Unveiling Fv1's Potential: Insights into its Interaction with the HIV-1 Capsid

Unveiling Fv1's Potential: Insights into its Interaction with the HIV-1 Capsid | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Unveiling Fv1's Potential: Insights into its Interaction with the HIV-1 Capsid Behzad Dehghani, Ava Hashempour This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5423642/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Virus susceptibility factor 1 (Fv1) serves as the prototype restriction factor guarding against infection by murine leukemia virus (MLV). Analysis of the Fv1 sequences revealed several residues in the C-terminal region that had undergone positive selection during evolution and might have played a role in various retroviral infections. For the first time, various bioinformatic tools have been applied to reveal specific residues involved in the interaction between Fv1 and the HIV-1 capsid as the target. Molecular dynamics (MD) simulation analysis of the Fv1-capsid complex confirmed the stability of the protein-protein complex. Docking and molecular dynamic simulation analyses demonstrated the potential of Fv1 to inhibit HIV-1 infection and supported the possibility that the HIV-1 capsid could be a target for novel anti-HIV medications. Furthermore, we revealed conserved regions, postmodification sites, and secondary and tertiary structures, which provided valuable data about the nature of the FV1 protein. Virus susceptibility factor 1 (Fv1) HIV-1 Bioinformatics Anti-HIV Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Introduction Retroviral infections exert selective pressure, leading to the evolution of antiviral cellular factors that serve as defence mechanisms against retroviruses. Famous factors include tripartite motif 5 (TRIM5), Friend virus susceptibility factor-1 (Fv1), Trim5Cyp and Mx2, which constitute a new class of restriction factors that inhibit retroviruses that target almost all viral capsids to prevent the establishment of a provirus[ 1 , 2 ]. They possess the ability to recognize specific domains on capsids, thereby defining their restriction specificities[ 2 – 4 ]. Recently, mechanisms of restriction of such antiviral cellular factors have been under focus; they are important not only for understanding viral tropism and species barriers but also for providing great opportunities for their use as novel antiretroviral therapies[ 5 , 6 ]. In the early 1970s, Fv1 was identified as a gene that regulates the susceptibility of mice to murine leukemia virus (MLV); since then, two primary alleles of Fv1 have been characterized: Fv1n and Fv1b. Fv1b is present in BALB/c mice, which are susceptible to infection by B-MLV but not N-MLV[ 3 , 7 , 8 ]. In contrast, Fv1n is expressed in NIH-Swiss mice, rendering them susceptible to N-tropic MLV infection but resistant to B-tropic MLV infection. Studies have indicated that the MLV capsid (CA) protein serves as the target of Fv1[ 9 ]. While the precise mechanism underlying Fv1 restriction remains unknown, it has been established that Fv1 impedes the virus at a stage occurring after reverse transcription but before integration[ 10 ]. The Fv1 protein consists of two domains: an N-terminal domain (Fv1NTD) and a C-terminal domain (Fv1CTD), connected by a flexible linker. It is believed that Fv1CTD serves as the capsid-targeting domain, whereas Fv1NTD contains a coiled-coil region and forms an antiparallel dimer[ 11 ]. TRIM5α is the best known for its ability to restrict HIV-1; despite the difference between Fv1 and TRIM5α at the primary sequence level, both proteins have a similar domain organization[ 12 ]. In both proteins, the N-terminal domain has a coil‒coil motif involved in multimerization, and the C-terminal domain is essential for specific virus binding. It was suggested that the C-terminal domain of Fv1 has an ability similar to that of cyclophilin A (CypA), a molecule known to bind to the HIV-1 capsid; therefore, this similarity in binding capacity suggests that Fv1 may also restrict HIV[ 13 ]. During the last decade, bioinformatics tools have been introduced and developed to investigate the function, structure, and interactions of different proteins[ 14 – 16 ]. Several studies have employed them to study viral inhibitors, which has provided a better understanding of their ability. While studies have suggested the potential role of Fv1 in inhibiting the HIV-1 virus, no studies have explored the interaction between Fv1 and HIV. Therefore, this study aimed to examine the possible interaction between Fv1 and the HIV capsid protein. Several reliable bioinformatics tools have investigated all the physicochemical properties, postmodification sites, and secondary and tertiary structures of Fv1. Materials and methods Sequence availability Eight Fv1 sequences available from different mouse species were collected from NCBI GenBank with the following accession numbers: rusty-bellied brush-furred rat (Lophuromys sikapusi): MH270656; yellow-spotted brush-furred rat (Lophuromys flavopunctatus): MH270655; rock rat (Praomys fumatus): MH270651; Jackson's soft-furred mouse (Praomys jacksoni): MH270650; typical striped grass mouse (Lemniscomys striatus): MH270654; woodland thicket rat (Grammomys dolichurus): MH270652; Barbary striped grass mouse (Lemniscomys barbarus): MH270653; African grass rat (Arvicanthis niloticus): MH270649. To define the homology among 8 sequences, CLC-sequence viewer software was employed with the following parameters: gap opening cost, 10; gap extension cost, 1.0; and a very accurate progressive alignment algorithm. Furthermore, phylogenetic trees were examined by the CLC-sequence viewer via the neighbor‒joining method (bootstrap: 1000) to confirm the reliability of the phylogenetic trees. For structural analysis and docking analysis, we used a consensus sequence for Fv1 and a reference sequence for the Gag protein (AB703607) ( the DNA and amino acid sequences are provided in supplementary data 1). In addition, ConservFold (https://www.rodrigueslab.com/resources) was used, which allows for automatic conservation analysis; it checks all and downloads the weblogo.png and .txt files to understand the most conserved residues [17-19]. It then also adds this to the b-factor of an alphafold-generated model to show this in 3D. Signal peptide prediction: The signal peptides of the Fv1 and HIV Gag P24 proteins were predicted by “Predisi” (http://www.predisi.de/predisi/startprediction) and “phobius” (http://phobius.sbc.su.se/cgi-bin/predict.pl)[20, 21]. Physicochemical analysis The overall characteristics of Fv1 and HIV Gag P24 were analyzed via the "ExPASy's ProtParam" online tool (http://ExPASy.org/tools/protparam.html) [22]. Postmo dification Serine, threonine, and tyrosine phosphorylation site predictions were made via DISPHOS (http://www.dabi.temple.edu/disphos/pred.html) and NetPhos (http://www.cbs.dtu.dk/services/NetPhos/)[23, 24]. Kinase-specific phosphorylation sites were determined via NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/)[25]. NetNGlyc (http://www.cbs.dtu.dk/services/NetNGlyc/) and GlycoEP (http://www.imtech.res.in/raghava/glycoep/submit.html) were employed for N-glycosylation site prediction[26, 27]. DIpro (https://scratch.proteomics.ics.uci.edu/) was used to predict disulfide bonds. Prediction of Secondary and Tertiary Structures To predict secondary and tertiary structures, SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html) was employed[28]. 3D structures were predicted via I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER), and the suggested model was refined via GalaxyRefine. Finally, the refined models were evaluated via "Qmean" (http://swissmodel.ExPASy.org/qmean/cgi/index.cgi), "Rampage" (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php), ERRAT (https://servicesn.mbi.ucla.edu/ERRAT/), and ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php)[29-33]. Docking analysis: The docking of Fv1 and the HIV Gag P24 protein (AB703607) was predicted via Hex 8.0.0 docking software [34] . The parameters considered for the docking were as follows: correction type , shape only ; FFT mode, 3D fast lite ; grid dimension, 0.6; receptor range, 180; ligand range, 180; twist range, 360; and distance range, 40. The docking results were analyzed via Discovery Studio 2017 R2 to define the interaction sites. In addition, we conducted a molecular docking analysis of Fv1 with the HIV-1 capsid via the ClusPro 2.0 online server (https://cluspro.bu.edu/login.php). Molecular dynamic simulation MD simulation is commonly accepted as an effective technique for examining biological systems at the molecular scale. In this study, Linux-based GROMACS software was used to analyze the effectiveness of the interaction between Fv1 and the HIV-1 capsid protein. The GROMACS software is compatible with various force fields, such as AMBER, OPLS, GROMOS, and CHARMM. In our study, we utilized the GROMACS 2018—x series (version 05) for simulation, implementing the OPLS‒AA force field (Optimized Potential for Liquid Simulation). In the initial phase of preparation, the Fv1‒capsid complexes were analyzed via OPLS‒AA force field parameters. This process created coordinate and topology files for the complex system. The system was solvated using the transferable intermolecular potential 3P (TIP3P) water model and then neutralized with chloride (Cl) ions to maintain the stability of the structural and topological coordinates.[35] Next, the final structure was achieved by conducting an energy minimization process (EM).[36] The equilibration of the NVT ensemble continued for 100 ps, and 50,000 steps were taken to achieve the target temperature. This method made it possible to create velocities, which in turn allowed the simulation to be conducted at various speeds. A 50,000-step NPT ensemble was then employed to investigate the density, potential, pressure, and temperature of the stabilized Fv1-capsid complex during the entire process. After allowing the system to stabilize, MD simulations consisting of 50,000,000 steps and lasting 100 nanoseconds were conducted on the structure. The backbone energy's root mean square deviation (RMSD) is reduced following the MD simulation, and the outcomes are displayed graphically. Furthermore, an analysis was conducted on the radius of gyration (Rg), density plots, and hydrogen bonding in the MD simulations. Results Sequences and phylogenetic tree analysis The alignment results of eight selected sequences are presented in Figure 1. The substitutions observed in the Fv1 protein across different species are highlighted. In addition, the ConservFold results revealed that the C-terminus of FV1 has several highly variable regions, which were previously indicated as possible regions to restrict different viruses (Figure 2 and Figure 4-D). Figure 3 shows the phylogenetic tree of the Fv1 sequences, revealing the presence of two distinct clades. The upper clade contained two sequences ( Lophuromys sikapusi : MH270656 and Lophuromys flavopunctatus : MH270655) that were grouped together, indicating their close phylogenetic relationship. On the other hand, the lower clade contained other species. Notably, all bootstraps were 100, which indicates the high reliability of the tree's results. " ProtParam" analysis Despite several substitutions, physicochemical analysis of Fv1 in 8 species revealed that its isoelectric point (pI) consistently increased to approximately 5, indicating its acidic nature. Stability assessments of Fv1 in various host systems, including mammalian cells, yeast, and E. coli , indicated proper stability across different hosts. However, while Fv1 demonstrated high stability in vivo, predictions suggested that it may be unstable in vitro, potentially leading to rapid degradation postextraction. Furthermore, Fv1 was found to be a thermostable protein, offering an advantage for laboratory use, and it exhibited hydrophilic properties, as summarized in Table 1. In addition, our prediction showed that HIV Gag p24 is a basic protein that was predicted to be thermostable and stable in all the indicated hosts. Signal peptide prediction Two software programs detected a signal peptide that showed a region from amino acids 1 to 20 for Fv1, although the software could not identify the type of signal peptide. However, it might be suggested that this region must be omitted after protein secretion; therefore, in all protein expression systems in the laboratory, this region must be deleted to reach the proper tertiary structure. In addition, the software did not find any signal peptide for the HIV Gag p24 protein. Postmodification analysis The disulfide bond prediction revealed that two species (MH270656 and MH270655) presented four disulfide bonds each, whereas the other species presented different patterns of predicted bonds (see Table 2). This variance in disulfide bonds could cause significant changes in the structure and function of Fv1. Notably, the pattern of disulfide bonds closely mirrored the phylogenetic tree, with two species closely grouped in the upper clade and the remaining species clustered in the lower clade. Considering the disulfide bonds, spices can be categorized into four groups. The first group (MH270656, MH270655) has 4 bonds; however, the bonds are not in the exact same positions. Group 2, MH270651 and MH270650, had 2 bonds (114 – 369 and 374 – 400), and the third group (MH270654, MH270652, and MH270653) had two bonds (114 – 367 and 372 – 408), and the fourth group (MH270649) had two bonds (114 – 365 and 370 – 406). The cysteine at position 114 was highly conserved across all the species. While this amino acid formed a disulfide bond in 6 species, it was not predicted to do so in the two other species (MH270656 and MH270655). Phosphorylation prediction analysis revealed that Fv1 is a highly phosphorylated protein, with numerous phosphorylation sites identified across various positions (see Table 2). However, the distribution of phosphorylation sites varied among the 8 species studied. Despite differences in the distribution of phosphorylation sites, certain positions were conserved among the majority of the species. For example, position 26 was completely conserved, with all sequences containing a phosphorylation site at this position. Additionally, positions 52, 23, and 53 were found in 7, 6, and 5 species, respectively. Finally, positions 60, 184, 198, and 202 were present in 4 species each. The glycosylation prediction analysis revealed that only two species (MH270656 and MH270655) presented a glycosylation site at position 42 (see Table 2). In contrast, other species presented different glycosylation sites, although position 58 was conserved among them. Additionally, for HIV Gag p24, four disulfide bonds, several phosphorylation sites, and two glycosylation sites were identified, indicating that these posttranslational modifications could influence the structure and function of this protein. Secondary and tertiary structure prediction The results of secondary structure prediction for all 8 Fv1 sequences and HIV Gag p24 software are summarized in Table 3. The analysis revealed that the primary structure in all the species consisted of an alpha helix and a random coil, although the percentages varied among the species. The assessment data of the 3D models suggested by I-Tasser are summarized in Table 4, and the selected model is bolded. The tertiary structures of Fv1 and the HIV-1 capsid are illustrated in Figure 4 (A and B). Docking results Docking analysis via Hex revealed a high energy value for HIV Gag p24 and Fv1 docking (-618), and interaction site analysis revealed several amino acids involved in the interaction site (Table 5 and Figure 4-C). In addition, the interaction between Fv1 and the HIV-1 capsid structure was examined via protein-protein docking analysis via ClusPro 2.0. A total of all the models were generated through docking, and the least energy score was utilized to choose the models that interacted well with the receptor. According to our results, the docking complex of the Fv1 and HIV-1 capsid proteins with the lowest energy scores of -238.9 was considered for further analysis (Table 6, Figure 5). Molecular dynamic analysis Figure 6 (A-E) shows the results of the molecular dynamics simulations of the Fv1-capsid complex. The simulations were expected to determine the movement of molecules and atoms in the complex formed by the Fv1-capsid complex. Moreover, the interaction between the Fv1 and HIV-1 capsid proteins was calculated via Rg computation, energy minimization, potential energy determination, density assessment, pressure evaluation, and temperature analysis. We obtained the RMSD value by analyzing the trajectory generated in a 100 ns simulation. The RMSD value of the Fv1 and HIV-1 capsid molecules was 0.95 nm, suggesting that the complex is stable and devoid of fluctuations. RMSF analysis was used to assess the structural stability and mobility of the complex. The results indicated that the residues at the binding site fluctuated less. In addition, the Rg results revealed that the structure of the construct remained stable throughout the molecular dynamics simulation. In other words, the few fluctuations in RG supported our hypothesis of the compactness of the protein-ligand complex. The density analysis showed stability, suggesting that the Fv1-capsid complex was adequately equilibrated in terms of pressure and density. Our findings revealed that the Fv1-capsid complex achieves a balance between flexibility and stability, which helps to suppress HIV infection. Discussion The capsid of HIV-1 plays crucial roles in various stages of the virus replication cycle, including assembly, release, maturation, and establishment of infection[ 37 ]. Research has revealed its importance; however, there are currently no approved antiretroviral therapies that specifically target the Gag precursor protein or its mature forms[ 37 ]. Recent advancements in the understanding of the structure and cell biology of the HIV-1 capsid have paved the way for the identification of potential targets useful for therapeutic intervention[ 38 ]. This study, for the first time, examined the possible interaction between Fv1, an intrinsic factor that inhibits retroviruses, and the HIV P24 protein via a bioinformatics approach and revealed a strong attachment between the two proteins (E value: -618). These results could confirm the ability of this protein to inhibit the HIV virus. Our analysis revealed several residues involved in this interaction, in which tyrosine 123 and proline 350 are conserved in all the selected sequences, indicating that these amino acids may play important roles in the possible inhibitory effects of Fv1 and could be interesting targets for generating mutant proteins to determine their possible roles. Our findings revealed several conserved regions in the Fv1 protein and, in agreement with our results, two studies by Anthony Stevens et al. (2004) and Bishop et al. identified 3 variable regions (VR) in the Fv1 protein: VRA (amino acids 247–276), VRB (amino acids 345–358), and variable region C (amino acids 375–401) [ 39 , 40 ]. VRB contains most of the residues we identified via interaction analysis, and VRC, which can alter restriction specificity, contains glutamine 399, which is found in two selected sequences. Variable domains, collectively or individually, are involved in target selection and binding, which are important for the possible inhibition of Fv1. In addition, it was suggested that residue 399 was involved in determining tropism. Amino acid 358 has been reported to frequently play the main role in interactions with the HIV capsid (amino acid 110 in the HIV capsid), and mutation of residue 358 to alanine might abolish the activity of Fv1[ 2 , 39 – 42 ]. While our prediction showed that this residue is conserved among most sequences, the docking results could not reveal any interaction between this amino acid and the HIV capsid, possibly because of the different resources used in previous studies. Yuhe Yan et al. (2009) identified six codons, specifically Fv1 amino acids 261, 265, 270, 362, 399, and 401, that displayed evidence of positive selection during Mus evolution[ 43 ]. Amino acids 261, 362, and 399 were highly conserved in the selected sequences studied here. However, amino acid 401, while not conserved as either C, S, or T, still plays a significant role in interactions within the HIV-1 capsid. In 2014, Melvyn W. Yap et al. demonstrated that the C-terminal region of Fv1, which is believed to contain determinants of restriction specificity, is significantly different[ 44 ]. Consistent with Yap's findings, our analysis also suggested that many of the amino acids involved in potential interactions are in the C-terminal region, which comprises coil structures and represents a variable part of the protein. Consequently, certain Fv1 alleles may lack interaction sites and associated restriction activities. It would be of great interest to investigate whether these alleles recognize alternative targets, revealing the possible varied functions of Fv1 in viral restriction. MD simulation analysis verified that the Fv1-capsid complex remains stable under various environmental conditions, even with changes in pressure and temperature. Furthermore, the initial evaluation, which involved calculating parameters such as the RMSD, radius of gyration, and hydrogen bonds, indicated that the Fv1-capsid complex demonstrated remarkable stability in a biological setting. It can be inferred that in cases of natural HIV infection, one way the virus is suppressed is through the interaction between FV-1 and the HIV-1 capsid protein, resulting in the inhibition of capsid function. These findings suggest that developing drugs that mimic the binding of FV-1 to the HIV-1 capsid, thus impeding the ability of the virus to infect cells at different stages, could be a promising approach for effectively combating the virus. Our predictions suggest that mammalian cells, yeast, and E. coli are suitable hosts for expressing the Fv1 protein. These findings are supported by several studies, including those by Wilson Li et al. (2016), Luca D. Passerini (2006), Anthony Stevens (2004), and Melvyn W. Yap (2003)[ 2 , 3 , 40 , 45 ]. These studies have expressed Fv1 in various cell lines, such as Dunni tail fibroblasts, the human TE671 cell line, mouse fibroblasts, NIH3T3 cells, and BALB3T3 cells, confirming the stability of Fv1 in these cell lines. Additionally, Kate N. Bishop conducted two investigations demonstrating the stability of Fv1 in E. coli , whereas Mark P. Dodding (2005) and Anthony Stevens (2004) suggested the ability of yeast to express Fv1[ 39 , 40 , 46 , 47 ]. After reviewing publications, it became evident that more data are needed regarding postmodifications, such as phosphorylation, disulfide bonds, and glycosylation sites, in the Fv1 protein. This is the first comprehensive study to identify several modification sites that might be useful in defining their possible effects on the function and structure of this protein. Conclusion Host restriction factors are cellular proteins that inhibit specific steps of the viral life cycle. In recent decades, several proteins have been identified, confirming the potential of these factors to inhibit viral infections. The present study, for the first time, suggests the probable inhibitory role of Fv1, a recognized host restriction factor, through its interaction with the HIV-1 capsid. Additionally, it predicts several characteristics of FV1 that could be valuable for subsequent investigations. In addition, MD analysis of the Fv1-capsid complex indicated that the interaction between Fv1 and the HIV-1 capsid led to significant conformational alterations, resulting in a strong affinity between the two proteins. However, to validate this claim, several experiments need to be conducted. Abbreviations Fv1: susceptibility factor 1 MLV: murine leukemia virus MD: Molecular dynamics TRIM5: factors include tripartite motif 5 HIV: human immunodeficiency virus Declarations Ethics approval and consent to participate: This study was approved by the local Ethics Committee of Shiraz University of Medical Sciences, Shiraz, Iran. All methods were carried out according to relevant guidelines and regulations. Clinical Trial: Not applicable Availability of data and material: Data that support the findings of this study are available from the corresponding author (Dr. Ava Hashempour) upon reasonable request. Competing interests: The authors declare that they have no competing interests. Funding : This study was funded by Shiraz University of Medical Sciences (grant number 13787). Authors' contributions : BD: design of the work, the acquisition, analysis and providing the first draft. AH: providing main funds, data analysis, and editing the final draft. Acknowledgements : This study was supported by Shiraz University of Medical Sciences. References Nakayama, E.E. and T. Shioda, Role of Human TRIM5α in Intrinsic Immunity. Frontiers in Microbiology, 2012. 3 . Passerini, L.D., Z. Keckesova, and G.J. Towers, Retroviral restriction factors Fv1 and TRIM5alpha act independently and can compete for incoming virus before reverse transcription. J Virol, 2006. 80 (5): p. 2100-5. Li, W., M.W. Yap, V. 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Towers, and J.P. Stoye, Identification of the regions of Fv1 necessary for murine leukemia virus restriction. J Virol, 2001. 75 (11): p. 5182-8. Stevens, A., et al., Retroviral capsid determinants of Fv1 NB and NR tropism. J Virol, 2004. 78 (18): p. 9592-8. Zheng, Y.H. and B.M. Peterlin, Intracellular immunity to HIV-1: newly defined retroviral battles inside infected cells. Retrovirology, 2005. 2 : p. 25. Schaller, T., et al., Fusion of cyclophilin A to Fv1 enables cyclosporine-sensitive restriction of human and feline immunodeficiency viruses. J Virol, 2007. 81 (18): p. 10055-63. Yan, Y., A. Buckler-White, K. Wollenberg, and C.A. Kozak, Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus. Proc Natl Acad Sci U S A, 2009. 106 (9): p. 3259-63. Yap, M.W., E. Colbeck, S.A. Ellis, and J.P. Stoye, Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses. PLoS Pathog, 2014. 10 (3): p. e1003968. Yap, M.W. and J.P. Stoye, Intracellular localisation of Fv1. Virology, 2003. 307 (1): p. 76-89. Bishop Kate, N., et al., Characterization of an Amino-Terminal Dimerization Domain from Retroviral Restriction Factor Fv1. Journal of Virology, 2006. 80 (16): p. 8225-8235. Dodding, M.P., M. Bock, M.W. Yap, and J.P. Stoye, Capsid processing requirements for abrogation of Fv1 and Ref1 restriction. J Virol, 2005. 79 (16): p. 10571-7. Tables Table 1: Protparam analysis of the FV1 proteins for 8 selected sequences and HIV Gag P24. MH270656 MH270655 MH270651 MH270650 MH270654 MH270652 MH270653 MH270649 gag Number of amino acids 413 413 430 430 437 438 437 435 497 Molecular weight 46867.25 46933.4 48552.81 48579.92 49517.77 49501.06 49415.76 49242.49 55149.14 Theoretical pI 5.25 5.52 5.02 5.11 5.34 5.17 5.23 5.23 9.18 half-life mammalian reticulocytes 30 30 30 30 30 30 30 30 30 yeast >20 >20 >20 >20 >20 >20 >20 >20 >20 Escherichia coli >10 >10 >10 >10 >10 >10 >10 >10 >10 Instability index Unstable Unstable Unstable Unstable Unstable Stable Unstable Unstable Unstable Aliphatic index 86.61 88.77 84.79 85 83.43 84.36 85.22 84.48 70.72 GRAVY -0.391 -0.394 -0.481 -0.482 -0.509 -0.466 -0.473 -0.452 -0.579 Table 2: The post-modification sites of FV1 and HIV Gag P24 , where various residues have undergone modifications such as disulfide bond formation, phosphorylation, and glycosylation. MH270656 MH270655 MH270651 MH270650 MH270654 MH270652 MH270653 MH270649 g ag disulphide bonds 150-318 150-154 114 - 369 114 - 369 114 - 367 114 - 157 114 - 367 114 – 365 57-87 268-283 263-278 374 - 400 374 - 400 372 - 408 372 - 408 372 - 408 370 – 406 329-349 274-339 269-334 392-410 344-380 339-375 382-402 phosphorylation sites 23,26,52,60,157, 206,211,216,324, 373 23,26,46,50,52, 53,60,184, 211 26,52,53,187,201, 205,225,229,246, 250,307 26,43,52,201,205, 210,225,229 23,26,52,53,60, 95,152,182,184, 198,202,226,241, 243,247,263,301, 398,428 23,26,122,125,184, 198,202,207,222,226, 241,247,304,346,398 23,26,52,53,95, 152,182,184,198, 202,207,226,241, 243,247,428 23,26,52,53,60, 63,184,198,202, 207,210,227,245, 261,302,426 6, 9,49,66,70,77,8411 124,128,145,147,164,175 179,203,233,240,241 250,261,277,280 302,309,341,356 424,437,448,453 459,467,469,481 485,496 glycosylation sites 42 42 58 ,227 58 ,227 58 ,224, 344 58 ,224 58 ,224,344 58 ,222,342 47, 126 Table 3: Secondary structure prediction estimated by SOPMA; most of the structures were alpha helix and random coil in all sequences. MH270656 MH270655 MH270651 MH270650 MH270654 MH270652 MH270653 MH270649 gag Alpha helix 0.5085 0.4891 0.4744 0.4605 0.4577 0.4726 0.4622 0.4598 44.06 Extended strand 0.0605 0.0847 0.0837 0.0837 0.0572 0.0913 0.0732 0.0759 3.02 Beta turn 0.0218 0.0533 0.0349 0.0419 0.0297 0.032 0.0503 0.0437 0.00 Random coil 0.4092 0.3729 0.407 0.414 0.4554 0.4041 0.4142 0.4207 52.92 Table 4: The final results of 4 servers used to define the best 3D structure for Fv1 and HIV gag protein. The selected structure is bolded. FV1 Models Qmean ERRAT ProSA-web Rampage (Ramachandran plot) favor region % I-TASSER without refinement -12.61 78.2716 -3.65 75.1% GalaxyRefine 1 -6.47 76.4851 -4.72 83.10% 2 -6.85 77.9703 -4.64 81.70% 3 -6.8 71.2871 -4.8 83.10% 4 -6.69 76.2963 -4.87 83.10% 5 -6.6 76.4851 -4.9 83.70% gag Models Qmean ERRAT ProSA-web Rampage (Ramachandran plot) favor region % I-TASSER without refinement -11.11 75.2716 -4.25 74.1% GalaxyRefine 1 -5.57 75.4111 -4.12 82.11% 2 -5.85 77.1233 -4.44 82.70% 3 -5.18 72.2871 -4.18 84.30% 4 -5.69 75.2963 -4.27 82.50% 5 -5.4 79.2351 -4.81 87.80% Table 5: The amino acid residues identified in the interaction sites during the docking analysis of Fv1 and HIV gag P24 proteins. Each row lists two amino acids predicted to interact with each other. Fv1 P24 HIV GLU149 LYS330 GLU399 VAL352 TYR123 ASP283 GLY349 ARG334 PRO350 LYS330 VAL353 CYS349 ARG357 CYS349 PRO152 LEU321 Table 6: Molecular docking results of Fv1 and HIV-1 capsid proteins generated using the Cluspro2.0 tool. (The best model is shown in bold font.). Predicted models Members Representative Weighted Score 0 50 Center -206.1 Lowest Energy -221.1 1 49 Center -223.9 Lowest Energy -238.9 2 24 Center -203.4 Lowest Energy -245.9 3 24 Center -182.8 Lowest Energy -214.2 4 23 Center -228.8 Lowest Energy -231.9 5 19 Center -226.9 Lowest Energy -226.9 6 18 Center -197.9 Lowest Energy -213.6 7 18 Center -224.3 Lowest Energy -224.3 8 16 Center -211.8 Lowest Energy -211.8 Additional Declarations No competing interests reported. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5423642","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":379678299,"identity":"4364f157-cb14-47b3-baee-bf979c3f4930","order_by":0,"name":"Behzad Dehghani","email":"","orcid":"","institution":"Shiraz University of Medical Sciences","correspondingAuthor":false,"prefix":"","firstName":"Behzad","middleName":"","lastName":"Dehghani","suffix":""},{"id":379678300,"identity":"c7fae782-52fd-42e2-b989-756f9d62c5ae","order_by":1,"name":"Ava Hashempour","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAx0lEQVRIiWNgGAWjYDACCQYGZiAlBxdgI6SDB6rFmHQtiQ1Eu8teuvnx54KKbenzZ2Qnf2CosWPgkz5AwBaZY2bSM87czt1wI3ebBMOxZAY2vgRCDkswY+ZtA2qRyN0G9MgBBjYeAg7jkUj//Jn33+10+Rm5mz8w/CNKS46BNG/D7QSGG0CLGNuI0XIjp0ya59htww1n3m6TSOxL5iGohX1G+ubPPDW35eXbgQ778M1OTr6HgBZUkAC0liQNo2AUjIJRMAqwAwBDyzqfxaoo5AAAAABJRU5ErkJggg==","orcid":"","institution":"Shiraz University of Medical Sciences","correspondingAuthor":true,"prefix":"","firstName":"Ava","middleName":"","lastName":"Hashempour","suffix":""}],"badges":[],"createdAt":"2024-11-09 22:23:08","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5423642/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5423642/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":70104042,"identity":"4a187aaa-f52f-4551-8aab-0c88dbab0de4","added_by":"auto","created_at":"2024-11-28 11:05:05","extension":"jpeg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1227958,"visible":true,"origin":"","legend":"\u003cp\u003eThe alignment results of Fv1 protein sequences. Notably, several amino acid substitutions, which could impact the function of the protein, were recorded among the selected sequences.\u003c/p\u003e","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/ef4627de0f1913636c704215.jpeg"},{"id":70104035,"identity":"2d3c60d6-c400-4149-8920-0f3aef8d5bbd","added_by":"auto","created_at":"2024-11-28 11:05:05","extension":"jpeg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1480996,"visible":true,"origin":"","legend":"\u003cp\u003eConservFold output which indicated Fv1 conserved regions, with the larger letters having higher conservation.\u003c/p\u003e","description":"","filename":"floatimage3.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/aeaf7457e520b61cea2ca365.jpeg"},{"id":70104039,"identity":"31de1d5e-e4d8-4f8e-8ff2-fc503144fe61","added_by":"auto","created_at":"2024-11-28 11:05:05","extension":"jpeg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":127297,"visible":true,"origin":"","legend":"\u003cp\u003ethe results of the phylogenetic tree of 8 Fv1 sequences, constructed using the neighbor-joining method with a bootstrap value of 1000. The tree reveals two main clades: the upper clade comprises two sequences (Lophuromys sikapusi and Lophuromys flavopunctatus), while the lower clade further divides into two main clusters containing the remaining sequences.\u003c/p\u003e","description":"","filename":"floatimage4.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/59a0f3247db754dc0ce9e748.jpeg"},{"id":70104838,"identity":"aa966be2-3694-420a-bb1c-fbb6354efd7a","added_by":"auto","created_at":"2024-11-28 11:13:05","extension":"jpeg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":262574,"visible":true,"origin":"","legend":"\u003cp\u003estructural analysis of Fv1 and HIV-1 capsid proteins. A) Tertiary structure of HIV-1 capsid, B) Tertiary structure of FV1 protein, C) the predicted position of FV1 and HIV-1 capsid, which showed possible interaction between them, and D) ConservFold result which indicated conserved regions, with red being high and blue being low entropy/conservation.\u003c/p\u003e","description":"","filename":"floatimage5.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/2420fdde0eba7fe28b5b7ede.jpeg"},{"id":70104040,"identity":"d6b699af-dfd0-427b-8c83-c45c5e0a4d37","added_by":"auto","created_at":"2024-11-28 11:05:05","extension":"jpeg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":742532,"visible":true,"origin":"","legend":"\u003cp\u003eDocked complexes of the Fv1 and HIV-1 capsid proteins using ClusPro server. Among all six suggested models (A-I), the complex formation data obtained by docking indicated that model 1 exhibited the highest affinity for binding Fv1 with HIV-1 capsid.\u003c/p\u003e","description":"","filename":"floatimage6.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/19bd906136b38441dc65ce87.jpeg"},{"id":70104036,"identity":"577fbf5e-8e37-4c50-a127-bbadd0cae4e9","added_by":"auto","created_at":"2024-11-28 11:05:05","extension":"jpeg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":266387,"visible":true,"origin":"","legend":"\u003cp\u003eThe RMSD (a), RMSF (b), RG (c), density (d), pressure (e), and temperature (f) plots for the complex of Fv1-capsid.\u003c/p\u003e","description":"","filename":"floatimage7.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/9db5f9528a22f34bf9a91cbd.jpeg"},{"id":74153739,"identity":"d2bb7568-d1b8-420f-8e05-5c003260f4b9","added_by":"auto","created_at":"2025-01-18 19:46:26","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":5425422,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/bc5b39f5-e287-4415-96df-8aea0f2c3641.pdf"},{"id":70104839,"identity":"f37e9341-53f7-4bc0-ac9f-72f3fb814d13","added_by":"auto","created_at":"2024-11-28 11:13:05","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":13831,"visible":true,"origin":"","legend":"","description":"","filename":"S1.docx","url":"https://assets-eu.researchsquare.com/files/rs-5423642/v1/ad1a7b51c110307bdeef5f44.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Unveiling Fv1's Potential: Insights into its Interaction with the HIV-1 Capsid","fulltext":[{"header":"Introduction","content":"\u003cp\u003eRetroviral infections exert selective pressure, leading to the evolution of antiviral cellular factors that serve as defence mechanisms against retroviruses. Famous factors include tripartite motif 5 (TRIM5), Friend virus susceptibility factor-1 (Fv1), Trim5Cyp and Mx2, which constitute a new class of restriction factors that inhibit retroviruses that target almost all viral capsids to prevent the establishment of a provirus[\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. They possess the ability to recognize specific domains on capsids, thereby defining their restriction specificities[\u003cspan additionalcitationids=\"CR3\" citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Recently, mechanisms of restriction of such antiviral cellular factors have been under focus; they are important not only for understanding viral tropism and species barriers but also for providing great opportunities for their use as novel antiretroviral therapies[\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn the early 1970s, Fv1 was identified as a gene that regulates the susceptibility of mice to murine leukemia virus (MLV); since then, two primary alleles of Fv1 have been characterized: Fv1n and Fv1b. Fv1b is present in BALB/c mice, which are susceptible to infection by B-MLV but not N-MLV[\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. In contrast, Fv1n is expressed in NIH-Swiss mice, rendering them susceptible to N-tropic MLV infection but resistant to B-tropic MLV infection. Studies have indicated that the MLV capsid (CA) protein serves as the target of Fv1[\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. While the precise mechanism underlying Fv1 restriction remains unknown, it has been established that Fv1 impedes the virus at a stage occurring after reverse transcription but before integration[\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. The Fv1 protein consists of two domains: an N-terminal domain (Fv1NTD) and a C-terminal domain (Fv1CTD), connected by a flexible linker. It is believed that Fv1CTD serves as the capsid-targeting domain, whereas Fv1NTD contains a coiled-coil region and forms an antiparallel dimer[\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTRIM5α is the best known for its ability to restrict HIV-1; despite the difference between Fv1 and TRIM5α at the primary sequence level, both proteins have a similar domain organization[\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. In both proteins, the N-terminal domain has a coil‒coil motif involved in multimerization, and the C-terminal domain is essential for specific virus binding. It was suggested that the C-terminal domain of Fv1 has an ability similar to that of cyclophilin A (CypA), a molecule known to bind to the HIV-1 capsid; therefore, this similarity in binding capacity suggests that Fv1 may also restrict HIV[\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eDuring the last decade, bioinformatics tools have been introduced and developed to investigate the function, structure, and interactions of different proteins[\u003cspan additionalcitationids=\"CR15\" citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Several studies have employed them to study viral inhibitors, which has provided a better understanding of their ability.\u003c/p\u003e \u003cp\u003eWhile studies have suggested the potential role of Fv1 in inhibiting the HIV-1 virus, no studies have explored the interaction between Fv1 and HIV. Therefore, this study aimed to examine the possible interaction between Fv1 and the HIV capsid protein. Several reliable bioinformatics tools have investigated all the physicochemical properties, postmodification sites, and secondary and tertiary structures of Fv1.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cp\u003e\u003cstrong\u003eSequence\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEight Fv1 sequences available from different mouse species were collected from NCBI\u003cspan dir=\"RTL\"\u003e\u0026nbsp;\u003c/span\u003eGenBank with the following accession numbers: rusty-bellied brush-furred rat (Lophuromys sikapusi): MH270656; yellow-spotted brush-furred rat (Lophuromys flavopunctatus): MH270655; rock rat (Praomys fumatus): MH270651; Jackson\u0026apos;s soft-furred mouse (Praomys jacksoni): MH270650; typical striped grass mouse (Lemniscomys striatus): MH270654; woodland thicket rat (Grammomys dolichurus): MH270652; Barbary striped grass mouse (Lemniscomys barbarus): MH270653; African grass rat (Arvicanthis niloticus): MH270649. To define the homology among 8 sequences, CLC-sequence viewer software was employed with the following parameters: gap opening cost, 10; gap extension cost, 1.0; and a very accurate progressive alignment algorithm. Furthermore, phylogenetic trees were examined by the CLC-sequence viewer via the neighbor‒joining method (bootstrap: 1000) to confirm the reliability of the phylogenetic trees.\u003c/p\u003e\n\u003cp\u003eFor structural analysis and docking analysis, we used a consensus sequence for Fv1 and a reference sequence for the Gag protein (AB703607) \u003cem\u003e(\u003c/em\u003e\u003cem\u003ethe\u003c/em\u003e\u003cem\u003e\u0026nbsp;DNA and amino acid sequences\u0026nbsp;\u003c/em\u003e\u003cem\u003eare\u003c/em\u003e\u003cem\u003e\u0026nbsp;provided in supplementary data 1).\u003c/em\u003e In addition, ConservFold (https://www.rodrigueslab.com/resources) was used, which allows for automatic conservation analysis; it checks all and downloads the weblogo.png and .txt files to understand the most conserved residues [17-19]. It then also adds this to the b-factor of an alphafold-generated model to show this in 3D.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSignal\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;peptide prediction:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe signal peptides of the Fv1 and \u003cem\u003eHIV Gag P24\u0026nbsp;\u003c/em\u003eproteins were predicted by \u0026ldquo;Predisi\u0026rdquo; (http://www.predisi.de/predisi/startprediction) and \u0026ldquo;phobius\u0026rdquo; (http://phobius.sbc.su.se/cgi-bin/predict.pl)[20, 21].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePhysicochemical analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe overall characteristics of Fv1 and \u003cem\u003eHIV Gag P24\u0026nbsp;\u003c/em\u003ewere analyzed via the \u0026quot;ExPASy\u0026apos;s ProtParam\u0026quot; online tool (http://ExPASy.org/tools/protparam.html) [22].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePostmo\u003c/strong\u003e\u003cstrong\u003edification\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSerine, threonine, and tyrosine phosphorylation site predictions were made via DISPHOS (http://www.dabi.temple.edu/disphos/pred.html) and NetPhos (http://www.cbs.dtu.dk/services/NetPhos/)[23, 24]. Kinase-specific phosphorylation sites were determined via NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/)[25]. NetNGlyc (http://www.cbs.dtu.dk/services/NetNGlyc/) and GlycoEP (http://www.imtech.res.in/raghava/glycoep/submit.html) were employed for N-glycosylation site prediction[26, 27]. DIpro (https://scratch.proteomics.ics.uci.edu/) was used to predict disulfide bonds.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePrediction of Secondary and Tertiary Structures\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo predict secondary and tertiary structures, SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html) was employed[28]. 3D structures were predicted via I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER), and the suggested model was refined via GalaxyRefine. Finally, the refined models were evaluated via \u0026quot;Qmean\u0026quot; (http://swissmodel.ExPASy.org/qmean/cgi/index.cgi), \u0026quot;Rampage\u0026quot; (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php), ERRAT (https://servicesn.mbi.ucla.edu/ERRAT/), and ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php)[29-33].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDocking analysis:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eThe docking\u003c/em\u003e\u003cem\u003e\u0026nbsp;of\u0026nbsp;\u003c/em\u003e\u003cem\u003eFv1\u003c/em\u003e\u003cem\u003e\u0026nbsp;\u003c/em\u003e\u003cem\u003eand\u0026nbsp;\u003c/em\u003e\u003cem\u003ethe\u0026nbsp;\u003c/em\u003e\u003cem\u003eHIV Gag P24 protein (AB703607) was\u0026nbsp;\u003c/em\u003epredicted\u003cem\u003e\u0026nbsp;\u003c/em\u003e\u003cem\u003evia\u003c/em\u003e\u003cem\u003e\u0026nbsp;Hex 8.0.0 docking software\u003c/em\u003e\u003cem\u003e[34]\u003c/em\u003e\u003cem\u003e. The parameters considered for the docking were\u003c/em\u003e\u003cem\u003e\u0026nbsp;as follows: correction\u003c/em\u003e\u003cem\u003e\u0026nbsp;type\u003c/em\u003e\u003cem\u003e,\u003c/em\u003e\u003cem\u003e\u0026nbsp;\u003c/em\u003e\u003cem\u003eshape\u003c/em\u003e\u003cem\u003e\u0026nbsp;only\u003c/em\u003e\u003cem\u003e;\u003c/em\u003e\u003cem\u003e\u0026nbsp;FFT\u0026nbsp;\u003c/em\u003e\u003cem\u003emode,\u003c/em\u003e\u003cem\u003e\u0026nbsp;3D\u0026nbsp;\u003c/em\u003e\u003cem\u003efast\u003c/em\u003e\u003cem\u003e\u0026nbsp;lite\u003c/em\u003e\u003cem\u003e; grid dimension, 0.6; receptor range, 180; ligand range, 180; twist range, 360; and distance range,\u003c/em\u003e\u003cem\u003e\u0026nbsp;40. The docking results were analyzed\u0026nbsp;\u003c/em\u003e\u003cem\u003evia\u003c/em\u003e\u003cem\u003e\u0026nbsp;Discovery Studio 2017 R2 to define the interaction sites.\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eIn addition, we conducted a molecular docking analysis of Fv1 with the HIV-1 capsid via the ClusPro 2.0 online server (https://cluspro.bu.edu/login.php).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMolecular dynamic simulation\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eMD simulation is commonly accepted as an effective technique for examining biological systems at the molecular scale. In this study, Linux-based GROMACS software was used to analyze the effectiveness of the interaction between Fv1 and the HIV-1 capsid protein. The GROMACS software is compatible with various force fields, such as AMBER, OPLS, GROMOS, and CHARMM. In our study, we utilized the GROMACS 2018\u0026mdash;x series (version 05) for simulation, implementing the OPLS‒AA force field (Optimized Potential for Liquid Simulation). In the initial phase of preparation, the Fv1‒capsid complexes were analyzed via OPLS‒AA force field parameters. This process created coordinate and topology files for the complex system. The system was solvated using the transferable intermolecular potential 3P (TIP3P) water model and then neutralized with chloride (Cl) ions to maintain the stability of the structural and topological coordinates.[35] Next, the final structure was achieved by conducting an energy minimization process (EM).[36] The equilibration of the NVT ensemble continued for 100 ps, and 50,000 steps were taken to achieve the target temperature. This method made it possible to create velocities, which in turn allowed the simulation to be conducted at various speeds. A 50,000-step NPT ensemble was then employed to investigate the density, potential, pressure, and temperature of the stabilized Fv1-capsid complex during the entire process. After allowing the system to stabilize, MD simulations consisting of 50,000,000 steps and lasting 100 nanoseconds were conducted on the structure. The backbone energy\u0026apos;s root mean square deviation (RMSD) is reduced following the MD simulation, and the outcomes are displayed graphically. Furthermore, an analysis was conducted on the radius of gyration (Rg), density plots, and hydrogen bonding in the MD simulations.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003eSequences and phylogenetic tree analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe alignment results of eight selected sequences are presented in Figure 1. The substitutions observed in the Fv1 protein across different species are highlighted. In addition, the ConservFold results revealed that the C-terminus of FV1 has several highly variable regions, which were previously indicated as possible regions to restrict different viruses (Figure 2 and Figure 4-D).\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;Figure 3 shows the phylogenetic tree of the Fv1 sequences, revealing the presence of two distinct clades. The upper clade contained two sequences (\u003cem\u003eLophuromys sikapusi\u003c/em\u003e: MH270656 and \u003cem\u003eLophuromys flavopunctatus\u003c/em\u003e: MH270655) that were grouped together, indicating their close phylogenetic relationship. On the other hand, the lower clade contained other species. Notably, all bootstraps were 100, which indicates the high reliability of the tree\u0026apos;s results.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026quot;\u003c/strong\u003e\u003cstrong\u003eProtParam\u0026quot; analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDespite several substitutions, physicochemical analysis of Fv1 in 8 species revealed that its isoelectric point (pI) consistently increased to approximately 5, indicating its acidic nature.\u003c/p\u003e\n\u003cp\u003eStability assessments of Fv1 in various host systems, including mammalian cells, yeast, and \u003cem\u003eE. coli\u003c/em\u003e, indicated proper stability across different hosts. However, while Fv1 demonstrated high stability in vivo, predictions suggested that it may be unstable in vitro, potentially leading to rapid degradation postextraction. Furthermore, Fv1 was found to be a thermostable protein, offering an advantage for laboratory use, and it exhibited hydrophilic properties, as summarized in Table 1. In addition, our prediction showed that \u003cem\u003eHIV Gag p24 is a basic protein that was predicted to be thermostable and stable in all\u0026nbsp;\u003c/em\u003e\u003cem\u003ethe\u0026nbsp;\u003c/em\u003e\u003cem\u003eindicated hosts.\u003c/em\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSignal peptide prediction\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTwo software programs detected a signal peptide that showed a region from amino acids 1 to 20 for Fv1, although the software could not identify the type of signal peptide. However, it might be suggested that this region must be omitted after protein secretion; therefore, in all protein expression systems in the laboratory, this region must be deleted to reach the proper tertiary structure. In addition, the software did not find any signal peptide for the \u003cem\u003eHIV Gag p24\u0026nbsp;\u003c/em\u003eprotein.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePostmodification\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe disulfide bond prediction revealed that two species (MH270656 and MH270655) presented four disulfide bonds each, whereas the other species presented different patterns of predicted bonds (see Table 2). This variance in disulfide bonds could cause significant changes in the structure and function of Fv1. Notably, the pattern of disulfide bonds closely mirrored the phylogenetic tree, with two species closely grouped in the upper clade and the remaining species clustered in the lower clade. Considering the disulfide bonds, spices can be categorized into four groups. The first group (MH270656, MH270655) has 4 bonds; however, the bonds are not in the exact same positions. Group 2, MH270651 and MH270650, had 2 bonds (114 \u0026ndash; 369 and 374 \u0026ndash; 400), and the third group (MH270654, MH270652, and MH270653) had two bonds (114 \u0026ndash; 367 and 372 \u0026ndash; 408), and the fourth group (MH270649) had two bonds (114 \u0026ndash; 365 and 370 \u0026ndash; 406). The cysteine at position 114 was highly conserved across all the species. While this amino acid formed a disulfide bond in 6 species, it was not predicted to do so in the two other species (MH270656 and MH270655).\u003c/p\u003e\n\u003cp\u003ePhosphorylation prediction analysis revealed that Fv1 is a highly phosphorylated protein, with numerous phosphorylation sites identified across various positions (see Table 2). However, the distribution of phosphorylation sites varied among the 8 species studied. Despite differences in the distribution of phosphorylation sites, certain positions were conserved among the majority of the species. For example, position 26 was completely conserved, with all sequences containing a phosphorylation site at this position. Additionally, positions 52, 23, and 53 were found in 7, 6, and 5 species, respectively. Finally, positions 60, 184, 198, and 202 were present in 4 species each.\u003c/p\u003e\n\u003cp\u003eThe glycosylation prediction analysis revealed that only two species (MH270656 and MH270655) presented a glycosylation site at position 42 (see Table 2). In contrast, other species presented different glycosylation sites, although position 58 was conserved among them.\u003c/p\u003e\n\u003cp\u003eAdditionally, for HIV Gag p24, four disulfide bonds, several phosphorylation sites, and two glycosylation sites were identified, indicating that these posttranslational modifications could influence the structure and function of this protein.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSecondary and tertiary\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003estructure\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;prediction\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe results of secondary structure prediction for all 8 Fv1 sequences and HIV Gag p24 software are summarized in Table 3. The analysis revealed that the primary structure in all the species consisted of an alpha helix and a random coil, although the percentages varied among the species. The assessment data of the 3D models suggested by I-Tasser are summarized in Table 4, and the selected model is bolded. The tertiary structures of Fv1 and the HIV-1 capsid are illustrated in Figure 4 (A and B).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDocking results\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDocking analysis via Hex revealed a high energy value for HIV Gag p24 and Fv1 docking (-618), and interaction site analysis revealed several amino acids involved in the interaction site (Table 5 and Figure 4-C). In addition, the interaction between Fv1 and the HIV-1 capsid structure was examined via protein-protein docking analysis via ClusPro 2.0. A total of all the models were generated through docking, and the least energy score was utilized to choose the models that interacted well with the receptor. According to our results, the docking complex of the Fv1 and HIV-1 capsid proteins with the lowest energy scores of -238.9 was considered for further analysis (Table 6, Figure 5).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMolecular dynamic analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFigure 6 (A-E) shows the results of the molecular dynamics simulations of the Fv1-capsid complex. The simulations were expected to determine the movement of molecules and atoms in the complex formed by the Fv1-capsid complex. Moreover, the interaction between the Fv1 and HIV-1 capsid proteins was calculated via Rg computation, energy minimization, potential energy determination, density assessment, pressure evaluation, and temperature analysis. We obtained the RMSD value by analyzing the trajectory generated in a 100 ns simulation. The RMSD value of the Fv1 and HIV-1 capsid molecules was 0.95 nm, suggesting that the complex is stable and devoid of fluctuations. RMSF analysis was used to assess the structural stability and mobility of the complex. The results indicated that the residues at the binding site fluctuated less. In addition, the Rg results revealed that the structure of the construct remained stable throughout the molecular dynamics simulation. In other words, the few fluctuations in RG supported our hypothesis of the compactness of the protein-ligand complex. The density analysis showed stability, suggesting that the Fv1-capsid complex was adequately equilibrated in terms of pressure and density. Our findings revealed that the Fv1-capsid complex achieves a balance between flexibility and stability, which helps to suppress HIV infection.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe capsid of HIV-1 plays crucial roles in various stages of the virus replication cycle, including assembly, release, maturation, and establishment of infection[\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]. Research has revealed its importance; however, there are currently no approved antiretroviral therapies that specifically target the Gag precursor protein or its mature forms[\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]. Recent advancements in the understanding of the structure and cell biology of the HIV-1 capsid have paved the way for the identification of potential targets useful for therapeutic intervention[\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. This study, for the first time, examined the possible interaction between Fv1, an intrinsic factor that inhibits retroviruses, and the HIV P24 protein via a bioinformatics approach and revealed a strong attachment between the two proteins (E value: -618). These results could confirm the ability of this protein to inhibit the HIV virus. Our analysis revealed several residues involved in this interaction, in which tyrosine 123 and proline 350 are conserved in all the selected sequences, indicating that these amino acids may play important roles in the possible inhibitory effects of Fv1 and could be interesting targets for generating mutant proteins to determine their possible roles.\u003c/p\u003e \u003cp\u003eOur findings revealed several conserved regions in the Fv1 protein and, in agreement with our results, two studies by Anthony Stevens et al. (2004) and Bishop et al. identified 3 variable regions (VR) in the Fv1 protein: VRA (amino acids 247\u0026ndash;276), VRB (amino acids 345\u0026ndash;358), and variable region C (amino acids 375\u0026ndash;401) [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. VRB contains most of the residues we identified via interaction analysis, and VRC, which can alter restriction specificity, contains glutamine 399, which is found in two selected sequences. Variable domains, collectively or individually, are involved in target selection and binding, which are important for the possible inhibition of Fv1. In addition, it was suggested that residue 399 was involved in determining tropism.\u003c/p\u003e \u003cp\u003eAmino acid 358 has been reported to frequently play the main role in interactions with the HIV capsid (amino acid 110 in the HIV capsid), and mutation of residue 358 to alanine might abolish the activity of Fv1[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan additionalcitationids=\"CR40 CR41\" citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. While our prediction showed that this residue is conserved among most sequences, the docking results could not reveal any interaction between this amino acid and the HIV capsid, possibly because of the different resources used in previous studies.\u003c/p\u003e \u003cp\u003eYuhe Yan et al. (2009) identified six codons, specifically Fv1 amino acids 261, 265, 270, 362, 399, and 401, that displayed evidence of positive selection during Mus evolution[\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. Amino acids 261, 362, and 399 were highly conserved in the selected sequences studied here. However, amino acid 401, while not conserved as either C, S, or T, still plays a significant role in interactions within the HIV-1 capsid.\u003c/p\u003e \u003cp\u003eIn 2014, Melvyn W. Yap et al. demonstrated that the C-terminal region of Fv1, which is believed to contain determinants of restriction specificity, is significantly different[\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. Consistent with Yap's findings, our analysis also suggested that many of the amino acids involved in potential interactions are in the C-terminal region, which comprises coil structures and represents a variable part of the protein. Consequently, certain Fv1 alleles may lack interaction sites and associated restriction activities. It would be of great interest to investigate whether these alleles recognize alternative targets, revealing the possible varied functions of Fv1 in viral restriction.\u003c/p\u003e \u003cp\u003eMD simulation analysis verified that the Fv1-capsid complex remains stable under various environmental conditions, even with changes in pressure and temperature. Furthermore, the initial evaluation, which involved calculating parameters such as the RMSD, radius of gyration, and hydrogen bonds, indicated that the Fv1-capsid complex demonstrated remarkable stability in a biological setting. It can be inferred that in cases of natural HIV infection, one way the virus is suppressed is through the interaction between FV-1 and the HIV-1 capsid protein, resulting in the inhibition of capsid function. These findings suggest that developing drugs that mimic the binding of FV-1 to the HIV-1 capsid, thus impeding the ability of the virus to infect cells at different stages, could be a promising approach for effectively combating the virus.\u003c/p\u003e \u003cp\u003eOur predictions suggest that mammalian cells, yeast, and \u003cem\u003eE. coli\u003c/em\u003e are suitable hosts for expressing the Fv1 protein. These findings are supported by several studies, including those by Wilson Li et al. (2016), Luca D. Passerini (2006), Anthony Stevens (2004), and Melvyn W. Yap (2003)[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. These studies have expressed Fv1 in various cell lines, such as Dunni tail fibroblasts, the human TE671 cell line, mouse fibroblasts, NIH3T3 cells, and BALB3T3 cells, confirming the stability of Fv1 in these cell lines. Additionally, Kate N. Bishop conducted two investigations demonstrating the stability of Fv1 in \u003cem\u003eE. coli\u003c/em\u003e, whereas Mark P. Dodding (2005) and Anthony Stevens (2004) suggested the ability of yeast to express Fv1[\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e, \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e, \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAfter reviewing publications, it became evident that more data are needed regarding postmodifications, such as phosphorylation, disulfide bonds, and glycosylation sites, in the Fv1 protein. This is the first comprehensive study to identify several modification sites that might be useful in defining their possible effects on the function and structure of this protein.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eHost restriction factors are cellular proteins that inhibit specific steps of the viral life cycle. In recent decades, several proteins have been identified, confirming the potential of these factors to inhibit viral infections. The present study, for the first time, suggests the probable inhibitory role of Fv1, a recognized host restriction factor, through its interaction with the HIV-1 capsid. Additionally, it predicts several characteristics of FV1 that could be valuable for subsequent investigations. In addition, MD analysis of the Fv1-capsid complex indicated that the interaction between Fv1 and the HIV-1 capsid led to significant conformational alterations, resulting in a strong affinity between the two proteins. However, to validate this claim, several experiments need to be conducted.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eFv1: susceptibility factor 1\u003c/p\u003e\n\u003cp\u003eMLV: murine leukemia virus\u003c/p\u003e\n\u003cp\u003eMD: Molecular dynamics\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTRIM5: factors\u0026nbsp;include\u0026nbsp;tripartite motif 5\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eHIV: human immunodeficiency virus\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate:\u003c/strong\u003e This study was approved by the local Ethics Committee of Shiraz University of Medical Sciences, Shiraz, Iran. All methods were carried out according to relevant guidelines and regulations.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eClinical Trial:\u003c/strong\u003e Not applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and material: \u003c/strong\u003eData that support the findings of this study are available from the corresponding author (Dr. Ava Hashempour) upon reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests: \u003c/strong\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e: This study was funded by Shiraz University of Medical Sciences (grant number 13787).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026apos; contributions :\u003c/strong\u003e BD: design of the work, the acquisition, analysis and providing the first draft. AH: providing main funds, data analysis, and editing the final draft.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e: This study was supported by Shiraz University of Medical Sciences.\u0026nbsp;\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eNakayama, E.E. and T. Shioda, \u003cem\u003eRole of Human TRIM5\u0026alpha; in Intrinsic Immunity.\u003c/em\u003e Frontiers in Microbiology, 2012. \u003cstrong\u003e3\u003c/strong\u003e.\u003c/li\u003e\n\u003cli\u003ePasserini, L.D., Z. Keckesova, and G.J. Towers, \u003cem\u003eRetroviral restriction factors Fv1 and TRIM5alpha act independently and can compete for incoming virus before reverse transcription.\u003c/em\u003e J Virol, 2006. \u003cstrong\u003e80\u003c/strong\u003e(5): p. 2100-5.\u003c/li\u003e\n\u003cli\u003eLi, W., M.W. Yap, V. Voss, and J.P. 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Stoye, \u003cem\u003eCapsid processing requirements for abrogation of Fv1 and Ref1 restriction.\u003c/em\u003e J Virol, 2005. \u003cstrong\u003e79\u003c/strong\u003e(16): p. 10571-7.\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 1:\u0026nbsp;\u003c/strong\u003eProtparam analysis of the FV1 proteins for 8 selected sequences and \u003cem\u003eHIV Gag P24.\u003c/em\u003e\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"921\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270656\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270655\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270651\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270650\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270654\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270652\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270653\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270649\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e\u003cstrong\u003egag\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNumber of amino acids\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e413\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e413\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e430\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e430\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e438\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e435\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e497\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMolecular weight\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e46867.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e46933.4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e48552.81\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e48579.92\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e49517.77\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e49501.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e49415.76\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e49242.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e55149.14\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTheoretical pI\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e5.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e5.52\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e5.02\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e5.11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e5.34\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e5.17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e5.23\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e5.23\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e9.18\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"3\" valign=\"top\" style=\"width: 53px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ehalf-life\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 114px;\"\u003e\n \u003cp\u003e\u003cstrong\u003emammalian reticulocytes\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e30\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 114px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eyeast\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e\u0026gt;20\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 114px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eEscherichia coli\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e\u0026gt;10\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eInstability index\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eUnstable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eUnstable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003eUnstable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003eUnstable\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eUnstable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eStable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e\u0026nbsp;Unstable\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u0026nbsp;Unstable\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003eUnstable\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eAliphatic index\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e86.61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e88.77\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e84.79\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e85\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e83.43\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e84.36\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e85.22\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e84.48\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e70.72\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 167px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eGRAVY\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e-0.391\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e-0.394\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e-0.481\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 89px;\"\u003e\n \u003cp\u003e-0.482\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e-0.509\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e-0.466\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003e-0.473\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e-0.452\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 91px;\"\u003e\n \u003cp\u003e-0.579\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 2:\u0026nbsp;\u003c/strong\u003eThe post-modification sites of FV1 and \u003cem\u003eHIV Gag P24\u003c/em\u003e, where various residues have undergone modifications such as disulfide bond formation, phosphorylation, and glycosylation.\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"1143\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" valign=\"top\" style=\"width: 164px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270656\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270655\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;MH270651\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;MH270650\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270654\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270652\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;MH270653\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;MH270649\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eg\u003c/strong\u003e\u003cstrong\u003eag\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"4\" valign=\"top\" style=\"width: 130px;\"\u003e\n \u003cp\u003e\u003cstrong\u003edisulphide bonds\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e150-318\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e150-154\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e - 369\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e - 369\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e - 367\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e - 157\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e - 367\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e114\u003c/strong\u003e \u0026ndash; 365\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e57-87\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e268-283\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e263-278\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e374 - 400\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e374 - 400\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e372 - 408\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e372 - 408\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e372 - 408\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e370 \u0026ndash; 406\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e329-349\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e274-339\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e269-334\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e392-410\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e344-380\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e339-375\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e382-402\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 130px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ephosphorylation sites\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e23,26,52,60,157,\u003c/p\u003e\n \u003cp\u003e206,211,216,324,\u003c/p\u003e\n \u003cp\u003e373\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e23,26,46,50,52,\u003c/p\u003e\n \u003cp\u003e53,60,184, 211\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e26,52,53,187,201,\u003c/p\u003e\n \u003cp\u003e205,225,229,246,\u003c/p\u003e\n \u003cp\u003e250,307\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e26,43,52,201,205,\u003c/p\u003e\n \u003cp\u003e210,225,229\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e23,26,52,53,60,\u003c/p\u003e\n \u003cp\u003e95,152,182,184,\u003c/p\u003e\n \u003cp\u003e198,202,226,241,\u003c/p\u003e\n \u003cp\u003e243,247,263,301,\u003c/p\u003e\n \u003cp\u003e398,428\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e23,26,122,125,184,\u003c/p\u003e\n \u003cp\u003e198,202,207,222,226,\u003c/p\u003e\n \u003cp\u003e241,247,304,346,398\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e23,26,52,53,95,\u003c/p\u003e\n \u003cp\u003e152,182,184,198,\u003c/p\u003e\n \u003cp\u003e202,207,226,241,\u003c/p\u003e\n \u003cp\u003e243,247,428\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e23,26,52,53,60,\u003c/p\u003e\n \u003cp\u003e63,184,198,202,\u003c/p\u003e\n \u003cp\u003e207,210,227,245,\u003c/p\u003e\n \u003cp\u003e261,302,426\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e6, 9,49,66,70,77,8411\u003c/p\u003e\n \u003cp\u003e124,128,145,147,164,175\u003c/p\u003e\n \u003cp\u003e179,203,233,240,241\u003c/p\u003e\n \u003cp\u003e250,261,277,280\u003c/p\u003e\n \u003cp\u003e302,309,341,356\u003c/p\u003e\n \u003cp\u003e424,437,448,453\u003c/p\u003e\n \u003cp\u003e459,467,469,481\u003c/p\u003e\n \u003cp\u003e485,496\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 33px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 130px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eglycosylation sites\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 97px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e42\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 93px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e42\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,227\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 100px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,227\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,224, 344\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 118px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,224\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,224,344\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e58\u003c/strong\u003e,222,342\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e47, 126\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003ch1\u003e\u0026nbsp;\u0026nbsp;\u003c/h1\u003e\n\u003cp\u003e\u003cstrong\u003eTable 3:\u003c/strong\u003e Secondary structure prediction estimated by SOPMA; most of the structures were alpha helix and random coil in all sequences. \u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"727\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270656\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270655\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270651\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270650\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270654\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270652\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270653\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMH270649\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 41px;\"\u003e\n \u003cp\u003e\u003cstrong\u003egag\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eAlpha helix\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.5085\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4891\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4744\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4605\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4577\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4726\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4622\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4598\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 41px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e44.06\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eExtended strand\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0605\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0847\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0837\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0837\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0572\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0913\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0732\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0759\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 41px;\"\u003e\n \u003cp\u003e3.02\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eBeta turn\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0218\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0533\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0349\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0419\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0297\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.032\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0503\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e0.0437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 41px;\"\u003e\n \u003cp\u003e0.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eRandom coil\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4092\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.3729\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.407\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.414\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4554\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4041\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4142\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 73px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e0.4207\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 41px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e52.92\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 4:\u003c/strong\u003e\u0026nbsp; The final results of 4 servers used to define the best 3D structure for Fv1 and HIV gag protein. The selected structure is bolded.\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"613\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFV1\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eModels\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eQmean\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eERRAT\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eProSA-web\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 170px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eRampage (Ramachandran plot) favor region %\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eI-TASSER\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003ewithout refinement\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-12.61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e78.2716\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-3.65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e75.1%\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"5\" valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eGalaxyRefine\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-6.47\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e76.4851\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e83.10%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-6.85\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e77.9703\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.64\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e81.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-6.8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e71.2871\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e83.10%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-6.69\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e76.2963\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.87\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e83.10%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e5\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e-6.6\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e76.4851\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e-4.9\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e83.70%\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"613\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003egag\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eModels\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eQmean\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eERRAT\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eProSA-web\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 170px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eRampage (Ramachandran plot) favor region %\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eI-TASSER\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003ewithout refinement\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-11.11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e75.2716\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e74.1%\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"5\" valign=\"top\" style=\"width: 16.8502%;\"\u003e\n \u003cp\u003e\u003cstrong\u003eGalaxyRefine\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-5.57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e75.4111\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e82.11%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-5.85\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e77.1233\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e82.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-5.18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e72.2871\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e84.30%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-5.69\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e75.2963\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e-4.27\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e82.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 17.388%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e5\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e-5.4\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e79.2351\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 15.0576%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e-4.81\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 19.0013%;\"\u003e\n \u003cp\u003e\u003cstrong\u003e87.80%\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 5:\u003c/strong\u003e The amino acid residues identified in the interaction sites during the docking analysis of Fv1 and HIV gag P24 proteins. Each row lists two amino acids predicted to interact with each other.\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"180\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFv1\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eP24 HIV\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eGLU149\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eLYS330\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eGLU399\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eVAL352\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eTYR123\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eASP283\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eGLY349\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eARG334\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003ePRO350\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eLYS330\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eVAL353\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eCYS349\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003eARG357\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eCYS349\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003ePRO152\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 107px;\"\u003e\n \u003cp\u003eLEU321\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003e6:\u0026nbsp;\u003c/strong\u003eMolecular docking results of Fv1 and HIV-1 capsid proteins generated using the Cluspro2.0 tool. (The best model is shown in bold font.).\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003ePredicted\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;models\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003eMembers\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003eRepresentative\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003eWeighted Score\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e0\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e50\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-206.1\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-221.1\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e1\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e49\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003eCenter\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e-223.9\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003eLowest Energy\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e-238.9\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e2\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-203.4\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-245.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e3\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-182.8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-214.2\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e4\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e23\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-228.8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-231.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e5\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-226.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-226.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e6\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-197.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-213.6\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e7\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-224.3\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-224.3\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e\u003cstrong\u003e8\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" valign=\"top\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eCenter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-211.8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003eLowest Energy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\"\u003e\n \u003cp\u003e-211.8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Virus susceptibility factor 1 (Fv1), HIV-1, Bioinformatics, Anti-HIV","lastPublishedDoi":"10.21203/rs.3.rs-5423642/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5423642/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eVirus susceptibility factor 1 (Fv1) serves as the prototype restriction factor guarding against infection by murine leukemia virus (MLV). Analysis of the Fv1 sequences revealed several residues in the C-terminal region that had undergone positive selection during evolution and might have played a role in various retroviral infections. For the first time, various bioinformatic tools have been applied to reveal specific residues involved in the interaction between Fv1 and the HIV-1 capsid as the target. Molecular dynamics (MD) simulation analysis of the Fv1-capsid complex confirmed the stability of the protein-protein complex. Docking and molecular dynamic simulation analyses demonstrated the potential of Fv1 to inhibit HIV-1 infection and supported the possibility that the HIV-1 capsid could be a target for novel anti-HIV medications. Furthermore, we revealed conserved regions, postmodification sites, and secondary and tertiary structures, which provided valuable data about the nature of the FV1 protein.\u003c/p\u003e","manuscriptTitle":"Unveiling Fv1's Potential: Insights into its Interaction with the HIV-1 Capsid","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-11-28 11:05:00","doi":"10.21203/rs.3.rs-5423642/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"a91460dc-afb5-44e9-b2d6-7e8610b65279","owner":[],"postedDate":"November 28th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-01-18T19:38:13+00:00","versionOfRecord":[],"versionCreatedAt":"2024-11-28 11:05:00","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5423642","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5423642","identity":"rs-5423642","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}