Skip to main content

Advertisement

SpringerLink
Log in

Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Human immunodeficiency virus type 1 protease (HIV-1 PR) cleaves two viral precursor proteins, Gag and Gag-Pol, at multiple sites. Although the processing proceeds in the rank order to assure effective viral replication, the molecular mechanisms by which the order is regulated are not fully understood. In this study, we used bioinformatics approaches to examine whether the folding preferences of the cleavage junctions influence their cleavabilities by HIV-1 PR. The folding of the eight-amino-acid peptides corresponding to the seven cleavage junctions of the HIV-1HXB2 Gag and Gag-Pol precursors were simulated in the PR-free and PR-bound states with molecular dynamics and homology modeling methods, and the relationships between the folding parameters and the reported kinetic parameters of the HIV-1HXB2 peptides were analyzed. We found that a folding preference for forming a dihedral angle of Cβ (P1)-Cα (P1)- Cα (P1’)-Cβ (P1’) in the range of 150 to 180 degrees in the PR-free state was positively correlated with the 1/Km (R = 0.95, P = 0.0008) and that the dihedral angle of the O (P2)-C (P2)- C (P1)- O (P1) of the main chains in the PR-bound state was negatively correlated with kcat (R = 0.94, P = 0.001). We further found that these two folding properties influenced the overall cleavability of the precursor protein when the sizes of the side chains at the P1 site were similar. These data suggest that the dihedral angles at the specific positions around the cleavage junctions before and after binding to PR are both critical for regulating the cleavability of precursor proteins by HIV-1 PR.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Leis J, Baltimore D, Bishop JM et al. (1988) Standardized and simplified nomenclature for proteins common to all retroviruses. J Virol 62:1808–1809

    CAS  Google Scholar 

  2. Partin K, Krausslich HG, Ehrlich L et al. (1990) Mutational analysis of a native substrate of the human immunodeficiency virus type 1 proteinase. J Virol 64:3938–3947

    CAS  Google Scholar 

  3. Wondrak EM, Louis JM, de Rocquigny H et al. (1993) The gag precursor contains a specific HIV-1 protease cleavage site between the NC (P7) and P1 proteins. FEBS Lett 333:21–24

    Article  CAS  Google Scholar 

  4. Louis JM, Dyda F, Nashed NT et al. (1998) Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. Biochemistry 37:2105–2110

    Article  CAS  Google Scholar 

  5. Mervis RJ, Ahmad N, Lillehoj EP et al. (1988) The gag gene products of human immunodeficiency virus type 1: alignment within the gag open reading frame, identification of posttranslational modifications, and evidence for alternative gag precursors. J Virol 62:3993–4002

    CAS  Google Scholar 

  6. Gowda SD, Stein BS, Engleman EG (1989) Identification of protein intermediates in the processing of the p55 HIV-1 gag precursor in cells infected with recombinant vaccinia virus. J Biol Chem 264:8459–8462

    CAS  Google Scholar 

  7. Krausslich HG, Ingraham RH, Skoog MT et al. (1989) Activity of purified biosynthetic proteinase of human immunodeficiency virus on natural substrates and synthetic peptides. Proc Natl Acad Sci USA 86:807–811

    Article  CAS  Google Scholar 

  8. Pettit SC, Moody MD, Wehbie RS et al. (1994) The p2 domain of human immunodeficiency virus type 1 Gag regulates sequential proteolytic processing and is required to produce fully infectious virions. J Virol 68:8017–8027

    CAS  Google Scholar 

  9. Lindhofer H, von der Helm K, Nitschko H (1995) In vivo processing of Pr160gag-pol from human immunodeficiency virus type 1 (HIV) in acutely infected, cultured human T-lymphocytes. Virology 214:624–627

    Article  CAS  Google Scholar 

  10. Almog N, Roller R, Arad G et al. (1996) A p6Pol-protease fusion protein is present in mature particles of human immunodeficiency virus type 1. J Virol 70:7228–7232

    CAS  Google Scholar 

  11. Wiegers K, Rutter G, Kottler H et al. (1998) Sequential steps in human immunodeficiency virus particle maturation revealed by alterations of individual Gag polyprotein cleavage sites. J Virol 72:2846–2854

    CAS  Google Scholar 

  12. Pettit SC, Henderson GJ, Schiffer CA et al. (2002) Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol 76:10226–10233

    Article  CAS  Google Scholar 

  13. Pettit SC, Everitt LE, Choudhury S et al. (2004) Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism. J Virol 78:8477–8485

    Article  CAS  Google Scholar 

  14. Pettit SC, Clemente JC, Jeung JA et al. (2005) Ordered processing of the human immunodeficiency virus type 1 GagPol precursor is influenced by the context of the embedded viral protease. J Virol 79:10601–10607

    Article  CAS  Google Scholar 

  15. Pettit SC, Lindquist JN, Kaplan AH et al. (2005) Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates. Retrovirology 2:66

    Article  Google Scholar 

  16. Jupp RA, Phylip LH, Mills JS et al. (1991) Mutating P2 and P1 residues at cleavage junctions in the HIV-1 pol polyprotein. Effects on hydrolysis by HIV-1 proteinase. FEBS Lett 283:180–184

    Article  CAS  Google Scholar 

  17. Tritch RJ, Cheng YE, Yin FH et al. (1991) Mutagenesis of protease cleavage sites in the human immunodeficiency virus type 1 gag polyprotein. J Virol 65:922–930

    CAS  Google Scholar 

  18. Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2000) How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol 301:1207–1220

    Article  CAS  Google Scholar 

  19. Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2002) Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure 10:369–381

    Article  CAS  Google Scholar 

  20. King NM, Prabu-Jeyabalan M, Nalivaika EA et al. (2004) Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chem Biol 11:1333–1338

    CAS  Google Scholar 

  21. King NM, Prabu-Jeyabalan M, Nalivaika EA et al. (2004) Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor. J Virol 78:12012–12021

    Article  CAS  Google Scholar 

  22. Prabu-Jeyabalan M, Nalivaika EA, King NM et al. (2004) Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J Virol 78:12446–12454

    Article  CAS  Google Scholar 

  23. Tyndall JD, Nall T, Fairlie DP (2005) Proteases universally recognize beta strands in their active sites. Chem Rev 105:973–999

    Article  CAS  Google Scholar 

  24. Fairlie DP, Tyndall JD, Reid RC et al. (2000) Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. J Med Chem 43:1271–1281

    Article  CAS  Google Scholar 

  25. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314:141–151

    Article  CAS  Google Scholar 

  26. Pitera JW, Swope W (2003) Understanding folding and design: replica-exchange simulations of “Trp-cage” miniproteins. Proc Natl Acad Sci USA 100:7587–7592

    Article  CAS  Google Scholar 

  27. Andrec M, Felts AK, Gallicchio E et al. (2005) Protein folding pathways from replica exchange simulations and a kinetic network model. Proc Natl Acad Sci USA 102:6801–6806

    Article  CAS  Google Scholar 

  28. Im W, Brooks CL (2005) Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci USA 102:6771–6776

    Article  CAS  Google Scholar 

  29. Seibert MM, Patriksson A, Hess B et al. (2005) Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J Mol Biol 354:173–183

    Article  CAS  Google Scholar 

  30. Marti-Renom MA, Stuart AC, Fiser A et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325

    Article  CAS  Google Scholar 

  31. Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93–96

    Article  CAS  Google Scholar 

  32. Shirakawa K, Takaori-Kondo A, Yokoyama M et al. (2008) Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nat Struct Mol Biol 15:1184–1191

    Article  CAS  Google Scholar 

  33. Maschera B, Darby G, Palu G et al. (1996) Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J Biol Chem 271:33231–33235

    Article  CAS  Google Scholar 

  34. Zoete V, Michielin O, Karplus M (2002) Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol 315:21–52

    Article  CAS  Google Scholar 

  35. Perryman AL, Lin JH, McCammon JA (2004) HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci 13:1108–1123

    Article  CAS  Google Scholar 

  36. Ode H, Neya S, Hata M et al. (2006) Computational simulations of HIV-1 proteases–multi-drug resistance due to nonactive site mutation L90M. J Am Chem Soc 128:7887–7895

    Article  CAS  Google Scholar 

  37. Ode H, Matsuyama S, Hata M et al. (2007) Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease. J Mol Biol 370:598–607

    Article  CAS  Google Scholar 

  38. Pearlman DA, Case DA, Caldwell JW et al. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 91:1–41

    Article  CAS  Google Scholar 

  39. Kollman PA, Massova I, Reyes C et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897

    Article  CAS  Google Scholar 

  40. Hornak V, Abel R, Okur A et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712–725

    Article  CAS  Google Scholar 

  41. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55:383–394

    Article  CAS  Google Scholar 

  42. Tie Y, Boross PI, Wang YF et al. (2005) Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. FEBS J 272:5265–5277

    Article  CAS  Google Scholar 

  43. Sayer JM, Liu F, Ishima R et al. (2008) Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease. J Biol Chem 283:13459–13470

    Article  CAS  Google Scholar 

  44. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calcluating conformational energies of organic and biological molecules? J Comput Chem 29:1693–1698

    Google Scholar 

  45. Labute P (2008) The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area. J Comput Chem 29:1693–1698

    Article  CAS  Google Scholar 

  46. Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85

    Article  CAS  Google Scholar 

  47. Kontijevskis A, Prusis P, Petrovska R et al. (2007) A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol 3:e48

    Article  Google Scholar 

  48. Szeltner Z, Polgar L (1996) Rate-determining steps in HIV-1 protease catalysis. The hydrolysis of the most specific substrate. J Biol Chem 271:32180–32184

    Article  CAS  Google Scholar 

  49. Tozser J, Gustchina A, Weber IT et al. (1991) Studies on the role of the S4 substrate binding site of HIV proteinases. FEBS Lett 279:356–360

    Article  CAS  Google Scholar 

  50. You L, Garwicz D, Rognvaldsson T (2005) Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease. J Virol 79:12477–12486

    Article  CAS  Google Scholar 

  51. Dogra SK. “Y Scrmabling” from QSARWorld - A Strand Life Sciences Web Resource. Available from: http://www.qsarworld.com/qsar-statistics-y-scrambling.php

  52. Zamyatin AA (1972) Protein volume in solution. Prog Biophys Mol Biol 24:107–123

    Article  Google Scholar 

  53. Prabu-Jeyabalan M, King NM, Nalivaika EA et al. (2006) Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother 50:1518–1521

    Article  CAS  Google Scholar 

  54. Okimoto N, Tsukui T, Hata M et al. (1999) Hydrolysis mechanism of the phenylalanine-proline peptide bond specific to HIV-1 protease: investigation by the ab initio melecular orbital method. J Am Chem Soc 121:7349–7354

    Article  CAS  Google Scholar 

  55. Okimoto N, Tsukui T, Kitayama K et al. (2000) Molecular dynamics study of HIV-1 protease-substrate complex: roles of the water molecules at the loop structures of the active site. J Am Chem Soc 122:5613–5622

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by a Grant-in-Aid for Japan Society for the Promotion of Science (JSPS) Research Fellowships, and a Grant for HIV/AIDS Research from the Ministry of Health, Labor and Welfare of Japan.

Author contributions

Designed the research: H.O. and H.S. Performed the research: H.O. Contributed analytic tools: M.Y. and T.K. Analyzed the data: H.O. Wrote the paper: H.O. and H.S.

Author information

Authors and Affiliations

  1. Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, MusashiMurayama-shi, Tokyo, 208-0011, Japan

    Hirotaka Ode, Masaru Yokoyama, Tadahito Kanda & Hironori Sato

Authors
  1. Hirotaka Ode
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masaru Yokoyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tadahito Kanda
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hironori Sato
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hirotaka Ode.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 367 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ode, H., Yokoyama, M., Kanda, T. et al. Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability. J Mol Model 17, 391–399 (2011). https://doi.org/10.1007/s00894-010-0739-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-010-0739-z

Keywords

Search

Navigation