Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways

Proteins: Structure, Function and Genetics

Volumn 43, Issue 4, 2001, Pages 365-372

  Cecconi, Fabio ^a,b   Micheletti, Cristian ^a,b   Carloni, Paolo ^a,b,c   Maritan, Amos ^a,b  

^a SISSA   (Italy)

^b INFM   (Italy)

^c INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

Drug resistance; Folding pathways; HIV 1 protease

Indexed keywords

AMPRENAVIR; ANTIINFECTIVE AGENT; INDINAVIR; NELFINAVIR; PROTEINASE; RITONAVIR; SAQUINAVIR;

ANTIBIOTIC RESISTANCE; ARTICLE; CALCULATION; CORRELATION FUNCTION; ENZYME ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; PHENOTYPE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; SIMULATION;

AMINO ACID SEQUENCE; DRUG RESISTANCE, MICROBIAL; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; HUMANS; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; STATISTICS; THERMODYNAMICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0035371215     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1049     Document Type: Article

References (36)

1. Gulnik S, Erickson JW, Xie D. HIV protease: enzyme function and drug resistance. Vitam Horm 2000;58:213-256.
2. Wlodawer A, Erickson JW. Structure-based inhibitors of HIV-1 protease. Annu Rev Biochem 1993;62:543-585.
3. Reddy P, Ross J. A protease inhibitor for the treatment of patients with HIV-1 infection. Formulary 1999;34:567-675.
4. Ala PJ, Huston EE, Klabe RM, Jadhav PK, Lam PY, Chang CH. Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities. Biochemistry 1998;37:15042-15049.
5. Condra JH, Schleif WA, Blahy OM, Gabryelski LJ, Graham DJ, Quintero JC, Rhodes A, Robbing HL, Roth E, Shivaprakash M, et al. In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature 1995;374:569-571.
6. Brown AJ, Korber BT, Condra JH. Associations between amino acids in the evolution of HIV type 1 protease sequences under indinavir therapy. AIDS Res Hum Retroviruses 1999;15:247-253.
7. Durant J, Clevenbergh P, Halfon P, Delgiudice P, Porsin S, Simonet P, Montagne N, Boucher CA, Schapiro JM, Dellamonica P. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet 1999;353:2195-2199.
8. Boucher C. Rational approaches to resistance: using saquinavir. AIDS 1996(suppl 1):S15-S19.
9. Micheletti C, Banavar JR, Maritan A, Seno F. Protein structures and optimal folding from a geometrical variational principle. Phys Rev Lett 1999;82:3372-3375.
10. Fersht AR. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc Natl Acad Sci USA 1995;92:10869-10873.
11. Maritan A, Micheletti C, Banavar JR. Role of secondary motifs in fast folding polymers: a dynamical variational principle. Phys Rev Lett 2000;84:3009-3012.
12. Galzitskaya OV, Finkelstein AV. A theoretical search for folding/ unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci USA 1999;96:11299-11304.
13. Munoz V, Henry ER, Hofrichter J, Eaton WA. A statistical mechanical model for beta-hairpin kinetics. Proc Natl Acad Sci USA 199826;95:5872-5879.
14. Aim E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci USA 1999;96:11305-11310.
15. Chiti F, Taddei N, White PM, Bucciantini M, Magherini F, Stefani M, Dobson CM. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Struct Biol 1999;6:1005-1009.
16. Martinez JC, Pisabarro MT, Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Struct Biol 1998;5:721-729.
17. Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 2000;298: 937-953.
18. Martinez JC, Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct Biol 1999;6:1010-1016.
19. Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct Biol 1999;6:1016-1024.
20. Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
21. Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
22. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
23. Wolynes PG, Onuchic JN, Thirumalai D. Navigating the folding routes. Science 1995;267:1619-1620.
24. Go N, Scheraga HA. On the use of classical statistical mechanics in the treatment of polymer chain conformations. Macromolecules 1976;9:535-542.
25. Clementi C, Carloni P, Maritan A. Protein design is a key factor for subunit-subunit association. Proc Natl Acad Sci USA 1999;96: 9616-9621.
26. Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins 1998;30:2-33.
27. Evans DJ, Hoover WG, Failor BH, Moran B, Ladd AJC. Phys Rev A 1983;28:1016-1021.
28. Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1989;63:1195-1198.
29. Hao MH, Scheraga HA. On foldable protein-like models; a statistical-mechanical study with Montecarlo simulations. Physica A 1997;244:124-145.
30. Molla A, Korneyeva M, Gao Q, Vasavanonda S, Schipper PJ, Mo HM, Markowitz M, Chernyavskiy T, Niu P, Lyons N, Hsu A, Granneman GR, Ho DD, Boucher CA, Leonard JM, Norbeck DW, Kempf DJ. Ordered accumulation of mutations in HIV protease confers resistance to ritonavir. Nature Med 1996;2:760-766.
31. Markowitz M, Mo H, Kempf DJ, Norbeck DW, Bhat TN, Erickson JW, Ho DD. Selection and analysis of human immunodeficiency virus type 1 variants with increased resistance to ABT-538, a novel protease inhibitor. J Virol 1995;69:701-706.
32. Patick AK, Mo H, Markowitz M, Appelt K, Wu B, Musick L, Kalish V, Kaldor S, Reich S, Ho D, Webber S. Antiviral and resistance studies of AG1343, an orally bioavailable inhibitor of human immunodeficiency virus protease. Antimicrob Agents Chemother 1996;40:292-297.
33. Tisdale M, Myers RE, Maschera B, Parry NR, Oliver NM, Blair ED. Cross-resistance analysis of human immunodeficiency virus type 1 variants individually selected for resistance to five different protease inhibitors. Antimicrob Agents Chemother 1995;39:1704-1710.
34. Jacobsen H, Hanggi M, Ott M, Duncan IB, Owen S, Andreoni M, Vella S, Mous J. In vivo resistance to a human immunodeficiency virus type 1 proteinase inhibitor: mutations, kinetics, and frequencies. J Infect Dis 1996;173:1379-1387.
35. Chen Z, Li Y, Schock HB, Hall D, Chen E, Kuo LC. Three-dimensional structure of a mutant HIV-1 protease displaying cross-resistance to all protease inhibitors in clinical trials. J Biol Chem 1995;270:21433-21436.
36. Nair AC, Miertus S, Tossi A, Romeo D. A computational study of the resistance of HIV-1 aspartic protease to the inhibitors ABT-538 and VX-478 and design of new analogues. Biochem Biophys Res Commun 1998;242:545-551.