The molecular evolution of HIV-1 protease simulated at atomic detail

Proteins: Structure, Function and Bioinformatics

Volumn 76, Issue 4, 2009, Pages 895-910

  Tiana, G ^a   Broglia, R A ^a,b  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Computational models; Evolution; HIV 1 protease

Indexed keywords

PROTEINASE;

AMINO ACID SEQUENCE; ARTICLE; ENZYME CONFORMATION; ENZYME STABILITY; HUMAN IMMUNODEFICIENCY VIRUS 1; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION; STRUCTURAL PROTEOMICS; VIRUS RESISTANCE;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; HIV PROTEASE; HIV-1; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; SEQUENCE ALIGNMENT; THERMODYNAMICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 68149132087     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22395     Document Type: Article

References (43)

1. Tomasselli AG, Heinrikson RL. Targeting the HIV-protease in AIDS therapy: a current clinical perspective. Biochim Biophys Acta 2000;1477:189-214.
2. Kelly JK. Replication rate and evolution in the human immunodeficiency virus. J Theor Biol 1996;180:359-364. (Pubitemid 26258554)
3. Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis and therapy. Science 1995;373:382-389.
4. Rodriguez-Barros F, Gago F. HIV protease inhibition: limited recent progress and advances in understanding current pitfalls. Curr Top Med Chem 2004;4:991-1007. (Pubitemid 38854851)
5. Dixit NM, Perelson AS. HIV dynamics with multiple infections of target cells. Proc Natl Acad Sci USA 2005;102:8198-8203. (Pubitemid 40800066)
6. Broglia RA, Tiana G, Sutto L, Provasi D, Simona F. Design of HIV- 1-PR inhibitors that do not create resistance: blocking the folding of single monomers. Protein Sci 2005;14:2668-2681. (Pubitemid 41395593)
7. Broglia RA, Levy Y, Tiana G. HIV-1 protease folding and the design of drugs which do not create resistance. Curr Opin Struct Biol 2008;18:60-66.
8. Broglia RA, Provasi D, Vasile F, Ottolina G, Longhi R, Tiana G. A folding inhibitor of the HIV-1 protease. Proteins 2006;62:928-933.
9. Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387. (Pubitemid 34722226)
10. Shakhnovich E, Gutin AM. A new approach to the design of stable proteins. Protein Eng 1993;6:793-800. (Pubitemid 23347353)
11. Shakhnovich EI, Gutin AM. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA 1993;90:7195-7199. (Pubitemid 23222416)
12. Tiana G, Broglia RA, Shakhnovich EI. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins 2000;39:244-251. (Pubitemid 30226506)
13. Dokholyan NV, Shakhnovich EI. Understanding hierarchical protein evolution from first principles. J Mol Biol 2001;312:289-307.
14. Jung A, Maier R, Vartanian JP, Bocharov G, Jung V, Fischer U, Meese E, Wain-Hobson S, Meyerhans A. Multiply infected spleen cells in HIV patients. Nature 2002;418:144. (Pubitemid 34773761)
15. Branden C, Tooze J. Introduction to protein structure. Garland Publishing, Inc., New York; 1999.
16. Abkevich VI, Gutin AM, Shakhnovich E. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 1994;33:10026-10036. (Pubitemid 24286081)
17. Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151. (Pubitemid 129556751)
18. Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
19. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comp Chem 2005;26:1701-1718.
20. Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991;9:56-68.
21. Holm L, Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res 1996;24:206-209. (Pubitemid 26085767)
22. Mirny LA, Shakhnovich EI. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 1999;291:177-196.
23. Mirny L, Shakhnovich E. Evolutionary conservation of the folding nucleus. J Mol Biol 2001;308:123-129.
24. Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Meth Enzymol 1990;183:63-98.
25. Xie D, Gulnik S, Gustchina E, Yu B, Shao W, Qoronfleh W, Nathan A, Erickson JW. Drug resistance mutations can effect dimer stability of HIV-1 protease at neutral pH. Protein Sci 1999;8:1702-1707. (Pubitemid 29379953)
26. Tiana G, Broglia RA. Design and folding of dimeric proteins. Proteins 2002;49:82-94.
27. Tiana G, Provasi D, Broglia RA. Role of bulk and of interface contacts in the behaviour of lattice model dimeric proteins. Phys Rev E 2003;67:051909.
28. Farber PJ, Mittermainer A. Side chain burial and hydrophobic core packing in protein folding transition states. Protein Sci 2008;17: 644-651.
29. Broglia RA, Tiana G. Hierarchy of events in the folding of model proteins. J Chem Phys 2001;114:7267-7273. (Pubitemid 32445505)
30. Tiana G, Broglia RA. Statistical analysis of native contact formation in the folding of designed model proteins. J Chem Phys 2001;114: 2503-2510. (Pubitemid 32873126)
31. Ding F, Dokholyan NV. Emergence of protein fold families through rational design. PLoS Comput Biol 2006;2:e85. (Pubitemid 44147383)
32. Wallqvist A, Smythers GW, Covell DG. A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations. Protein Eng 1998;11:999-1005.
33. Broglia RA, Tiana G, Sutto L, Provasi D, Simona F. The physics of protein folding and of non-conventional drug design: attacking AIDS with its own weapons. La Rivista del Nuovo Cimento 2007;29:1-119.
34. Szeltner Z, Polgár L. Conformational stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration. J Biol Chem 1996;271:5458-5463. (Pubitemid 26083878)
35. Derrida B. Random energy model: an exactly solvable model of disordered systems. Phys Rev B 1981;24:2613-2626.
36. Ramanathan S, Shakhnovich EI. Statistical mechanics of proteins with evolutionary selected sequences. Phys Rev E 1994;50:1303-1312.
37. Mezard M, Parisi G, Virasoro MA. Spin Glasses and beyond. World Scientific, Singapore; 1987.
38. Govindarajan S, Goldstein RA. The foldability landscape of model proteins. Biopolymers 1997;42:427-438.
39. Govindarajan S, Goldstein RA. Evolution of model proteins on a foldability landscape. Proteins 1997;29:461-466. (Pubitemid 27520199)
40. Rhee S-Y, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 2003;31:298-303. (Pubitemid 36150389)
41. Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA. Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol 2006;80:3607-3616.
42. Rost B. Protein structures sustain evolutionary drift. Fold Des 1997;2:S19-S24. (Pubitemid 127740475)
43. Frauenfelder H, Wolynes PG. Biomolecules: where the physics of complexity and simplicity meet. Phys Today 1994;47:58-64. (Pubitemid 24976454)