The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 4, 2014, Pages 633-639

  Kimura, Sachie ^a   Caldarini, Martina ^a   Broglia, Ricardo A ^a,b   Dokholyan, Nikolay V ^c   Tiana, Guido ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Computational model; Equilibrium properties; MD simulations; Non native interactions; Protein dimerization

Indexed keywords

DIMER; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; MONOMER;

ARTICLE; CALORIMETRY; CONFORMATION; DIMERIZATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROCESSING; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

COMPUTATIONAL MODEL; EQUILIBRIUM PROPERTIES; MD SIMULATIONS; NON-NATIVE INTERACTIONS; PROTEIN DIMERIZATION;

CALORIMETRY; ENZYME PRECURSORS; HIV PROTEASE; HIV-1; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY;

EID: 84895519880     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24440     Document Type: Article

References (28)

1. Ishima R, Torchia DA, Louis JM. Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor. J Biol Chem 2007;282:17190-17199.
2. Louis JM, Nashed NT, Parris KD, Kimmel AR, Jerina DM. Kinetics and mechanism of autoprocessing of human immunodeficiency virus type 1 protease from an analog of the Gag-Pol polyprotein. Proc Natl Acad Sci USA 1994;91:7970-7974.
3. Louis JM, Wondrak EM, Kimmel AR, Wingfield PT, Nashed NT. Proteolytic processing of HIV-1 protease precursor, kinetics and mechanism. J Biol Chem 1999;274:23437-23442.
4. Louis JM, Aniana A, Weber IT, Sayer JM. Inhibition of autoprocessing of natural variants and multidrug resistant mutant precursors of HIV-1 protease by clinical inhibitors. Proc Natl Acad Sci USA 2011;108:9072-9077.
5. Ishima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM. Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor. J Biol Chem 2003;278:43311-43319.
6. Cecconi F, Micheletti C, Carloni P, Maritan A. Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways. Proteins 2001;43:365-372.
7. Levy Y, Caflisch A, Onuchic JN, Wolynes PG. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. J Mol Biol 2004;340:67-79.
8. Bonomi M, Barducci A, Gervasio FL, Parrinello M. Multiple routes and milestones in the folding of HIV-1 protease monomer. PLoS One 2010;5:e13208.
9. Tozzini V, Trylska J, Chang C-E, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007;157:606-615.
10. Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci USA 2006;103:915-920.
11. Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci USA 2012;109:17845-17850.
12. Ding F, Tsao D, Nie H, Dokholyan NV. Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure 2008;16:1010-1018.
13. Shirvanyants D, Ding F, Tsao D, Ramachandran S, Dokholyan NV. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B 2012;116:8372-8382.
14. Yin S, Ding F, Dokholyan NV. Eris: an automated estimator of protein stability. Nat Methods 2007;4:466-467.
15. Dokholyan NV, Buldryev SV, Stanley HE, Shakhnovich EI. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 1998;3:577-587.
16. Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics. WIREs Comput Mol Sci 2011;1:80-92.
17. Tang C, Louis JM, Aniana A, Suh J-Y, Clore GM. Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease. Nature 2008;455:693-696.
18. Ferrenberg A, Swendsen R. Optimized Monte Carlo data analysis. Phys Rev Lett 1989;63:1195-1198.
19. Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN. SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res 2010;38:W657-W661.
20. Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Peptide folding: when simulation meets experiment. Angew Chem Int Ed Engl 1999;38:236-240.
21. Yamazaki T, Hinck AP, Wang Y-X, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, Kaufman JD, Chang CH, Domaille PJ, Lam PY. Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. Protein Sci 1996;5:495-506.
22. Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008;18:342-348.
23. Sayer JM, Liu F, Ishima R, Weber IT, Louis JM. Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease. J Biol Chem 2008;283:13459-13470.
24. Noel AF, Bilsel O, Kundu A, Wu Y, Zitzewitz JA, Matthews CR. The folding free-energy surface of HIV-1 protease: insights into the thermodynamic basis for resistance to inhibitors. J Mol Biol 2009;387:1002-1016.
25. Liwo A, Khalili M, Scheraga HA. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci USA 2005;102:2362-2367.
26. Louis JM, Clore GM, Gronenborn AM. Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat Struct Biol 1999;6:868-875.
27. Spinelli S, Liu QZ, Alzari PM, Hirel PH, Poljak RJ. The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie 1991;73:1391-1396.
28. Limongelli V, Bonomi M, Parrinello M. Funnel metadynamics as accurate binding free-energy method. Proc Natl Acad Sci USA 2013;110:6358-6363.