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Volumn 70, Issue 4, 2008, Pages 1408-1415

A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps

Author keywords

AIDS; Dynamics; Molecular dynamics; Relaxation; Retrovirus

Indexed keywords

DIMER; MONOMER; PROTEINASE;

EID: 39749086224     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21632     Document Type: Article
Times cited : (36)

References (33)
  • 2
    • 0027218692 scopus 로고
    • Structure-based inhibitors of HIV-1 protease
    • Wlodawer A, Erickson JW. Structure-based inhibitors of HIV-1 protease. Annu Rev Biochem 1993;62:543-585.
    • (1993) Annu Rev Biochem , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 3
    • 0027137058 scopus 로고
    • Catalytic contribution of flap-substrate hydrogen bonds in "HIV-1 protease" explored by chemical synthesis
    • Baca M, Kent SB. Catalytic contribution of flap-substrate hydrogen bonds in "HIV-1 protease" explored by chemical synthesis. Proc Natl Acad Sci USA 1993;90:11638-11642.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11638-11642
    • Baca, M.1    Kent, S.B.2
  • 4
    • 0030910583 scopus 로고    scopus 로고
    • Sequence requirements of the HIV-1 protease flap region determined by saturation mutagenesis and kinetic analysis of flap mutants
    • Shao W, Everitt L, Manchester M, Loeb DD, Hutchison CA III, Swanstrom R. Sequence requirements of the HIV-1 protease flap region determined by saturation mutagenesis and kinetic analysis of flap mutants. Proc Natl Acad Sci USA 1997;94:2243-2248.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 2243-2248
    • Shao, W.1    Everitt, L.2    Manchester, M.3    Loeb, D.D.4    Hutchison III, C.A.5    Swanstrom, R.6
  • 5
    • 0026344399 scopus 로고
    • The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU
    • 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.
    • (1991) Biochimie , vol.73 , pp. 1391-1396
    • Spinelli, S.1    Liu, Q.Z.2    Alzari, P.M.3    Hirel, P.H.4    Poljak, R.J.5
  • 7
    • 0027309442 scopus 로고
    • Inhibitor binding to the Phe53Trp mutant of HIV-1 protease promotes conformational changes detectable by spectrofluorometry
    • Rodriguez EJ, Debouck C, Deckman IC, Abu-Soud H, Raushel FM, Meek TD. Inhibitor binding to the Phe53Trp mutant of HIV-1 protease promotes conformational changes detectable by spectrofluorometry. Biochemistry 1993;32:3557-3563.
    • (1993) Biochemistry , vol.32 , pp. 3557-3563
    • Rodriguez, E.J.1    Debouck, C.2    Deckman, I.C.3    Abu-Soud, H.4    Raushel, F.M.5    Meek, T.D.6
  • 9
    • 0027468137 scopus 로고
    • Molecular dynamics simulation of HIV-1 protease in a crystalline
    • York DM, Darden TA, Pedersen LG, Anderson MW. Molecular dynamics simulation of HIV-1 protease in a crystalline. Biochemistry 1993;32:1443-1453.
    • (1993) Biochemistry , vol.32 , pp. 1443-1453
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3    Anderson, M.W.4
  • 10
    • 0028958868 scopus 로고
    • Flap opening in HIV-1 protease simulated by activated molecular-dynamics
    • Collins JR, Burt SK, Erickson JW. Flap opening in HIV-1 protease simulated by activated molecular-dynamics. Nat Struct Biol 1995; 2:334-338.
    • (1995) Nat Struct Biol , vol.2 , pp. 334-338
    • Collins, J.R.1    Burt, S.K.2    Erickson, J.W.3
  • 11
    • 0032127391 scopus 로고    scopus 로고
    • Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease
    • Rick SW, Erickson JW, Burt SK. Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease. Proteins 1998;32:7-16.
    • (1998) Proteins , vol.32 , pp. 7-16
    • Rick, S.W.1    Erickson, J.W.2    Burt, S.K.3
  • 12
    • 26444548978 scopus 로고    scopus 로고
    • Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease
    • Hamelberg D, McCammon JA. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc 2005;127:13778-13779.
    • (2005) J Am Chem Soc , vol.127 , pp. 13778-13779
    • Hamelberg, D.1    McCammon, J.A.2
  • 13
    • 0034483901 scopus 로고    scopus 로고
    • Urling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
    • Scott WRP, Schiffer CA. Urling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 2000;8:1259-1265.
    • (2000) Structure , vol.8 , pp. 1259-1265
    • Scott, W.R.P.1    Schiffer, C.A.2
  • 14
    • 11344292848 scopus 로고    scopus 로고
    • A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the. active site
    • Kovalskyy D, Dubyna V, Mark AE, Kornelyuk A. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: the role of Na+ ions in stabilizing the. active site. Proteins 2005;58:450-458.
    • (2005) Proteins , vol.58 , pp. 450-458
    • Kovalskyy, D.1    Dubyna, V.2    Mark, A.E.3    Kornelyuk, A.4
  • 15
    • 1842454635 scopus 로고    scopus 로고
    • 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
    • Perryman AL, Lin JH, McCammon JA. 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 2004;13:1108-1123.
    • (2004) Protein Sci , vol.13 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 16
    • 10844257486 scopus 로고    scopus 로고
    • Solvation influences flap collapse in HIV-1 protease
    • Meagher KL, Carlson HA. Solvation influences flap collapse in HIV-1 protease. Proteins 2005;58:119-125.
    • (2005) Proteins , vol.58 , pp. 119-125
    • Meagher, K.L.1    Carlson, H.A.2
  • 17
    • 32244437816 scopus 로고    scopus 로고
    • HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
    • 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.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 915-920
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 18
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF. Protein flexibility predictions using graph theory. Proteins 2001;44:150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 19
    • 0037963159 scopus 로고    scopus 로고
    • Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
    • Kurt N, Scott WRP, Schiffer CA, Haliloglu T. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins 2003;51:409-422.
    • (2003) Proteins , vol.51 , pp. 409-422
    • Kurt, N.1    Scott, W.R.P.2    Schiffer, C.A.3    Haliloglu, T.4
  • 20
    • 2942615093 scopus 로고    scopus 로고
    • The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations
    • 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.
    • (2004) J Mol Biol , vol.340 , pp. 67-79
    • Levy, Y.1    Caflisch, A.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 21
    • 33744730369 scopus 로고    scopus 로고
    • Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases
    • Toth G, Borics A. Closing of the flaps of HIV-1 protease induced by substrate binding: a model of a flap closing mechanism in retroviral aspartic proteases. Biochemistry 2006;45:6606-6614.
    • (2006) Biochemistry , vol.45 , pp. 6606-6614
    • Toth, G.1    Borics, A.2
  • 22
    • 33644948688 scopus 로고    scopus 로고
    • HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
    • Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. J Am Chem Soc 2006;128:2812-2813.
    • (2006) J Am Chem Soc , vol.128 , pp. 2812-2813
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 23
    • 0034927324 scopus 로고    scopus 로고
    • Nuclear magnetic resonance relaxation in determination of residue-specific N-15 chemical shift tensors in proteins in solution: Protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Nuclear magnetic resonance of biological macromolecules, Part B
    • Fushman D, Cowburn D. Nuclear magnetic resonance relaxation in determination of residue-specific N-15 chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Nuclear magnetic resonance of biological macromolecules, Part B. Methods Enzymol 2001;339:109.
    • (2001) Methods Enzymol , vol.339 , pp. 109
    • Fushman, D.1    Cowburn, D.2
  • 24
    • 0034984208 scopus 로고    scopus 로고
    • Nmr probes of molecular dynamics: Overview and comparison with other techniques
    • Palmer AG III. Nmr probes of molecular dynamics: overview and comparison with other techniques. Annu Rev Biophys Biomol Struct 2001;30:129-155.
    • (2001) Annu Rev Biophys Biomol Struct , vol.30 , pp. 129-155
    • Palmer III, A.G.1
  • 25
    • 14844361989 scopus 로고    scopus 로고
    • NMR studies of protein structure and dynamics
    • Kay LE. NMR studies of protein structure and dynamics. J Magn Reson 2005;173:193-207.
    • (2005) J Magn Reson , vol.173 , pp. 193-207
    • Kay, L.E.1
  • 26
    • 33646911358 scopus 로고    scopus 로고
    • Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences
    • Jarymowycz VA, Stone MJ. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 2006;106:1624-1671.
    • (2006) Chem Rev , vol.106 , pp. 1624-1671
    • Jarymowycz, V.A.1    Stone, M.J.2
  • 27
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
    • Igumenova TI, Frederick KK, Wand AJ. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 2006;106:1672-1699.
    • (2006) Chem Rev , vol.106 , pp. 1672-1699
    • Igumenova, T.I.1    Frederick, K.K.2    Wand, A.J.3
  • 28
    • 0033200247 scopus 로고    scopus 로고
    • Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function
    • Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 1999;7:1047-1055.
    • (1999) Structure , vol.7 , pp. 1047-1055
    • Ishima, R.1    Freedberg, D.I.2    Wang, Y.X.3    Louis, J.M.4    Torchia, D.A.5
  • 31
    • 0242353303 scopus 로고    scopus 로고
    • Solution structure of the mature HIV-1 protease monomer: Insight into the tertiary fold and stability of a precursor
    • 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.
    • (2003) J Biol Chem , vol.278 , pp. 43311-43319
    • Ishima, R.1    Torchia, D.A.2    Lynch, S.M.3    Gronenborn, A.M.4    Louis, J.M.5
  • 32
    • 17444392445 scopus 로고    scopus 로고
    • Autoprocessing of HIV-1 protease is tightly coupled to protein folding
    • Louis JM, Clore GM, Gronenborn AM. Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat Struct Biol 1999; 6:868-875.
    • (1999) Nat Struct Biol , vol.6 , pp. 868-875
    • Louis, J.M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 33
    • 0034328380 scopus 로고    scopus 로고
    • HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations
    • de la Torre JG, Huertas ML, Carrasco B. HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J Magn Reson 2000;147:138-146.
    • (2000) J Magn Reson , vol.147 , pp. 138-146
    • de la Torre, J.G.1    Huertas, M.L.2    Carrasco, B.3


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