메뉴 건너뛰기




Volumn 10, Issue 8, 2014, Pages 3438-3448

Drug resistance mutations alter dynamics of inhibitor-bound HIV-1 protease

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84906274179     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct4010454     Document Type: Article
Times cited : (30)

References (44)
  • 3
    • 80051739212 scopus 로고    scopus 로고
    • Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope
    • Ozen, A.; Haliloglu, T.; Schiffer, C. A. Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope J. Mol. Biol. 2011, 410, 726-744
    • (2011) J. Mol. Biol. , vol.410 , pp. 726-744
    • Ozen, A.1    Haliloglu, T.2    Schiffer, C.A.3
  • 4
    • 33645767675 scopus 로고    scopus 로고
    • Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease
    • Prabu-Jeyabalan, M.; King, N. M.; Nalivaika, E. A.; Heilek-Snyder, G.; Cammack, N.; Schiffer, C. A. Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease Antimicrob. Agents Chemother. 2006, 50, 1518-21
    • (2006) Antimicrob. Agents Chemother. , vol.50 , pp. 1518-1521
    • Prabu-Jeyabalan, M.1    King, N.M.2    Nalivaika, E.A.3    Heilek-Snyder, G.4    Cammack, N.5    Schiffer, C.A.6
  • 6
    • 0346333382 scopus 로고    scopus 로고
    • Secondary mutations M36I and A71V in the human immunodeficiency virus type 1 protease can provide an advantage for the emergence of the primary mutation D30N
    • Clemente, J. C.; Hemrajani, R.; Blum, L. E.; Goodenow, M. M.; Dunn, B. M. Secondary mutations M36I and A71V in the human immunodeficiency virus type 1 protease can provide an advantage for the emergence of the primary mutation D30N Biochemistry (Moscow) 2003, 42, 15029-35
    • (2003) Biochemistry (Moscow) , vol.42 , pp. 15029-15035
    • Clemente, J.C.1    Hemrajani, R.2    Blum, L.E.3    Goodenow, M.M.4    Dunn, B.M.5
  • 8
    • 33846798356 scopus 로고    scopus 로고
    • Hydrophobic sliding: A possible mechanism for drug resistance in human immunodeficiency virus type 1 protease
    • Foulkes-Murzycki, J. E.; Scott, W. R.; Schiffer, C. A. Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease Structure 2007, 15, 225-33
    • (2007) Structure , vol.15 , pp. 225-233
    • Foulkes-Murzycki, J.E.1    Scott, W.R.2    Schiffer, C.A.3
  • 9
    • 84857804736 scopus 로고    scopus 로고
    • Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease
    • Mittal, S.; Cai, Y.; Nalam, M. N.; Bolon, D. N.; Schiffer, C. A. Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease J. Am. Chem. Soc. 2012, 134, 4163-8
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 4163-4168
    • Mittal, S.1    Cai, Y.2    Nalam, M.N.3    Bolon, D.N.4    Schiffer, C.A.5
  • 10
    • 0036147844 scopus 로고    scopus 로고
    • Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations
    • Freedberg, D. I.; Ishima, R.; Jacob, J.; Wang, Y. X.; Kustanovich, I.; Louis, J. M.; Torchia, D. A. Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations Protein Sci. 2002, 11, 221-32
    • (2002) Protein Sci. , vol.11 , pp. 221-232
    • Freedberg, D.I.1    Ishima, R.2    Jacob, J.3    Wang, Y.X.4    Kustanovich, I.5    Louis, J.M.6    Torchia, D.A.7
  • 11
    • 34548737701 scopus 로고    scopus 로고
    • Interflap distances in HIV-1 protease determined by pulsed EPR measurements
    • Galiano, L.; Bonora, M.; Fanucci, G. E. Interflap distances in HIV-1 protease determined by pulsed EPR measurements J. Am. Chem. Soc. 2007, 129, 11004-5
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11004-11005
    • Galiano, L.1    Bonora, M.2    Fanucci, G.E.3
  • 12
    • 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, R. C.; 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, 2812-3
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2812-2813
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 13
    • 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, D. I.; Wang, Y. X.; Louis, J. M.; Torchia, D. A. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function Structure 1999, 7, 1047-55
    • (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
  • 14
    • 39749086224 scopus 로고    scopus 로고
    • A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps
    • Ishima, R.; Louis, J. M. A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps Proteins 2008, 70, 1408-15
    • (2008) Proteins , vol.70 , pp. 1408-1415
    • Ishima, R.1    Louis, J.M.2
  • 16
    • 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, A. L.; Lin, J. H.; McCammon, J. A. 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, 1108-23
    • (2004) Protein Sci. , vol.13 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 17
    • 0034483901 scopus 로고    scopus 로고
    • Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
    • Scott, W. R.; Schiffer, C. A. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance Structure 2000, 8, 1259-65
    • (2000) Structure , vol.8 , pp. 1259-1265
    • Scott, W.R.1    Schiffer, C.A.2
  • 18
    • 84867374992 scopus 로고    scopus 로고
    • Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation
    • Cai, Y.; Yilmaz, N. K.; Myint, W.; Ishima, R.; Schiffer, C. A. Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation J. Chem. Theory Comput. 2012, 8, 3452-3462
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3452-3462
    • Cai, Y.1    Yilmaz, N.K.2    Myint, W.3    Ishima, R.4    Schiffer, C.A.5
  • 19
    • 0032947107 scopus 로고    scopus 로고
    • Human immunodeficiency virus reverse transcriptase and protease sequence database
    • Shafer, R. W.; Stevenson, D.; Chan, B. Human immunodeficiency virus reverse transcriptase and protease sequence database Nucleic Acids Res. 1999, 27, 348-352
    • (1999) Nucleic Acids Res. , vol.27 , pp. 348-352
    • Shafer, R.W.1    Stevenson, D.2    Chan, B.3
  • 24
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 26
    • 0029162947 scopus 로고
    • Comparison of Md Simulations and Nmr Experiments for Hen Lysozyme - Analysis of Local Fluctuations, Cooperative Motions, and Global Changes
    • Smith, L. J.; Mark, A. E.; Dobson, C. M.; Vangunsteren, W. F. Comparison of Md Simulations and Nmr Experiments for Hen Lysozyme-Analysis of Local Fluctuations, Cooperative Motions, and Global Changes Biochemistry (Moscow) 1995, 34, 10918-10931
    • (1995) Biochemistry (Moscow) , vol.34 , pp. 10918-10931
    • Smith, L.J.1    Mark, A.E.2    Dobson, C.M.3    Vangunsteren, W.F.4
  • 27
    • 0026684043 scopus 로고
    • A 500-Ps Molecular-Dynamics Simulation Study of Interleukin-1-Beta in Water - Correlation with Nuclear-Magnetic-Resonance Spectroscopy and Crystallography
    • Chandrasekhar, I.; Clore, G. M.; Szabo, A.; Gronenborn, A. M.; Brooks, B. R. A 500-Ps Molecular-Dynamics Simulation Study of Interleukin-1-Beta in Water-Correlation with Nuclear-Magnetic-Resonance Spectroscopy and Crystallography J. Mol. Biol. 1992, 226, 239-250
    • (1992) J. Mol. Biol. , vol.226 , pp. 239-250
    • Chandrasekhar, I.1    Clore, G.M.2    Szabo, A.3    Gronenborn, A.M.4    Brooks, B.R.5
  • 28
    • 44949262025 scopus 로고    scopus 로고
    • An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins
    • Hansen, D. F.; Vallurupalli, P.; Kay, L. E. An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins J. Phys. Chem. B 2008, 112, 5898-904
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5898-5904
    • Hansen, D.F.1    Vallurupalli, P.2    Kay, L.E.3
  • 29
    • 44949167605 scopus 로고    scopus 로고
    • Characterization of specific protein association by 15N CPMG relaxation dispersion NMR: The GB1(A34F) monomer-dimer equilibrium
    • Jee, J.; Ishima, R.; Gronenborn, A. M. Characterization of specific protein association by 15N CPMG relaxation dispersion NMR: the GB1(A34F) monomer-dimer equilibrium J. Phys. Chem. B 2008, 112, 6008-12
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6008-6012
    • Jee, J.1    Ishima, R.2    Gronenborn, A.M.3
  • 30
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G.; Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity J. Am. Chem. Soc. 1982, 104, 4546-4559
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 31
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
    • Lipari, G.; Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results J. Am. Chem. Soc. 1982, 104, 4559-4570
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 32
    • 0028941877 scopus 로고
    • Backbone Dynamics of Escherichia-Coli Ribonuclease Hi - Correlations with Structure and Function in an Active Enzyme
    • Mandel, A. M.; Akke, M.; Palmer, A. G. Backbone Dynamics of Escherichia-Coli Ribonuclease Hi-Correlations with Structure and Function in an Active Enzyme J. Mol. Biol. 1995, 246, 144-163
    • (1995) J. Mol. Biol. , vol.246 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer, A.G.3
  • 34
    • 84867475489 scopus 로고    scopus 로고
    • Correlating conformational shift induction with altered inhibitor potency in a multidrug resistant HIV-1 protease variant
    • de Vera, I. M.; Blackburn, M. E.; Fanucci, G. E. Correlating conformational shift induction with altered inhibitor potency in a multidrug resistant HIV-1 protease variant Biochemistry (Moscow) 2012, 51, 7813-5
    • (2012) Biochemistry (Moscow) , vol.51 , pp. 7813-7815
    • De Vera, I.M.1    Blackburn, M.E.2    Fanucci, G.E.3
  • 35
    • 84877768643 scopus 로고    scopus 로고
    • Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease
    • de Vera, I. M.; Smith, A. N.; Dancel, M. C.; Huang, X.; Dunn, B. M.; Fanucci, G. E. Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease Biochemistry (Moscow) 2013, 52, 3278-88
    • (2013) Biochemistry (Moscow) , vol.52 , pp. 3278-3288
    • De Vera, I.M.1    Smith, A.N.2    Dancel, M.C.3    Huang, X.4    Dunn, B.M.5    Fanucci, G.E.6
  • 36
    • 84864651001 scopus 로고    scopus 로고
    • Protein activity regulation by conformational entropy
    • Tzeng, S. R.; Kalodimos, C. G. Protein activity regulation by conformational entropy Nature 2012, 488, 236-40
    • (2012) Nature , vol.488 , pp. 236-240
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 37
    • 0030601792 scopus 로고    scopus 로고
    • Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: Application to protein folding
    • Yang, D.; Kay, L. E. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding J. Mol. Biol. 1996, 263, 369-82
    • (1996) J. Mol. Biol. , vol.263 , pp. 369-382
    • Yang, D.1    Kay, L.E.2
  • 38
    • 3543005385 scopus 로고    scopus 로고
    • Thermodynamics of protein-ligand interactions: History, presence, and future aspects
    • Perozzo, R.; Folkers, G.; Scapozza, L. Thermodynamics of protein-ligand interactions: history, presence, and future aspects J. Recept. Signal Transduction Res. 2004, 24, 1-52
    • (2004) J. Recept. Signal Transduction Res. , vol.24 , pp. 1-52
    • Perozzo, R.1    Folkers, G.2    Scapozza, L.3
  • 39
    • 77951133082 scopus 로고    scopus 로고
    • Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV
    • Cai, Y.; Schiffer, C. A. Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV J. Chem. Theory Comput. 2010, 6, 1358-1368
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1358-1368
    • Cai, Y.1    Schiffer, C.A.2
  • 40
    • 79957585828 scopus 로고    scopus 로고
    • Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases
    • Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases ChemMedChem 2011, 6, 1049-66
    • (2011) ChemMedChem , vol.6 , pp. 1049-1066
    • Abel, R.1    Salam, N.K.2    Shelley, J.3    Farid, R.4    Friesner, R.A.5    Sherman, W.6
  • 42
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
    • Fenley, A. T.; Muddana, H. S.; Gilson, M. K. Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 20006-11
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 20006-20011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 43
    • 77955567116 scopus 로고    scopus 로고
    • Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding
    • Ward, J. M.; Gorenstein, N. M.; Tian, J.; Martin, S. F.; Post, C. B. Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding J. Am. Chem. Soc. 2010, 132, 11058-70
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 11058-11070
    • Ward, J.M.1    Gorenstein, N.M.2    Tian, J.3    Martin, S.F.4    Post, C.B.5
  • 44
    • 80051739212 scopus 로고    scopus 로고
    • Dynamics of preferential substrate recognition in HIV-1 protease: Redefining the substrate envelope
    • Ozen, A.; Haliloglu, T.; Schiffer, C. A. Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope J. Mol. Biol. 2011, 410, 726-44
    • (2011) J. Mol. Biol. , vol.410 , pp. 726-744
    • Ozen, A.1    Haliloglu, T.2    Schiffer, C.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.