메뉴 건너뛰기




Volumn 118, Issue 44, 2014, Pages 12577-12585

pH-REMD simulations indicate that the catalytic aspartates of HIV-1 protease exist primarily in a monoprotonated state

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTATES; HIV-1 PROTEASE;

EID: 84908612291     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp504011c     Document Type: Article
Times cited : (39)

References (63)
  • 1
    • 0018097388 scopus 로고
    • Relationship of Retrovirus Polyprotein Cleavages to Virion Maturation Studied with Temperature-Sensitive Murine Leukemia Virus Mutants
    • Witte, O. N.; Baltimore, D. Relationship of Retrovirus Polyprotein Cleavages to Virion Maturation Studied with Temperature-Sensitive Murine Leukemia Virus Mutants. J. Virol. 1978, 26, 750-761.
    • (1978) J. Virol. , vol.26 , pp. 750-761
    • Witte, O.N.1    Baltimore, D.2
  • 4
    • 45149083375 scopus 로고    scopus 로고
    • Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease
    • Sayer, J. M.; Liu, F.; Ishima, R.; Weber, I. T.; Louis, J. M. 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.
    • (2008) J. Biol. Chem. , vol.283 , pp. 13459-13470
    • Sayer, J.M.1    Liu, F.2    Ishima, R.3    Weber, I.T.4    Louis, J.M.5
  • 5
    • 0029065893 scopus 로고
    • Relative Binding Free Energies of Peptide Inhibitors of HIV-1 Protease: The Influence of the Active Site Protonation State
    • Chen, X.; Tropsha, A. Relative Binding Free Energies of Peptide Inhibitors of HIV-1 Protease: The Influence of the Active Site Protonation State. J. Med. Chem. 1995, 38, 42-48.
    • (1995) J. Med. Chem. , vol.38 , pp. 42-48
    • Chen, X.1    Tropsha, A.2
  • 6
    • 0031423107 scopus 로고    scopus 로고
    • Dissection of the pH Dependence of Inhibitor Binding Energetics for an Aspartic Protease: Direct Measurement of the Protonation States of the Catalytic Aspartic Acid Residues
    • Xie, D.; Gulnik, S.; Collins, L.; Gustchina, E.; Suvorov, L.; Erickson, J. W. Dissection of the pH Dependence of Inhibitor Binding Energetics for an Aspartic Protease: Direct Measurement of the Protonation States of the Catalytic Aspartic Acid Residues. Biochemistry 1997, 36, 16166-16172.
    • (1997) Biochemistry , vol.36 , pp. 16166-16172
    • Xie, D.1    Gulnik, S.2    Collins, L.3    Gustchina, E.4    Suvorov, L.5    Erickson, J.W.6
  • 7
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins 2006, 65, 712-725.
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 8
    • 0034602373 scopus 로고    scopus 로고
    • Free Energy Calculations on Dimer Stability of the HIV Protease Using Molecular Dynamics and a Continuum Solvent Model
    • Wang, W.; Kollman, P. A. Free Energy Calculations on Dimer Stability of the HIV Protease Using Molecular Dynamics and a Continuum Solvent Model. J. Mol. Biol. 2000, 303, 567-582.
    • (2000) J. Mol. Biol. , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.A.2
  • 9
    • 77749305127 scopus 로고    scopus 로고
    • Crucial Roles of the Subnanosecond Local Dynamics of the Flap Tips in the Global Conformational Changes of HIV-1 Protease
    • Li, D.; Ji, B.; Hwang, K.; Huang, Y. Crucial Roles of the Subnanosecond Local Dynamics of the Flap Tips in the Global Conformational Changes of HIV-1 Protease. J. Phys. Chem. B 2010, 114, 3060-3069.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 3060-3069
    • Li, D.1    Ji, B.2    Hwang, K.3    Huang, Y.4
  • 10
    • 0027181741 scopus 로고
    • Prediction of the Protonation State of the Active Site Aspartyl Residues in HIV-1 Protease-Inhibitor Complexes via Molecular Dynamics Simulation
    • Harte, W. E.; Beveridge, D. L. Prediction of the Protonation State of the Active Site Aspartyl Residues in HIV-1 Protease-Inhibitor Complexes via Molecular Dynamics Simulation. J. Am. Chem. Soc. 1993, 115, 3883-3886.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3883-3886
    • Harte, W.E.1    Beveridge, D.L.2
  • 11
    • 0029009434 scopus 로고
    • HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation
    • Chatfield, D. C.; Brooks, B. R. HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation. J. Am. Chem. Soc. 1995, 117, 5561-5572.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5561-5572
    • Chatfield, D.C.1    Brooks, B.R.2
  • 12
    • 0031049559 scopus 로고    scopus 로고
    • Analysis of the Structure of HIV-1 Protease Complexed with a Hexapeptide Inhibitor. Part II: Molecular Dynamic Studies of the Active Site Region
    • Geller, M.; Miller, M.; Swanson, S. M.; Maizel, J. Analysis of the Structure of HIV-1 Protease Complexed with a Hexapeptide Inhibitor. Part II: Molecular Dynamic Studies of the Active Site Region. Proteins: Struct., Funct., Bioinf. 1997, 27, 195-203.
    • (1997) Proteins: Struct., Funct., Bioinf. , vol.27 , pp. 195-203
    • Geller, M.1    Miller, M.2    Swanson, S.M.3    Maizel, J.4
  • 13
    • 0033998647 scopus 로고    scopus 로고
    • Conformational Flexibility of the Catalytic Asp Dyad in HIV-1 Protease: An ab Initio Study on the Free Enzyme
    • Piana, S.; Carloni, P. Conformational Flexibility of the Catalytic Asp Dyad in HIV-1 Protease: An ab Initio Study on the Free Enzyme. Proteins: Struct., Funct., Bioinf. 2000, 39, 26-36.
    • (2000) Proteins: Struct., Funct., Bioinf. , vol.39 , pp. 26-36
    • Piana, S.1    Carloni, P.2
  • 14
    • 0035850539 scopus 로고    scopus 로고
    • Ab Initio Molecular Dynamics-Based Assignment of the Protonation State of Pepstatin A/HIV-1 Protease Cleavage Site
    • Piana, S.; Sebastiani, D.; Carloni, P.; Parrinello, M. Ab Initio Molecular Dynamics-Based Assignment of the Protonation State of Pepstatin A/HIV-1 Protease Cleavage Site. J. Am. Chem. Soc. 2001, 123, 8730-8737.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 8730-8737
    • Piana, S.1    Sebastiani, D.2    Carloni, P.3    Parrinello, M.4
  • 15
    • 40549107752 scopus 로고    scopus 로고
    • Accurate Prediction of Protonation State as a Prerequisite for Reliable MM-PB(GB)SA Binding Free Energy Calculations of HIV-1 Protease Inhibitors
    • Wittayanarakul, K.; Hannongbua, S.; Feig, M. Accurate Prediction of Protonation State as a Prerequisite for Reliable MM-PB(GB)SA Binding Free Energy Calculations of HIV-1 Protease Inhibitors. J. Comput. Chem. 2008, 29, 673-685.
    • (2008) J. Comput. Chem. , vol.29 , pp. 673-685
    • Wittayanarakul, K.1    Hannongbua, S.2    Feig, M.3
  • 16
    • 0027231964 scopus 로고
    • A Quantum Mechanical Study of the Active Site of Aspartic Proteinases
    • Beveridge, A. J.; Heywood, G. C. A Quantum Mechanical Study of the Active Site of Aspartic Proteinases. Biochemistry 1993, 32, 3325-3333.
    • (1993) Biochemistry , vol.32 , pp. 3325-3333
    • Beveridge, A.J.1    Heywood, G.C.2
  • 17
    • 0029863567 scopus 로고    scopus 로고
    • Inhibition and Catalytic Mechanism of HIV-1 Aspartic Protease
    • Silva, A. M.; Cachau, R. E.; Sham, H. L.; Erickson, J. W. Inhibition and Catalytic Mechanism of HIV-1 Aspartic Protease. J. Mol. Biol. 1996, 255, 321-340.
    • (1996) J. Mol. Biol. , vol.255 , pp. 321-340
    • Silva, A.M.1    Cachau, R.E.2    Sham, H.L.3    Erickson, J.W.4
  • 18
    • 0041565315 scopus 로고    scopus 로고
    • Investigation of the Protonated State of HIV-1 Protease Active Site
    • Nam, K.-Y.; Chang, B. H.; Han, C. K.; Ahn, S. G.; No, K. T. Investigation of the Protonated State of HIV-1 Protease Active Site. Bull. Korean Chem. Soc. 2003, 24, 817-823.
    • (2003) Bull. Korean Chem. Soc. , vol.24 , pp. 817-823
    • Nam, K.-Y.1    Chang, B.H.2    Han, C.K.3    Ahn, S.G.4    No, K.T.5
  • 19
    • 0029885915 scopus 로고    scopus 로고
    • An ab Initio Quantum Mechanical Model for the Catalytic Mechanism of HIV-1 Protease
    • Lee, H.; Darden, T. A.; Pedersen, L. G. An ab Initio Quantum Mechanical Model for the Catalytic Mechanism of HIV-1 Protease. J. Am. Chem. Soc. 1996, 118, 3946-3950.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3946-3950
    • Lee, H.1    Darden, T.A.2    Pedersen, L.G.3
  • 21
    • 34547657456 scopus 로고    scopus 로고
    • Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study
    • Czodrowski, P.; Sotriffer, C. A.; Klebe, G. Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study. J. Chem. Inf. Model. 2007, 47, 1590-1598.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1590-1598
    • Czodrowski, P.1    Sotriffer, C.A.2    Klebe, G.3
  • 22
    • 0026344399 scopus 로고
    • The Three-Dimensional Structure of the Aspartyl Protease from the HIV-1 Isolate BRU
    • Spinelli, S.; Liu, Q. Z.; Alzari, P. M.; Hirel, P. H.; Poljak, R. J. 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
  • 23
    • 0030970305 scopus 로고    scopus 로고
    • Simulation of Protein Conformational Freedom as a Function of pH: Constant-pH Molecular Dynamics Using Implicit Titration
    • Baptista, A. M.; Martel, P. J.; Petersen, S. B. Simulation of Protein Conformational Freedom as a Function of pH: Constant-pH Molecular Dynamics Using Implicit Titration. Proteins: Struct., Funct., Bioinf. 1997, 27, 523-544.
    • (1997) Proteins: Struct., Funct., Bioinf. , vol.27 , pp. 523-544
    • Baptista, A.M.1    Martel, P.J.2    Petersen, S.B.3
  • 24
    • 0036732086 scopus 로고    scopus 로고
    • Constant-pH Molecular Dynamics Using Stochastic Titration
    • Baptista, A. M.; Teixeira, V. H.; Soares, C. M. Constant-pH Molecular Dynamics Using Stochastic Titration. J. Chem. Phys. 2002, 117, 4184-4200.
    • (2002) J. Chem. Phys. , vol.117 , pp. 4184-4200
    • Baptista, A.M.1    Teixeira, V.H.2    Soares, C.M.3
  • 25
    • 4043132337 scopus 로고    scopus 로고
    • Constant-pH Molecular Dynamics Using Continuous Titration Coordinates
    • Lee, M. S.; Salsbury, F. R.; Brooks, C. L. Constant-pH Molecular Dynamics Using Continuous Titration Coordinates. Proteins: Struct., Funct., Bioinf. 2004, 56, 738-752.
    • (2004) Proteins: Struct., Funct., Bioinf. , vol.56 , pp. 738-752
    • Lee, M.S.1    Salsbury, F.R.2    Brooks, C.L.3
  • 26
    • 9244223045 scopus 로고    scopus 로고
    • Constant pH Molecular Dynamics in Generalized Born Implicit Solvent
    • Mongan, J.; Case, D. A.; McCammon, J. A. Constant pH Molecular Dynamics in Generalized Born Implicit Solvent. J. Comput. Chem. 2004, 25, 2038-2048.
    • (2004) J. Comput. Chem. , vol.25 , pp. 2038-2048
    • Mongan, J.1    Case, D.A.2    McCammon, J.A.3
  • 28
    • 84869051811 scopus 로고    scopus 로고
    • Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics
    • Swails, J. M.; Roitberg, A. E. Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics. J. Chem. Theory Comput. 2012, 8, 4393-4404.
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 4393-4404
    • Swails, J.M.1    Roitberg, A.E.2
  • 30
    • 84896282058 scopus 로고    scopus 로고
    • Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
    • Swails, J. M.; York, D. M.; Roitberg, A. E. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J. Chem. Theory Comput. 2014, 10, 1341-1352.
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 1341-1352
    • Swails, J.M.1    York, D.M.2    Roitberg, A.E.3
  • 31
    • 80051643867 scopus 로고    scopus 로고
    • Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange
    • Wallace, J. A.; Shen, J. K. Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange. J. Chem. Theory Comput. 2011, 7, 2617-2629.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2617-2629
    • Wallace, J.A.1    Shen, J.K.2
  • 33
    • 84855710487 scopus 로고    scopus 로고
    • Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent
    • Goh, G. B.; Knight, J. L.; Brooks, C. L. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J. Chem. Theory Comput. 2012, 8, 36-46.
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 36-46
    • Goh, G.B.1    Knight, J.L.2    Brooks, C.L.3
  • 34
    • 0033003998 scopus 로고    scopus 로고
    • Small Dipeptide-Based HIV Protease Inhibitors Containing the Hydroxymethylcarbonyl Isostere as an Ideal Transition-State Mimic
    • Kiso, Y.; Matsumoto, H.; Mizumoto, S.; Kimura, T.; Fujiwara, Y.; Akaji, K. Small Dipeptide-Based HIV Protease Inhibitors Containing the Hydroxymethylcarbonyl Isostere as an Ideal Transition-State Mimic. Pept. Sci. 1999, 51, 59-68.
    • (1999) Pept. Sci. , vol.51 , pp. 59-68
    • Kiso, Y.1    Matsumoto, H.2    Mizumoto, S.3    Kimura, T.4    Fujiwara, Y.5    Akaji, K.6
  • 37
    • 77956326486 scopus 로고    scopus 로고
    • Amprenavir Complexes with HIV-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters
    • Shen, C.-H.; Wang, Y.-F.; Kovalevsky, A. Y.; Harrison, R. W.; Weber, I. T. Amprenavir Complexes with HIV-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. FEBS J. 2010, 277, 3699-3714.
    • (2010) FEBS J. , vol.277 , pp. 3699-3714
    • Shen, C.-H.1    Wang, Y.-F.2    Kovalevsky, A.Y.3    Harrison, R.W.4    Weber, I.T.5
  • 38
    • 34248336220 scopus 로고    scopus 로고
    • Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations
    • Muzammil, S.; Armstrong, A. A.; Kang, L. W.; Jakalian, A.; Bonneau, P. R.; Schmelmer, V.; Amzel, L. M.; Freire, E. Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations. J. Virol. 2007, 81, 5144-5154.
    • (2007) J. Virol. , vol.81 , pp. 5144-5154
    • Muzammil, S.1    Armstrong, A.A.2    Kang, L.W.3    Jakalian, A.4    Bonneau, P.R.5    Schmelmer, V.6    Amzel, L.M.7    Freire, E.8
  • 39
    • 84859383561 scopus 로고    scopus 로고
    • HIV-1 Protease with 20 Mutations Exhibits Extreme Resistance to Clinical Inhibitors through Coordinated Structural Rearrangements
    • Agniswamy, J.; Shen, C.-H.; Aniana, A.; Sayer, J. M.; Louis, J. M.; Weber, I. T. HIV-1 Protease with 20 Mutations Exhibits Extreme Resistance to Clinical Inhibitors through Coordinated Structural Rearrangements. Biochemistry 2012, 51, 2819-2828.
    • (2012) Biochemistry , vol.51 , pp. 2819-2828
    • Agniswamy, J.1    Shen, C.-H.2    Aniana, A.3    Sayer, J.M.4    Louis, J.M.5    Weber, I.T.6
  • 40
    • 0032169572 scopus 로고    scopus 로고
    • Rapid X-ray Diffraction Analysis of HIV-1 Protease-Inhibitor Complexes: Inhibitor Exchange in Single Crystals of the Bound Enzyme
    • Munshi, S.; Chen, Z.; Li, Y.; Olsen, D. B.; Fraley, M. E.; Hungate, R. W.; Kuo, L. C. Rapid X-ray Diffraction Analysis of HIV-1 Protease-Inhibitor Complexes: Inhibitor Exchange in Single Crystals of the Bound Enzyme. Acta Crystallogr., Sect. D 1998, 54, 1053-1060.
    • (1998) Acta Crystallogr., Sect. D , vol.54 , pp. 1053-1060
    • Munshi, S.1    Chen, Z.2    Li, Y.3    Olsen, D.B.4    Fraley, M.E.5    Hungate, R.W.6    Kuo, L.C.7
  • 43
    • 9544235162 scopus 로고    scopus 로고
    • Cyclic HIV Protease Inhibitors: Syn
    • thesis, Conformational Analysis, P2/ P2′ Structure-Activity Relationship, and Molecular Recognition of Cyclic Ureas.
    • Lam, P. Y. S.; Ru, Y.; Jadhav, P. K.; Aldrich, P. E.; DeLucca, G. V.; Eyermann, C. J.; Chang, C.-H.; Emmett, G.; Holler, E. R.; Daneker, W. F.; et al. Cyclic HIV Protease Inhibitors: Synthesis, Conformational Analysis, P2/ P2′ Structure-Activity Relationship, and Molecular Recognition of Cyclic Ureas. J. Med. Chem. 1996, 39, 3514-3525.
    • (1996) J. Med. Chem. , vol.39 , pp. 3514-3525
    • Lam, P.Y.S.1    Ru, Y.2    Jadhav, P.K.3    Aldrich, P.E.4    DeLucca, G.V.5    Eyermann, C.J.6    Chang, C.-H.7    Emmett, G.8    Holler, E.R.9    Daneker, W.F.10
  • 45
    • 70350052784 scopus 로고    scopus 로고
    • Subtype Polymorphisms among HIV-1 Protease Variants Confer Altered Flap Conformations and Flexibility
    • Kear, J. L.; Blackburn, M. E.; Veloro, A. M.; Dunn, B. M.; Fanucci, G. E. Subtype Polymorphisms among HIV-1 Protease Variants Confer Altered Flap Conformations and Flexibility. J. Am. Chem. Soc. 2009, 131, 14650-14651.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 14650-14651
    • Kear, J.L.1    Blackburn, M.E.2    Veloro, A.M.3    Dunn, B.M.4    Fanucci, G.E.5
  • 48
    • 0036890178 scopus 로고    scopus 로고
    • Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation
    • Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation. J. Comput. Chem. 2002, 23, 1623-1641.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 50
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems
    • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 51
    • 67650072432 scopus 로고    scopus 로고
    • Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules
    • Sindhikara, D. J.; Kim, S.; Voter, A. F.; Roitberg, A. E. Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules. J. Chem. Theory Comput. 2009, 5, 1624-1631.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1624-1631
    • Sindhikara, D.J.1    Kim, S.2    Voter, A.F.3    Roitberg, A.E.4
  • 52
    • 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
  • 53
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model. Proteins 2004, 55, 383-394.
    • (2004) Proteins , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 54
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
    • Roe, D. R.; Cheatham, T. E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. J. Chem. Theory Comput. 2013, 9, 3084-3095.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 57
    • 0026005186 scopus 로고
    • Human Immunodeficiency Virus-1 Protease. 2. Use of pH Rate Studies and Solvent Kinetic Isotope Effects To Elucidate Details of Chemical Mechanism
    • Hyland, L. J.; Tomaszek, T. A.; Meek, T. D. Human Immunodeficiency Virus-1 Protease. 2. Use of pH Rate Studies and Solvent Kinetic Isotope Effects To Elucidate Details of Chemical Mechanism. Biochemistry 1991, 30, 8454-8463.
    • (1991) Biochemistry , vol.30 , pp. 8454-8463
    • Hyland, L.J.1    Tomaszek, T.A.2    Meek, T.D.3
  • 58
    • 0026325601 scopus 로고
    • Kinetic Studies of Human Immunodeficiency Virus Type 1 Protease and Its Active-Site Hydrogen Bond Mutant A28S
    • Ido, E.; Han, H. P.; Kezdy, F. J.; Tang, J. Kinetic Studies of Human Immunodeficiency Virus Type 1 Protease and Its Active-Site Hydrogen Bond Mutant A28S. J. Biol. Chem. 1991, 266, 24359-24366.
    • (1991) J. Biol. Chem. , vol.266 , pp. 24359-24366
    • Ido, E.1    Han, H.P.2    Kezdy, F.J.3    Tang, J.4
  • 59
    • 0029859529 scopus 로고    scopus 로고
    • Ionization States of the Catalytic Residues in HIV-1 Protease
    • Smith, R.; Brereton, I. M.; Chai, R. Y.; Kent, S. B. Ionization States of the Catalytic Residues in HIV-1 Protease. Nat. Struct. Biol. 1996, 3, 946-950.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 946-950
    • Smith, R.1    Brereton, I.M.2    Chai, R.Y.3    Kent, S.B.4
  • 60
    • 0029757151 scopus 로고    scopus 로고
    • Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different Ionization States in the Complex Formed with the Asymmetric Drug KNI-272
    • Wang, Y.-X.; Freedberg, D. I.; Yamazaki, T.; Wingfield, P. T.; Stahl, S. J.; Kaufman, J. D.; Kiso, Y.; Torchia, D. A. Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different Ionization States in the Complex Formed with the Asymmetric Drug KNI-272. Biochemistry 1996, 35, 9945-9950.
    • (1996) Biochemistry , vol.35 , pp. 9945-9950
    • Wang, Y.-X.1    Freedberg, D.I.2    Yamazaki, T.3    Wingfield, P.T.4    Stahl, S.J.5    Kaufman, J.D.6    Kiso, Y.7    Torchia, D.A.8
  • 61
    • 84880148483 scopus 로고    scopus 로고
    • Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design
    • Weber, I. T.; Waltman, M. J.; Mustyakimov, M.; Blakeley, M. P.; Keen, D. A.; Ghosh, A. K.; Langan, P.; Kovalevsky, A. Y. Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design. J. Med. Chem. 2013, 56, 5631-5635.
    • (2013) J. Med. Chem. , vol.56 , pp. 5631-5635
    • Weber, I.T.1    Waltman, M.J.2    Mustyakimov, M.3    Blakeley, M.P.4    Keen, D.A.5    Ghosh, A.K.6    Langan, P.7    Kovalevsky, A.Y.8
  • 62
    • 0028114966 scopus 로고
    • NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor
    • Yamazaki, T.; Nicholson, L.; Torchia, D.; Wingfield, P.; Stahl, S.; Kaufman, J.; Eyermann, C.; Hodge, C. N.; Lam, P.; Ru, Y.; et al. NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor. J. Am. Chem. Soc. 1994, 116, 10791-10792.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 10791-10792
    • Yamazaki, T.1    Nicholson, L.2    Torchia, D.3    Wingfield, P.4    Stahl, S.5    Kaufman, J.6    Eyermann, C.7    Hodge, C.N.8    Lam, P.9    Ru, Y.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.