메뉴 건너뛰기




Volumn 117, Issue 22, 2013, Pages 6625-6634

NMR relaxation in proteins with fast internal motions and slow conformational exchange: Model-free framework and markov state simulations

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; MOLECULAR DYNAMICS; POPULATION STATISTICS;

EID: 84879184332     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp400797y     Document Type: Article
Times cited : (28)

References (91)
  • 1
    • 33748619206 scopus 로고    scopus 로고
    • An NMR Perspective on Enzyme Dynamics
    • Boehr, D. D.; Dyson, H. J.; Wright, P. E. An NMR Perspective on Enzyme Dynamics Chem. Rev. 2006, 106, 3055-3079
    • (2006) Chem. Rev. , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 2
    • 70350340728 scopus 로고    scopus 로고
    • The Role of Dynamic Conformational Ensembles in Biomolecular Recognition
    • Boehr, D. D.; Nussinov, R.; Wright, P. E. The Role of Dynamic Conformational Ensembles in Biomolecular Recognition Nat. Chem. Biol. 2009, 5, 789-796
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 3
    • 33846635484 scopus 로고    scopus 로고
    • Targeting Structural Flexibility in HIV-1 Protease Inhibitor Binding
    • Hornak, V.; Simmerling, C. Targeting Structural Flexibility in HIV-1 Protease Inhibitor Binding Drug Discovery Today 2007, 12, 132-138
    • (2007) Drug Discovery Today , vol.12 , pp. 132-138
    • Hornak, V.1    Simmerling, C.2
  • 4
    • 0036892381 scopus 로고    scopus 로고
    • HIVdb: A Database of the Structures of Human Immunodeficiency Virus Protease
    • Vondrasek, J.; Wlodawer, A. HIVdb: A Database of the Structures of Human Immunodeficiency Virus Protease Proteins: Struct., Funct. Genet. 2002, 49, 429-431
    • (2002) Proteins: Struct., Funct. Genet. , vol.49 , pp. 429-431
    • Vondrasek, J.1    Wlodawer, A.2
  • 6
    • 33750086969 scopus 로고    scopus 로고
    • The Open Structure of a Multi-drugresistant HIV-1 Protease is Stabilized by Crystal Packing Contacts
    • Layten, M.; Hornak, V.; Simmerling, C. The Open Structure of a Multi-drugresistant HIV-1 Protease is Stabilized by Crystal Packing Contacts J. Am. Chem. Soc. 2006, 128, 13360-13361
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 13360-13361
    • Layten, M.1    Hornak, V.2    Simmerling, C.3
  • 8
    • 0030253418 scopus 로고    scopus 로고
    • Anisotropic Rotational Diffusion of Perdeuterated HIV Protease from N-15 NMR Relaxation Measurements at Two Magnetic
    • Tjandra, N.; Wingfield, P.; Stahl, S.; Bax, A. Anisotropic Rotational Diffusion of Perdeuterated HIV Protease from N-15 NMR Relaxation Measurements at Two Magnetic J. Biomol. NMR 1996, 8, 273-284
    • (1996) J. Biomol. NMR , vol.8 , pp. 273-284
    • Tjandra, N.1    Wingfield, P.2    Stahl, S.3    Bax, A.4
  • 9
    • 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, 221-232
    • (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
  • 10
    • 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, 1047-1055
    • (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
  • 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, 11004-11005
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11004-11005
    • Galiano, L.1    Bonora, M.2    Fanucci, G.E.3
  • 12
    • 33646911358 scopus 로고    scopus 로고
    • Fast Time Scale Dynamics of Protein Backbones: NMR Relaxation Methods, Applications, and Functional Consequences
    • Jarymowycz, V. A.; Stone, M. J. 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
  • 13
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the Fast Dynamics of Protein Amino Acid Side Chains using NMR Relaxation in Solution
    • Igumenova, T. I.; Frederick, K. K.; Wand, A. J. 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
  • 14
    • 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
  • 15
    • 0025046144 scopus 로고
    • Deviations from the Simple 2-Parameter-Free Appoach to the Interpretation of N-15 Nuclear Magnetic-Relaxation of Proteins
    • Clore, G. M.; Szabo, A.; Bax, A.; Kay, L. E.; Driscoll, P. C.; Gronenborn, A. M. Deviations from the Simple 2-Parameter-Free Appoach to the Interpretation of N-15 Nuclear Magnetic-Relaxation of Proteins J. Am. Chem. Soc. 1990, 112, 4989-4991
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 4989-4991
    • Clore, G.M.1    Szabo, A.2    Bax, A.3    Kay, L.E.4    Driscoll, P.C.5    Gronenborn, A.M.6
  • 16
    • 4243155782 scopus 로고    scopus 로고
    • NMR Characterization of the Dynamics of Biomacromolecules
    • Palmer, A. G. NMR Characterization of the Dynamics of Biomacromolecules Chem. Rev. 2004, 104, 3623-3640
    • (2004) Chem. Rev. , vol.104 , pp. 3623-3640
    • Palmer, A.G.1
  • 17
    • 0032127391 scopus 로고    scopus 로고
    • Reaction Path and Free Energy Calculations of the Transition between Alternate Conformations of HIV-1 Protease
    • Rick, S. W.; Erickson, J. W.; Burt, S. K. Reaction Path and Free Energy Calculations of the Transition between Alternate Conformations of HIV-1 Protease Proteins: Struct., Funct. Genet. 1998, 32, 7-16
    • (1998) Proteins: Struct., Funct. Genet. , vol.32 , pp. 7-16
    • Rick, S.W.1    Erickson, J.W.2    Burt, S.K.3
  • 18
    • 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. P.; 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, 1259-1265
    • (2000) Structure , vol.8 , pp. 1259-1265
    • Scott, W.R.P.1    Schiffer, C.A.2
  • 20
    • 33744940504 scopus 로고    scopus 로고
    • Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model
    • Chang, C. E.; Shen, T.; Trylska, J.; Tozzini, V.; McCammon, J. A. Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model Biophys. J. 2006, 90, 3880-3885
    • (2006) Biophys. J. , vol.90 , pp. 3880-3885
    • Chang, C.E.1    Shen, T.2    Trylska, J.3    Tozzini, V.4    McCammon, J.A.5
  • 21
    • 33847116895 scopus 로고    scopus 로고
    • Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model
    • Tozzini, V.; Trylska, J.; Chang, C.-e.; McCammon, J. A. Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model J. Struct. Biol. 2007, 157, 606-615
    • (2007) J. Struct. Biol. , vol.157 , pp. 606-615
    • Tozzini, V.1    Trylska, J.2    Chang, C.-E.3    McCammon, J.A.4
  • 22
    • 32244437816 scopus 로고    scopus 로고
    • HIV-1 Protease Flaps Spontaneously Open and Reclose in Molecular Dynamics Simulations
    • Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 Protease Flaps Spontaneously Open and Reclose in Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 915-920
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 23
    • 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, 2812-2813
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2812-2813
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 24
    • 44949121782 scopus 로고    scopus 로고
    • Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments
    • Ding, F.; Layten, M.; Simmerling, C. Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments J. Am. Chem. Soc. 2008, 130, 7184-7185
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 7184-7185
    • Ding, F.1    Layten, M.2    Simmerling, C.3
  • 25
    • 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
  • 26
    • 77957948558 scopus 로고    scopus 로고
    • Explicit Solvent Dynamics and Energetics of HIV-1 Protease Flap Opening and Closing
    • Kashif Sadiq, S.; De Fabritiis, G. Explicit Solvent Dynamics and Energetics of HIV-1 Protease Flap Opening and Closing Proteins: Struct., Funct. Bioinf. 2010, 78, 2873-2885
    • (2010) Proteins: Struct., Funct. Bioinf. , vol.78 , pp. 2873-2885
    • Kashif Sadiq, S.1    De Fabritiis, G.2
  • 27
    • 79959209742 scopus 로고    scopus 로고
    • Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations
    • Deng, N.-J.; Zheng, W.; Gallicchio, E.; Levy, R. M. Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations J. Am. Chem. Soc. 2011, 133, 9387-9394
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 9387-9394
    • Deng, N.-J.1    Zheng, W.2    Gallicchio, E.3    Levy, R.M.4
  • 28
    • 0028958868 scopus 로고
    • Flap Opening in HIV-1 Protease Simulated by Activated molecular-dynamics
    • Collins, J. R.; Burt, S. K.; Erickson, J. W. 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
  • 29
    • 14244273182 scopus 로고    scopus 로고
    • Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations
    • Tsui, V.; Case, D. A. Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations Biopolymers 2000, 56, 275-291
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 32
    • 69049084558 scopus 로고    scopus 로고
    • Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations
    • Pietrucci, F.; Marinelli, F.; Carloni, P.; Laio, A. Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations J. Am. Chem. Soc. 2009, 131, 11811-11818
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 11811-11818
    • Pietrucci, F.1    Marinelli, F.2    Carloni, P.3    Laio, A.4
  • 33
    • 18744366086 scopus 로고    scopus 로고
    • Protein Folding Pathways from Replica Exchange Simulations and a Kinetic Network Model
    • Andrec, M.; Felts, A. K.; Gallicchio, E.; Levy, R. M. Protein Folding Pathways From Replica Exchange Simulations and a Kinetic Network Model Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6801-6806
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6801-6806
    • Andrec, M.1    Felts, A.K.2    Gallicchio, E.3    Levy, R.M.4
  • 34
    • 34848892169 scopus 로고    scopus 로고
    • Simulating Replica Exchange Simulations of Protein Folding with a Kinetic Network Model
    • Zheng, W.; Andrec, M.; Gallicchio, E.; Levy, R. M. Simulating Replica Exchange Simulations of Protein Folding with a Kinetic Network Model Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 15340-15345
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 15340-15345
    • Zheng, W.1    Andrec, M.2    Gallicchio, E.3    Levy, R.M.4
  • 35
    • 70349240373 scopus 로고    scopus 로고
    • Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics
    • Zheng, W.; Andrec, M.; Gallicchio, E.; Levy, R. M. Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics J. Phys. Chem. B 2009, 113, 11702-11709
    • (2009) J. Phys. Chem. B , vol.113 , pp. 11702-11709
    • Zheng, W.1    Andrec, M.2    Gallicchio, E.3    Levy, R.M.4
  • 36
    • 79951523268 scopus 로고    scopus 로고
    • Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations
    • Zheng, W.; Gallicchio, E.; Deng, N.; Andrec, M.; Levy, R. M. Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations J. Phys. Chem. B 2011, 115, 1512-1523
    • (2011) J. Phys. Chem. B , vol.115 , pp. 1512-1523
    • Zheng, W.1    Gallicchio, E.2    Deng, N.3    Andrec, M.4    Levy, R.M.5
  • 37
    • 0036074173 scopus 로고    scopus 로고
    • Fast-Folding Protein Kinetics, Hidden Intermediates, and the Sequential Stabilization model
    • Ozkan, S. B.; Dill, K. A.; Bahar, I. Fast-Folding Protein Kinetics, Hidden Intermediates, and the Sequential Stabilization model Protein Sci. 2002, 11, 1958-1970
    • (2002) Protein Sci. , vol.11 , pp. 1958-1970
    • Ozkan, S.B.1    Dill, K.A.2    Bahar, I.3
  • 38
    • 3142707288 scopus 로고    scopus 로고
    • Using Path Sampling to Build Better Markovian State Models: Predicting the Folding Rate and Mechanism of a Tryptophan Zipper Beta Hairpin
    • Singhal, N.; Snow, C. D.; Pande, V. S. Using Path Sampling to Build Better Markovian State Models: Predicting the Folding Rate and Mechanism of a Tryptophan Zipper Beta Hairpin J. Chem. Phys. 2004, 121, 415-425
    • (2004) J. Chem. Phys. , vol.121 , pp. 415-425
    • Singhal, N.1    Snow, C.D.2    Pande, V.S.3
  • 39
    • 2942567954 scopus 로고    scopus 로고
    • Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
    • Swope, W.; Pitera, J. W.; Suits, F. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory J. Chem. Phys. 2004, 108, 6571-6581
    • (2004) J. Chem. Phys. , vol.108 , pp. 6571-6581
    • Swope, W.1    Pitera, J.W.2    Suits, F.3
  • 40
    • 17444389688 scopus 로고    scopus 로고
    • Coarse Master Equation for Bayesian Analysis of Replica Molecular Dynamics Simulations
    • Sriraman, S.; Kevrekidis, I. G.; Hummer, G. Coarse Master Equation for Bayesian Analysis of Replica Molecular Dynamics Simulations J. Phys. Chem. B 2005, 109, 6479-6484
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6479-6484
    • Sriraman, S.1    Kevrekidis, I.G.2    Hummer, G.3
  • 41
    • 33846184750 scopus 로고    scopus 로고
    • Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins
    • Noe, F.; Krachtus, D.; Smith, J. C.; Fischer, S. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins J. Chem. Theory Comput. 2006, 2, 840-857
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 840-857
    • Noe, F.1    Krachtus, D.2    Smith, J.C.3    Fischer, S.4
  • 42
    • 0001616080 scopus 로고    scopus 로고
    • Replica-Exchange Molecular Dynamics Method for Protein Folding
    • Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 43
    • 66849091890 scopus 로고    scopus 로고
    • Reactive Flux and Folding Pathways in Network Models of Coarse-Grained Protein Dynamics
    • Berezhkovskii, A.; Hummer, G.; Szabo, A. Reactive Flux and Folding Pathways in Network Models of Coarse-Grained Protein Dynamics J. Chem. Phys. 2009, 130, 205102-205106
    • (2009) J. Chem. Phys. , vol.130 , pp. 205102-205106
    • Berezhkovskii, A.1    Hummer, G.2    Szabo, A.3
  • 44
    • 33645429016 scopus 로고
    • Exact Stochastic Simulation of Coupled Chemical Reactions
    • Gillespie, D. T. Exact Stochastic Simulation of Coupled Chemical Reactions J. Phys. Chem. 1977, 81, 2340-2361
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 45
    • 0001200931 scopus 로고
    • Increase of Carbon-13 NMR relaxation times in Proteins due to Picosecond Motional averaging
    • Levy, R. M.; Karplus, M.; McCammon, J. A. Increase of Carbon-13 NMR relaxation times in Proteins due to Picosecond Motional averaging J. Am. Chem. Soc. 1981, 103, 994-996
    • (1981) J. Am. Chem. Soc. , vol.103 , pp. 994-996
    • Levy, R.M.1    Karplus, M.2    McCammon, J.A.3
  • 46
    • 0000459946 scopus 로고
    • NMR Relaxation Parameters in Molecules with Internal Motion: Exact Langevin Trajectory Results Compared with Simplified Relaxation Models
    • Levy, R. M.; Karplus, M.; Wolynes, P. G. NMR Relaxation Parameters in Molecules with Internal Motion: Exact Langevin Trajectory Results Compared with Simplified Relaxation Models J. Am. Chem. Soc. 1981, 103, 5998-6011
    • (1981) J. Am. Chem. Soc. , vol.103 , pp. 5998-6011
    • Levy, R.M.1    Karplus, M.2    Wolynes, P.G.3
  • 47
    • 0019960215 scopus 로고
    • Protein Dynamics and NMR Relaxation: Comparison of Simulations with Experiment
    • Lipari, G.; Szabo, A.; Levy, R. M. Protein Dynamics and NMR Relaxation: Comparison of Simulations with Experiment Nature 1982, 300, 197-198
    • (1982) Nature , vol.300 , pp. 197-198
    • Lipari, G.1    Szabo, A.2    Levy, R.M.3
  • 48
    • 0020714519 scopus 로고
    • Combined Effect of Restricted Rotational Diffusion Plus Jumps on Nuclear Magnetic Resonance and Fluorescence Probes of Aromatic Ring Motions in Proteins
    • Levy, R. M.; Sheridan, R. P. Combined Effect of Restricted Rotational Diffusion Plus Jumps on Nuclear Magnetic Resonance and Fluorescence Probes of Aromatic Ring Motions in Proteins Biophys. J. 1983, 41, 217-221
    • (1983) Biophys. J. , vol.41 , pp. 217-221
    • Levy, R.M.1    Sheridan, R.P.2
  • 49
    • 44949176027 scopus 로고    scopus 로고
    • Evaluating Rotational Diffusion from Protein MD Simulations
    • Wong, V.; Case, D. A. Evaluating Rotational Diffusion from Protein MD Simulations J. Phys. Chem. B 2008, 112, 6013-6024
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6013-6024
    • Wong, V.1    Case, D.A.2
  • 50
    • 35948943745 scopus 로고    scopus 로고
    • Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field
    • Showalter, S. A.; Bruschweiler, R. Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field J. Chem. Theory Comput. 2007, 3, 961-975
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 961-975
    • Showalter, S.A.1    Bruschweiler, R.2
  • 51
    • 0034846397 scopus 로고    scopus 로고
    • Calculation of NMR-Relaxation Parameters for Flexible Molecules from Molecular Dynamics Simulations
    • Peter, C.; Daura, X.; van Gunsteren, W. F. Calculation of NMR-Relaxation Parameters for Flexible Molecules from Molecular Dynamics Simulations J. Biomol. NMR 2001, 20, 297-310
    • (2001) J. Biomol. NMR , vol.20 , pp. 297-310
    • Peter, C.1    Daura, X.2    Van Gunsteren, W.F.3
  • 53
    • 84857637811 scopus 로고    scopus 로고
    • Sucrose in Aqueous Solution Revisited. Part 1:. Molecular Dynamics Simulations and Direct and Indirect Dipolar Coupling Analysis
    • Xia, J.; Case, D. A. Sucrose in Aqueous Solution Revisited. Part 1:. Molecular Dynamics Simulations and Direct and Indirect Dipolar Coupling Analysis Biopolymers 2012, 97, 276-288
    • (2012) Biopolymers , vol.97 , pp. 276-288
    • Xia, J.1    Case, D.A.2
  • 54
    • 84857637851 scopus 로고    scopus 로고
    • Sucosae in Aqueous Solution Revisted. Part 2: Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation
    • Xia, J.; Case, D. A. Sucosae in Aqueous Solution Revisted. Part 2: Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation Biopolymers 2012, 97, 289-302
    • (2012) Biopolymers , vol.97 , pp. 289-302
    • Xia, J.1    Case, D.A.2
  • 55
    • 3042846786 scopus 로고    scopus 로고
    • Model-Free Analysis of Protein Dynamics: Assessment of Accuracy and Model Selection Protocols Based on Molecular Dynamics Simulation
    • Chen, J. H.; Brooks, C. L.; Wright, P. E. Model-Free Analysis of Protein Dynamics: Assessment of Accuracy and Model Selection Protocols Based on Molecular Dynamics Simulation J. Biomol. NMR 2004, 29, 243-257
    • (2004) J. Biomol. NMR , vol.29 , pp. 243-257
    • Chen, J.H.1    Brooks, C.L.2    Wright, P.E.3
  • 56
    • 0344791680 scopus 로고    scopus 로고
    • Influence of Internal Dynamics on Accuracy of Protein NMR Structures: Derivation of Realistic Model Distance Data from a Long Molecular Dynamics Trajectory
    • Schneider, T. R.; Brunger, A. T.; Nilges, M. Influence of Internal Dynamics on Accuracy of Protein NMR Structures: Derivation of Realistic Model Distance Data from a Long Molecular Dynamics Trajectory J. Mol. Biol. 1999, 285, 727-740
    • (1999) J. Mol. Biol. , vol.285 , pp. 727-740
    • Schneider, T.R.1    Brunger, A.T.2    Nilges, M.3
  • 57
    • 42149175435 scopus 로고    scopus 로고
    • Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules
    • Noe, F.; Fischer, S. Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules Curr. Opin. Struct. Biol. 2008, 18, 154-162
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 154-162
    • Noe, F.1    Fischer, S.2
  • 58
    • 77956220940 scopus 로고    scopus 로고
    • Everything You Wanted to Know about Markov State Models but were Afraid to Ask
    • Pande, V. S.; Beauchamp, K.; Bowman, G. R. Everything You Wanted to Know about Markov State Models but were Afraid to Ask Methods 2010, 52, 99-105
    • (2010) Methods , vol.52 , pp. 99-105
    • Pande, V.S.1    Beauchamp, K.2    Bowman, G.R.3
  • 60
    • 62649161772 scopus 로고    scopus 로고
    • Mapping the Conformational Transition in Src Activation by Cumulating the Information from Multipe Molecular Dynamics Trajectories
    • Yang, S.; Banavali, N. K.; Roux, B. Mapping the Conformational Transition in Src Activation by Cumulating the Information from Multipe Molecular Dynamics Trajectories Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 3776-3781
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 3776-3781
    • Yang, S.1    Banavali, N.K.2    Roux, B.3
  • 61
    • 84863069608 scopus 로고    scopus 로고
    • Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II
    • Da, L.-T.; Wang, D.; Huang, X. Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II J. Am. Chem. Soc. 2012, 134, 2399-2406
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 2399-2406
    • Da, L.-T.1    Wang, D.2    Huang, X.3
  • 62
    • 80755172456 scopus 로고    scopus 로고
    • Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
    • Lane, T. J.; Bowman, G. R.; Beauchamp, K.; Voelz, V. A.; Pande, V. S. Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories J. Am. Chem. Soc. 2011, 133, 18413-18419
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 18413-18419
    • Lane, T.J.1    Bowman, G.R.2    Beauchamp, K.3    Voelz, V.A.4    Pande, V.S.5
  • 63
    • 44949178407 scopus 로고    scopus 로고
    • Coarse Master Equations for Peptide Folding Dynamics
    • Buchete, N.-V.; Hummer, G. Coarse Master Equations for Peptide Folding Dynamics J. Phys. Chem. B 2008, 112, 6057-6069
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6057-6069
    • Buchete, N.-V.1    Hummer, G.2
  • 64
    • 79960007037 scopus 로고    scopus 로고
    • Complete Reconstruction of an Enzyme Inhibitor Binding Process by Molecular Dynamics Simulations
    • Buch, I.; Giorgino, T.; De Fabritiis, G. Complete Reconstruction of an Enzyme Inhibitor Binding Process by Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 10184-10189
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 65
    • 0000231955 scopus 로고
    • Conjugate Peak Refinement - An Algorithm for Finding Reaction Paths and Accurate Transition-States in Systems with Many Degrees Freedom
    • Fischer, S.; Karplus, M. Conjugate Peak Refinement-an Algorithm for Finding Reaction Paths and Accurate Transition-States in Systems with Many Degrees Freedom Chem. Phys. Lett. 1992, 194, 252-261
    • (1992) Chem. Phys. Lett. , vol.194 , pp. 252-261
    • Fischer, S.1    Karplus, M.2
  • 66
    • 70450255797 scopus 로고    scopus 로고
    • Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
    • Noe, F.; Schuette, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19011-19016
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 19011-19016
    • Noe, F.1    Schuette, C.2    Vanden-Eijnden, E.3    Reich, L.4    Weikl, T.R.5
  • 67
    • 34247382025 scopus 로고    scopus 로고
    • Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
    • Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Dill, K. A. Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations Multiscale Model Simul. 2006, 5, 1214-1226
    • (2006) Multiscale Model Simul. , vol.5 , pp. 1214-1226
    • Chodera, J.D.1    Swope, W.C.2    Pitera, J.W.3    Dill, K.A.4
  • 68
    • 68249105984 scopus 로고    scopus 로고
    • Bayesian Comparison of Markov Models of Molecular Dynamics with Detailed Balance Constraint
    • Bacallado, S.; Chodera, J. D.; Pande, V. Bayesian Comparison of Markov Models of Molecular Dynamics with Detailed Balance Constraint J. Chem. Phys. 2009, 131, 045106-045115
    • (2009) J. Chem. Phys. , vol.131 , pp. 045106-045115
    • Bacallado, S.1    Chodera, J.D.2    Pande, V.3
  • 69
    • 46149122776 scopus 로고    scopus 로고
    • Probability Distributions of Molecular Observables Computed from Markov Models
    • Noe, F. Probability Distributions of Molecular Observables Computed from Markov Models J. Chem. Phys. 2008, 128, 244103-244115
    • (2008) J. Chem. Phys. , vol.128 , pp. 244103-244115
    • Noe, F.1
  • 70
    • 28344441228 scopus 로고    scopus 로고
    • Error Analysis and Efficient Sampling in Markovian State Models for Molecular Dynamics
    • Singhal, N.; Pande, V. S. Error Analysis and Efficient Sampling in Markovian State Models for Molecular Dynamics J. Chem. Phys. 2005, 123, 204909-204921
    • (2005) J. Chem. Phys. , vol.123 , pp. 204909-204921
    • Singhal, N.1    Pande, V.S.2
  • 72
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tiradorives, J.3
  • 73
    • 1442330396 scopus 로고    scopus 로고
    • AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling
    • Gallicchio, E.; Levy, R. M. AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling J. Comput. Chem. 2004, 25, 479-499
    • (2004) J. Comput. Chem. , vol.25 , pp. 479-499
    • Gallicchio, E.1    Levy, R.M.2
  • 75
    • 17444366185 scopus 로고    scopus 로고
    • Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths
    • Gallicchio, E.; Andrec, M.; Felts, A. K.; Levy, R. M. Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths J. Phys. Chem. B 2005, 109, 6722-6731
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6722-6731
    • Gallicchio, E.1    Andrec, M.2    Felts, A.K.3    Levy, R.M.4
  • 76
    • 0042274585 scopus 로고
    • Evaluating the Assumptions Underlying Force-Field Development and Application Using Free-Energy Conformational Maps for Nucleosides
    • Pearlman, D. A.; Kollman, P. A. Evaluating the Assumptions Underlying Force-Field Development and Application Using Free-Energy Conformational Maps for Nucleosides J. Am. Chem. Soc. 1991, 113, 7167-7177
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 7167-7177
    • Pearlman, D.A.1    Kollman, P.A.2
  • 77
    • 36149012348 scopus 로고
    • Theory of the Rotational Brownian Motion of a Free Rigid Body
    • Favro, L. D. Theory of the Rotational Brownian Motion of a Free Rigid Body Phys. Rev. 1960, 119, 53-62
    • (1960) Phys. Rev. , vol.119 , pp. 53-62
    • Favro, L.D.1
  • 78
    • 33644625296 scopus 로고
    • Nuclear Spin Relaxation in Ellipsoids Undergoing Rotational Brownian Motion
    • Woessner, D. E. Nuclear Spin Relaxation in Ellipsoids Undergoing Rotational Brownian Motion J. Chem. Phys. 1962, 37, 647-654
    • (1962) J. Chem. Phys. , vol.37 , pp. 647-654
    • Woessner, D.E.1
  • 79
    • 36849100949 scopus 로고
    • Nuclear Spin-Lattice Relaxation in Axially Symmetric Ellipsoids with Internal Motion
    • Woessner, D. E.; Snowden, B. S.; Meyer, G. H. Nuclear Spin-Lattice Relaxation in Axially Symmetric Ellipsoids with Internal Motion J. Chem. Phys. 1969, 50, 719-721
    • (1969) J. Chem. Phys. , vol.50 , pp. 719-721
    • Woessner, D.E.1    Snowden, B.S.2    Meyer, G.H.3
  • 80
    • 36849105774 scopus 로고
    • Effect of Internal Rotation on Angular Correlation Functions
    • Wallach, D. Effect of Internal Rotation on Angular Correlation Functions J. Chem. Phys. 1967, 47, 5258-5268
    • (1967) J. Chem. Phys. , vol.47 , pp. 5258-5268
    • Wallach, D.1
  • 81
    • 0001030227 scopus 로고
    • Theory of NMR Relaxation in Macromolecules: Restricted Diffusion and Jump models for Multiple Internal Rotations in Amino Acide Side Chains
    • Wittebort, R. J.; Szabo, A. Theory of NMR Relaxation in Macromolecules: Restricted Diffusion and Jump models for Multiple Internal Rotations in Amino Acide Side Chains J. Chem. Phys. 1978, 69, 1722-1736
    • (1978) J. Chem. Phys. , vol.69 , pp. 1722-1736
    • Wittebort, R.J.1    Szabo, A.2
  • 82
    • 67650482706 scopus 로고    scopus 로고
    • Influence of the Coupling of Interdomain and Overall Motions on NMR Relaxation
    • Wong, V.; Case, D. A.; Szabo, A. Influence of the Coupling of Interdomain and Overall Motions on NMR Relaxation Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 11016-11021
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 11016-11021
    • Wong, V.1    Case, D.A.2    Szabo, A.3
  • 83
    • 84856477155 scopus 로고    scopus 로고
    • Coupling between Internal Dynamics and Rotational Diffusion in the Presence of Exchange between Discrete Molecular Conformations
    • Ryabov, Y.; Clore, G. M.; Schwieters, C. D. Coupling between Internal Dynamics and Rotational Diffusion in the Presence of Exchange between Discrete Molecular Conformations J. Chem. Phys. 2012, 136, 034108-034112
    • (2012) J. Chem. Phys. , vol.136 , pp. 034108-034112
    • Ryabov, Y.1    Clore, G.M.2    Schwieters, C.D.3
  • 84
    • 33947411739 scopus 로고    scopus 로고
    • A Model of Interdomain Mobility in a Multidomain Protein
    • Ryabov, Y. E.; Fushman, D. A Model of Interdomain Mobility in a Multidomain Protein J. Am. Chem. Soc. 2007, 129, 3315-3327
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 3315-3327
    • Ryabov, Y.E.1    Fushman, D.2
  • 85
    • 0037165750 scopus 로고    scopus 로고
    • General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation
    • Prompers, J. J.; Bruschweiler, R. General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation J. Am. Chem. Soc. 2002, 124, 4522-4534
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4522-4534
    • Prompers, J.J.1    Bruschweiler, R.2
  • 86
    • 1842454635 scopus 로고    scopus 로고
    • HIV-1 Protease Molecular Dynamics of a Wide-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 Wide-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
  • 88
    • 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
  • 89
    • 70349153078 scopus 로고    scopus 로고
    • Monitoring Inhibitor-Induced Conformational Population Shifts in HIV-1 Protease by Pulsed EPR Spectroscopy
    • Blackburn, M. E.; Veloro, A. M.; Fanucci, G. E. Monitoring Inhibitor-Induced Conformational Population Shifts in HIV-1 Protease by Pulsed EPR Spectroscopy Biochemistry 2009, 48, 8765-8767
    • (2009) Biochemistry , vol.48 , pp. 8765-8767
    • Blackburn, M.E.1    Veloro, A.M.2    Fanucci, G.E.3
  • 90
    • 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
  • 91
    • 69049099679 scopus 로고    scopus 로고
    • A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
    • Marinelli, F.; Pietrucci, F.; Laio, A.; Piana, S. A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations PLOS Comput. Biol. 2009, 5, e1000452
    • (2009) PLOS Comput. Biol. , vol.5 , pp. 1000452
    • Marinelli, F.1    Pietrucci, F.2    Laio, A.3    Piana, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.