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Volumn 48, Issue 2, 2015, Pages 414-422

Markov state models provide insights into dynamic modulation of protein function

Author keywords

[No Author keywords available]

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; PROTEIN;

EID: 84923101774     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar5002999     Document Type: Review
Times cited : (213)

References (59)
  • 1
    • 0014034807 scopus 로고
    • The Photochemical and Macromolecular Aspects of Vision
    • Abrahamson, E. W.; Ostroy, S. E. The Photochemical and Macromolecular Aspects of Vision Prog. Biophys. Mol. Biol. 1967, 17, 179-215
    • (1967) Prog. Biophys. Mol. Biol. , vol.17 , pp. 179-215
    • Abrahamson, E.W.1    Ostroy, S.E.2
  • 2
    • 0036513485 scopus 로고    scopus 로고
    • The Molecular Basis of CaMKII Function in Synaptic and Behavioural Memory
    • Lisman, J.; Schulman, H.; Cline, H. The Molecular Basis of CaMKII Function in Synaptic and Behavioural Memory Nat. Rev. Neurosci. 2002, 3, 175-190
    • (2002) Nat. Rev. Neurosci. , vol.3 , pp. 175-190
    • Lisman, J.1    Schulman, H.2    Cline, H.3
  • 3
    • 84897019862 scopus 로고    scopus 로고
    • Dazzling History
    • Sumner, T. Dazzling History Science 2014, 343, 1092-1093
    • (2014) Science , vol.343 , pp. 1092-1093
    • Sumner, T.1
  • 4
    • 0001266102 scopus 로고
    • A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis
    • Kendrew, J. C.; Bodo, G.; Dintzis, H. M.; Parrish, R. G.; Wyckoff, H.; Phillips, D. C. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis Nature 1958, 181, 662-666
    • (1958) Nature , vol.181 , pp. 662-666
    • Kendrew, J.C.1    Bodo, G.2    Dintzis, H.M.3    Parrish, R.G.4    Wyckoff, H.5    Phillips, D.C.6
  • 6
    • 84896774627 scopus 로고    scopus 로고
    • Developments in X-Ray Crystallographic Structure Determination of Biological Macromolecules
    • Garman, E. F. Developments in X-Ray Crystallographic Structure Determination of Biological Macromolecules Science 2014, 343, 1102-1108
    • (2014) Science , vol.343 , pp. 1102-1108
    • Garman, E.F.1
  • 7
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic Personalities of Proteins
    • Henzler-Wildman, K.; Kern, D. Dynamic Personalities of Proteins Nature 2007, 450, 964-972
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 8
    • 84900548447 scopus 로고    scopus 로고
    • Markov State Models of Biomolecular Conformational Dynamics
    • Chodera, J. D.; Noé, F. Markov State Models of Biomolecular Conformational Dynamics Curr. Opin. Struct. Biol. 2014, 25, 135-144
    • (2014) Curr. Opin. Struct. Biol. , vol.25 , pp. 135-144
    • Chodera, J.D.1    Noé, F.2
  • 10
    • 84873526912 scopus 로고    scopus 로고
    • To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding
    • Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding Curr. Opin. Struct. Biol. 2013, 23, 58-65
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 58-65
    • Lane, T.J.1    Shukla, D.2    Beauchamp, K.A.3    Pande, V.S.4
  • 11
    • 84919832780 scopus 로고    scopus 로고
    • Activation Pathway of Src Kinase Reveals Intermediate States as Targets for Drug Design
    • Shukla, D.; Meng, Y.; Roux, B.; Pande, V. S. Activation Pathway of Src Kinase Reveals Intermediate States as Targets for Drug Design Nat. Commun. 2014, 5 3397
    • (2014) Nat. Commun. , vol.5 , pp. 3397
    • Shukla, D.1    Meng, Y.2    Roux, B.3    Pande, V.S.4
  • 12
    • 84862909284 scopus 로고    scopus 로고
    • Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer
    • Lin, Y.-S.; Bowman, G. R.; Beauchamp, K. A.; Pande, V. S. Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer Biophys. J. 2012, 102, 315-324
    • (2012) Biophys. J. , vol.102 , pp. 315-324
    • Lin, Y.-S.1    Bowman, G.R.2    Beauchamp, K.A.3    Pande, V.S.4
  • 13
    • 84887066152 scopus 로고    scopus 로고
    • Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation
    • Qiao, Q.; Bowman, G. R.; Huang, X. Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation J. Am. Chem. Soc. 2013, 135, 16092-16101
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 16092-16101
    • Qiao, Q.1    Bowman, G.R.2    Huang, X.3
  • 15
    • 80052003642 scopus 로고    scopus 로고
    • Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments
    • Chodera, J. D.; Pande, V. S. Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments Phys. Rev. Lett. 2011, 107 098102
    • (2011) Phys. Rev. Lett. , vol.107 , pp. 098102
    • Chodera, J.D.1    Pande, V.S.2
  • 17
    • 84904118937 scopus 로고    scopus 로고
    • Application of Molecular-Dynamics Based Markov State Models to Functional Proteins
    • Malmstrom, R. D.; Lee, C. T.; Van Wart, A. T.; Amaro, R. E. Application of Molecular-Dynamics Based Markov State Models to Functional Proteins J. Chem. Theory Comput. 2014, 10, 2648-2657
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 2648-2657
    • Malmstrom, R.D.1    Lee, C.T.2    Van Wart, A.T.3    Amaro, R.E.4
  • 18
    • 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
  • 19
    • 84863939894 scopus 로고    scopus 로고
    • Equilibrium Fluctuations of a Single Folded Protein Reveal a Multitude of Potential Cryptic Allosteric Sites
    • Bowman, G. R.; Geissler, P. L. Equilibrium Fluctuations of a Single Folded Protein Reveal a Multitude of Potential Cryptic Allosteric Sites Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 11681-11686
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 11681-11686
    • Bowman, G.R.1    Geissler, P.L.2
  • 20
    • 80053254053 scopus 로고    scopus 로고
    • Probing Molecular Kinetics with Markov Models: Metastable States, Transition Pathways and Spectroscopic Observables
    • Prinz, J.-H.; Keller, B.; Noé, F. Probing Molecular Kinetics with Markov Models: Metastable States, Transition Pathways and Spectroscopic Observables Phys. Chem. Chem. Phys. 2011, 13, 16912-16927
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 16912-16927
    • Prinz, J.-H.1    Keller, B.2    Noé, F.3
  • 21
    • 70349631761 scopus 로고    scopus 로고
    • Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems
    • Bowman, G. R.; Beauchamp, K. A.; Boxer, G.; Pande, V. S. Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems J. Chem. Phys. 2009, 131 124101
    • (2009) J. Chem. Phys. , vol.131 , pp. 124101
    • Bowman, G.R.1    Beauchamp, K.A.2    Boxer, G.3    Pande, V.S.4
  • 22
    • 77951688892 scopus 로고    scopus 로고
    • Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
    • E, W.; Vanden-Eijnden, E. Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events Annu. Rev. Phys. Chem. 2010, 61, 391-420
    • (2010) Annu. Rev. Phys. Chem. , vol.61 , pp. 391-420
    • Vanden-Eijnden, E.1
  • 23
    • 77950159292 scopus 로고    scopus 로고
    • Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
    • Bowman, G. R.; Ensign, D. L.; Pande, V. S. Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models J. Chem. Theory Comput. 2010, 6, 787-794
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 787-794
    • Bowman, G.R.1    Ensign, D.L.2    Pande, V.S.3
  • 24
    • 80053954164 scopus 로고    scopus 로고
    • Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies
    • Weber, J. K.; Pande, V. S. Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies J. Chem. Theory Comput. 2011, 7, 3405-3411
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3405-3411
    • Weber, J.K.1    Pande, V.S.2
  • 25
    • 57749188299 scopus 로고    scopus 로고
    • Targeting Cancer with Small Molecule Kinase Inhibitors
    • Zhang, J.; Yang, P. L.; Gray, N. S. Targeting Cancer with Small Molecule Kinase Inhibitors Nat. Rev. Cancer 2009, 9, 28-39
    • (2009) Nat. Rev. Cancer , vol.9 , pp. 28-39
    • Zhang, J.1    Yang, P.L.2    Gray, N.S.3
  • 26
    • 84934436648 scopus 로고    scopus 로고
    • Principal component analysis: A method for determining the essential dynamics of proteins
    • David, C. C.; Jacobs, D. J. Principal component analysis: a method for determining the essential dynamics of proteins Methods Mol. Biol. 2014, 1084, 193-226
    • (2014) Methods Mol. Biol. , vol.1084 , pp. 193-226
    • David, C.C.1    Jacobs, D.J.2
  • 27
    • 84876005630 scopus 로고    scopus 로고
    • Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
    • Schwantes, C. R.; Pande, V. S. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9 J. Chem. Theory Comput. 2013, 9, 2000-2009
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2000-2009
    • Schwantes, C.R.1    Pande, V.S.2
  • 30
    • 84901608851 scopus 로고    scopus 로고
    • Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models
    • Razavi, A. M.; Wuest, W. M.; Voelz, V. A. Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models J. Chem. Inf. Model. 2014, 54, 1425-1432
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1425-1432
    • Razavi, A.M.1    Wuest, W.M.2    Voelz, V.A.3
  • 31
    • 80052082999 scopus 로고    scopus 로고
    • Structural Insights into Agonist-Induced Activation of G-Protein-Coupled Receptors
    • Deupi, X.; Standfuss, J. Structural Insights into Agonist-Induced Activation of G-Protein-Coupled Receptors Curr. Opin. Struct. Biol. 2011, 21, 541-551
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 541-551
    • Deupi, X.1    Standfuss, J.2
  • 34
    • 84876477790 scopus 로고    scopus 로고
    • Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics
    • Weber, J. K.; Jack, R. L.; Pande, V. S. Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics J. Am. Chem. Soc. 2013, 135, 5501-5504
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 5501-5504
    • Weber, J.K.1    Jack, R.L.2    Pande, V.S.3
  • 35
    • 84907344348 scopus 로고    scopus 로고
    • Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscape
    • Weber, J. K.; Jack, R. L.; Schwantes, C. R.; Pande, V. S. Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscape Biophys. J. 2014, 107 (4) 974-982
    • (2014) Biophys. J. , vol.107 , Issue.4 , pp. 974-982
    • Weber, J.K.1    Jack, R.L.2    Schwantes, C.R.3    Pande, V.S.4
  • 36
    • 0033246864 scopus 로고    scopus 로고
    • A Gallavotti-Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics
    • Lebowitz, J. L.; Spohn, H. A Gallavotti-Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics J. Stat. Phys. 1999, 95, 333-365
    • (1999) J. Stat. Phys. , vol.95 , pp. 333-365
    • Lebowitz, J.L.1    Spohn, H.2
  • 37
    • 0000186593 scopus 로고    scopus 로고
    • Path-Ensemble Averages in Systems Driven far from Equilibrium
    • Crooks, G. E. Path-Ensemble Averages in Systems Driven far from Equilibrium Phys. Rev. E 2000, 61, 2361-2366
    • (2000) Phys. Rev. e , vol.61 , pp. 2361-2366
    • Crooks, G.E.1
  • 38
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium Equality for Free Energy Differences
    • Jarzynski, C. Nonequilibrium Equality for Free Energy Differences Phys. Rev. Lett. 1997, 78, 2690-2693
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 41
    • 0033945124 scopus 로고    scopus 로고
    • Structure of the Negative Regulatory Domain of p53 Bound to S100B(ββ)
    • Rustandi, R. R.; Baldisseri, D. M.; Weber, D. J. Structure of the Negative Regulatory Domain of p53 Bound to S100B(ββ) Nat. Struct. Biol. 2000, 7, 570-574
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 570-574
    • Rustandi, R.R.1    Baldisseri, D.M.2    Weber, D.J.3
  • 42
    • 0001858251 scopus 로고
    • Application of a Theory of Enzyme Specificity to Protein Synthesis
    • Koshland, D. E. Application of a Theory of Enzyme Specificity to Protein Synthesis Proc. Natl. Acad. Sci. U. S. A. 1958, 44, 98-104
    • (1958) Proc. Natl. Acad. Sci. U. S. A. , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 43
    • 84892166712 scopus 로고
    • Einfluss der Configuration auf die Wirkung der Enzyme
    • Fischer, E. Einfluss der Configuration auf die Wirkung der Enzyme Ber. Dtsch. Chem. Ges. 1894, 27, 2985-2993
    • (1894) Ber. Dtsch. Chem. Ges. , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 44
    • 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
  • 45
    • 84907919370 scopus 로고    scopus 로고
    • Elements and Modulation of Functional Dynamics
    • Gibbs, A. C. Elements and Modulation of Functional Dynamics J. Med. Chem. 2014, 57, 7819-7837
    • (2014) J. Med. Chem. , vol.57 , pp. 7819-7837
    • Gibbs, A.C.1
  • 46
    • 77957228360 scopus 로고
    • O Dinamicseszkij Aszpektah Sztukturü Fermentov (On the Dynamic Aspects of Protein Structure)
    • Braunstein, A. E. Izdat. Nauka: Moscow.
    • Straub, F. B.; Szabolcsi, G. O Dinamicseszkij Aszpektah Sztukturü Fermentov (On the Dynamic Aspects of Protein Structure). Molecular Biology, Problems and Perspectives; Braunstein, A. E., Ed.; Izdat. Nauka: Moscow, 1964.
    • (1964) Molecular Biology, Problems and Perspectives
    • Straub, F.B.1    Szabolcsi, G.2
  • 48
  • 49
    • 33745744079 scopus 로고    scopus 로고
    • Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates
    • Snow, C. D.; Rhee, Y. M.; Pande, V. S. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates Biophys. J. 2006, 91, 14-24
    • (2006) Biophys. J. , vol.91 , pp. 14-24
    • Snow, C.D.1    Rhee, Y.M.2    Pande, V.S.3
  • 50
    • 0034255123 scopus 로고    scopus 로고
    • Speeding Molecular Recognition by Using the Folding Funnel: The Fly-Casting Mechanism
    • Shoemaker, B. A.; Portman, J. J.; Wolynes, P. G. Speeding Molecular Recognition by Using the Folding Funnel: The Fly-Casting Mechanism Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 8868-8873
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 8868-8873
    • Shoemaker, B.A.1    Portman, J.J.2    Wolynes, P.G.3
  • 51
    • 62849090890 scopus 로고    scopus 로고
    • The Courtship of Proteins: Understanding the Encounter Complex
    • Ubbink, M. The Courtship of Proteins: Understanding the Encounter Complex FEBS Lett. 2009, 583, 1060-1066
    • (2009) FEBS Lett. , vol.583 , pp. 1060-1066
    • Ubbink, M.1
  • 52
    • 0025048105 scopus 로고
    • Molecular Dynamics Simulations in Biology
    • Karplus, M.; Petsko, G. A. Molecular Dynamics Simulations in Biology Nature 1990, 347, 631-639
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 55
    • 0034623787 scopus 로고    scopus 로고
    • Screen Savers of the World Unite!
    • Shirts, M.; Pande, V. S. Screen Savers of the World Unite! Science 2000, 290, 1903-1904
    • (2000) Science , vol.290 , pp. 1903-1904
    • Shirts, M.1    Pande, V.S.2
  • 56
    • 84870997608 scopus 로고    scopus 로고
    • A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons
    • Paulechka, E.; Kroenlein, K.; Kazakov, A.; Frenkel, M. A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons J. Phys. Chem. B 2012, 116, 14389-14397
    • (2012) J. Phys. Chem. B , vol.116 , pp. 14389-14397
    • Paulechka, E.1    Kroenlein, K.2    Kazakov, A.3    Frenkel, M.4
  • 57
    • 84872142162 scopus 로고    scopus 로고
    • Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
    • Wang, L.-P.; Chen, J.; Van Voorhis, T. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data J. Chem. Theory Comput. 2013, 9, 452-460
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 452-460
    • Wang, L.-P.1    Chen, J.2    Van Voorhis, T.3
  • 58
    • 79953167530 scopus 로고    scopus 로고
    • Dynamical Fingerprints for Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments
    • Noé, F.; Doose, S.; Daidone, I.; Löllmann, M.; Sauer, M.; Chodera, J. D.; Smith, J. C. Dynamical Fingerprints for Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 4822-4827
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 4822-4827
    • Noé, F.1    Doose, S.2    Daidone, I.3    Löllmann, M.4    Sauer, M.5    Chodera, J.D.6    Smith, J.C.7


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