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Volumn 9, Issue 2, 2008, Pages 144-150

Molecular simulations of protein dynamics: New windows on mechanisms in biology

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE REDUCTASE; NUCLEAR FACTOR; PROTEIN P53; PROTEIN TYROSINE KINASE; SYNTAXIN;

EID: 38949151546     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/sj.embor.7401160     Document Type: Review
Times cited : (128)

References (45)
  • 2
    • 17044392602 scopus 로고    scopus 로고
    • Improving implicit solvent simulations: A Poisson-centric view
    • Baker M (2005) Improving implicit solvent simulations: A Poisson-centric view. Curr Opin Struct Biol 15: 137-143
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 137-143
    • Baker, M.1
  • 3
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase landscape
    • Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase landscape. Science 313: 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 4
    • 38949135781 scopus 로고    scopus 로고
    • The electrostatic surface of MDM2 modulates the specificity of its interaction with phosphorylated and unphosphorylated p53 peptides
    • in press
    • Brown CJ, Srinivasan D, Lee HJ, Coomber D, Verma CS, Lane DP (2008) The electrostatic surface of MDM2 modulates the specificity of its interaction with phosphorylated and unphosphorylated p53 peptides. Cell Cycle 7 (in press)
    • (2008) Cell Cycle , vol.7
    • Brown, C.J.1    Srinivasan, D.2    Lee, H.J.3    Coomber, D.4    Verma, C.S.5    Lane, D.P.6
  • 5
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67 922-930
    • (2007) Proteins , vol.67 , pp. 922-930
    • Chen, J.1    Brooks, C.L.2
  • 6
    • 34447632693 scopus 로고    scopus 로고
    • High throughput identification of interacting protein-protein binding sites
    • Chung JL, Wang W, Bourne PE (2007) High throughput identification of interacting protein-protein binding sites. BMC Bioinformatics 8 223-224
    • (2007) BMC Bioinformatics , vol.8 , pp. 223-224
    • Chung, J.L.1    Wang, W.2    Bourne, P.E.3
  • 7
    • 34147185256 scopus 로고    scopus 로고
    • Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
    • Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P (2007) Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struct Biol 17: 149-156
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 149-156
    • Dal Peraro, M.1    Ruggerone, P.2    Raugei, S.3    Gervasio, F.L.4    Carloni, P.5
  • 9
    • 30744478915 scopus 로고    scopus 로고
    • Protein flexibility: Its role in structure and mechanism revealed by molecuiar simulations
    • Dodson G, Verma CS (2006) Protein flexibility: Its role in structure and mechanism revealed by molecuiar simulations. Cell Mol Life Sci 63: 207-219.
    • (2006) Cell Mol Life Sci , vol.63 , pp. 207-219
    • Dodson, G.1    Verma, C.S.2
  • 10
    • 17044425870 scopus 로고    scopus 로고
    • Long-timescale simulation methods
    • Elber R (2005) Long-timescale simulation methods. Curr Opin Struct Biol 15: 151-156
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 151-156
    • Elber, R.1
  • 11
    • 33746592161 scopus 로고    scopus 로고
    • Molecular simulations of cotranslational protein folding fragment stabilities, folding cooperativity and trapping in the ribosome
    • Elcock A (2006) Molecular simulations of cotranslational protein folding fragment stabilities, folding cooperativity and trapping in the ribosome. PLos Comput Biol 2: E98
    • (2006) PLos Comput Biol , vol.2
    • Elcock, A.1
  • 12
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a ptotein hydrophobic cavity by NMR
    • Ernst JA, Clubb RT, Zhou HX, Gronenborn AM, Clore GM (1995) Demonstration of positionally disordered water within a ptotein hydrophobic cavity by NMR. Science 267: 1813-1817
    • (1995) Science , vol.267 , pp. 1813-1817
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 14
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: Analysis by modern rate theory and computer simulations
    • Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science 303: 186-195
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 15
  • 17
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman KA et al (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450: 838-844
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1
  • 18
    • 33845922103 scopus 로고    scopus 로고
    • The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading
    • Johnson A, Yao NY, Bowman GD, Kuriyan J, O'Donnell M (2006) The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading. J Biol Chem 281: 35531-35543
    • (2006) J Biol Chem , vol.281 , pp. 35531-35543
    • Johnson, A.1    Yao, N.Y.2    Bowman, G.D.3    Kuriyan, J.4    O'Donnell, M.5
  • 19
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102: 6679-6685
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 20
    • 25444469141 scopus 로고    scopus 로고
    • Out-of-plane sliding motions in open sliding clamps: Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
    • Kazmirski SL, Zhao Y, Bowman GD, O'Donnell M, Kuriyan J (2005) Out-of-plane sliding motions in open sliding clamps: Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen. Proc Natl Acad Sci USA 102: 13801-13806
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13801-13806
    • Kazmirski, S.L.1    Zhao, Y.2    Bowman, G.D.3    O'Donnell, M.4    Kuriyan, J.5
  • 21
    • 36849011121 scopus 로고    scopus 로고
    • Modulation of the p53-MDM2 interaction by phosphorylation of Thr 18: A computational study
    • Lee HJ, Srinivasan D, Coomber D, Lane DP, Verma CS (2007) Modulation of the p53-MDM2 interaction by phosphorylation of Thr 18: A computational study. Cell Cycle 6: 2604-2611
    • (2007) Cell Cycle , vol.6 , pp. 2604-2611
    • Lee, H.J.1    Srinivasan, D.2    Coomber, D.3    Lane, D.P.4    Verma, C.S.5
  • 24
    • 34147133371 scopus 로고    scopus 로고
    • Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
    • Meirovitch H (2007) Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Curr Opin Struct Biol 17: 181-186
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 181-186
    • Meirovitch, H.1
  • 26
    • 34547628903 scopus 로고    scopus 로고
    • Reaction coordinate of an enzymatic reaction revealed by transition path sampling
    • Quaytman SL, Schwartz SD (2007) Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc Natl Acad Sci USA 104: 12253-12258
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 12253-12258
    • Quaytman, S.L.1    Schwartz, S.D.2
  • 27
    • 33845957884 scopus 로고    scopus 로고
    • Determination of solvent content in cavities in IL-1β using experimentally phased electron density
    • Quillin ML, Wingfield Fr, Matthews BW (2006) Determination of solvent content in cavities in IL-1β using experimentally phased electron density. Proc Natl Acad Sci USA 103: 19749-19753
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 19749-19753
    • Quillin, M.L.1    Wingfield, F.2    Matthews, B.W.3
  • 28
    • 33847175935 scopus 로고    scopus 로고
    • High performance computing in biology: Multimillion atom simulations of nanoscale systems
    • Sanbonmatsu KY, Tung CS (2007) High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol 157: 470-480
    • (2007) J Struct Biol , vol.157 , pp. 470-480
    • Sanbonmatsu, K.Y.1    Tung, C.S.2
  • 29
    • 35649018226 scopus 로고    scopus 로고
    • Atomic-level structural and functional model of a bacterial photosynthetic membrane-vesicle
    • Sener MK, Olsen JD, Hunter CN, Schulten K (2007) Atomic-level structural and functional model of a bacterial photosynthetic membrane-vesicle. Proc Natl Acad Sci USA 104: 15723-15728
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 15723-15728
    • Sener, M.K.1    Olsen, J.D.2    Hunter, C.N.3    Schulten, K.4
  • 31
    • 24644442164 scopus 로고    scopus 로고
    • The folding energy landscape and phosphorylation: Modeling the conformational switch of the NFAT regulatory domain
    • Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG (2005) The folding energy landscape and phosphorylation: Modeling the conformational switch of the NFAT regulatory domain. FASEB J 19: 1389-1395
    • (2005) FASEB J , vol.19 , pp. 1389-1395
    • Shen, T.1    Zong, C.2    Hamelberg, D.3    McCammon, J.A.4    Wolynes, P.G.5
  • 32
    • 34548256844 scopus 로고    scopus 로고
    • Anatomy and dynamics of a supramolecular membrane protein cluster
    • Sieber JJ et al (2007) Anatomy and dynamics of a supramolecular membrane protein cluster. Science 317: 1072-1076
    • (2007) Science , vol.317 , pp. 1072-1076
    • Sieber, J.J.1
  • 33
    • 0016819380 scopus 로고    scopus 로고
    • (11975) Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor
    • Snyder GH, Rowan R 3rd, Karplus S, Sykes BD (11975) Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor. Biochemistry 14: 3765-3777
    • Biochemistry , vol.14 , pp. 3765-3777
    • Snyder, G.H.1    Rowan 3rd, R.2    Karplus, S.3    Sykes, B.D.4
  • 34
    • 34248572405 scopus 로고    scopus 로고
    • Hydration of a hydrophobic cavity and its functional role: A simulation study of human interleukin-1β
    • Somani S, Chng CP, Verma CS (2007) Hydration of a hydrophobic cavity and its functional role: A simulation study of human interleukin-1β. Proteins 67: 868-885
    • (2007) Proteins , vol.67 , pp. 868-885
    • Somani, S.1    Chng, C.P.2    Verma, C.S.3
  • 35
    • 34249930159 scopus 로고    scopus 로고
    • Single-molecule experiments in vitro and in silico
    • Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316: 1144-1148
    • (2007) Science , vol.316 , pp. 1144-1148
    • Sotomayor, M.1    Schulten, K.2
  • 36
    • 34147179524 scopus 로고    scopus 로고
    • Bridging from molecular simulation to biochemical networks
    • Stein M, Gabdoulline RR, Wade RC (2007) Bridging from molecular simulation to biochemical networks. Curr Opin Struct Biol 17 166-172
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 166-172
    • Stein, M.1    Gabdoulline, R.R.2    Wade, R.C.3
  • 37
    • 33746017658 scopus 로고    scopus 로고
    • Electric fields at the active site of an enzyme: Direct comparison of experiment with theory
    • Suydam IT, Snow CD, Pande VS, Boxer SG (2006) Electric fields at the active site of an enzyme: Direct comparison of experiment with theory. Science 313: 200-204
    • (2006) Science , vol.313 , pp. 200-204
    • Suydam, I.T.1    Snow, C.D.2    Pande, V.S.3    Boxer, S.G.4
  • 38
    • 33750805030 scopus 로고    scopus 로고
    • Molecular anatomy of a trafficking organelle
    • Takamori S et al (2006) Molecular anatomy of a trafficking organelle: Cell 127: 671-673
    • (2006) Cell , vol.127 , pp. 671-673
    • Takamori, S.1
  • 39
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form and shape: Guiding principles for robustness in macromolecular machines
    • Tama F, Brooks CL (2006) Symmetry, form and shape: Guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 35: 115-133
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 40
    • 33646191829 scopus 로고    scopus 로고
    • Size, motion and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes
    • Tian P, Andricioaei I (2006) Size, motion and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes. Biophys J 90: 2718-2730
    • (2006) Biophys J , vol.90 , pp. 2718-2730
    • Tian, P.1    Andricioaei, I.2
  • 42
    • 0016433835 scopus 로고
    • NMR investigations of the dynamics of the aromatic amino acid residues in the basic pancreatic trypsin inhibitor
    • Wuthrich K, Wagner G (1975) NMR investigations of the dynamics of the aromatic amino acid residues in the basic pancreatic trypsin inhibitor. FEBS Lett 50: 265-268
    • (1975) FEBS Lett , vol.50 , pp. 265-268
    • Wuthrich, K.1    Wagner, G.2
  • 43
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J (2001) Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105: 115-126
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 44
    • 0033524454 scopus 로고    scopus 로고
    • Disordered water within a hydrophobic protein cavity visualized by X-ray crystallography
    • Yu B, Blaber M, Gronenborn AM, Clore GM, Caspar DI (1999) Disordered water within a hydrophobic protein cavity visualized by X-ray crystallography. Proc Natl Acad Sci USA 96: 103-108
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 103-108
    • Yu, B.1    Blaber, M.2    Gronenborn, A.M.3    Clore, G.M.4    Caspar, D.I.5
  • 45
    • 33645033314 scopus 로고    scopus 로고
    • Comparing atomistic simulation data with NMR experiment: How much can NOEs actually tell us
    • Zagrovic B, van Gunsteren WF (2006) Comparing atomistic simulation data with NMR experiment: How much can NOEs actually tell us. Proteins 63: 210-218
    • (2006) Proteins , vol.63 , pp. 210-218
    • Zagrovic, B.1    van Gunsteren, W.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.