메뉴 건너뛰기




Volumn 5, Issue 4, 2009, Pages

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL EFFICIENCY; LIGANDS; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES; PROTEINS;

EID: 65349192770     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000343     Document Type: Article
Times cited : (51)

References (51)
  • 1
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450: 964-972.
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 2
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282: 740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 4
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • Swain JF, Gierasch LM (2006) The changing landscape of protein allostery. Curr Opin Struct Biol 16: 102-108.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 102-108
    • Swain, J.F.1    Gierasch, L.M.2
  • 5
    • 0343415156 scopus 로고    scopus 로고
    • The way things move: Looking under the hood of molecular motor proteins
    • Vale RD, Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288: 88-95.
    • (2000) Science , vol.288 , pp. 88-95
    • Vale, R.D.1    Milligan, R.A.2
  • 6
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11: 224-230.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 7
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • Haliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79: 3090-3093.
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 8
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins 44: 150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 9
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Wang YM, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147: 302-314.
    • (2004) J Struct Biol , vol.147 , pp. 302-314
    • Wang, Y.M.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 10
    • 14844300852 scopus 로고    scopus 로고
    • Maturation dynamics of bacteriophage HK97 capsid
    • Rader AJ, Vlad DH, Bahar I (2005) Maturation dynamics of bacteriophage HK97 capsid. Structure 13: 413-421.
    • (2005) Structure , vol.13 , pp. 413-421
    • Rader, A.J.1    Vlad, D.H.2    Bahar, I.3
  • 11
    • 0029000872 scopus 로고
    • Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand-gated
    • Williams JC, Mcdermott AE (1995) Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand-gated. Biochemistry 34: 8309-8319.
    • (1995) Biochemistry , vol.34 , pp. 8309-8319
    • Williams, J.C.1    Mcdermott, A.E.2
  • 12
    • 0026779802 scopus 로고
    • Segmental movement: Definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase
    • Sampson NS, Knowles JR (1992) Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry 31: 8482-8487.
    • (1992) Biochemistry , vol.31 , pp. 8482-8487
    • Sampson, N.S.1    Knowles, J.R.2
  • 14
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE (2001) Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry 40: 9846-9859.
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 15
    • 0029618368 scopus 로고
    • Steroid hormone receptors: Many actors in search of a plot
    • Beato M, Herrlich P, Schutz G (1995) Steroid hormone receptors: many actors in search of a plot. Cell 83: 851-857.
    • (1995) Cell , vol.83 , pp. 851-857
    • Beato, M.1    Herrlich, P.2    Schutz, G.3
  • 16
    • 0032446607 scopus 로고    scopus 로고
    • The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
    • Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, et al. (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95: 927-937.
    • (1998) Cell , vol.95 , pp. 927-937
    • Shiau, A.K.1    Barstad, D.2    Loria, P.M.3    Cheng, L.4    Kushner, P.J.5
  • 17
    • 0025015392 scopus 로고
    • Anatomy of a conformational change: Hinged lid motion of the triosephosphate isomerase loop
    • Joseph D, Petsko GA, Karplus M (1990) Anatomy of a conformational change: hinged lid motion of the triosephosphate isomerase loop. Science 249: 1425-1428.
    • (1990) Science , vol.249 , pp. 1425-1428
    • Joseph, D.1    Petsko, G.A.2    Karplus, M.3
  • 18
    • 0345540195 scopus 로고
    • Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phos- phate
    • Madura JD, Mccammon JA (1989) Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phos- phate. J Phys Chem 93: 7285-7287.
    • (1989) J Phys Chem , vol.93 , pp. 7285-7287
    • Madura, J.D.1    Mccammon, J.A.2
  • 19
    • 0031972864 scopus 로고    scopus 로고
    • The loop opening/closing motion of the enzyme triosephosphate isomerase
    • Derreumaux P, Schlick T (1998) The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys J 74: 72-81.
    • (1998) Biophys J , vol.74 , pp. 72-81
    • Derreumaux, P.1    Schlick, T.2
  • 20
    • 35348942279 scopus 로고    scopus 로고
    • Allosteric communication in dihydrofolate reductase: Signaling network and pathways for closed to occluded transition and back
    • Chen J, Dima RI, Thirumalai D (2007) Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol 374: 250-266.
    • (2007) J Mol Biol , vol.374 , pp. 250-266
    • Chen, J.1    Dima, R.I.2    Thirumalai, D.3
  • 21
    • 0031557394 scopus 로고    scopus 로고
    • Domain motions in dihydrofolate reductase: A molecular dynamics study
    • Verma CS, Caves LSD, Hubbard RE, Roberts GCK (1997) Domain motions in dihydrofolate reductase: a molecular dynamics study. J Mol Biol 266: 776-796.
    • (1997) J Mol Biol , vol.266 , pp. 776-796
    • Verma, C.S.1    Caves, L.S.D.2    Hubbard, R.E.3    Roberts, G.C.K.4
  • 22
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
    • Radkiewicz JL, Brooks CL (2000) Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J Am Chem Soc 122: 225-231.
    • (2000) J Am Chem Soc , vol.122 , pp. 225-231
    • Radkiewicz, J.L.1    Brooks, C.L.2
  • 23
    • 0038810233 scopus 로고    scopus 로고
    • Correlated motion and the effect of distal mutations in dihydrofolate reductase
    • Rod TH, Radkiewicz JL, Brooks CL (2003) Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A 100: 6980-6985.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 6980-6985
    • Rod, T.H.1    Radkiewicz, J.L.2    Brooks, C.L.3
  • 24
    • 6344294816 scopus 로고    scopus 로고
    • Thorpe IF, Brooks CL 3rd (2004) The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 57: 444-457.
    • Thorpe IF, Brooks CL 3rd (2004) The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 57: 444-457.
  • 25
    • 0034966704 scopus 로고    scopus 로고
    • Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions
    • Ota N, Agard DA (2001) Enzyme specificity under dynamic control II: principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Protein Sci 10: 1403-1414.
    • (2001) Protein Sci , vol.10 , pp. 1403-1414
    • Ota, N.1    Agard, D.A.2
  • 27
    • 47349128896 scopus 로고    scopus 로고
    • Toward better refinement of comparative models: Predicting loops in inexact environments
    • Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP (2008) Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 72: 959-971.
    • (2008) Proteins , vol.72 , pp. 959-971
    • Sellers, B.D.1    Zhu, K.2    Zhao, S.3    Friesner, R.A.4    Jacobson, M.P.5
  • 28
    • 45649083705 scopus 로고    scopus 로고
    • A simple model of backbone flexibility improves modeling of side-chain conformational variability
    • Friedland GD, Linares AJ, Smith CA, Kortemme T (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 380: 757-774.
    • (2008) J Mol Biol , vol.380 , pp. 757-774
    • Friedland, G.D.1    Linares, A.J.2    Smith, C.A.3    Kortemme, T.4
  • 29
    • 0030580089 scopus 로고    scopus 로고
    • Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
    • Hilser VJ, Freire E (1996) Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J Mol Biol 262: 756-772.
    • (1996) J Mol Biol , vol.262 , pp. 756-772
    • Hilser, V.J.1    Freire, E.2
  • 30
    • 33748281380 scopus 로고    scopus 로고
    • Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
    • Shehu A, Clementi C, Kavraki LE (2006) Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins 65: 164-179.
    • (2006) Proteins , vol.65 , pp. 164-179
    • Shehu, A.1    Clementi, C.2    Kavraki, L.E.3
  • 31
    • 33847776838 scopus 로고    scopus 로고
    • On the characterization of protein native state ensembles
    • Shehu A, Kavraki LE, Clementi C (2007) On the characterization of protein native state ensembles. Biophys J 92: 1503-1511.
    • (2007) Biophys J , vol.92 , pp. 1503-1511
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 33
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • Ota N, Agard DA (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol 351: 345-354.
    • (2005) J Mol Biol , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 34
    • 33749029273 scopus 로고    scopus 로고
    • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    • Sharp K, Skinner JJ (2006) Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Proteins 65: 347-361.
    • (2006) Proteins , vol.65 , pp. 347-361
    • Sharp, K.1    Skinner, J.J.2
  • 35
    • 0029633186 scopus 로고
    • Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, et al. (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91: 1-41.
    • (1995) Comput Phys Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5
  • 36
    • 0025762996 scopus 로고
    • The crystal-structure of the open and the closed conformation of the flexible loop of trypanosomal triosephosphate isomerase
    • Wierenga RK, Noble MEM, Postma JPM, Groendijk H, Kalk KH, et al. (1991) The crystal-structure of the open and the closed conformation of the flexible loop of trypanosomal triosephosphate isomerase. Proteins 10: 33-49.
    • (1991) Proteins , vol.10 , pp. 33-49
    • Wierenga, R.K.1    Noble, M.E.M.2    Postma, J.P.M.3    Groendijk, H.4    Kalk, K.H.5
  • 37
    • 0029102089 scopus 로고
    • Dynamics of the dihydrofolate- reductase folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features
    • Epstein DM, Benkovic SJ, Wright PE (1995) Dynamics of the dihydrofolate- reductase folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry 34: 11037-11048.
    • (1995) Biochemistry , vol.34 , pp. 11037-11048
    • Epstein, D.M.1    Benkovic, S.J.2    Wright, P.E.3
  • 39
    • 0032558779 scopus 로고    scopus 로고
    • Unfolded conformations of alpha-lytic protease are more stable than its native state
    • Sohl JL, Jaswal SS, Agard DA (1998) Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature 395: 817-819.
    • (1998) Nature , vol.395 , pp. 817-819
    • Sohl, J.L.1    Jaswal, S.S.2    Agard, D.A.3
  • 40
    • 65349192770 scopus 로고    scopus 로고
    • Protein Flexibility from Perturbations PLoS Computational Biology | www.ploscompbiol.org 13 April 2009 | 5 | Issue 4 | e1000343
    • Protein Flexibility from Perturbations PLoS Computational Biology | www.ploscompbiol.org 13 April 2009 | Volume 5 | Issue 4 | e1000343
  • 41
    • 0037122769 scopus 로고    scopus 로고
    • Energetic landscape of alpha- lytic protease optimizes longevity through kinetic stability
    • Jaswal SS, Sohl JL, Davis JH, Agard DA (2002) Energetic landscape of alpha- lytic protease optimizes longevity through kinetic stability. Nature 415: 343-346.
    • (2002) Nature , vol.415 , pp. 343-346
    • Jaswal, S.S.1    Sohl, J.L.2    Davis, J.H.3    Agard, D.A.4
  • 42
    • 0034851838 scopus 로고    scopus 로고
    • The conserved residues of the ligand-binding domains of steroid receptors are located in the core of the molecules
    • Maeda M (2001) The conserved residues of the ligand-binding domains of steroid receptors are located in the core of the molecules. J Mol Graph Model 19: 543-551.
    • (2001) J Mol Graph Model , vol.19 , pp. 543-551
    • Maeda, M.1
  • 43
    • 33750008686 scopus 로고    scopus 로고
    • Structural analysis of E-coli hsp90 reveals dramatic nucleotide-dependent conformational rearrange- ments
    • Shiau AK, Harris SF, Southworth DR, Agard DA (2006) Structural analysis of E-coli hsp90 reveals dramatic nucleotide-dependent conformational rearrange- ments. Cell 127: 329-340.
    • (2006) Cell , vol.127 , pp. 329-340
    • Shiau, A.K.1    Harris, S.F.2    Southworth, D.R.3    Agard, D.A.4
  • 44
    • 33750407288 scopus 로고    scopus 로고
    • Anisotropic network model: Systematic evaluation and a new web interface
    • Eyal E, Yang LW, Bahar I (2006) Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 22: 2619.
    • (2006) Bioinformatics , vol.22 , pp. 2619
    • Eyal, E.1    Yang, L.W.2    Bahar, I.3
  • 45
    • 33748663254 scopus 로고    scopus 로고
    • THESEUS: Maximum likelihood super- positioning and analysis of macromolecular structures
    • Theobald DL, Wuttke DS (2006) THESEUS: maximum likelihood super- positioning and analysis of macromolecular structures. Bioinformatics 22: 2171.
    • (2006) Bioinformatics , vol.22 , pp. 2171
    • Theobald, D.L.1    Wuttke, D.S.2
  • 46
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9: 646-652.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 47
    • 0034663710 scopus 로고    scopus 로고
    • Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a- amylase inhibitor
    • Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to a- amylase inhibitor. Proteins 40: 512-524.
    • (2000) Proteins , vol.40 , pp. 512-524
    • Doruker, P.1    Atilgan, A.R.2    Bahar, I.3
  • 48
    • 2442543557 scopus 로고    scopus 로고
    • Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
    • Micheletti C, Carloni P, Maritan A (2004) Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins 55: 635-645.
    • (2004) Proteins , vol.55 , pp. 635-645
    • Micheletti, C.1    Carloni, P.2    Maritan, A.3
  • 49
    • 31544444687 scopus 로고    scopus 로고
    • Loop motions of triosephosphate isomerase observed with elastic networks
    • Kurkcuoglu O, Jernigan RL, Doruker P (2006) Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 45: 1173-1182.
    • (2006) Biochemistry , vol.45 , pp. 1173-1182
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 50
    • 29444446536 scopus 로고    scopus 로고
    • Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small a/b protein: A unified picture of high probability, fast atomic motions in proteins
    • Clore GM, Schwieters CD (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small a/b protein: a unified picture of high probability, fast atomic motions in proteins. J Mol Biol 355: 879-886.
    • (2006) J Mol Biol , vol.355 , pp. 879-886
    • Clore, G.M.1    Schwieters, C.D.2
  • 51
    • 40549107133 scopus 로고    scopus 로고
    • Conformational selection in silico: Loop latching motions and ligand binding in enzymes
    • Wong S, Jacobson MP (2007) Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins 71: 153-164.
    • (2007) Proteins , vol.71 , pp. 153-164
    • Wong, S.1    Jacobson, M.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.