메뉴 건너뛰기




Volumn 350, Issue 5, 2005, Pages 1035-1050

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

Author keywords

Folding nucleus; Molecular dynamics simulations; Protein folding; src SH3 protein domain; Transition state ensemble

Indexed keywords

PROTEIN; SRC SH3 PROTEIN; UNCLASSIFIED DRUG;

EID: 21744452297     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.05.017     Document Type: Article
Times cited : (68)

References (72)
  • 2
    • 0033871781 scopus 로고    scopus 로고
    • Protein folding intermediates and pathways studied by hydrogen exchange
    • S.W. Englander Protein folding intermediates and pathways studied by hydrogen exchange Annu. Rev. Biophys. Biomol. Struct. 29 2000 213 238
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 213-238
    • Englander, S.W.1
  • 3
    • 0028270634 scopus 로고
    • Kinetics of protein-folding - A lattice model study of the requirements for folding to the native-state
    • A. Sali, E. Shakhnovich, and M. Karplus Kinetics of protein-folding - a lattice model study of the requirements for folding to the native-state J. Mol. Biol. 235 1994 1614 1636
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 5
    • 0036535895 scopus 로고    scopus 로고
    • Protein folding: The free energy surface
    • M. Gruebele Protein folding: the free energy surface Curr. Opin. Struct. Biol. 12 2002 161 168
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 161-168
    • Gruebele, M.1
  • 6
    • 36448999595 scopus 로고
    • Free-energy landscape for protein-folding kinetics - Intermediates, traps, and multiple pathways in theory and lattice model simulations
    • V.I. Abkevich, A.M. Gutin, and E.I. Shakhnovich Free-energy landscape for protein-folding kinetics - intermediates, traps, and multiple pathways in theory and lattice model simulations J. Chem. Phys. 101 1994 6052 6062
    • (1994) J. Chem. Phys. , vol.101 , pp. 6052-6062
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 7
    • 0029940033 scopus 로고    scopus 로고
    • Molecular collapse: The rate-limiting step in two-state cytochrome c folding
    • T.R. Sosnick, L. Mayne, and S.W. Englander Molecular collapse: the rate-limiting step in two-state cytochrome c folding Proteins: Struct. Funct. Genet. 24 1996 413 426
    • (1996) Proteins: Struct. Funct. Genet. , vol.24 , pp. 413-426
    • Sosnick, T.R.1    Mayne, L.2    Englander, S.W.3
  • 8
    • 0034681133 scopus 로고    scopus 로고
    • Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration
    • H. Nymeyer, N.D. Socci, and J.N. Onuchic Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration Proc. Natl Acad. Sci. USA 97 2000 634 639
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 634-639
    • Nymeyer, H.1    Socci, N.D.2    Onuchic, J.N.3
  • 9
    • 0035252685 scopus 로고    scopus 로고
    • Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis
    • M. Oliveberg Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis Curr. Opin. Struct. Biol. 11 2001 94 100
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 94-100
    • Oliveberg, M.1
  • 10
    • 0026511656 scopus 로고
    • The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding
    • A.R. Fersht, A. Matouschek, and L. Serrano The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 224 1992 771 782
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 11
    • 2542599277 scopus 로고    scopus 로고
    • Phi-value analysis and the nature of protein-folding transition states
    • A.R. Fersht, and S. Sato Phi-value analysis and the nature of protein-folding transition states Proc. Natl Acad. Sci. USA 101 2004 7976 7981
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7976-7981
    • Fersht, A.R.1    Sato, S.2
  • 12
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of Phi-values in protein folding kinetics
    • S.B. Ozkan, I. Bahar, and K.A. Dill Transition states and the meaning of Phi-values in protein folding kinetics Nature Struct. Biol. 8 2001 765 769
    • (2001) Nature Struct. Biol. , vol.8 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 13
    • 0345304461 scopus 로고    scopus 로고
    • Origin of unusual Phi-values in protein folding: Evidence against specific nucleation sites
    • I.E. Sanchez, and T. Kiefhaber Origin of unusual Phi-values in protein folding: evidence against specific nucleation sites J. Mol. Biol. 334 2003 1077 1085
    • (2003) J. Mol. Biol. , vol.334 , pp. 1077-1085
    • Sanchez, I.E.1    Kiefhaber, T.2
  • 14
    • 0032555115 scopus 로고    scopus 로고
    • Synergy between simulation and experiment in describing the energy landscape of protein folding
    • A.G. Ladurner, L.S. Itzhaki, V. Daggett, and A.R. Fersht Synergy between simulation and experiment in describing the energy landscape of protein folding Proc. Natl Acad. Sci. USA 95 1998 8473 8478
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 8473-8478
    • Ladurner, A.G.1    Itzhaki, L.S.2    Daggett, V.3    Fersht, A.R.4
  • 15
    • 0036435907 scopus 로고    scopus 로고
    • Determination of a transition state at atomic resolution from protein engineering data
    • E. Paci, M. Vendruscolo, C.M. Dobson, and M. Karplus Determination of a transition state at atomic resolution from protein engineering data J. Mol. Biol. 324 2002 151 163
    • (2002) J. Mol. Biol. , vol.324 , pp. 151-163
    • Paci, E.1    Vendruscolo, M.2    Dobson, C.M.3    Karplus, M.4
  • 16
    • 0842332830 scopus 로고    scopus 로고
    • Commitment and nucleation in the protein G transition state
    • I.A. Hubner, J. Shimada, and E.I. Shakhnovich Commitment and nucleation in the protein G transition state J. Mol. Biol. 336 2004 745 761
    • (2004) J. Mol. Biol. , vol.336 , pp. 745-761
    • Hubner, I.A.1    Shimada, J.2    Shakhnovich, E.I.3
  • 18
    • 0033607208 scopus 로고    scopus 로고
    • Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein a
    • J.E. Shea, J.N. Onuchic, and C.L. Brooks Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A Proc. Natl Acad. Sci. USA 96 1999 12512 12517
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 12512-12517
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 19
    • 0034321011 scopus 로고    scopus 로고
    • Energetic frustration and the nature of the transition state in protein folding
    • J.E. Shea, J.N. Onuchic, and C.L. Brooks Energetic frustration and the nature of the transition state in protein folding J. Chem. Phys. 113 2000 7663 7671
    • (2000) J. Chem. Phys. , vol.113 , pp. 7663-7671
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 20
    • 0036927818 scopus 로고    scopus 로고
    • Direct molecular dynamics observation of protein folding transition state ensemble
    • F. Ding, N.V. Dokholyan, S.V. Buldyrev, H.E. Stanley, and E.I. Shakhnovich Direct molecular dynamics observation of protein folding transition state ensemble Biophys. J. 83 2002 3525 3532
    • (2002) Biophys. J. , vol.83 , pp. 3525-3532
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 21
    • 0035370662 scopus 로고    scopus 로고
    • Multiple protein folding nuclei and the transition state ensemble in two-state proteins
    • D.K. Klimov, and D. Thirumalai Multiple protein folding nuclei and the transition state ensemble in two-state proteins Proteins: Struct. Funct. Genet. 43 2001 465 -475
    • (2001) Proteins: Struct. Funct. Genet. , vol.43 , pp. 465-475
    • Klimov, D.K.1    Thirumalai, D.2
  • 22
    • 36449000646 scopus 로고
    • Transition states and the folding dynamics of proteins and heteropolymers
    • H.S. Chan, and K.A. Dill Transition states and the folding dynamics of proteins and heteropolymers J. Chem. Phys. 100 1994 9238 9257
    • (1994) J. Chem. Phys. , vol.100 , pp. 9238-9257
    • Chan, H.S.1    Dill, K.A.2
  • 23
    • 1542345514 scopus 로고    scopus 로고
    • Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations
    • G. Settanni, J. Gsponer, and A. Caflisch Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations Biophys. J. 86 2004 1691 1701
    • (2004) Biophys. J. , vol.86 , pp. 1691-1701
    • Settanni, G.1    Gsponer, J.2    Caflisch, A.3
  • 24
    • 0034743155 scopus 로고    scopus 로고
    • From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
    • J.E. Shea, and C.L. Brooks From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding Annu. Rev. Phys. Chem. 52 2001 499 535
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 499-535
    • Shea, J.E.1    Brooks, C.L.2
  • 25
    • 0037340910 scopus 로고    scopus 로고
    • Folding of a highly conserved diverging turn motif from the SH3 domain
    • S. Gnanakaran, and A.E. Garcia Folding of a highly conserved diverging turn motif from the SH3 domain Biophys. J. 84 2003 1548 1562
    • (2003) Biophys. J. , vol.84 , pp. 1548-1562
    • Gnanakaran, S.1    Garcia, A.E.2
  • 26
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica-exchange simulations of "trp-cage" miniproteins
    • J.W. Pitera, and W. Swope Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins Proc. Natl Acad. Sci. USA 100 2003 7587 7592
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 27
    • 0041877561 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of reversible folding
    • F. Rao, and A. Caflisch Replica exchange molecular dynamics simulations of reversible folding J. Chem. Phys. 119 2003 4035 4042
    • (2003) J. Chem. Phys. , vol.119 , pp. 4035-4042
    • Rao, F.1    Caflisch, A.2
  • 28
    • 0000888146 scopus 로고    scopus 로고
    • Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
    • Y. Sugita, and Y. Okamoto Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape Chem. Phys. Letters 329 2000 261 270
    • (2000) Chem. Phys. Letters , vol.329 , pp. 261-270
    • Sugita, Y.1    Okamoto, Y.2
  • 30
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a -hairpin fragment of protein G
    • V.S. Pande, and D.S. Rokhsar Molecular dynamics simulations of unfolding and refolding of a -hairpin fragment of protein G Proc. Natl Acad. Sci. USA 96 1999 9062 9067
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 32
    • 0032443390 scopus 로고    scopus 로고
    • Discrete molecular dynamics studies of the folding of a protein-like model
    • N.V. Dokholyan, S.V. Buldyrev, H.E. Stanley, and E.I. Shakhnovich Discrete molecular dynamics studies of the folding of a protein-like model Fold. Des. 3 1998 577 587
    • (1998) Fold. Des. , vol.3 , pp. 577-587
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Stanley, H.E.3    Shakhnovich, E.I.4
  • 33
    • 0031475159 scopus 로고    scopus 로고
    • Folding thermodynamics of a model three-helix-bundle protein
    • Y. Zhou, and M. Karplus Folding thermodynamics of a model three-helix-bundle protein Proc. Natl Acad. Sci. USA 94 1997 14429 14432
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 14429-14432
    • Zhou, Y.1    Karplus, M.2
  • 34
    • 0031444104 scopus 로고    scopus 로고
    • Folding dynamics of the src SH3 domain
    • V.P. Grantcharova, and D. Baker Folding dynamics of the src SH3 domain Biochemistry 36 1997 15685 15692
    • (1997) Biochemistry , vol.36 , pp. 15685-15692
    • Grantcharova, V.P.1    Baker, D.2
  • 35
    • 0032538302 scopus 로고    scopus 로고
    • Prediction and structural characterization of an independently folding substructure in the src SH3 domain
    • Q. Yi, C. Bystroff, P. Rajagopal, R.E. Klevit, and D. Baker Prediction and structural characterization of an independently folding substructure in the src SH3 domain J. Mol. Biol. 283 1998 293 300
    • (1998) J. Mol. Biol. , vol.283 , pp. 293-300
    • Yi, Q.1    Bystroff, C.2    Rajagopal, P.3    Klevit, R.E.4    Baker, D.5
  • 36
    • 0345411345 scopus 로고    scopus 로고
    • Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
    • J. Tsai, M. Levitt, and D. Baker Hierarchy of structure loss in MD simulations of src SH3 domain unfolding J. Mol. Biol. 291 1999 215 225
    • (1999) J. Mol. Biol. , vol.291 , pp. 215-225
    • Tsai, J.1    Levitt, M.2    Baker, D.3
  • 39
    • 0037974485 scopus 로고    scopus 로고
    • Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
    • W.H. Guo, S. Lampoudi, and J.E. Shea Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain Biophys. J. 85 2003 61 69
    • (2003) Biophys. J. , vol.85 , pp. 61-69
    • Guo, W.H.1    Lampoudi, S.2    Shea, J.E.3
  • 41
    • 0035946940 scopus 로고    scopus 로고
    • Role of native topology investigated by multiple unfolding simulations of four SH3 domains
    • J. Gsponer, and A. Caflisch Role of native topology investigated by multiple unfolding simulations of four SH3 domains J. Mol. Biol. 309 2001 285 298
    • (2001) J. Mol. Biol. , vol.309 , pp. 285-298
    • Gsponer, J.1    Caflisch, A.2
  • 42
    • 1842584557 scopus 로고    scopus 로고
    • Temperature dependence of the free energy landscape of the src-SH3 protein domain
    • W.H. Guo, S. Lampoudi, and J.E. Shea Temperature dependence of the free energy landscape of the src-SH3 protein domain Proteins: Struct. Funct. Genet. 55 2004 395 406
    • (2004) Proteins: Struct. Funct. Genet. , vol.55 , pp. 395-406
    • Guo, W.H.1    Lampoudi, S.2    Shea, J.E.3
  • 43
    • 11844285690 scopus 로고    scopus 로고
    • Temperature dependence of three-body hydrophobic interactions: Potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity
    • M.S. Moghaddam, S. Shimizu, and H.S. Chan Temperature dependence of three-body hydrophobic interactions: potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity J. Am. Chem. Soc. 127 2005 303 316
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 303-316
    • Moghaddam, M.S.1    Shimizu, S.2    Chan, H.S.3
  • 46
    • 0031853167 scopus 로고    scopus 로고
    • Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
    • V.P. Grantcharova, D.S. Riddle, J.V. Santiago, and D. Baker Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain Nature Struct. Biol. 5 1998 714 720
    • (1998) Nature Struct. Biol. , vol.5 , pp. 714-720
    • Grantcharova, V.P.1    Riddle, D.S.2    Santiago, J.V.3    Baker, D.4
  • 47
    • 0015987426 scopus 로고
    • Prediction of protein conformation
    • P.Y. Chou, and G.D. Fasman Prediction of protein conformation Biochemistry 13 1974 222 245
    • (1974) Biochemistry , vol.13 , pp. 222-245
    • Chou, P.Y.1    Fasman, G.D.2
  • 48
    • 0034598947 scopus 로고    scopus 로고
    • Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix
    • V. Forge, M. Hoshino, K. Kuwata, M. Arai, K. Kuwajima, C.A. Batt, and Y. Goto Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix J. Mol. Biol. 296 2000 1039 1051
    • (2000) J. Mol. Biol. , vol.296 , pp. 1039-1051
    • Forge, V.1    Hoshino, M.2    Kuwata, K.3    Arai, M.4    Kuwajima, K.5    Batt, C.A.6    Goto, Y.7
  • 49
    • 0034687774 scopus 로고    scopus 로고
    • Topology to geometry in protein folding: Beta-lactoglobulin
    • A. Fernandez, A. Colubri, and R.S. Berry Topology to geometry in protein folding: beta-lactoglobulin Proc. Natl Acad. Sci. USA 97 2000 14062 14066
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 14062-14066
    • Fernandez, A.1    Colubri, A.2    Berry, R.S.3
  • 50
    • 2342451295 scopus 로고    scopus 로고
    • Transition states for protein folding have native topologies despite high structural variability
    • K. Lindorff-Larsen, M. Vendruscolo, E. Paci, and C.M. Dobson Transition states for protein folding have native topologies despite high structural variability Nature Struct. Mol. Biol. 11 2004 443 449
    • (2004) Nature Struct. Mol. Biol. , vol.11 , pp. 443-449
    • Lindorff-Larsen, K.1    Vendruscolo, M.2    Paci, E.3    Dobson, C.M.4
  • 51
    • 0028143603 scopus 로고
    • Characterization of the transition-state of protein unfolding by use of molecular-dynamics - Chymotrypsin inhibitor-2
    • A.J. Li, and V. Daggett Characterization of the transition-state of protein unfolding by use of molecular-dynamics - chymotrypsin inhibitor-2 Proc. Natl Acad. Sci. USA 91 1994 10430 10434
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 10430-10434
    • Li, A.J.1    Daggett, V.2
  • 52
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
    • H. Kaya, and H.S. Chan Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? J. Mol. Biol. 326 2003 911 931
    • (2003) J. Mol. Biol. , vol.326 , pp. 911-931
    • Kaya, H.1    Chan, H.S.2
  • 53
    • 0033200251 scopus 로고    scopus 로고
    • Folding studies of immunoglobulin-like -sandwich proteins suggest that they share a common folding path
    • J. Clarke, E. Cota, S.B. Fowler, and S.J. Hamill Folding studies of immunoglobulin-like -sandwich proteins suggest that they share a common folding path Structure 7 1999 1145 1153
    • (1999) Structure , vol.7 , pp. 1145-1153
    • Clarke, J.1    Cota, E.2    Fowler, S.B.3    Hamill, S.J.4
  • 54
    • 0032708771 scopus 로고    scopus 로고
    • Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein foldi
    • F. Chiti, N. Taddei, P. White, M. Bucciantini, F. Magherini, M. Stefani, and C.M. Dobson Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein foldi Nature Struct. Biol. 6 1999 1005 1009
    • (1999) Nature Struct. Biol. , vol.6 , pp. 1005-1009
    • Chiti, F.1    Taddei, N.2    White, P.3    Bucciantini, M.4    Magherini, F.5    Stefani, M.6    Dobson, C.M.7
  • 55
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • C. Clementi, H. Nymeyer, and J.N. Onuchic Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 2000 937 953
    • (2000) J. Mol. Biol. , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 56
    • 18844459862 scopus 로고    scopus 로고
    • Nucleation and the transition state of the SH3 domain
    • I.A. Hubner, K.A. Edmonds, and E. Shakhnovich Nucleation and the transition state of the SH3 domain J. Mol. Biol. 349 2005 424 434
    • (2005) J. Mol. Biol. , vol.349 , pp. 424-434
    • Hubner, I.A.1    Edmonds, K.A.2    Shakhnovich, E.3
  • 57
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding knetics and function
    • L. Mirny, and E. Shakhnovich Universally conserved positions in protein folds: reading evolutionary signals about stability, folding knetics and function J. Mol. Biol. 291 1999 177 196
    • (1999) J. Mol. Biol. , vol.291 , pp. 177-196
    • Mirny, L.1    Shakhnovich, E.2
  • 58
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • L. Li, L. Mirny, and E. Shakhnovich Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus Nature Struct. Biol. 7 2000 336 342
    • (2000) Nature Struct. Biol. , vol.7 , pp. 336-342
    • Li, L.1    Mirny, L.2    Shakhnovich, E.3
  • 59
    • 0036923039 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    • F. Ding, N.V. Dokholyan, S.V. Buldyrev, H.E. Stanley, and E.I. Shakhnovich Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism J. Mol. Biol. 324 2002 851 857
    • (2002) J. Mol. Biol. , vol.324 , pp. 851-857
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 60
    • 0035191642 scopus 로고    scopus 로고
    • Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil
    • B.A. Krantz, and T.R. Sosnick Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil Nature Struct. Biol. 8 2001 1042 1047
    • (2001) Nature Struct. Biol. , vol.8 , pp. 1042-1047
    • Krantz, B.A.1    Sosnick, T.R.2
  • 61
    • 10644261303 scopus 로고    scopus 로고
    • Differences in the folding transition state of ubiquitin indicated by φ and ψ analyses
    • T.R. Sosnick, R.S. Dothager, and B.A. Krantz Differences in the folding transition state of ubiquitin indicated by φ and ψ analyses Proc. Natl Acad. Sci. USA 101 2004 17377 17382
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17377-17382
    • Sosnick, T.R.1    Dothager, R.S.2    Krantz, B.A.3
  • 62
    • 10644295536 scopus 로고    scopus 로고
    • φ Values versus ψ analysis
    • A.R. Fersht φ Values versus ψ analysis Proc. Natl Acad. Sci. USA 101 2004 17327 17328
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17327-17328
    • Fersht, A.R.1
  • 65
    • 0000764091 scopus 로고
    • Constant-temperature free energy surfaces for physical and chemical processes
    • E.M. Boczko, and C.L. Brooks III Constant-temperature free energy surfaces for physical and chemical processes J. Phys. Chem. 97 1993 4509 4513
    • (1993) J. Phys. Chem. , vol.97 , pp. 4509-4513
    • Boczko, E.M.1    Brooks III, C.L.2
  • 66
    • 0032080053 scopus 로고    scopus 로고
    • Calculations on folding of segment B1 of streptococcal protein G
    • F.B. Sheinerman, and C.L. Brooks Calculations on folding of segment B1 of streptococcal protein G J. Mol. Biol. 278 1998 439 456
    • (1998) J. Mol. Biol. , vol.278 , pp. 439-456
    • Sheinerman, F.B.1    Brooks, C.L.2
  • 68
    • 0035823222 scopus 로고    scopus 로고
    • Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model
    • A.V. Smith, and C.K. Hall Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model J. Mol. Biol. 312 2001 187 202
    • (2001) J. Mol. Biol. , vol.312 , pp. 187-202
    • Smith, A.V.1    Hall, C.K.2
  • 69
    • 0033598375 scopus 로고    scopus 로고
    • Interpreting the folding kinetics of helical proteins
    • Y. Zhou, and M. Karplus Interpreting the folding kinetics of helical proteins Nature 401 1999 400 403
    • (1999) Nature , vol.401 , pp. 400-403
    • Zhou, Y.1    Karplus, M.2
  • 70
    • 0019569599 scopus 로고
    • Non-interacting local-structure model of folding and unfolding transition in globular-proteins. 1. Formulation
    • N. Go, and H. Abe Non-interacting local-structure model of folding and unfolding transition in globular-proteins. 1. Formulation Biopolymers 20 1981 991 1011
    • (1981) Biopolymers , vol.20 , pp. 991-1011
    • Go, N.1    Abe, H.2
  • 71
    • 0027393187 scopus 로고
    • Statistical clustering techniques for analysis of long molecular dynamics trajectories. I: Analysis of 2.2 ns trajectories of YPGDV
    • M.E. Karpen, D.T. Tobias, and C.L. Brooks III Statistical clustering techniques for analysis of long molecular dynamics trajectories. I: analysis of 2.2 ns trajectories of YPGDV Biochemistry 32 1993 412 420
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.T.2    Brooks III, C.L.3
  • 72
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • M. Feig, J. Karanicolas, and C.L. Brooks III MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology J. Mol. Graph. Model. 22 2004 377 395
    • (2004) J. Mol. Graph. Model. , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.