메뉴 건너뛰기




Volumn 63, Issue 3, 2006, Pages 555-570

Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β-hairpins

Author keywords

hairpin folding; Monte Carlo simulations; Structural stability

Indexed keywords

PROTEIN;

EID: 33646064742     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20846     Document Type: Article
Times cited : (19)

References (86)
  • 1
    • 0003932766 scopus 로고
    • New York: W. H. Freeman. 507 p.
    • Creighton TE. Proteins. New York: W. H. Freeman; 1993. 507 p.
    • (1993) Proteins
    • Creighton, T.E.1
  • 2
    • 0029155035 scopus 로고
    • Helix design, prediction and stability
    • Muñoz V, Serrano L. Helix design, prediction and stability. Curr Opin Biotechnol 1995;6:382-386.
    • (1995) Curr Opin Biotechnol , vol.6 , pp. 382-386
    • Muñoz, V.1    Serrano, L.2
  • 5
    • 33751391161 scopus 로고
    • Helix/coil theories: A comparative study for finite length polypeptides
    • Qian H, Schellman JA. Helix/coil theories: a comparative study for finite length polypeptides. J Phys Chem 1992;96:3987-3994.
    • (1992) J Phys Chem , vol.96 , pp. 3987-3994
    • Qian, H.1    Schellman, J.A.2
  • 6
    • 0037059026 scopus 로고    scopus 로고
    • Recent advances in helix-coil theory
    • Doig AJ. Recent advances in helix-coil theory. Biophys Chem 2002;101-102:281-293.
    • (2002) Biophys Chem , vol.101-102 , pp. 281-293
    • Doig, A.J.1
  • 7
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of β-hairpin formation
    • Muñoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of β-hairpin formation. Nature 1997;390:196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Muñoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 8
    • 0031038377 scopus 로고    scopus 로고
    • Local interactions in protein folding: Lessons from the α-helix
    • Aurora R, Creamer TP, Srinivasan R, Rose GD. Local interactions in protein folding: lessons from the α-helix. J Biol Chem 1997;272:1413-1416.
    • (1997) J Biol Chem , vol.272 , pp. 1413-1416
    • Aurora, R.1    Creamer, T.P.2    Srinivasan, R.3    Rose, G.D.4
  • 9
    • 0034743055 scopus 로고    scopus 로고
    • Peptide models of protein β-sheets: Design, folding and insights into stabilising weak interactions
    • Searle MS. Peptide models of protein β-sheets: design, folding and insights into stabilising weak interactions. J Chem Soc Perkin Trans 2001;2:1011-1020.
    • (2001) J Chem Soc Perkin Trans , vol.2 , pp. 1011-1020
    • Searle, M.S.1
  • 10
    • 1942531291 scopus 로고    scopus 로고
    • Insights into stabilizing weak interactions in designed peptide β-hairpins
    • Searle MS. Insights into stabilizing weak interactions in designed peptide β-hairpins. Biopolymer 2004;76:185-195.
    • (2004) Biopolymer , vol.76 , pp. 185-195
    • Searle, M.S.1
  • 11
    • 4143070403 scopus 로고    scopus 로고
    • Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding
    • Searle MS, Ciani B. Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr Opin Struc Biol 2004;14:458-464.
    • (2004) Curr Opin Struc Biol , vol.14 , pp. 458-464
    • Searle, M.S.1    Ciani, B.2
  • 12
    • 0032246263 scopus 로고    scopus 로고
    • Minimal model systems for β-sheet secondary structure in proteins
    • Gellman SH. Minimal model systems for β-sheet secondary structure in proteins. Curr Opin Chem Biol 1998;2:717-725.
    • (1998) Curr Opin Chem Biol , vol.2 , pp. 717-725
    • Gellman, S.H.1
  • 13
    • 0032006708 scopus 로고    scopus 로고
    • Formation and stability of β-hairpin structures in polypeptides
    • Blanco F, Ramírez-Alvarado M, Serrano L. Formation and stability of β-hairpin structures in polypeptides. Curr Opin Struc Biol 1998;8:107-111.
    • (1998) Curr Opin Struc Biol , vol.8 , pp. 107-111
    • Blanco, F.1    Ramírez-Alvarado, M.2    Serrano, L.3
  • 15
    • 0028500779 scopus 로고
    • A short linear peptide that folds into a native stable bold β-hairpin in aqueous solution
    • Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable bold β-hairpin in aqueous solution. Nat Struct Biol 1994;1:584-590.
    • (1994) Nat Struct Biol , vol.1 , pp. 584-590
    • Blanco, F.J.1    Rivas, G.2    Serrano, L.3
  • 16
    • 0035936697 scopus 로고    scopus 로고
    • Interplay between hydrophobic cluster and loop propensity in β-hairpin formation
    • Espinosa JF, Muñoz V, Gellman SH. Interplay between hydrophobic cluster and loop propensity in β-hairpin formation. J Mol Biol 2001;306:397-402.
    • (2001) J Mol Biol , vol.306 , pp. 397-402
    • Espinosa, J.F.1    Muñoz, V.2    Gellman, S.H.3
  • 17
    • 0034488879 scopus 로고    scopus 로고
    • Position effect of cross-strand side-chain interactions on β-hairpin formation
    • Santiveri CM, Rico M, Jiménez MA. Position effect of cross-strand side-chain interactions on β-hairpin formation. Protein Sci 2000;9:2151-2160.
    • (2000) Protein Sci , vol.9 , pp. 2151-2160
    • Santiveri, C.M.1    Rico, M.2    Jiménez, M.A.3
  • 18
    • 0142236215 scopus 로고    scopus 로고
    • Sequence dependence of β-hairpin structure: Comparison of a salt bridge and an aromatic interaction
    • Kiehna SE, Waters ML. Sequence dependence of β-hairpin structure: comparison of a salt bridge and an aromatic interaction. Protein Sci 2003;12:2657-2667.
    • (2003) Protein Sci , vol.12 , pp. 2657-2667
    • Kiehna, S.E.1    Waters, M.L.2
  • 19
    • 0033536659 scopus 로고    scopus 로고
    • Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding
    • Griffiths-Jones SR, Maynard AJ, Searle MS. Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding. J Mol Biol 1999;292:1051-1069.
    • (1999) J Mol Biol , vol.292 , pp. 1051-1069
    • Griffiths-Jones, S.R.1    Maynard, A.J.2    Searle, M.S.3
  • 20
    • 0041866611 scopus 로고    scopus 로고
    • Stabilization of β-hairpin peptides by salt bridges: Role of preorganization in the energetic contribution of weak interactions
    • Ciani B, Jourdan M, Searle MS. Stabilization of β-hairpin peptides by salt bridges: role of preorganization in the energetic contribution of weak interactions. J Am Chem Soc 2003;125:9038-9047.
    • (2003) J Am Chem Soc , vol.125 , pp. 9038-9047
    • Ciani, B.1    Jourdan, M.2    Searle, M.S.3
  • 21
    • 2942562092 scopus 로고    scopus 로고
    • Enhanced hairpin stability through loop design: The case of the protein G B1 domain hairpin
    • Fesinmeyer RM, Hudson FM, Andersen NH. Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin. J Am Chem Soc 2004;126:7238-7243.
    • (2004) J Am Chem Soc , vol.126 , pp. 7238-7243
    • Fesinmeyer, R.M.1    Hudson, F.M.2    Andersen, N.H.3
  • 22
    • 0347480547 scopus 로고    scopus 로고
    • Infrared study of the stability and folding kinetics of a 15-residue β-hairpin
    • Xu Y, Oyola R, Gai F. Infrared study of the stability and folding kinetics of a 15-residue β-hairpin. J Am Chem Soc 2003;125:15388-15394.
    • (2003) J Am Chem Soc , vol.125 , pp. 15388-15394
    • Xu, Y.1    Oyola, R.2    Gai, F.3
  • 24
    • 8644237364 scopus 로고    scopus 로고
    • Understanding the key factors that control the rate of beta-hairpin folding
    • Du DG, Zhu YJ, Huang CY, Gai F. Understanding the key factors that control the rate of beta-hairpin folding. Proc Natl Acad Sci USA 2004;1:15915-15920.
    • (2004) Proc Natl Acad Sci USA , vol.1 , pp. 15915-15920
    • Du, D.G.1    Zhu, Y.J.2    Huang, C.Y.3    Gai, F.4
  • 25
    • 0037132665 scopus 로고    scopus 로고
    • Thermodynamic analysis of beta-hairpin-forming peptides from the thermal dependence of (1)H NMR chemical shifts
    • Santiveri CM, Santoro J, Rico M, Jiménez MA. Thermodynamic analysis of beta-hairpin-forming peptides from the thermal dependence of (1)H NMR chemical shifts. J Am Chem Soc 2002;124:14903-14909.
    • (2002) J Am Chem Soc , vol.124 , pp. 14903-14909
    • Santiveri, C.M.1    Santoro, J.2    Rico, M.3    Jiménez, M.A.4
  • 29
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G
    • Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G. Proc Natl Acad Sci USA 1999;96:9062-9067.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 30
    • 0035850758 scopus 로고    scopus 로고
    • β-hairpin folding simulations in atomistic detail using an implicit solvent mode
    • Zagrovic B, Sorin EJ, Pande V. β-hairpin folding simulations in atomistic detail using an implicit solvent mode. J Mol Biol 2001;313:151-169.
    • (2001) J Mol Biol , vol.313 , pp. 151-169
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3
  • 31
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a β hairpin in explicit solvent
    • García AE, Sanbonmatsu KY. Exploring the energy landscape of a β hairpin in explicit solvent. Proteins 2001;42:345-354.
    • (2001) Proteins , vol.42 , pp. 345-354
    • García, A.E.1    Sanbonmatsu, K.Y.2
  • 32
    • 0036568318 scopus 로고    scopus 로고
    • Role of hydrophilic and hydrophobic contacts in folding of the second β-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model
    • Zhou Y, Linhananta A. Role of hydrophilic and hydrophobic contacts in folding of the second β-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model. Proteins 2002;47:154-162.
    • (2002) Proteins , vol.47 , pp. 154-162
    • Zhou, Y.1    Linhananta, A.2
  • 33
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for β-hairpin folding in explicit water
    • Zhou R, Berne BJ, Germain R. The free energy landscape for β-hairpin folding in explicit water. Proc Natl Acad Sci USA 2001;98:14931-14936.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14931-14936
    • Zhou, R.1    Berne, B.J.2    Germain, R.3
  • 34
    • 0036789950 scopus 로고    scopus 로고
    • Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?
    • Zhou R, Berne BJ. Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc Natl Acad Sci USA 2002;99:12777-12782.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12777-12782
    • Zhou, R.1    Berne, B.J.2
  • 35
    • 0037461487 scopus 로고    scopus 로고
    • Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique
    • Wei GH, Derreumaux P, Mousseau N. Exploring the energy landscape of proteins: a characterization of the activation-relaxation technique. J Chem Phys 2002;117:11379-11387.
    • (2002) J Chem Phys , vol.117 , pp. 11379-11387
    • Wei, G.H.1    Derreumaux, P.2    Mousseau, N.3
  • 36
    • 0142116251 scopus 로고    scopus 로고
    • Sampling the complex energy landscape of a simple β-hairpin
    • Wei GH, Derreumaux P, Mousseau N. Sampling the complex energy landscape of a simple β-hairpin. J Chem Phys 2003;119:6403-6406.
    • (2003) J Chem Phys , vol.119 , pp. 6403-6406
    • Wei, G.H.1    Derreumaux, P.2    Mousseau, N.3
  • 37
    • 3142737884 scopus 로고    scopus 로고
    • Complex folding pathways in a simple β-hairpin
    • Wei GH, Mousseau N, Derreumaux P. Complex folding pathways in a simple β-hairpin. Proteins 2004;56:464-474.
    • (2004) Proteins , vol.56 , pp. 464-474
    • Wei, G.H.1    Mousseau, N.2    Derreumaux, P.3
  • 38
    • 0032764074 scopus 로고    scopus 로고
    • Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques
    • Kolinski A, Ilkowski B, Skolnick J. Dynamics and thermodynamics of β-hairpin assembly: insights from various simulation techniques. Biophys J 1999;77:2942-2952.
    • (1999) Biophys J , vol.77 , pp. 2942-2952
    • Kolinski, A.1    Ilkowski, B.2    Skolnick, J.3
  • 39
    • 0034646218 scopus 로고    scopus 로고
    • Mechanisms and kinetics of β-hairpin formation
    • Klimov DK, Thirumalai D. Mechanisms and kinetics of β-hairpin formation. Proc Natl Acad Sci USA 2000;97:2544-2549.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 2544-2549
    • Klimov, D.K.1    Thirumalai, D.2
  • 40
    • 0036295960 scopus 로고    scopus 로고
    • Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
    • Klimov DK, Thirumalai D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 2002;317:721-737.
    • (2002) J Mol Biol , vol.317 , pp. 721-737
    • Klimov, D.K.1    Thirumalai, D.2
  • 41
    • 0041629626 scopus 로고    scopus 로고
    • Thermodynamics of α- and β-structure formation in proteins
    • Irbäck A, Samuelsson B, Sjunnesson F, Wallin S. Thermodynamics of α- and β-structure formation in proteins. Biophys J 2003;85:1466-1473.
    • (2003) Biophys J , vol.85 , pp. 1466-1473
    • Irbäck, A.1    Samuelsson, B.2    Sjunnesson, F.3    Wallin, S.4
  • 42
    • 0034718550 scopus 로고    scopus 로고
    • How does a β-hairpin fold/unfold?: Competition between topology and heterogeneity in a solvable model
    • Guo C, Levine H, Kessler DA. How does a β-hairpin fold/unfold?: competition between topology and heterogeneity in a solvable model. Proc Natl Acad Sci USA 2000;97:10775-10779.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10775-10779
    • Guo, C.1    Levine, H.2    Kessler, D.A.3
  • 43
    • 0037379625 scopus 로고    scopus 로고
    • Universal model for alpha-helix and beta-sheet structures in protein
    • Chen JZY, Imamura H. Universal model for alpha-helix and beta-sheet structures in protein. Physica A 2003;321:181-188.
    • (2003) Physica A , vol.321 , pp. 181-188
    • Chen, J.Z.Y.1    Imamura, H.2
  • 44
    • 0037403052 scopus 로고    scopus 로고
    • Minimal model for studying prion-like folding pathways
    • Chen JZY, Lemak AS, Lepock JR, Kemp JP. Minimal model for studying prion-like folding pathways. Proteins 2003;51:283-288.
    • (2003) Proteins , vol.51 , pp. 283-288
    • Chen, J.Z.Y.1    Lemak, A.S.2    Lepock, J.R.3    Kemp, J.P.4
  • 45
    • 3843125162 scopus 로고    scopus 로고
    • Conformational conversion of proteins due to mutation
    • Imamura H, Chen JYZ. Conformational conversion of proteins due to mutation. Europhys Lett 2004;67:491-497.
    • (2004) Europhys Lett , vol.67 , pp. 491-497
    • Imamura, H.1    Chen, J.Y.Z.2
  • 46
    • 0037398844 scopus 로고    scopus 로고
    • Minimalist models for protein folding and design
    • Head-Gordon T, Brown S. Minimalist models for protein folding and design. Curr Opin Struct Biol 2003;13:160-167.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 160-167
    • Head-Gordon, T.1    Brown, S.2
  • 47
    • 0347753603 scopus 로고    scopus 로고
    • Reduced models of proteins and their applications
    • Kolinski A, Skolnick J. Reduced models of proteins and their applications. Polymer 2004;45:511-524.
    • (2004) Polymer , vol.45 , pp. 511-524
    • Kolinski, A.1    Skolnick, J.2
  • 48
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and uctuations by computer simulations
    • Taketomi H, Ueda Y, Gō N. Studies on protein folding, unfolding and uctuations by computer simulations. Int J Pep Protein Res 1975;7:445-459.
    • (1975) Int J Pep Protein Res , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 49
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Gō N. Theoretical studies of protein folding. Ann Rev Biophys Bioeng 1983;12:183-210.
    • (1983) Ann Rev Biophys Bioeng , vol.12 , pp. 183-210
    • Go, N.1
  • 50
    • 0032742688 scopus 로고    scopus 로고
    • Gō-ing for the prediction of protein folding mechanisms
    • Takada S. Gō-ing for the prediction of protein folding mechanisms. Proc Natl Acad Sci USA 1999;96:11698-11700.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 11698-11700
    • Takada, S.1
  • 51
    • 0027500601 scopus 로고
    • Folding proteins: Finding a needle in a haystack
    • Dill KA. Folding proteins: finding a needle in a haystack. Curr Opin Struct Biol 1993;3:99-103.
    • (1993) Curr Opin Struct Biol , vol.3 , pp. 99-103
    • Dill, K.A.1
  • 52
    • 0000508285 scopus 로고    scopus 로고
    • Identification of relaxation and diffusion mechanisms in amorphous silicon
    • Barkema GT, Mousseau N. Identification of relaxation and diffusion mechanisms in amorphous silicon. Phys Rev Lett 1998;81:1865-1868.
    • (1998) Phys Rev Lett , vol.81 , pp. 1865-1868
    • Barkema, G.T.1    Mousseau, N.2
  • 53
    • 0034505723 scopus 로고    scopus 로고
    • Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
    • Malek R, Mousseau N. Dynamics of Lennard-Jones clusters: a characterization of the activation-relaxation technique. Phys Rev E 2000;62:7723-7728.
    • (2000) Phys Rev E , vol.62 , pp. 7723-7728
    • Malek, R.1    Mousseau, N.2
  • 54
    • 0026643094 scopus 로고
    • The nature of folded states of globular proteins
    • Honeycutt JD, Thirumalai D. The nature of folded states of globular proteins. Biopolymers 1992;32:695-709.
    • (1992) Biopolymers , vol.32 , pp. 695-709
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 55
    • 0036156804 scopus 로고    scopus 로고
    • Folding thermodynamics of model four-strand antiparallel β-sheet proteins
    • Jang H, Hall CK, Zhou Y. Folding thermodynamics of model four-strand antiparallel β-sheet proteins. Biophys J 2002;82:646-659.
    • (2002) Biophys J , vol.82 , pp. 646-659
    • Jang, H.1    Hall, C.K.2    Zhou, Y.3
  • 56
    • 0001738398 scopus 로고    scopus 로고
    • Formation of helical states in wormlike polymer chains
    • Kemp JP, Chen ZY. Formation of helical states in wormlike polymer chains. Phys Rev Lett 1998;81:3880-3883,
    • (1998) Phys Rev Lett , vol.81 , pp. 3880-3883
    • Kemp, J.P.1    Chen, Z.Y.2
  • 57
    • 0036568327 scopus 로고    scopus 로고
    • Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
    • Favrin G, Irbäck A, Wallin S. Folding of a small helical protein using hydrogen bonds and hydrophobicity forces. Proteins 2002;47:99-105.
    • (2002) Proteins , vol.47 , pp. 99-105
    • Favrin, G.1    Irbäck, A.2    Wallin, S.3
  • 58
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990;29:7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 59
    • 0028920098 scopus 로고
    • Prolines and amyloidogenicity in fragments of the Alzheimer's peptide β/A4
    • Wood SJ, Wetzel R, Martin JD, Hurle MR. Prolines and amyloidogenicity in fragments of the Alzheimer's peptide β/A4. Biochemistry 1995;34:724-730.
    • (1995) Biochemistry , vol.34 , pp. 724-730
    • Wood, S.J.1    Wetzel, R.2    Martin, J.D.3    Hurle, M.R.4
  • 60
    • 0035045429 scopus 로고    scopus 로고
    • Solvent-induced beta-hairpin to helix conformational transition in a designed peptide
    • Awasthi SK, Shankaramma SC, Raghothama S, Balaram P. Solvent-induced beta-hairpin to helix conformational transition in a designed peptide. Biopolymers 2001;58:465-476.
    • (2001) Biopolymers , vol.58 , pp. 465-476
    • Awasthi, S.K.1    Shankaramma, S.C.2    Raghothama, S.3    Balaram, P.4
  • 64
    • 0001646306 scopus 로고    scopus 로고
    • Applications of Monte Carlo methods to statistical physics
    • Binder K. Applications of Monte Carlo methods to statistical physics. Rep Prog Phys 1997;60:487-559.
    • (1997) Rep Prog Phys , vol.60 , pp. 487-559
    • Binder, K.1
  • 65
    • 0024034830 scopus 로고
    • Monte Carlo simulation of lattice models for macromolecules
    • Kremer K, Binder K. Monte Carlo simulation of lattice models for macromolecules. Comp Phys Rep 1988;7:259-310.
    • (1988) Comp Phys Rep , vol.7 , pp. 259-310
    • Kremer, K.1    Binder, K.2
  • 66
    • 0000464832 scopus 로고
    • Metropolis Monte Carlo method as a numerical technique to solve the Fokker-Planck equation
    • Kikuchi K, Yoshida M, Maekawa T, Watanabe H. Metropolis Monte Carlo method as a numerical technique to solve the Fokker-Planck equation. Chem Phys Lett 1991;185:335-338.
    • (1991) Chem Phys Lett , vol.185 , pp. 335-338
    • Kikuchi, K.1    Yoshida, M.2    Maekawa, T.3    Watanabe, H.4
  • 68
    • 33645675171 scopus 로고
    • Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins
    • Rey A, Skolnick J. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins. Chem Phys 1991;158:199-219.
    • (1991) Chem Phys , vol.158 , pp. 199-219
    • Rey, A.1    Skolnick, J.2
  • 69
    • 0028270634 scopus 로고
    • Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
    • Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J Mol Biol 1994;235:1614-1636.
    • (1994) J Mol Biol , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 70
    • 36449000646 scopus 로고
    • Transition states and folding dynamics of proteins and heteropolymers
    • Chan HS, Dill KA. Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 1994;100:9238-9257.
    • (1994) J Chem Phys , vol.100 , pp. 9238-9257
    • Chan, H.S.1    Dill, K.A.2
  • 71
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
    • Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins 1998;30:2-33.
    • (1998) Proteins , vol.30 , pp. 2-33
    • Chan, H.S.1    Dill, K.A.2
  • 72
    • 0002770218 scopus 로고
    • Protein folding: Theoretical studies of thermodynamics and dynamics
    • Creighton TE, editor. New York: W. H. Freeman
    • Karplus M, Shakhnovich E. Protein folding: theoretical studies of thermodynamics and dynamics. In: Creighton TE, editor. Protein folding. New York: W. H. Freeman; 1992. p 127-196.
    • (1992) Protein Folding , pp. 127-196
    • Karplus, M.1    Shakhnovich, E.2
  • 74
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 1995;21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 75
    • 0000239504 scopus 로고    scopus 로고
    • Master equation approach to protein folding and kinetic traps
    • Cieplak M, Henkel M, Karbowski J, Banavar JR. Master equation approach to protein folding and kinetic traps. Phys Rev Lett 1998;80:3654-3657.
    • (1998) Phys Rev Lett , vol.80 , pp. 3654-3657
    • Cieplak, M.1    Henkel, M.2    Karbowski, J.3    Banavar, J.R.4
  • 77
    • 0001274615 scopus 로고
    • Quantitative measure of efficiency of Monte Carlo simulations
    • Mountain R, Thirumalai D. Quantitative measure of efficiency of Monte Carlo simulations. Physica A 1994;210:453-460.
    • (1994) Physica A , vol.210 , pp. 453-460
    • Mountain, R.1    Thirumalai, D.2
  • 78
    • 43949158791 scopus 로고
    • Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem
    • Hansmann UHE, Okamoto Y. Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 1994;212:415-437.
    • (1994) Physica A , vol.212 , pp. 415-437
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 79
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg J. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comp Chem 1992;13:1011-1021.
    • (1992) J Comp Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.5
  • 80
    • 0141457398 scopus 로고    scopus 로고
    • Rotamer-specific potentials of mean force for residue pair interactions
    • Lemak AS, Gunn JR. Rotamer-specific potentials of mean force for residue pair interactions. J Phys Chem B 2000;104:1097-1107.
    • (2000) J Phys Chem B , vol.104 , pp. 1097-1107
    • Lemak, A.S.1    Gunn, J.R.2
  • 81
    • 0030601851 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
    • Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol 1996;263:323-343.
    • (1996) J Mol Biol , vol.263 , pp. 323-343
    • Guo, Z.1    Thirumalai, D.2
  • 82
    • 0035839115 scopus 로고    scopus 로고
    • Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus
    • Viguera AR, Serrano L. Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus. J Mol Biol 2001;311:357-371.
    • (2001) J Mol Biol , vol.311 , pp. 357-371
    • Viguera, A.R.1    Serrano, L.2
  • 83
    • 0001720011 scopus 로고    scopus 로고
    • Molecular dynamics of folding of secondary structures in Go-type models of proteins
    • Hoang TX, Cieplak M. Molecular dynamics of folding of secondary structures in Go-type models of proteins. J Chem Phys 2000;112:6851-6862.
    • (2000) J Chem Phys , vol.112 , pp. 6851-6862
    • Hoang, T.X.1    Cieplak, M.2
  • 84
    • 0034645735 scopus 로고    scopus 로고
    • Thermodynamics of a β-hairpin structure: Evidence for cooperative formation of folding nucleus
    • Honda S, Kobayashi N, Munekata E. Thermodynamics of a β-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol 2000;295:269-278.
    • (2000) J Mol Biol , vol.295 , pp. 269-278
    • Honda, S.1    Kobayashi, N.2    Munekata, E.3
  • 85
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson CM, Sǎli A, Karplus M. Protein folding: a perspective from theory and experiment. Angew Chem Int Ed Engl 1998;37:868-893.
    • (1998) Angew Chem Int Ed Engl , vol.37 , pp. 868-893
    • Dobson, C.M.1    Sǎli, A.2    Karplus, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.