메뉴 건너뛰기




Volumn 86, Issue 3, 2004, Pages 1691-1701

Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN FOLDING; STRUCTURE ANALYSIS;

EID: 1542345514     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74238-1     Document Type: Article
Times cited : (24)

References (53)
  • 2
    • 0036308818 scopus 로고    scopus 로고
    • Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics
    • Borreguero, J. M., N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, and H. E. Stanley. 2002. Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics. J. Mol. Biol. 318:863-876.
    • (2002) J. Mol. Biol. , vol.318 , pp. 863-876
    • Borreguero, J.M.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Shakhnovich, E.I.4    Stanley, H.E.5
  • 4
    • 0037093655 scopus 로고    scopus 로고
    • Weak temperature dependence of the free energy surface and folding pathways of structured peptides
    • Cavalli, A., P. Ferrara, and A. Caflisch. 2002. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins Struct. Funct. Gen. 47:305-314.
    • (2002) Proteins Struct. Funct. Gen. , vol.47 , pp. 305-314
    • Cavalli, A.1    Ferrara, P.2    Caflisch, A.3
  • 5
    • 0041842498 scopus 로고    scopus 로고
    • Fast protein folding on downhill energy landscape
    • Cavalli, A., U. Haberthur, E. Paci, and A. Caflisch. 2003. Fast protein folding on downhill energy landscape. Protein Sci. 12:1801-1803.
    • (2003) Protein Sci. , vol.12 , pp. 1801-1803
    • Cavalli, A.1    Haberthur, U.2    Paci, E.3    Caflisch, A.4
  • 6
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung, M. S., A. E. Garcia, and J. N. Onuchic. 2002. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.N.3
  • 7
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • Daggett, V., and A. R. Fersht. 2003. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28:18-25.
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 18-25
    • Daggett, V.1    Fersht, A.R.2
  • 8
    • 0029981188 scopus 로고    scopus 로고
    • Structure of the transition state for folding of a protein derived from experiment and simulation
    • Daggett, V., A. Li, L. Itzhaki, D. Otzen, and A. Fersht. 1996. Structure of the transition state for folding of a protein derived from experiment and simulation. J. Mol. Biol. 257:430-440.
    • (1996) J. Mol. Biol. , vol.257 , pp. 430-440
    • Daggett, V.1    Li, A.2    Itzhaki, L.3    Otzen, D.4    Fersht, A.5
  • 9
    • 0032917075 scopus 로고    scopus 로고
    • De novo design of a monomeric three-stranded antiparallel β-sheet
    • De Alba, E., J. Santoro, M. Rico, and M. A. Jiménez. 1999. De novo design of a monomeric three-stranded antiparallel β-sheet. Protein Sci. 8:854-865.
    • (1999) Protein Sci. , vol.8 , pp. 854-865
    • De Alba, E.1    Santoro, J.2    Rico, M.3    Jiménez, M.A.4
  • 11
    • 0036927818 scopus 로고    scopus 로고
    • Direct molecular dynamics observation of protein folding transition state ensemble
    • Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83:3525-3532.
    • (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
  • 12
    • 0009519484 scopus 로고    scopus 로고
    • The thermodynamics and kinetics of protein folding: A lattice model analysis of multiple pathways with intermediates
    • Dinner, A., and M. Karplus. 1999a. The thermodynamics and kinetics of protein folding: a lattice model analysis of multiple pathways with intermediates. J. Phys. Chem. B. 103:7976-7994.
    • (1999) J. Phys. Chem. B. , vol.103 , pp. 7976-7994
    • Dinner, A.1    Karplus, M.2
  • 13
    • 0033578828 scopus 로고    scopus 로고
    • Is protein unfolding the reverse of protein folding? A lattice simulation analysis
    • Dinner, A. R., and M. Karplus. 1999b. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J. Mol. Biol. 292:403-419.
    • (1999) J. Mol. Biol. , vol.292 , pp. 403-419
    • Dinner, A.R.1    Karplus, M.2
  • 16
    • 0031273621 scopus 로고    scopus 로고
    • Continuum solvation model for studying protein hydration thermodynamics at high temperatures
    • Elcock, A. H., and J. A. McCammon. 1997. Continuum solvation model for studying protein hydration thermodynamics at high temperatures. J. Phys. Chem. B. 101:9624-9634.
    • (1997) J. Phys. Chem. B. , vol.101 , pp. 9624-9634
    • Elcock, A.H.1    McCammon, J.A.2
  • 17
    • 0001767031 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
    • Ferrara, P., J. Apostolakis, and A. Caflisch. 2000. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B. 104:5000-5010.
    • (2000) J. Phys. Chem. B. , vol.104 , pp. 5000-5010
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 18
    • 0036138028 scopus 로고    scopus 로고
    • Evaluation of a fast implicit solvent model for molecular dynamics simulations
    • Ferrara, P., J. Apostolakis, and A. Caflisch. 2002. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins. 46:24-33.
    • (2002) Proteins , vol.46 , pp. 24-33
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 19
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel β-sheet peptide
    • Ferrara, P., and A. Caflisch. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA. 97:10780-10785.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10780-10785
    • Ferrara, P.1    Caflisch, A.2
  • 20
    • 0035793713 scopus 로고    scopus 로고
    • Native topology or specific interactions: What is more important for peptide folding?
    • Ferrara, P., and A. Caflisch. 2001. Native topology or specific interactions: what is more important for peptide folding? J. Mol. Biol. 306:837-850.
    • (2001) J. Mol. Biol. , vol.306 , pp. 837-850
    • Ferrara, P.1    Caflisch, A.2
  • 21
    • 0037195097 scopus 로고    scopus 로고
    • On the simulation of protein folding by short time scale molecular dynamics and distributed computing
    • Fersht, A. R. 2002. On the simulation of protein folding by short time scale molecular dynamics and distributed computing. Proc. Natl. Acad. Sci. USA. 99:14122-14125.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14122-14125
    • Fersht, A.R.1
  • 22
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman, D., and P. Argos. 1995. Knowledge-based protein secondary structure assignment. Proteins. 23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 24
    • 0031853167 scopus 로고    scopus 로고
    • Important role of hydrogen bonds in the structurally polarized transition state for folding of the src-SH3 domain
    • Grantcharova, V. P., D. S. Riddle, J. V. Santiago, and D. Baker. 1998. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src-SH3 domain. Nat. Struc. Biol. 5:714-720.
    • (1998) Nat. Struc. Biol. , vol.5 , pp. 714-720
    • Grantcharova, V.P.1    Riddle, D.S.2    Santiago, J.V.3    Baker, D.4
  • 25
    • 0035946940 scopus 로고    scopus 로고
    • Role of native topology investigated by multiple unfolding simulations of four SH3 domains
    • Gsponer, J., and A. Caflisch. 2001. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J. Mol. Biol. 309:285-298.
    • (2001) J. Mol. Biol. , vol.309 , pp. 285-298
    • Gsponer, J.1    Caflisch, A.2
  • 26
    • 0037076334 scopus 로고    scopus 로고
    • Molecular dynamics simulations of protein folding from the transition state
    • Gsponer, J., and A. Caflisch. 2002. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA. 99:6719-6724.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6719-6724
    • Gsponer, J.1    Caflisch, A.2
  • 27
    • 0037974485 scopus 로고    scopus 로고
    • Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
    • Guo, W. H., S. Lampoudi, and J. E. Shea. 2003. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. Biophys. J. 85:61-69.
    • (2003) Biophys. J. , vol.85 , pp. 61-69
    • Guo, W.H.1    Lampoudi, S.2    Shea, J.E.3
  • 28
    • 0001308921 scopus 로고
    • A rapid approximation to the solvent accessible surface areas of atoms
    • Hasel, W., T. F. Hendrickson, and W. C. Still. 1988. A rapid approximation to the solvent accessible surface areas of atoms. Tetrahedron Comput. Methodol. 1:103-116.
    • (1988) Tetrahedron Comput. Methodol. , vol.1 , pp. 103-116
    • Hasel, W.1    Hendrickson, T.F.2    Still, W.C.3
  • 30
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson, S. E., and A. R. Fersht. 1991. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry. 30:10428-10435.
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 31
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein 1
    • Kim, D. E., C. Fisher, and D. Baker. 2000. A breakdown of symmetry in the folding transition state of protein 1. J. Mol. Biol. 298:971-984.
    • (2000) J. Mol. Biol. , vol.298 , pp. 971-984
    • Kim, D.E.1    Fisher, C.2    Baker, D.3
  • 32
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis, T., and M. Karplus. 1999. Effective energy function for proteins in solution. Proteins Struct. Funct. Gen. 35:133-152.
    • (1999) Proteins Struct. Funct. Gen. , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 33
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li, A. J., and V. Daggett. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-429.
    • (1996) J. Mol. Biol. , vol.257 , pp. 412-429
    • Li, A.J.1    Daggett, V.2
  • 34
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics-chymotrypsin inhibitor-2
    • Li, A. J., and V. Daggett. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics-chymotrypsin inhibitor-2. Proc. Natl. Acad. Sci. USA. 91:10430-10434.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10430-10434
    • Li, A.J.1    Daggett, V.2
  • 35
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • Li, L., L. A. Mirny, and E. I. Shakhnovich. 2000. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat. Struct. Biol. 7:336-342.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 336-342
    • Li, L.1    Mirny, L.A.2    Shakhnovich, E.I.3
  • 36
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek, A., J. T. Kellis, Jr., L. Serrano, and A. R. Fersht. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 340:122-126.
    • (1989) Nature , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis Jr., J.T.2    Serrano, L.3    Fersht, A.R.4
  • 38
    • 0033871567 scopus 로고    scopus 로고
    • Critical role of β-hairpin formation in protein-G folding
    • McCallister, E. L., E. Alm, and D. Baker. 2000. Critical role of β-hairpin formation in protein-G folding. Nat. Struct. Biol. 7:669-673.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 669-673
    • McCallister, E.L.1    Alm, E.2    Baker, D.3
  • 39
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the SH3 domain folding transition state
    • Northey, J. G. B., A. Di Nardo, and A. R. Davidson. 2002a. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9:126-130.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 126-130
    • Northey, J.G.B.1    Di Nardo, A.2    Davidson, A.R.3
  • 40
    • 0036296248 scopus 로고    scopus 로고
    • Protein folding kinetics beyond the φ-value: Using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state
    • Northey, J. G. B., K. L. Maxwell, and A. R. Davidson. 2002b. Protein folding kinetics beyond the φ-value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J. Mol. Biol. 320:389-402.
    • (2002) J. Mol. Biol. , vol.320 , pp. 389-402
    • Northey, J.G.B.1    Maxwell, K.L.2    Davidson, A.R.3
  • 41
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of φ-values in protein folding kinetics
    • Ozkan, S. B., I. Bahar, and K. A. Dill. 2001. Transition states and the meaning of φ-values in protein folding kinetics. Nat. Struct. Biol. 8:765-769.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 42
    • 0037478676 scopus 로고    scopus 로고
    • Analysis of the distributed computing approach applied to the folding of a small β-peptide
    • Paci, E., A. Cavalli, M. Vendruscolo, and A. Caflisch. 2003. Analysis of the distributed computing approach applied to the folding of a small β-peptide. Proc. Natl. Acad. Sci. USA. 100:8217-8222.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 8217-8222
    • Paci, E.1    Cavalli, A.2    Vendruscolo, M.3    Caflisch, A.4
  • 43
    • 0036435907 scopus 로고    scopus 로고
    • Determination of a transition state at atomic resolution from protein engineering data
    • Paci, E., M. Vendruscolo, C. M. Dobson, and M. Karplus. 2002. Determination of a transition state at atomic resolution from protein engineering data. J. Mol. Biol. 324:151-163.
    • (2002) J. Mol. Biol. , vol.324 , pp. 151-163
    • Paci, E.1    Vendruscolo, M.2    Dobson, C.M.3    Karplus, M.4
  • 46
    • 0034743155 scopus 로고    scopus 로고
    • From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
    • Shea, J. E., and C. L. Brooks. 2001. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:499-535.
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 499-535
    • Shea, J.E.1    Brooks, C.L.2
  • 47
    • 0037058992 scopus 로고    scopus 로고
    • Probing the folding free energy landscape of the src-SH3 protein domain
    • Shea, J. E., J. N. Onuchic, and C. L. Brooks. 2002. Probing the folding free energy landscape of the src-SH3 protein domain. Proc. Natl. Acad. Sci. USA. 99:16064-16068.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16064-16068
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 48
    • 0035962955 scopus 로고    scopus 로고
    • Mathematical analysis of coupled parallel simulations
    • Shirts, M. R., and V. S. Pande. 2001. Mathematical analysis of coupled parallel simulations. Phys. Rev. Lett. 86:4983-4987.
    • (2001) Phys. Rev. Lett. , vol.86 , pp. 4983-4987
    • Shirts, M.R.1    Pande, V.S.2
  • 49
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow, C. D., N. Nguyen, V. S. Pande, and M. Gruebele. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, N.2    Pande, V.S.3    Gruebele, M.4
  • 50
    • 0345411345 scopus 로고    scopus 로고
    • Hierarchy of structure loss in MD simulations of src-SH3 domain unfolding
    • Tsai, J., M. Levitt, and D. Baker. 1999. Hierarchy of structure loss in MD simulations of src-SH3 domain unfolding. J. Mol. Biol. 291:215-225.
    • (1999) J. Mol. Biol. , vol.291 , pp. 215-225
    • Tsai, J.1    Levitt, M.2    Baker, D.3
  • 51
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo, M., E. Paci, C. M. Dobson, and M. Karplus. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 53
    • 0031025991 scopus 로고    scopus 로고
    • Three-dimensional structure of the tyrosine kinase c-src
    • Xu, W. Q., S. C. Harrison, and M. J. Eck. 1997. Three-dimensional structure of the tyrosine kinase c-src. Nature. 385:595-602.
    • (1997) Nature , vol.385 , pp. 595-602
    • Xu, W.Q.1    Harrison, S.C.2    Eck, M.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.