메뉴 건너뛰기




Volumn 355, Issue 3, 2006, Pages 536-547

Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

Author keywords

Molecular dynamics; Protein folding kinetics; Protein folding pathways; Staphylococcal protein A; United residue force field

Indexed keywords

POLYPEPTIDE; STAPHYLOCOCCUS PROTEIN A;

EID: 28944442465     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.10.056     Document Type: Article
Times cited : (63)

References (31)
  • 1
    • 0030755502 scopus 로고    scopus 로고
    • Absence of a stable intermediate on the folding pathway of protein a
    • Y.W. Bai, A. Karimi, H.J. Dyson, and P.E. Wright Absence of a stable intermediate on the folding pathway of protein A Protein Sci. 6 1997 1449 1457
    • (1997) Protein Sci. , vol.6 , pp. 1449-1457
    • Bai, Y.W.1    Karimi, A.2    Dyson, H.J.3    Wright, P.E.4
  • 2
    • 28944439568 scopus 로고
    • PhD thesis, chapt. 3, University of California, San Diego.
    • Karimi, A. (1995). PhD thesis, chapt. 3, University of California, San Diego.
    • (1995)
    • Karimi, A.1
  • 3
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • J.K. Myers, and T.G. Oas Preorganized secondary structure as an important determinant of fast protein folding Nature Struct. Biol. 8 2001 552 558
    • (2001) Nature Struct. Biol. , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 4
    • 1642290710 scopus 로고    scopus 로고
    • Microsecond folding dynamics of the F13W, G29A mutant of the B domain of staphylococcal protein a by laser-induced temperature jump
    • G. Dimitriadis, A. Drysdale, J.K. Myers, P. Arora, S.E. Radford, T.G. Oas, and D.A. Smith Microsecond folding dynamics of the F13W, G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump Proc. Natl Acad. Sci. USA 101 2004 3809 3814
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 3809-3814
    • Dimitriadis, G.1    Drysdale, A.2    Myers, J.K.3    Arora, P.4    Radford, S.E.5    Oas, T.G.6    Smith, D.A.7
  • 5
    • 2342449128 scopus 로고    scopus 로고
    • Testing protein-folding simulations by experiment: B domain of protein a
    • S. Sato, T.L. Religa, V. Daggett, and A.R. Fersht Testing protein-folding simulations by experiment: B domain of protein A Proc. Natl Acad. Sci. USA 101 2004 6952 6956
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6952-6956
    • Sato, S.1    Religa, T.L.2    Daggett, V.3    Fersht, A.R.4
  • 6
    • 0034602807 scopus 로고    scopus 로고
    • Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and e domains
    • D.O.V. Alonso, and V. Daggett Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains Proc. Natl Acad. Sci. USA 97 2000 133 138
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 133-138
    • Alonso, D.O.V.1    Daggett, V.2
  • 7
    • 0035854476 scopus 로고    scopus 로고
    • Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model
    • G.F. Berriz, and E.I. Shakhnovich Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model J. Mol. Biol. 310 2001 673 685
    • (2001) J. Mol. Biol. , vol.310 , pp. 673-685
    • Berriz, G.F.1    Shakhnovich, E.I.2
  • 8
    • 0036678831 scopus 로고    scopus 로고
    • An atomically detailed study of the folding pathways of protein a with the stochastic difference equation
    • A. Ghosh, R. Elber, and H.A. Scheraga An atomically detailed study of the folding pathways of protein A with the stochastic difference equation Proc. Natl Acad. Sci. USA 99 2002 10394 10398
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 10394-10398
    • Ghosh, A.1    Elber, R.2    Scheraga, H.A.3
  • 9
    • 0036568327 scopus 로고    scopus 로고
    • Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
    • G. Farvin, A. Irbäck, and S. Wallin Folding of a small helical protein using hydrogen bonds and hydrophobicity forces Proteins: Struct. Funct. Genet. 47 2002 99 105
    • (2002) Proteins: Struct. Funct. Genet. , vol.47 , pp. 99-105
    • Farvin, G.1    Irbäck, A.2    Wallin, S.3
  • 10
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein a
    • A.E. García, and J.N. Onuchic Folding a protein in a computer: an atomic description of the folding/unfolding of protein A Proc. Natl Acad. Sci. USA 100 2003 13903 13989
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13903-13989
    • García, A.E.1    Onuchic, J.N.2
  • 11
    • 0345724787 scopus 로고    scopus 로고
    • Ab initio folding of helix bundle proteins using molecular dynamics simulations
    • S. Jang, E. Kim, S. Shin, and Y. Pak Ab initio folding of helix bundle proteins using molecular dynamics simulations J. Am. Chem. Soc. 125 2003 14841 14846
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14841-14846
    • Jang, S.1    Kim, E.2    Shin, S.3    Pak, Y.4
  • 12
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • A. Liwo, M. Khalili, and H.A. Scheraga Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains Proc. Natl Acad. Sci. USA 102 2005 2362 2367
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 13
    • 28944453362 scopus 로고    scopus 로고
    • Experimental resolution of the early steps in the folding of a three-helix bundle protein. Nineteenth Symposium of the Protein Society, Boston, Massachussetts, July 30-August 3, 2005
    • D.M. Vu, S.H. Brewer, S. Sato, A.R. Fersht, and R.B. Dyer Experimental resolution of the early steps in the folding of a three-helix bundle protein. Nineteenth Symposium of the Protein Society, Boston, Massachussetts, July 30-August 3, 2005 Protein Sci. 14 2005 184
    • (2005) Protein Sci. , vol.14 , pp. 184
    • Vu, D.M.1    Brewer, S.H.2    Sato, S.3    Fersht, A.R.4    Dyer, R.B.5
  • 14
    • 28944450112 scopus 로고    scopus 로고
    • Phi value analysis of protein a using moving optical probes. Nineteenth Symposium of the Protein Society, Boston, Massachussetts, July 30-August 3, 2005
    • S. Sato, T.L. Religa, and A.R. Fersht Phi value analysis of protein A using moving optical probes. Nineteenth Symposium of the Protein Society, Boston, Massachussetts, July 30-August 3, 2005 Protein Sci. 14 2005 186
    • (2005) Protein Sci. , vol.14 , pp. 186
    • Sato, S.1    Religa, T.L.2    Fersht, A.R.3
  • 15
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • A. Kolinski, and J. Skolnick Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme Proteins: Struct. Funct. Genet. 18 1994 338 352
    • (1994) Proteins: Struct. Funct. Genet. , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 16
    • 0029151245 scopus 로고
    • First-principles calculation of the folding free-energy of a 3-helix bundle protein
    • E.M. Boczko, and C.L. Brooks First-principles calculation of the folding free-energy of a 3-helix bundle protein Science 269 1995 393 396
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks, C.L.2
  • 17
    • 0030967896 scopus 로고    scopus 로고
    • Exploring the folding free energy surface of a three-helix bundle protein
    • Z.Y. Guo, C.L. Brooks, and E.M. Boczko Exploring the folding free energy surface of a three-helix bundle protein Proc. Natl Acad. Sci. USA 94 1997 10161 10166
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 10161-10166
    • Guo, Z.Y.1    Brooks, C.L.2    Boczko, E.M.3
  • 18
    • 23144463330 scopus 로고    scopus 로고
    • Molecular dynamics with the united-residue (UNRES) model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems
    • M. Khalili, A. Liwo, A. Jagielska, and H.A. Scheraga Molecular dynamics with the united-residue (UNRES) model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems J. Phys. Chem. ser. B 109 2005 13798 13810
    • (2005) J. Phys. Chem. Ser. B , vol.109 , pp. 13798-13810
    • Khalili, M.1    Liwo, A.2    Jagielska, A.3    Scheraga, H.A.4
  • 20
    • 0025113815 scopus 로고
    • Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random Poly(hydroxybutylglutamine-co- S-methylthio-l-cysteine)
    • J. Wojcik, K.H. Altmann, and H.A. Scheraga Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random Poly(hydroxybutylglutamine-co-S-methylthio-l-cysteine) Biopolymers 30 1990 121 134
    • (1990) Biopolymers , vol.30 , pp. 121-134
    • Wojcik, J.1    Altmann, K.H.2    Scheraga, H.A.3
  • 21
    • 8344277888 scopus 로고    scopus 로고
    • Optimization of the UNRES force field by hierarchical design of the potential-energy landscape: II. Off-lattice tests of the method with single proteins
    • S. Ołdziej, A. Liwo, C. Czaplewski, J. Pillardy, and H.A. Scheraga Optimization of the UNRES force field by hierarchical design of the potential-energy landscape: II. Off-lattice tests of the method with single proteins J. Phys. Chem. ser. B 108 2004 16934 16949
    • (2004) J. Phys. Chem. Ser. B , vol.108 , pp. 16934-16949
    • Ołdziej, S.1    Liwo, A.2    Czaplewski, C.3    Pillardy, J.4    Scheraga, H.A.5
  • 22
    • 0033117927 scopus 로고    scopus 로고
    • Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
    • D. Thirumalai, and D.K. Klimov Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models Curr. Opin. Struct. Biol. 9 1999 197 207
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 197-207
    • Thirumalai, D.1    Klimov, D.K.2
  • 23
    • 0036783392 scopus 로고    scopus 로고
    • Thermal folding and mechanical unfolding pathways of protein secondary structures
    • M. Cieplak, T.X. Hoang, and M.O. Robbins Thermal folding and mechanical unfolding pathways of protein secondary structures Proteins: Struct. Funct. Genet. 49 2002 104 113
    • (2002) Proteins: Struct. Funct. Genet. , vol.49 , pp. 104-113
    • Cieplak, M.1    Hoang, T.X.2    Robbins, M.O.3
  • 24
    • 4544223597 scopus 로고    scopus 로고
    • Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations
    • S. Chowdhury, M.C. Lee, and Y. Duan Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations J. Phys. Chem. B 108 2004 13855 13865
    • (2004) J. Phys. Chem. B , vol.108 , pp. 13855-13865
    • Chowdhury, S.1    Lee, M.C.2    Duan, Y.3
  • 25
    • 23144450194 scopus 로고    scopus 로고
    • Molecular dynamics with the united-residue (UNRES) model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode
    • M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, and H.A. Scheraga Molecular dynamics with the united-residue (UNRES) model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode J. Phys. Chem. ser. B 109 2005 13785 13797
    • (2005) J. Phys. Chem. Ser. B , vol.109 , pp. 13785-13797
    • Khalili, M.1    Liwo, A.2    Rakowski, F.3    Grochowski, P.4    Scheraga, H.A.5
  • 26
    • 0035424584 scopus 로고    scopus 로고
    • Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
    • A. Liwo, C. Czaplewski, J. Pillardy, and H.A. Scheraga Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field J. Chem. Phys. 115 2001 2323 2347
    • (2001) J. Chem. Phys. , vol.115 , pp. 2323-2347
    • Liwo, A.1    Czaplewski, C.2    Pillardy, J.3    Scheraga, H.A.4
  • 27
    • 0027435091 scopus 로고
    • Prediction of protein conformation on the basis of a search for compact structures; Test on avian pancreatic polypeptide
    • A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide Protein Sci. 2 1993 1715 1731
    • (1993) Protein Sci. , vol.2 , pp. 1715-1731
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 28
    • 0000095892 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
    • A. Liwo, S. Ołdziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data J. Comput. Chem. 18 1997 849 873
    • (1997) J. Comput. Chem. , vol.18 , pp. 849-873
    • Liwo, A.1    Ołdziej, S.2    Pincus, M.R.3    Wawak, R.J.4    Rackovsky, S.5    Scheraga, H.A.6
  • 29
    • 3142681595 scopus 로고    scopus 로고
    • Parameterization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems
    • A. Liwo, S. Ołdziej, C. Czaplewski, U. Kozłowska, and H.A. Scheraga Parameterization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems J. Phys. Chem. ser. B 108 2004 9421 9438
    • (2004) J. Phys. Chem. Ser. B , vol.108 , pp. 9421-9438
    • Liwo, A.1    Ołdziej, S.2    Czaplewski, C.3    Kozłowska, U.4    Scheraga, H.A.5
  • 30
    • 8344262957 scopus 로고    scopus 로고
    • Optimization of the UNRES force field by hierarchical design of the potential-energy landscape: III. Use of many proteins in optimization
    • S. Ołdziej, J. Łagiewka, A. Liwo, C. Czaplewski, M. Chinchio, M. Nanias, and H.A. Scheraga Optimization of the UNRES force field by hierarchical design of the potential-energy landscape: III. Use of many proteins in optimization J. Phys. Chem. ser. B 108 2004 16950 16959
    • (2004) J. Phys. Chem. Ser. B , vol.108 , pp. 16950-16959
    • Ołdziej, S.1    Łagiewka, J.2    Liwo, A.3    Czaplewski, C.4    Chinchio, M.5    Nanias, M.6    Scheraga, H.A.7
  • 31
    • 0036733958 scopus 로고    scopus 로고
    • Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach
    • M.P. Eastwood, C. Hardin, Z. Luthey-Schulten, and P.G. Wolynes Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach J. Chem. Phys. 117 2002 4602 4615
    • (2002) J. Chem. Phys. , vol.117 , pp. 4602-4615
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.