메뉴 건너뛰기




Volumn 36, Issue 2, 1999, Pages 249-261

Direct computation of long time processes in peptides and proteins: Reaction path study of the coil-to-helix transition in polyalanine

Author keywords

Continuum solvation; Diffusion; Helix coil transition; Peptide dynamics; Polyalanine; Reaction paths

Indexed keywords

ALANINE DERIVATIVE; PEPTIDE; POLYALANINE; PROTEIN; UNCLASSIFIED DRUG;

EID: 0033181019     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990801)36:2<249::AID-PROT10>3.0.CO;2-1     Document Type: Article
Times cited : (53)

References (39)
  • 1
    • 0000668407 scopus 로고
    • Theory of phase transition between helix and random coil in polypeptide chains
    • Zimm BH, Bragg JK. Theory of phase transition between helix and random coil in polypeptide chains. J Chem Phys 1959;31:526.
    • (1959) J Chem Phys , vol.31 , pp. 526
    • Zimm, B.H.1    Bragg, J.K.2
  • 2
    • 33751391161 scopus 로고
    • Helix-coil theories: A comparative study for finit length polypeptides
    • Qian H, Schellman J. Helix-coil theories: a comparative study for finit length polypeptides. J Phys Chem 1992;96:3987.
    • (1992) J Phys Chem , vol.96 , pp. 3987
    • Qian, H.1    Schellman, J.2
  • 4
    • 0026209013 scopus 로고
    • The helical s constant for alanine in water derived from template-nucleated helices
    • Kemp DS, Boyd JG, Muendel CC. The helical s constant for alanine in water derived from template-nucleated helices. Nature 1991;352:451.
    • (1991) Nature , vol.352 , pp. 451
    • Kemp, D.S.1    Boyd, J.G.2    Muendel, C.C.3
  • 5
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 1994;3:843.
    • (1994) Protein Sci , vol.3 , pp. 843
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 6
    • 0026254055 scopus 로고
    • Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water
    • Scholtz JM, Qian H, York EJ, Stewart JM, Baldwin RL. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers 1991;31:1463.
    • (1991) Biopolymers , vol.31 , pp. 1463
    • Scholtz, J.M.1    Qian, H.2    York, E.J.3    Stewart, J.M.4    Baldwin, R.L.5
  • 7
    • 0025113815 scopus 로고
    • Helix-coil stability constants for the naturally occuring amino acids in water. XXIV. half-cystine parameters from random poly (hydroxybutlglutamineco-s-methylthio-l-cysteine)
    • Wójcik J, Altmann KH, Scheraga HA. Helix-coil stability constants for the naturally occuring amino acids in water. xxiv. half-cystine parameters from random poly (hydroxybutlglutamineco-s-methylthio-l-cysteine). Biopolymers 1990;30:121.
    • (1990) Biopolymers , vol.30 , pp. 121
    • Wójcik, J.1    Altmann, K.H.2    Scheraga, H.A.3
  • 8
    • 0028847038 scopus 로고
    • Thermodynamic parameters for the helix-coil transition of oligopeptides: Molecular dynamics simulation with the peptide growth method
    • Wang L, O'Connell T, Tropsha A, Hermans J. Thermodynamic parameters for the helix-coil transition of oligopeptides: molecular dynamics simulation with the peptide growth method. Proc Natl Acad Sci USA 1995;92:10924.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 10924
    • Wang, L.1    O'Connell, T.2    Tropsha, A.3    Hermans, J.4
  • 9
    • 0029887269 scopus 로고    scopus 로고
    • A microscopic view of helix propagation: N and c-terminal helix growth in alanine helices
    • Young WS, Brooks CL III. A microscopic view of helix propagation: N and c-terminal helix growth in alanine helices. J Mol Biol 1996;259:260.
    • (1996) J Mol Biol , vol.259 , pp. 260
    • Young, W.S.1    Brooks C.L. III2
  • 10
    • 0026525048 scopus 로고
    • Molecular dynamics simulations of helix denaturation
    • Daggett V, Levitt M. Molecular dynamics simulations of helix denaturation. J Mol Biol 1992;223:1121.
    • (1992) J Mol Biol , vol.223 , pp. 1121
    • Daggett, V.1    Levitt, M.2
  • 11
    • 0031587288 scopus 로고    scopus 로고
    • Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
    • Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol 1997;272:423.
    • (1997) J Mol Biol , vol.272 , pp. 423
    • Mohanty, D.1    Elber, R.2    Thirumalai, D.3    Beglov, D.4    Roux, B.5
  • 12
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Proc Natl Acad Sci USA 1998;282:740.
    • (1998) Proc Natl Acad Sci USA , vol.282 , pp. 740
    • Duan, Y.1    Kollman, P.A.2
  • 13
    • 0001842441 scopus 로고    scopus 로고
    • Adding backbone to protein folding: Why proteins are polypeptides
    • Honig B, Cohen FE. Adding backbone to protein folding: why proteins are polypeptides. Fold Des 1996;1:R17-R20.
    • (1996) Fold Des , vol.1
    • Honig, B.1    Cohen, F.E.2
  • 14
    • 0032424129 scopus 로고    scopus 로고
    • Virtual atom representation of hydrogen bonds in minimal off-lattice models of α-helices: Effect on stability, cooperativity and kinetics
    • Klimov DK, Betancourt MR, Virtual atom representation of hydrogen bonds in minimal off-lattice models of α-helices: effect on stability, cooperativity and kinetics. Thirumalai D. Fold Des 1998;3:481-496.
    • (1998) Thirumalai D. Fold Des , vol.3 , pp. 481-496
    • Klimov, D.K.1    Betancourt, M.R.2
  • 15
    • 33645675171 scopus 로고
    • Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins
    • Rey J, Skolnick J. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins. Chem Phys 1991;158:199.
    • (1991) Chem Phys , vol.158 , pp. 199
    • Rey, J.1    Skolnick, J.2
  • 16
    • 0026643094 scopus 로고
    • The nature of folded states in globular proteins
    • Honeycutt JD, Thirumalai D. The nature of folded states in globular proteins. Biopolymers 1992;32:695.
    • (1992) Biopolymers , vol.32 , pp. 695
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 17
    • 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.
    • (1996) J Mol Biol , vol.263 , pp. 323
    • Guo, Z.1    Thirumalai, D.2
  • 18
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1: 227.
    • (1992) Protein Sci , vol.1 , pp. 227
    • Wesson, L.1    Eisenberg, D.2
  • 19
    • 0031256658 scopus 로고    scopus 로고
    • The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body system at finite temperature
    • Huo S, Straub JE. The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body system at finite temperature. J Chem Phys 1997;107: 5000.
    • (1997) J Chem Phys , vol.107 , pp. 5000
    • Huo, S.1    Straub, J.E.2
  • 20
    • 0017251893 scopus 로고
    • Protein-folding dynamics
    • Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976; 260:404.
    • (1976) Nature , vol.260 , pp. 404
    • Karplus, M.1    Weaver, D.L.2
  • 21
    • 84985656311 scopus 로고
    • Diffusion-collision model for protein folding
    • Karplus M, Weaver DL. Diffusion-collision model for protein folding. Biopolymers 1979;18:1421.
    • (1979) Biopolymers , vol.18 , pp. 1421
    • Karplus, M.1    Weaver, D.L.2
  • 22
    • 0024391879 scopus 로고
    • How does protein folding get started?
    • Baldwin RL. How does protein folding get started? Trends Biochem Sci 1989;14:291.
    • (1989) Trends Biochem Sci , vol.14 , pp. 291
    • Baldwin, R.L.1
  • 23
    • 0026205054 scopus 로고
    • A molecular dynamics simulations of polyalanine: An analysis of equilibrium motions and helix-coil transitions
    • Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulations of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers 1991;31:1115.
    • (1991) Biopolymers , vol.31 , pp. 1115
    • Daggett, V.1    Kollman, P.A.2    Kuntz, I.D.3
  • 24
    • 0344557043 scopus 로고
    • Molecular dynamics and monte carlo simulations favor the alpha-helical form for alanine-based peptides in water
    • Tirado-Rives J, Maxwell DS, Jorgensen WL. Molecular dynamics and Monte Carlo simulations favor the alpha-helical form for alanine-based peptides in water. J Am Chem Soc 1993; 115:11590.
    • (1993) J Am Chem Soc , vol.115 , pp. 11590
    • Tirado-Rives, J.1    Maxwell, D.S.2    Jorgensen, W.L.3
  • 25
  • 26
    • 0028317634 scopus 로고
    • 10 helix versus α-helix: A molecular dynamics study of conformational preferences of aib and alanine
    • 10 helix versus α-helix: a molecular dynamics study of conformational preferences of aib and alanine. J Am Chem Soc 1994;116:11915.
    • (1994) J Am Chem Soc , vol.116 , pp. 11915
    • Zhang, L.1    Hermans, J.2
  • 27
    • 0028921182 scopus 로고
    • 10-helix along the thermodynamic folding pathway
    • 10-helix along the thermodynamic folding pathway. Biochemistry 1995;34:3873.
    • (1995) Biochemistry , vol.34 , pp. 3873
    • Millhauser, G.L.1
  • 30
    • 0030006074 scopus 로고    scopus 로고
    • Molecular dynamics simulations of synthetic peptide folding
    • Sung S, Wu X. Molecular dynamics simulations of synthetic peptide folding. Proteins 1996;25:202.
    • (1996) Proteins , vol.25 , pp. 202
    • Sung, S.1    Wu, X.2
  • 31
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983.
    • (1994) J Mol Biol , vol.235 , pp. 983
    • Abagyan, R.1    Totrov, M.2
  • 32
    • 0345246954 scopus 로고    scopus 로고
    • Molecular Simulations, Inc
    • Molecular Simulations, Inc. (1997).
    • (1997)
  • 34
    • 0000055722 scopus 로고
    • Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate
    • Berkowitz M, Morgan JD, McCammon JA, Northrup SH. Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate. J Chem Phys 1983;79:5563.
    • (1983) J Chem Phys , vol.79 , pp. 5563
    • Berkowitz, M.1    Morgan, J.D.2    McCammon, J.A.3    Northrup, S.H.4
  • 35
    • 84987058840 scopus 로고
    • Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems
    • Czerminski R, Elber R. Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems. Int J Quant Chem 1990;24:167.
    • (1990) Int J Quant Chem , vol.24 , pp. 167
    • Czerminski, R.1    Elber, R.2
  • 36
  • 37
    • 0028835443 scopus 로고
    • Nucleation mechanism for protein-folding and theoretical predictions for hydrogen-exchange labeling experiments
    • Guo Z, Thirumalai D. Nucleation mechanism for protein-folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers 1994;35:137.
    • (1994) Biopolymers , vol.35 , pp. 137
    • Guo, Z.1    Thirumalai, D.2
  • 38
    • 0031285905 scopus 로고    scopus 로고
    • Kinetics partitioning mechanism as a unifying theme in the folding of biomolecules
    • Thirumalai D, Klimov DK, Woodson SA. Kinetics partitioning mechanism as a unifying theme in the folding of biomolecules. Theor Chem Ace 1997;1:23.
    • (1997) Theor Chem Ace , vol.1 , pp. 23
    • Thirumalai, D.1    Klimov, D.K.2    Woodson, S.A.3
  • 39
    • 0030970740 scopus 로고    scopus 로고
    • Curious structure in canonical alanine-based peptides
    • Shirley WA, Brooks CL III. Curious structure in canonical alanine-based peptides. Proteins 1997;28:59.
    • (1997) Proteins , vol.28 , pp. 59
    • Shirley, W.A.1    Brooks C.L. III2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.