메뉴 건너뛰기




Volumn 86, Issue 4, 2004, Pages 1946-1958

β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water

Author keywords

[No Author keywords available]

Indexed keywords

AMYLASE INHIBITOR; PEPTIDE; TENDAMISTAT;

EID: 1942519803     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74258-7     Document Type: Article
Times cited : (39)

References (32)
  • 1
    • 0030745939 scopus 로고    scopus 로고
    • Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
    • Beachy, M. D., D. Chasman, R. B. Murphy, T. A. Halgren, and R. A. Friesner. 1997. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J. Am. Chem. Soc. 119:5908-5920.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5908-5920
    • Beachy, M.D.1    Chasman, D.2    Murphy, R.B.3    Halgren, T.A.4    Friesner, R.A.5
  • 2
    • 0000349003 scopus 로고
    • NMR Evidence of a short linear peptide that folds into a β-hairpin in aqueous solution
    • Blanco, F. J., M. A. Jiménez, J. Herranz, M. Rico, J. Santoro, and J. L. Nieto. 1993. NMR Evidence of a short linear peptide that folds into a β-hairpin in aqueous solution. J. Am. Chem. Soc. 115:5887-5888.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 5887-5888
    • Blanco, F.J.1    Jiménez, M.A.2    Herranz, J.3    Rico, M.4    Santoro, J.5    Nieto, J.L.6
  • 3
    • 0034635340 scopus 로고    scopus 로고
    • Beta-hairpin stability and folding: Molecular dynamics studies of the first beta-hairpin of tendamistat
    • Bonvin, A. M., and W. F. van Gunsteren. 2000. Beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. J. Mol. Biol. 296:255-268.
    • (2000) J. Mol. Biol. , vol.296 , pp. 255-268
    • Bonvin, A.M.1    Van Gunsteren, W.F.2
  • 4
    • 0034081255 scopus 로고    scopus 로고
    • Mechanical unfolding of a beta-hairpin using molecular dynamics
    • Bryant, Z., V. S. Pande, and D. S. Rokhsar. 2000. Mechanical unfolding of a beta-hairpin using molecular dynamics. Biophys. J. 78:584-589.
    • (2000) Biophys. J. , vol.78 , pp. 584-589
    • Bryant, Z.1    Pande, V.S.2    Rokhsar, D.S.3
  • 7
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel beta-sheet peptide
    • Ferrara, P., and A. Caflisch. 2000. Folding simulations of a three-stranded antiparallel beta-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
  • 8
    • 0036250489 scopus 로고    scopus 로고
    • Alpha-helix and beta-hairpin folding from experiment, analytical theory and molecular dynamics simulations
    • Galzitskaya, O. V., J. Higo, and A. V. Finkelstein. 2002. Alpha-helix and beta-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Curr. Protein Pept. Sci. 3:191-200.
    • (2002) Curr. Protein Pept. Sci. , vol.3 , pp. 191-200
    • Galzitskaya, O.V.1    Higo, J.2    Finkelstein, A.V.3
  • 10
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a beta-hairpin in explicit solvent
    • Garcia, A. E., and K. Y. Sanbonmatsu. 2001. Exploring the energy landscape of a beta-hairpin in explicit solvent. Proteins. 42:345-354.
    • (2001) Proteins , vol.42 , pp. 345-354
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 11
    • 0037022662 scopus 로고    scopus 로고
    • Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds
    • Garcia, A. E., and K. Y. Sanbonmatsu. 2002. Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. USA. 99:2782-2787.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 2782-2787
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 12
    • 0034645735 scopus 로고    scopus 로고
    • Thermodynamics of a beta-hairpin structure: Evidence for cooperative formation of folding nucleus
    • Honda, S., N. Kobayashi, and E. Munekata. 2000. Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J. Mol. Biol. 295:269-278.
    • (2000) J. Mol. Biol. , vol.295 , pp. 269-278
    • Honda, S.1    Kobayashi, N.2    Munekata, E.3
  • 13
    • 0000043930 scopus 로고    scopus 로고
    • Solvation free energy of biomacromolecules: Parameters for a modified Generalized Bom model consistent with the AMBER force field
    • Jayaram, B., D. Sprous, and D. L. Beveridge. 2000. Solvation free energy of biomacromolecules: parameters for a modified Generalized Bom model consistent with the AMBER force field. J. Phys. Chem. B. 102:9571-9576.
    • (2000) J. Phys. Chem. B , vol.102 , pp. 9571-9576
    • Jayaram, B.1    Sprous, D.2    Beveridge, D.L.3
  • 15
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of beta-hairpin formation
    • Munoz, V., P. A. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390:196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 16
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
    • Pande, V. S., and D. S. Rokhsar. 1999. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA. 96:9062-9067.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 17
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties
    • Perlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. Debolt, D. Ferguson, G. L. Seibel, and P. A. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties. Comp. Phys. Commun. 91:1-41.
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 1-41
    • Perlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham III, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.L.8    Kollman, P.A.9
  • 19
    • 0032484151 scopus 로고    scopus 로고
    • Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
    • Schaefer, M., C. Bartels, and M. Karplus. 1998. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J. Mol. Biol. 284:835-848.
    • (1998) J. Mol. Biol. , vol.284 , pp. 835-848
    • Schaefer, M.1    Bartels, C.2    Karplus, M.3
  • 20
    • 0001740994 scopus 로고    scopus 로고
    • Self-guided molecular dynamics in the isothermal-isobaric ensemble
    • Shinoda, W., and M. Mikami. 2001. Self-guided molecular dynamics in the isothermal-isobaric ensemble. Chem. Phys. Lett. 335:265-272.
    • (2001) Chem. Phys. Lett. , vol.335 , pp. 265-272
    • Shinoda, W.1    Mikami, M.2
  • 21
    • 0021844602 scopus 로고
    • β-hairpin families in globular proteins
    • Sibanda, B., and J. Thomton. 1985. β-hairpin families in globular proteins. Nature. 316:170-174.
    • (1985) Nature , vol.316 , pp. 170-174
    • Sibanda, B.1    Thomton, J.2
  • 22
    • 0037046768 scopus 로고    scopus 로고
    • Competitive and reversible binding of a guest molecule to its host in aqueous solution through molecular dynamics simulation: Benzyl alcohol/a-cyclodextrin system
    • Varady, J., X. Wu, and S. Wang. 2002. Competitive and reversible binding of a guest molecule to its host in aqueous solution through molecular dynamics simulation: benzyl alcohol/a-cyclodextrin system. J. Phys. Chem. B. 106:4863-4872.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 4863-4872
    • Varady, J.1    Wu, X.2    Wang, S.3
  • 23
    • 0032735468 scopus 로고    scopus 로고
    • Molecular dynamics simulations of beta-hairpin folding
    • Wang, H., J. Varady, L. Ng, and S. S. Sung. 1999. Molecular dynamics simulations of beta-hairpin folding. Proteins. 37:325-333.
    • (1999) Proteins , vol.37 , pp. 325-333
    • Wang, H.1    Varady, J.2    Ng, L.3    Sung, S.S.4
  • 24
    • 0037093874 scopus 로고    scopus 로고
    • Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation
    • Wu, X., S. Wang, and B. R. Brooks. 2002. Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J. Am. Chem. Soc. 124:5282-5283.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5282-5283
    • Wu, X.1    Wang, S.2    Brooks, B.R.3
  • 25
    • 0000515108 scopus 로고    scopus 로고
    • Self-guided molecular dynamics simulation for efficient conformational search
    • Wu, X.-W., and S. Wang. 1998. Self-guided molecular dynamics simulation for efficient conformational search. J. Phys. Chem. B. 102:7238-7250.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 7238-7250
    • Wu, X.-W.1    Wang, S.2
  • 26
    • 0032607091 scopus 로고    scopus 로고
    • Enhancing systematic motion in molecular dynamics simulation
    • Wu, X.-W., and S. Wang. 1999. Enhancing systematic motion in molecular dynamics simulation. J. Chem. Phys. 110:9401-9410.
    • (1999) J. Chem. Phys. , vol.110 , pp. 9401-9410
    • Wu, X.-W.1    Wang, S.2
  • 27
    • 0034710426 scopus 로고    scopus 로고
    • Folding study of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation
    • Wu, X.-W., and S. Wang. 2000. Folding study of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation. J. Phys. Chem. B. 104:8023-8034.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 8023-8034
    • Wu, X.-W.1    Wang, S.2
  • 28
    • 0035932703 scopus 로고    scopus 로고
    • Helix folding of an alanine-based peptide in explicit water
    • Wu, X., and S. Wang. 2001. Helix folding of an alanine-based peptide in explicit water. J. Phys. Chem. B. 105:2227-2235.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 2227-2235
    • Wu, X.1    Wang, S.2
  • 29
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • York, D. M., T. A. Darden, and L. G. Pedersen. 1993. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:8345-8348.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 30
    • 0036789950 scopus 로고    scopus 로고
    • Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
    • Zhou, R., and B. J. Beme. 2002. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl. Acad. Sci. USA. 99:12777-12782.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12777-12782
    • Zhou, R.1    Beme, B.J.2
  • 31
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for beta hairpin folding in explicit water
    • Zhou, R., B. J. Beme, and R. Germain. 2001. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA. 98:14931-14936.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 14931-14936
    • Zhou, R.1    Beme, B.J.2    Germain, R.3
  • 32
    • 0036568318 scopus 로고    scopus 로고
    • Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model
    • Zhou, Y., and A. Linhananta. 2002. Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model. Proteins. 47:154-162.
    • (2002) Proteins , vol.47 , pp. 154-162
    • Zhou, Y.1    Linhananta, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.