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Volumn 87, Issue 6, 2004, Pages 3786-3798

Equilibrium structure and folding of a helix-forming peptide: Circular dichroism measurements and replica-exchange molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLTRYPTOPHYLALANYLALANYLALANYLHISTIDYLTRIS(ALANYLALANYLALANYLARGINYLALA NYL)ALANINAMIDE; PEPTIDE; UNCLASSIFIED DRUG;

EID: 10044247242     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.045419     Document Type: Article
Times cited : (46)

References (44)
  • 1
    • 0024278714 scopus 로고
    • Helix geometry in proteins
    • Barlow, D. J., and J. M. Thomton. 1988. Helix geometry in proteins. J. Mol. Biol. 201:601-619.
    • (1988) J. Mol. Biol. , vol.201 , pp. 601-619
    • Barlow, D.J.1    Thomton, J.M.2
  • 3
    • 0036816569 scopus 로고    scopus 로고
    • Probing protein dynamics using temperature jump relaxation spectroscopy
    • Callender, R., and R. B. Dyer. 2002. Probing protein dynamics using temperature jump relaxation spectroscopy. Curr. Opin. Struct. Biol. 12: 628-633.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 628-633
    • Callender, R.1    Dyer, R.B.2
  • 7
    • 0033557181 scopus 로고    scopus 로고
    • Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations
    • Daura, X., W. F. Van Gunsteren, and A. E. Mark. 1999. Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins. 34:269-280.
    • (1999) Proteins , vol.34 , pp. 269-280
    • Daura, X.1    Van Gunsteren, W.F.2    Mark, A.E.3
  • 8
    • 0000810764 scopus 로고    scopus 로고
    • Infrared studies of fast events in protein folding
    • Dyer, R. B., F. Gai, and W. H. Woodruff. 1998. Infrared studies of fast events in protein folding. Acc. Chem. Res. 31:709-716.
    • (1998) Acc. Chem. Res. , vol.31 , pp. 709-716
    • Dyer, R.B.1    Gai, F.2    Woodruff, W.H.3
  • 10
    • 0542397796 scopus 로고    scopus 로고
    • Kinetics and dynamics of loops, alpha-helices, beta-hairpins, and fast-folding proteins
    • Eaton, W. A., V. Munoz, P. A. Thompson, E. R. Henry, and J. Hofrichter. 1998. Kinetics and dynamics of loops, alpha-helices, beta-hairpins, and fast-folding proteins. Acc. Chem. Res. 31:745-753.
    • (1998) Acc. Chem. Res. , vol.31 , pp. 745-753
    • Eaton, W.A.1    Munoz, V.2    Thompson, P.A.3    Henry, E.R.4    Hofrichter, J.5
  • 11
    • 0041814016 scopus 로고    scopus 로고
    • MMTSB NIH Research Resource. The Scripps Institute, La Jolla, CA
    • Feig, M., J. Karanicolas, and C. L. Brooks III. 2001. MMTSB Tool Set. MMTSB NIH Research Resource. The Scripps Institute, La Jolla, CA.
    • (2001) MMTSB Tool Set
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 12
    • 0038054912 scopus 로고    scopus 로고
    • Force field influence on the observation of a-helical protein structures in molecular dynamics simulations
    • Feig, M., A. D. MacKerrel, Jr., and C. L. B. Brooks III. 2003. Force field influence on the observation of a-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2831-2836.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 2831-2836
    • Feig, M.1    MacKerrel Jr., A.D.2    Brooks III, C.L.B.3
  • 13
    • 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
  • 15
    • 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
  • 16
    • 0037022662 scopus 로고    scopus 로고
    • α-helical stabilization by side chain shielding of backbone hydrogen bonds
    • Garcia, A. E., and K. Y. Sanbonmatsu. 2002. α-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
  • 18
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 19
    • 0035128362 scopus 로고    scopus 로고
    • Effect of viscosity on the kinetics of alpha-helix and beta-hairpin formation
    • Jas, G. S., W. A. Eaton, and J. Hofrichter. 2001. Effect of viscosity on the kinetics of alpha-helix and beta-hairpin formation. J. Phys. Chem. B. 105:261-272.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 261-272
    • Jas, G.S.1    Eaton, W.A.2    Hofrichter, J.3
  • 21
    • 1842500993 scopus 로고    scopus 로고
    • Unfolded state of polyalanine is a segmented polyproline II helix
    • Kentsis, A., M. Mezei, T. Gindin, and R. Osman. 2004. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins. 55:493-501.
    • (2004) Proteins , vol.55 , pp. 493-501
    • Kentsis, A.1    Mezei, M.2    Gindin, T.3    Osman, R.4
  • 22
    • 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. 35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 24
    • 0037022332 scopus 로고    scopus 로고
    • The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation
    • Lopez, M. M., D.-H. Chin, R. L. Baldwin, and G. I. Makhatadze. 2002. The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation. Proc. Natl. Acad. Sci. USA. 99:1298-1302.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1298-1302
    • Lopez, M.M.1    Chin, D.-H.2    Baldwin, R.L.3    Makhatadze, G.I.4
  • 26
    • 0024707204 scopus 로고
    • Unusually stable helix formation in short alanine-based peptides
    • Marqusee, S., V. H. Robbins, and R. L. Baldwin. 1989. Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad. Sci. USA. 86:5286-5290.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 5286-5290
    • Marqusee, S.1    Robbins, V.H.2    Baldwin, R.L.3
  • 27
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is the preferred conformation of unfolded polyalanine in water
    • Mezei, M., P. J. Fleming, R. Srinivasan, and G. D. Rose. 2004. Polyproline II helix is the preferred conformation of unfolded polyalanine in water. Proteins. 55:502-507.
    • (2004) Proteins , vol.55 , pp. 502-507
    • Mezei, M.1    Fleming, P.J.2    Srinivasan, R.3    Rose, G.D.4
  • 28
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulation in the canonical ensemble
    • Nose, S. 1984. A molecular dynamics method for simulation in the canonical ensemble. Mol. Phys. 52:255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nose, S.1
  • 29
    • 0344702698 scopus 로고    scopus 로고
    • Simulations of the folding equilibrium of a-helical peptides: A comparison of generalized Bom approximation with explicit solvent
    • Nymeyer, H., and A. E. Garcia. 2003. Simulations of the folding equilibrium of a-helical peptides: A comparison of generalized Bom approximation with explicit solvent. Proc. Natl. Acad. Sci. USA. 100: 13934-13939.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13934-13939
    • Nymeyer, H.1    Garcia, A.E.2
  • 30
    • 0345564821 scopus 로고    scopus 로고
    • Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix-coil transitions in polyalanine and the c-peptide from RNase A
    • Ohkubo, Y. Z., and C. L. Brooks III. 2003. Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the c-peptide from RNase A. Proc. Natl. Acad. Sci. USA. 100: 13916-13921.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13916-13921
    • Ohkubo, Y.Z.1    Brooks III, C.L.2
  • 31
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica exchange simulations of Trp-cage miniproteins
    • Pitera, J. W., and W. Swope. 2003. Understanding folding and design: Replica exchange simulations of Trp-cage miniproteins. Proc. Natl. Acad. Sci. USA. 100:7587-7592.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 32
    • 0041877561 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of reversible folding
    • Rao, F., and A. Caflisch. 2003. Replica exchange molecular dynamics simulations of reversible folding. J. Chem. Phys. 119:4035-4042.
    • (2003) J. Chem. Phys. , vol.119 , pp. 4035-4042
    • Rao, F.1    Caflisch, A.2
  • 33
    • 0037305918 scopus 로고    scopus 로고
    • Multiplexed-replica exchange molecular dynamics method for protein folding simulations
    • Rhee, M. H., and V. S. Pande. 2003. Multiplexed-replica exchange molecular dynamics method for protein folding simulations. Biophys. J. 84:775-786.
    • (2003) Biophys. J , vol.84 , pp. 775-786
    • Rhee, M.H.1    Pande, V.S.2
  • 34
    • 0347753737 scopus 로고    scopus 로고
    • Temperature dependence of the thermodynamics of helix-coil transition
    • Richardson, J. M., and G. I. Makhatadze. 2004. Temperature dependence of the thermodynamics of helix-coil transition. J. Mol. Biol. 335:1029-1037.
    • (2004) J. Mol. Biol. , vol.335 , pp. 1029-1037
    • Richardson, J.M.1    Makhatadze, G.I.2
  • 35
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the cartesian equations of motion with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 37
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • Simonson, T., and A. Brunger. 1994. Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment. J. Phys. Chem. 98:4683-4694.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4683-4694
    • Simonson, T.1    Brunger, A.2
  • 38
    • 0041375556 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent
    • Suenaga, A. 2003. Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent. J. Mol. Struct. 634:235-241.
    • (2003) J. Mol. Struct. , vol.634 , pp. 235-241
    • Suenaga, A.1
  • 39
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita. Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 40
    • 36749110571 scopus 로고
    • A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules, application to water clusters
    • Swope, W. C., H. C. Andersen, P. H. Berens, and K. R. Wilson. 1982. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules, application to water clusters. J. Chem. Phys. 76:637-649.
    • (1982) J. Chem. Phys. , vol.76 , pp. 637-649
    • Swope, W.C.1    Andersen, H.C.2    Berens, P.H.3    Wilson, K.R.4
  • 43
    • 0036789950 scopus 로고    scopus 로고
    • Can a continuum solvent model reproduce the free energy landscape for beta-hairpin folding in water?
    • Zhou, R. H., and B. J. Berne. 2002. Can a continuum solvent model reproduce the free energy landscape for beta-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.H.1    Berne, B.J.2
  • 44
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for beta hairpin folding in explicit water
    • Zhou, R. H., B. J. Berne, 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.H.1    Berne, B.J.2    Germain, R.3


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