journal article Apr 17, 2002

Molecular Dynamics Study of Peptides in Implicit Water:  Ab Initio Folding of β-Hairpin, β-Sheet, and ββα-motif

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References
49
[1]
Berne B. J. Curr. Opin. Struct. Biol. (1997) 10.1016/s0959-440x(97)80023-1
[2]
FROMFOLDINGTHEORIES TOFOLDINGPROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

Joan-Emma Shea, Charles L Brooks III

Annual Review of Physical Chemistry 2001 10.1146/annurev.physchem.52.1.499
[3]
Protein Structure Prediction and Structural Genomics

David Baker, Andrej Šali

Science 2001 10.1126/science.1065659
[4]
Wu X. J. Phys. Chem. B (1998) 10.1021/jp9817372
[5]
Samudrala R. Proteins (Suppl.) (1999)
[6]
Ab initio folding of proteins using restraints derived from evolutionary information

Angel R. Ortiz, Andrzej Kolinski, Piotr Rotkiewicz et al.

Proteins: Structure, Function, and Bioinformatics 1999 10.1002/(sici)1097-0134(1999)37:3+<177::aid-prot22>3.0.co;2-e
[7]
Recent improvements in prediction of protein structure by global optimization of a potential energy function

Jarosław Pillardy, Cezary Czaplewski, Adam Liwo et al.

Proceedings of the National Academy of Sciences 2001 10.1073/pnas.041609598
[8]
Jones D. T. Proteins (Suppl.) (1997) 10.1002/(sici)1097-0134(1997)1+<185::aid-prot24>3.0.co;2-j
[9]
Prospects for ab initio protein structural genomics

Kim T Simons, Charlie Strauss, David Baker

Journal of Molecular Biology 2000 10.1006/jmbi.2000.4459
[10]
Dinner A. Proc. Natl. Acad. Sci. U.S.A. (1999)
[11]
Hansman L. Curr. Opin. Struct. Biol. (1999) 10.1016/s0959-440x(99)80025-6
[12]
Bartels C. J. Phys. Chem. B (1998) 10.1021/jp972280j
[13]
Hukushima K. J. Phys. Soc. Jpn. (1996) 10.1143/jpsj.65.1604
[14]
Replica-exchange molecular dynamics method for protein folding

Yuji Sugita, Yuko Okamoto

Chemical Physics Letters 1999 10.1016/s0009-2614(99)01123-9
[15]
Generalized-ensemble algorithms for molecular simulations of biopolymers

Ayori Mitsutake, Yuji Sugita, Yuko Okamoto

Biopolymers 2001 10.1002/1097-0282(2001)60:2<96::aid-bip1007>3.0.co;2-f
[16]
Stolovitzky G. J. Proc. Natl. Acad. Sci. U.S.A. (2000) 10.1073/pnas.97.21.11164
[17]
Constanciel R. Theor. Chim. Acta (1984) 10.1007/bf02427575
[18]
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii

Di Qiu, Peter S. Shenkin, Frank P. Hollinger et al.

The Journal of Physical Chemistry A 1997 10.1021/jp961992r
[19]
Still W. C. J. Am. Chem. Soc. (1990) 10.1021/ja00172a038
[20]
Pairwise solute descreening of solute charges from a dielectric medium

Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar

Chemical Physics Letters 1995 10.1016/0009-2614(95)01082-k
[21]
Edinger S. R. J. Phys. Chem. B (1997) 10.1021/jp962156k
[22]
Dominy B. H. J. Phys. Chem. B (1999) 10.1021/jp984440c
[23]
Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects

Jayashree Srinivasan, Megan W. Trevathan, Paul Beroza et al.

Theoretical Chemistry Accounts 1999 10.1007/s002140050460
[24]
Bursulaya B. D. J. Am. Chem. Soc. (1999) 10.1021/ja991764l
[25]
MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y, Karplus, M.CHARMM:The Encyclopedia of ComputationalChemistry; Schleyer, P. R., Eds.; John Wiley & Sons:  New York, 1998; Vol. 1, p 271.
[26]
Cramer C. J. Chem. Rev. (1999) 10.1021/cr960149m
[27]
Generalized Born Models of Macromolecular Solvation Effects

Donald Bashford, David A. Case

Annual Review of Physical Chemistry 2000 10.1146/annurev.physchem.51.1.129
[28]
Zerella R. Protein Sci. (2000) 10.1110/ps.9.11.2142
[29]
A short linear peptide that folds into a native stable β-hairpin in aqueous solution

Francisco J. Blanco, Germán Rivas, Luis Serrano

Nature Structural &amp; Molecular Biology 1994 10.1038/nsb0994-584
[30]
Folding dynamics and mechanism of β-hairpin formation

Victor Muñoz, Peggy A. Thompson, James Hofrichter et al.

Nature 1997 10.1038/36626
[31]
Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G

Vijay S. Pande, Daniel S. Rokhsar

Proceedings of the National Academy of Sciences 1999 10.1073/pnas.96.16.9062
[32]
Mechanisms and kinetics of β-hairpin formation

Dmitri K. Klimov, D. Thirumalai

Proceedings of the National Academy of Sciences 2000 10.1073/pnas.97.6.2544
[33]
A molecular dynamics study of the 41‐56 β‐hairpin from B1 domain of protein G

Danilo Roccatano, Andrea Amadei, Alfredo Di Nola et al.

Protein Science 1999 10.1110/ps.8.10.2130
[34]
Exploring the energy landscape of a ? hairpin in explicit solvent

Angel E. Garc�a, Kevin Y. Sanbonmatsu

Proteins: Structure, Function, and Bioinformatics 10.1002/1097-0134(20010215)42:3<345::aid-prot50>3.0.co;2-h
[35]
Lee J. Biophys. J. (2001) 10.1016/s0006-3495(01)75896-1
[36]
de Alba E. Protein Sci. (1999) 10.1110/ps.8.4.854
[37]
De Novo Protein Design: Fully Automated Sequence Selection

Bassil I. Dahiyat, Stephen L. Mayo

Science 1997 10.1126/science.278.5335.82
[38]
DeGrado W. F. Science (1997) 10.1126/science.278.5335.80
[39]
β-hairpin folding simulations in atomistic detail using an implicit solvent model 1 1Edited by F. Cohen

Bojan Zagrovic, Eric J Sorin, Vijay Pande

Journal of Molecular Biology 2001 10.1006/jmbi.2001.5033
[40]
Zhou R. Proc. Natl. Acad. Sci. U.S.A. (2001)
[41]
Jorgensen W. L. J. Am. Chem. Soc. (1988) 10.1021/ja00214a002
[42]
Screen Savers of the World Unite!

Michael Shirts, Vijay S. Pande

Science 2001 10.1126/science.290.5498.1903
[43]
Ferrara P. Proc. Natl. Acad. Sci. U.S.A. (2000) 10.1073/pnas.190324897
[44]
Wang H. J. Am. Chem. Soc. (2000) 10.1021/ja992359x
[45]
Sung S. S. Biophys. J. (1994)
[46]
Solvation energy in protein folding and binding

David Eisenberg, Andrew D. McLachlan

Nature 1986 10.1038/319199a0
[47]
Derreumaux P. J. Chem. Phys. (1999) 10.1063/1.479501
[48]
Pak Y. J. Chem. Phys. (1999) 10.1063/1.480270
[49]
Chem. Eng. News (2001)
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Citations
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References
Details
Published
Apr 17, 2002
Vol/Issue
124(18)
Pages
4976-4977
Cite This Article
Soonmin Jang, Seokmin Shin, Youngshang Pak (2002). Molecular Dynamics Study of Peptides in Implicit Water:  Ab Initio Folding of β-Hairpin, β-Sheet, and ββα-motif. Journal of the American Chemical Society, 124(18), 4976-4977. https://doi.org/10.1021/ja025675b
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