journal article May 18, 2002

Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent

View at Publisher Save 10.1021/ja025789n
Topics

No keywords indexed for this article. Browse by subject →

References
46
[1]
Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between the chain ends

Elisha Haas, Ephraim Katchalski‐Katzir, Izchak Z. Steinberg

Biopolymers 1978 10.1002/bip.1978.360170103
[2]
Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding.

S J Hagen, James Hofrichter, A Szabo et al.

Proceedings of the National Academy of Sciences 1996 10.1073/pnas.93.21.11615
[3]
Peptide Conformational Dynamics and Vibrational Stark Effects Following Photoinitiated Disulfide Cleavage

Martin Volk, Yuriy Kholodenko, Helen S. M. Lu et al.

The Journal of Physical Chemistry B 1997 10.1021/jp971951a
[4]
Bonnet G. Proc. Natl. Acad. Sci. U.S.A. (1998) 10.1073/pnas.95.15.8602
[5]
The speed limit for protein folding measured by triplet–triplet energy transfer

Oliver Bieri, Jakob Wirz, Bruno Hellrung et al.

Proceedings of the National Academy of Sciences 1999 10.1073/pnas.96.17.9597
[6]
McGimpsey W. G. J. Phys. Chem. A (1999) 10.1021/jp9901592
[7]
Lapidus L. J. Proc. Natl. Acad. Sci. U.S.A. (2000) 10.1073/pnas.97.13.7220
[8]
Wallace M. I. Proc. Natl. Acad. Sci. U.S.A. (2001) 10.1073/pnas.101523498
[9]
Hagen S. J. J. Mol. Biol. (2001) 10.1006/jmbi.2000.4366
[10]
Hudgins R. R. J. Am. Chem. Soc. (2002) 10.1021/ja010493n
[11]
First passage time approach to diffusion controlled reactions

Attila Szabo, Klaus Schulten, Zan Schulten

The Journal of Chemical Physics 1980 10.1063/1.439715
[12]
Zwanzig R. Proc. Natl. Acad. Sci. U.S.A. (1988) 10.1073/pnas.85.7.2029
[13]
Zhou H. X. Biophys. J. (1996) 10.1016/s0006-3495(96)79437-7
[14]
Diffusion limited first contact of the ends of a polymer: Comparison of theory with simulation

Richard W. Pastor, Robert Zwanzig, Attila Szabo

The Journal of Chemical Physics 1996 10.1063/1.472208
[15]
Thirumalai D. J. Phys. Chem. B (1999) 10.1021/jp982362n
[16]
Klenin K. V. J. Chem. Phys. (2001) 10.1063/1.1350579
[17]
Dua A. J. Chem. Phys. (2002) 10.1063/1.1423937
[18]
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly et al.

Journal of the American Chemical Society 1995 10.1021/ja00124a002
[19]
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

A. D. Mackerell, D. Bashford, M. Bellott et al.

The Journal of Physical Chemistry B 1998 10.1021/jp973084f
[20]
Comparison of simple potential functions for simulating liquid water

William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura et al.

The Journal of Chemical Physics 1983 10.1063/1.445869
[21]
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

Tom Darden, Darrin York, Lee G. Pedersen

The Journal of Chemical Physics 1993 10.1063/1.464397
[22]
A smooth particle mesh Ewald method

Ulrich Essmann, Lalith Perera, Max L. Berkowitz et al.

The Journal of Chemical Physics 1995 10.1063/1.470117
[23]
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J.C Berendsen

Journal of Computational Physics 1977 10.1016/0021-9991(77)90098-5
[24]
Molecular dynamics with coupling to an external bath

H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren et al.

The Journal of Chemical Physics 1984 10.1063/1.448118
[26]
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson et al.

Journal of Computational Chemistry 1983 10.1002/jcc.540040211
[27]
NAMD2: Greater Scalability for Parallel Molecular Dynamics

Laxmikant Kalé, Robert Skeel, Milind Bhandarkar et al.

Journal of Computational Physics 1999 10.1006/jcph.1999.6201
[28]
MOLMOL: A program for display and analysis of macromolecular structures

Reto Koradi, Martin Billeter, Kurt Wüthrich

Journal of Molecular Graphics 1996 10.1016/0263-7855(96)00009-4
[29]
Durell S. R. J. Phys. Chem. (1994) 10.1021/j100059a038
[30]
Feller S. E. J. Phys. Chem. (1996) 10.1021/jp9614658
[31]
The Role of Solvent Viscosity in the Dynamics of Protein Conformational Changes

Anjum Ansari, C M Jones, Eric R. Henry et al.

Science 1992 10.1126/science.1615323
[32]
Viscosity Dependence of the Folding Rates of Proteins

Dmitri K. Klimov, D. Thirumalai

Physical Review Letters 1997 10.1103/physrevlett.79.317
[33]
Portman J. J. J. Chem. Phys. (2001) 10.1063/1.1334663
[34]
Samuelson S. J. Phys. Chem. B (1997) 10.1021/jp9704269
[35]
Wilemski G. J. Chem. Phys. (1974) 10.1063/1.1681162
[36]
Bicout D. J. J. Chem. Phys. (1997) 10.1063/1.474066
[37]
Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor.

C J Camacho, D Thirumalai

Proceedings of the National Academy of Sciences 1995 10.1073/pnas.92.5.1277
[38]
Lapidus L. J. Phys. Rev. Lett. (2001) 10.1103/physrevlett.87.258101
[39]
Bicout D. J. J. Chem. Phys. (1998) 10.1063/1.476800
[40]
Lapidus L. J. (2002)
[41]
Large-amplitude nonlinear motions in proteins

Angel E. Garcia

Physical Review Letters 1992 10.1103/physrevlett.68.2696
[42]
Helix nucleation kinetics from molecular simulations in explicit solvent

Gerhard Hummer, Angel E. Garcia, Shekhar Garde

Proteins: Structure, Function, and Bioinformatics 10.1002/1097-0134(20010101)42:1<77::aid-prot80>3.0.co;2-#
[43]
Jeppesen C. Science (2001) 10.1126/science.293.5529.465
[44]
Reversible peptide folding in solution by molecular dynamics simulation 1 1Edited by R. Huber

Xavier Daura, Bernhard Jaun, Dieter Seebach et al.

Journal of Molecular Biology 1998 10.1006/jmbi.1998.1885
[45]
Daura X. J. Am. Chem. Soc. (2001) 10.1021/ja003689g
[46]
Hummer G. Phys. Rev. Lett. (2000) 10.1103/physrevlett.85.2637
Cited By
109
Physical Chemistry Chemical Physics
Progress in Nuclear Magnetic Resona...
Proceedings of the National Academy...
Annual Reports in Computational Che...
The Journal of Physical Chemistry B
The Journal of Physical Chemistry A
Journal of Chemical Theory and Comp...
Biophysical Journal
Are Current Molecular Dynamics Force Fields too Helical?

Robert B. Best, Nicolae-Viorel Buchete · 2008

Biophysical Journal
Annual Review of Physical Chemistry
Journal of Computational Chemistry
Biophysical Journal
Insight into the role of hydration on protein dynamics

Donald Hamelberg, Tongye Shen · 2006

The Journal of Chemical Physics
Chemical Physics
AIChE Journal
Angewandte Chemie International Edi...
Metrics
109
Citations
46
References
Details
Published
May 18, 2002
Vol/Issue
124(23)
Pages
6563-6568
Cite This Article
In-Chul Yeh, Gerhard Hummer (2002). Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent. Journal of the American Chemical Society, 124(23), 6563-6568. https://doi.org/10.1021/ja025789n
Related

You May Also Like

Preparation of Graphitic Oxide

William S. Hummers, Richard E. Offeman · 1958

28,428 citations

Adsorption of Gases in Multimolecular Layers

Stephen Brunauer, P. H. Emmett · 1938

24,134 citations

Organometal Halide Perovskites as Visible-Light Sensitizers for Photovoltaic Cells

Akihiro Kojima, Kenjiro Teshima · 2009

21,478 citations