Peptide folding driven by Van der Waals interactions

Shen‐Shu Sung

doi:10.1002/pro.2710

journal article Jun 11, 2015

Peptide folding driven by Van der Waals interactions

Shen‐Shu Sung

Protein Science Vol. 24 No. 9 pp. 1383-1388 · Wiley

View at Publisher Save 10.1002/pro.2710

Abstract

AbstractContrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin‐like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide‐solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge‐charge interactions, these simulation results will give us a new view of the folding mechanism.

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References

25

[1]

The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain

Linus Pauling, Robert B. Corey, H. R. Branson

Proceedings of the National Academy of Sciences 10.1073/pnas.37.4.205

[2]

Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds

Linus Pauling, Robert B. Corey

Proceedings of the National Academy of Sciences 10.1073/pnas.37.11.729

[3]

Nelson DL (2008)

[4]

Berg JM. (2002)

[5]

Van Der Waals Interaction and the Stability of Helical Polypeptide Chains

P. DE SANTIS, E. GIGLIO, A. M. Liquori et al.

Nature 10.1038/206456a0

[6]

10.1073/pnas.1414556111

[7]

10.1021/j100262a010

[8]

Fine Structure Analysis of a Protein Folding Transition State; Distinguishing Between Hydrophobic Stabilization and Specific Packing

Burcu Anil, Satoshi Sato, Jae-Hyun Cho et al.

Journal of Molecular Biology 10.1016/j.jmb.2005.08.054

[9]

10.1073/pnas.1012668108

[10]

Schulz GE (1990)

[11]

10.1016/s0006-3495(94)80973-7

[12]

10.1021/ja992359x

[13]

A neutral, water-soluble, .alpha.-helical peptide: the effect of ionic strength on the helix-coil equilibrium

J. Martin Scholtz, Eunice J. York, John M. Stewart et al.

Journal of the American Chemical Society 10.1021/ja00013a079

[14]

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 10.1021/ja00124a002

[15]

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 of molecules

David A. Pearlman, David A. Case, James W. Caldwell et al.

Computer Physics Communications 10.1016/0010-4655(95)00041-d

[16]

Molecular dynamics simulations of helix denaturation

Valerie Daggett, Michael Levitt

Journal of Molecular Biology 10.1016/0022-2836(92)90264-k

[17]

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

Robert B. Best, Gerhard Hummer

The Journal of Physical Chemistry B 10.1021/jp901540t

[18]

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 10.1002/jcc.540040211

[19]

Scalable molecular dynamics with NAMD

James C. Phillips, Rosemary Braun, Wei Wang et al.

Journal of Computational Chemistry 10.1002/jcc.20289

[20]

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten

Journal of Molecular Graphics 10.1016/0263-7855(96)00018-5

[21]

10.1021/ja00066a092

[22]

Direct Observation of the Folding and Unfolding of a β-Hairpin in Explicit Water through Computer Simulation

Xiongwu Wu, Shaomeng Wang, Bernard R. Brooks

Journal of the American Chemical Society 10.1021/ja0257321

[23]

Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search

Xiongwu Wu, Shaomeng Wang

The Journal of Physical Chemistry B 10.1021/jp9817372

[24]

The Protein Folding Problem

Ken A. Dill, S. Banu Ozkan, M. Scott Shell et al.

Annual Review of Biophysics 10.1146/annurev.biophys.37.092707.153558

[25]

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 10.1016/0021-9991(77)90098-5

Metrics

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Citations

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References

Details

Published: Jun 11, 2015
Vol/Issue: 24(9)
Pages: 1383-1388
License: View

Authors

S

Shen‐Shu Sung

Department of Pharmacology, College of Medicine Penn State University Hershey Pennsylvania 17033

Funding

College of Medicine, Penn State University

Cite This Article

Shen‐Shu Sung (2015). Peptide folding driven by Van der Waals interactions. Protein Science, 24(9), 1383-1388. https://doi.org/10.1002/pro.2710

Peptide folding driven by Van der Waals interactions

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