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Molecules 2017, 22(10), 1716; doi:10.3390/molecules22101716

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins

1
Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan
2
Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
3
Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
4
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
*
Author to whom correspondence should be addressed.
Received: 20 September 2017 / Revised: 5 October 2017 / Accepted: 10 October 2017 / Published: 12 October 2017
(This article belongs to the Section Green Chemistry)
View Full-Text   |   Download PDF [4890 KB, uploaded 13 October 2017]   |  

Abstract

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton’s equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10–46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10–34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems. View Full-Text
Keywords: molecular dynamics simulation; protein structure prediction; replica exchange molecular dynamics; secondary structure molecular dynamics simulation; protein structure prediction; replica exchange molecular dynamics; secondary structure
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Kato, K.; Nakayoshi, T.; Fukuyoshi, S.; Kurimoto, E.; Oda, A. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins. Molecules 2017, 22, 1716.

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