Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins
| Autor: | Akifumi Oda, Tomoki Nakayoshi, Shuichi Fukuyoshi, Koichi Kato, Eiji Kurimoto |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Models Molecular Protein Conformation Pharmaceutical Science Peptide Protein Structure Secondary Article Analytical Chemistry lcsh:QD241-441 03 medical and health sciences Molecular dynamics Structure-Activity Relationship Protein structure lcsh:Organic chemistry Computational chemistry Drug Discovery Physical and Theoretical Chemistry Protein secondary structure chemistry.chemical_classification Chemistry Organic Chemistry Equations of motion Proteins secondary structure Protein structure prediction Test protein molecular dynamics simulation protein structure prediction replica exchange molecular dynamics Molecular Weight 030104 developmental biology Chemistry (miscellaneous) Molecular Medicine Biological system |
| Zdroj: | Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry Molecules; Volume 22; Issue 10; Pages: 1716 Molecules, Vol 22, Iss 10, p 1716 (2017) |
| ISSN: | 1420-3049 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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