Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters
Joint Authors
Shimosato, Taku
Dedachi, Kenichi
Iwaoka, Michio
Minezaki, Toshiya
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-13, 13 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-02-28
Country of Publication
Egypt
No. of Pages
13
Main Subjects
Abstract EN
Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials (ESAAP) and electrostatic (EES) and Lennard-Jones (ELJ) potentials between the amino acid units.
In this study, the SAAP force field (SAAPFF) parameters were improved, and classical canonical Monte Carlo (MC) simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model.
Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin.
The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides.
A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness) was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.
American Psychological Association (APA)
Dedachi, Kenichi& Shimosato, Taku& Minezaki, Toshiya& Iwaoka, Michio. 2013. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters. Journal of Chemistry،Vol. 2013, no. 2013, pp.1-13.
https://search.emarefa.net/detail/BIM-469728
Modern Language Association (MLA)
Dedachi, Kenichi…[et al.]. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters. Journal of Chemistry No. 2013 (2013), pp.1-13.
https://search.emarefa.net/detail/BIM-469728
American Medical Association (AMA)
Dedachi, Kenichi& Shimosato, Taku& Minezaki, Toshiya& Iwaoka, Michio. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters. Journal of Chemistry. 2013. Vol. 2013, no. 2013, pp.1-13.
https://search.emarefa.net/detail/BIM-469728
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-469728