Skip Navigation


Bioinformatics Advance Access originally published online on January 15, 2009
Bioinformatics 2009 25(5):628-635; doi:10.1093/bioinformatics/btp032
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
25/5/628    most recent
btp032v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Nishima, W.
Right arrow Articles by Kitao, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nishima, W.
Right arrow Articles by Kitao, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins

Wataru Nishima 1, Guoying Qi 2, Steven Hayward 2,3 and Akio Kitao 4,5,*

1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Japan, 2School of Computing Sciences, 3School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 4Institute of Molecular and Cellular Biosciences, The University of Tokyo and 5JST, CREST, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan

*To whom correspondence should be addressed.


  Abstract

Motivation: The biological function of proteins is associated with a variety of motions, ranging from global domain motion to local motion of side chain. We propose a method, dihedral transition analysis (DTA), to identify significant dihedral angle changes between two distinct protein conformations and for characterization of the effect of these transitions on both local and global conformation.

Results: Applying DTA to a comprehensive and non-redundant dataset of 459 high-resolution pairs of protein structures, we found that a dihedral transition occurs in 82% of proteins. Multiple dihedral transitions are shown to occur cooperatively along the sequence, which allows us to separate a polypeptide chain into fragments with and without transitions, namely transition fragments (TFs) and stable fragments (SFs), respectively. By characterizing the magnitude of TF conformational change and the effect of the transition on the neighboring fragments, flap and hinge motions are identified as typical motions. DTA is also useful to detect protein motions, subtle in RMSD but significant in terms of dihedral angle changes, such as the peptide-plane flip, the side-chain flip and path-preserving motions. We conclude that DTA is a useful tool to extract potential functional motions, some of which might have been missed using conventional methods for protein motion analysis.

Availability: http://dynamics.iam.u-tokyo.ac.jp/DTA/

Contact: kitao{at}iam.u-tokyo.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on November 4, 2008; revised on December 25, 2008; accepted on January 10, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.