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Author, Editor(s)

Author(s):

Zhu, Hongbo
Sommer, Ingolf
Lengauer, Thomas
Domingues, Francisco S.

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BibTeX cite key*:

Zhu2008

Title

Title*:

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces


Zhu2008.pdf (303.07 KB)

Journal

Journal Title*:

PLoS ONE

Journal's URL:

http://www.plosone.org/home.action

Download URL
for the article:

http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=0A3D7EC41A43F97C3C099904D033004B?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0001926&representation=PDF

Language:

English

Publisher

Publisher's
Name:

Public Library of Science

Publisher's URL:

http://www.plos.org/

Publisher's
Address:

San Francisco

ISSN:

1932-6203

Vol, No, pp, Date

Volume*:

3

Number:

4

Publishing Date:

April 2008

Pages*:

e1926

Number of
VG Pages:

23

Page Start:

1

Page End:

9

Sequence Number:


DOI:

10.1371/journal.pone.0001926

Note, Abstract, ©

Note:


(LaTeX) Abstract:

Background
The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces.

Methodology/Principal Findings
Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions.

Conclusions/Significance
The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

URL for the Abstract:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001926

Categories,
Keywords:


HyperLinks / References / URLs:


Copyright Message:

Copyright: © 2008 Zhu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Personal Comments:


Download
Access Level:

Public

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort


BibTeX Entry:

@ARTICLE{Zhu2008,
AUTHOR = {Zhu, Hongbo and Sommer, Ingolf and Lengauer, Thomas and Domingues, Francisco S.},
TITLE = {Alignment of Non-Covalent Interactions at Protein-Protein Interfaces},
JOURNAL = {PLoS ONE},
PUBLISHER = {Public Library of Science},
YEAR = {2008},
NUMBER = {4},
VOLUME = {3},
PAGES = {e1926},
ADDRESS = {San Francisco},
MONTH = {April},
ISBN = {1932-6203},
DOI = {10.1371/journal.pone.0001926},
}


Entry last modified by Ruth Schneppen-Christmann, 03/03/2009
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Editor(s)
Hongbo Zhu
Created
11/18/2008 02:14:18 PM
Revisions
8.
7.
6.
5.
4.
Editor(s)
Ruth Schneppen-Christmann
Francisco S. Domingues
Francisco S. Domingues
Francisco S. Domingues
Francisco S. Domingues
Edit Dates
22.01.2009 14:39:09
01/13/2009 11:02:22 AM
01/13/2009 11:00:41 AM
01/13/2009 11:00:17 AM
01/13/2009 10:59:51 AM
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