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Bioinformatics Advance Access originally published online on September 18, 2009
Bioinformatics 2009 25(22):2921-2928; doi:10.1093/bioinformatics/btp541
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Understanding hydrogen-bond patterns in proteins using network motifs

Ofer Rahat 1, Uri Alon 2, Yaakov Levy 3,* and Gideon Schreiber 1,*

1Department of Biological Chemistry, 2Department of Molecular Cell Biology and 3Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel

*To whom correspondence should be addressed.


  Abstract

Summary: Protein structures can be viewed as networks of contacts (edges) between amino-acid residues (nodes). Here we dissect proteins into sub-graphs consisting of six nodes and their corresponding edges, with an edge being either a backbone hydrogen bond (H-bond) or a covalent interaction. Six thousand three hundred and twenty-two such sub-graphs were found in a large non-redundant dataset of high-resolution structures, from which 35 occur much more frequently than in a random model. Many of these significant sub-graphs (also called network motifs) correspond to sub-structures of {alpha} helices and β-sheets, as expected. However, others correspond to more exotic sub-structures such as 310 helix, Schellman motif and motifs that were not defined previously. This topological characterization of patterns is very useful for producing a detailed differences map to compare protein structures. Here we analyzed in details the differences between NMR, molecular dynamics (MD) simulations and X-ray structures for Lysozyme, SH3 and the lambda repressor. In these cases, the same structures solved by NMR and simulated by MD showed small but consistent differences in their motif composition from the crystal structures, despite a very small root mean square deviation (RMSD) between them. This may be due to differences in the pair-wise energy functions used and the dynamic nature of these proteins.

Availability: A web-based tool to calculate network motifs is available at http://bioinfo.weizmann.ac.il/protmot/.

Contact: gideon.schreiber{at}weizmann.ac.il; koby.levy{at}weizmann.ac.il

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on January 25, 2009; revised on September 8, 2009; accepted on September 10, 2009

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