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Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model

Ofer Rahat¹, Uri Alon², Yaakov Levy³, & Gideon Schreiber¹

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1. Weizmann Institute of Science, Biological Chemistry
2. Weizmann Institute of Science, Molecular Cell Biology
3. Weizmann Institute of Science, Department of Structural Biology

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Document Type:

Manuscript

Date:

Received 04 January 2008 13:12 UTC; Posted 04 January 2008

Subjects:

Biotechnology, Bioinformatics

Tags:

• Network motifs analysis
• X-ray crystallography
• molecular dynamics simulations
• protein contact map patterns
• NMR

Abstract:

Proteins are built from basic structural elements and their systematic characterization is of interest. Searching for recurring patterns in protein contact maps, we found several network motifs, patterns that occur more frequently in experimentally determined protein contact maps than in randomized contact maps with the same properties. Some of these network motifs correspond to sub-structures of alpha helices, including topologies not previously recognized in this context. Other motifs characterize beta-sheets, again some of which appear to be novel. This topological characterization of patterns serves as a tool to characterize proteins, and to reveal a high detailed differences map for comparing protein structures solved by X-ray crystallography, NMR and molecular dynamics (MD) simulations. Both NMR and MD show small but consistent differences from the crystal structures of the same proteins, possibly due to the pair-wise energy functions used. Network motifs analysis can serve as a base for many-body energy statistical energy potential, and suggests a dictionary of basic elements of which protein secondary structure is made.

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Rahat, Ofer, Alon, Uri, Levy, Yaakov, and Schreiber, Gideon. Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1490.1> (2008)

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