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Nucleic Acids Research 2004 32(17):5147-5162; doi:10.1093/nar/gkh785
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Published online 30 September 2004

Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved

A new hydrogen-bonding potential for the design of protein–RNA interactions predicts specific contacts and discriminates decoys

Yu Chen1, Tanja Kortemme2, Tim Robertson2, David Baker2 and Gabriele Varani1,2,*

1 Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA and 2 Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195-7350, USA

* To whom correspondence should be addressed. Tel: +1 206 543 7113; Fax: +1 206 685 8665; Email: varani{at}chem.washington.edu

Received June 5, 2004; Revised July 21, 2004; Accepted August 3, 2004

RNA-binding proteins play many essential roles in the regulation of gene expression in the cell. Despite the significant increase in the number of structures for RNA–protein complexes in the last few years, the molecular basis of specificity remains unclear even for the best-studied protein families. We have developed a distance and orientation-dependent hydrogen-bonding potential based on the statistical analysis of hydrogen-bonding geometries that are observed in high-resolution crystal structures of protein–DNA and protein–RNA complexes. We observe very strong geometrical preferences that reflect significant energetic constraints on the relative placement of hydrogen-bonding atom pairs at protein–nucleic acid interfaces. A scoring function based on the hydrogen-bonding potential discriminates native protein–RNA structures from incorrectly docked decoys with remarkable predictive power. By incorporating the new hydrogen-bonding potential into a physical model of protein–RNA interfaces with full atom representation, we were able to recover native amino acids at protein–RNA interfaces.


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