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Protein surface analysis for function annotation in high-throughput structural genomics pipeline

¹ Structural Biology Center & Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
² Department of Bioengineering, The University of Illinois at Chicago, Chicago, Illinois 60607-7052, USA

(RECEIVED August 5, 2005; FINAL REVISION September 16, 2005; ACCEPTED September 16, 2005)

Structural genomics (SG) initiatives are expanding the universe of protein fold space by rapidly determining structures of proteins that were intentionally selected on the basis of low sequence similarity to proteins of known structure. Often these proteins have no associated biochemical or cellular functions. The SG success has resulted in an accelerated deposition of novel structures. In some cases the structural bioinformatics analysis applied to these novel structures has provided specific functional assignment. However, this approach has also uncovered limitations in the functional analysis of uncharacterized proteins using traditional sequence and backbone structure methodologies. A novel method, named pvSOAR (pocket and void Surface of Amino Acid Residues), of comparing the protein surfaces of geometrically defined pockets and voids was developed. pvSOAR was able to detect previously unrecognized and novel functional relationships between surface features of proteins. In this study, pvSOAR is applied to several structural genomics proteins. We examined the surfaces of YecM, BioH, and RpiB from Escherichia coli as well as the CBS domains from inosine-5'-monosphate dehydrogenase from Streptococcus pyogenes, conserved hypothetical protein Ta549 from Thermoplasm acidophilum, and CBS domain protein mt1622 from Methanobacterium thermoautotrophicum with the goal to infer information about their biochemical function.

Keywords: structural genomics; protein surface; surface pattern; protein function; pocket sequence; pocket shape; surface matching; functional genomics

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051759005.

Reprint requests to: Jie Liang, Department of Bioengineering, The University of Illinois, 851 South Morgan St., Room 218, Chicago, IL 60607, USA; e-mail: jliang{at}uic.edu; fax: (312) 996-5921.

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