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Protein surface analysis for function annotation in high‐throughput structural genomics pipeline
Author(s) -
Binkowski T. Andrew,
Joachimiak Andrzej,
Liang Jie
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.051759005
Subject(s) - structural genomics , computational biology , biology , comparative genomics , functional genomics , protein domain , sequence alignment , peptide sequence , protein structure , genomics , structural biology , structural similarity , genetics , biochemistry , gene , genome
Abstract 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 ( p ocket and v oid S urface of A mino Acid R esidues), 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.

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