title: Functional classification of protein 3D structures from predicted local interaction sites.
abstract: A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.
authors.affiliation: Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.
authors.forename: Ramya
authors.initials: R
authors.lastname: Parasuram
authors.forename: Joslynn S
authors.initials: JS
authors.lastname: Lee
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Yin
authors.forename: Srinivas
authors.initials: S
authors.lastname: Somarowthu
authors.forename: Mary Jo
authors.initials: MJ
authors.lastname: Ondrechen
mesh_terms: D000818:Animals; D001185:Artificial Intelligence; D001426:Bacterial Proteins / Q000737:chemistry; D001441:Bacteroides fragilis / Q000201:enzymology; D002238:Carbohydrate Epimerases / Q000737:chemistry; D020134:Catalytic Domain; D019295:Computational Biology; D004746:Enoyl-CoA Hydratase / Q000737:chemistry; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry; D008958:Models, Molecular; D010963:Plasmodium falciparum / Q000201:enzymology; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D040901:Proteomics / Q000706:statistics & numerical data; D015800:Protozoan Proteins / Q000737:chemistry; D012984:Software; D055672:Static Electricity; D048372:Streptomyces coelicolor / Q000201:enzymology; D040681:Structural Homology, Protein
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D015800:Protozoan Proteins; D005087:Glucan 1,4-alpha-Glucosidase; D004746:Enoyl-CoA Hydratase; D002238:Carbohydrate Epimerases; C022553:ribulosephosphate 3-epimerase