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PMID: 8433995 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 90 ·No. 4 ·1993-02-15 ·Pages 1379-83

Wilmanns M, Eisenberg D

Abstract

The three-dimensional profile method expresses the three-dimensional structure of a protein as a table, the profile, which represents the local environment of each residue. The score of an amino acid sequence, aligned with the three-dimensional profile, reflects its compatibility with the profiled structure. In the original implementation, each local environment was characterized by its polarity, the area buried of its side chain, and its secondary structure. Here we describe a modified three-dimensional profile algorithm that characterizes the local environment in terms of the statistical preferences of the profiled residue for neighbors of specific residue types, main-chain conformations, or secondary structure. Combined profiles of the original and the three new types were tested on beta/alpha-barrel protein structures. The method identified the following enzymes of unknown three-dimensional structure as probable beta/alpha-barrels, all of which catalyze reactions in the biosynthesis of aromatic amino acids: anthranilate phosphoribosyltransferase (trpD), glutamine amidotransferase (trpG), and phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA).

MeSH Terms
Aldose-Ketose Isomerases Algorithms Amino Acid Sequence Anthranilate Phosphoribosyltransferase/chemistry Anthranilate Synthase Databases, Factual Enzymes/chemistry Isomerases/chemistry Models, Molecular Nitrogenous Group Transferases Protein Conformation Protein Folding Protein Structure, Secondary Proteins/chemistry Transferases/chemistry
Chemicals
Enzymes Proteins Transferases Anthranilate Phosphoribosyltransferase Nitrogenous Group Transferases Anthranilate Synthase anthranilate synthase, glutamine amidotransferase subunit Isomerases Aldose-Ketose Isomerases Phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Wilmanns M
Molecular Biology Institute, University of California, Los Angeles 90024-1570.
Eisenberg D
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28 references, click to expand
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.90.4.1379
Published
1993-02-15
Pages
1379-83
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC45876
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.90.4.1379 PMC Full Text View journal details
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