Catalogo Articoli (Spogli Riviste)

OPAC HELP

Titolo:
A GRAPH-THEORETIC APPROACH TO THE IDENTIFICATION OF 3-DIMENSIONAL PATTERNS OF AMINO-ACID SIDE-CHAINS IN PROTEIN STRUCTURES
Autore:
ARTYMIUK PJ; POIRRETTE AR; GRINDLEY HM; RICE DW; WILLETT P;
Indirizzi:
UNIV SHEFFIELD,KREBS INST BIOMOLEC RES,DEPT MOLEC BIOL & BIOTECHNOL,WESTERN BANK SHEFFIELD S10 2TN S YORKSHIRE ENGLAND UNIV SHEFFIELD,KREBS INST BIOMOLEC RES,DEPT INFORMAT STUDIES SHEFFIELD S10 2TN S YORKSHIRE ENGLAND
Titolo Testata:
Journal of Molecular Biology
fascicolo: 2, volume: 243, anno: 1994,
pagine: 327 - 344
SICI:
0022-2836(1994)243:2<327:AGATTI>2.0.ZU;2-T
Fonte:
ISI
Lingua:
ENG
Soggetto:
PHOTOSYNTHETIC REACTION CENTER; PORCINE PANCREATIC ELASTASE; REFINED CRYSTAL-STRUCTURE; VISION-BASED TECHNIQUE; CARBOXYPEPTIDASE-A; CRYSTALLOGRAPHIC REFINEMENT; ALPHA-CHYMOTRYPSIN; SERINE PROTEASE; RHODOPSEUDOMONAS-VIRIDIS; SUBTILISIN CARLSBERG;
Keywords:
GRAPH THEORY; STRUCTURAL COMPARISON; SIDE-CHAIN; CATALYTIC TRIAD; SERINE PROTEASES;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Citazioni:
80
Recensione:
Indirizzi per estratti:
Citazione:
P.J. Artymiuk et al., "A GRAPH-THEORETIC APPROACH TO THE IDENTIFICATION OF 3-DIMENSIONAL PATTERNS OF AMINO-ACID SIDE-CHAINS IN PROTEIN STRUCTURES", Journal of Molecular Biology, 243(2), 1994, pp. 327-344

Abstract

This paper discusses the use of graph-theoretic methods for the representation and searching of three-dimensional patterns of side-chains in protein structures. The position of a side-chain is represented by pseudo-atoms, and the relative positions of pairs of side-chains by thedistances between them. This description of the geometry can be represented by a labelled graph in which the nodes and the edges of the graph represent the pseudo-atoms and the sets of inter-pseudo-atomic distances, respectively. Given such a representation, a protein can be searched for the presence of a user-defined query pattern of side-chains by means of a subgraph-isomorphism algorithm which is implemented in the program ASSAM. Experiments with one such algorithm, that due to Ullmann, show that it provides both an effective and a highly efficient way of searching for patterns of side-chains. The method is illustratedby searches for the serine protease catalytic triad, for residues involved in the catalytic activity of staphyloccocal nuclease, and for the zinc-binding side-chains of thermolysin. The catalytic triad patternsearch revealed the existence of a second Asp-His-Ser triad-like arrangement of residues in trypsinogen and chymotrypsinogen, in addition to the catalytic residues. In addition the program can be used to search for hypothetical patterns, as is shown for a pattern of three tryptophan side-chains. These searches demonstrate that the search algorithmcan successfully retrieve the great majority of the expected proteins, as well as other, previously unreported proteins that contain the. pattern of interest.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 28/11/20 alle ore 04:18:34