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Titolo:
3-DIMENSIONAL, SEQUENCE ORDER-INDEPENDENT STRUCTURAL COMPARISON OF A SERINE-PROTEASE AGAINST THE CRYSTALLOGRAPHIC DATABASE REVEALS ACTIVE-SITE SIMILARITIES - POTENTIAL IMPLICATIONS TO EVOLUTION AND TO PROTEIN-FOLDING
Autore:
FISCHER D; WOLFSON H; LIN SL; NUSSINOV R;
Indirizzi:
NCI,FREDERICK CANC RES FACIL,PRI DYNCORP,MATH BIOL LAB,BLDG 469,ROOM 151 FREDERICK MD 21702 NCI,FREDERICK CANC RES FACIL,PRI DYNCORP,MATH BIOL LAB FREDERICK MD 21702 TEL AVIV UNIV,SCH MATH SCI,DEPT COMP SCI IL-69978 TEL AVIV ISRAEL TEL AVIV UNIV,FAC MED,SACKLER INST MOLEC MED IL-69978 TEL AVIV ISRAEL
Titolo Testata:
Protein science
fascicolo: 5, volume: 3, anno: 1994,
pagine: 769 - 778
SICI:
0961-8368(1994)3:5<769:3SOSCO>2.0.ZU;2-Z
Fonte:
ISI
Lingua:
ENG
Soggetto:
RESOLUTION; MOTIFS; REFINEMENT; CRYSTAL;
Keywords:
COMPUTER VISION; PROTEASE ACTIVE SITES; PROTEIN DATABASE STRUCTURAL COMPARISON; PROTEIN FOLDING; 3D PROTEIN MOTIFS;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Citazioni:
24
Recensione:
Indirizzi per estratti:
Citazione:
D. Fischer et al., "3-DIMENSIONAL, SEQUENCE ORDER-INDEPENDENT STRUCTURAL COMPARISON OF A SERINE-PROTEASE AGAINST THE CRYSTALLOGRAPHIC DATABASE REVEALS ACTIVE-SITE SIMILARITIES - POTENTIAL IMPLICATIONS TO EVOLUTION AND TO PROTEIN-FOLDING", Protein science, 3(5), 1994, pp. 769-778

Abstract

We have recently developed a fast approach to comparisons of 3-dimensional structures. Our method is unique, treating protein structures ascollections of unconnected points (atoms) in space. It is completely independent of the amino acid sequence order. It is unconstrained by insertions, deletions, and chain directionality. It matches single, isolated amino acids between 2 different structures strictly by their spatial positioning regardless of their relative sequential position in the amino acid chain. It automatically detects a recurring 3D motif in protein molecules. No predefinition of the motif is required. The motif can be either in the interior of the proteins or on their surfaces. In this work, we describe an enhancement over our previously developedtechnique, which considerably reduces the complexity of the algorithm. This results in an extremely fast technique. A typical pairwise comparison of 2 protein molecules requires less than 3 s on a workstation. We have scanned the structural database with dozens of probes, successfully detecting structures that are similar to the probe. To illustrate the power of this method, we compare the structure of a trypsin-like serine protease against the structural database. Besides detecting homologous trypsin-like proteases, we automatically obtain 3D, sequenceorder-independent, active-site similarities with subtilisin-like and sulfhydryl proteases. These similarities equivalence isolated residues, not conserving the linear order of the amino acids in the chains. The active-site similarities are well known and have been detected by manually inspecting the structures in a time-consuming, laborious procedure. This is the first time such equivalences are obtained automatically from the comparison of full structures. The far-reaching advantagesand the implications of our novel algorithm to studies of protein folding, to evolution, and to searches for pharmacophoric patterns are discussed.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 29/11/20 alle ore 02:09:50