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Titolo:
CONFORMATIONAL-ANALYSIS AND CLUSTERING OF SHORT AND MEDIUM-SIZE LOOPSCONNECTING REGULAR SECONDARY STRUCTURES - A DATABASE FOR MODELING ANDPREDICTION
Autore:
DONATE LE; RUFINO SD; CANARD LHJ; BLUNDELL TL;
Indirizzi:
UNIV LONDON BIRKBECK COLL,DEPT CRYSTALLOG,IMPERIAL CANC RES FUND,UNITSTRUCT MOL BIOL LONDON WC1E 7HX ENGLAND UNIV LONDON BIRKBECK COLL,DEPT CRYSTALLOG,IMPERIAL CANC RES FUND,UNITSTRUCT MOL BIOL LONDON WC1E 7HX ENGLAND
Titolo Testata:
Protein science
fascicolo: 12, volume: 5, anno: 1996,
pagine: 2600 - 2616
SICI:
0961-8368(1996)5:12<2600:CACOSA>2.0.ZU;2-X
Fonte:
ISI
Lingua:
ENG
Soggetto:
ACID SUBSTITUTION TABLES; PROTEIN STRUCTURES; ALPHA-HELICES; GLOBULAR-PROTEINS; DNA RECOGNITION; BETA-HAIRPINS; KEY RESIDUES; BINDING; REGIONS; DESIGN;
Keywords:
LOOP ANALYSIS; BIOLOGICAL FUNCTIONS OF; CLASSES; CONFORMATION; STRUCTURE MODELING AND PREDICTION; PROTEIN SECONDARY STRUCTURE;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Citazioni:
61
Recensione:
Indirizzi per estratti:
Citazione:
L.E. Donate et al., "CONFORMATIONAL-ANALYSIS AND CLUSTERING OF SHORT AND MEDIUM-SIZE LOOPSCONNECTING REGULAR SECONDARY STRUCTURES - A DATABASE FOR MODELING ANDPREDICTION", Protein science, 5(12), 1996, pp. 2600-2616

Abstract

Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residuesin length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loopclass suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferencesas key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Mostof these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin-like calcium-binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix-turn-helix DNA-binding loops. This article provides a systematic and coherentconformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted.

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Documento generato il 01/12/20 alle ore 07:54:25