Catalogo Articoli (Spogli Riviste)

OPAC HELP

Titolo:
Structure-based prediction of DNA target sites by regulatory proteins
Autore:
Kono, H; Sarai, A;
Indirizzi:
RIKEN,panst Phys & Chem Res, Tsukuba Life Sci Ctr, Tsukuba, Ibaraki 305, Ja RIKEN Tsukuba Ibaraki Japan 305 ba Life Sci Ctr, Tsukuba, Ibaraki 305, Ja
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 1, volume: 35, anno: 1999,
pagine: 114 - 131
SICI:
0887-3585(19990401)35:1<114:SPODTS>2.0.ZU;2-W
Fonte:
ISI
Lingua:
ENG
Soggetto:
RESOLUTION CRYSTAL-STRUCTURE; BINDING-SITES; ZINC FINGERS; TRANSCRIPTION FACTORS; GLOBULAR-PROTEINS; RECOGNITION CODE; HYDROGEN-BOND; PROBE HELIX; C-MYB; SEQUENCE;
Keywords:
protein-DNA recognition; specific binding; binding site prediction; statistical potential; spatial distribution;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
62
Recensione:
Indirizzi per estratti:
Indirizzo: Sarai, A RIKEN,Ibarakihys & Chem Res, Tsukuba Life Sci Ctr, 3-1-1 Koyadai,Tsukuba, RIKEN 3-1-1 Koyadai Tsukuba Ibaraki Japan 305 1 Koyadai, Tsukuba,
Citazione:
H. Kono e A. Sarai, "Structure-based prediction of DNA target sites by regulatory proteins", PROTEINS, 35(1), 1999, pp. 114-131

Abstract

Regulatory proteins play a critical role in controlling complex spatial and temporal patterns of gene expression in higher organism, by recognizing multiple DNA sequences and regulating multiple target genes. Increasing amounts of structural data on the protein-DNA complex provides clues for the mechanism of target recognition by regulatory proteins. The analyses of the propensities of base-amino acid interactions observed in those structural data show that there is no one-to-one correspondence in the interaction, but clear preferences exist. On the other hand, the analysis of spatial distribution of amino acids around bases shows that even those amino acids with strong base preference such as Arg with G are distributed in a wide space around bases. Thus, amino acids with many different geometries can form a similar type of interaction with bases, The redundancy and structural flexibility in the interaction suggest that there are no simple rules in the sequence recognition, and its prediction is not straightforward, However, the spatial distributions of amino acids around bases indicate a possibility that the structural data can be used to derive empirical interaction potentials between amino acids and bases. Such information extracted from structural databases has been successfully used to predict amino acid sequences that fold into particular protein structures, We surmised that the structures of protein-DNA complexes could be used to predict DNA target sites for regulatory proteins, because determining DNA sequences that bind to a particular protein structure should be similar to finding amino acid sequences that fold into a particular structure, Here we demonstrate that the structural data can be used to predict DNA target sequences for regulatory proteins. Pairwise potentials that determine the interaction between bases and amino acids were empirically derived from the structural data, These potentials were then used to examine the compatibility between DNA sequences and the protein-DNA complex structure in a combinatorial "threading" procedure, We applied this strategy to the structures of protein-DNA complexes to predict DNA binding sites recognized by regulatory proteins, To test the applicability of this method in target-site prediction, we examined the effects of cognate and noncognate binding, cooperative binding, and DNA deformation on the binding specificity, and predicted binding sites in real promoters and compared with experimental data, These results show that target binding sites for several regulatory proteins are successfully predicted, and our data suggest that this method can serve as a powerful tool for predicting multiple target sites and target genes for regulatory proteins. Proteins 1999;35:114-131,(C) 1999 Wiley-Liss, Inc.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 27/09/20 alle ore 13:36:05