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Titolo:
How common is the funnel-like energy landscape in protein-protein interactions?
Autore:
Tovchigrechko, A; Vakser, IA;
Indirizzi:
Med Univ S Carolina, Dept Cell & Mol Pharmacol, Charleston, SC 29425 USA Med Univ S Carolina Charleston SC USA 29425 col, Charleston, SC 29425 USA
Titolo Testata:
PROTEIN SCIENCE
fascicolo: 8, volume: 10, anno: 2001,
pagine: 1572 - 1583
SICI:
0961-8368(200108)10:8<1572:HCITFE>2.0.ZU;2-Z
Fonte:
ISI
Lingua:
ENG
Soggetto:
DIFFUSION EQUATION METHOD; MULTIPLE-MINIMA PROBLEM; MOLECULAR RECOGNITION; CYTOCHROME-P450 2B4; DOCKING; COMPLEXES; CONTACTS; PACKING;
Keywords:
docking; protein modeling; structure prediction; binding; structural bioinformatics; low-resolution methods;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
26
Recensione:
Indirizzi per estratti:
Indirizzo: Vakser, IA Med Univ S Carolina, Dept Cell & Mol Pharmacol, Charleston, SC 29425 USA Med Univ S Carolina Charleston SC USA 29425 ston, SC 29425 USA
Citazione:
A. Tovchigrechko e I.A. Vakser, "How common is the funnel-like energy landscape in protein-protein interactions?", PROTEIN SCI, 10(8), 2001, pp. 1572-1583

Abstract

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a seriesof computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because ofthe uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether thisminimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding nl ea was mole populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.

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Documento generato il 23/09/20 alle ore 16:07:48