Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition.

Tópicos

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Resumo

Defining the amino acid composition of protein cores is fundamental for understanding protein folding, as different architectures might achieve structural stability only in the presence of specific amino acid networks. Quantitative characterization of protein cores in relation to the corresponding structures and dynamics is needed to increase the reliability of protein engineering procedures. Unambiguous criteria based on atom depth considerations were established to assign amino acid residues to protein cores and, hence, for classifying inner and outer molecular moieties. These criteria were summarized in a new tool named ProCoCoA, Protein Core Composition Analyzer. An user-friendly web interface was developed, available at the URL: http://www.sbl.unisi.it/prococoa. An accurate estimate of protein core composition for six protein architectures selected from the CATH database of solved structures has been carried out, and the obtained results indicate the presence of specific patterns of amino acid core composition in different protein folds.

Resumo Limpo

defin amino acid composit protein core fundament understand protein fold differ architectur might achiev structur stabil presenc specif amino acid network quantit character protein core relat correspond structur dynam need increas reliabl protein engin procedur unambigu criteria base atom depth consider establish assign amino acid residu protein core henc classifi inner outer molecular moieti criteria summar new tool name prococoa protein core composit analyz userfriend web interfac develop avail url httpwwwsblunisiitprococoa accur estim protein core composit six protein architectur select cath databas solv structur carri obtain result indic presenc specif pattern amino acid core composit differ protein fold

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