ProCoCoA: A quantitative approach for analyzing protein core composition

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.

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► Unambiguous criteria are established for defining protein cores from PDB files.
► Atom depth calculations yield structure-based residue assignment to protein cores.
► A possible relationship between protein folds and core composition was studied.
► Different protein folds were found to have specific amino acid core compositions.
► URL: http://www.sbl.unisi.it/prococoa gives an user-friendly interface for ProCoCoA.