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ProCoCoA: A quantitative approach for analyzing protein core composition

Paper ID Volume ID Publish Year Pages File Format Full-Text
15152 1382 2013 6 PDF Available
Title
ProCoCoA: A quantitative approach for analyzing protein core composition
Abstract

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.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► 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.

Keywords
Protein core composition; Protein folding; Atom depth
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ProCoCoA: A quantitative approach for analyzing protein core composition
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 43, April 2013, Pages 29–34
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us