Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins

José Augusto Salim; Luiz Borro; Ivan Mazoni; Inácio Yano; José G Jardine; Goran Neshich

doi:10.1093/bioinformatics/btw082

Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins

Bioinformatics. 2016 Jun 15;32(12):1885-7. doi: 10.1093/bioinformatics/btw082. Epub 2016 Feb 15.

Authors

José Augusto Salim¹, Luiz Borro¹, Ivan Mazoni², Inácio Yano², José G Jardine², Goran Neshich²

Affiliations

¹ EMBRAPA Agriculture Informatics, Computational Biology Research Group, Brazilian Agricultural Research Corporation, Campinas 13083-886, Brazil and State University of Campinas/UNICAMP, Campinas, 13081-970, Brazil.
² EMBRAPA Agriculture Informatics, Computational Biology Research Group, Brazilian Agricultural Research Corporation, Campinas 13083-886, Brazil and.

PMID: 27153716
DOI: 10.1093/bioinformatics/btw082

Abstract

Motivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a web-based tool called multiple structure single parameter (MSSP) was developed and here presented.

Results: MSSP produces a two-dimensional plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected of >1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Y-axis contains the descriptor's numerical values for each aligned structure. To illustrate one of possible MSSP contributions to the investigation of changes in physicochemical and structural properties of mutants, comparing them with the cognate wild-type structure, the oncogenic mutation of M918T in RET kinase is presented. The comparative analysis of wild-type and mutant structures shows great changes in their electrostatic potential. These variations are easily depicted at the MSSP-generated XY-plot.

Availability and implementation: The web server is freely available at http://www.cbi.cnptia.embrapa.br/SMS/STINGm/MPA/index.html Web server implemented in Perl, Java and JavaScript and JMol or Protein Viewer as structure visualizers.

Contact: goran.neshich@embrapa.br or gneshich@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Amino Acids
Databases, Protein
Proteins / chemistry*
Software

Substances

Amino Acids
Proteins