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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
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Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared
José Augusto Salim1, Luiz Borro1, Ivan Mazoni2
1EMBRAPA Agriculture Informatics, Computational Biology Research Group, Brazilian Agricultural Research Corporation, Campinas 13083-886, Brazil and State University of Campinas/UNICAMP, Campinas, 13081-970, Brazil.
Bioinformatics (Oxford, England)
|May 7, 2016
Summary
A new web tool, Multiple Structure Single Parameter (MSSP), visually represents protein structural variations. This tool aids in understanding how amino acid changes affect protein function by analyzing physicochemical descriptors.
Area of Science:
- * Structural bioinformatics
- * Computational biology
- * Protein structure-function relationships
Background:
- * Analyzing variations in structurally aligned proteins requires intuitive methods to link structural changes to functional implications.
- * Physicochemical and structural descriptors of amino acid residues can provide insights into protein characteristics.
- * Observing amino acid characteristics and their nano-environments aids in understanding structural variations.
Purpose of the Study:
- * To develop a web-based tool for visualizing protein structural and physicochemical properties.
- * To facilitate the association of functional implications with identified variations in structural characteristics.
- * To present the Multiple Structure Single Parameter (MSSP) tool for analyzing protein descriptor variations.
Main Methods:
- * Development of the Multiple Structure Single Parameter (MSSP) web-based tool.
- * Utilization of 150 protein descriptors from the STING database (>1500 parameters).
- * Generation of 2D XY-plots showing amino acid position versus descriptor values for aligned protein chains.
Main Results:
- * MSSP generates informative XY-plots for comparing single protein descriptors across multiple aligned protein chains.
- * The tool effectively visualizes changes in physicochemical properties, such as electrostatic potential, between wild-type and mutant protein structures.
- * Analysis of the oncogenic M918T mutation in RET kinase demonstrates MSSP's utility in identifying significant structural variations.
Conclusions:
- * MSSP provides an intuitive graphical representation for associating protein structural variations with potential functional implications.
- * The tool enhances the investigation of physicochemical and structural property changes in mutants compared to wild-type structures.
- * MSSP facilitates the understanding of how specific mutations impact protein behavior through visual analysis of descriptors.
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