GCAT: A network model of mutational influences between amino acid positions in PSD95 pdz3 .

Autor:	Pacini L; University Lyon, CNRS, INSA Lyon, Ecole Centrale de Lyon, UMR5005, Université Claude Bernard Lyon 1, Villeurbanne, France.; Institut Rhônalpin des Systèmes Complexes, IXXI-ENS-Lyon, Lyon, France., Lesieur C; University Lyon, CNRS, INSA Lyon, Ecole Centrale de Lyon, UMR5005, Université Claude Bernard Lyon 1, Villeurbanne, France.; Institut Rhônalpin des Systèmes Complexes, IXXI-ENS-Lyon, Lyon, France.
Jazyk:	angličtina
Zdroj:	Frontiers in molecular biosciences [Front Mol Biosci] 2022 Oct 31; Vol. 9, pp. 1035248. Date of Electronic Publication: 2022 Oct 31 (Print Publication: 2022).
DOI:	10.3389/fmolb.2022.1035248
Abstrakt:	Proteins exist for more than 3 billion years: proof of a sustainable design. They have mechanisms coping with internal perturbations (e.g., amino acid mutations), which tie genetic backgrounds to diseases or drug therapy failure. One difficulty to grasp these mechanisms is the asymmetry of amino acid mutational impact: a mutation at position i in the sequence, which impact a position j does not imply that the mutation at position j impacts the position i . Thus, to distinguish the influence of the mutation of i on j from the influence of the mutation of j on i , position mutational influences must be represented with directions. Using the X ray structure of the third PDZ domain of PDS-95 (Protein Data Bank 1BE9) and in silico mutations, we build a directed network called GCAT that models position mutational influences. In the GCAT, a position is a node with edges that leave the node (out-edges) for the influences of the mutation of the position on other positions and edges that enter the position (in-edges) for the influences of the mutation of other positions on the position. 1BE9 positions split into four influence categories called G, C, A and T going from positions influencing on average less other positions and influenced on average by less other positions (category C) to positions influencing on average more others positions and influenced on average by more other positions (category T). The four categories depict position neighborhoods in the protein structure with different tolerance to mutations. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Pacini and Lesieur.)
Databáze:	MEDLINE
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