Most yeast SH3 domains bind peptide targets with high intrinsic specificity

PloS One
Tom BrownElliott J Stollar

Abstract

A need exists to develop bioinformatics for predicting differences in protein function, especially for members of a domain family who share a common fold, yet are found in a diverse array of proteins. Many domain families have been conserved over large evolutionary spans and representative genomic data during these periods are now available. This allows a simple method for grouping domain sequences to reveal common and unique/specific binding residues. As such, we hypothesize that sequence alignment analysis of the yeast SH3 domain family across ancestral species in the fungal kingdom can determine whether each member encodes specific information to bind unique peptide targets. With this approach, we identify important specific residues for a given domain as those that show little conservation within an alignment of yeast domain family members (paralogs) but are conserved in an alignment of its direct relatives (orthologs). We find most of the yeast SH3 domain family members have maintained unique amino acid conservation patterns that suggest they bind peptide targets with high intrinsic specificity through varying degrees of non-canonical recognition. For a minority of domains, we predict a less diverse binding surface, likely...Continue Reading

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Citations

Sep 15, 2020·PLoS Computational Biology·Gabriella J GerlachK Aurelia Ball
Mar 14, 2021·Nature Communications·Ugo DionneChristian R Landry
Dec 24, 2021·Protein Science : a Publication of the Protein Society·Melody GaoJeanine F Amacher

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Methods Mentioned

BETA
phage display

Software Mentioned

ENTREZ Global Query Cross - Database Search System
scikit
BLAST
ENTREZ
learn
ClustalW

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