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Updated: Jun 24, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Friends and relatives: insight into conformational regulation from orthologues and evolutionary lineages using KIF
Dariia Yehorova1, Rory M Crean2, Peter M Kasson3,4,5
1School of Chemistry and Biochemistry, Georgia Institute of Technology, USA. skamerlin3@gatech.edu.
Abstract:
Noncovalent interaction networks provide a powerful means to represent and analyze protein structure. Such networks can represent both static structures and dynamic conformational ensembles. We have recently developed two tools for analyzing such interaction networks and generating hypotheses for protein engineering. Here, we apply these tools to the conformational regulation of substrate specificity in class A β-lactamases, particularly the evolutionary development from generalist to specialist catalytic function and how that can be recapitulated or reversed by protein engineering. These tools, KIF and KIN, generate a set of prioritized residues and interactions as targets for experimental protein engineering.
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