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Friends and relatives : insight into conformational regulation from orthologues and evolutionary lineages using KIF and KIN

Yehorova, Dariia ; Crean, Rory M ; Kasson, Peter M and Kamerlin, Shina Caroline Lynn (2024) In Faraday Discussions 252. p.341-353
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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author
; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Protein Conformation, beta-Lactamases/chemistry, Evolution, Molecular, Protein Engineering, Substrate Specificity, Models, Molecular
in
Faraday Discussions
volume
252
pages
13 pages
publisher
Royal Society of Chemistry
external identifiers
  • pmid:38842247
  • scopus:85195392889
ISSN
1359-6640
DOI
10.1039/d4fd00018h
language
English
LU publication?
no
id
9ab192db-8804-4b8a-87f3-4c080a003f76
date added to LUP
2025-01-11 18:18:01
date last changed
2025-07-13 18:37:25
@article{9ab192db-8804-4b8a-87f3-4c080a003f76,
  abstract     = {{<p>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.</p>}},
  author       = {{Yehorova, Dariia and Crean, Rory M and Kasson, Peter M and Kamerlin, Shina Caroline Lynn}},
  issn         = {{1359-6640}},
  keywords     = {{Protein Conformation; beta-Lactamases/chemistry; Evolution, Molecular; Protein Engineering; Substrate Specificity; Models, Molecular}},
  language     = {{eng}},
  month        = {{09}},
  pages        = {{341--353}},
  publisher    = {{Royal Society of Chemistry}},
  series       = {{Faraday Discussions}},
  title        = {{Friends and relatives : insight into conformational regulation from orthologues and evolutionary lineages using KIF and KIN}},
  url          = {{http://dx.doi.org/10.1039/d4fd00018h}},
  doi          = {{10.1039/d4fd00018h}},
  volume       = {{252}},
  year         = {{2024}},
}