Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations

I. Can Kazan, Prerna Sharma, Mohammad Imtiazur Rahman, Andrey Bobkov, Raimund Fromme, Giovanna Ghirlanda, S. Banu Ozkan

Research output: Contribution to journalArticlepeer-review

Abstract

We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.

Original languageEnglish (US)
JournaleLife
Volume11
DOIs
StatePublished - Dec 6 2022
Externally publishedYes

Keywords

  • allostery
  • enzyme
  • glycan
  • lectin
  • molecular biophysics
  • molecular mechanism
  • none
  • protein dynamics
  • structural biology

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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