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Exploring the dynamics of holo-shikimate kinase through molecular mechanics
Umeå University, Faculty of Science and Technology, High Performance Computing Center North (HPC2N).
2023 (English)In: Biophysica, ISSN 2673-4125, Vol. 3, no 3, p. 463-475Article in journal (Refereed) Published
Abstract [en]

Understanding the connection between local and global dynamics can provide valuable insights into enzymatic function and may contribute to the development of novel strategies for enzyme modulation. In this work, we investigated the dynamics at both the global and local (active site) levels of Shikimate Kinase (SK) through microsecond time-scale molecular dynamics (MD) simulations of the holoenzyme in the product state. Our focus was on the wild-type (WT) enzyme and two mutants (R116A and R116K) which are known for their reduced catalytic activity. Through exploring the dynamics of these variants, we gained insights into the role of residue R116 and its contribution to overall SK dynamics. We argue that the connection between local and global dynamics can be attributed to local frustration near the mutated residue which perturbs the global protein dynamics.

Place, publisher, year, edition, pages
MDPI, 2023. Vol. 3, no 3, p. 463-475
Keywords [en]
shikimate kinase, mutants, molecular, dynamics, binding, frustration
National Category
Biophysics
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:umu:diva-212302DOI: 10.3390/biophysica3030030ISI: 001274265200001Scopus ID: 2-s2.0-85176214833OAI: oai:DiVA.org:umu-212302DiVA, id: diva2:1783566
Available from: 2023-07-21 Created: 2023-07-21 Last updated: 2025-04-24Bibliographically approved

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Ojeda-May, Pedro

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CiteExportLink to record
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Citation style
  • apa
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Output format
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