ArticleScientific reports2019
Universality of fold-encoded localized vibrations in enzymes.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters.Biophysical journal · 2023Article
- Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins.Frontiers in molecular biosciences · 2021Article
- The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity.Scientific reports · 2020Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.
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