ArticleJACS Au2024
A Fresh Look at the Normal Mode Analysis of Proteins: Introducing Allosteric Co-Vibrational Modes.
Article in JACS Au, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.Acta crystallographica. Section D, Structural biology · 2026Article
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Structural Insights and Bioactivity Correlations of Heteroleptic Zn(II)/Cd(II) Complexes: Experimental Characterization, Theoretical Modelling, and Evaluation of Antimicrobial, Anticancer, and Lipase Inhibitory Potentials.Applied biochemistry and biotechnology · 2026Article
- Calculation of minimum energy pathways in transport proteins.Communications chemistry · 2025Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Engineering Protein Dynamics through Mutational Energy Landscape Traps.Journal of chemical information and modeling · 2025Article
- Complementing Adiabatic and Nonadiabatic Methods To Understand Internal Conversion Dynamics in Porphyrin Derivatives.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose a new way of utilizing normal modes to study protein conformational transitions. Instead of considering individual modes independently, we show that a weighted mixture of low-frequency vibrational modes can reveal dynamic information about the conformational mechanism in more detail than any single mode can. The weights in the mixed mode, termed the allosteric covibrational mode, are determined using a simple model where the conformational transition is viewed as a perturbation of the coupled harmonic oscillator associated with either of the two conformations. We demonstrate our theory in a biologically relevant example of high pharmaceutical interest involving the V617F mutation of Janus 2 tyrosine kinase (JAK2).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.