ArticlePLoS computational biology2020
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 46 citations in OpenAlex.
- Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations.Journal of computational chemistry · 2026Article
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- Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of the influenza A virus.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Learning molecular traits of human pain disease via voltage-gated sodium channel structure renormalization.Computational and structural biotechnology journal · 2025Article
- A strategy for Cas13 miniaturization based on the structure and AlphaFold.Nature communications · 2023Article
- Increasing the OACS catalysis · 2023Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.Computational biology and chemistry · 2022Article
- Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase.Entropy (Basel, Switzerland) · 2022Article
- Comparative protein structure network analysis on 3CLProteins · 2021Article
- Box scaling as a proxy of finite size correlations.Scientific reports · 2021Article
- Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.PLoS computational biology · 2021Article
- Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors.International journal of molecular sciences · 2020Article
- Inferring couplings in networks across order-disorder phase transitions.Physical review researchArticle
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins in cellular environments are highly susceptible. Local perturbations to any residue can be sensed by other spatially distal residues in the protein molecule, showing long-range correlations in the native dynamics of proteins. The long-range correlations of proteins contribute to many biological processes such as allostery, catalysis, and transportation. Revealing the structural origin of such long-range correlations is of great significance in understanding the design principle of biologically functional proteins. In this work, based on a large set of globular proteins determined by X-ray crystallography, by conducting normal mode analysis with the elastic network models, we demonstrate that such long-range correlations are encoded in the native topology of the proteins. To understand how native topology defines the structure and the dynamics of the proteins, we conduct scaling analysis on the size dependence of the slowest vibration mode, average path length, and modularity. Our results quantitatively describe how native proteins balance between order and disorder, showing both dense packing and fractal topology. It is suggested that the balance between stability and flexibility acts as an evolutionary constraint for proteins at different sizes. Overall, our result not only gives a new perspective bridging the protein structure and its dynamics but also reveals a universal principle in the evolution of proteins at all different sizes.
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