ArticleBiophysical journal2004
Small-world communication of residues and significance for protein dynamics.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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Who cites it
106 citing papers in PubMed.
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- Network reorganization of a cold-adapted β-glucosidase couples conformational flexibility to catalytic efficiency under low-temperature conditions.Frontiers in microbiology · 2026Article
- The multimerization pathway of the glucocorticoid receptor.Nucleic acids research · 2025Article
- Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction.Structure (London, England : 1993) · 2025Article
- Revealing SARS-CoV-2 MComputational and structural biotechnology journal · 2024Article
- Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families.Protein science : a publication of the Protein Society · 2024Article
- Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine.Biophysical journal · 2024Article
- Einstein Model of a Graph to Characterize Protein Folded/Unfolded States.Molecules (Basel, Switzerland) · 2023Article
- A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance.Science advances · 2023Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Deciphering Isoniazid Drug Resistance Mechanisms on DimericACS omega · 2022Article
- Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations.Nature communications · 2022Article
- The Structural Basis ofMolecules (Basel, Switzerland) · 2022Article
- Network approach to understand biological systems: From single to multilayer networks.Journal of biosciences · 2022Article
- Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins.Computational and structural biotechnology journal · 2022Article
- Role of a high centrality residue in protein dynamics and thermal stability.Journal of structural biology · 2021Article
- Comparative protein structure network analysis on 3CLProteins · 2021Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is not merely the position of residues that is critically important for a protein's function and stability, but also their interactions. We illustrate, by using a network construction on a set of 595 nonhomologous proteins, that regular packing is preserved in short-range interactions, but short average path lengths are achieved through some long-range contacts. Thus, lying between the two extremes of regularity and randomness, residues in folded proteins are distributed according to a "small-world" topology. Using this topology, we show that the core residues have the same local packing arrangements irrespective of protein size. Furthermore, we find that the average shortest path lengths are highly correlated with residue fluctuations, providing a link between the spatial arrangement of the residues and protein dynamics.
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