ArticleComputational and structural biotechnology journal2021
Protein conformational switch discerned via network centrality properties.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
- Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.bioRxiv : the preprint server for biology · 2026Article
- Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes.Journal of chemical information and modeling · 2026Article
- Conformational transition of a polycationic hinge domain contributes to DNA binding.Biophysical chemistry · 2026Article
- Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates.The Biochemical journal · 2025Article
- Computational model predicts function of Rho-GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes.Protein science : a publication of the Protein Society · 2025Article
- Multiple intramolecular triggers converge to preferential G protein coupling in the CBNature communications · 2025Article
- Single-cell network biology enabling cell-type-resolved disease genetics.Genomics & informatics · 2025Review
- Allosteric modulation of Plasmodium falciparum Isoleucyl tRNA synthetase by South African natural compounds.PloS one · 2025Article
- Mitigation of QingLuoTongMai Pills on Chemotherapy-induced Phlebitis: A Network Pharmacology Study and Experimental Validation.Combinatorial chemistry & high throughput screening · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- Novel Impact of Colchicine on Interleukin-10 Expression in Acute Myocardial Infarction: An Integrative Approach.Journal of clinical medicine · 2024Article
- Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics.Journal of chemical information and modeling · 2024Article
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- Temperature sensitive contact modes allosterically gate TRPV3.PLoS computational biology · 2023Article
- Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins.BMC bioinformatics · 2023Article
- Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding.Journal of chemical theory and computation · 2023Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs.Life (Basel, Switzerland) · 2022Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.
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