ArticleThe journal of physical chemistry. B2019
Exploring Allosteric Pathways of a V-Type Enzyme with Dynamical Perturbation Networks.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches.International journal of molecular sciences · 2024Review
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase.ACS catalysis · 2023Article
- Connected Component Analysis of Dynamical Perturbation Contact Networks.The journal of physical chemistry. B · 2023Article
- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- MDiGest: A Python package for describing allostery from molecular dynamics simulations.The Journal of chemical physics · 2023Article
- Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase.Nature communications · 2023Article
- Calculation of centralities in protein kinase A.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis.Journal of chemical information and modeling · 2022Article
- Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase.Journal of the American Chemical Society · 2022Article
- Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria.Biophysical journal · 2022Article
- Community Network Analysis of Allosteric Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Elucidating the Activation Mechanism of AMPK by Direct Pan-Activator PF-739.Frontiers in molecular biosciences · 2021Article
- Mapping Function from Dynamics: Future Challenges for Network-Based Models of Protein Structures.Frontiers in molecular biosciences · 2021Article
- Decrypting the Information Exchange Pathways across the Spliceosome Machinery.Journal of the American Chemical Society · 2020Article
- Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement.Scientific reports · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Elucidation of the allosteric pathways in proteins is a computational challenge that strongly benefits from combination of atomistic molecular dynamics (MD) simulations and coarse-grained analysis of the complex dynamical network of chemical interactions based on graph theory. Here, we introduce and assess the performances of the dynamical perturbation network analysis of allosteric pathways in a prototypical V-type allosteric enzyme. Dynamical atomic contacts obtained from MD simulations are used to weight the allosteric protein graph, which involves an extended network of contacts perturbed by the effector binding in the allosteric site. The outcome showed good agreement with previously reported theoretical and experimental extended studies and it provided recognition of new potential allosteric spots that can be exploited in future mutagenesis experiments. Overall, the dynamical perturbation network analysis proved to be a powerful computational tool, complementary to other network-based approaches that can assist the full exploitation of allosteric phenomena for advances in protein engineering and rational drug design.
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