ArticlePloS one2015
Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.Journal of chemical information and modeling · 2023Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
- Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.International journal of molecular sciences · 2021Review
- Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.Biophysical journal · 2020Article
- Hydration of Aromatic Heterocycles as an Adversary of π-Stacking.Journal of chemical information and modeling · 2019Article
- Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.Journal of biomolecular structure & dynamics · 2019Article
- Electrostatic recognition in substrate binding to serine proteases.Journal of molecular recognition : JMR · 2018Article
- Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.Journal of chemical information and modeling · 2018Article
- Conformational Flexibility Differentiates Naturally Occurring Bet v 1 Isoforms.International journal of molecular sciences · 2017Article
- 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases.MedChemComm · 2017Article
- Binding Pose Flip Explained via Enthalpic and Entropic Contributions.Journal of chemical information and modeling · 2017Article
- Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data.Current protein & peptide science · 2017Review
- Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD.Journal of chemical theory and computation · 2016Article
- Enzyme Selectivity Fine-Tuned through Dynamic Control of a Loop.Angewandte Chemie (International ed. in English) · 2016Article
- Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases.The journal of physical chemistry. B · 2016Article
- Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization.Protein science : a publication of the Protein Society · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.
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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 OpenQuestion graph.