ArticleThe journal of physical chemistry. B2013
Correlated motions and residual frustration in thrombin.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 41 citations in OpenAlex.
- Redesign of energetically frustrated regions rescues function in defective T4 clamp loaders.Molecular biology and evolution · 2026Article
- Possible Thrombus-clearing Mechanism and Modification Suggestion of β-sitosterol.Current drug targets · 2026Article
- Dynamic nature of Staphylococcus aureus type I signal peptidases.Biophysical journal · 2025Article
- Aggregation-Prone Pathogenic SOD1 Variants in Amyotrophic Lateral Sclerosis: Insights from Computational Genomics and Evolutionary Conservation.Journal of molecular neuroscience : MN · 2025Article
- Frustration in physiology and molecular medicine.Molecular aspects of medicine · 2025Review
- A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa.Scientific reports · 2022Article
- Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin.Biochemistry · 2021Article
- Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.International journal of molecular sciences · 2021Review
- Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex.Scientific reports · 2021Article
- Article
- Sodium-induced population shift drives activation of thrombin.Scientific reports · 2020Article
- Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.Journal of biomolecular structure & dynamics · 2019Article
- Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I.Biochemistry · 2019Article
- NaPhysical chemistry chemical physics : PCCP · 2019Article
- Structure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins.Science advances · 2018Article
- Self-organization, entropy and allostery.Biochemical Society transactions · 2018Review
- Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43.RSC advances · 2018Article
- Frustration, function and folding.Current opinion in structural biology · 2018Review
- Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I.Biochemistry · 2017Article
- Mechanistic insights into thrombin's switch between "slow" and "fast" forms.Physical chemistry chemical physics : PCCP · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Thrombin is the central protease in the cascade of blood coagulation proteases. The structure of thrombin consists of a double β-barrel core surrounded by connecting loops and helices. Compared to chymotrypsin, thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity. Previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites. We present a combined approach of molecular dynamics (MD), accelerated molecular dynamics (AMD), and analysis of the residual local frustration of apo-thrombin and active-site-bound (PPACK-thrombin). Community analysis of the MD ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts. AMD simulations, calibrated on measured residual dipolar couplings, reveal that upon active site ligation, correlated loop motions are quenched, but new ones connecting the active site with distal sites where allosteric regulators bind emerge. Residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics. The results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states.
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What OpenQuestion holds
Registered trials
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.