ArticleBiophysical journal2012
The dynamic structure of thrombin in solution.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 51 citations in OpenAlex.
- DNA-Guided Robust Single-Protein Electronic Readout.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The Prothrombin-Prothrombinase Interaction.Sub-cellular biochemistry · 2024Review
- Dynamic allostery in thrombin-a review.Frontiers in molecular biosciences · 2023Review
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- How Thrombomodulin Enables W215A/E217A Thrombin to Cleave Protein C but Not Fibrinogen.Biochemistry · 2022Article
- Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin.Biochemistry · 2021Article
- Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex.Scientific reports · 2021Article
- Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System.Life (Basel, Switzerland) · 2021Review
- Article
- Sodium-induced population shift drives activation of thrombin.Scientific reports · 2020Article
- Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin.Scientific reports · 2019Article
- 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
- Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.Biophysical journal · 2019Article
- Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.Biophysical journal · 2019Article
- Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.Journal of chemical information and modeling · 2018Article
- Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin.Biochemistry · 2018Article
- Interplay between conformational selection and zymogen activation.Scientific reports · 2018Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R(1), R(2), and heteronuclear NOE experiments, variable temperature TROSY 2D [(1)H-(15)N] correlation spectra, and R(ex) measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na(+) binding site have order parameters below 0.8. Significant R(ex) was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales.
Indexed as
Identifiers
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.