ArticleNature structural & molecular biology2011
Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site.
Article in Nature structural & molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed.
- Enzyme Reset: Water-Mediated Tautomerization Restores the Catalytic Asparagine in ProteinJournal of chemical information and modeling · 2026Article
- Single-engineered-residue solvation perturbations regulate global protein architecture and function.Nature communications · 2026Article
- Membrane Composition Reshapes the Folding Landscape of a pH-Responsive Peptide.The journal of physical chemistry letters · 2026Article
- Water Under Molecular Crowding: From Femtosecond H-Bond Networks Dynamics to Biological Function.Sub-cellular biochemistry · 2026Review
- Fast product release requires active-site water dynamics in carbonic anhydrase.Nature communications · 2025Article
- Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations.Biomolecules · 2025Article
- Impact of water models on the structure and dynamics of enzyme tunnels.Computational and structural biotechnology journal · 2024Article
- Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy.Communications chemistry · 2024Article
- Catalytic Mechanism of Collagen Hydrolysis by Zinc(II)-Dependent Matrix Metalloproteinase-1.The journal of physical chemistry. B · 2023Article
- Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.The Journal of chemical physics · 2023Article
- Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules.Biophysical reviews · 2023Review
- Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.Journal of the American Chemical Society · 2023Article
- Increase in the Intracellular Bulk Water Content in the Early Phase of Cell Death of Keratinocytes, Corneoptosis, as Revealed by 65 GHz Near-Field CMOS Dielectric Sensor.Molecules (Basel, Switzerland) · 2022Article
- Article
- Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case.The journal of physical chemistry letters · 2021Article
- Continuous noninvasive glucose monitoring; water as a relevant marker of glucose uptake in vivo.Biophysical reviews · 2019Review
- Article
- Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme.Nature chemistry · 2019Article
- Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase.The journal of physical chemistry. B · 2019Article
- Strong coupling of collective intermolecular vibrations in organic materials at terahertz frequencies.Nature communications · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme-inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.
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.