ArticleProceedings of the National Academy of Sciences of the United States of America2014
Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. 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.
- Review
- Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions.International journal of molecular sciences · 2021Article
- Article
- Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin.Biophysical journal · 2021Article
- Terahertz radiation and the skin: a review.Journal of biomedical optics · 2021Review
- Water is a biomarker of changes in the cellular environment in live animals.Scientific reports · 2020Article
- Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics.Journal of chemical information and modeling · 2019Article
- Entropy connects water structure and dynamics in protein hydration layer.Physical chemistry chemical physics : PCCP · 2018Article
- How Does Solvation Layer Mobility Affect Protein Structural Dynamics?Frontiers in molecular biosciences · 2018Article
- Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy.Biomedical optics express · 2017Article
- Article
- Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Cross-linked dry bonding: A new etch-and-rinse technique.Dental materials : official publication of the Academy of Dental Materials · 2016Article
- Water Determines the Structure and Dynamics of Proteins.Chemical reviews · 2016Review
- Surface water retardation around single-chain polymeric nanoparticles: critical for catalytic function?Chemical science · 2016Article
- Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP.Biophysical journal · 2015Article
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Authors and funding
8 authors.
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Abstract
The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz- based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.
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