ArticleMolecular simulation
To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.
Article in Molecular simulation. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers.Computational and structural biotechnology journal · 2024Article
- Article
- Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents.Methods in molecular biology (Clifton, N.J.) · 2022Article
- 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
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.
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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.