Related Experiment Video
Updated: Oct 12, 2025
09:42
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
9.2K
Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents
Haiyang Cui1,2, Markus Vedder1, Ulrich Schwaneberg1,2
1Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
Methods in Molecular Biology (Clifton, N.J.)
|November 23, 2021
Summary
Molecular dynamics simulations enhance understanding of enzyme stability in organic solvents (OSs). This protocol guides researchers in engineering robust enzymes for improved biocatalysis in OS media.
Area of Science:
- Biocatalysis
- Computational Chemistry
- Enzyme Engineering
Background:
- Organic solvents (OSs) offer industrial advantages for chemical synthesis but often reduce enzyme performance.
- Enzyme instability (reduced activity, poor stability) in OSs limits their application.
- Molecular dynamics (MD) simulations can elucidate enzyme dynamics and stability in OSs.
Purpose of the Study:
- To describe a computational protocol for MD simulations of enzymes in OSs.
- To provide a transferable procedure for enzyme-OS system setup and analysis.
- To guide protein engineering for enhanced enzyme resistance to OSs.
Main Methods:
- Utilized GROMACS software for MD simulations.
- Focused on Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO).
- Discussed force field selection, parameterization, simulation setup, and trajectory analysis.
Main Results:
- Presented a detailed computational procedure for MD simulations of enzymes in OSs.
- Highlighted transferable methods for system setup and analysis of structural and solvation properties.
- Demonstrated the potential to guide rational protein engineering for OS-resistant enzymes.
Conclusions:
- The described MD simulation protocol is adaptable for various enzymes and OS systems.
- Molecular insights gained can facilitate the development of engineered enzymes for OS-based biocatalysis.
- Further research is needed to address remaining challenges in computational biocatalysis in OSs.
More Related Videos
Related Concept Videos
01:13Introduction to Mechanisms of Enzyme Catalysis
9.2K
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
9.2K
01:07Catalytically Perfect Enzymes
4.3K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Most enzymes...
Most enzymes...
4.3K
01:19Enzyme Kinetics
100.2K
Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
100.2K
01:13Induced-fit Model
85.0K
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
85.0K