Enzyme Molecular Dynamics Simulation
Summary
In order to fully understand the catalytic activity of enzymes, researchers have conducted a wide range of MD simulation studies on several types of enzyme catalytic processes and discussed the whole process in detail.- Author Name: Tylor
Enzyme catalysis includes complex processes such as the transport of substrates to the active area, selective catalysis of chemical reactions, and product release. Any chemical or non-chemical process may be a crucial step in determining enzyme activity due to the complex environmental effects of proteins. Molecular dynamics (MD) method is a motion equations of the multi-particle system developed based on Newtonian classical mechanics. MD simulates the microscopic process of the system over time to obtain the particle phase trajectory of the system, and studies the equilibrium thermodynamic properties and structural dynamic properties of the system. In order to fully understand the catalytic activity of enzymes, researchers have conducted a wide range of MD simulation studies on several types of enzyme catalytic processes and discussed the whole process in detail. Investigation of the molecular mechanism of enzyme catalysis, the role of key residues and protein environmental effects have deepen the understanding of enzyme catalytic activity. With the further improvement and development of MD models, it is possible to provide support for related research in the field of enzyme engineering through the simulation study of the complex biological enzyme catalytic process.
Figure 1. A molecular dynamics simulation method in enzyme catalyzed reactions. (Boehr, D. D.; et al. 2018)
Scope of Application
- Study the conformational changes of enzymes in polar inorganic solvents and non-polar organic solvents.
- Investigate the influence of solvents on the thermal stability of enzymes.
- Reveal how mutations alter the structure and organization of enzyme active sites.
- Study the fluctuations between active and inactive conformations normally concealed to static crystallography.
- Predict changes in the enzyme systems containing proteins, DNA/RNA, lipids and other small ligands over time, to explore important biological and pharmaceutical events.
- Study biocatalytic processes by evaluating enzyme-ligand binding and optimizing the study biocatalytic processes.
- Identify hidden or isotope binding points, assisting in traditional virtual screening methods by directly predicting the binding energy of small molecules.
