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Enzyme Molecular Dynamics Simulation


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.

Enzyme Molecular Dynamics SimulationFigure 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.

Our Molecular Dynamics Simulation Process

  • Create the initial model

We prepare suitable structure including biological macromolecules and small molecules, coenzymes, solvent molecules and other structural treatments to create the initial model.

  • Optimize the model

Unreasonable conformations in the initial model are eliminated in this step.

  • Long-term molecular dynamics simulation

We conduct dynamic simulations, including energy optimization, heating, equilibrium phase and production phase. Our teams collect the equilibrium data and analyze the thermodynamic properties of the system through statistical methods when the system reaches equilibrium.

Our Services

Alfa Chemistry is committed to providing enzyme molecular dynamics simulation services for the biopharmaceutical field. Our fast and high-quality services include the following:

  • Free energy calculation

Compared to other static structure and energy information, free energy changes can more reasonably describe the characteristics of enzyme-catalyzed reactions. We use the MD method combined with umbrella sampling technology to simulate the entire process of the enzyme-catalyzed reaction. The influence of protein and medium environmental kinetics on the catalytic reaction process and the free energy properties of the reaction process can be obtained. Moreover, we provide the panoramic view of free energy changes.

  • Study the protein conformation changes

Alfa Chemistry has developed random accelerated molecular dynamics (RAMD) and classical molecular dynamics simulation methods to obtain possible pathways for substrate/product transport in the process of enzyme catalysis, and the conformational changes of proteins in the process of delivery. Our scientists use RAMD and MD methods to simulate the non-chemical steps of substrate/product transportation and explore possible pathways for reactants to enter the active site and product release. We also combine the MD technology with umbrella sampling method to calculate and analyze the energy properties of transport, so as to obtain one-dimensional and two-dimensional relative free energy maps and detailed transport mechanisms.

  • Analysis of the role of key residues

Key residues play very important roles in substrate/product transport and enzyme-catalyzed chemical reactions. The residue mutation method is widely used to discuss the influence of conserved residues in the enzyme catalysis process. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. Our teams use MD simulation to study the structural or functional roles of key residues at different stages of the enzyme catalysis process. As a binding free energy calculation method based on molecular mechanics and continuum model, molecular mechanics generalized born surface/poisson-boltzmann surface area approach is applied to evaluate the role of key residues in substrate binding including protein-ligand, protein-protein, protein-peptide interaction.

Alfa Chemistry provides enzyme molecular dynamics simulation services. We simulate the microscopic process of the enzyme-catalyzed reaction over time, monitor the phase trajectory of the system particles, and analyze the equilibrium thermodynamic properties and structural dynamics properties, etc. If you have any questions, please feel free to contact us.


  • Boehr, D. D.; et al. Engineered control of enzyme structural dynamics and function. Protein Science, 2018, 27(4).

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