Biological Enzyme Catalysis Calculation

Enzymes are high molecular weight proteins that act on substrate or reactant molecules to form one or more products. In biological systems, enzymes act as catalysts and play a key role in accelerating reactions. Each enzyme exhibits selectivity for a single reactant or substrate. Understanding enzyme catalysis is crucial for both basic research and real-world applications, such as enzyme reaction processes that are crucial to the logical design of pharmaceuticals. It helps to have a thorough understanding of the mechanics governing reactions and the variables affecting specificity and selectivity when designing enzyme engineering to achieve desired results.

The main area of Alfa Chemistry's study has been enzymatic reaction mechanistic investigations. By offering specialist services for computing the catalytic effects of biological enzymes, we may assist our clients in finding solutions to their research-related challenges. These computer simulations, which are based on quantum theory and classical mechanics, can considerably offset the shortcomings of experimental methods and offer essential data on structure and energy for comprehending the mechanism of enzyme processes at the atomic level.

Our Service

Researchers at Alfa Chemistry have developed a variety of computational techniques that can be used to address various issues in enzyme catalysis. Molecular docking, molecular dynamics simulation, free energy perturbation, empirical valence bonding, quantum mechanics and molecular mechanics (QM/MM), and cluster approaches are examples of popular techniques. These methods might be seen as complementary to one another. Depending on the experimental demands of our clients, we will choose one or a combination of complimentary methodologies for computing the catalytic activity of biological enzymes.

The comprehensive strategy we present here is general and widely applicable to other cases of enzyme-substrate selectivity and reactivity.

Example-Limonene 1,2-epoxide hydrolases (LEHs)

Fig 1. LEH dimeric structure with limonene-1,2-epoxide shown in the active site. (Rinaldi S, et al. 2018)

Moderate enantioselectivity for unnatural ligands, coupled with narrow substrate specificity, limits the use of LEHs as general biocatalytic tools. In order to demonstrate how the presence of natural or artificial substrates differentially modulates the dynamics and catalytic behavior of LEHs, we combined QM/MM free energy calculations of reactions with MD simulations of enzyme internal kinetics. We also calculated binding affinities for different representatives of enzyme conformational combinations. The choice of specific substrate-dependent interactions at the binding site is made easier by the contact between the protein and the ligand, enabling the reactive complexes to choose various favored reaction pathways. The knowledge gained through our integrated approach provides a molecular rationale for LEH substrate preference.

Our Computational Method

• Molecular docking and molecular dynamics simulations are frequently utilized in the field of asymmetric biocatalysis and aid in qualitatively explaining the observed selectivity as well as providing rational or semi-rational guidance for enzyme engineering.
• In the QM/MM approach, a small fraction of the enzyme around the active site is treated with quantum mechanical methods and the rest of the enzyme, as well as the surrounding water, is treated with molecular force fields. Today, this approach has many applications in the stereoselectivity of enzymes.
• In the EVB approach, the reaction is first studied in a reference system and the parameters are adjusted to reproduce experimentally observable values or higher level calculations. These parameters are then used to model the reaction in an enzymatic environment in which a new free energy map can be calculated.
• The cluster modeling method (full QM method) is a simple but powerful method used to study the reaction mechanism at the active site of an enzyme. The model of the active site is usually designed based on the crystal structure of the enzyme. In the cluster approach, the choice of quantification method is usually made using density flooding theory (DFT).

Our biological enzyme catalysis calculation services significantly reduce costs, facilitate further experimentation, and accelerate the drug design process for our global customers. Our personalized, full-service approach will meet your innovative learning needs. If you are interested in our services, please feel free to contact us. We would be happy to work with you and see you succeed!

Reference

• Rinaldi S, et al. (2018). "Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases." ACS Catal. 8(7): 5698-5707.