Glycan-related Enzymatic Reaction Mechanism Prediction Service
Unlocking Glycan Enzymatic Reactions with Precision Prediction!
Oligosaccharides and glycoconjugates are indispensable entities, with glycan-related enzymes standing out in the precise biosynthesis of glycan structures. Due to their fundamental importance, CD BioGlyco provides a service to analyze the catalytic mechanisms. We use hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Methodologies, a formidable strategy, to deliver precise descriptions of intricate biological systems. By employing QM to scrutinize the electronic structure of the active site alongside molecular mechanics for the glycan-related enzyme's broader environment, these approaches enable comprehensive modeling of glycan-related enzymatic reactions. They facilitate the exploration of diverse reaction pathways such as transition states and intermediates, crucially enhancing our comprehension of enzymatic mechanisms.
Structure preparation
The first thing to do is to prepare the enzyme for calculations, and then assemble the enzyme-substrate complex. Experimental structures such as X-ray or nuclear magnetic resonance (NMR) coordinates from the PDB database are preferred for obtaining complex coordinates. We use diverse software tools like Modeller and Chimera, Maestro for preparing X-ray crystal structures. The preparation process includes several steps:
- Initial selection of amino acid residues, resolving any dual conformations by choosing one
- Removal of water oxygen atoms from the structure initially
- Identification and addition of missing amino acid residues using tools like Modeller, refining their orientation
- The addition of hydrogen atoms and determination of protonation states based on residue pKa values, facilitated by software methods like Chimera
- Utilization of restraints to improve accuracy during substrate docking into the active site of the enzyme
- Addition of relevant water molecules to the complex structure
This structured approach ensures that the prepared structure is optimized for subsequent computational calculations, facilitating accurate substrate docking and analysis.
QM/MM partition
The next task is to tackle the issue of selecting a computational model. This involves dividing the entire system into QM and MM regions and choosing suitable QM and MM methods for each region. Typically, use QM for the reactive part of the active site and MM for the rest of the system. We define the boundary between QM and MM regions meticulously, often moving it away from active residues as recommended. After selecting the QM and MM methods using standard criteria, the next step is to optimize the overall system's geometry to fix any inaccuracies in the initial coordinates derived from X-ray, NMR, or modeling.
Mapping catalytic reaction
When modeling the catalytic reaction of glycan-related enzymes, we calculate a potential energy surface (PES) that accurately describes chemical changes involving electron redistribution. The PES of the entire system (enzyme and substrates) typically encompasses numerous transition states and stationary states, influenced by various degrees of freedom that shape its structure. Therefore, to track the progress of the catalytic reaction, we focus on observing structural changes in a specific set of reaction coordinates. Choosing the correct reaction coordinate(s) is crucial, an improper selection can introduce biases into the calculations and result in slower convergence.
By adopting this methodology, we delve into the intricacies of enzymatic functionality, predicated upon the three-dimensional architecture and the dynamicity of the glycan-related enzyme-substrate conjugations. We employ these computational methodologies to unravel the intricate structural configurations of transition states and to elucidate the energetic landscapes, encompassing activation barriers, in glycan-related enzyme-catalyzed reaction environments. Through this approach, we aim to elucidate the fundamental principles of glycan-related enzymatic efficacy.
Publication Data
Technology: QM-only cluster calculations, QM/MM free energy simulations
Journal: The Journal of Physical Chemistry B
Published: 2022
IF: 3.466
Results: The paper delves into the intricate workings of urease, a crucial enzyme catalyzing the hydrolysis of urea to ammonia and carbamate. This process significantly impacts both human health and agricultural practices. Extensive studies employing inhibition, mutagenesis, and kinetic analyses have provided valuable insights into urease's enzymatic function, yet debates persist regarding its substrate binding mode and the exact mechanism of the catalytic reaction. In this study, the authors employed advanced computational techniques including QM-only and QM/MM MD simulations. They have elucidated the binding mode of urea within the enzyme's active site and uncovered the detailed steps involved in the urease-catalyzed hydrolysis reaction. The research highlights the preference for a bidentate-bound urea complex over a monodentate-bound one, showing it to be more favorable for both the nucleophilic attack and subsequent proton transfer steps. This bidentate coordination not only fits snugly into the active site, particularly when the mobile flap is in a closed conformation, but also facilitates the stabilization of transition states and intermediates through multiple hydrogen bonds with specific residues. Furthermore, the study explores the role of the bridging hydroxide ion, which acts both as a nucleophile and a general acid during the reaction. Importantly, the simulations underscore that the dissociation of certain ions is a critical trigger for positioning urea optimally before the onset of hydrolysis. The authors also reveal significant insights into the proton transfer reactions mediated by specific active site residues, crucially demonstrating the influence of the protein environment on these processes.
Fig.1 QM regions of 1 and 2 after the QM(GFN2-xTB)/MM MD equilibrations (top). Key bond distances are also presented in Å (bottom). (Saito & Takano, 2022)
Advantages
- We possess a skilled team proficient in molecular simulation and biochemistry to deliver high-level support and analytical capabilities for studying complex glycan-related enzymatic mechanisms.
- Our researchers integrate cutting-edge computational techniques with experimental data, providing clients with precise predictions and deep insights.
- Our research team helps investigate three-dimensional enzyme-substrate interactions to elucidate structural configurations and energetic landscapes, enhancing understanding of enzymatic efficacy in glycan-related processes.
Applications
- Glycan-related enzymatic reaction mechanism prediction services can be used to design drugs that target specific enzymes involved in glycan processing or modification, potentially for researching diseases related to glycosylation disorders or other glycan-related diseases.
- Glycan-related enzymatic reaction mechanism prediction services can be utilized in the engineering of enzymes for industrial applications, such as glycan synthesis or modification in biotechnological processes by predicting enzymatic reaction mechanisms.
- Glycan-related enzymatic reaction mechanism prediction service can be applied to study disease mechanisms by enhancing our understanding of diseases associated with glycan dysregulation, such as cancer, autoimmune disorders, and metabolic conditions.
Frequently Asked Questions
- Why apply QM/MM methods in enzyme catalysis research?
- The method partitions the entire system into two regions: a QM region and a MM region. QM region is typically centered on the active site where the chemical reaction occurs. It includes the structural moieties involved in the catalytic reactions and amino acids that interact with the reacting substrate(s). MM region includes the remaining parts of the substrate(s), the enzyme, and, if necessary, solvent molecules. The MM region is treated with classical force fields, which are less computationally demanding than QM calculations. The QM/MM method allows for a compromise between the high accuracy of quantum mechanics for the active site and the efficiency of molecular mechanics for the rest of the system. Such attributes render QM/MM methods, with their diverse versions and sophistication levels, particularly compelling choices for investigating enzymatic reactions.
- Are there additional services for glycoinformatics-assisted glycan-molecular interaction analysis available in CD BioGlyco?
CD BioGlyco helps clients explore the catalytic mechanism of glycosyltransferases with a QM/MM approach. Our modeling process encompasses three key stages, constructing a structural model, developing a QM/MM model, and simulating an enzymatic reaction. In general, Glycan-Molecular Interaction is of fundamental interest in glycobiology, contact us to obtain more information about our Glycoinformatics Service.
Reference
- Saito, T.; Takano, Y. QM/MM molecular dynamics simulations revealed the catalytic mechanism of urease. The Journal of Physical Chemistry B. 2022, 126(10): 2087-2097.
For research use only. Not intended for any diagnostic use.
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