QZyme WorkbenchTM is a fully automated proprietary in silico protein engineering platform, evolved by integrating open source computational chemistry tools in combination with customised algorithms and scripts. QZyme WorkbenchTM is capable of tackling several important aspects of protein modelling and engineering including structural refinement, ligand docking, conformational sampling, estimating substrate binding affinity, modelling catalytic reaction, identifying mutable hotspots, further hotspot optimization, and so on.
QZyme WorkbenchTM is a fully automated proprietary in silico protein engineering platform of Quantumzyme LLP, evolved by integrating open source computational chemistry tools (such as Modeller, AmberTools, Gromacs, Gamess-US, AutoDock) in combination with in-house developed algorithms and scripts. QZyme WorkbenchTM is comprised of five modules namely: QZyme Pilot, QZyme Modeller, QZyme CatMec, QZyme Hotspot and QZyme Designer which is capable of tackling several important aspects of protein modeling and engineering including structural refinement, ligand docking, conformational sampling, estimating substrate binding affinity, modeling catalytic reaction, identifying mutable hotspots, further hotspot optimization, and so on.
QZyme PilotTM deals with literature review for the reaction of interest. In this phase we understand the entire reaction, the structure of the enzyme, ligand, enzyme – substrate - product (E-S-P) disassociation. This particular model is unique because there is a cursory level patent search carried out for the identified enzyme, to provide freedom to operate. This allows the customer to file for a patent, if needed.
QZyme ModellerTM is based on the enzyme identification done during the QZyme Pilot phase. This module deals with modelling of the 3D structure of the protein and ligand and understanding the Michaelis complex. Here, a grid like structure is created for the reaction of interest, to understand amino acid interaction at the substrate entry and exit pathway, the retention time of the substrate and product disassociation.
QZyme CatMecTM determines “near attack” conformations of the substrate for the reaction by docking, and conduct Molecular Dynamics simulations of the enzyme-substrate (E-S) complexes. Post simulation analyses are carried out to explore the distribution of the substrate conformation in the enzyme’s entrance tunnel and the active site. The simulated trajectories are analysed to determine the atomic contacts between the enzyme and the substrate to obtain a consolidated list of residues for the computational alanine scanning (CAS) in next step.
QZyme HotspotTM module is based on the transition state conformations of the E-S complex. The amino acids of interest are subjected to alanine substitution resulting in those amino acids which give better performance. These are then shortlisted for QZyme Designer
QZyme DesignerTM deals with the in silico mutagenesis of the identified hotspot residues affecting the binding of substrate, transitions state barrier. The enzyme variants are screened and ranked according to the interaction energies of E-S complex, probability of binding affinity of substrate in near attack conformation, activation energy barrier and so on.
The main objective of “QZyme WorkBenchTM ” is to reduce time taken for execution of Enzyme Engineering Projects from 4+ months to 3 months or less and enable scientists to handle multiple projects at a given time. Some of the other objectives include
Abstracting IT related tasks from Scientists,
Managing efficient Server utilization.
Delight the Customer with Prompt Deliverables.
The enzyme penicillin G acylase (PGA; EC 188.8.131.52) is a heterodimeric protein consisting of a small subunit and a large subunit, which are formed by the processing of a single polypeptide precursor.
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