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 Pilot deals with bioinformatics study such as sequence alignment, structure alignment and gather all the available information in the literature.
The second module, QZyme Modeller deals with prediction of three-dimensional structure, missing regions of enzyme from the given primary sequence of an enzyme. This module is optional depending on the availability of the crystal structure of protein.
QZyme CatMec 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.
Representative E-S conformations obtained from MD simulations from the tunnel entrance to active site are subjected to CAS analysis in QZyme Hotspot module.
The identified hotspot residues affecting the binding of substrate, transitions state barrier, are then subjected to in silico mutagenesis using the fifth module QZyme Designer. 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. Earlier study demonstrated the successful implementation of QZyme WorkbenchTM and few stories are described in the case studies.
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 18.104.22.168) 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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