Mechanical understanding of the correlation between actin assembly and ATP hydrolysis has been an object of intensive studies in biochemistry and structural biology. Azadirachtin(A) (AZA), a potential insecticide from neem, binds to actin and induces depolymerization in Drosophila. AZA binds to the pocket the same as that of Latrunculin A (LAT), but LAT inhibits actin...
One of the major problems in the use of enzymes in the industry is their instability under strict process conditions. As the use of organic solvents in industries for hydrophobic substrate solubility or the suppression of water-dependent reactions has become inevitable, the need to engineer enzymes to accommodate the varying solvent conditions and high substrate...
The current study demonstrates the significant progress made in computational enzymology and exemplifies the power and advantages of employing CPMD simulations in characterizing enzyme mechanisms. Here Acetylcholinesterase inhibitors such as Rivastigmine, Physostigmine, Neostigmine, and Edrophonium binding mechanisms were explored through the metadynamics approach. (In Preparation)
The invention is specific to the engineering of enzymes. The Michaelis Complex of E-S reaction is simulated using QM/MM, and MD methods. Using the QM polarized grid maps, MMPBSA. MMGBSA, low energy ES conformations that lead to the formation of attack conformation are identified. Subsequently, the enzyme is designed around the Michaelis complex where the...
Congratulations Swissmodel for completing 25 years of service!An excellent and powerful protein modeling server, the first ever modeling server since 2002. Modeled 1000s of protein, cytoskeletal proteins like tubulin, actin, and enzymes for engineering studies like Penicillin G Acylase. A tool that can be used for teaching and as well for research purposes.
Kcat Enzymatic we are working on the similar reactions of Cytochromes as in the Nobel Laureate Dr. Arnold’s lab, however by a different technology that uses Quantum Molecular Dynamics. We wonder if enzymatic reactions take the aid of quantum tunneling effects; specifically, could it be heavy atom tunneling! A quantum mechanical phenomenon where particles penetrate...
Cryptic pockets are sites on enzymes that only become apparent when ligands (substrate, co-substrate, cofactor) binds. They do not correspond to local minima in the computed conformational free energy landscape of the un-liganded proteins. Hence, they close in all the molecular dynamics simulations performed. Their formation is also known to be an interplay between both...
Schematic representation of Kcat’s Technology used to derive variants to achieve kg level substrate conversion with desired regioselectivity, stereospecificity, and enantiomeric excess. A system of Micrometer size with higher enzyme and substrate concentrations at varying pH, temperature, cofactor, co-substrate, and solvent conditions is simulated for microseconds. Information Capturing Technologies:A 7th Dimensional Grid made of Quantum beads that captures...
The patented technology works on Quantum mechanics-based probes/grid points, and real solvation using semi-empirical QM simulations. The dynamic probes atoms in the grid are replaced based on the neighbor-neighbor contacts in the conformational transitions. The Dynamic grid points capture high-resolution details of the enzymatic reaction. The method was implemented on an R-specific transaminase enzyme and...
Since its first appearance in December 2019, scientists all over the world are working towards treatment for COVID-19.We are happy to announce that Kcat Enzymatic is funded by the UKRI grant for in-vitro screening and validation of molecules to target spike protein a Mpro of COVID-19. The test is being carried out at the University...
