Molecular simulations of enzymes under non-natural conditions

Beyond the Chemical Step: The Role of Substrate Access in Acyltransferase from Mycobacterium smegmatis

“…At the same time, the role of the enzyme is to protect the active site from unwanted compounds, which might block the active site and compete with the desired substrates. Attraction of uncharged substrates is achieved by binding to the protein surface, 30,66 followed by a two-dimensional diffusion on the protein surface.…”

Applied biocatalysis beyond just buffers – from aqueous to unconventional media. Options and guidelines

“…New modelling and simulation tools currently under development may also facilitate solvent selection in the near future. 140 Also non-scientific aspects come into play. When the reaction target is a high-value compound, increased product concentrations and decreased catalyst costs may have a relative small impact on the economic viability of a reaction.…”

“…New modelling and simulation tools currently under development may also facilitate solvent selection in the near future. 140 …”

Molecular Mechanism of Methanol Inhibition in CALB-Catalyzed Alcoholysis: Analyzing Molecular Dynamics Simulations by a Markov State Model

“…39 This interpretation is supported by the fact that this binding site is too far from the active site to interfere directly with productive binding while presenting less negative binding free energy. In the process of fitting experimental data by a kinetic model, macroscopic constants such as K M and K I are fitting parameters, which depend not only on the active site but also on alternative sites such as the substrate access channel 70 and on the solvent. 71 Similarly, the rate constants k 1 and k −1 result from a combination of multiple microscopic binding steps and conformational changes of the enzyme.…”