Studies on enzyme-catalysed reactions

Maria João Ramos
2020 Zenodo  
Part of the BioExcel Virtual Workshop on Best Practices in QM/MM Simulation of Biomolecular Systems Abstract This talk is concerned with the computational needs that we come across to figure out results within computational enzymology. Specific problems related to the establishment of enzymatic catalytic mechanisms are put forward, as well as a way to recognise the correct one. Single conformation QM/MM calculations, as well as multiple PES, more specifically related to the catalytic mechanism
more » ... atalytic mechanism of human pancreatic alpha-amylase are reported and, at the end, averaging over an ensemble of conformations is also explained. Comparisons are made with the previously mentioned calculations. Included is also the benchmarking of density functionals that we usually carry out to find the best suited one for the system under study. Therefore, we have resorted to different methodologies and altogether different studies [1-4] in order to analyze the energetics of processes related to the systems under study and evaluate their feasibility according to the available experimental data. References [1] SF. Sousa, AJM Ribeiro, RPP Neves, NF Bras, NMFSA Cerqueira, PA. Fernandes, MJ. Ramos, WIREs, 2017, 7, 1-29. https://doi.org/10.1002/wcms.1281 [2] RPP. Neves, PA. Fernandes, MJ. Ramos, PNAS, 2017, 114, E4724-E4733. https://doi.org/10.1073/pnas.1618985114 [3] D. Santos-Martins, AR. Calixto, PA. Fernandes, MJ. Ramos, MJ, ACS Catalysis, 2018, 8, 4055-4063. https://doi.org/10.1021/acscatal.7b04400 [4] P. Ferreira, NMFSA. Cerqueira, PA. Fernandes, MJ. Romão, MJ. Ramos, ACS Catalysis, 2020, 10, 16, 9276-9286. https://doi.org/10.1021/acscatal.0c02627
doi:10.5281/zenodo.4320762 fatcat:jazfg3ay2fbgxjkns7dk2xqhfm