| Resumo: |
Recent single molecule studies have confirmed that the catalytic rate is in fact an average of distinct catalytic rate constants even for the catalysis of one molecule only. This research project proposes to identify local and collective motions during the catalysis of 1-4 glycoside bonds by the human pancreatic a-amylase, which is representative of the glycoside hydrolase family of enzymes. The study will comprehend an accurate characterization of the minimum free energy path (MFEP) for the cleavage of the 1-4 glycosidic bond by a-amylase with the string method approach, and an efficient sampling of the resulting MFEP through umbrella sampling QM/MM MD simulations along the converged string. Ultimately, through extensive sampling, the underlying features of a-amylase's catalysis should be determined, shedding light on the nature of the catalysis by the enzyme. |