Theoretical Physics

10 November 2015
Time: 16:00 to 17:00
Location: EC Stoner 8.90

Theoretical Physics Seminar: David Reha (INSB)

EC Stoner 8.90 at 4pm

A Beginner's Guide to how Proteins Speed up Chemical Reactions with Quantum Mechanics


Biomolecules that participate in chemical reactions, such as the proteins involved in photosynthesis or the enzymes that catalyze metabolic interactions, are particularly challenging to describe theoretically because they combine chemical complexity with quantum mechanical behavior. This lecture will provide a non-technical introduction to the simulation techniques used to understand quantum processes in biomolecules, with a focus on the hybrid quantum/molecular mechanical (QM/MM) approaches that are used to span the multiple time and length-scales relevant to biomolecular catalysis. It will be then shown how these methods can be applied to understand metabolic enzymes in plants and bacteria.

Several examples of applications of computational methods on biomolecules will be demonstrated. First, the methods were applied to study the mechanisms of NADH:quinone oxidation reduction reaction in flavoprotein WrbA. The protein WrbA from E. coli belongs to the family of flavodoxine-like proteins and participates in protection of bacterial cell from oxidative stress. We have studied the detail mechanism of its enzymatic reaction and found the most suitable position of its substrates. The methods were also applied to calculate activation energy of typical model of enzymatic reaction, chorismate to prephenate within the chorismate mutase enzyme. Finally, the methods were also used to study binding affinity of progesterone, propranolol and warfarin (typically used as medicine) to human α1-acid glycoprotein (blood protein).



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