Modelling Reactions in Biomolecules

Biomolecules are the most complex materials that exist. Moreover, at room temperature they are highly dynamic structures.

Therefore, the theoretical/computational analysis of enzymatic or photochemical reactions in biomolecules is a very challenging problem that usually involves the exploration of a large conformational space. Recently we have developed a quantum mechanics / molecular mechanics (QM/MM) method for the simulation of reactions in biomolecules: Fireball / Amber [1].

This technique presents a very appealing balance between accuracy and computational efficiency. In this talk the application of this technique will be illustrated by means of three examples: (I) an enzymatic reaction (enzyme: triosephosphate isomerase) [2]; (II) proton transfer reactions in DNA [3]; and (III) a photochemical reaction in DNA [4].

References

[1] J.I. Mendieta-Moreno et al. , J. Chem. Theory Comput. 10, 2185 (2014).
[2] J.I. Mendieta-Moreno et al. , Advances in Protein Chemistry and Structural Biology 100, 67 (2015).
[3] Diego Soler-Polo et al. , to be published (2018).
[4] J.I. Mendieta-Moreno et al. , J. Phys. Chem. Lett. 7, 4391 (2016).