WP 3 In silico design and implementation of a polyketide synthesis system for production of virtual libraries of macrolides

The RIO family [1] of atypical protein kinases are present in organism varying from archea to humans. RIO1 and RIO2 are required for proper ribosome processing in yeast, and for proper cell cycle progression. Deletion of either RIO1 or RIO2 is lethal. Although the biological substrates of RIO kinases are still not known, this family is an important member of the regulation network in a cell. Hence, we decided to search for potential candidates as inhibitors, using a modelling approach. Crystallographic structures of RIO1 [2] are the basis for this approach. They are, however, not sufficient. The starting point for modeling is, apart from modeling the missing loops, determination of the protonation states of the more than one hundred ionizable groups of the protein. Poisson-Boltzmann equations were solved (MEAD program package), using the OPLS force-field parameters in the GROMACS program. To determine the probabilities of protonation of different ionizable groups of the protein at different pH values, the DOPS package [3, 4] was used. Analysis of protonation states within different potential binding sites will be presented.