In our previous work, a NAD(H)-dependent carbonyl reductase (GoCR) was identified from Gluconobacter oxydans, which showed moderate to high enantiospecificity for the reduction of different kinds of prochiral ketones. In the present study, the crystal structure of GoCR was determined at 1.65Å resolution, and a computational strategy concerning substrate-enzyme docking and all-atom molecular dynamics (MD) simulation was established to help understand the molecular basis of enantiopreference and enantiorecognition for GoCR, and to further guide the design and engineering of GoCR enantioselectivity. For the reduction of ethyl 2-oxo-4-phenylbutyrate (OPBE), three binding pocket residues, Cys93, Tyr149, and Trp193 were predicted to play a critical role in determining the enantioselectivity. Through site-directed mutagenesis, single-point mutant W193A was constructed and proved to reduce OPBE to ethyl (R)-2-hydroxy-4-phenylbutyrate (R-HPBE) with a significantly improved ee of >99% compared to 43.2% for the wild type (WT). Furthermore, double mutant C93V/Y149A was proved to even invert the enantioselectivity of GoCR to afford S-HPBE at 79.8% ee.

Systems Biology is a multi-disciplinary research field with the aim of understanding the function of complex processes in living organisms. These intracellular processes are described by biochemical networks. Experimental studies in alliance with computer simulation lead to a continually increasing amount of data in liaison with different layers of biochemical networks. Thus, visualization is very important for getting an overview of data in association with the network components. Omix is a software for the visualization of any data in biochemical networks. The unique feature of Omix is: the software is programmable by a scripting language called Omix Visualization Language (OVL). In Omix, the visualization of data coming from experiment or simulation is completely performed by the software user realized in concise OVL scripts. By this, visualization becomes most flexible and adaptable to the requirements of the user and can be adapted to new application fields. We present four case studies of visualizing data of diverse kind in biochemical networks on metabolic level by using Omix and the OVL scripting language. These worked examples demonstrate the power of OVL in conjunction with pleasing visualization, an important requirement for successful interdisciplinary communication in the interface between more experimental and more theoretical researchers.