Over the past 50 years, over 40% of new approved drugs have been based on natural products. Thus, understanding how nature fine-tunes its biological machinery involved in the synthesis of such natural products has become crucial for advances in bioengineering and therapeutic drug development. Mononuclear, non-heme Fe(II), alpha-ketoglutarate (aKG) dependent enzymes are a class of natural product biosynthesis enzymes that catalyze a variety of reactions such as hydroxylation, halogenation, and stereoinversion. SyrB2 is a representative enzyme of this diverse family and reacts only on substrates delivered to its active site via phosphopantetheine (PPant) arm attached to a carrier protein SyrB1. The SyrB2/SyrB1 complex exhibits substrate selectivity, chlorinating its native substrate but hydroxylating structurally-similar but non-native substrates. The source of this difference cannot be understood through any available structural data, as there are no co-crystallized SyrB2/SyrB1 complexes and only limited spectroscopic (i.e., HYSCORE) data. Recent experiment and simulations have promoted the hypothesis that substrate position strongly influences reaction outcome. In order to investigate this hypothesis with atomic scale resolution of active site dynamics, we have employed long-time classical molecular dynamics and large-scale QM/MM calculations on the SyrB2/SyrB1 complex. Energy decomposition analysis at the classical and quantum levels of theory help us identify a unique double hydrogen bond configuration for the native substrate that places it at an optimum distance from the active site, thus allowing it to be chlorinated instead of hydroxylated. The variations in these substrate-protein interactions also allow us to resolve the uncertainty regarding the three possible coordination isomers of Fe(II) active site. We believe this approach can be useful in elucidating the reactivity trends in multi-protein biosynthetic complexes.

Elucidating the role of substrate positioning in non-heme Fe(II) and alpha-ketoglutarate dependent halogenase SyrB2: A computational study

256th National Meeting (2018)

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