Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases |
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| Authors: | Dr Vikram V Shende Natalia R Harris Dr Jacob N Sanders Dr Sean A Newmister Dr Yogan Khatri Prof Mohammad Movassaghi Prof Kendall N Houk Prof David H Sherman |
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| Institution: | 1. Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109 USA;2. Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA USA;3. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA |
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| Abstract: | In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp2?N bond forming dimerase, AspB. Overlay of the AspB structure onto C?C and C?N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C?N bond formation. MD simulations also suggest that intermolecular C?C or C?N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic. |
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| Keywords: | Biosynthesis Diketopiperazine Enzyme Mechanisms Molecular Dynamics Natural Products |
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