Molecular dynamics are well known to reveal the dynamical information beyond static X-ray structures. In this study, we show that molecular dynamics of multifunctional P450 MycG explains its selectivity to the natural substrate M-IV, and predict mutations that improve reactivities to the unreactive substrates (M-VI and M-III with 99% identity in structure with M-IV). Conformational search of substrates in enzyme using restrained MD clarify the interactions during hydroxylation and epoxidation. The deoxysugar of all substrates reside in a hydrophobic cavity composed of three leucines. The polarity of the deoxysugars effects their affinity to the hydrophobic cavity and also the gating between R75 and E173 in the FG and BC loops, further enlarging the difference between three substrates. MD simulations on possible mutants predict that enhancing the gating between R75 and E173 is beneficial to improving reactivity for M-VI and M-III. Experimental data further confirms that the yield of oxidation products for M-III and M-VI is doubled or quadrupled respectively. These findings demonstrate the power of molecular dynamics in studying enzymatic reactions even when subtle difference between substrates, and more importantly, is capable to guide experiments to improve the performance of enzymes.

Studying the substrate specificity and reactivity of MycG: A multifunctional enzyme

253rd National Meeting (2017)

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