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Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation

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Abstract

Macrolide biosensor protein MphR(A) has been known as a key regulatory protein in metabolite sensing and genetic expression regulating. MphR(A) protein binds to macrolide antibiotic erythromycin (Ery) and releases the gene operon, thus activates expression of the mphA gene and initiates Ery resistance. The two mutant amino acid residues (V66L and V126L) might potentially disrupt Ery binding to MphR(A). In these studies, the binding of macrolide antibiotic Ery to wild type (Wt) MphR(A) and double mutant (V66L/V126L) MphR(A) are explored by molecular dynamics simulations. Compared to the Apo-MphR(A) protein and Wt-MphR(A)–Ery complex, many interesting effects owing to the double mutant (V66L/V126L) are discovered. In the case of Ery, Helix I which plays an important role in transcription shows itself a right-hand α helix in Wt-MphR(A)–Ery, whereas the activated helix is broken down in double mutant-V66L/V126L-MphR(A)–Ery. The calculated results exhibit that the double mutant V66L/V126L reduces the binding affinity of the V66L/V126L-MphR(A) to Ery, resulting in the block of Ery resistance. The binding free energy decomposition analysis reveals that the decrease of the binding affinity for the variant V66L/V126L-MphR(A)–Ery is mainly attributed to the gas phase electrostatic energies. The residue Leu66, Thr154, and Arg122 enhance the binding affinity of V66L/V126L-MphR(A) to Ery. The residues Tyr103 and His147 contributes mainly to binding energies in the Wt-MphR(A)–Ery complex, whereas the two residues have no contribution to the binding free energy inV66L/V126L-MphR(A)–Ery complex. Our study gives useful insights into the nature of amino acids mutation effect, the mechanism of blocking drug resistance at the atomic level and the characteristics in binding affinity for Ery to double mutant (V66L/V126L) MphR(A), which will contribute to the design of more effective macrolide antibiotics.

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Acknowledgments

The calculations of this paper were performed partly on the Supercomputing Center of University of Science and Technology of China.

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Authors and Affiliations

  1. National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People’s Republic of China

    Tingting Feng, Yanjun Zhang, Jing-Na Ding & Ju-Guang Han

  2. College of Basic Medical Sciences of Anhui Medical University, Hefei, 230024, People’s Republic of China

    Tingting Feng & Song Fan

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  1. Tingting Feng
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  2. Yanjun Zhang
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  3. Jing-Na Ding
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  4. Song Fan
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  5. Ju-Guang Han
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Correspondence to Ju-Guang Han.

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Feng, T., Zhang, Y., Ding, JN. et al. Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation. J Comput Aided Mol Des 29, 1123–1136 (2015). https://doi.org/10.1007/s10822-015-9881-0

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  • DOI: https://doi.org/10.1007/s10822-015-9881-0

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