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Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations

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Abstract

In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1–3)-a-L-rhamnopyranosyl-(1–6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4”-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. The free energies are consistent with available experimental results and suggest that the binding site of BSA-drug1 is more stable than those of BSA-drug2 and BSA-drug3. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of BSA-drug1 while the van der Waals interactions contribute largely to stabilization of the binding site of BSA-drug2 and BSA-drug3. The key residues stabilizing the binding sites of BSA-drug1, BSA-drug2 and BSA-drug3 are identified based on the residue decomposition analysis.

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Acknowledgments

The authors acknowledge the financial support by the research startup fund of Jilin University (No. 4305050102H8; No. 4305050102B5), the basic research and operational costs of Jilin University (No. 421031196604 and No. 450060445293), the Specialized Research Fund for the Doctoral Program of Higher Education (20090061120101), and the Natural Science Foundation of Jilin Province in China (20101552).

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Authors and Affiliations

  1. Department of Food quality and Safety, Jilin University, Changchun, 130062, People’s Republic of China

    Xiaodi Niu, Xiaohan Gao, Hongsu Wang, Xin Wang & Song Wang

  2. State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130061, People’s Republic of China

    Xiaodi Niu & Song Wang

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  1. Xiaodi Niu
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  2. Xiaohan Gao
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  3. Hongsu Wang
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  4. Xin Wang
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  5. Song Wang
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Correspondence to Song Wang.

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Niu, X., Gao, X., Wang, H. et al. Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations. J Mol Model 19, 1039–1047 (2013). https://doi.org/10.1007/s00894-012-1649-z

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  • DOI: https://doi.org/10.1007/s00894-012-1649-z

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