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Physicochemical stability study of protein–benzoic acid complexes using molecular dynamics simulations

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Abstract

Carboxyl-modified substrates are the most common chemical moieties that are frequently used as protein defibrillators. We studied the stability of protein–benzoic acid complexes with bovine serum albumin (BSA), zein and lysozyme proteins using various computational methods. Structural model for zein was built using homology modelling technique and molecular docking was used to prepare complex structures of all three proteins with benzoic acid. Molecular dynamics calculations performed on these complex structures provided a strong support for the stability of protein–benzoic acid complexes. The results from various analyses including root-mean-square deviation (RMSD) and radius of gyration showed the stability and compactness of all proteins–benzoic acid complexes. Moreover, exploration of structural fluctuations in proteins revealed the stability of active site residues. Two potential binding modes of benzoic acid with all three proteins were identified via cluster analysis. The binding mode which was retrieved from top cluster containing 86–91% of total conformations displayed very strong binding interactions for zein, BSA and lysozyme proteins. In addition, the results of binding mode showed that various interactions, including hydrogen binding, hydrophobic and electrostatic interactions were important for the optimal binding of benzoic acid with the active sites of proteins. Exploration of solvent accessible surface area showed that lysozyme-binding cavity was more exposed to the surface as compared to the other two proteins. Free energy analysis of all protein systems showed the stability of protein–benzoic acid complexes with lysozyme and BSA relatively more stable than zein system. The results of our study provided important insights to the dynamic and structural information about protein–benzoic acid interactions with BSA, zein and lysozyme proteins. This work is important in enhancing the stability of therapeutic protein drugs loaded on carboxyl substrates.

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Acknowledgements

MA acknowledges SEED research Grant (1902144083) from the University of Sharjah. AAM acknowledges the University of Sharjah support of competitive grants (160-2142-029-P and 150-2142-017-P), Organometallic Research Group Grant (RISE-046-2016) and Functionalized Nanomaterials Synthesis Lab Grant (151-0039). The authors acknowledge the use of the HPC Facility at the University of Sharjah for part of the work reported in this paper.

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  1. Mahreen Arooj and Ihsan Shehadi authors contributed equally to this manuscript.

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  1. Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates

    Mahreen Arooj, Ihsan Shehadi, Chahlaa N. Nassab & Ahmed A. Mohamed

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  1. Mahreen Arooj
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  2. Ihsan Shehadi
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  3. Chahlaa N. Nassab
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  4. Ahmed A. Mohamed
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Correspondence to Ahmed A. Mohamed.

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Arooj, M., Shehadi, I., Nassab, C.N. et al. Physicochemical stability study of protein–benzoic acid complexes using molecular dynamics simulations. Amino Acids 52, 1353–1362 (2020). https://doi.org/10.1007/s00726-020-02897-2

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