MM/PBSA binding free energy calculations of heparin binding domain of fibronectin with self-assembled monolayers Viswanath Vittaladevaram 2 and David Cheung 1 1 Department of Biological & Chemical Sciences, University of Galway, Ireland 2 University of Galway, Ireland
Figure 1: Workflow of MM-PBSA free energy calculations Understanding protein-surface interactions is critical for designing biomaterials which enables to have a control over biological responses during interactions. A thorough understanding of protein adsorption onto surfaces is essential to optimize formation of functional biomaterials. Quantitative estimation of protein-surface binding affinities is critical towards understanding specific interactions that favours in revealing molecular mechanism in detail. In this research, we performed molecular mechanics Poison-Boltzmann surface area (MM-PBSA) analysis to compute binding free energies of Heparin binding fragments fibronectin with hydrophobic methyl (CH3)-self- assembled monolayer(SAM)surface. Average binding free energies of snapshots were determined by Δ G bind after removing the solvent molecules from the system. The mean and standard deviation defining each portion of Delta G calculated using MM-PBSA computing method. Results showed mobility of fibronectin fragments is enhanced on adsorption to hydrophobic surface and further interactions between protein, surface and solvent were quantified. The research study highlights the importance of MM-PBSA in computing binding free energies of a complex system which favours the process of optimisation of biomaterials and design of novel medical devices. References 1. C. Masato Nakano,Heng Ma, andTao Wei, "Study of lysozyme mobility and binding free energy during adsorption on a graphene surface", Appl. Phys. Lett.106, 153701(2015)https://doi.org/10.1063/1.4918292 2. Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.Chemical reviews,119(16), 9478–9508. https:// doi.org/10.1021/acs.chemrev.9b00055
V09
© The Author(s), 2023
Made with FlippingBook Learn more on our blog