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ISSN 1511-3701

Home / Regular Issue / JTAS Vol. 31 (6) Oct. 2023 / JST-3967-2022


Effect of Scaling the Electrostatic Interactions on the Free Energy of Transfer of Azurin from Water to Lipid Membrane Determined by Coarse-Grained Simulations

Dian Fitrasari, Acep Purqon and Suprijadi

Pertanika Journal of Tropical Agricultural Science, Volume 31, Issue 6, October 2023


Keywords: Coarse-Grained MARTINI method, electrostatic scaling, free energy analysis, protein-lipid membrane model, windows separation

Published on: 12 October 2023

Azurin protein potentially plays an important role as an anti-cancer therapeutic agent, particularly in treating breast cancer in experiments and showing without having a negative effect on normal cells. Although the interaction mechanism between protein and lipid membrane is complicated, it can be modeled as protein-lipid interaction. Since the all-atom (AA) model simulation is cost computing, we apply a coarse-grained (CG-MARTINI) model to calculate the protein-lipid interaction. We investigate the binding free energy value dependency by varying the windows separation and electrostatic scale parameters. After scaling the electrostatic interactions by a factor of 0.04, the best result in terms of free energy is -140.831 kcal/mol, while after window-separation optimization, it reaches -71.859 kcal/mol. This scaling was necessary because the structures from the CG MARTINI model have a higher density than the corresponding all-atom structures. We thus postulate that electrostatic interactions should be scaled down in this case of CG-MARTINI simulations.

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