Enhancing Martini 3 for protein self-interaction simulations.

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Tác giả: Jonas Binder, Robin Curtis, Wolfgang Friess, Martin Huelsmeyer, Michael Siedler, Matja Zalar

Ngôn ngữ: eng

Ký hiệu phân loại:

Thông tin xuất bản: Netherlands : European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 718008

Coarse-grained molecular dynamics simulations are highly valuable for studying protein-protein interactions. Unfortunately, commonly used force fields often overestimate these interactions. Here, we investigate the performance of the Martini 3 force field in predicting the self-interaction behavior of lysozyme and subtilisin using Metadynamics. The original Martini 3, despite improvements over its predecessor, overestimates interaction strength. Through reparameterization of bead interactions, we achieve good agreement with experimental data of the second virial coefficient and the diffusion coefficient. The new, refined force field enables more accurate CG-MD simulations, with potential applications in understanding and prediction of protein stability, aggregation tendencies, and solubility, with the possibility to aid in the development of protein-based drugs.
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