| Title: | Enhancing Martini3 for protein self-interaction simulations |
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| Authors: | ID Binder, Jonas (Author)
ID Zalar, Matja (Author)
ID Huelsmeyer, Martin (Author)
ID Siedler, Michael (Author)
ID Curtis, Robin (Author)
ID Frieß, Wolfgang (Author) |
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| Files: |  1-s2.0-S0928098725000673-main.pdf (6,83 MB)
MD5: BFF4B77B6ADD7A75886A9BED9A7DFC95
 https://www.sciencedirect.com/science/article/pii/S0928098725000673?via%3Dihub
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| Language: | English |
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| Work type: | Article |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: | FKKT - Faculty of Chemistry and Chemical Engineering
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| Abstract: | 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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| Keywords: | coarse-grained molecular dynamics, Martini 3 force field, protein-protein interactions, B22, reparameterization, NMR, diffusion coefficient |
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Submitted for review: | 14.11.2024 |
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| Article acceptance date: | 09.03.2025 |
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| Publication date: | 10.03.2025 |
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| Publisher: | Elsevier |
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| Year of publishing: | 2025 |
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| Number of pages: | 28 str. |
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| Numbering: | [article no.] 107068 |
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| PID: | 20.500.12556/DKUM-92203  |
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| UDC: | 543.2/.9 |
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| ISSN on article: | 1879-0720 |
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| COBISS.SI-ID: | 228983811 |
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| DOI: | 10.1016/j.ejps.2025.107068 |
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| Copyright: | © 2025 The Authors |
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| Publication date in DKUM: | 20.03.2025 |
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| Views: | 286 |
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| Downloads: | 11 |
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| Metadata: |    |
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| Categories: | Misc.
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