Coarse grained protein- lipid model with application to lipoprotein particles
Open accessAbstract
A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model developed previously by Marrink et al., although future versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces the system size about 10-fold and allows integration time steps of 25-50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved to be reliable in maintaining the shape of preassembled particles and in reproducing the overall structural features of high-density lipoproteins accurately. Microsecond simulations of lipoprotein assembly revealed the formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer.
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Traditional molecular modeling methods usually provide reliable simulation results but require heavy computational resources, limiting their applicability.
“The methods in the first category, such as coarse-grained molecular dynamics simulations [9, 10], usually provide reliable simulation results but require heavy computational resources, which limits their applicability [11].”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [9]
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‘Improved parameters for the Martini coarse-grained protein force field’
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- Authors
- Shih, A. Y., Arkhipov, A., Freddolino, L., & Schulten, K.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Schulten, Klaus
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-01-06
- Volume
- 110
- Issue
- 8
- Pages
- 3674-3684
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- PMC
- PMC2535944
- OpenAlex
- W2093795463
- Cited by
- 267
- References
- 59
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 6 · 2023: 2 · 2022: 5 · 2021: 5 · 2020: 7 · 2019: 12 · 2018: 11 · 2017: 9 · 2016: 25 · 2015: 14 · 2014: 17 · 2013: 13 · 2012: 16
- FWCI
- 10.75
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM067887)
- National Center for Research Resources (5P41 RR 05969, P41RR005969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- coarse-grained molecular dynamics, protein-lipid interactions, high-density lipoprotein, effective potential, lipoprotein assembly, protein-lipid complex, lipid bilayers, helical proteins
- MeSH terms
- Algorithms, Computer Simulation, Lipids, Lipoproteins, Micelles, Models, Molecular, Proteins, Nanoparticles
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