ReviewInternational journal of molecular sciences2010
Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems.
Review in International journal of molecular sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Phosphatidic Acid Homeostasis and Membrane Lipid Remodeling Confer Salt Tolerance inPlants (Basel, Switzerland) · 2025Article
- Development of Transferable Coarse-Grained Lipid Models with Optimized Structural and Elastic Membrane Properties.Journal of chemical theory and computation · 2025Article
- Computational Methods to Target Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Modeling Polyzwitterion-Based Drug Delivery Platforms: A Perspective of the Current State-of-the-Art and Beyond.ACS engineering Au · 2022Review
- Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19.International journal of molecular sciences · 2019Article
- A generic force field for protein coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2012Article
- Latest developments in experimental and computational approaches to characterize protein-lipid interactions.Proteomics · 2012Review
- Medicinal chemistry for 2020.Future medicinal chemistry · 2011Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
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Registered trials
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