ArticlePeerJ2018
Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Impact of Single-Walled Carbon Nanotube Functionalization on Ion and Water Molecule Transport at the Nanoscale.Nanomaterials (Basel, Switzerland) · 2024Article
- Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions.The journal of physical chemistry. B · 2022Article
- Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments.Current issues in molecular biology · 2021Article
- Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19.International journal of molecular sciences · 2021Article
- The degree and position of phosphorylation determine the impact of toxic and trace metals on phosphoinositide containing model membranes.BBA advances · 2021Article
- Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches.Antibiotics (Basel, Switzerland) · 2020Review
- Membrane permeability of small molecules from unbiased molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.Chemical reviews · 2020Review
- Permeability of membranes in the liquid ordered and liquid disordered phases.Nature communications · 2019Article
- Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.Journal of chemical theory and computation · 2019Article
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
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2 authors.
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Abstract
The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification when calculating membrane physical properties. The water permeability predicted by these models is significantly different; the mTIP3P-model diffusion in solution and at the lipid-water interface is anomalously fast due to the spuriously low viscosity of mTIP3P-model water, but the potential of mean force of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials. As a result, the rates of water permeation calculated the FB water models are slower than the experimental value by a factor of 15-17, while simulations with the mTIP3P model only underestimate the water permeability by a factor of 3.
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