ArticleBiophysical journal2007
A generalized born implicit-membrane representation compared to experimental insertion free energies.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.International journal of molecular sciences · 2018Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.Journal of chemical theory and computation · 2016Article
- Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor.The journal of physical chemistry. B · 2016Article
- Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.Journal of chemical information and modeling · 2015Article
- Peptide Folding in Translocon-Like Pores.The Journal of membrane biology · 2015Article
- Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.Biophysical journal · 2015Article
- Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers.Biochimica et biophysica acta · 2014Article
- Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.Journal of chemical theory and computation · 2014Article
- Introducing Charge Hydration Asymmetry into the Generalized Born Model.Journal of chemical theory and computation · 2014Article
- Peptide-lipid interactions: experiments and applications.International journal of molecular sciences · 2013Article
- Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models.Journal of molecular modeling · 2013Article
- Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.Chemical physics letters · 2013Article
- Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.Journal of chemical theory and computation · 2012Article
- Membrane bending is critical for the stability of voltage sensor segments in the membrane.The Journal of general physiology · 2012Article
- Testing physical models of passive membrane permeation.Journal of chemical information and modeling · 2012Article
- In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions.Journal of the American Chemical Society · 2011Article
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4 authors.
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Abstract
An implicit-membrane representation based on the generalized Born theory of solvation has been developed. The method was parameterized against the water-to-cyclohexane insertion free energies of hydrophobic side-chain analogs. Subsequently, the membrane was compared with experimental data from translocon inserted polypeptides and validated by comparison with an independent dataset of six membrane-associated peptides and eight integral membrane proteins of known structure and orientation. Comparison of the insertion energy of alpha-helical model peptides with the experimental values from the biological hydrophobicity scale of Hessa et al. gave a correlation of 93% with a mean unsigned error of 0.64 kcal/mol, when charged residues were ignored. The membrane insertion energy was found to be dependent on residue position. This effect is particularly pronounced for charged and polar residues, which strongly prefer interfacial locations. All integral membrane proteins investigated orient and insert correctly into the implicit-membrane model. Remarkably, the membrane model correctly predicts a partially inserted configuration for the monotopic membrane protein cyclooxygenase, matching experimental and theoretical predictions. To test the applicability and usefulness of the implicit-membrane method, molecular simulations of influenza A M2 as well as the glycophorin A dimer were performed. Both systems remain structurally stable and integrated into the membrane.
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