Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An Implicit Membrane Model with a Dynamically Varying Bilayer Thickness

Panahi, Afra; Feig, Michael

doi:10.1021/ct300975k

Cited by 44 publications

(78 citation statements)

References 89 publications

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“…As discussed previously, 52,56,60 CHARMM/HDGB is in good agreement with the explicit lipid results for most residues except for the charged amino acids where membrane deformations play a dominant role. Therefore, we focus the comparison here on reproducing the profiles obtained from CHARMM/HDGB with PRIMO-M.…”

Section: Resultssupporting

confidence: 84%

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association

Kar¹,

Gopal²,

Cheng³

et al. 2014

J. Chem. Theory Comput.

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An extension of the recently developed PRIMO coarse-grained force field to membrane environments, PRIMO-M, is described. The membrane environment is modeled with the heterogeneous dielectric generalized Born (HDGB) methodology that simply replaces the standard generalized Born model in PRIMO without further parametrization. The resulting model was validated by comparing amino acid insertion free energy profiles and application in molecular dynamics simulations of membrane proteins and membrane-interacting peptides. Membrane proteins with 148–661 amino acids show stable root-mean-squared-deviations (RMSD) between 2 and 4 Å for most systems. Transmembrane helical peptides maintain helical shape and exhibit tilt angles in good agreement with experimental or other simulation data. The association of two glycophorin A (GpA) helices was simulated using replica exchange molecular dynamics simulations yielding the correct dimer structure with a crossing angle in agreement with previous studies. Finally, conformational sampling of the influenza fusion peptide also generates structures in agreement with previous studies. Overall, these findings suggest that PRIMO-M can be used to study membrane bound peptides and proteins and validates the transferable nature of the PRIMO coarse-grained force field.

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Section: Resultssupporting

confidence: 84%

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association

Kar¹,

Gopal²,

Cheng³

et al. 2014

J. Chem. Theory Comput.

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“…They coupled the membrane elastic energy with a dynamic heterogeneous generalized Born (DHDBG) formalism for fast dynamics simulations in the presence of an implicit membrane. The authors found that when using the dynamic version that allows for membrane bending, instead of a static implicit model of the membrane, the insertion of charged and polar molecules (amino acid side chain analogs, the WALP23 peptide, gramicidin channels and arginine-containing helices) is much more in-line with results from fully-atomistic simulations [130]. Another important advance has been to more realistically treat the membrane-protein boundary.…”

Section: Towards a More Realistic Geometric And Chemical Representmentioning

confidence: 97%

“…The Feig group has extended this mechanical deformation model to include a more dynamic view of small molecules, peptides, and proteins [130]. They coupled the membrane elastic energy with a dynamic heterogeneous generalized Born (DHDBG) formalism for fast dynamics simulations in the presence of an implicit membrane.…”

Section: Towards a More Realistic Geometric And Chemical Representmentioning

confidence: 99%

Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models

Argudo

Bethel

Marcoline

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches.

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“…This model was optimized to reproduce the solvation free energy profile of a solute upon insertion into the explicit lipid bilayers [121]. The HDGB model has been further extended to allow dynamic membrane deformations with an additional energy term for the free energy of deformation from an elasticity theory [122]. …”

Section: Molecular Models For Membranes and Membrane Proteinsmentioning

confidence: 99%

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori

Miyashita²,

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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108

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This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov.

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Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An Implicit Membrane Model with a Dynamically Varying Bilayer Thickness

Cited by 44 publications

References 89 publications

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association

Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

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