ArticleThe journal of physical chemistry. B2013
Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 50 citations in OpenAlex.
- A Global Review on Short Peptides: Frontiers and Perspectives.Molecules (Basel, Switzerland) · 2021Review
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.International journal of molecular sciences · 2018Article
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- New Continuum Approaches for Determining Protein-Induced Membrane Deformations.Biophysical journal · 2017Article
- An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.Chemical reviews · 2016Review
- Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.Journal of chemical information and modeling · 2016Article
- Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface.Chemistry and physics of lipids · 2016Article
- The Molecular Mechanism Underlying Recruitment and Insertion of Lipid-Anchored LC3 Protein into Membranes.Biophysical journal · 2015Article
- Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca(2+) Channels.Biophysical journal · 2015Article
- Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics.Langmuir : the ACS journal of surfaces and colloids · 2015Article
- Structural and Thermodynamic Insight into Spontaneous Membrane-Translocating Peptides Across Model PC/PG Lipid Bilayers.The Journal of membrane biology · 2015Article
- Membrane permeation of a peptide: it is better to be positive.The journal of physical chemistry. B · 2015Article
- Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.The journal of physical chemistry. B · 2014Article
- Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model.The journal of physical chemistry letters · 2014Review
- Continuum approaches to understanding ion and peptide interactions with the membrane.The Journal of membrane biology · 2014Article
- Translocation thermodynamics of linear and cyclic nonaarginine into model DPPC bilayer via coarse-grained molecular dynamics simulation: implications of pore formation and nonadditivity.The journal of physical chemistry. B · 2014Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a monoarginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged monoarginine peptide unit from water to the center of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.