Free energetics of arginine permeation into model DMPC lipid bilayers: Coupling of effective counterion concentration and lateral bilayer dimensions

Yuan Hu, Shuching Ou, Sandeep Patel

Research output: Contribution to journalArticle

36 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)11641-11653
Number of pages13
JournalJournal of Physical Chemistry B
Volume117
Issue number39
DOIs
StatePublished - Oct 3 2013
Externally publishedYes

Fingerprint

Arginine
Lipid bilayers
Phosphorylcholine
Permeation
Peptides
Free energy
peptides
lipids
free energy
Molecular dynamics
Cell-Penetrating Peptides
Water
molecular dynamics
simulation
estimates
determinants
Experiments
Lipids
water
seats

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Free energetics of arginine permeation into model DMPC lipid bilayers : Coupling of effective counterion concentration and lateral bilayer dimensions. / Hu, Yuan; Ou, Shuching; Patel, Sandeep.

In: Journal of Physical Chemistry B, Vol. 117, No. 39, 03.10.2013, p. 11641-11653.

Research output: Contribution to journalArticle

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