Why Can Hydrogen Sulfide Permeate Cell Membranes?

Riahi, Saleh; Rowley, Christopher N.

doi:10.1021/ja508063s

Cited by 99 publications

(82 citation statements)

References 29 publications

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“…42 Several theoretical models have been developed to predict the rates of permeation from molecular simulations, although the solubility-diffusion model has been particularly popular. 7,[43][44][45][46] This model predicts the rate of permeation from the potential of mean force and the diffusivity of the permeating solute as a function of its position, z, along the trans- These results are in line with previous simulations. 46,47 The TIP3P-FB and TIP4P-FB water models have viscosity/self-diffusion coefficients that are much closer to the experimental values and the diffusivity of the permeating water molecule is lower accordingly.…”

Section: Water Permeabilitysupporting

confidence: 87%

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

Sajadi¹,

Rowley²

2018

Preprint

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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 TIP3P 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 DPPC and POPC 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. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid-water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and a TIP4P-FB models due to their high excess chemical potentials.

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Section: Water Permeabilitysupporting

confidence: 87%

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

Sajadi¹,

Rowley²

2018

Preprint

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“…Several studies for small molecules do report increased diffusion rates at the center of the lipid bilayer. 15,[18][19][20][21] In contrast, most studies of larger molecules that are at least the size of the amino acids studied in this work show relatively flat diffusion profiles in homogenous lipid bilayers. 25,27,30 Thus, our translational diffusion results are consistent with other reported values for larger molecules.…”

Section: Translational Diffusionmentioning

confidence: 59%

“…Our PMF profile for NATA qualitatively agrees with results of Cardenas et al, 43 and the calculated translational and rotational diffusion rates in the solution region agree with both computational results and experimental data. 15,[18][19][20][21]25,27,30 Thus, we believe that our combined experimental and computational study provides improved understanding of the process of transmembrane permeation of small aromatic peptides. Especially valuable are the microscopic insights from the simulations, including the large difference between translational and rotational diffusion rates and changes in peptide structure as a function of membrane insertion depth.…”

Section: Discussionmentioning

confidence: 91%

“…Previous studies, which focused on translational dynamics, typically found faster motions in the central region of lower relative density. 15,[18][19][20][21] Presence of slow reorientations in the course of membrane transport has been previously explored. 25,27,30 Our simulations suggest that translational diffusion in the z direction, along the elongated lipid molecules, is relatively easy; while rotational diffusion of the peptide sidechains, which are tethered to their backbones and must move in directions perpendicular to the tightly packed lipids, is unexpectedly slow.…”

Section: Fig 6 Insertion Angles θmentioning

confidence: 99%

“…14 Recent molecular dynamics studies have focused on a wide variety of molecules passively diffusing through membranes, such as water, [15][16][17] small molecules, [18][19][20][21][22][23] model drug compounds, 6,22,24,25 analgesics, [26][27][28] drug delivery systems, 29,30 dyes, 31,32 other lipids, 33,34 nanoparticles, [35][36][37] toxins, 38 small peptides, 39,40 and even transmembrane proteins. 41,42 However, only a handful of MD studies have examined amino acid-related systems and are confined to tryptophan, [43][44][45] arginine, 46,47 lysine, 47 and amino acid analogues.…”

Section: Introductionmentioning

confidence: 99%

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Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

Lee

Kuczera

Middaugh

et al. 2016

The Journal of Chemical Physics

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The time-resolved parallel artificial membrane permeability assay with fluorescence detection and comprehensive computer simulations are used to study the passive permeation of three aromatic dipeptides—N-acetyl-phenylalanineamide (NAFA), N-acetyltyrosineamide (NAYA), and N-acetyl-tryptophanamide (NATA) through a 1,2-dioleoyl-sn-glycero-3-phospocholine (DOPC) lipid bilayer. Measured permeation times and permeability coefficients show fastest translocation for NAFA, slowest for NAYA, and intermediate for NATA under physiological temperature and pH. Computationally, we perform umbrella sampling simulations to model the structure, dynamics, and interactions of the peptides as a function of z, the distance from lipid bilayer. The calculated profiles of the potential of mean force show two strong effects—preferential binding of each of the three peptides to the lipid interface and large free energy barriers in the membrane center. We use several approaches to calculate the position-dependent translational diffusion coefficients D(z), including one based on numerical solution the Smoluchowski equation. Surprisingly, computed D(z) values change very little with reaction coordinate and are also quite similar for the three peptides studied. In contrast, calculated values of sidechain rotational correlation times τrot(z) show extremely large changes with peptide membrane insertion—values become 100 times larger in the headgroup region and 10 times larger at interface and in membrane center, relative to solution. The peptides’ conformational freedom becomes systematically more restricted as they enter the membrane, sampling α and β and C7eq basins in solution, α and C7eq at the interface, and C7eq only in the center. Residual waters of solvation remain around the peptides even in the membrane center. Overall, our study provides an improved microscopic understanding of passive peptide permeation through membranes, especially on the sensitivity of rotational diffusion to position relative to the bilayer.

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The Ediacaran‐Cambrian Transition

Kaufman

2018

Chemostratigraphy Across Major Chronological Boundaries

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Why Can Hydrogen Sulfide Permeate Cell Membranes?

Cited by 99 publications

References 29 publications

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

The Ediacaran‐Cambrian Transition

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