Center for Molecular Modeling - O. De Vos

Effect of Chain Unsaturation and Temperature on Oxygen Diffusion through Lipid Membranes from Simulations

wim — Mon, 05 Feb 2018 11:49:32 +0000

O. De Vos, T. Van Hecke, A. Ghysels

Advances in Experimental Medicine and Biology

Oxygen Transport to Tissue XL, 399-404

2018

Open Access version available at UGent repository

Green Open Access

DOI

https://doi.org/10.1007/978-3-319-91287-5_64

Private attachment

paper_oxygen-in-ord-disord-membr_Ghysels_2018.pdf

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

wim — Mon, 05 Feb 2018 07:52:29 +0000

O. De Vos, R.M. Venable, T. Van Hecke, G. Hummer, R.W. Pastor, A. Ghysels

Journal of Chemical Theory and Computation (JCTC)

14 (7), 3811-3824

2018

Abstract

The balance of normal and radial (lateral) diffusion of oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski equation for the inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories of oxygen to extract the free energy and the normal and radial diffusion profiles. This paper derives a theoretical formalism to convert these profiles into characteristic times and lengths associated with entering, escaping, or completely crossing the membrane. The formalism computes mean first passage times and holds for any process described by rate equations between discrete states. BA of simulations of eight model membranes with varying lipid composition and temperature indicate that oxygen travels 3 to 5 times further in the radial than in the normal direction when crossing the membrane in a time of 15 to 32 ns, thereby confirming the anisotropy of passive oxygen transport in membranes. Moreover, the preceding times and distances estimated from the BA are compared to the aggregate of 280 membrane exits explicitly observed in the trajectories. BA predictions for the distances of oxygen radial diffusion within the membrane are statistically indistinguishable from the corresponding simulation values, yet BA oxygen exit times from the membrane interior are approximately 20% shorter than the simulation values, averaged over seven systems. The comparison supports the BA approach and, therefore, the applicability of the Smoluchowski equation to membrane diffusion. Given the shorter trajectories required for the BA, these results validate the BA as a computationally attractive alternative to direct observation of exits when estimating characteristic times and radial distances. The effect of collective membrane undulations on the BA is also discussed.

DOI

http://dx.doi.org/10.1021/acs.jctc.8b00115

Private attachment

paperII.pdf

Simulating oxygen transport through membranes at various temperatures

oriana — Mon, 06 Nov 2017 11:06:44 +0000

Description

Membranes are found in every cell and organelle. Oxygen must be transported through the membrane in order to supply energy to that cell/organelle. But how does oxygen diffuse through the membrane? Does the presence of ordered rafts in membranes influence this process? This project aims to investigate these questions through simulations of three model membranes with varying degree of lipid saturation, and hence varying degree of ordering. The effect of temperature will be investigated by comparing oxygen diffusion at room temperature and body temperature, which will help towards the understanding of oxygen transport in ordered rafts.

Period

Wednesday, 1 November, 2017 to Monday, 30 April, 2018

Node days

660.00 days

Users

O. De Vos, A. Ghysels

Downloads

O. De Vos, T. Van Hecke, A. Ghysels

ISBN/ISSN:

Poster

Conference / event / venue

Chemical Research in Flanders Symposium (CRF-1)

Blankenberge, Belgium

Monday, 24 October, 2016 to Wednesday, 26 October, 2016

Abstract (private)

DeVosOriana_DiffusionOfO2InCellMembranes_correct.pdf

Modeling oxygen diffusion through biological lipid membranes using inverse Monte Carlo

wim — Mon, 07 Mar 2016 13:20:24 +0000

Study of oxygen diffusion through cell membranes

oriana — Mon, 29 Feb 2016 12:18:03 +0000

Period

Monday, 29 February, 2016 to Wednesday, 31 August, 2016

Node days

1 125.00 days

Users

O. De Vos, A. Ghysels

Remaining days

1 125.00 days

Downloads

AanvraagTIER1_feb2016_v2.pdf

TIER1 reference n°

2016-20

Status

Approved