Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

[Display omitted] •WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo.•Protein surface coverage characterized by atomic force microscopy.•Models indicate transport characteristics depend strongly on surface coverage.•Results resolve of a four orders of magnitude difference in...

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Bibliographic Details
Published in:Chemical physics 2015-08, Vol.457 (C), p.19-27
Main Authors: Tringe, J.W., Ileri, N., Levie, H.W., Stroeve, P., Ustach, V., Faller, R., Renaud, P.
Format: Article
Language:English
Subjects:
BASIC BIOLOGICAL SCIENCES
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
Membrane
Molecular Dynamics
Monte Carlo
Nanochannel
Nanopore
NANOSCIENCE AND NANOTECHNOLOGY
Protein
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Summary:[Display omitted] •WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo.•Protein surface coverage characterized by atomic force microscopy.•Models indicate transport characteristics depend strongly on surface coverage.•Results resolve of a four orders of magnitude difference in diffusion coefficient values. We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
ISSN:0301-0104
DOI:10.1016/j.chemphys.2015.04.021