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

Abstract

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 1000 s 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.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1249923
Alternate Identifier(s):
OSTI ID: 1201667; OSTI ID: 1376018
Report Number(s):
LLNL-JRNL-665540
Journal ID: ISSN 0301-0104; S0301010415001287; PII: S0301010415001287
Grant/Contract Number:  
AC52-07NA27344; 12-LR-237353; DMR0844115
Resource Type:
Journal Article: Published Article
Journal Name:
Chemical Physics
Additional Journal Information:
Journal Name: Chemical Physics Journal Volume: 457 Journal Issue: C; Journal ID: ISSN 0301-0104
Publisher:
Elsevier
Country of Publication:
Netherlands
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; molecular dynamics; Monte Carlo; nanochannel; protein; nanopore; membrane; 77 NANOSCIENCE AND NANOTECHNOLOGY; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE

Citation Formats

Tringe, J. W., Ileri, N., Levie, H. W., Stroeve, P., Ustach, V., Faller, R., and Renaud, P. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels. Netherlands: N. p., 2015. Web. doi:10.1016/j.chemphys.2015.04.021.
Tringe, J. W., Ileri, N., Levie, H. W., Stroeve, P., Ustach, V., Faller, R., & Renaud, P. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels. Netherlands. https://doi.org/10.1016/j.chemphys.2015.04.021
Tringe, J. W., Ileri, N., Levie, H. W., Stroeve, P., Ustach, V., Faller, R., and Renaud, P. 2015. "Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels". Netherlands. https://doi.org/10.1016/j.chemphys.2015.04.021.
@article{osti_1249923,
title = {Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels},
author = {Tringe, J. W. and Ileri, N. and Levie, H. W. and Stroeve, P. and Ustach, V. and Faller, R. and Renaud, P.},
abstractNote = {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 1000 s 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.},
doi = {10.1016/j.chemphys.2015.04.021},
url = {https://www.osti.gov/biblio/1249923}, journal = {Chemical Physics},
issn = {0301-0104},
number = C,
volume = 457,
place = {Netherlands},
year = {Sat Aug 01 00:00:00 EDT 2015},
month = {Sat Aug 01 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1016/j.chemphys.2015.04.021

Citation Metrics:
Cited by: 5 works
Citation information provided by
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Works referencing / citing this record:

The raspberry model for protein-like particles: Ellipsoids and confinement in cylindrical pores
journal, October 2016