skip to main content

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

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:
 [1] ;  [2] ;  [1] ;  [3] ;  [3] ;  [3] ;  [4]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of California, Davis, CA (United States)
  3. Univ. of California, Davis, CA (United States)
  4. Swiss Federal Institute of Technology, Lausanne (Switzerland)
Publication Date:
OSTI Identifier:
1249923
Grant/Contract Number:
12-LR-237353; DMR0844115; AC52-07NA27344
Type:
Published Article
Journal Name:
Chemical Physics
Additional Journal Information:
Journal Volume: 457; Journal Issue: C; Journal ID: ISSN 0301-0104
Publisher:
Elsevier
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; molecular dynamics; Monte Carlo; nanochannel; protein; nanopore; membrane