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

Tringe J., İLERİ ERCAN N., Levie H., Stroeve P., Ustach V., Faller R., ...Daha Fazla

Chemical Physics, cilt.457, ss.19-27, 2015 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 457
  • Basım Tarihi: 2015
  • Doi Numarası: 10.1016/j.chemphys.2015.04.021
  • Dergi Adı: Chemical Physics
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.19-27
  • Anahtar Kelimeler: Membrane, Molecular Dynamics, Monte Carlo, Nanochannel, Nanopore, Protein
  • Orta Doğu Teknik Üniversitesi Adresli: Hayır

Özet

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.