Gating and conduction of nano-channel forming proteins: a computational approach

J Biomol Struct Dyn. 2013;31(8):818-28. doi: 10.1080/07391102.2012.712460. Epub 2012 Aug 28.

Abstract

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used to measure the possible amplitude of vibration in channel forming proteins. The current approach complements theoretical and experimental techniques including HOLE, Molecular Dynamics (MD), and voltage clamp used to address the channel's structure and dynamics and provides the means to conduct a theoretical simultaneous study of the structure and function of the channel. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:3.

MeSH terms

  • Bacterial Proteins / chemistry
  • Ion Channels / chemistry*
  • Ion Channels / metabolism
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Porins / chemistry
  • Protein Conformation

Substances

  • Bacterial Proteins
  • Ion Channels
  • Porins