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

Besya, A. B ; Sharif University of Technology | 2013

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  1. Type of Document: Article
  2. DOI: 10.1080/07391102.2012.712460
  3. Publisher: 2013
  4. Abstract:
  5. 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
  6. Keywords:
  7. Biophysics ; Elastic network model ; Membrane proteins ; Normal mode analysis ; Alpha hemolysin ; Outer membrane protein ; Outer membrane protein A ; Outer membrane protein F ; Porin ; TolC protein ; Channel gating ; Mathematical computing ; Membrane channel ; Membrane structure ; Molecular dynamics ; Molecular model ; Porosity ; Priority journal ; Protein function ; Protein structure ; Structure analysis ; Vibration ; Voltage clamp ; Bacterial Proteins ; Ion Channels ; Models, Molecular ; Molecular Dynamics Simulation ; Porins ; Protein Conformation
  8. Source: Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN)
  9. URL: http://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712460