Sharif Digital Repository

Bacterial outer membrane porins (Omp) that have robust β -barrel structures, show potential applications for nanomedicine devices in synthetic membranes and single molecule detection biosensors. Here, we explore the conformational dynamics of a set of 22 outer membrane porins, classified into five major groups: general porins, specific porins, transport Omps, poreless Omps and composed pores. Normal mode analysis, based on mechanical vibration theory and elastic network model, is performed to study the fluctuations of residues of aforementioned porins around their equilibrium positions. We find that a simple modification in this model considering weak interaction between protein and... 

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...