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outer-membrane-protein
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Vibration Modes of Membrane Proteins by Application of Elastic Network Model
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Mobasheri, Hamid (Supervisor) ; Naghdabadi, Reza (Co-Advisor)
Abstract
Outer membrane proteins play the role of molecular machines in the outer membrane of bacteria to regulate their basic functions. These macromolecules have nano-scale dimensions and they are involved in the classifications of nano-machines and nano-pores. Protein structure is constructed of chain of amino acids. Coarse grained elastic network model of the protein introduces a network of selected point masses, which is located on α-carbon of each amino acid, linked together with harmonic springs that represent the interactions between residues, both the chemical (protein backbone) and physical bonds. Using the harmonic network potential and theory of mechanical vibration, normal modes of...
Gating and conduction of nano-channel forming proteins: A computational approach
, Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2013
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...