Membrane interactions control residue fluctuations of outer membrane porins.
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 membrane, dramatically enhance the stability of results and improve the correlation coefficient between computational output and experimental results.
Besya
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AB
Institute for Nano Science and Technology, Sharif University of Technology, P.O. Box 14588-89694, Tehran, Iran.
Mobasheri
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H
Ejtehadi
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MR
D000465:Algorithms; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D001703:Biophysics / Q000379:methods*; D015374:Biosensing Techniques; D029968:Escherichia coli Proteins / Q000737:chemistry; D006460:Hemolysin Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D018272:Porins / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; D006460:Hemolysin Proteins; C036507:Hlya protein, E coli; D018272:Porins