Fast-time scale dynamics of outer membrane protein A by extended model-free analysis of NMR relaxation data.
In order to better understand the dynamics of an integral membrane protein, backbone amide (15)N NMR dynamics measurements of the beta-barrel membrane protein OmpA have been performed at three magnetic fields. A total of nine relaxation data sets were globally analyzed using an extended model-free formalism. The diffusion tensor was found to be prolate axially symmetric with an axial ratio of 5.75, indicating a possible rotation of the protein within the micelle. The generalized order parameters gradually decreased from the mid-plane towards the two ends of the barrel, counteracting the dynamic gradient of the lipids in a matching bilayer, and were dramatically reduced in the extracellular loops. Large-scale internal motions on the ns time scale indicate that entire loops most likely undergo concerted ("sea anemone"-like) motions emanating from their anchoring points on the barrel. The case of OmpA in DPC micelles also illustrates inherent limitations of analyzing the data with even the most sophisticated current models of the model-free formalism. It is likely that conformational exchange processes on the ms-mus also play a role in describing the motions of some residues, but their analysis did not produce unique results that could be independently verified.
Liang
Binyong
B
Center for Membrane Biology and Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 800736, Charlottesville, VA 22908, USA.
Arora
Ashish
A
Tamm
Lukas K
LK
D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D008823:Micelles; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017433:Protein Structure, Secondary / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000502:physiology
D001425:Bacterial Outer Membrane Proteins; D008051:Lipid Bilayers; D008823:Micelles; C078167:OMPA outer membrane proteins