Insertion Of X-Ray Structures Of Proteins In Membranes

Few structures of membrane proteins are known and their relationships with the
membrane are unclear. In a previous report, 20 X-ray structures of transmembrane
proteins were analyzed in silico for their orientation in a 36A-thick membrane
[J. Mol. Graph. Model. 20 (2001) 235]. In this paper, we use the same approach to
analyze how the insertion of the X-ray structures varies with the bilayer
thickness. The protein structures are kept constant and, at each membrane
thickness, the protein is allowed to tilt and rotate in order to accommodate at
their best. The conditions are said to be optimal when the energy of insertion is
minimal. The results show that most helix bundles require thicker membranes than
porin barrels. Moreover, in a few instances, the ideal membrane thickness is
unrealistic with respect to natural membranes supporting that the X-ray structure
requires adaptation to stabilize in membrane. For instance, the squalene cyclase
could adapt by bending the side chains of its ring of lysine and arginine in
order to increase the hydrophobic surface in contact with membranes. We analyzed
the distribution of amino acids in the water, interface and acyl chain layers of
the membrane and compared with the literature.