Membrane transport through alpha-heltical bundles. IV. Preliminary model building investigation of helix-helix interactions.

Abstract

Abstract Previously we made order of magnitude estimates that suggested the possibility of forming proton wires between facing α-helices joined by knobs-into-holes packing (Dunker, Marvin, Zaleske & Jones, 1976; Dunker & Marvin, 1978). Such structures may be a feature of membrane proteins. Since our original work, another type of packing, called ridges-into-grooves, has been identified as a way of meshing adjoining α-helices. Using precision (CPK) molecular models, we have investigated the possibility of forming proton wires: (1) in order to improve on our previous order of magnitude estimates, and (2) in order to evaluate the different kinds of packing interfaces for their ability to support stereochemically feasible proton wires. We found knobs-into-holes and ridges-into=grooves packing to support exactly the same proton wires. The positions of the side chains are determined more by the geometry of the hydrogen-bonding network rather than by the type of packing originally used to locate the appropriate residues. Thus, we suggest that a new name is needed for such packing, which we propose to call “H-bond packing”. In our earlier investigations we arbitrarily restricted our attention to proton wires parallel to the packing interface. By lifting this restriction, we found it possible to construct many additional types of wires. The model building exercises suggested that both parallel-to-the-interface and non-parallel-to-the-interface wires are feasible, except that the non-parallel wires are restricted in length depending on the angle with the interface, whereas the parallel wires apparently can be continued indefinitely. The various types of wires share local hydrogen bonding patterns and so could easily connect together. In our model building of several representative wires, we investigated the limitations with regard to type of and combinations of side chains. We also determined possible variations in the origins of such side chains on the helical backbones. These preliminary model building studies provide the basis for determining possible hydrogen bonding between the helical segments of membrane proteins. From these data we are formulating preliminary proposals for the helix-helix interactions of the bacteriorhodopsin molecule, which are to be presented in future paper.