Myrta S. Montal

Synthetic peptides and proteins as models for pore-forming structure of channel proteins.

Publisher Summary This chapter discusses a strategy to identify, in the primary structure of channel proteins, segments that determine the functional characteristics of the protein. Amphipathic α-helical segments are identified in the primary structure using secondary structure prediction algorithms. Segments are selected based on sequence similarity between members of a superfamily of channel proteins. Synthesis of the four-helix bundle protein is accomplished by a two-step procedure: the template molecule is synthesized using orthogonal lysine side-chain protection followed by the simultaneous assembly of peptide blocks. Oligomeric clusters of amphipathic α-helices, whether self-assembled in the lipid bilayer or covalently attached to a template molecule in a four-helix bundle configuration, form ionic channels in bilayers. The evidence that fundamental pore properties may be reproduced within a bundle of α-helices representing selected sequences from the primary structure of a channel protein lends credence to the notion that a cluster of amphipathic α-helices constitutes a general pore-forming motif for channel proteins.

CHANNEL PROTEINS: FROM ANATOMY TO DESIGN

The precise mechanisms of action of channel proteins have not been delineated; accordingly, we aim to identify principles that define the biological design of channel proteins, to realize the molecular design of a pore forming structure, and to use it towards understanding the molecular basis of ionic selectivity and channel blockade. As a first step towards the design of channel proteins, we set out to model only the inner pore-forming element. This endeavor has suggested a molecular blueprint for the pore-forming structure of channel proteins: a bundle of amphipathic a-helices that cluster together to generate a central hydrophilic channel. The pore-forming structures are engineered from functional modules that represent the amino acid sequence of authentic proteins and refined to accommodate specific functional characteristics. The strength of the strategy is that the design can be realized and the validity of the proposed structural motif evaluated experimentally. Accordingly, four-helix bundle proteins that span the lipid bilayer and provide binding sites for permeant ions and for specific channel modulators have been generated; these synthetic channel proteins mimic properties of corresponding authentic proteins. Since high resolution structural information is not yet available, the uniqueness and significance of this approach is evident: the ability to produce proteins with predicted functional attributes by emulating the authentic sequences affords, for the first time, clues to the biological design of channel proteins. The emergence of the structure model integrated with the benefits of chemical synthesis provides, a means to evaluate sites of action for channel modifiers and may facilitate the conceptual design of channel blocking drugs.