Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation

Abstract

The fact that natural β-sheet proteins are usually soluble but that fragments or designs of β structure usually aggregate suggests that natural β proteins must somehow be designed to avoid this problem. Regular β-sheet edges are dangerous, because they are already in the right conformation to interact with any other β strand they encounter. We surveyed edge strands in a large sample of all-β proteins to tabulate features that could protect against further β-sheet interactions. β-barrels, of course, avoid edges altogether by continuous H-bonding around the barrel cylinder. Parallel β-helix proteins protect their β-sheet ends by covering them with loops of other structure. β-propeller and single-sheet proteins use a combination of β-bulges, prolines, strategically placed charges, very short edge strands, and loop coverage. β-sandwich proteins favor placing an inward-pointing charged side chain on one of the edge strands where it would be buried by dimerization; they also use bulges, prolines, and other mechanisms. One recent β-hairpin design has a constrained twist too great for accommodation into a larger β-sheet, whereas some β-sheet edges are protected by the bend and reverse twist produced by an Lβ glycine. All free edge strands were seen to be protected, usually by several redundant mechanisms. In contrast, edge strands that natively form β H-bonded dimers or rings have long, regular stretches without such protection. These results are relevant to understanding how proteins may assemble into β-sheet amyloid fibers, and they are especially applicable to the de novo design of β structure. Many edge-protection strategies used by natural proteins are beyond our current abilities to constrain by design, but one possibility stands out as especially useful: a single charged side chain near the middle of what would ordinarily be the hydrophobic side of the edge β strand. This minimal negative-design strategy changes only one residue, requires no backbone distortion, and is easy to design. The accompanying paper [Wang, W. & Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760–2765] makes use of the inward-pointing charge strategy with great success, turning highly aggregated β-sandwich designs into soluble monomers.