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Unformatted text preview: Natural b-sheet proteins use negative design to avoid edge-to-edge aggregation Jane S. Richardson* and David C. Richardson Department of Biochemistry, Duke University, Durham, NC 27710-3711 Contributed by Jane S. Richardson, December 28, 2001 The fact that natural b-sheet proteins are usually soluble but that fragments or designs of b structure usually aggregate suggests that natural b proteins must somehow be designed to avoid this problem. Regular b-sheet edges are dangerous, because they are already in the right conformation to interact with any other b strand they encounter. We surveyed edge strands in a large sample of all- b proteins to tabulate features that could protect against further b-sheet interactions. b-barrels, of course, avoid edges altogether by continuous H-bonding around the barrel cylinder. Parallel b-helix proteins protect their b-sheet ends by covering them with loops of other structure. b-propeller and single-sheet proteins use a combination of b-bulges, prolines, strategically placed charges, very short edge strands, and loop coverage. b-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 mecha- nisms. One recent b-hairpin design has a constrained twist too great for accommodation into a larger b-sheet, whereas some b-sheet edges are protected by the bend and reverse twist pro- duced by an L b glycine. All free edge strands were seen to be protected, usually by several redundant mechanisms. In contrast, edge strands that natively form b H-bonded dimers or rings have long, regular stretches without such protection. These results are relevant to understanding how proteins may assemble into b-sheet amyloid fibers, and they are especially applicable to the de novo design of b 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 b 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 b-sandwich de- signs into soluble monomers. A ll- b folds are a common, major category of protein struc- ture, and as produced in the cell they fold up successfully with only a few isolated cases of aggregation or insolubility. In contrast, fragments or peptides from b-sheet proteins have long had a reputation for insolubility (1), and it is now known that the amyloid fibrils produced in some disease states or by harsh treatment in vitro have a b-sheet structure (2). Also, de novo designs of b proteins almost all have severe problems of insol-...
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