Inside the beta sheet

Charlotte Deane1, Oxford University

Beta sheets are one of the two common repeating structures found in protein structures. They make up approximately 25% of globular proteins. Despite their importance in structure they are not well or fully understood. The non-local nature of beta sheet interactions makes them far harder to predict both with secondary structure prediction algorithms and in 3D novel fold predictors [1] . It has also been shown repeatedly that proteins, fragments or peptides designed to show beta sheet behaviour often aggregate and are insoluble [2-5] This aggregation has become of interest in the light of our understanding that the amyloid fibrils produced in some disease states or by harsh treatment in vitro have a beta sheet structure [6]. A subset of 1152 non-homologus chains from the Protein Data Bank with less than 30% identity and resolution better than 1.8A and R factor less than 25 were used to investigate the properties of beta sheets. In order to improve the prediction of protein structure/folding and better understand amyloid (and general aggregate) formation. It has previously been established that different amino acid residues have measurably different propensities for forming beta sheets [7]. This propensity is now also shown to depend upon the type of beta strand parallel/anti-parallel as well as its position as a central or edge strand. These propensities are not just dependent upon the buried or exposed nature of the strand. We further investigate those residues that act as beta caps (residues found at the terminus of a strand) clear patterns of behaviour indicate that not only do certain residues act as beta caps preferentially but these preferences can also be further sub divided by N and C termini positions of the strand as well as strand type. 1. Ruczinski, I., et al., Distributions of beta sheets in proteins with application to structure prediction. Proteins, 2002. 48(1): p. 85-97. 2. Richardson, J.S. and D.C. Richardson, Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A, 2002. 99(5): p. 2754-9. 3. Richardson, J.S., et al., Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J, 1992. 63(5): p. 1185-209. 4. Mattice, W.L., The beta-sheet to coil transition. Annu Rev Biophys Biophys Chem, 1989. 18: p. 93-111. 5. Mutter, M., Nature's rules and chemist's tools: a way for creating novel proteins. Trends Biochem Sci, 1988. 13(7): p. 260-5. 6. Sunde, M. and C. Blake, The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv Protein Chem, 1997. 50: p. 123-59. 7. Swindells, M.B., M.W. MacArthur, and J.M. Thornton, Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol, 1995. 2(7): p. 596-603.