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beta-bulge-pnas - Proc Natl Acad Sd USA Vol 75 No 6 pp...

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Proc. Natl. Acad. Sd. USA Vol. 75, No. 6, pp. 2574-2578, June 1978 Biochemistry The v3 bulge: A common small unit of nonrepetitive protein structure (I sheet/,8 barrel/secondary structure/tight turn/strand twist) JANE S. RICHARDSONt, ELIZABETH D. GETZOFFt, AND DAVID C. RICHARDSONt t Anatomy Department and * Biochemistry Department, Duke University, Durham, North Carolina 27710 Communicated by C. B. Anfinsen, February 16,1978 ABSTRACr A ft bulge is a region between two consecutive a-4ype hydrogen bonds which includes two residues (positions 1 and 2) on one strand opposite a single residue (position x) on the other strand. Compared to regular I structure, a ,B bulge puts the usual alternation of side-chain direction out of register on one of the strands, introduces a slight bend in the P sheet, and locally accentuates the usual right-handed strand twist. Almost all , bulges are between antiparallel strands, usually between a narrow rather than a wide pair of hydrogen bonds. Ninety-one examples are listed. The two commonest types arethe "classic" P bulge, with position 1 in approximately a-helical conforma- tion, and the "GI" B bulge, with a required glycine at position 1 in approximately left-handed a-helical conformation. GI bulges almost always occur in combination with a type Iltight turn. The functional roles of 0 bulges probably include com- pensating for the effects of a single-residue insertion or deletion within P structure and providing the strong local twist required to form closed P barret structures. One of the outstanding problems in globular protein structure is the task of describing the nonrepetitive "coil" regions that are neither helices nor (3 sheets. The one really major advance in this regard was identification of the tight turn (1), a loop in which the carbonyl oxygen of residue n hydrogen bonds to, or at least is close to, the NH group of residue n + 3. If all four residues are counted as part of the tight turn and the hydrogen bond is not required, thensuch turns account for up to a third of protein structure, and their occurrence can be predicted from the sequence with a moderate degree of success (e.g., ref. 2). Several other non-a, non-,8 conformations have been described, but except for the transition to 310 or all conformation at the ends of a-helices (3), it happens that each of them has been identified for only one or a very few examples. The y turn (4), which occurs in thermolysin (5), is a tighter turn involving only three residues and a highly bent hydrogen bond. Short pieces of polyproline II structure have been identified in pancreatic trypsin inhibitor (6) and in cytochrome cssm (7). An extended- chain "e-helix" (rather similar to polyproline) has been iden- tified in chymotrypsin (8). Two cis-prolines have been dem- onstrated in the Bence-Jones dimer REI, which form a distinct subclass of tight turns with a cis-proline in position 3 (9). Al- though, surely, additional examples of all these conformations could be found in other protein structures, each of them is ap- parently rather rare.
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