P-bulge

Fig. 43. Four superimposed examples of G1 p bulges with associated type II tight turns trypsin Gly-133, Thr-134 opposite Ile-162 elastase Gly-204, Gly-205 opposite Thr-221 Bence-Jones REI VL Gly-16, Asp-17 opposite Leu-78 and cytochrome c Gly-37, Arg-38 opposite Trp-59. The tight turn is the small hydrogen-bonded loop at the lower left its plane is approximately perpendicular to the plane of the bulge. The a-carbon in the lower right comer of the loop is the required glycine in position 3 of the turn and position 1 of the bulge.

Bromoperoxidase(s) 856 Bronsted equation in basicity 490 Bronsted plot 309, 490 Brown, Michael S. 84 Brownian movement 461 Brucellosis 7 Bryophyta 29 Buchner, Edward 83,456 Buffer(s) 97-98 table 99 volatile 98 P Bulge 66,67s Burkitt s lymphoma 572, 576 Butyrylcholinesterase 634... 

Considering the second cluster of E-L2-E, about one fourth of the linkers adopt turn type II conformation, although they are known to occur seldom in haiipins. Few of the members of this structural sub-family have medium to heavily twisted P-strands and the linker has both C -O(i) to N-H(i+3) as well as has both C -O(i) to N-H(i+3) as well as N-H(i) to C -0(i+3) hytogen bonds (Figure 4). The alx)ve clusters correspond to chain-reversal linkers of E-L2-E. A third cluster is found to be quite variable and constitutes the "non-chain-reversal linker", as found in the distance cluster (Fig.3a). Some of these correspond to P-bulges, where (]), /... 

The tendency for a P sheet to fold into a cylinder is encouraged in antiparallel P structures by the existence of a common irregularity called the p bulge. Tizs As illustrated in Fig. 2-18, a p bulge contains an extra residue inserted into one of the chains. In the second... 

Figure 2-18 Typical P bulges in antiparallel pleated sheets. The residues Rj, R2, and R identify the bulges. (A) A "classic" P bulge, in which ( )j and /j are nearly those of an a helix while other torsion angles are approximately those of regular P structures. (B) The G1 bulge in which the first residue is glycine with

Between the nucleophilic and acid-base glutamates in the linear sequence lies a catalytically important assisting aspartate. GH 16 can be divided into two sub-families. The first, including laminarases and agarases, has an active site linear sequence Glu(nucleophile)-Hph-Asp(assist)-Hph-Met-Glu(acid/base), where Hph is a hydrophobic amino acid such as isoleucine. The second subfamily does not possess the methionine. The X-ray structures of the enzymes indicate that this extra Met residue distorts a p-strand to make a p-bulge . 

A p-bulge is a common nonrepetitive irregularity found in antiparallel p-sheets. A misalignment occurs between strands of the p-sheet, causing one side to bow outward. 

The P-strand at two diagonally opposite comers passes from one layer to the next without interruption. The bend in the P packing is usually produced by local coiUng of the strand, a P-tum of a P bulge. The large majority of the known assemblies of p sheets are two-layer stractures with limited chain topologies, namely hairpin, Greek key and jelly roll for two, four and six strands respectively. 

Fig. 2.20. The P bulge (according to Richardson et ai, 1978). A P bulge indicated by the outlined region is at the edge of an antiparallel p sheet. Smaller triangles represent side chains that are below the sheet, larger triangles those that are above it.

---