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Document The first strand of each sheet is connected across the top of the submit to the fourth strand of the preceding sheet. The N-terminus lies across the bottom of the subunit, and builds the fourth strand of the sixth sheet before entering the first sheet. The C-terminus strand builds the third strand of the sixth sheet, enters the subunit interface from the bottom, and runs parallel with the outermost (fourth) strand of the sixth β sheet. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_466.html (2 of 2) [4/9/2004 12:15:39 AM]
Document B. Protein Structure Page 467 The 6 β sheets of the subunit, although topologically identical, vary in size and detailed structure. However, the six sheets can be considered as maintaining an approximate 6-fold symmetry relationship to each other about an axis parallel to the mean direction of the first strand of each sheet and through the centroid of these directions. Four disulfide bridges are formed between adjacent sheets as well as two between the sheets, which distort the sheet structure. Similar pairing has now been found in one of the domains of CD4 [57]. Also short β bulges occur on the inner and outer strands of most of the sheets. The packing of the β sheets is stabilized by hydrophobic interactions at the sheet interfaces and hydrogen bonding at the periphery of the sheets. In addition the intersheet disulfide bonds and ion pairs stabilize the structure. In general the loops connectioning the β sheets are shorter and tighter on the bottom of the subunit compared to the outer loops, which tends to be more elaborate. The intersheet loop connecting the fourth and fifth loop is the most extensive in the structure and is stabilized primarily by a disulfide bridge between Cys318 (sequence numbering of A/Tokyo/3/67 will be used throughout) and Cys337, a conserved ion pair Asp330—Arg364, and a putative Ca 2+ ion binding site. This calcium binding site has approximate octahedral coordination with the main-chain oxygens of residues 293, 297, 345, and 348, a carboxylate oxygen of Asp324, and a water molecule in N2 and type B neuraminidases. In N9, the mainchain oxygen at 343 is replaced by a water molecule. Calcium has been shown to be necessary for neuraminidase activity [58] and this site is connected to the active site via conserved residues; however, the functional role of calcium in the structure is unknown, although it has been shown that calcium is essential for the thermostability of the molecule [59]. C. Carbohydrate Structure Carbohydrate at four N-linked glycosylation sites were observed in N2 neuraminidase at residues 86, 146, 200, and 234 in the x-ray structure. Two N-acetylglucosamines were resolved at Asp86 and Asp234, both at the bottom surface of the monomer. The carbohydrate at Asp200 consists of eight sugar residues with linkages consistent with known mannose-rich simple N-linked carbohydrates [60]. This oligosaccharide emerges from the side of the monomer and covers a neighboring subunit (see Figure 4). The oligosaccharide site at Asn146 is the most conserved of all neuraminidase glucosylation sites, except that of the neurovirulent virus A/WSN/33 [61]. The absence of this glycosylation site in A/WSN/33 has been shown to confer neurovirulence in mice [62]. It is a complex sugar containing Nacetylgalactosamine [63] that is not found in any other of the known oligosaccharides of influenza virus glycoproteins and is the only glycopeptide antigenically related to chick embryo “host antigen” http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_467.html [4/9/2004 12:16:34 AM]
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Structure-based Drug Design 14 Stru
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