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Document Figure3 (a) Stereo diagram of the secondary structural elements of IL-1β. Produced by Molscript [106]. (b) Stereo plot of all the atoms of IL-1β viewed parallel to the axis of the barrel. Page 404 42,44], and once by NMR [43]. The four crystal structures, each to 2.0 Å, were all solved in the same space group, P4 3, each structure being in relatively good agreement with the others [53]. As pointed out previously, the molecule adopts a β-trefoil fold with about 65% of the molecule in beta sheet and 35% in random coil/turn (Figure 3a). The IL-1β molecule resembles a conical barrel with a shallow open face on one end and a closed face on the other. The length of the long tubular core of the molecule is about 23 Å. Twelve antiparallel β http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_404.html (1 of 2) [4/5/2004 5:44:35 PM]
Document Page 405 strands constitute the secondary structural elements of IL-1β. Three pairs of β strands (one pair from each of the fragments) form the six-stranded barrel and the other three pairs cover one end of the barrel, referred to as the “closed end”. The amino and carboxy termini are close to each other at the “open end” of the barrel (Figure 3b). The overall structure of the molecule consists of three similar fragments (F1, F2, F3) related by a pseudo-3-fold symmetry, with each fragment having a βββLβ motif. Residues 1 to 52 (F1), 53 to 107 (F2), and 108 to 153 (F3) form these fragments. These βββLβ motifs can be superposed to display structural similarities. The core of the molecule consists entirely of hydrophobic residues, two-thirds of which are leucines and phenylalanines—a feature that seems to be essential to maintain the structural integrity of the molecule. Most of the aromatic groups have their planes aligned along the barrel axis and both ends of the barrel have concentrations of exposed polar residues that may be involved in binding interactions with the receptor (see below). No alpha-helical structure is observed in IL-1β although one short region of 3 10 helix is observed between residues Gln34 and Gln38. Two of the β hairpins are in the open end and three are at the closed end. Residues 18 to 28, 69 to 82, and 122 to 135 form the three β hairpins at the closed end where three strands (residues 24–28, 78–82, and 129–135) are in close proximity and form three sides of a triangle, covering this end of the barrel. C. Open End of the Barrel Analysis of the surface of IL-1 reveals an epitope consisting of many polar residues widely spaced, approximately in an annular fashion, around the open end of the barrel (Figure 3b). It has a broad surface area containing many polar residues [42]. Residues from six β-turns [type I, β turn 1 (T1=11- 17); type III, β turn 3 (T3=33-36); type I', β turn 6 (T6=52-55); type I, β turn 7 (T7=62-65); type I, β turn 9 (T9=86-89); type I', β turn 10 (T10=106-109)] are present in this open end. There is a β bulge between strands β4 and β5 in one of the hairpins; this bulge may play a key role in the formation of the putative binding surface. The β bulge in IL-1 is of the “wide” type stabilized by multiple interactions, whose conformation is such as to place the side chains of polar residues (Glu51, Asn53, Asp54) in the proposed binding surface, fanning out in the direction of the open end of the barrel. Multiple interactions serve to stabilize the strained conformation of the loop, between residue 86 and 94, presenting the side chains of Asp86, Lys88, Asn89, and Lys93 at the open end of the barrel. In well-defined residues having abnormal φ, ψ values, strained conformations often may be related to functional properties and are observed either in the active site or in the region responsible for its activity. The reason for having such strains in the loop at this open end may be to place these charged side chains in the putative receptor binding surface. There is a short 3 10-helix in the region between β3 and http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_405.html [4/5/2004 5:44:42 PM]
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Structure-based Drug Design 14 Stru
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Document D ddI, 152 tumour necrosis
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