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Document Figure 6 (a) CPK representation of the individual structure of AP-B [47], which is closest to the average over the whole molecule, showing residues thought to contribute to the cardioactive pharmacophore. The surfaces of residues 7 and 9 are shaded black, those of 14, 37, 39, and 48 dark grey, and that of 35 lighter grey. As discussed in the text, the primary functions of Asp9 (the side chain of which is hardly visible in this view) and Asn35 may be to maintain the local structure in an active conformation, but it cannot be excluded that they also interact directly with the sodium channel. In AP-B the cationic side chains of Arg12 and Lys49 are also important, but it appears that their roles can be compensated for by nearby cationic side chains (Arg14 and Lys48, respectively) and that they favor binding to the neuronal sodium channel rather than the cardiac channel [53]. (b) Connolly surface of AP-B in the same orientation as in part a, with the charged residues Asp7, Asp9, Arg14, Lys37, and Lys48 highlighted. This figure was generated using Insight (Biosym Technologies). http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_311.html (2 of 2) [4/5/2004 5:24:01 PM]
Document Page 312 In peptide—protein and protein—protein interactions the size of the buried surface area ranges from 400 Å 2 to 1400 Å 2 [66]. In the potassium channel blocker charybdotoxin, 5–8 residues with surface areas of 530–850 Å 2 were found to be essential for binding, depending on the type of potassium channel investigated [67,68]. In the calcium channel blocker ω-conotoxin GVIA, an alanine scan identified only two residues, Lys2 and Tyr13, that were important for activity [69]. It is likely, however, that the number of residues contributing to the binding surface is greater than this, particularly given the high affinity of this toxin for its receptor. If we consider a larger ligand such as human growth hormone, eight of the 31 residues in the growth hormone-receptor interface contribute 85% of the binding energy and more than half make no significant contribution to the affinity [70]. A similar result was found for a growth hormone-monoclonal antibody complex, where only five residues were critical for binding [71]. In fact, the example of growth hormone may be more relevant to the anthopleurins than those of charybdotoxin and conotoxin, which function simply as ion channel blockers. Thus, we expect the essential residues in the anthopleurins to number between five and ten, a total somewhat less than previously anticipated [24]. If we ignore Asp9 and assume that only one of Arg12 or Arg14 and one of Lys48 or Lys49 are necessary, then it is likely that the residues highlighted in Figure 6 make a significant contribution to the sodium channel binding surface of the anthopleurins. They span a larger area on the surface than the essential residues in charybdotoxin, but it is important to note that the conformation of the Arg14 loop in solution is not fixed and that conformations in which the Arg14 side chain is closer to the region around Asp7 could be more representative of the sodium-channel-bound structure. For example, the distance between the Arg14 guanidino group and the Asp7 carboxylate varies from 13 to 26 Å over the family of structures of AP-A and 10 to 22 Å in AP-B. By analogy with other protein—protein interactions, it is likely that the sodium channel binding surface of the anthopleurins will include side chains that mutagenesis studies will not identify as having a significant role in binding or activity. As indicated above, alanine scanning of residues in the human growth hormone—receptor interface indicated that less than a quarter of the contact residues provided most of the binding energy [70]. Thus, we believe that the residues identified above will contribute to the sodium channel binding surface of the anthopleurins by virtue of their location on the protein surface in the immediate vicinity of residues, which clearly are important for activity. Nevertheless, some of them may make only modest contributions to binding affinity and could be altered without destroying activity. Other residues, as yet unidentified, may also make significant contributions. By analogy with other protein—protein interactions characterized to date, it is reasonable to anticipate that some of these residues will be hydrophobic, in contrast to the charged http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_312.html [4/5/2004 5:24:03 PM]
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Structure-based Drug Design 14 Stru
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