Structural and functional analysis of caspase active sites
Structural and functional analysis of caspase active sites
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DOI：
10.1021/bi020593l
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发表时间：
2003-04-15
期刊：
影响因子：
2.9
通讯作者：
Wu, JC
中科院分区：
文献类型：
--
作者：
Chéreau, D;Kodandapani, L;Wu, JC
将caspase1、3、7和8的氨基酸序列与其已发表的三维结构进行比对。将得到的比对作为模板来比较caspase 2、4-6和9-11的一级结构，以建立3D同源模型。随后使用从一系列底物类抑制剂获得的结构-活性关系数据对结构模型进行了改进和验证。所有半胱氨酸天冬氨酸氨基转移酶都具有相同的S 1和催化二聚体结构，但具有不同的S2-S4结构。这11个caspase的S2片段可以简单地分为两类：Csp3、-6和-7为一类，Csp1、-2、-4、-5、-8、-9、-10和-11为另一类。Csp3、-6和-7的S2片段比其他8个caspase的片段小，仅限于结合小的P2残基，如Ala和Val。在S3位点，所有caspase中都存在保守的Arg，这表明Glu可能是普遍首选的P3残基。Csp8和Csp9在这个口袋中有一个额外的Arg，可以进一步增强P3 Glu的结合，而Csp2在保守的Arg附近有一个Glu。因此，Csp2是唯一能同时容纳正负电荷P3的caspase。在S4，Csp1、-4、-5和-11与它们的结构和结合基团偏好密切相关；都有一个大的疏水口袋，并喜欢大的疏水残基，如Trp。Csp2、-3和-7的S4代表具有高度特异地结合天冬氨酸的构象的相反基团。Csp6、-8、-9和-10的S4结构似乎是两个极端的杂交，对任何P4几乎没有特异性。这项工作揭示的信息为设计具有理想特异性的有效caspase抑制剂提供了指导。
Amino acid sequences of caspases 1, 3, 7, and 8 were aligned with their published three-dimensional (3D) structures. The resultant alignment was used as a template to compare the primary structures of caspases 2, 4-6, and 9-11 to build 3D homology models. The structural models were subsequently refined and validated using structure-activity relationship data obtained from an array of substrate-like inhibitors. All caspases were shown to have identical S 1 and catalytic dyad architecture but diverse S2-S4 structures. S2 pockets of these 11 caspases can be briefly categorized into two groups: Csp3, -6, and -7 as one and Csp1, -2, -4, -5, -8, -9, -10, and -11 as the other. S2 pockets of Csp3, -6, and -7 are smaller than those of the other eight caspases, and are limited to binding small P2 residues such as Ala and Val. At the S3 site, the presence of a conserved Arg in all caspases suggests that Glu would be a universally preferred P3 residue. Csp8 and Csp9 have an additional Arg in this pocket that can further enhance the binding of a P3 Glu, whereas Csp2 has a Glu adjacent to the conserved Arg. As such, Csp2 is the only caspase that can accommodate both positively and negatively charged P3. At S4, Csp1, -4, -5, and -11 are closely related with respect to their structures and binder preferences; all have a large hydrophobic pocket and prefer large hydrophobic residues such as Trp. S4 of Csp2, -3, and -7 represents an opposite group with a conformation that is highly specific in binding an Asp. The S4 structures of Csp6, -8, -9, and -10 appear to be hybrids of the two extremes, and have little specificity for any P4. Information revealed from this work provides a guide for designing potent caspase inhibitors with desirable specificity.