Pisabarro M T, Serrano L, Wilmanns M
EMBL, Structures & Biocomputing, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
J Mol Biol. 1998 Aug 21;281(3):513-21. doi: 10.1006/jmbi.1998.1932.
The Abl-SH3 domain is implicated in negative regulation of the Abl kinase by mediating protein-protein interactions. High-affinity SH3 ligands could compete for these interactions and specifically activate the Abl kinase, providing control and a better understanding of the molecular interactions that underlie diseases where SH3 domains are involved. The p41 peptide (APSYSPPPPP) is a member of a group of peptide ligands designed to bind specifically the Abl-SH3 domain. It binds to Abl-SH3 with a Kd of 1.5 microM, whereas its affinity for the Fyn-SH3 domain is 273 microM. We have determined the crystal structure of the Abl-SH3 domain in complex with the high-affinity peptide ligand p41 at 1.6 A resolution. In the crystal structure, this peptide adopts a polyproline type II helix conformation through residue 5 to 10, and it binds in type I orientation to the Abl-SH3 domain. The tyrosine side-chain in position 4 of the peptide is hydrogen bonded to two residues in the RT-loop of the Abl-SH3 domain. The tight fit of this side-chain into the RT-loop pocket is enhanced by conformational adjustment of the main chain at position 5. The SH3 ligand peptides can be divided into two distinct parts. The N-terminal part binds to the SH3 domain in the region formed by the valley between the nSrc and RT-loops. It determines the specificity for different SH3 domains. The C-terminal part adopts a polyproline type II helix conformation. This binds to a well-conserved hydrophobic surface of the SH3 domain. Analysis of two "half"-peptides, corresponding to these ligand parts, shows that both are essential components for strong binding to the SH3 domains. The crystal structure of the Abl-SH3:p41 complex explains the high affinity and specificity of the p41 peptide towards the Abl-SH3 domain, and reveals principles that will be exploited for future design of small, high-affinity ligands to interfere efficiently with the in vivo regulation of Abl kinase activity.
Abl-SH3结构域通过介导蛋白质-蛋白质相互作用参与对Abl激酶的负调控。高亲和力的SH3配体可竞争这些相互作用并特异性激活Abl激酶，从而为涉及SH3结构域的疾病背后的分子相互作用提供调控手段并加深理解。p41肽（APSYSPPPPP）是一组设计用于特异性结合Abl-SH3结构域的肽配体中的一员。它以1.5微摩尔的解离常数（Kd）与Abl-SH3结合，而其对Fyn-SH3结构域的亲和力为273微摩尔。我们已确定了Abl-SH3结构域与高亲和力肽配体p41复合物的晶体结构，分辨率为1.6埃。在晶体结构中，该肽通过第5至10位残基呈现多聚脯氨酸II型螺旋构象，并以I型方向与Abl-SH3结构域结合。肽第4位的酪氨酸侧链与Abl-SH3结构域RT环中的两个残基形成氢键。该侧链紧密嵌入RT环口袋，这通过第5位主链的构象调整而增强。SH3配体肽可分为两个不同部分。N端部分在由nSrc环和RT环之间的谷形成的区域与SH3结构域结合。它决定了对不同SH3结构域的特异性。C端部分呈现多聚脯氨酸II型螺旋构象。它与SH3结构域一个保守的疏水表面结合。对对应于这些配体部分的两个“半”肽的分析表明，两者都是与SH3结构域强结合的必需成分。Abl-SH3:p41复合物的晶体结构解释了p41肽对Abl-SH3结构域的高亲和力和特异性，并揭示了将用于未来设计小的、高亲和力配体以有效干扰Abl激酶活性体内调控的原理。
