A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site.
A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site.
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DOI：
10.1039/c7ob00526a
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发表时间：
2017-05-16
影响因子：
3.2
通讯作者：
Wipf P
中科院分区：
文献类型：
--
作者：
Burnett JC;Lim C;Peyser BD;Samankumara LP;Kovaliov M;Colombo R;Bulfer SL;LaPorte MG;Hermone AR;McGrath CF;Arkin MR;Gussio R;Huryn DM;Wipf P
两个相邻的苏氨酸的旋转门运动建立了一个动态的侧链相互作用，可以在小分子变构蛋白结合位点容纳极性和非极性配体。基于SAR数据以及AAA ATP酶p97的X射线和冷冻-EM结构的计算模型用于分析成对苏氨酸在抑制剂位点的作用。具体而言，Thr侧链羟基形成易于容纳小的高极性配体取代基的氢键网络。相反，X1扭转的直径旋转150-180°将侧链β-甲基定向到结合裂缝中，产生可以容纳小的非极性取代基的疏水口袋。发现该基序对于合理化p97抑制剂的结构集中集的亲和力至关重要，其涵盖效力的> 2，000倍变化，偏好小-高极性或小-非极性基团。通过PDB搜索进一步验证了苏氨酸旋转门基序，该搜索确定了PKB中配体相互作用中的类似结合模式，以及通过NMR结构分析证明了相邻Thr对之间的额外齿轮样相互作用。结合，这些数据表明，苏氨酸旋转门基序可能是一个一般的功能感兴趣的蛋白质结合口袋。两个相邻的苏氨酸的旋转门运动在变构结合位点中容纳极性和非极性配体。
The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents. Conversely, diametric rotation of the χ1 torsion by 150–180° orients the side chain β-methyl groups into the binding cleft, creating a hydrophobic pocket that can accommodate small, apolar substituents. This motif was found to be critical for rationalizing the affinities of a structurally focused set of inhibitors of p97 covering a >2,000-fold variation in potencies, with a preference for either small-highly polar or small-apolar groups. The threonine turnstile motif was further validated by a PDB search that identified analogous binding modes in ligand interactions in PKB, as well as by an analysis of NMR structures demonstrating additional gear-like interactions between adjacent Thr pairs. Combined, these data suggest that the threonine turnstile motif may be a general feature of interest in protein binding pockets. The turnstile motion of two neighboring threonines accommodates both polar and apolar ligands in an allosteric binding site.