Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA.
Department of Nanobioscience, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA.
Acta Crystallogr F Struct Biol Commun. 2024 Jan 1;80(Pt 1):1-12. doi: 10.1107/S2053230X23010749.
Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.
蛋白酪氨酸磷酸酶 1B（PTP1B）在细胞内稳态中发挥着重要作用，是治疗多种人类疾病（包括糖尿病、肥胖症和乳腺癌）的高度验证的治疗靶点。然而，关于构象变化如何通过 PTP1B 的结构传递信息，以实现配体的变构调节或对突变的功能响应，仍有许多需要了解。高分辨率 X 射线晶体学可以提供蛋白质构象集合体的独特窗口，但即使是高分辨率结构的比较也常常因数据集之间的差异而变得复杂，包括非同晶性。在这里，目前共解析了约 350 个 PTP1B 结构，展示了迄今为止apo 野生型（WT）PTP1B 的最高分辨率晶体结构。该结构是 PTP1B 中罕见的晶体形式，有两个独特的蛋白质拷贝，表现出不同的构象异质性模式，允许在同一不对称单元内的两条链之间进行局部无序的对照比较。在apo 结构中以及在最近报道的几种高分辨率配体结合结构之间对这些链之间的构象差异进行了检测。还检查了最近报道的激活双突变体的高分辨率结构的电子密度图，并发现了突变体结构中未建模的替代构象，这些构象与新 WT 结构中增强的构象异质性区域相吻合。这些结果验证了这些突变通过增强局部动力学起作用的观点，并表明 WT 酶中存在对这种变化的潜在敏感性。这些新数据和分析共同提供了 PTP1B 构象集合体的详细视图，并强调了高分辨率晶体学在阐明与功能相关的构象异质性方面的实用性。
