D. E. Shaw Research, New York, New York 10036, United States.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States.
J Chem Inf Model. 2023 Jul 10;63(13):4115-4124. doi: 10.1021/acs.jcim.3c00286. Epub 2023 Jun 28.
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin signaling pathways, making it a highly attractive target for the treatment of type II diabetes. For PTP1B to perform its enzymatic function, a loop referred to as the "WPD loop" must transition between open (catalytically incompetent) and closed (catalytically competent) conformations, which have both been resolved by X-ray crystallography. Although prior studies have established this transition as the rate-limiting step for catalysis, the transition mechanism for PTP1B and other PTPs has been unclear. Here we present an atomically detailed model of WPD loop transitions in PTP1B based on unbiased, long-timescale molecular dynamics simulations and weighted ensemble simulations. We found that a specific WPD loop region─the PDFG motif─acted as the key conformational switch, with structural changes to the motif being necessary and sufficient for transitions between long-lived open and closed states of the loop. Simulations starting from the closed state repeatedly visited open states of the loop that quickly closed again unless the infrequent conformational switching of the motif stabilized the open state. The functional importance of the PDFG motif is supported by the fact that it is well conserved across PTPs. Bioinformatic analysis shows that the PDFG motif is also conserved, and adopts two distinct conformations, in deiminases, and the related DFG motif is known to function as a conformational switch in many kinases, suggesting that PDFG-like motifs may control transitions between structurally distinct, long-lived conformational states in multiple protein families.
蛋白酪氨酸磷酸酶 1B（PTP1B）是胰岛素和瘦素信号通路的负调节剂，使其成为治疗 2 型糖尿病的极具吸引力的靶点。为了使 PTP1B 发挥其酶促功能，一个称为“WPD 环”的环必须在开放（催化无能力）和封闭（催化有能力）构象之间转变，这两种构象都已经通过 X 射线晶体学解析。尽管先前的研究已经确定这种转变是催化的限速步骤，但 PTP1B 和其他 PTP 的转变机制尚不清楚。在这里，我们根据无偏、长时程分子动力学模拟和加权组合模拟，提出了 PTP1B 中 WPD 环转变的原子细节模型。我们发现，一个特定的 WPD 环区域——PDFG 基序——充当了关键的构象开关，基序的结构变化对于环的长寿命开放和关闭状态之间的转变是必要和充分的。从封闭状态开始的模拟反复访问环的开放状态，但很快再次关闭，除非基序的罕见构象转换稳定了开放状态。PDFG 基序的功能重要性得到了支持，它在 PTP 中得到了很好的保守。生物信息学分析表明，PDFG 基序在脱氨酶中也是保守的，并采用两种不同的构象，而相关的 DFG 基序在许多激酶中被认为是构象开关，这表明 PDFG 样基序可能控制多个蛋白家族中结构不同、长寿命构象状态之间的转变。
