Ganguly Debabani, Chen Jianhan
Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America; Indian Institute of Engineering Science and Technology, Shibpur Howrah, India.
Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America.
PLoS Comput Biol. 2015 Apr 21;11(4):e1004247. doi: 10.1371/journal.pcbi.1004247. eCollection 2015 Apr.
Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles.
内在无序蛋白（IDP）常常与癌症等人类疾病相关，并且约四分之一与疾病相关的错义突变已被定位到预测的无序区域。了解这些突变如何影响IDP的结构-功能关系是一项艰巨的任务，需要对无序构象集合进行详细表征。有人提出，隐式溶剂与增强采样相结合，能够在对突变以及翻译后修饰对IDP结构和相互作用的影响进行系统和比较评估所需的准确性和效率之间取得平衡。在此，我们利用最近开发的引导退火增强采样的副本交换技术，在隐式溶剂中计算肿瘤抑制因子p53的内在无序反式激活结构域（TAD）以及几种癌症相关突变体的收敛良好的原子构象集合。通过与提供二级和三级结构信息的几种实验数据进行定量比较，对模拟结果进行了严格评估。结果表明，计算得到的集合定量地再现了野生型p53-TAD的局部结构特征以及K24N突变的影响。在三级水平上，模拟的集合过于紧凑，尽管它们似乎定性地概括了瞬时长程接触的整体特征。一个关键发现是，虽然p53-TAD及其癌症突变体采样了一组相似的构象状态，但癌症突变体可能会引入局部和长程结构调制，从而可能扰乱p53与各种调节蛋白结合的平衡，并进一步改变这种平衡如何通过p53-TAD的多位点磷酸化来调节。当前的研究清楚地证明了原子模拟在详细表征IDP构象方面的前景，同时也揭示了当前隐式溶剂蛋白质力场中的重要局限性，为了可靠地描述无序集合的长程结构特征，必须充分解决这些局限性。
