Multi-scale enhanced sampling of disordered proteins

 描述(申请人提供)：抑癌基因P53是人类癌症中最常见的突变蛋白。对乳腺癌的临床研究表明，P53突变类型可能与癌症预后、对药物治疗的反应和患者生存有关。因此，了解不同类型P53失活的分子基础是至关重要的 以了解突变的生物学后果，并评估潜在的癌症干预策略。该项目通过确定肿瘤突变体在其反式激活结构域(TAD)中的P53失活的结构和功能机制，为这一重要目标做出了贡献。有趣的是，P53-TAD是一种固有的无序蛋白(IDP)。它的性质是由不同种类的构象集合控制的，不适合用传统的方法来描述，传统的方法倾向于描述一组连贯的相似结构。在描述IDP集合及其相互作用方面，可靠的原子模拟具有重要和变革性的作用。同时，像P53-TAD这样的IDPs的异质性和动态性也提出了重要的挑战，推动了蛋白质力场精度和构象采样能力的极限。在这个项目中，我们将利用我们在开发先进技术方面的丰富经验和最新贡献，对国内流离失所者进行原子模拟，并追求两个平行的具体目标。在目标1中，我们将开发新的多尺度增强采样技术，用于高效和准确地对IDP系综及其相互作用进行原子模拟。在目标2中，我们将把这些先进的模拟技术与核磁共振和其他生物物理实验相结合，以确定p53-TAD癌症突变的结构和功能后果。具体地说，我们将测试一个新的假设，即TAD癌症突变可以调节未结合的构象集合，扰乱P53与负调控因子MDM2和一般转录共激活因子CBP之间的平衡，并进一步改变这种平衡是如何通过P53-TAD的多位点磷酸化来调节的。该项目的成功完成将为蛋白质构象平衡和转变的从头模拟提供尖端计算工具。这项拟议的研究还代表了对疾病突变如何影响p53-TAD结构-功能关系的生物物理基础的首次系统研究，并为理解许多其他IDPs提供了一个范例，这些IDPs是细胞调控网络的关键组成部分，在主要疾病途径中过度表达。

 DESCRIPTION (provided by applicant): The tumor suppressor p53 is the most frequently mutated protein in human cancers. Clinical studies of breast cancer have suggested that the type of p53 mutation can be linked to cancer prognosis, response to drug treatment, and patient survival. It is thus crucial to understand the molecular basis of p53 inactivation by various types of mutations, so as to understand the biological consequences and assess potential cancer intervention strategies. This project contributes to this important goal by determining the structural and functional mechanisms of p53 inactivation by cancer mutants in its transactivation domain (TAD). Intriguingly, p53-TAD is an intrinsically disordered protein (IDP). Its properties are governed by a heterogeneous ensemble of conformations that does not lend itself to description using traditional methods that are geared toward describing a coherent set of similar structures. Reliable atomistic simulations have an important and transformative role to play in terms of describing IDP ensembles and their interactions. At the same time, the heterogeneous and dynamic nature of IDPs like p53-TAD also present important challenges that push the limit of the protein force field accuracy and conformational sampling capability. In this project, we wil leverage our extensive experience and recent contributions in developing advanced techniques for atomistic simulation of IDPs and pursue two parallel specific aims. In Aim 1, we will develop novel multi-scale enhanced sampling techniques for efficient and accurate atomistic simulations of IDP ensembles and their interaction. In Aim 2, we will integrate these advanced simulation techniques with NMR and other biophysical experiments to determine the structural and functional consequences of p53-TAD cancer mutations. Specifically, we will test a novel hypothesis that TAD cancer mutations can modulate unbound conformational ensembles, perturb the balance between p53 binding to negative regulator MDM2 and the general transcriptional co-activator CBP, and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. Successful completion of this project will provide cutting-edge computational tools for de novo simulation of protein conformational equilibria and transitions. The proposed research also represents the first systematic study of the biophysical basis of how disease mutants affect the structure-function relationship of p53-TAD, and provides a paradigm for understanding many other IDPs that are key components of cellular regulatory networks and over-represented in major disease pathways.