Allosteric Interactions between Proteins on DNA and Membranes

细胞中基因的调节是由蛋白质与DNA的结合/解离控制的。通常，一种蛋白质的结合会改变DNA分子上另一种不同蛋白质在远处的结合亲和力。这种现象被称为“变构”；它在酶中得到了广泛的研究，但还没有通过DNA进行研究，因为DNA大多被认为是为蛋白质提供结合位点的刚性物体。通过DNA的变构作用在以前的许多实验研究中都有涉及，包括在药物分子的结合中，但还没有通过将DNA视为由结合蛋白局部变形的弹性(而不是刚性)分子的力学理论来理解。与脂质双层结合的蛋白质引起的类似的弹性变形也会导致变构相互作用，这是细胞过程的关键，例如，物质进出细胞所需的胞内和胞外作用。通常，变构还涉及蛋白质之间的熵力，这是分隔蛋白质的弹性介质(DNA或类脂膜)的布朗运动引起的波动的结果。这项研究的总体目标是通过一种数学理论来定量描述蛋白质在DNA和脂膜上的变构相互作用，该理论将蛋白质视为弹性物体，同时解释它们的布朗波动。该模型将显著提高对活细胞中基因调控方式的理解。该项目将包括对研究生的指导，对本科生和硕士研究生的指导。PI还将通过在国际会议上组织研讨会和高级学校，与宾夕法尼亚大学MRSEC和纳米生物界面中心合作开展针对高中(少数族裔)学生和教师的NanoDay和其他活动，开展外联活动。该项目将通过DNA促进对变构相互作用的基本理解，从而解决该领域长期存在的悬而未决的问题，并为该主题的丰富实验数据提供量化解释。特别是，这个项目将展示DNA的双杆模型如何描述蛋白质在单个碱基对水平上引起的变形，以及由于DNA的螺旋性质，这些变形产生的能量是如何正弦调制的。对于脂膜上的蛋白质，这个项目将展示它们的弹性和熵相互作用的竞争如何导致自组装。该项目开发的新理论方法将能够定量预测蛋白质之间的变构相互作用，这是DNA或膜的机械性能以及结合蛋白质施加于它们的边界条件的函数。在这个项目中进行的分析将把蛋白质在DNA和脂膜上的变构相互作用置于弹性固体中缺陷相互作用的更广泛的理论背景中。

The regulation of genes in cells is controlled by the binding/unbinding of proteins on DNA. Often, the binding of one protein changes the binding affinity of a different protein at a distant site on the DNA molecule. This phenomenon is called "allostery"; it has been extensively studied in enzymes, but not through DNA which has mostly been regarded as a rigid object that provides binding sites for proteins. Allostery through DNA has been implicated in many previous experimental studies, including in the binding of drug molecules, but it has not been understood through a mechanical theory which regards DNA as an elastic (not rigid) molecule that is locally deformed by the binding proteins. Similar elastic deformations caused by proteins binding to lipid bilayers also result in allosteric interactions that are responsible for cellular processes, such as, endo- and exo-cytosis required for transport of materials into and out of cells. Often, allostery also involves entropic forces between the proteins that are the result of fluctuations caused by Brownian motion of the elastic media (DNA or lipid membrane) separating them. The overall goal of this research program is to quantitatively describe allosteric interactions between proteins on DNA and lipid membranes through a mathematical theory that regards them as elastic objects while accounting for their Brownian fluctuations. The model will significantly improve understanding of how genes are regulated in living cells. The project will include instruction of graduate students, mentoring of undergraduates and masters students. The PI will also perform outreach through organizing symposia and advanced schools in international conferences, and working with the Penn MRSEC and the Nano Bio Interface Center for NanoDay and other activities targeted at high school (minority) students and teachers.This project will advance the fundamental understanding of allosteric interactions through DNA, thus addressing long-standing open questions in the field and providing quantitative explanations for the wealth of experimental data on the subject. In particular, this project will show how a birod model for DNA can describe the deformations caused by proteins at a single base-pair level, and how the energy due to these deformations is sinusoidally modulated due the helical nature of DNA. For proteins on lipid membranes this project will show how self-assembly may be caused by the competition of their elastic and entropic interactions. The new theoretical approaches developed in this project will enable quantitative predictions of allosteric interactions between proteins as a function of the mechanical properties of the DNA or membrane and the boundary conditions imposed on them by the binding proteins. The analysis performed in this project will place allosteric interactions of proteins on DNA and lipid membranes in the broader context of theories for the interactions of defects in elastic solids.