Allosteric Interactions between Proteins on DNA and Membranes

细胞中基因的调控是由蛋白质在DNA上的结合/解结合控制的。通常，一种蛋白质的结合会改变DNA分子上远处另一种蛋白质的结合亲和力。这种现象被称为“变构”；它已经在酶中得到了广泛的研究，但没有通过DNA进行研究，DNA主要被认为是一种为蛋白质提供结合位点的刚性物体。DNA的变构在以前的许多实验研究中都有涉及，包括药物分子的结合，但它还没有通过机械理论来理解，这种理论认为DNA是一种弹性（而不是刚性）分子，被结合蛋白质局部变形。由蛋白质与脂质双分子层结合引起的类似弹性变形也会导致变构相互作用，这种作用负责细胞过程，例如物质进出细胞运输所需的内胞和外胞作用。通常，变构也涉及蛋白质之间的熵力，这是由分离它们的弹性介质（DNA或脂质膜）的布朗运动引起的波动的结果。本研究计划的总体目标是通过数学理论定量描述DNA和脂质膜上蛋白质之间的变构相互作用，将它们视为弹性物体，同时考虑它们的布朗波动。该模型将显著提高对活细胞中基因如何调控的理解。该项目将包括研究生指导、本科生和硕士生指导。PI还将通过组织专题讨论会和高级学校参加国际会议，并与宾夕法尼亚大学MRSEC和纳米生物界面中心合作开展纳米日活动，以及针对高中（少数民族）学生和教师的其他活动，来开展外展活动。该项目将促进对DNA变构相互作用的基本理解，从而解决该领域长期存在的开放性问题，并为该主题的丰富实验数据提供定量解释。特别是，该项目将展示DNA的生物模型如何在单个碱基对水平上描述由蛋白质引起的变形，以及由于DNA的螺旋性质而导致这些变形的能量如何被正弦调制。对于脂质膜上的蛋白质，该项目将展示它们的弹性和熵相互作用的竞争如何引起自组装。在这个项目中开发的新的理论方法将能够定量预测蛋白质之间的变构相互作用，作为DNA或膜的机械特性和结合蛋白质施加在它们上的边界条件的函数。在这个项目中进行的分析将把蛋白质在DNA和脂质膜上的变构相互作用置于弹性固体中缺陷相互作用理论的更广泛背景下。

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.