Allosteric Interactions between Proteins on DNA and Membranes

DNA 和膜上蛋白质之间的变构相互作用

• 批准号: 1662101
• 负责人: Prashant Purohit
• 金额: $ 32.91万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-06-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1662101&HistoricalAwards=false
• 关键词: Allosteric; Interactions; between; Proteins; DNA

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.

细胞中基因的调节是通过蛋白质与 DNA 的结合/解除结合来控制的。通常，一种蛋白质的结合会改变 DNA 分子上较远位点的不同蛋白质的结合亲和力。这种现象称为“变构”；它已经在酶中得到了广泛的研究，但还没有通过 DNA 进行研究，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 进行的变构已涉及许多先前的实验研究，包括药物分子的结合，但尚未通过机械理论来理解它，该理论将 DNA 视为弹性（而非刚性）分子，会因结合蛋白而局部变形。由蛋白质与脂质双层结合引起的类似弹性变形也会导致变构相互作用，这种相互作用负责细胞过程，例如将物质转运入和运出细胞所需的胞吞作用和胞吐作用。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 或脂质膜）的布朗运动引起的波动的结果。该研究项目的总体目标是通过数学理论定量描述 DNA 和脂质膜上的蛋白质之间的变构相互作用，该数学理论将它们视为弹性物体，同时考虑其布朗波动。 该模型将显着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还将通过在国际会议中组织研讨会和先进学校，以及与宾夕法尼亚大学MRSEC和纳米生物界面中心合作开展NanoDay以及其他针对高中（少数族裔）学生和教师的活动来进行推广。该项目将推进基础科学的发展通过 DNA 了解变构相互作用，从而解决该领域长期存在的悬而未决的问题，并为该主题的大量实验数据提供定量解释。特别是，该项目将展示 DNA 的 birod 模型如何描述蛋白质在单碱基对水平上引起的变形，以及如何由于 DNA 的螺旋性质而对这些变形产生的能量进行正弦调制。对于脂膜上的蛋白质，该项目将展示如何通过其弹性和熵相互作用的竞争引起自组装。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，作为 DNA 或膜的机械特性以及结合蛋白施加于它们的边界条件的函数。该项目中进行的分析将把 DNA 和脂质膜上蛋白质的变构相互作用置于弹性固体缺陷相互作用理论的更广泛背景下。

项目成果

Discontinuous growth of DNA plectonemes due to atiomic scale friction

由于原子尺度摩擦，DNA plectoneme 的不连续生长

• DOI: 10.1039/c8m00852c
• 发表时间: 2018
• 期刊: Soft matter
• 影响因子: 3.4
• 作者: Min, Yifei;Purohit, Prashant K.
• 通讯作者: Purohit, Prashant K.

Self-assembly on a lipid membrane viewed as a first passage time problem

脂质膜上的自组装被视为首次通过时间问题

• DOI: 10.1016/j.jmps.2019.103787
• 发表时间: 2020
• 期刊: Journal of the Mechanics and Physics of Solids
• 影响因子: 5.3
• 作者: Liao, Xinyu;Purohit, Prashant K.
• 通讯作者: Purohit, Prashant K.

Biomechanical origins of inherent tension in fibrin networks.

• DOI: 10.1016/j.jmbbm.2022.105328
• 发表时间: 2022-09
• 期刊: JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
• 影响因子: 3.9
• 作者: Spiewak, Russell;Gosselin, Andrew;Merinov, Danil;Litvinov, Rustem I.;Weisel, John W.;Tutwiler, Valerie;Purohit, Prashant K.
• 通讯作者: Purohit, Prashant K.

Statistical mechanics of a double-stranded rod model for DNA melting and elasticity

DNA 熔解和弹性双链棒模型的统计力学

• DOI: 10.1039/d0sm00521e
• 发表时间: 2020
• 期刊: Soft Matter
• 影响因子: 3.4
• 作者: Singh, Jaspreet;Purohit, Prashant K.
• 通讯作者: Purohit, Prashant K.

Analytical solutions for a conical elastic sheet under a live normal load

活法向载荷下锥形弹性片的解析解

• DOI: 10.1016/j.ijnonlinmec.2019.04.003
• 发表时间: 2019
• 期刊: International Journal of Non-Linear Mechanics
• 影响因子: 3.2
• 作者: Singh, Jaspreet;Purohit, Prashant K.
• 通讯作者: Purohit, Prashant K.