Quantifying the effects of ions and collective rearrangements during ribosome function

量化核糖体功能过程中离子和集体重排的影响

• 批准号: 1915843
• 负责人: Paul Whitford
• 金额: $ 79.73万
• 依托单位: Northeastern University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1915843&HistoricalAwards=false
• 关键词: Quantifying; effects; ions; collective; rearrangements

This project focuses on understanding the molecular factors that govern gene expression. To this end, large-scale simulations will be applied to study how the ribosome can accurately and efficiently synthesize proteins. The production of proteins is essential for nearly all biological functions, making the ribosome one of the most important biological machines. While modern experiments can resolve static configurations of the ribosome, detailed simulations will allow the research community to understand how molecular structure enables specific biological function. This can reveal strategies for controlling cellular dynamics, as well as provide a "rule book" that can aid in the design of novel molecular-scale machines. This project will involve a range of activities that will provide introductory science seminars for high school students, valuable training experiences for undergraduate and graduate student researcher and workshops for experimental researchers.Theoretical models will be developed and applied to identify the detailed role of localized, "diffuse" ions during ribosome function. Characterizing several critical substeps of the elongation cycle (tRNA accommodation, hybrid-state formation, translocation and domain rotations) will elucidate how the ionic environment shapes the energy landscape of the ribosome. This will help uncover the modes by which ions can enable conformationally-complex biological dynamics. With the high negative charge density of RNA, the dynamics of ribonucleoprotein assemblies rely critically on a locally diffuse ionic environment, which can lead to attraction between negatively charged RNA molecules. Accordingly, to fully characterize the energetics of large-scale biological assemblies, one must properly describe the statistical properties of the ionic environment. To address this challenge, simplified energetic models will be developed that employ all-atom resolution, as well as explicitly represented monovalent and divalent ions. Calibration of the energetic parameters will be established through comparison with experiments and explicit-solvent simulations of prototypical systems. These simplified models will then enable the simulation of large-scale (20-100 Angstroms) conformational transitions in the ribosome. This will implicate the influence of fluctuations/changes in local ionic distributions. While this study will focus on ribosome dynamics, the models and computational methods will be transferrable to a broad range of biological assemblies.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该项目的重点是了解控制基因表达的分子因素。 为此，将应用大规模模拟来研究核糖体如何准确有效地合成蛋白质。蛋白质的产生对于几乎所有生物功能都至关重要，这使得核糖体成为最重要的生物机器之一。虽然现代实验可以解决核糖体的静态构型，但详细的模拟将使研究界能够了解分子结构如何实现特定的生物功能。这可以揭示控制细胞动力学的策略，并提供一本可以帮助设计新型分子尺度机器的“规则手册”。该项目将涉及一系列活动，为高中生提供入门科学研讨会，为本科生和研究生研究人员提供宝贵的培训经验，并为实验研究人员提供研讨会。将开发并应用理论模型来确定核糖体功能过程中局部“扩散”离子的详细作用。表征延伸循环的几个关键子步骤（tRNA 调节、混合态形成、易位和结构域旋转）将阐明离子环境如何塑造核糖体的能量景观。这将有助于揭示离子实现构象复杂的生物动力学的模式。由于 RNA 的高负电荷密度，核糖核蛋白组装体的动力学关键依赖于局部扩散的离子环境，这可能导致带负电荷的 RNA 分子之间的吸引力。因此，为了充分表征大规模生物组装体的能量学特征，必须正确描述离子环境的统计特性。为了应对这一挑战，将开发采用全原子分辨率以及明确表示的单价和二价离子的简化能量模型。将通过与原型系统的实验和显式溶剂模拟进行比较来建立能量参数的校准。这些简化的模型将能够模拟核糖体中的大规模（20-100 埃）构象转变。这将暗示局部离子分布的波动/变化的影响。虽然这项研究将重点关注核糖体动力学，但模型和计算方法将可转移到广泛的生物组装中。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Diffusion of tRNA inside the ribosome is position-dependent

tRNA 在核糖体内的扩散具有位置依赖性

• DOI: 10.1063/1.5113814
• 发表时间: 2019
• 期刊: The Journal of Chemical Physics
• 作者: Yang, Huan;Bandarkar, Prasad;Horne, Ransom;Leite, Vitor B. P.;Chahine, Jorge;Whitford, Paul C.
• 通讯作者: Whitford, Paul C.

How Nanopore Translocation Experiments Can Measure RNA Unfolding

• DOI: 10.1016/j.bpj.2020.01.030
• 发表时间: 2020-04-07
• 期刊: BIOPHYSICAL JOURNAL
• 影响因子: 3.4
• 作者: Bandarkar, Prasad;Yang, Huan;Whitford, Paul C.
• 通讯作者: Whitford, Paul C.

Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly

核糖核蛋白组装中的扩散离子协调动力学

• DOI: 10.1021/jacs.2c04082
• 发表时间: 2022
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Wang, Ailun;Levi, Mariana;Mohanty, Udayan;Whitford, Paul C.
• 通讯作者: Whitford, Paul C.

Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.

• DOI: 10.1073/pnas.2105739118
• 发表时间: 2021-07-27
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Staquicini DI;Tang FHF;Markosian C;Yao VJ;Staquicini FI;Dodero-Rojas E;Contessoto VG;Davis D;O'Brien P;Habib N;Smith TL;Bruiners N;Sidman RL;Gennaro ML;Lattime EC;Libutti SK;Whitford PC;Burley SK;Onuchic JN;Arap W;Pasqualini R
• 通讯作者: Pasqualini R

The dynamics of subunit rotation in a eukaryotic ribosome.

• DOI: 10.3390/biophysica1020016
• 发表时间: 2021-06
• 期刊: Biophysica