The Mechanism of Polyvalent Ion Competition with Membranes and Membrane-Associated Proteins

多价离子与膜和膜相关蛋白竞争的机制

• 批准号: 2003912
• 负责人: Jeffery Klauda
• 金额: $ 64.6万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2003912&HistoricalAwards=false
• 关键词: Mechanism; Polyvalent; Ion; Competition; Membranes

With this award, the Chemistry of Life Processes Program is funding Drs. Jeffery Klauda and Sergei Sukharev at the University of Maryland to study the binding competition of polyvalent ions with lipids and membrane-associated proteins. Calcium ions in solution play multiple critical roles as signaling agents and cofactors that mediate muscle contraction, nerve signal transmission, blood clotting, and, importantly, dead cell removal. Positively charged calcium ions assist in recognition of injured and dying cells by special biological processes, which depend on calcium binding to negatively-charged lipid molecules exposed during cell death. Specific proteins recognize these calcium-coated dying (apoptotic) cells and are key to removing these cells. However, some toxic metal ions, such as beryllium, can compete with, displace, and suppress natural functions mediated by calcium. Drs. Jeffery Klauda and Sergei Sukharev use a combined experimental and computational approach to understand the basic aspects of binding and competition of calcium and beryllium to model compounds, lipids, and proteins. This project provides insight into the mechanisms of how beryllium interferes with multiple calcium-dependent processes and specifically disrupts apoptotic cell recognition and the associated cleaning cascade in the body. This project provides training for undergraduate and graduate student researchers, and the research results are disseminated through presentations at scientific meetings and publications. This project involves educational outreach through summer research internships for high school students at minority-serving institutions. A series of magnet practicums will allow students to actively perform supervised research in the labs of Drs. Klauda and Sukharev. In addition, course lectures and practical examples from the project research are integrated into undergraduate and graduate engineering and science courses to increase engagement and exposure.Probing the structure and thermodynamics for ions binding to lipids in cellular membranes has been challenging. This project aims to use isothermal titration calorimetry (ITC) to obtain free energies of binding for calcium(II) and beryllium(II) to model compounds for lipids and peptide carbonyls/carboxylates. Fourier Transform-Infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopic techniques are used to determine the structure of ions binding to liposomes with the aid of quantum mechanical (QM) calculations of model clusters. QM and experimental measures (ITC, FTIR, Langmuir monolayer experiments, and NMR) are used to parametrize an additive and a polarizable Drude force field for ion-water, -lipid and -protein interactions. These force fields will be used in molecular dynamics (MD) simulations with enhanced sampling approaches to study the coordination and competitive binding of calcium(II) and beryllium(II). The final aspect of this project is probing the binding of model phosphatidylserine (PS) receptors to liposomes and/or apoptotic cells in the presence of calcium(II) and beryllium(II) with fluorescent microscopy, flow cytometry and electron paramagnetic resonance. In parallel, calcium(II) displacement by beryllium(II) in the calcium(II)-arranged PS contacts with these protein receptors is studied with MD simulations to probe the critical role of coordination and the strength of these interactions. Together these studies are expected to provide insight into the mechanism of how beryllium(II) disrupts intracellular signaling, including details of extracellular PS recognition and of Be(II)-disruption of the apoptotic cell cleaning cascade.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.

通过这一奖项，生命过程化学计划资助马里兰大学的Jeffery Klauda博士和Sergei Sukharev博士研究多价离子与脂质和膜相关蛋白质的结合竞争。溶液中的钙离子作为信号媒介和辅助因子扮演着多种关键角色，它们介导肌肉收缩、神经信号传递、血液凝固，以及更重要的是，清除死亡细胞。带正电荷的钙离子通过特殊的生物学过程帮助识别受损和死亡的细胞，这依赖于细胞死亡过程中暴露的带负电荷的脂分子与钙的结合。特定的蛋白质识别这些被钙包裹的死亡(凋亡)细胞，并是移除这些细胞的关键。然而，一些有毒的金属离子，如铍，可以与钙竞争、取代和抑制钙介导的自然功能。Jeffery Klauda博士和Sergei Sukharev博士使用实验和计算相结合的方法来了解钙和铍与模型化合物、脂类和蛋白质的结合和竞争的基本方面。该项目深入了解了铍如何干扰多种钙依赖过程，并具体扰乱体内凋亡细胞识别和相关的清洁级联的机制。该项目为本科生和研究生研究人员提供培训，并通过在科学会议和出版物上发表演讲来传播研究成果。该项目涉及通过为少数族裔服务机构的高中生进行暑期研究实习来进行教育推广。一系列的磁铁练习将允许学生在Klauda博士和Sukharev博士的实验室中积极进行有指导的研究。此外，该项目研究的课程讲座和实际例子被整合到本科生和研究生的工程和科学课程中，以增加参与和接触。探索细胞膜中离子与脂质结合的结构和热力学一直是具有挑战性的。本项目的目标是使用等温滴定热法(ITC)获得钙(II)和铍(II)的结合自由能，以模拟脂质和多肽/羧酸盐的化合物。采用傅里叶变换红外光谱(FTIR)和核磁共振(NMR)光谱技术，借助模型团簇的量子力学(QM)计算，确定了离子与脂质体结合的结构。QM和实验方法(ITC、FTIR、朗缪尔单分子层实验和核磁共振)被用来对离子-水、-脂和-蛋白质相互作用的添加剂和可极化的Drude力场进行参数化。这些力场将用于分子动力学(MD)模拟和增强的采样方法，以研究钙(II)和铍(II)的配位和竞争结合。本项目的最后一个方面是用荧光显微镜、流式细胞仪和电子顺磁共振来探索在钙(II)和铍(II)存在的情况下模型磷脂酰丝氨酸(PS)受体与脂质体和/或凋亡细胞的结合。同时，用分子动力学模拟研究了钙(II)排列的PS与这些蛋白受体接触时，铍(II)对钙(II)的置换作用，以探讨配位的关键作用和这些相互作用的强度。总而言之，这些研究有望深入了解铍(II)如何扰乱细胞内信号传递的机制，包括细胞外PS识别和Be(II)-破坏凋亡细胞清除级联的细节。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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

Considerations of Recent All-Atom Lipid Force Field Development

• DOI: 10.1021/acs.jpcb.1c02417
• 发表时间: 2021-05-28
• 期刊: JOURNAL OF PHYSICAL CHEMISTRY B
• 影响因子: 3.3
• 作者: Klauda, Jeffery B.

Estimating localization of various statins within a POPC bilayer

• DOI: 10.1016/j.chemphyslip.2021.105074
• 发表时间: 2021-03-10
• 期刊: CHEMISTRY AND PHYSICS OF LIPIDS
• 影响因子: 3.4
• 作者: Kuba, Jacob Olondo;Yu, Yalun;Klauda, Jeffery B.
• 通讯作者: Klauda, Jeffery B.

Simulations of Diabetic and Non-Diabetic Peripheral Nerve Myelin Lipid Bilayers

糖尿病和非糖尿病周围神经髓磷脂双层的模拟

• DOI: 10.1021/acs.jpcb.1c01621
• 发表时间: 2021
• 期刊: The Journal of Physical Chemistry B
• 作者: Yuan, Yiding;Yu, Yalun;Klauda, Jeffery B.
• 通讯作者: Klauda, Jeffery B.

All-Atom Modeling of Complex Cellular Membranes

• DOI: 10.1021/acs.langmuir.1c02084
• 发表时间: 2021-12-28
• 期刊: LANGMUIR
• 影响因子: 3.9
• 作者: Hsieh, Min-Kang;Yu, Yalun;Klauda, Jeffery B.
• 通讯作者: Klauda, Jeffery B.

Molecular dynamics simulations of the human ocular lens with age and cataract

• DOI: 10.1016/j.bbamem.2022.184025
• 发表时间: 2022-08-17
• 期刊: BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
• 影响因子: 3.4
• 作者: Fernandes, Joshua B.;Yu, Yalun;Klauda, Jeffery B.
• 通讯作者: Klauda, Jeffery B.