Probing the rules governing domain formation and protein partitioning in membrane
探索膜中结构域形成和蛋白质分配的规则
基本信息
- 批准号:1900416
- 负责人:
- 金额:$ 51万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing 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:
- 关键词:
项目摘要
Professor John E. Straub at Boston University is supported by an award from the Chemical Theory, Models and Computational Methods (CTMC) Program in the Chemistry Division to perform theoretical and computational research on predictions of the structure of the lipid membrane. The lipid membrane plays a key role in the organization and function of the cell. The systematic investigation of lipid membranes is essential to our understanding of fundamental aspects of cellular function, including cellular transport and signaling. At the present time, state-of-the-art computational models fail to capture key aspects of membrane structure and function. The Straub group is developing novel theoretical models of membrane and membrane proteins that aspire to a new level of realism in the computational modeling of the cell. As such, the successful development of the methods and their applications may be transformative to the field. This project includes the training and mentoring of undergraduate and graduate research students as well as the development of simulation methods, codes, and datasets. A complete textbook on the topic "Mathematical Methods for Chemists" is being developed that will be made freely available to instructors and students.The program of analyzing multi-component protein mixtures partitioning with lipid domains in heterogeneous membrane surface structure is extremely challenging. For direct comparison with experiment, it is necessary to perform all-atom simulations, so the free energy calculations use Umbrella Sampling and Energy Representation methods for speed and accuracy and Simulated Tempering in dihedral space and free volume space for enhanced conformational sampling. The multi-component mixtures are complex, containing cholesterol, sphingolipids, glycolipids and other agents important in determining lipid phase domains. The goal of this research is to enable the first de novo studies of membrane domain formation and membrane protein partitioning using atomistic models. The models are validated against average experimental measurements of nanoscopic membrane structures in membrane mixtures and protein partitioning between lipid domains.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.
波士顿大学的John E.Straub教授获得了化学部化学理论、模型和计算方法(CTMC)项目的支持,负责对脂膜结构的预测进行理论和计算研究。脂膜在细胞的组织和功能中起着关键作用。对脂膜的系统研究对于我们理解细胞功能的基本方面是必不可少的,包括细胞运输和信号传递。目前,最先进的计算模型无法捕捉膜结构和功能的关键方面。Straub小组正在开发膜和膜蛋白的新理论模型,希望在细胞计算建模方面达到一个新的现实水平。因此,这些方法的成功开发及其应用可能会对该领域产生变革。该项目包括对本科生和研究生的培训和指导,以及模拟方法、代码和数据集的开发。一本完整的《化学工作者的数学方法》教材正在编写中,将向教师和学生免费提供。分析具有非均相膜表面结构的类脂结构域的多组分蛋白质混合物的程序极具挑战性。为了与实验直接比较,有必要进行全原子模拟,因此自由能计算采用伞采样和能量表示法来提高速度和精度,并在二面体空间和自由体积空间进行模拟回火来增强构象采样。多组分混合物是复杂的,包含胆固醇、鞘脂、糖脂和其他在确定脂相结构域中重要的试剂。这项研究的目标是使用原子模型首次从头研究膜结构域的形成和膜蛋白的分配。这些模型通过对膜混合物中纳米膜结构和脂域之间蛋白质分配的平均实验测量进行了验证。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
期刊论文数量(9)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Finite-Size Effects and Optimal System Sizes in Simulations of Surfactant Micelle Self-Assembly
- DOI:10.1021/acs.jpcb.1c01186
- 发表时间:2021-05-07
- 期刊:
- 影响因子:3.3
- 作者:Harris, Jonathan J.;Pantelopulos, George A.;Straub, John E.
- 通讯作者:Straub, John E.
Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model.
- DOI:10.1021/acs.jctc.0c01253
- 发表时间:2021-04-13
- 期刊:
- 影响因子:5.5
- 作者:Majumder A;Straub JE
- 通讯作者:Straub JE
On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes
计算膜中蛋白质-蛋白质缔合的平衡结合常数
- DOI:10.1021/acs.jctc.2c00106
- 发表时间:2022
- 期刊:
- 影响因子:5.5
- 作者:Majumder, Ayan;Kwon, Seulki;Straub, John E.
- 通讯作者:Straub, John E.
Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers.
- DOI:10.1021/acs.jpcb.0c10631
- 发表时间:2021-02-25
- 期刊:
- 影响因子:0
- 作者:Elkins MR;Bandara A;Pantelopulos GA;Straub JE;Hong M
- 通讯作者:Hong M
Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A
- DOI:10.1016/j.jmb.2020.01.029
- 发表时间:2020-03-27
- 期刊:
- 影响因子:5.6
- 作者:Frame, Nicholas M.;Kumanan, Meera;Gursky, Olga
- 通讯作者:Gursky, Olga
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John Straub其他文献
Cu2p X線分光でみる銅酸化物系のキャリアドーピングに伴う電子構造変化
Cu2p X 射线光谱观察到铜氧化物中载流子掺杂导致的电子结构变化
- DOI:
- 发表时间:
2014 - 期刊:
- 影响因子:0
- 作者:
Yasuhiro Matsunaga;Akinori Baba;Chun Biu Li;John Straub;Mikito Toda;Tamiki Komatsuzaki;R. Berry;藤内博記,雀部矩正,魚住孝幸;高安美佐子;播木敦,市野塚義行,魚住孝幸 - 通讯作者:
播木敦,市野塚義行,魚住孝幸
Transition from power law to monopoly in complex business firm network
复杂企业网络中从幂律到垄断的转变
- DOI:
- 发表时间:
2012 - 期刊:
- 影响因子:0
- 作者:
Yasuhiro Matsunaga;Akinori Baba;Chun Biu Li;John Straub;Mikito Toda;Tamiki Komatsuzaki;R. Berry;藤内博記,雀部矩正,魚住孝幸;高安美佐子 - 通讯作者:
高安美佐子
Office of Administration
行政办公室
- DOI:
- 发表时间:
2006 - 期刊:
- 影响因子:0
- 作者:
John Straub;Sandy Evans;Clara Patterson;James Knodell;Victor Bersen;Theresa Payton - 通讯作者:
Theresa Payton
Ce金属間化合物の多極子秩序を考慮した内殻X線分光の理論
考虑Ce金属间化合物多极级的核心X射线光谱理论
- DOI:
- 发表时间:
2014 - 期刊:
- 影响因子:0
- 作者:
Yasuhiro Matsunaga;Akinori Baba;Chun Biu Li;John Straub;Mikito Toda;Tamiki Komatsuzaki;R. Berry;藤内博記,雀部矩正,魚住孝幸 - 通讯作者:
藤内博記,雀部矩正,魚住孝幸
窒素分子イオン四重極遷移周波数の精密計測
氮分子离子四极跃迁频率的精确测量
- DOI:
- 发表时间:
2016 - 期刊:
- 影响因子:0
- 作者:
Yasuhiro Matsunaga;Akinori Baba;Chun Biu Li;John Straub;Mikito Toda;Tamiki Komatsuzaki;R. Berry;梶田雅稔 - 通讯作者:
梶田雅稔
John Straub的其他文献
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{{ truncateString('John Straub', 18)}}的其他基金
Complex role of solvation in protein structure and dynamics in micelles and membranes
溶剂化在胶束和膜的蛋白质结构和动力学中的复杂作用
- 批准号:
1362524 - 财政年份:2014
- 资助金额:
$ 51万 - 项目类别:
Standard Grant
Algorithms for the simulation of strong phase changes in complex molecular systems
复杂分子系统中强相变的模拟算法
- 批准号:
1114676 - 财政年份:2011
- 资助金额:
$ 51万 - 项目类别:
Continuing Grant
Acquisition of an EPR spectrometer for cyber-enabled research and education
采购 EPR 光谱仪用于网络研究和教育
- 批准号:
0840418 - 财政年份:2009
- 资助金额:
$ 51万 - 项目类别:
Standard Grant
Probing the principles of dynamics and energy transfer in proteins
探索蛋白质动力学和能量转移的原理
- 批准号:
0750309 - 财政年份:2008
- 资助金额:
$ 51万 - 项目类别:
Continuing Grant
Algorithms for the simulation of short and long time dynamics of proteins
模拟蛋白质短期和长期动态的算法
- 批准号:
0316551 - 财政年份:2003
- 资助金额:
$ 51万 - 项目类别:
Standard Grant
Algorithms for enhanced sampling and global optimization
增强采样和全局优化的算法
- 批准号:
9975494 - 财政年份:1999
- 资助金额:
$ 51万 - 项目类别:
Continuing Grant
Algorithms for Global Optimization, Enhanced Sampling and Reaction Pathway Determination
全局优化、增强采样和反应途径确定的算法
- 批准号:
9632236 - 财政年份:1996
- 资助金额:
$ 51万 - 项目类别:
Continuing Grant
Novel Algorithms for Many-Body Classical Dynamics and Global Optimization
多体经典动力学和全局优化的新算法
- 批准号:
9306375 - 财政年份:1993
- 资助金额:
$ 51万 - 项目类别:
Continuing Grant
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