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Solvation dynamics and structure around proteins and peptides: collective network motions or weak interactions

蛋白质和肽周围的溶剂化动力学和结构：集体网络运动或弱相互作用

基本信息

批准号：
EP/K034995/1
负责人：
Klaas Wynne
金额：
$ 53.68万
依托单位：
University of Glasgow
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2014
资助国家：
英国
起止时间：
2014 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FK034995%2F1
关键词：
Solvation dynamics structure around proteins

项目摘要

Virtually all biological processes take place in an aqueous environment and the presence of water is essential to life. Chemistry enabled by proteins relies on the fluctuations and flexibility of the protein scaffold. This flexibility is largely determined by water while at the same time the protein is known to affect the structure and dynamics of the surrounding water. A number of recent studies using very different techniques have come to the conclusion that a protein ties many water layers (7 to 10) to itself in an intimate embrace that has been termed the "protein dance". Some experiments, such as those by the Zewail group, suggest a dramatic slowing down of the dynamics of water near a protein suggesting that this water has become a glass. However, other studies such as femtosecond infrared pump-probe studies on smaller solutes have clearly shown no effect on water structure and dynamics beyond the first solvation shell. Thus, we are in the highly unsatisfactory position where state-of-the-art studies by reputable groups completely disagree on the interaction of biomolecules with the surrounding aqueous medium.Here we propose that this conflict can be resolved through a wider and more appropriate spectral coverage. The low frequency infrared and Raman spectroscopy that yielded the highly controversial results is only sensitive to dynamics in a narrow range of timescales around ~1 ps and cannot resolve slower and faster processes. To remedy this, we will apply a very high dynamic range time-domain version of Raman spectroscopy covering the spectral range <125 MHz to ~30 THz. This will be combined with broadband dielectric spectroscopy covering the spectral range 100 MHz to 200 THz. These complementary techniques will be used to solve the controversies relating to the interaction of proteins, peptides, and other molecules of biological significance with the surrounding water as well as to characterise low-frequency modes in the biomolecules themselves. Low temperature studies will address the controversial protein dynamical transition and particularly the role of the solvent in this. Finally, we propose to study changes in the collective modes of proteins as they undergo changes in tertiary and quaternary structure caused by environmental parameters.The research programme addresses the microscopic structural dynamics of proteins, peptides, other biomolecules, and the surrounding aqueous solvent. This is critical to the understanding of the function of the living cell, to the design of synthetic life, and to the fundamental physics of life. This area is at the cusp of physics, biology, and chemistry and underpins future synthetic-biology engineering. Current research into synthetic life will only lead to the development of future industries if the physical design principles have been laid down first; this is the primary aim of this proposal. Our strong links with theory collaborators will ensure that fundamental insights will propagate effectively to the 'users' of such information.

事实上，所有生物过程都发生在水环境中，水的存在对于生命至关重要。蛋白质实现的化学依赖于蛋白质支架的波动和灵活性。这种灵活性很大程度上取决于水，同时已知蛋白质会影响周围水的结构和动态。最近使用非常不同的技术进行的许多研究得出的结论是，蛋白质将许多水层（7 至 10 个）以紧密的拥抱方式与自身结合在一起，这被称为“蛋白质之舞”。一些实验，例如泽维尔小组的实验，表明蛋白质附近的水动力学急剧减慢，表明这种水已经变成了玻璃。然而，其他研究，例如对较小溶质的飞秒红外泵浦探针研究，已清楚地表明对第一个溶剂化壳层之外的水结构和动力学没有影响。因此，我们处于非常不令人满意的境地，信誉良好的团体的最新研究在生物分子与周围水介质的相互作用方面完全不同意。在这里，我们建议可以通过更广泛和更合适的光谱覆盖范围来解决这一冲突。低频红外和拉曼光谱产生了备受争议的结果，仅对约 1 ps 左右的狭窄时间尺度范围内的动力学敏感，无法解析较慢和较快的过程。为了解决这个问题，我们将应用拉曼光谱的非常高动态范围时域版本，覆盖光谱范围<125 MHz至~30 THz。这将与覆盖 100 MHz 至 200 THz 光谱范围的宽带介电光谱相结合。这些互补技术将用于解决与蛋白质、肽和其他具有生物学意义的分子与周围水的相互作用有关的争议，以及表征生物分子本身的低频模式。低温研究将解决有争议的蛋白质动态转变，特别是溶剂在其中的作用。最后，我们建议研究蛋白质集体模式的变化，因为它们经历了由环境参数引起的三级和四级结构的变化。该研究项目致力于蛋白质、肽、其他生物分子和周围水溶剂的微观结构动力学。这对于理解活细胞的功能、合成生命的设计以及生命的基础物理学至关重要。该领域处于物理学、生物学和化学的尖端，为未来的合成生物工程奠定了基础。目前对合成生命的研究只有在物理设计原则先定下来的情况下才能促进未来产业的发展；这是本提案的主要目的。我们与理论合作者的紧密联系将确保基本见解能够有效地传播给此类信息的“用户”。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids.

DOI：
10.1039/d0cp05404f
发表时间：
2021-06-21
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
0
作者：
González-Jiménez M ;Ramakrishnan G ;Tukachev NV ;Senn HM ;Wynne K
通讯作者：
Wynne K

Understanding the emergence of the boson peak in molecular glasses.

DOI：
10.1038/s41467-023-35878-6
发表时间：
2023-01-13
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Gonzalez-Jimenez, Mario;Barnard, Trent;Russell, Ben A.;Tukachev, Nikita V.;Javornik, Uros;Hayes, Laure-Anne;Farrell, Andrew J.;Guinane, Sarah;Senn, Hans M.;Smith, Andrew J.;Wilding, Martin;Mali, Gregor;Nakano, Motohiro;Miyazaki, Yuji;McMillan, Paul;Sosso, Gabriele C.;Wynne, Klaas
通讯作者：
Wynne, Klaas

Characterisation of the Boson Peak from the Glass into the Liquid

从玻璃到液体的玻色子峰的表征