Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis.

IF 7.2 2区 生物学 Q1 BIOPHYSICS Quarterly Reviews of Biophysics Pub Date : 2020-08-10 DOI:10.1017/S0033583520000062
Robin A Richardson, Benjamin S Hanson, Daniel J Read, Oliver G Harlen, Sarah A Harris
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引用次数: 7

Abstract

Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject to explicit thermal noise, we have quantified the constraints on the range of molecular conformations that can be explored by dynein-c within the crowded architecture of the axoneme. We subsequently assess the influence of crowding on the 3D exploration of microtubule-binding sites, and specifically on the axial step length. Our calculations combine experimental information on the shape, flexibility and environment of dynein-c from three distinct sources; negative stain electron microscopy, cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET). Our FFEA simulations show that the super-macromolecular organisation of multiple protein complexes into higher-order structures can have a significant influence on the effective flexibility of the individual molecular components, and may, therefore, play an important role in the physical mechanisms underlying their biological function.

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用波动有限元分析探讨轴突内鞭毛动力蛋白的动态。
鞭毛动力蛋白是产生纤毛和鞭毛弯曲运动的分子马达。它们位于被称为轴突的密集排列和高度组织的超大分子细胞骨架结构中。使用中尺度模拟技术波动有限元分析(FFEA),将蛋白质表示为受显热噪声影响的粘弹性连续体物体,我们量化了轴素拥挤结构中dynein-c可以探索的分子构象范围的限制。我们随后评估了拥挤对微管结合位点三维探测的影响,特别是对轴向步长的影响。我们的计算结合了三个不同来源的关于dynein-c的形状、灵活性和环境的实验信息;负染色电镜,冷冻电镜(cryo-EM)和冷冻电子断层扫描(cryo-ET)。我们的FFEA模拟表明,多种蛋白质复合物的高阶结构的超大分子组织可以对单个分子组分的有效柔韧性产生重大影响,因此,可能在其生物功能的物理机制中发挥重要作用。
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来源期刊
Quarterly Reviews of Biophysics
Quarterly Reviews of Biophysics 生物-生物物理
CiteScore
12.90
自引率
1.60%
发文量
16
期刊介绍: Quarterly Reviews of Biophysics covers the field of experimental and computational biophysics. Experimental biophysics span across different physics-based measurements such as optical microscopy, super-resolution imaging, electron microscopy, X-ray and neutron diffraction, spectroscopy, calorimetry, thermodynamics and their integrated uses. Computational biophysics includes theory, simulations, bioinformatics and system analysis. These biophysical methodologies are used to discover the structure, function and physiology of biological systems in varying complexities from cells, organelles, membranes, protein-nucleic acid complexes, molecular machines to molecules. The majority of reviews published are invited from authors who have made significant contributions to the field, who give critical, readable and sometimes controversial accounts of recent progress and problems in their specialty. The journal has long-standing, worldwide reputation, demonstrated by its high ranking in the ISI Science Citation Index, as a forum for general and specialized communication between biophysicists working in different areas. Thematic issues are occasionally published.
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