The physics and structural biology of supramolecular protein self-assembly in meiotic chromosome synapsis

细胞中最大的蛋白质结构之一是联会复合体（SC），它将同源染色体联会在一起，以促进它们在减数分裂期间的重组。因此，SC对生育力至关重要，其缺陷导致人类不育、复发性流产和非整倍体。SC的拉链状结构长度可达25微米，并通过其八种卷曲螺旋蛋白质成分的自组装形成。这是通过形成三个不同的建筑自组装单元来实现的。首先，SYCP 3组装成一个准晶体阵列，使染色质在线性染色体轴内成环并压实（Syrjanen et al 2014）。然后，SYCP 1形成递归格子状阵列，以100 nm的间隔将同源染色体结合在一起（Dunce et al 2018）。最后，SYCE 2-TEX 12经历从2：2复合物到4：4结构的分级组装成微米长度的纤维，其类似于中间丝，并为SC沿着染色体长度的生长提供结构支持（Dunce et al 2021）。该博士项目旨在揭示SC的卷曲螺旋蛋白组分如何自组装成其主要结构单元的物理学。我们将使用计算方法来设计突变体和重新设计具有改变的自组装特性（如刚性，重复单元，宽度和长度）的蛋白质，以探索生物学并扩大SC相关生物材料的范围。我们将测试这些生物化学，确定结构和组装动力学的生物物理学和结构生物学。我们的研究结果将导致实验确定的大规模大分子组装体的结构和动态卷曲螺旋蛋白质自组装的数学模型。这个综合实验和计算项目的成果是广泛的。首先，工程蛋白组装体的高分辨率结构将提供对SC分子结构的前所未有的理解，克服目前研究天然SC蛋白的技术限制。这些生物学发现将由我们的合作者在MRC人类遗传学单位（https：//www.ed.ac.uk/mrc-human-genetics-unit）通过产生小鼠突变体进行测试。其次，它将为卷曲螺旋蛋白的超分子自组装建立物理基础，这将适用于广泛的生物系统。最后，它将确定我们如何能够操纵由SC蛋白形成的独特生化结构用于研究和用作生物材料。该项目将涉及广泛的生物化学，生物物理，结构生物学，计算和理论建模方法。基于实验室的方法包括重组蛋白表达和纯化、光和X射线散射、X射线晶体学、cryo-EM和cryo-ET，其中包括在钻石光源同步加速器设施（www.diamond.ac.uk）收集数据。计算和理论方法包括基于人工智能的结构建模，分子动力学，以及构建和模拟生物组装的数学模型，这将与凝聚态物质和复杂系统研究所（https：//www.ph.ed.ac.uk/icmcs）合作进行。该博士学位为具有生物化学/结构生物学，计算或物理学背景的学生提供了一个极好的机会，可以从事生命物理学的前沿研究。

One of the largest protein structures in the cell is the synaptonemal complex (SC), which synapses together homologous chromosomes to facilitate their recombination during meiosis. As such, the SC is essential for fertility, and its defects lead to human infertility, recurrent miscarriage, and aneuploidy. The zipper-like structure of the SC is up to 25 micrometres in length, and forms through self-assembly of its eight coiled-coil protein constituents. This occurs by formation of three distinct architectural self-assembled units. Firstly, SYCP3 assembles into a paracrystalline array that loops and compacts chromatin within linear chromosome axes (Syrjanen et al 2014). Then, SYCP1 forms a recursive lattice-like array that binds together homologous chromosome with a 100 nm separation (Dunce et al 2018). Finally, SYCE2-TEX12 undergoes hierarchical assembly from a 2:2 complex through a 4:4 structure into micrometre-length fibres, which resemble intermediate filaments, and provide structural support for SC growth along the chromosome length (Dunce et al 2021).This PhD project aims to uncover the physics of how the SC's coiled-coil protein components self-assemble into its principal architectural units. We will use computational methods to design mutants and re-engineer proteins with altered self-assembly characteristics, such as rigidity, repeating units, width and length, to probe the biology and widen the range of SC-related biomaterials. We will test these biochemically, determining structures and assembly dynamics by biophysics and structural biology. Our findings will lead to experimentally-determined structures of large-scale macromolecular assemblies and mathematical models of dynamic coiled-coil protein self-assembly. The outcomes of this integrated experimental and computational project are wide-reaching. Firstly, high-resolution structures of engineered protein assemblies will provide unprecedented understanding of the molecular structure of the SC, overcoming the current technical limitations of studying native SC proteins. These biological findings will be tested through the generation of mouse mutants by our collaborators at the MRC Human Genetics Unit (https://www.ed.ac.uk/mrc-human-genetics-unit). Secondly, it will establish a physical basis for supramolecular self-assembly of coiled-coil proteins that will be applicable to a wide range of biological systems. Finally, it will determine how we can manipulate the unique biochemical structures formed by SC proteins for research and for use as biomaterials.This project will involve a wide range of biochemical, biophysical, structural biology, computational and theoretical modelling methods. The laboratory-based methods include recombinant protein expression and purification, light and X-ray scattering, X-ray crystallography, cryo-EM and cryo-ET, which will include data collection at the Diamond Light Source synchrotron facility (www.diamond.ac.uk). Computational and theoretical methods include AI-based structural modelling, molecular dynamics, and building and simulating mathematical models of bio-assemblies, which will be performed in collaboration with the Institute for Condensed Matter and Complex Systems (https://www.ph.ed.ac.uk/icmcs).This PhD provides an excellent opportunity for a student with a biochemical/structural biology, computational or physics background to engage in cutting-edge research into the physics of life.