Atomistic reconstruction of large biomolecular systems from low-resolution cryo-electron microscopy data - RECKON

该项目的目的是开发一种现成的技术，用于使用分辨率差的低温电子显微镜（cryo-EM）数据重建生物分子的全原子结构。目标包括开发一种智能协议，用于处理低分辨率的cryo-EM密度，开发一个脚本或软件模块工具包，以促进这一过程，并从新获得的cryo-EM数据中产生噬菌体的全原子结构。这个问题是高度相关的，因为发表的冷冻EM数据量增长迅速，特别是大的生物分子对象，如整个病毒。从这些数据重建分子结构的方法远远落后。这极大地限制了这种复杂而昂贵的实验的科学产出。冷冻EM实验的最终目标是目标的原子模型，可以形成进一步生物化学研究的基础。目前，只有当收集的冷冻EM密度具有足够高的分辨率以应用现有的重建算法时，才能实现该目标。然而，由于仪器或基础的限制，通常存在分辨率较低的大区域，使得常用的算法失败。我们的方法在重建过程中考虑了目标的其他信息（化学结构，生物分子约束等）。智能算法开发将能够处理以前无法访问的区域的冷冻EM数据，从而使它有可能重建的目标在其原子的完整性。为了测试它，将进行Qbeta噬菌体的冷冻EM测量，这是一种重要的生物靶标。所产生的基因组加载噬菌体的全原子模型将引起病毒学家和分子生物学家的高度兴趣，并且该技术本身将吸引专门从事cryo-EM的研究小组的注意，包括工业。

The project's aim is to develop a ready-to-use technique for all-atom structure reconstruction of biomolecules using poorly resolved cryo-electron microscopy (cryo-EM) data. The objectives include developing an intelligent protocol for dealing with low-resolution cryo-EM density, developing a toolkit of scripts or software modules for facilitating the process, and producing all-atom structure of a bacteriophage from newly-acquired cryo-EM data. The problem is highly relevant because the amount of published cryo-EM data growth rapidly, especially of large biomolecular objects such as whole viruses. Methodologies of reconstructing molecular structures from these data lag far behind. This strongly limits scientific output of such elaborate and expensive experiments. The ultimate goal of a cryo-EM experiment is an atomistic model of the target that can form the basis for further biochemical research. Currently, the goal can only be achieved if the collected cryo-EM density has high enough resolution to apply the existing reconstruction algorithms. However, often large regions with low resolution are present due to either instrumental or fundamental limitations, making commonly used algorithms to fail.Our methodology takes additional information on the target into account (chemical structure, biomolecular constraints, etc) in the reconstruction process. The intelligent algorithm to be developed will be able to deal with previously inaccessible regions of cryo-EM data and thus make it possible to reconstruct the target in its atomistic completeness. To test it, a cryo-EM measurement of a Qbeta bacteriophage will be done, which is an important biological target. The produced all-atom model of genome-loaded phage will be of high interest for virologists and molecular biologists, and the technique itself will attract attention of research groups specialising in cryo-EM, including industry.