Flexibility analysis on the cryo-EM data of a small protein
Title: Flexibility analysis on the cryo-EM data of a small protein
DNr: Berzelius-2024-52
Project Type: LiU Berzelius
Principal Investigator: Szabolcs Bódizs <szabolcs.bodizs@kemi.uu.se>
Affiliation: Uppsala universitet
Duration: 2024-03-01 – 2024-09-01
Classification: 10601
Homepage: http://www.westenhofflab.net/


Phytochromes are an essential part of plants’ photosensory repertoire. They detect red and far-red light and are responsible for the positioning and regulation of the photosynthetic apparatus in bacteria, while in higher plants they control growth and reproduction. Recombinant phytochrome constructs are used in neurology as optogenetic tools which are subjects to constant optimization. The structures of light sensing domains of different phytochromes and the photoactivation mechanism are relatively well described, thanks to the application of time-resolved X-ray crystallography. Structural information on full-length phytochromes is more scarce, which my project is aiming to solve. In this work I combine traditional cryo-EM with a novel microsecond time-resolved approach to gather dynamic structural data on the full-length Pseudomonas aeruginosa bacteriophytochrome. The usage of a HPC resource is necessary in this project as phytochromes are flexible proteins, and resolving this flexibility in cryo-EM data, while possible with established methods, is a computationally intensive task. The pre-processing of data happens on our group's in-house workstation computer, but we are looking to delegate the task of 3D reconstruction and variability analysis to a more capable machine.