Breaking the cage – Implementing photocages to address spatiotemporal challenges in chemical biology
Abstract
Visualizing atoms and molecules in motion remains a formidable challenge within structural chemical biology. Significant advances in the generation of ultrashort and bright X-ray pulses have provided the technical framework to facilitate the study of complex biomolecules with atomic resolution. For the first time, it was possible to convince nature’s machinery to reveal their temporal structural dynamics by initiating native reactions in photoresponsive systems and observe the molecular dance of life by ultrafast time-resolved serial femtosecond crystallography. However, given the exceedingly small fraction of naturally photoactive proteins within nature’s diverse repertoire of proteins, the vast majority remain elusive to detailed, time-resolved structural studies.
A major objective in the forefront of structural biology is to extend the scope of time-resolved X-ray diffraction beyond light responsive proteins to include substrate dependent systems. Photocages constitute a generic method of introducing a biologically relevant substrate to its associated protein with spatiotemporal control. Numerous challenges remain, some of which are addressed in this thesis.
In this work, the native reaction between cytochrome c oxidase and oxygen released from an oxygen photocage is studied by time-resolved serial femtosecond crystallography. These are difficult experiments, both from a theoretical and technical perspective. Nevertheless, we can provide structural evidence for enzymatic turnover following the release of oxygen from the photocage. In this thesis, novel oxygen photocages and singlet oxygen responsive materials have been developed towards addressing contemporary challenges in various scientific fields. An unexpectedly successful study of structural rearrangements in a pH-responsive ion channel following acidification by a photoacid via time-resolved X-ray solution scattering further cements the scientific versatility provided by photocages in the study of temporal dynamics of proteins.
Parts of work
Paper I. Characterization and evaluation of photolabile (µ-peroxo)(µ hydroxo)bis[bis(bipyridyl)cobalt caged oxygen compounds towards enabling time-resolved crystallographic studies of cytochrome c oxidase Emil Sandelin; Jonatan Johannesson; Ola Wendt; Gisela Brändén; Richard Neutze; Carl-Johan Wallentin. Photochem. Photobiol. Sci. https://doi.org/10.1007/s43630-024-00558-x Paper II. Structural changes in cytochrome c oxidase following the reduction of dioxygen to water. Doris Zorić† ;Jonatan Johannesson†; Adams Vallejos ; Emil Sandelin ;Arpitha Kabbinale; Swagatha Ghosh; Aaron Flink ;Monika Bjelčić ;John Rönnholm; Peter Dahl; Emma Victoria Beale; Christoph Bostedt; Claudio Cirelli ;Camila Bacellar Cases da Silveira; Philip Johnson; Dmitry Ozerov; Alex Batyuk; Sebastien Boutet; Chris Kupitz; Ariana N. Peck; Fred Poitevin; Ray Sierra; Stella Lisova; Carl-Johan Wallentin; Gisela Brändén; Richard Neutze. Manuscript (2024) †These authors contributed equally to this work. Paper III. Spatiotemporal release of singlet oxygen in low molecular weight organo-gels upon thermal or photochemical external stimuli. Emil Sandelin; Leonard Schilling; Ekata Saha; Andrea Ruiu; Richard Neutze; Henrik Sundén; Carl-Johan Wallentin. Manuscript (2024). Accepted for publication in Small. Paper IV. Time-resolved studies of pH induced conformational changes in a potassium channel. Andrea Cellini†; Greger Hammarin†; Analia Banacore; Emil Sandelin; Jonatan Johannesson; Beatrice Keller; Lucija Ostojic; Leona Cesar; Ayaan Ali; Giorgia Ortolani; Taru Larkiala; Céline Mariette; Mikhail Kozhaev; Kévin Pounot; Matteo Levantino; Carl-Johan Wallentin; Richard Neutze; Julia Morud. Manuscript, (2024). †These authors contributed equally to this work.
Degree
Doctor of Philosophy
University
University of Gothenburg. Faculty of Science
Institution
Department of Chemistry and Molecular Biology ; Institutionen för kemi och molekylärbiologi
Disputation
Fredagen den 10 maj 2024, kl. 9.00, 3401 Korallrevet, Natrium, Medicinaregatan 7B
Date of defence
2024-05-10
emil1svensson@gmail.com
Date
2024-04-16Author
Sandelin, Emil
Keywords
Photocages
cytochrome c oxidase
time-resolved serial femtosecond crystallography (TR-SFX)
spatiotemporal release of oxygen
Publication type
Doctoral thesis
ISBN
978-91-8069-708-8 (PDF)
978-91-8069-707-1 (PRINT)
Language
swe