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Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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2018 (English)In: Nature Plants, ISSN 2055-026X, Vol. 4, p. 212-217Article in journal (Refereed) Published
Abstract [en]

Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3,4,5,6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9–3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.

Place, publisher, year, edition, pages
2018. Vol. 4, p. 212-217
National Category
Biological Sciences Chemical Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
URN: urn:nbn:se:su:diva-156633DOI: 10.1038/s41477-018-0129-6ISI: 000430648300011OAI: oai:DiVA.org:su-156633DiVA, id: diva2:1210400
Available from: 2018-05-28 Created: 2018-05-28 Last updated: 2020-03-13Bibliographically approved
In thesis
1. Fast and reliable alignment and classification of biological macromolecules in electron microscopy images
Open this publication in new window or tab >>Fast and reliable alignment and classification of biological macromolecules in electron microscopy images
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In the last century, immense progress has been made to charter and understand a wide range of biological phenomena. The origin of genetic inheritance was determined, showing that DNA holds genes that determine the architecture of proteins, utilized by the cell for most functions. Mapping of the human genome eventually revealed around 20000 genes, showing a vast complexity of biology at its most fundamental level.

To study the molecular structure, function and regulation of proteins, spectroscopic techniques and microscopy are employed. Until just over a decade ago, the determination of atomic detail of biomolecules like proteins was limited to those that were small or possible to crystallize. However recent technological advances in cryogenic electron microscopy (cryo-EM) now allows it to routinely reach resolutions where it can provide a wealth of new information on molecular biological phenomena by permitting new targets to be structurally characterized.

In cryo-EM, biological molecules are suspended in thin vitreous sheet of ice and imaged in projection. Collecting millions of such images permits the reconstruction of the original molecular structure, by appropriate alignment and averaging of the particle images. This however requires immense computational effort, which just a few years ago was prohibitive to full use of the image data.

In this thesis, I describe the development of fast algorithms for processing of cryo-EM data, utilizing GPUs by exposing the inherent parallelism of its alignment and classification. The acceleration of this processing has changed how biological research can utilize cryo-EM data. The drastically reduced processing time now allows more extensive processing, development of new and more demanding processing tools, and broader access to cryo-EM as a method for biological investigation. As an example of what is now possible, I show the processing of the fungal pyruvate dehydrogenase complex (PDC), which poses unique processing challenges. Through extensive processing, new biological information can be inferred, reconciling numerous previous findings from biochemical research. The processing of PDC also exemplifies current limitations to established.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik, Stockholms Universitet, 2020. p. 100
Keywords
cryo-EM, electron microscopy, GPU, parallel processing, protein structure
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-179802 (URN)978-91-7911-050-5 (ISBN)978-91-7911-051-2 (ISBN)
Public defence
2020-04-24, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.

Available from: 2020-04-01 Created: 2020-03-10 Last updated: 2020-05-25Bibliographically approved

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Perez Boerema, AnnemarieAibara, ShintaroTobiasson, VictorKimanius, DariForsberg, Björn O.Walldén, KarinLindahl, ErikAmunts, Alexey
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