A 2023 Crick PhD project with David Balchin.
Project background and description
Proteins are synthesised on the ribosome as linear polypeptides that in most cases must fold into defined 3-D structures to be biologically active. How this occurs is a fundamental problem in biology. Although few proteins fold efficiently in a test tube, in vitro studies of isolated model proteins underpin our current understanding of the folding process. Folding in vivo is a much more sophisticated operation. Folding begins during synthesis, and is aided by a complex network of protein biogenesis factors: molecular chaperones that stimulate folding reactions, reverse misfolding, and inhibit aggregation[1, 2]. Failure of the cellular protein folding machinery has severe consequences. Protein misfolding is a hallmark of neurodegenerative disease, cystic fibrosis and type II diabetes, and a key contributor to the process of aging.
The overarching goal of our lab is to understand protein biogenesis in molecular detail. To do this, we study cellular protein synthesis and folding networks in vitro and in vivo using a range of cell biological, biochemical, biophysical and structural approaches [3, 4]. By studying the molecular principles underlying protein folding in the cell, we also hope to understand why proteins misfold in disease.
Many large eukaryotic proteins with complex structures do not fold when expressed in bacteria, implying that eukaryotes have evolved unique solutions to the folding problem. For example, eukaryotic cells express a large array of molecular chaperones that are not found in simpler organisms. However, it is not well understood how this complex network of “folding-helpers” is coordinated with protein synthesis at the ribosome, nor how exactly it contributes to folding newly-made proteins. Using novel methods developed in our lab, the PhD candidate will explore the chaperone network associated with the human ribosome. We will determine which chaperones engage a spectrum of structurally diverse nascent proteins during translation. We will then use fluorescence microscopy and ribosome profiling to study chaperone interactions in cells, and characterise the complexes in molecular detail using structural proteomics and cryo-electron microscopy. The ultimate goal of the project is to understand how chaperones enable protein biogenesis in human cells.
Candidates should have a degree in Biochemistry, Molecular Biology, or a related subject. Familiarity with basic molecular biology techniques would be advantageous. This project would particularly suit candidates with a background in protein biochemistry or cell biology, and an interest in protein folding, structure and dynamics.
1. Balchin, D., Hayer-Hartl, M. and Hartl, F.U. (2016)
In vivo aspects of protein folding and quality control.
Science 353: aac4354. PubMed abstract
2. Balchin, D., Hayer-Hartl, M. and Hartl, F.U. (2020)
Recent advances in understanding catalysis of protein folding by molecular chaperones.
FEBS Letters 594: 2770-2781. PubMed abstract
3. Balchin, D., Miličić, G., Strauss, M., Hayer-Hartl, M. and Hartl, F.U. (2018)
Pathway of actin folding directed by the eukaryotic chaperonin TRiC.
Cell 174: 1507-1521.e1516. PubMed abstract
4. Wales, T.E., Pajak, A., Roeselová, A., Shivakumaraswamy, S., Howell, S., Hartl, F.U., . . . Balchin, D. (2022)
Preprint: Resolving chaperone-assisted protein folding on the ribosome at the peptide level.
Available at: bioRxiv. https://www.biorxiv.org/content/biorxiv/early/2022/09/23/2022.09.23.509153.full.pdf
5. Albanése, V., Yam, A.Y., Baughman, J., Parnot, C. and Frydman, J. (2006)
Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells.
Cell 124: 75-88. PubMed abstract