How do proteins fold biologically?
For nearly as long as scientists have had access to protein structure we have understood that the primary amino acid sequence is what determines that protein's native structure and consequently its function (Anfinsen's dogma). However, studying how a protein folds into its native conformation has classically been done in vitro with purified proteins. This has provided a wealth of valuable data on the biochemical and biophysical properties of proteins and how the primary sequence contributes to their folding. Nonetheless, this is not how proteins fold in vivo. They are produced by a ribosome where even during translation (cotranslationally) they may begin to fold. There is now significant evidence that protein folding on the ribosome can differ significantly from the folding of full-length proteins in solution. By using so-called force-sensitive translational arrest peptides we study protein folding cotranslationally by indirectly observing forces acting on the nascent chain during translation. This method is a cost-effective biochemical method that is even accessible in vivo and yields comparable results to more labour and cost intensive biophysical cotranslational measurements.
How are large bioenergetic protein complexes assembled and function?
Complex I is the first enzyme complex in the electron transport chain that generates energy in living cells. It is an incredibly efficient machine that couples NADH reduction to the pumping of protons and the generation of a proton gradient that is used for ATP synthesis. The molecular details of how protein pumping is activated by the electron transfer from NADH to conenzyme Q are still unclear. By combining "top-down" and "bottom-up" approaches in both the wet lab and via molecular simulation, we hope to dissect these details and ultimately learn how they can be applied to make synthetic molecular machines more efficient.
Research group: Ville Kaila
A selection from Stockholm University publication database
Force-Profile Analysis of the Cotranslational Folding of HemK and Filamin Domains
2019. Grant Kemp (et al.). Journal of Molecular Biology 431 (6), 1308-1314Article
We have characterized the cotranslational folding of two small protein domains of different folds-the alpha-helical N-terminal domain of HemK and the beta-rich FLN5 filamin domain-by measuring the force that the folding protein exerts on the nascent chain when located in different parts of the ribosome exit tunnel (force-profile analysis, or FPA), allowing us to compare FPA to three other techniques currently used to study cotranslational folding: real-time FRET, photo induced electron transfer, and NMR. We find that FPA identifies the same cotranslational folding transitions as do the other methods, and that these techniques therefore reflect the same basic process of cotranslational folding in similar ways.
Small membrane proteins - elucidating the function of the needle in the haystack
2014. Grant Kemp, Florian Cymer. Biological chemistry (Print) 395 (12), 1365-1377Article
Membrane proteins are important mediators between the cell and its environment or between different compartments within a cell. However, much less is known about the structure and function of membrane proteins compared to water-soluble proteins. Moreover, until recently a subset of membrane proteins, those shorter than 100 amino acids, have almost completely evaded detection as a result of technical difficulties. These small membrane proteins (SMPs) have been underrepresented in most genomic and proteomic screens of both pro-and eukaryotic cells and, hence, we know much less about their functions in both. Currently, through a combination of bioinformatics, ribosome profiling, and more sensitive proteomics, large numbers of SMPs are being identified and characterized. Herein we describe recent advances in identifying SMPs from genomic and proteomic datasets and describe examples where SMPs have been successfully characterized biochemically. Finally we give an overview of identified functions of SMPs and speculate on the possible roles SMPs play in the cell.