Monitoring dynamics of protein nascent chain on the ribosome using PET-FCS

by Marija Liutkute
Doctoral thesis
Date of Examination:2020-05-20
Date of issue:2020-06-24
Advisor:Prof. Dr. Marina Rodnina
Referee:Prof. Dr. Jörg Enderlein
Referee:Prof. Dr. Kai Tittmann
Referee:Prof. Dr. Patrick Cramer
Referee:Prof. Dr. Holger Stark
Referee:Dr. Alexis Caspar Faesen
Persistent Address: http://dx.doi.org/10.53846/goediss-8042

 

 

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Abstract

English

The ribosome synthesizes proteins according to the sequence of the messenger RNA (mRNA) by progressively adding amino acids to the C-terminus of the nascent peptide. For a protein to become fully functional, it has to fold into a specific three-dimensional structure, called the native state. Experimental work on protein folding in solution has shown several possible models of protein folding. However, currently there is no unifying model for protein folding on the ribosome. Recent experimental work has shown that in the cell nascent polypeptides begin to fold during ongoing translation and in the constrained space of the ribosomal peptide exit tunnel. Here we propose to utilize two novel experimental techniques, force profile assay (FPA) and photoinduced electron transfer with fluorescence correlation spectroscopy (PET-FCS) to map the folding trajectory and obtain temporal information on rapid local structural fluctuations of dynamic cotranslational intermediates. We studied how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally using a high-resolution force profile assay. FPA reveals that the protein starts to compact as soon as the N-terminal α-helical segments are synthesized. Compaction proceeds vectorially – as nascent chain grows, emerging helical segments dock onto the preceding structures and rearrangements continue after emergence out of the tunnel and near the ribosomal surface. PET-FCS shows that at each stage of translation the nascent peptide undergoes structural fluctuations on the µs time scale. As the domain grows in length and the complexity of tertiary interactions and moves away from the ribosome the fluctuations slow down. Native state destabilizing mutations have little effect on the folding pathway inside the ribosome exit tunnel, but disrupt the final domain stabilization. The results presented in this thesis show how FPA and PET-FCS method can be utilized in solving the trajectory of cotranslational protein folding and characterizing the dynamic properties of folding intermediates.
Keywords: Cotranslational folding; Nascent chain dynamics; Ribosome
 
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