Co-translational protein folding on the ribosome monitored in real time
Proteins are biopolymers assembled from 20 naturally occurring amino acids connected via peptide bonds. In living cells the process of protein synthesis is catalyzed by ribosomes which translate the sequence of the messenger RNA into the respective sequence of amino acids in a protein. To carry out their various vital functions in the cell, proteins must fold into their three-dimensional structures. The process of protein folding is remarkably rapid, as peptides fold within fractions of seconds while the ribosome continues to attach amino acids to the polypeptide. However, sometimes protein folding can go wrong. Misfolding is the source of many diseases such as Alzheimer's, Parkinson's, and other neurodegenerative diseases. There is a huge gap in our knowledge of how the ribosome synthesizes peptides and how the newly-made proteins attain their biological functions. Dissecting the mechanism of protein folding will help to understand how proteins attain their native shape.
Folding of many cellular proteins begins co-translationally, when the nascent peptide is still attached to the synthesizing ribosome. Contrary to folding of isolated proteins in vitro, co-translational folding is vectorial, that is, it starts as soon as the protein emerges from the peptide exit tunnel of the ribosome. The key questions are: When does folding start in relation to translation and what is the structure of the polypeptide emerging from the ribosome?
To investigate co-translational protein folding in real time, researchers of the Department of Physical Chemistry headed by Marina Rodnina at the Max Planck Institute for Biophysical Chemistry followed folding of a domain of an N5-glutamine methyltransferase termed PrmC in vitro, as it is synthesized on synchronized ribosomes in a translation system. They employed Förster Resonance Energy Transfer, Photoinduced-Electron Transfer, and limited proteolysis as sensitive methods for structure formation of growing polypeptide chains on ribosomes.
The scientist's results show that the protein folds sequentially: At first, the nascent chain folds into a compact, non-native state at an early stage when a large part of the nascent peptide is enclosed in the exit tunnel of the ribosome. It then rearranges into a near-native fold when the nascent chain is long enough to emerge from the ribosome. This sequence of folding events may be typical of small spontaneously folding protein domains. The compaction and native state formation are intrinsically rapid and limited by the rate of translation. Each time an amino acid is added, the nascent polypeptide rapidly scans the accessible conformations within the restricted environment of the exit tunnel. Thus, the ribosome defines the time and space for protein folding, which may help to prevent kinetic trapping of non-native structures and unproductive protein folding. The novel findings of Marina Rodnina's team show how the ribosome can, in principle, define the pathway for co-translational folding.