Nature Chemistry: A new approach to the study of ribosome function

In tiny cellular machines called ribosomes, strands of genetic material called messenger RNAs (mRNAs) match the corresponding transfer RNAs (tRNAs) to form sequences of amino acids that leave the ribosome
as proteins.
Unfinished proteins are called nascent strands, and they are left on ribosomes
.

Scientists know that some of these nascent chains regulate ribosome activity, and that the nascent chains sometimes interfere with antibiotics — many by targeting bacterial ribosome activity
.
Scientists don't know why this happens, mainly because it's hard to imagine what the ribosome-peptide-drug interaction looks like when the unfinished protein is still attached to the ribosome
.

Now, scientists at the University of Illinois at Chicago are the first to report a method for peptides to attach stably to trna, which gives them a new basic understanding
of ribosome function by determining their atomic-scale structure and the shape of these peptides in ribosomes.

"Our challenge is to get a closer look at the structure of ribosomes and the exit pathways when nascent peptides are present, because in nature, ribosomes are very easy for us to capture images or conduct experiments," said
Yury Polikanov, associate professor in the Department of Biological Sciences in the College of Arts and Sciences.
"Until this new method emerged, we could largely not see what was happening at
the active site of the ribosome at this critical moment.
"

Polikanov and his colleague Egor Syroegin (a PhD candidate in biological sciences at UIC) used a method called primary chemical ligation to fuse custom peptides with tRNA to generate so-called peptide-based tRNAs
.

"Obtaining tRNA molecules linked to peptides, similar to those found in ribosomes during protein synthesis, has been the dream
of many researchers in the field for almost 20 years," Polikanov said.
"This is very challenging because there is no enzyme that can directly attach peptides to tRNA
.
"

"This method has been used in chemistry for a long time, but it has never been
applied in this way.
It's basically mimicking nature, and with advanced imaging experience, we can now see how nature works at high resolution," Syroegin said
.

With this new method, Polikanov and Syroegin determined the high-resolution structure
of a group of ribosomes carrying peptidyl trnas of different lengths.

Detailed analysis of these structures provides new and surprising insights into the mechanisms of ribosome catalysis centers and answers several long-standing fundamental questions
in the ribosome field, Polikanov said.

Syroegin said: "We found that depending on the sequence, different peptides can form different shapes or folds within the ribosome tunnel, and we can synthesize different peptides from different sequences and then follow their shapes very precisely because our structure has high resolution
.
" "So now, we can say with great confidence, 'These peptides, this sequence, have this shape' or 'Another peptide has another shape
.
' This is important because nascent peptide folding determines whether a drug inhibits ribosomes
.
”

"This approach opens up countless avenues for structural and functional studies aimed at understanding the mechanisms of ribosome function, as well as sequence-specific ribosome arrest induced by certain antibiotics," Polikanov said
.

Polikanov and Syroegin, co-authors of the paper, "Insights into ribosome function from the structure of non-blocking ribosome nascent chain complexes," as well as "Insights into ribosome function from the structure of non-blocking ribosome nascent chain complexes," as well as "Insights into the structure of non-blocking ribosome nascent chain complexes," as well as "Insights into ribosome function," as well as the absence of a new chain of ribosome Elena Aleksandrova, Research Specialist
, Department of Biological Sciences, UIC.

This work was supported
by the National Institutes of Health (R01-GM132302, R21-AI163466), the National Science Foundation (MCB-1907273), and the Illinois Startup Fund.
This work is based on research
conducted at the Northeast Cooperation Visiting Group Beamline (DE-AC02-06CH11357) at Argonne National Laboratory Advanced Photon Source.