, to establish a collaboration through UC Berkeley’s California Institute for Quantitative Bioscience (QB3) to further investigate the questions of selectivity and mechanism of action. Cate is also director of UC Berkeley’s Center for RNA Systems Biology, while Doudna is a professor of molecular and cell biology and of chemistry, a Howard Hughes Medical Institute investigator and executive director of the Innovative Genomics Institute.
“Pfizer brought a significant depth of knowledge and resources to the collaboration, including fundamental cell biology, disease-relevant expertise, chemical biology and medicinal chemistry,“said Liras. “We aimed at building a strong cross-institutional collaboration which would complement our strengths in drug discovery with UC Berkeley’s strengths in ribosome biochemistry and structural biology.“
In the PLOS Biology paper, Cate, Robert Dullea at Pfizer and their teams at UC Berkeley and Pfizer describe how the drug interacts with the ribosome to halt protein production.
According to Cate, the ribosome assembles amino acids into a chain inside a tunnel that holds about 30 to 40 amino acids before the end begins to poke out of the tunnel. The chemical studied appears to bind to specific amino acid sequences of the growing protein within that tunnel in the ribosome and make them kink enough to stop progress down the tunnel, halting protein synthesis.
“We found that the proteins that are stalled are too short to stick outside the ribosome,” Cate said. “So we think the compound is actually trapping this snake-like chain, the starting part of the protein, in the tunnel — not completely blocking the tunnel, but just partially blocking it, in a way that prevents this particular protein from making its way out.”
While it’s still unclear what the two dozen proteins affected have in common that makes them susceptible to stalling by the small molecule, Cate sees these findings as clear evidence that ribosomal stalling can occur very specifically, something most researchers thought unlikely.
“We think that we now have enough understanding of the mechanism that we have our foot in the door to explore the relevance of this biology more broadly,” said Cate.
Co-authors of the paper are Cate, Doudna and postdoctoral scholar Nathanael Lintner of UC Berkeley and Pfizer researchers Kim McClure, Donna Petersen, Allyn Londregan, David Piotrowski, Liuqing Wei, Jun Xiao, Michael Bolt, Paula Loria, Bruce Maguire, Kieran Geoghegan, Austin Huang, Tim Rolph and Spiros Liras.
The work was funded by Pfizer, with computing and gene sequencing assistance through resources supported by the National Institutes of Health.