Lost lab notes hamper attempts to repeat crucial experiment.
The retraction of two papers from the lab of prominent US chemist Peter Schultz is a setback for researchers trying to synthesize and study glycoproteins — proteins with sugar chains attached.
The papers, published in Science1 and the Journal of the American Chemical Society2 (JACS), seemed to show that technology enabling the bacterium Escherichia coli to make proteins from many non-natural amino acids could also incorporate sugars at specific sites.
Schultz, of the Scripps Research Institute in La Jolla, California, says that while attempting to replicate the work in the two papers, members of his lab discovered that non-natural glycosylated amino acids — ones with attached sugars — behave differently from all other non-natural amino acids his lab has studied. The researchers were unable to get any glycosylated amino acids to integrate into proteins, Schultz says. He and his colleagues retracted the JACS paper on 4 September3 and the Science paper on 27 November4.
“This takes away one of the benchmarks people would cite to show how far the method could go. , ”
In August, a paper co-authored by Eric Tippmann, a former postdoc of Schultz's who is now at Cardiff University, UK, argued that the method described in the papers could not have worked anyway5. E. coli, he reported, has insufficient levels of the relevant enzymes necessary to process the glycosylated amino acids that were used in the experiment. He and his colleagues suggest5 that the proteins reported in the retracted papers contained natural rather than non-natural glycosylated amino acids.
Schultz says it could be true that the proteins incorporated natural rather than non-natural amino acids, but adds that there are other possible explanations for his results.
He says that the conditions of the original experiments may have allowed the E. coli to process the glycosylated amino acids, which had been modified to allow them to enter the bacteria easily. However, the lab no longer has the notebooks detailing the original experiments, so the team can't replicate those conditions, Schultz explains.
Schultz says that he had members of his lab try to replicate the papers for more than two years. "We worked hard on it, and there are real peculiarities associated with the glycosylated amino acids that we still don't understand," Schultz says. "We couldn't get it to work." Only then did the team decide to retract the papers. "I think we did the right thing," says Schultz.
Glycoproteins are ubiquitous in biology and pharmacology, but difficult to make artificially in living cell systems, so the ability to direct bacteria to make specific glycoproteins would have been a boon.
Chemist David Tirrell of the California Institute of Technology in Pasadena, who also studies methods for incorporating non-natural amino acids into proteins, says the retractions will be a blow for glycobiologists. But because the glycobiology work was often seen as proof of principle, it is also a disappointment for anyone working on making proteins from non-natural amino acids, he says. "This takes away one of the benchmarks people would cite to show how far the method could go," says Tirrell.
Another former postdoc of Schultz's, Ryan Mehl, who is now at Franklin & Marshall College in Lancaster, Pennsylvania, agrees. "[Glycobiologists] went from something where they had the potential for great tools to zero, so it's a big deal for that field."
Schultz's underlying method for incorporating non-natural amino acids into proteins has been reproduced by other labs, note Tirrell, Mehl and other scientists. But the ability to incorporate glycoproteins "would have been a killer application", says Steven Benner of the Foundation for Applied Molecular Evolution in Gainesville, Florida. "I'm disappointed that it didn't work."
Zhang, Z. et al. Science 303, 371-373 (2004).
Xu, R. et al. J. Am. Chem. Soc. 126, 15654-15655 (2004).
Xu, R. et al. J. Am. Chem. Soc. 131, 13883 (2009).
Zhang, Z. et al. Science 326, 1187 (2009).
Antonczak, A. K., Simova, Z. & Tippmann, E. M. J. Biol. Chem. 284, 28795-28800 (2009).
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Check Hayden, E. 'Killer application' for protein synthesis is retracted. Nature 462, 707 (2009). https://doi.org/10.1038/462707a
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