Navigating the intricate world of tryptophan interactions: the art of blocking and rescuing

Scientists have developed a new method to control and manipulate specific tryptophan residues in proteins, allowing for precise control over protein function. This new technology, published in Nature Chemistry, utilizes a vinyl-caged tryptophan analogue that can be selectively decaged to rescue protein activity.

The field of genetic code expansion (GCE) has rapidly advanced in recent years, with new technologies in codon reassignment, synthetic genomes, and evolved aaRS/tRNA systems. The incorporation of non-canonical amino acids (ncAAs) into proteins allows for the manipulation of protein function by targeting specific residues within an active site. However, until now, this technology has primarily been applied to amino acid residues that contain polar side chains, such as lysine, serine, tyrosine, and histidine.

In this new study, researchers have developed a method to cage the indole nitrogen of tryptophan with a vinyl handle, creating a "vinyl tryptophan" (vyW) that can be selectively decaged through the fast, specific, and bio-orthogonal inverse electron demand Diels–Alder (IEDDA) reaction. This method allows for precise control over any protein that has a tryptophan residue that is critical to its normal function.

"This technology brings precision control that can enable researchers to better understand the potential importance of select tryptophan residues in proteins of interest," said the study's lead author, Dr. Chen.

The researchers demonstrate the broad utility of their chemical activation of genetically encoded caged-tryptophan system, termed Trp-CAGE, in a variety of protein families and show that their optimized IEDDA diene reagent effectively rescues tryptophan interactions, thereby restoring protein functionality.

"This methodology has the potential to enable researchers to better understand the potential importance of select tryptophan residues in proteins of interest," said Dr. Chen.

The researchers also developed a bespoke aaRS for vyW and extensively tested the system in a wide variety of classes of proteins, demonstrating its high-fidelity, high-efficiency, and broad utility in establishing control over the activity of many proteins.

"In future works, this IEDDA-decaging model might be applicable for studying other amino acids of catalytic or structural importance in proteins," said Dr. Chen.

This new technology has the potential to have a significant impact on the field of protein research and could have numerous applications in the development of new drugs and therapies.

Source:
Zhu, Y. et al. (2024) Blocking and rescuing tryptophan interactions with a vinyl-caged tryptophan analogue. Nature Chemistry. doi: 10.1038/s41557-024-01463-7.