Ribosomes translate the information encoded in DNA into proteins in a precise process. Certain enzymes, known as aminoacyl-tRNA synthetases, play a crucial role in this process. They ensure that the correct amino acid is activated during translation and binds to the respective tRNA. However, the question of how this precisely coordinated process originated remains unanswered. The question arises, in particular, as to how amino acids could combine selectively in the absence of enzymes, enabling the formation of complex molecular machinery.
Dr. Charalampos Pappas, Dr. Kun Dai and Lenard Saile from the University of Freiburg and the Cluster of Excellence Living, Adaptive and Energy-autonomous Materials Systems (livMatS), have demonstrated in an experiment that amino acids can organize themselves selectively into peptide oligomers without the addition of enzymes. The scientists utilised phase separation to control the selection of the chemical building blocks involved. Both the binding of the amino acids and the liquid-liquid-phase-separation were achieved using just one acyl transfer reaction cycle. The team has published these results in the scientific journal Chem.
Shift from randomness to selectivity
“We are inspired by biological processes, but our goal is to reduce complexity and use simplified versions of Nature’s building blocks that can mimic such processes without enzymes,” says Charalampos Pappas. “Our study shows how droplets formed from simple amino acids can channel oligomerization pathways and help chemistry shift from randomness to selectivity.”
In living organisms, aminoacyl-tRNA synthetases recognize different amino acids and activate them by consuming ATP. This process results in the formation of the intermediate aminoacyl adenylate, which, however, cannot be recognized by the ribosomes. This is only achieved through aminoacyl transfer to a tRNA, whereby the amino acid is bound to the tRNA via an ester bond.
Acyl transfer reaction similar to that found in living organisms
In the experiment, the research team coupled a reaction cycle to the amino acid oligomerisation, triggering an acyl transfer reaction similar to that found in living organisms. During this reaction cycle, aminoacyl phenolic esters formed, organizing the amino acids in compartments to create linear or cyclic peptide chains depending on the type of side chain.
Assembling reactive amino acids in liquid-liquid phase separated compartments enabled precise control over the recognition of specific side chains and subsequent linkage of amino acids. During this process, only specific amino acids are concentrated and shielded from hydrolytic deactivation. The Freiburg researchers succeeded in enabling the monomers to simultaneously act as a reactive substance and the component that triggers phase separation.
- Original publication:
Dai, K., Saile, L., Pol, M. D., Sharma, A., Pramod, T., & Pappas, C. Phase Behavior and Pathway-Selective Oligomerization Driven by Amino Acid Side Chain Recognition, Chem, 2025.
DOI: 10.1016/j.chempr.2025.102589
- Charalampos Pappas has been a junior research group leader at the Cluster of Excellence Living, Adaptive and Energy-autonomous Materials Systems (livMatS) at the University of Freiburg since 2020. He is also a member of the Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT). His research focuses on Phosphate-driven Systems Chemistry.
- Kun Dai is a postdoctoral researcher at the livMatS Cluster of Excellence. He develops spontaneous peptide chemical networks capable of dynamic adaptation and mimicking biological behavior by constructing non-equilibrium self-assembling systems.
- Lenard Saile is a PhD student in the group of Charalampos Pappas at the livMatS Cluster of Excellence. His focus lies on the molecular design of dynamic reaction networks that adapt and respond to self-assembly mechanisms.