2’ vs. 3’ Aminoacylation in Biological Translation

Genetic information all in living organisms is stored in the form of long-chain molecules called nucleic acids, such as DNA or RNA. This information is then read and interpreted to produce proteins, another type of long-chain molecules, which are chiefly responsible for the functioning of cells. The process of translation of genetic information contained in nucleic acids into proteins is one of the most important biological processes and many of its aspects are universally conserved. The central element of the translation apparatus in the cells are transfer RNAs (tRNAs), in which a nucleic-acid molecule is covalently attached to a single amino acid, the basic building block of proteins, via a process of aminoacylation. In fact, tRNAs can be seen as the point at which the world of nucleic acids in the cell most directly contacts the world of proteins. Importantly, the amino acid can be attached at two possible positions (termed 2 and 3) in the terminal ribose of the tRNA and, once attached, the amino acid can change positions between the two. However, only the 3 attachment is used in the process of translation. Although they represent the very heart of the translation apparatus, the two points of amino-acid attachment still remain underexplored. What are the conformational differences between the two types of attachment? How do they impact the stability of tRNAs and their reactivity in the process of translation? How are the interactions of the tRNA with the rest of the translation apparatus affected depending on where the amino acid is attached? The present proposal utilizes a combination of advanced computational simulations, to be performed by us, and NMR experiments, to be performed by our collaborator John D. Sutherland (LMB Cambridge), aimed at addressing these important questions. The foundation for the project is a series of preliminary results in which we could show that 2 attachment of amino acids to tRNA may induce a collapsed, folded-back conformation, while 3 attachment may induce an extended conformation, two possibilities with potentially major mechanistic consequences. As a whole, our project will provide novel information about one of the most central biological processes, with implications concerning both the fundamental aspects of its present-day mechanism as well as its evolutionary origins. Moreover, we expect that our project will also impact other fields including biotechnology and biomedicine. Concerning the latter, approximately 50% of all antibiotics target the bacterial translation apparatus and it is our hope that the advances to be made in our project will pave way for new strategies for drug design as well.

A major characteristic of all living organisms is that they encode genetic information in long-chain molecules called nucleic acids, including DNA and RNA. In a process called translation, the information encoded in nucleic acids is used to produce proteins, another type of long-chain molecules, which are built of amino acids and carry out different functions in living cells. The translation of genetic information is one of the most important biological processes and many of its features are universally conserved, including the usage of transfer RNAs (tRNAs). tRNAs are nucleic acids which are covalently attached to single amino acids and are thought to serve as adaptors that connect the genetic information with what that information stands for. In many ways, tRNAs are the very nexus at which the world of nucleic acids comes most directly in contact with the world of proteins. The overarching goal of the present project was to analyze and compare at the atomistic level the implications of the two principal ways the amino acids are attached to the corresponding tRNAs, with a larger ambition to contribute to a detailed understanding of both present-day features of the biological translation and its evolutionary origins. In particular, we have used atomistic computer simulations in comparison with experimental data, to show that the site of amino-acid attachment has major repercussions on the conformational properties of RNAs and directly affects their stability and potential for long-range information transfer. In particular, we could show that the specific way of amino-acid attachment used in biology may have been selected as it induces an extended conformation, which is particularly conducive for the protein synthesis reaction. Moreover, our work has provided strong indications that a specific interaction between a nucleic acid and a bound amino acid could provide selection of some particular pairings of the two and could have led to the development of a primitive genetic code. Finally, as a part of the present project, we have also further developed and tested computational tools for the characterization of coupled motions in biomolecules and applied them in the case of tRNA. Overall, our project has provided novel information about the essential, atomistic details of one of the key biological processes when it comes to both its present-day mechanism as well as its evolutionary beginnings. As such, we expect its impact will extend to both fundamentally scientific fields such as mechanistic biochemistry and evolutionary biology, but also more practical fields such as biomedicine and biotechnology.