Ribosomes are ribonucleoprotein particles responsible for synthesis of a nascent peptide, also known as translation, wherein a sequence of messenger ribonucleic acid (mRNA) is translated into a sequence of amino acids. They are essential in all three domains of life - Archaea, Bacteria, and Eukarya. Although the critical parts of ribosomes are conserved across the domains, still there are sites where ribosomes differ.
The nascent chain is released from the ribosome through an exit tunnel located within the large ribosomal subunit and some difference between bacteria and higher organisms lie here. Numerous interactions occur between the nascent peptide and the tunnel walls, with the narrowest part formed by extended loops of two ribosomal proteins, namely uL4 and uL22. Additionally, uL4 and uL22 have globular parts on the surface of the ribosome, through which they can interact with other proteins associated with the ribosomes [1].
The roles played by the two domains of ribosomal proteins contributing to the tunnel walls and why these proteins evolved into their shapes are not fully understood. In this study, we address these questions by analysing a set of experimental ribosome structures from the Protein Data Bank. Our analysis includes root-mean-square fluctuation analysis to reveal the flexible and rigid sections of the proteins. Principal component analysis of Cartesian coordinates suggests that some elements are structurally correlated. In addition, sequence alignment complements our analyses by offering insight into the conserved sections of the proteins.
The research was supported by the Czech Science Foundation (project 23-05557S).