Abstract
The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30S small ribosomal subunit of Thermus thermophilus. We determined the causal influence of the presence and absence of proteins in the 30S complex on the binding free energies of other proteins. The predicted dependencies are in overall agreement with the experimentally determined assembly map for another organism, Escherichia coli. We found that the causal influences result from two distinct mechanisms: one is pure internal energy change, the other originates from the entropy change. We discuss the implications on how to target the ribosomal assembly most effectively by suggesting six proteins as targets for mutations or other hindering of their binding. Our results show that by blocking one out of this set of proteins, the association of other proteins is eventually reduced, thus reducing the translation efficiency even more. We could additionally determine the binding dependency of THX—a peptide not present in the ribosome of E. coli—and suggest its assembly path.
Highlights
Ribosomes are large ribonucleoprotein assemblies that conduct the process of translation of the genetic code
We have to emphasize that we study the T. thermophilus bacteria, we expect that our map may differ from that of E. coli, and those differences may be interesting to note
We applied an analytic procedure to the problem of the stability of proteins in the small subunit of the ribosome of T. thermophilus
Summary
Ribosomes are large ribonucleoprotein assemblies that conduct the process of translation of the genetic code They are composed of two asymmetric subunits, small and large, which associate through a network of intermolecular interactions. In the early 1970s, it was found that the Escherichia coli small ribosomal subunit can reassemble in vitro from the 16S rRNA and a mixture of the 30S proteins [4,5]. Such reassembly produces an active 30S particle, and these experiments revealed that subunit complexation is a sequential and ordered process. The pathway and the mechanism of the assembly have been of significant interest (for review see [6]), many details of this process still remain unclear
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