Dependency Map of Proteins in the Small Ribosomal Subunit

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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. The ribosome acts as the protein–production facility of the cell. Interfering with its assembly will shut down the function of the cell. The bacterial ribosome differs from the eukaryotic one. Both properties together prompt for the development of antibiotics targeting the bacterial ribosome. To target this macromolecular complex most efficiently, one needs to understand the assembly process. The smaller subunit consists of 21 proteins and a ≈ 1500 nucleotide long RNA chain. This size makes it unfeasible to treat the assembly process with conventional computational techniques. To overcome this size limit, this paper introduces a new approach which computes energetic and entropic contributions to the binding energy of individual proteins. By systematic Gedankenexperiments and an accompanying analysis procedure we were able to deduce the binding dependencies of the proteins and the influences of their respective absence or presence onto other proteins. From the obtained influence map we can deduce potential target proteins for drug development or other binding hindering experiments.