Ribosomes are the universal cellular machines that act as very efficient polymerases that translate the genetic code into proteins. They posses spectacular architecture accompanied by inherent mobility, which facilitate their smooth performance as RNA enzymes. The peptide bond formation site is located within a universal internal symmetrical region connecting all of the remote ribosomal features involved in its functions. The elaborate architecture of this region positions ribosomal substrates in appropriates stereochemistry for peptide bond formation, for substrate-mediated catalysis, and for substrate translocation. The high conservation of this symmetrical region implies its existence irrespective of environmental conditions and indicates that it may be a remnant of a prebiotic RNA machine that is still functioning in the contemporary ribosomes.
Adjacent to the peptide bond formation site is an elongated tunnel, along which nascent chains progress until they emerge out of the ribosome. This tunnel is involved in signaling and gating functions, provides the binding site of the first cellular chaperone that encounters the emerging nascent chain, and hosts a major family of antibiotics that target the ribosome.
A decade of structural studies on antibiotics targeting ribosomes yielded several imperative take-home lessons. Among them are the structural bases for the antibiotics modes of function, including induced fit and remote intersections; the basis for antibiotics synergism; the differentiation between ribosomes of pathogens vs. those of higher organism; the mechanisms of resistance to antibiotics, including secondary conformational rearrangements caused by remote mutations; cross-resistance to ribosomal antibiotics. Within this frame, parameters allowing for clinical usage of antibiotics targeting fully conserved regions, such is the peptidyl transferase center, have been identified; common and specific pathways of cross resistance have been proposed; and minute chemical differences that can turn competition into synergism, have been characterized. Based on those insights, the feasibility of design of advanced efficient antibiotics and/or of the improvement of the existing compounds could be assessed, thus paving the way to exciting developments in this area.