In the E. coli ribosome A901 is involved in tertiary contacts with the ribose of residue 811C at the base of b-h24, and with the backbone of residue A1513 in b-h45 (39), underscoring its important role in the stabilization of the complicated structure of the region.
These bulged-out bases are in the large ribosomal subunit of H. marismortui (13) (as well as in Deinococcus radiodurans (80), Escherichia coli (81), and Thermus thermophilus (82) ribosomal crystal structures) involved in tertiary contacts with bases of adjacent stem-loop of 23S rRNA (Fig. 5 B ).
In addition, ·OH protections constituting each side of a tertiary contact are not coincident in some cases, consistent with the formation of transient non-native interactions.
In Figure 1, we provide data for the dynamic variation of the tertiary contact formation and the hydrogen-bond formation of 10 pathways.
The preferred folding pathway involves initial formation of the proximal tertiary contact.
The helical hairpin is one of the most ubiquitous and elementary secondary structural motifs in nucleic acids, capable of serving functional roles and participating in long-range tertiary contacts.
The set of residue pairs within a small C β distance in tertiary structure in a representative crystal structure is recognized as a coarse criteria because it is not clear that close physical proximity is an essential precondition for coevolution [ 32], and because a single crystal structure may not accurately describe the tertiary contacts in all sequences in the alignment.
Our results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics.
They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts.
The split receptor approach could be a general, rapid, and easy assay for the routine determination of tertiary contacts in single chain, polytopic, integral membrane proteins.
