The distribution of ribosomal protein binding sites on the 16S ribosomal RNA molecule has been analyzed by limited ribonuclease hydrolysis of RNA-protein complexes, as well as by the interaction of individual proteins with RNA fragments purified from partial enzymatic digests. Of the six 30S subunit proteins known to interact directly with 16S RNA, proteins S4, S8, S15, S20, and, probably, S13 ...

Extensive studies in our laboratory using different ribonucleases resulted in valuable data on the topography of the E.coli 16S ribosomal RNA within the native 30S subunit, within partially unfolded 30S subunits, in the free state, and in association with individual ribosomal proteins. Such studies have precise details on the accessibility of certain residues and delineated highly accessible RN...

The sequences of oligonucleotides released by T1 ribonuclease digestion of 32-P-labeled 16S (chloroplast) and 18S (cytoplasmic) ribosomal RNAs from a marine species of Porphyridium (Rhodophyta) have been determined. The resultant catalogs have been compared to those obtained for three prokaryotes:Escherichia coli, Bacillus subtilis, and Anacystis nidulans (a blud-green alga). There is extensive...

A fragment of the 16S RNA of Thermus thermophilus corresponding to the central domain (nucleotides 547-895) has been prepared by transcription in vitro. Incubation of this fragment with the total 30S ribosomal proteins has resulted in the formation of a compact 12S ribonucleoprotein particle. This particle contained five T. thermophilus proteins corresponding to Escherichia coli ribosomal prote...

Partially denatured 16S rRNA from 30S ribosomes shows features of secondary structure in electron microscopy that correspond to the well accepted secondary structure model derived from chemical modification and phylogenetic data. However, a very different conformation is seen in precursor 16S rRNA sequences contained within 30S pre-rRNA transcripts: the major 5'-terminal loop is absent, and sev...

In this paper a coarse-grained method called elastic network interpolation (ENI) is used to generate feasible transition pathways between two given conformations of the core central domain of 16S Ribosomal RNA (16S rRNA). The two given conformations are the extremes generated by a molecular dynamics (MD) simulation, which differ from each other by 10A in root-mean-square deviation (RMSD). It ta...

The properties of 30S ribosomal subunits from untreated and from colicin E3-treated (E3-30S) bacteria have been compared. Polyacrylamide gel electrophoresis of ribosomal proteins revealed no difference, but several studies indicated that the 16S RNA from E3-30S particles was modified. E3-16S RNA showed slightly increased resistance to heat-induced degradation and had a reduced (15 S) sedimentat...