Positions of proteins S6, S11 and S15 in the 30 S ribosomal subunit of Escherichia coli

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

Epigenetic marks of prenatal air pollution exposure found in multiple tissues relevant for child health

BACKGROUND

Prenatal air pollution exposure has been linked to many adverse health conditions in the offspring. However, little is known about the mechanisms underlying these associations. Epigenetics may be one plausible biologic link. Here, we sought to identify site-specific and global DNA methylation (DNAm) changes, in developmentally relevant tissues, associated with prenatal exposure to nitrogen dioxide (NO₂) and ozone (O₃). Additionally, we assessed whether sex-specific changes in methylation exist and whether DNAm changes are consistently observed across tissues.

METHODS

Genome-scale DNAm measurements were obtained using the Infinium HumanMethylation450k platform for 133 placenta and 175 cord blood specimens from Early Autism Risk Longitudinal Investigation (EARLI) neonates. Ambient NO₂ and O₃ exposure levels were based on prenatal address locations of EARLI mothers and the Environmental Protection Agency's AirNOW monitoring network using inverse distance weighting. We computed sample-level aggregate methylation measures for each of 5 types of genomic regions including genome-wide, open sea, shelf, shore, and island regions. Linear regression was performed for each genomic region; per-sample aggregate methylation measures were modeled as a function of quantitative exposure level with covariate adjustment. In addition, bumphunting was performed to identify differentially methylated regions (DMRs) associated with prenatal O₃ and NO₂ exposures in each tissue and by sex, with adjustment for technical and biological sources of variation.

RESULTS

We identified global and locus-specific changes in DNA methylation related to prenatal exposure to NO₂ and O₃ in 2 developmentally relevant tissues. Neonates with increased prenatal O₃ exposure had lower aggregate levels of DNAm at CpGs located in open sea and shelf regions of the genome. We identified 6 DMRs associated with prenatal NO₂ exposure, including 3 sex-specific. An additional 3 sex-specific DMRs were associated with prenatal O₃ exposure levels. DMRs initially detected in cord blood samples (n = 4) showed consistent exposure-related changes in DNAm in placenta. However, the DMRs initially detected in placenta (n = 5) did not show DNAm differences in cord blood and, thus, they appear to be tissue-specific.

CONCLUSIONS

We observed global, locus, and sex-specific methylation changes associated with prenatal NO₂ and O₃ exposures. Our findings support DNAm is a biologic target of prenatal air pollutant exposures and highlight epigenetic involvement in sex-specific differential susceptibility to environmental exposure effects in 2 developmentally relevant tissues.

Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering

In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology.

Neutron scattering techniques and applications in structural biology

Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.

Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA

S1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. It has a pivotal role in stabilizing the mRNA on the ribosome. Thus far, S1 has eluded structural determination. We have identified the S1 protein mass in the cryo-electron microscopic map of the Escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30S subunit, which lacks S1. According to our finding, S1 is located at the junction of head, platform, and main body of the 30S subunit, thus explaining all existing biochemical and crosslinking data. Protein S1 as identified in our map has a complex, elongated shape with two holes in its central portion. The N-terminal domain, forming one of the extensions, penetrates into the head of the 30S subunit. Evidence for direct interaction of S1 with 11 nucleotides of the mRNA, immediately upstream of the Shine-Dalgarno sequence, explains the protein's role in the recognition of the 5' region of mRNA.

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution

The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.

On the global architecture of initiation factor IF3: a comparative study of the linker regions from the Escherichia coli protein and the Bacillus stearothermophilus protein

Initiation factor IF3 is a protein involved in the initiation stage of protein synthesis. It consists of two global domains linked by a 20 residue long, solvent-exposed linker. Recently, the structure of the N and C-terminal domains of the Bacillus stearothermophilus protein have been solved by X-ray crystallography and the structure of the intact Escherichia coli protein has been studied by NMR. These two studies have led to apparently contradictory models for the domain organization of IF3. The NMR study of the E. coli protein indicates that the linker region is flexible, while the studies of the isolated N and C-terminal domains of the B. stearothermophilus protein suggest that the linker forms a rigid helical rod. In order to resolve this discrepancy, a set of peptides corresponding to the linker regions of the B. stearothermophilus and the E. coli protein were synthesized. Circular dichroism and NMR spectroscopy were used to study the helical content as a function of pH, temperature, peptide concentration and ionic strength. Both peptides are monomeric. The estimated helical content of the linker fragment from B. stearothermophilus is 68% at high pH and 1 degree C. The measured helicity decreases to 53% at pH 7.0 and 1 degree C. In contrast, the peptide corresponding to the E. coli IF3 linker region is largely unstructured with a maximum helical content of 15% at high pH and only 8% at pH 7.0, 1 degree C. These results suggest that the different structures observed for the two intact proteins may be due to the different intrinsic stability of the two linker peptides. The helical content of the two linker peptides is, however, much closer when the peptides are compared at the respective temperatures of optimum growth for E. coli and B. stearothermophilus (3% versus 17%). The pH and ionic strength dependence of the helical content of the B. stearothermophilus peptide demonstrates that side-chain/side-chain interactions play an important role in stabilizing the helical structure. In addition, studies with mutant peptides show that the first Asp residue in the linker sequence helps to stabilize the helix via an N- capping interaction.

Heteronuclear NMR studies of E. coli translation initiation factor IF3. Evidence that the inter-domain region is disordered in solution

Initiation factor IF3 from Escherichia coli plays a critical role in the selection of the correct initiation codon. This protein is composed of two domains, connected by a lysin-rich hydrophilic linker. The conformation of native IF3 was investigated by heteronuclear NMR spectroscopy. The two domains are independent and show little or no interaction. Heteronuclear relaxation studies of a sample selectively labelled on lysine residues demonstrates that the inter-domain linker is highly flexible, exhibiting increased 15N T2 values and negative 1H[15N] nuclear Overhause effects over a length of at least eight residues. Analysis of the rotational correlation times further shows that the motions of the two domains are most likely uncorrelated. The inter-domain linker thus displays almost totally unrestricted motions. Accordingly, the amide protons in the central region are shown to be in fast exchange with water. Such a high degree of flexibility of the inter-domain linker might be required for IF3 domains to interact with distant regions of the ribosome.

A single mutation in 16S rRNA that affects mRNA binding and translation-termination

A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S subunits containing the mutation 726G had an altered binding affinity for mRNA by comparison to the wild type. In addition, expression of the mutant ribosomes in vivo resulted in exclusive suppression of the UGA nonsense codon. This effect was supported by in vitro studies that showed the mutant ribosomes to have an altered binding affinity for Release Factor-2.

Model for the three-dimensional folding of 16 S ribosomal RNA

We have derived a model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA, using interactive computer graphic methods. It is based on (1) the secondary structure derived from comparative sequence analysis, (2) the three-dimensional co-ordinates for the centers of mass of the 30 S subunit proteins, and (3) the locations of sites in 16 S rRNA that interact with specific ribosomal proteins, from footprinting and crosslinking studies. We present a detailed description of the derivation of the model. About 75% of the RNA chain is sufficiently constrained to provide a useful model. This contains most of the universally conserved core of the molecule. In all but a few instances, protected and crosslinked sites can be placed within or very close to their cognate proteins, while obeying stereochemical rules. The overall shape of the model and locations of specific regions of the RNA correspond well to data derived from electron micrographs of 30 S subunits, although such data were not used to construct the model. Phylogenetic variations in the structure are readily accommodated; as an example, we have modeled the 950-nucleotide mammalian mitochondrial 12 S rRNA by superimposing it on the E. coli structure. The three major RNA domains, as defined by secondary structure, appear to exist as autonomous structural units in three dimensions, for the most part. There is an extensive interface between the 5' and central domains, whereas the 3' major domain has relatively little apparent contact with the rest of the structure. The 5', central and 3' major domains form structures that resemble the body, platform and head, respectively, seen in electron micrographs of 30 S subunits. We discuss possible roles for the ribosomal proteins in stabilizing specific structural features of the RNA during ribosome assembly. The decoding site, as deduced from footprinting and crosslinking studies involving the tRNA anticodon stem-loop, is well-localized. Bases protected from chemical probing by the anticodon stem-loop line the cleft of the subunit. The conserved loop at position 530, which contains some of the bases protected by A site-bound tRNA, is remote (approx. 80 A) from the decoding site. Protection of these bases by the anticodon stem-loop is thus unlikely to be due to direct contact.

Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli

Neutron scattering distance data are presented for 33 protein pairs in the 30 S ribosomal subunit from Escherichia coli, along with the methods used for measuring distances between its exchangeable components. When combined with prior data, these new results permit the positioning of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit, completing the mapping of its proteins by neutron scattering. Comparisons with other data suggest that the neutron map is a reliable guide to the quaternary structure of the 30 S subunit.

A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli

The relative positions of the centers of mass of the 21 proteins of the 30S ribosomal subunit from Escherichia coli have been determined by triangulation using neutron scattering data. The resulting map of the quaternary structure of the small ribosomal subunit is presented, and comparisons are made with structural data from other sources.

Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences

Protein coding sequences carry an additional message in the form of a universal three-base periodical pattern (G-non-G-N)n, which is expressed as a strong preference for guanines in the first positions of the codons in mRNA and lack of guanines in the second positions. This periodicity appears immediately after the initiation codon and is maintained along the mRNA as far as the termination triplet, where it disappears abruptly. Known cases of ribosome slippage during translation (leaky frameshifts, out-of-frame gene fusion) are analyzed. At the sites of the slippage the G-periodical pattern is found to be interrupted. It reappears downstream from the slippage sites, in a new frame that corresponds to the new translation frame. This suggests that the (G-non-G-N)n pattern in the mRNA may be responsible for monitoring the correct reading frame during translation. Several sites with complementary C-periodical structure are found in the Escherichia coli 16 S rRNA sequence. Only three of them are exposed to various interactions at the surface of the small ribosomal subunit: (517)gcCagCagCegC, (1395)caCacCgcC and (1531)auCacCucC. A model of a frame-monitoring mechanism is suggested based on the weak complementarity of G-periodical mRNA to the C-periodical sites in the ribosomal RNA. The model is strongly supported by the fact that the hypothetical frame-monitoring sites in the 16 S rRNA that are derived from the nucleotide sequence analysis are also the only sites known to be actually involved or implicated in rRNA-mRNA interactions.

Three-dimensional arrangement of the Escherichia coli 16 S ribosomal RNA

A model for the arrangement of the Escherichia coli 16 S ribosomal RNA in the 30 S ribosomal subunit is given. This model is based on the 16 S ribosomal RNA secondary structure, intramolecular RNA crosslinking results, protein-RNA interactions, and the locations of proteins within the 30 S subunit. These considerations allow placement of most of the RNA helices in approximate positions. The overall shape (that of an asymmetric Y) is very reminiscent of the description of the shape of the RNA made by direct determinations and is reasonably correlated to the appearance of the 30 S subunit. The identities of the three major secondary-structure domains of the 16 S ribosomal RNA are, for the most part, preserved. In addition, many close contacts between the 5' and middle RNA domains occur in the body of the particle. The 3'-terminal domain is situated in the central part of the model. This position corresponds to the region between the head and the platform structure in the 30 S subunit. The regions that represent the general locations of the messenger RNA and transfer RNA binding sites can be identified in the model.

Location of protein S4 on the small ribosomal subunit of E. coli and B. stearothermophilus with protein- and hapten-specific antibodies

In spite of considerable effort there is still serious disagreement in the literature about the question of whether epitopes of ribosomal protein S4 are accessible for antibody binding on the intact small ribosomal subunit. We have attempted to resolve this issue using three independent approaches: (i) a re-investigation of the exposure and the location of epitopes of ribosomal protein S4 on the surface of the 30S subunit and 30S core particles of the E. coli ribosome, including rigorous controls of antibody specificity, (ii) a similar investigation of protein S4 from Bacillus stearothermophilus and (iii) the labelling of residue Cys-31 of E. coli S4 with a fluorescein derivative the accessibility of which towards a fluorescein-specific antibody was demonstrated directly by fluorimetry. In each of the three cases the antigen (E. coli S4, B. stearothermophilus S4 or fluorescein) was found to reside on the small lobe.

Positions of proteins S14, S18 and S20 in the 30 S ribosomal subunit of Escherichia coli

A map of the 30 S ribosomal subunit is presented giving the positions of 15 of its 21 proteins. The components located in the map are S1, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S14, S15, S18 and S20.

Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes

During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.

Structural elements of the 50 S subunit of E. coli ribosomes

The large (50 S) subunit from E. coli ribosomes consists of 32 different proteins and two RNA molecules of different length. In an attempt to determine the three-dimensional arrangement of the proteins in the subunit, we are also interested in obtaining direct information on the shape of the proteins within the subunit. This is possible only with ribosomal subunits which, unlike natural protonated subunits, are homogeneous for neutrons. These homogeneous particles are produced by reconstituting 50 S particles from RNA and proteins isolated from bacteria grown at different levels of D2O in the culture medium, 76% D2O for RNA and 84% D2O for proteins. Model calculations and test experiments reveal that the pursued strategy allows direct determination of radii of gyration of 50 S components within the particle with reasonable precision. Data evaluation and interpretation are significantly facilitated by contrast variation of the reconstituted particles. The determination of protein shape parameters is only one aspect of the new strategy. The pair distance measurements are completely independent of its success. Data on radii of gyration of five ribosomal proteins in situ are reported: L1 (26 +/- 2 A), L2 (22 +/- 2 A), L3 (22 +/- 2 A), L4 (20 +/- 2 A), and L23 (13 +/- 2 A).

Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids

Images

Location of eight ribosomal proteins on the surface of the 50S subunit from Escherichia coli

Eight ribosomal proteins, L9, L11, L15, L17, L18, L19, L23, and L29, have been localized on the surface of the 50S subunit from Escherichia coli by immunoelectron microscopy. The specificity of the antibody binding site was demonstrated by stringent absorption experiments. For each protein, the antibody attachment site was localized on the two characteristic views of the 50S subunit. Thus, each protein could be located in a confined region on the three-dimensional structural model of the 50S subunit.

Proteins of the Bacillus stearothermophilus ribosome. A 5 A structure analysis of protein S5

The structure of protein S5 from the small subunit of the Bacillus stearothermophilus ribosome is described to a resolution of 5 A. The molecular boundary is visible and shows the protein to be essentially compact although slightly elongated in one dimension.

X-ray solution-scattering studies of active and inactive Escherichia coli ribosomal subunits

That ribosomal subunits can exist in active and inactive functional states, and that subunits in the two states are interconvertible, has been known for some time (see Zamir et al., 1974). The magnitude of the conformational perturbation accompanying this functional transformation, however, was not known. In the present study 30 S and 50 S subunits in the two functional states have been compared by small-angle X-ray scattering. The results indicate that the structural differences between active and inactive subunits are small, at the limit of resolution of this technique. Model studies show that the data imply conformational differences at or below the limit of resolution of other physical methods now in use to examine the detailed structure of these particles.

Immunochemical accessibility of ribosomal protein S4 in the 30 S ribosome. The interaction of S4 with S5 and S12

The reactivity of protein S4-specific antibody preparations with 30 S ribosomal subunits and intermediates of in vitro subunit reconstitution has been characterized using a quantitative antibody binding assay. Anti-S4 antibody preparations did not react with native 30 S ribosomal subunits; however, they did react with various subunit assembly intermediates that lacked proteins S5 and S12. The inclusion of proteins S5 and S12 in reconstituted particles resulted in a large decrease in anti-S4 reactivity, and it was concluded that proteins S5 and S12 are primarily responsible for the masking of S4 antigenic determinants in the 30 S subunit. The effect of S5 and S12 on S4 accessibility is consistent with data from a variety of other approaches, suggesting that these proteins form a structural and functional domain in the small ribosomal subunit.

Protein-RNA crosslinking in Escherichia coli 30S ribosomal subunits. Identification of a 16S rRNA fragment crosslinked to protein S12 by the use of the chemical crosslinking reagent 1-ethyl-3-dimethyl-aminopropylcarbodiimide

1-ethyl-3-dimethyl aminopropylcarbodiimide (EDC) was used to cross-link 30S ribosomal proteins to 16S rRNA within the E. coli 3OS ribosomal subunit. Covalently linked complexes containing 30S proteins and 16S rRNA, isolated by sedimentation of dissociated crosslinked 30S subunits through SDS containing sucrose gradients, were digested with RNase T1, and the resulting oligonucleotide-protein complexes were fractionated on SDS containing polyacrylamide gels. Eluted complexes containing 30S proteins S9 and S12 linked to oligonucleotides were obtained in pure form. Oligonucleotide 5'terminal labelling was successful in the case of S12 containing but not of the S9 containing complex and led to identification of the S12 bound oligonucleotide as CAACUCG which is located at positions 1316-1322 in the 16S rRNA sequence. Protein S12 is crosslinked to the terminal G of this heptanucleotide.

Mapping evolution with ribosome structure: intralineage constancy and interlineage variation

Ribosomal small subunits are organized in three general structural patterns that correspond to the eubacterial, archaebacterial, and eukaryotic lineages. Within each of these lineages, ribosomal structure is highly conserved. Small subunits from all three lineages share a common overall structure except for the following differences: (i) small subunits from archaebacteria and from the cytoplasmic component of eukaryotes both contain a feature on the head of the subunit, the archaebacterial bill, that is absent in eubacteria, and (ii) eukaryotic small subunits contain additional regions of density at the base of the subunit, the eukaryotic lobes, that are absent in archaebacteria and in eubacteria. We interpret the intralineage conservation of ribosomal three-dimensional structure as forming a phylogenetic basis for regarding archaebacteria, eubacteria, and eukaryotes as primitive lines. Although our data are separate and independent from those of Woese and Fox, they lend further support to their proposal [Woese, C. R. & Fox, G. E. (1977) Proc. Natl. Acad. Sci. USA 74, 5088-5090]. These data also provide a simple, rapid, and accurate method for classifying organisms and for identifying new lineages. Finally, interlineage variation of ribosomal structure is used to establish a rigorous framework for considering the evolution of these three lines.

Ribosomal protein S4 is an internal protein: Localization by immunoelectron microscopy on protein-deficient subribosomal particles

The location of protein S4 in the small ribosomal subunit has been identified by immunoelectron microscopy. Although intact small subunits are not reactive with antibodies directed against protein S4, subribosomal particles reconstituted without proteins S5 and S12 are reactive. By using these "incomplete" subparticles, we have mapped the position of S4. It is located at a single site on the exterior (cytoplasmic) side of the subunit, at the partition that separates the one-third, or head, from two-thirds, or base, of the subunit. In this location, protein S4 is "beneath" proteins S5 and S12. All three proteins are members of a complex on, or near, the external surface of the small ribosomal subunit that plays an important role in regulation of translational fidelity.

A ribonucleoprotein fragment of the 30 S ribosome of E. coli containing two contiguous domains of the 16 S RNA

Ribonucleoprotein fragments of the 30 S ribosome of E. coli have been prepared by limited ribonuclease digestion and mild heating of the ribosome in a constant ionic environment. One such fragment has been described previously. A second electrophoretically homogeneous fragment has now been isolated and its RNA and protein moieties have been characterized. It contains the 5' half of the 16 S RNA, encompassing domains I and II except for the extreme 5' terminus and several small gaps. Seven proteins are present: S4, S5, S6, S8, S12, S15 and S20. The RNA binding sites of five of these proteins are known, and all are RNA sequences that are present in the fragment. Published neutron scattering and immuno-electron microscopic data indicate that six of the proteins are clustered together in a cross sectional slice through the center of the subunit. After deproteinization, the RNA moiety gives two bands in gel electrophoresis, one containing domains I and II and the other, essentially only domain II. The former, although larger, migrates faster in gel electrophoresis, indicating that RNA domains I and II interact with each other in such a way as to become more compact than domain II by itself.