High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit

Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the Triticum aestivum (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.

Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes

Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.

RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center

Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an Escherichia coli strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.

Perfect Hemihedral Twinning in Crystals of the γ-Subunit of Translation Initiation Factor 2 from Sulfolobus solfataricus: Cause and Effect

The crystal structure of the γ-subunit of translation initiation factor 2 from the archaeon Sulfolobus solfataricus (SsoIF2γ) has been solved based on perfectly hemihedral twinned data. The protein was cocrystallized with the 10-fold molar excess of GTP analog (GDPCP) over protein. However, no nucleotide was found in the structure, and the model demonstrated the apo form of the protein. Two slightly different molecules in the asymmetric unit of the crystal are related by the non-crystallographic 2-fold axis and form a tightly associated dimer. This dimer is stabilized by an intermolecular hydrophobic core and hydrogen bonds. Lack of GDPCP in the nucleotide-binding pocket of the γ-subunit and significant excess of dimers over monomers in the crystallization solution suggest that these dimers are the building blocks of the crystal. Contrary to SsoIF2γ monomers, these dimers are able to crystallize in two oppositely oriented slightly different crystal domains, thus forming a twinned crystal. Comparison of crystallization conditions for the twinned and untwinned crystals of apo SsoIF2γ showed that stabilization of the dimers in the solution may be caused by higher sodium salt concentration. Since amino acid residues involved in intermolecular contacts in the dimer are responsible for binding of the γ- and α-subunits within SsoIF2, increase in sodium salt concentration may prevent functioning of SsoIF2 in the cell.

[Determination of the Minimal Fragment of the Poliovirus IRES Necessary for the Formation of a Specific Complex with the Human Glycyl-tRNA Synthetase]

Aminoacyl-tRNA synthetases are an ancient enzyme family that specifically charge a tRNA molecule with a cognate amino acid required for protein synthesis. Glycyl-tRNA synthetase is one of the most interesting aminoacyl-tRNA synthetases due to its structure variability and functional features in the different organisms. It was shown recently that human glycyl-tRNA synthetase is a regulator of translational initiation of poliovirus mRNA. Details of this process and its mechanism still remain unknown. While exploring this stage of poliovirus functioning we have studied the interaction of the cytoplasmic form of human glycyl-tRNA synthetase and its domains with the fragments of the poliovirus IRES element. As a result, we have identified the minimal fragment of viral mRNA with which glycyl-tRNA synthetase fully interacts and estimated the contribution of some domains to the interaction of glycyl-tRNA synthetase with RNA.

Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate

The crystal structures of Erwinia carotovora L-asparaginase complexed with L-aspartate and L-glutamate were determined at 1.9 and 2.2 A, respectively, using the molecular-replacement method and were refined to R factors of about 21% in both cases. The positions of the ligands in the active site were located. A comparison of the new structures with the known structures of Escherichia coli L-asparaginase and Er. chrysanthemi L-asparaginase was performed. It was found that the arrangement of the ligands practically coincides in all three enzymes. The peculiarities of the quaternary structure of the enzyme, the possible role of water molecules in the enzyme action and the conformational changes during the catalyzed reaction are discussed.

[Distribution and cytogenetic features of triploid male goldfish from Azov basin]

When studying uni-bisexual goldfish (Carassius auratus gibelio) populations in the Azov basin in 1995-2000, we found triploid males, which constituted 2.5%, on average, of the total numbers of studied samples. The areas of nuclei of erythrocytes of triploid males were, on average, 1.35 times those in diploid males. At the same optical density of DNA, the sizes of mature spermatozoon heads in triploid males were, on average, 1.8 times smaller than in diploid males, as follows from the data obtained in 1966. The results of similar studies carried out during the period of natural spawning activity in 1997-1999 suggest that the sizes of spermatozoon heads suggest that the sizes of spermatozoon heads in triploid males were, on the contrary, 1.5 those in diploid males. Triploid males were characterized by mosaicism of spermatozoon size and chromosome mosaicism in somatic cells. Electrophoretic analysis for the locus of transferring confirmed the triploid status of this genetic group. The results of comparative crosses of goldfish with different ploidy suggest a high fertilizing capacity of triploid males, as well as normal viability of their progenies. A distinct positive correlation (r = 0.73) was found between the numbers of triploid females and triploid males in mixed di-triploid populations. No significant correlation was found between males and females within di- or triploid populations.

[Effect of polarized light on the immune status and cytokine levels of patients with bronchial asthma during immunotherapy with bronchomunal]

The influence of polarized polychromatic light on immunocompetent cells in complex with immunomodulated bronchomunal is studied. Data of content of the main cytokines taking part in development of inflammation are presented. It is cleared up that polarized light increases the number of T-lymphocyties, normalizes ratio of subpopulation of T-lymphocyties and level of serum FNO-alpha and level of interleukin-4 reaches the level of healthy people. It is ascertained that complex use bronchomunal and polarized polychromatic increases level of serum interferon-gamma.

[Ethanol injections in the integrated treatment of non-resectable malignant pancreatic tumor complicated by jaundice]

Results of treatment were analyzed in 28 patients with nonresectable pancreatic cancer (III-IV stages) complicated by jaundice, to whom in complex of treatment (biliodigestive shunting, in some of patients with hepatic dearterialyzation, gastroenterostomy, pancreatodigestive shunting) 96% ethanol was injected into the tumor. The complications frequency had constituted 21.4%, mortality--14.3%, the life span of operated patients--9 months at average. Sings of early and late "postethylizational" positive pancreatic cancer pathomorphosis were established.

[The initial experience of using the preparation Ukrain in treating cancer patients in Ukraine]

The chair of general surgery and the chair of oncology of the Ukrainian State Medical University have made a study into the use of the preparation "Ukrain" in the treatment of oncological patients. Early results of therapy of 23 patients confirm the evidence suggesting to us that "Ukrain" is endowed with cancerostatic activity, has immunopotentiating effect with no toxicity.

Certain biophysical properties of Ukrain

Ukrain was found to be relatively resistant in vitro to mean intensity radiation over the whole UV range. Of the seven peaks in the absorption spectrum of Ukraine those at 210 and 230 nm are conspicuous in the spectrum of the plasma of colorectal patients injected the previous day with this drug.