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Biomedical subjects

Alexander S Spirin

Publications and source records attributed to Alexander S Spirin.

11 recordsLinked to original sources
PubMed2006

Ribosomal protein S1 induces a conformational change of the 30S ribosomal subunit.

A comparative study of the 30S ribosomal subunit in the complex with protein S1 and the subunit depleted of this protein has been carried out by the hot tritium bombardment method. Differences in exposure of some ribosomal proteins within the 30S subunit depleted of S1 and within the 30S-S1 complex were found. It was concluded that protein S1 binds in the region of the neck of the 30S ribosomal subunit inducing a conformational change of its structure.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2005

Effective cotranslational folding of firefly luciferase without chaperones of the Hsp70 family.

Molecular chaperones of the Hsp70 family (bacterial DnaK, DnaJ, and GrpE) were shown to be strictly required for refolding of firefly luciferase from a denatured state and thus for effective restoration of its activity. At the same time the luciferase was found to be synthesized in an Escherichia coli cell-free translation system in a highly active state in the extract with no chaperone activity. The addition of the chaperones to the extract during translation did not raise the activity of the enzyme. The abrupt arrest of translation by the addition of a translational inhibitor led to immediate cessation of the enzyme activity accumulation, indicating the cotranslational character of luciferase folding. The results presented suggest that the chaperones of the Hsp70 family are not required for effective cotranslational folding of firefly luciferase.

Cell-Free System↗
PubMed2005

5'-poly(A) sequence as an effective leader for translation in eukaryotic cell-free systems.

Poly(A) sequence of 25 adenylic residues placed immediately before the start codons of the green fluorescent protein (GFP) and firefly luciferase (Luc) mRNAs is shown to provide a high rate of translation of the heterologous messages in eukaryotic cell-free translation systems. Also the poly(A) leader is found to provide the abolition of the inhibition of translation at excess mRNA concentrations. The possibility of the practical use of the constructs with the poly(A) leader for preparative protein production is demonstrated in the wheat germ continuous-exchange cell-free (CECF) translation system.

5' Untranslated Regions↗
PubMed2004

The ribosome-associated inhibitor A reduces translation errors.

Recently we have reported about a novel stress response protein (pY or RaiA) associated with Escherichia coli ribosomes that inhibits translation at the aminoacyl-tRNA binding stage. Here we show that leucine misincorporation during in vitro poly(U) translation is inhibited by this protein much stronger than the incorporation of phenylalanine. The miscoding counteraction by RaiA is especially strong at the concentrations of magnesium ions close to those observed in vivo and diminishes at higher magnesium concentrations. The results obtained suggest that the anti-miscoding activity of RaiA could be the main function of the protein, rather than the inhibition of translation. The role of the protein in adaptation of cells to environmental stress is discussed.

Escherichia coli↗
PubMed2004

The ribosome as an RNA-based molecular machine.

The ribosome is a protein-synthesizing ribonucleoprotein particle where RNA forms its structural and functional core. Compact self-folding of ribosomal RNA resulting in its specific tertiary structure and its conformational mobility underlie the functional behavior of the ribosome. In addition to the functions of ligand recognition (binding of mRNA, tRNA and translation factors) and catalysis (peptidyltransferase activity), the ribosomal RNA with its movable blocks principally contributes to the construction of the ribosome as a molecular machine. The oscillations between open (unlocked) and closed (locked) conformations are proposed to be necessary events in the processes of aminoacyl-tRNA binding, transpeptidation and translocation. Elongation factors EF-Tu and EF-G with GTP are considered as catalysts of conformational transitions during aminoacyl-tRNA binding and translocation, and the theory of NTP-dependent conformational catalysis via conformational intermediates is discussed. Thermal fluctuations are assumed to serve as the main "motive force" to move RNA parts and ligands in the translating ribosome. The binding of functional ligands, such as aminoacyl-tRNA and an elongation factor with GTP, and the chemical reactions of transpeptidation and GTP hydrolysis play the role of a Maxwell's Demon: they rectify the random fluctuations to produce the unidirectional conveyance process and translation ("thermal ratchet" model).

Guanosine Triphosphate↗
PubMed2004

High-throughput cell-free systems for synthesis of functionally active proteins.

Continuous cell-free translation systems with perpetual supply of consumable substrates and removal of reaction products made the process of in vitro synthesis of individual proteins sustainable and productive. Improvements of cell-free reaction mixtures, including new ways for efficient energy generation, had an additional impact on progress in cell-free protein synthesis technology. The requirement for gene-product identification in genomic studies, the development of high-throughput structural proteomics, the need for protein engineering without cell constraints (including the use of unnatural amino acids), and the need to produce cytotoxic, poorly expressed and unstable proteins have caused increased interest in cell-free protein synthesis technologies for molecular biologists, biotechnologists and pharmacologists.

Animals↗
PubMed2003

Compact globular structure of Thermus thermophilus ribosomal protein S1 in solution: sedimentation and calorimetric study.

Ribosomal protein S1 of Thermus thermophilus overexpressed in Escherichia coli cells has been isolated and subjected to studies by analytical sedimentation and differential scanning microcalorimetry techniques. It has been demonstrated that the protein of 60 kDa sediments at s020,w = 4.6 S and has the diffusion coefficient D020,w = 6.7 x 10(-7) cm2/s in 25 mm HEPES-NaOH buffer, pH 7.5 (similarly to bovine serum albumin of 66 kDa that sediments at s0 20,w = 4.4 S and D020,w =6.0 x 10(-7) cm2/s), indicating its compact globular conformation under these conditions. The microcalorimetry study has shown the presence of a cooperative tertiary structure melting at 90 degrees C, but with several (probably three) independent cooperative domains. In the presence of 100 mm NaCl the protein becomes more asymmetric (s020,w = 3.1 S) but does not lose its cooperativity and thermostability, this suggesting just the weakening of interdomain ionic interactions. The compact globular conformation of protein S1 seems to be most likely within the ribosome.

Calorimetry↗
PubMed2002

Omnipotent RNA.

The capability of polyribonucleotide chains to form unique, compactly folded structures is considered the basis for diverse non-genetic functions of RNA, including the function of recognition of various ligands and the catalytic function. Together with well-known genetic functions of RNA - coding and complementary replication - this has led to the concept of the functional omnipotence of RNA and the hypothesis that an ancient RNA world supposedly preceded the contemporary DNA-RNA-protein life. It is proposed that the Woese universal precursor in the ancient RNA world could be a cell-free community of mixed RNA colonies growing and multiplying on solid surfaces.

Catalysis↗
PubMed2002

Ribosome as a molecular machine.

General principles of structure and function of the ribosome are surveyed, and the translating ribosome is regarded as a molecular conveying machine. Two coupled conveying processes, the passing of compact tRNA globules and the drawing of linear mRNA chain through intraribosomal channel, are considered driven by discrete acts of translocation during translation. Instead of mechanical transmission mechanisms and power-stroke 'motors', thermal motion and chemically induced changes in affinities of ribosomal binding sites for their ligands (tRNAs, mRNA, elongation factors) are proposed to underlie all the directional movements within the ribosomal complex. The GTP-dependent catalysis of conformational transitions by elongation factors during translation is also discussed.

Animals↗
PubMed2002

Eukaryotic elongation factor 1A interacts with the upstream pseudoknot domain in the 3' untranslated region of tobacco mosaic virus RNA.

The genomic RNA of tobacco mosaic virus (TMV), like that of other positive-strand RNA viruses, acts as a template for both translation and replication. The highly structured 3' untranslated region (UTR) of TMV RNAs plays an important role in both processes; it is not polyadenylated but ends with a tRNA-like structure (TLS) preceded by a conserved upstream pseudoknot domain (UPD). The TLS of tobamoviral RNAs can be specifically aminoacylated and, in this state, can interact with eukaryotic elongation factor 1A (eEF1A)/GTP with high affinity. Using a UV cross-linking assay, we detected another specific binding site for eEF1A/GTP, within the UPDs of TMV and crucifer-infecting tobamovirus (crTMV), that does not require aminoacylation. A mutational analysis revealed that UPD pseudoknot conformation and some conserved primary sequence elements are required for this interaction. Its possible role in the regulation of tobamovirus gene expression and replication is discussed.

3' Untranslated Regions↗