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1

Recycling of eucaryotic ribosomes

100%
Tyczewska A., Bakowska-Zywicka K.
Biotechnologia
|
2009
|
issue 1
81-85
EN
Until recently protein biosynthesis has been viewed as a process involving only three steps: initiation of translation, elongation of the nascent polypeptide chain and release of the completed unfolded polypeptide. In recent years fourth step in translation has been distinguished ? it is the recycling of the ribosome. In this process posttermination complexes termed post-TC consisting of ribosomes with deacylated tRNA(s) and mRNA are dissociated with the help of ribosome recycling factor (RRF), elongation factor G (EF-G) and initiation factor 3 (IF3) in Procaryotes. The mechanism of this final step in Eucaryotes was unknown for a long time, but the work of Pisarev et al. sheds a light on splitting 80S ribosomes and preparing them for the next cycle of translation.
2

Computational modeling of the bacterial 70S ribosome and its subunits

80%
Trylska J.
Biotechnologia
|
2009
|
issue 1
36-47
EN
The computational modeling studies performed on the entire 70S bacterial ribosome and its subunits are reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to enormous size of the system theoretical efforts to study the ribosome are few and still pose a great challenge. For example, to extend the simulation time scales to biologically relevant ones, often reduced models requiring tedious parameterization procedures need to be applied. So far modeling of the ribosome involved its electrostatic properties, internal dynamics, binding of antibiotics, polypeptide folding in the ribosome tunnel, and assembly paths of proteins in the small ribosomal subunit.
3

The structure of the ribosome-short history

80%
Bakowska-Zywicka K., Tyczewska A.
Biotechnologia
|
2009
|
issue 1
99-103
EN
Ribosomes, which are ?the heart of the protein biosynthesis' have been the focus of structural studies for more than 50 years. The reconstitution of some of the morphological features of the ribosome was performed many years ago. In the past few years, high-resolution structures provided molecular details of different intermediates in ribosome-mediated translation. Together, these studies have revolutionized our understanding of the mechanism of protein biosynthesis. This success depended strictly on the advances in biochemical, biophysical and genetic studies and macromolecular crystallography that have been made during last decades.
4

Molecular basics of protein biosynthesis ? function of 23S rRNA

80%
Bakowska-Zywicka K., Kietrys A.
|
2007
|
issue 1
186-196
EN
The main function of ribosome is to serve as a site of mRNA translation into a sequence of amino acids in a process called protein biosynthesis. Most important for understanding the translational mechanism is how a ribosome interacts with the factors playing role in this complicated cellular process. The key elements of these interactions are the functional domains of rRNAs. In this paper, we present the functional importance of 23S rRNA in polypeptide biosynthesis.
5

Production of proteins in the cell-free expression systems

80%
Szaflarski W., Sujka P., Nowicki M., Zabel M.
Biotechnologia
|
2009
|
issue 1
86-97
EN
Efficient protein synthesis has become a critical issue in recent biotechnology and functional protemic studies. Traditional expression of protein performed in host cells such as Escherichia coli or Saccharomyces cerevisiae is generally lengthy and costly. Cell-free protein synthesis is an attractive alternative offering simplicity and fast rate of the reaction as well as the generation of functional proteins that are difficult to obtain using in vivo systems. Furthermore, the open nature of these systems makes it amenable to manipulation allowing the investigations into the mechanism of protein synthesis itself and into the inhibition of that process by interfering molecules such as antibiotics. Here we review all the main classes of cell-free protein expression system and we emphasize their potency and recent applications in biotechnology.
6

The function of conservative structural elements of ribosome in protein biosythesis

80%
Dudzinska B., Twardowski T.
Biotechnologia
|
2002
|
issue 3
178-188
EN
The mechanism of protein biosynthesis is common in all organism. The structural elements of ribosomes participating in substeps of this process are conserved. The best studied fragment of L-rRNA - a-sarcin domain is identical within all leaving ogranisms. In this paper, we described main steps of polypeptide synthesis carried out by ribosomes.
7

Structure and function of intersubunit bridges in procaryotic ribosome

80%
Kietrys A. M., Szopa A., Bakowska-Zywicka K.
Biotechnologia
|
2009
|
issue 1
48-58
EN
The main function of ribosome is decoding of the genetic message and formation of peptide bonds. Protein synthesis is a dynamic process during which tRNA and mRNA are translocated through the ribosome. Ribosomal subunits, small and large, are joined together by a series of bridges, which make possible forming of an active ribosome. It this paper we present the functional importance of ribosomal bridges.
8

Function of selected fragments of 16S rRNA of small ribosomal subunit in protein biosynthesis

80%
Bakowska K.
Biotechnologia
|
2005
|
issue 2
206-214
EN
The mechanism of protein biosynthesis and selected fragments of rRNAs are universally conserved. Understanding structural basis for the functional capabilities of rRNAs is essential to regulation of protein synthesis. In this paper I describe function of the most important fragments of 16S rRNA of small ribosomal subunit.
9

Codon recognition by tRNA

70%
Olejniczak M.
Biotechnologia
|
2009
|
issue 1
59-64
EN
Accurate codon recognition by tRNAs is necessary for correct translation of mRNA nucleotide sequence into the protein sequence. Here, different factors contributing to the correct codon reading by tRNAs are reviewed. In particular, the monitoring of codon-anticodon helix geometry by 16S rRNA bases, and the role of tRNA sequence elements and posttranscriptional modifications for modulating codon-anticodon interactions are discussed.
10

Application of high pressure in food technology and medicine

70%
Wandel A., Gensler I., Porowski S., Jurczak J., Barciszewski J.
|
|
issue 1
199-211
EN
For the first time, high pressure was used for milk sterilization at the beginning of this century. However, only recently attention has been paid to this method and its possible applications in food preservation and inactivation of some viruses. In this review, we summarize high pressure effects on biological macromolecules such as proteins, nucleic acids, ribosomes and other cell components. We also show examples of practical application of high pressure in food conservation and medicine.
11

Role of RNA backbone groups for ribosomal catalysis

61%
Erlacher M. D., Polacek N.
Biotechnologia
|
2009
|
issue 1
65-80
EN
The ribosomal peptidyl transferase ribozyme resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis, peptide bond formation and peptidyl-tRNA hydrolysis. With the presentations of atomic structures of the large ribosomal subunit, the questions how an RNA active site can catalyze these chemical reactions gained a new level of molecular significance. The peptidyl transferase center represents the most intense accumulation of universally conserved ribosomal RNA nucleotides in the entire ribosome. Thus, it came as a surprise that recent findings revealed that the nucleobase identities of active site residues are actually not critical for catalysis. Instead RNA backbone groups have been identified as key player in transpeptidation and peptide release. While the ribose 2' -OH of the 23S rRNA residue A2451 plays an important role in peptidyl transfer, its contribution to peptidyl-tRNA hydrolysis is only minor. On the other hand, the ribose 2'-OH of the terminal adenosine of P-site bound tRNA seems to play equally crucial roles in peptide bond formation and tRNA hydrolysis. While it seems that details of ribosome-catalyzed peptidyl-tRNA hydrolysis are just emerging, our molecular insights into transpeptidation are already very advanced. It has been realized that an intricate interaction between the ribose 2'-OH groups of 23S rRNA residue A2451 and tRNA nucleotide A76 are crucial for proton shuttling that is required for efficient amide bond synthesis.
12

Structural basis for the antibacterial activity of the 12-membered-ring mono-sugar macrolide methymycin

61%
Auerbach T., Mermershtain I., Bashan A., Davidovich C., Rozenberg H., Sherman D. H., Yonath A.
Biotechnologia
|
2009
|
issue 1
24-35
EN
The crystal structure of the complex of the large ribosomal subunit of the pathogen model Deinococcus radiodurans with the macrolide antibiotic methymycin, bearing a 12 membered macrolactone ring macrolide that contains a single amino sugar, shows that methymycin binds to the peptidyl transferase center (PTC) rather than to the high affinity macrolide binding pocket at the upper end of the ribosomal exit tunnel. This unexpected binding mode result in fairly efficient blockage of the 3'end of the A-site tRNA location, thus indicating the superiority of spatial-functional considerations over the formation of the typical high affinity macrolide interactions that due to the small size of methymycin could have led to incomplete blockage of the exit tunnel. Its binding involves rearrangements of several PTC nucleotides, some of which shown previously to be flexible. Comparisons between the binding modes of methymycin and other antibiotics are presented and discussed.
13

Ribophagy ? the novel degradation system of the ribosome

61%
Bakowska-Zywicka K., Tyczewska A.
Biotechnologia
|
2009
|
issue 1
99-103
EN
Recently biochemists have discovered a new pathway by which the cell selectively degrades ribosomes. The pathway is called ribophagy. Two proteins were identified as crucial for the selective degradation of ribosomes by autophagy: ubiquitin-specific protease 3 (Ubp3) and Ubp3-associated cofactor, Bre5. This fact strengthens the connections between the autophagy and proteasome pathways of protein degradations.
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