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1.
BBA Adv ; 3: 100089, 2023.
Article in English | MEDLINE | ID: mdl-37101685

ABSTRACT

As a person who has had a long scientific career in Ukraine, both before and after its re-acquisition of independence thirty years ago, I would like to share my observations with the readership of this Special Issue. By no means are these observations meant to provide a systematic presentation, which requires a different format. Rather, they are highly personal notes, providing snippets of the past and present and a discussion of the future of Ukrainian science. They also allow me to acknowledge my wonderful colleagues and bright students. I am delighted to see that many of them have contributed excellent reviews and original manuscripts to this Special Issue. (I am also keenly aware of the fact that because of the brutal invasion and bombardments by our imperial neighbor, many of my colleagues have been unable to share their latest work). It will be up to this next generation of Ukrainian scientists to develop Biological Sciences in Ukraine in the future.

2.
Nucleic Acids Res ; 50(16): 9490-9504, 2022 09 09.
Article in English | MEDLINE | ID: mdl-35971611

ABSTRACT

Protein synthesis in eukaryotic cell is spatially and structurally compartmentalized that ensures high efficiency of this process. One of the distinctive features of higher eukaryotes is the existence of stable multi-protein complexes of aminoacyl-tRNA synthetases and translation elongation factors. Here, we report a quaternary organization of the human guanine-nucleotide exchange factor (GEF) complex, eEF1B, comprising α, ß and γ subunits that specifically associate into a heterotrimeric form eEF1B(αßγ)3. As both the eEF1Bα and eEF1Bß proteins have structurally conserved GEF domains, their total number within the complex is equal to six. Such, so far, unique structural assembly of the guanine-nucleotide exchange factors within a stable complex may be considered as a 'GEF hub' that ensures efficient maintenance of the translationally active GTP-bound conformation of eEF1A in higher eukaryotes.


Subject(s)
Guanine Nucleotide Exchange Factors , Peptide Elongation Factor 1 , Humans , Peptide Elongation Factor 1/metabolism , Guanine Nucleotide Exchange Factors/genetics , Guanine Nucleotide Exchange Factors/metabolism , Protein Biosynthesis , Nucleotides/metabolism , Guanine
3.
Sensors (Basel) ; 20(15)2020 Aug 01.
Article in English | MEDLINE | ID: mdl-32752255

ABSTRACT

The combination of the generic mobile technology and inherent stability, versatility and cost-effectiveness of the synthetic receptors allows producing optical sensors for potentially any analyte of interest, and, therefore, to qualify as a platform technology for a fast routine analysis of a large number of contaminated samples. To support this statement, we present here a novel miniature sensor based on a combination of molecularly imprinted polymer (MIP) membranes and a smartphone, which could be used for the point-of-care detection of an important food contaminant, oestrogen-like toxin zearalenone associated with Fusarium contamination of cereals. The detection is based on registration of natural fluorescence of zearalenone using a digital smartphone camera after it binds to the sensor recognition element. The recorded image is further processed using a mobile application. It shows here a first example of the zearalenone-specific MIP membranes synthesised in situ using "dummy template"-based approach with cyclododecyl 2, 4-dihydroxybenzoate as the template and 1-allylpiperazine as a functional monomer. The novel smartphone sensor system based on optimized MIP membranes provides zearalenone detection in cereal samples within the range of 1-10 µg mL-1 demonstrating a detection limit of 1 µg mL-1 in a direct sensing mode. In order to reach the level of sensitivity required for practical application, a competitive sensing mode is also developed. It is based on application of a highly-fluorescent structural analogue of zearalenone (2-[(pyrene-l-carbonyl) amino]ethyl 2,4-dihydroxybenzoate) which is capable to compete with the target mycotoxin for the binding to zearalenone-selective sites in the membrane's structure. The competitive mode increases 100 times the sensor's sensitivity and allows detecting zearalenone at 10 ng mL-1. The linear dynamic range in this case comprised 10-100 ng mL-1. The sensor system is tested and found effective for zearalenone detection in maize, wheat and rye flour samples both spiked and naturally contaminated. The developed MIP membrane-based smartphone sensor system is an example of a novel, inexpensive tool for food quality analysis, which is portable and can be used for the "field" measurements and easily translated into the practice.


Subject(s)
Fusarium , Molecular Imprinting , Edible Grain , Food Contamination/analysis , Molecularly Imprinted Polymers , Polymers , Smartphone
4.
Talanta ; 201: 204-210, 2019 Aug 15.
Article in English | MEDLINE | ID: mdl-31122412

ABSTRACT

A novel smartphone-based optical biomimetic sensor based on free-standing molecularly imprinted polymer (MIP) membranes was developed for rapid and sensitive point-of-care detection of aflatoxin B1. The developed MIP membranes were capable of selective recognition of the target analyte and, at the same time, of generation of a fluorimetric sensor response, which could be registered using the camera of a smartphone and analysed using image analysis. The developed system provides a possibility of synchronous detection of aflatoxin B1 in 96 channels. UV irradiation of aflatoxin B1, selectively bound by the MIP membranes from the analysed samples, initiated fluorescence of aflatoxin B1 with intensity directly proportional to its concentration. The composition of the MIP membranes used as a recognition element was optimised taking into account data of computational modelling. Two functional monomers (2-acrylamido-2-methyl-1-propansulfonic acid and acrylamide) were identified as optimal for the formation of aflatoxin B1-selective binding sites in the structure of the MIP membranes. Working characteristics of the smartphone-based sensor system were also estimated. The influence of pH and of buffer and NaCl concentrations on the smartphone-based sensor responses were studied. High selectivity of the developed sensor system towards aflatoxin B1 was confirmed in experiments with the close structural analogue of the target analyte - aflatoxin G2, and ochratoxin A. The detection limit for aflatoxin B1 using the smartphone-based sensor systems was found to be 20 ng mL-1 for the sensor based on MIP membranes synthesised with acrylamide as a functional monomer. The storage stability of the recognition elements of the developed sensors was estimated as one year when stored at 22 °C. The possibility to detect the aflatoxin B1 in contaminated food samples was shown. The MIP-membrane-based sensor system provided a convenient point-of-care approach in food safety testing.


Subject(s)
Aflatoxin B1/analysis , Biomimetic Materials/chemistry , Fluorometry/methods , Food Contamination/analysis , Membranes, Artificial , Polymers/chemistry , Flour/analysis , Fluorometry/instrumentation , Limit of Detection , Molecular Imprinting , Smartphone , Zea mays/chemistry
5.
Int J Biol Macromol ; 126: 899-907, 2019 Apr 01.
Article in English | MEDLINE | ID: mdl-30590147

ABSTRACT

Translation elongation factor 1Bß (eEF1Bß) is a metazoan-specific protein involved into the macromolecular eEF1B complex, containing also eEF1Bα and eEF1Bγ subunits. Both eEF1Bα and eEF1Bß ensure the guanine nucleotide exchange on eEF1A while eEF1Bγ is thought to have a structural role. The structures of the eEF1Bß catalytic C-terminal domain and neighboring central acidic region are known while the structure of the protein-binding N-terminal domain remains unidentified which prevents clear understanding of architecture of the eEF1B complex. Here we show that the N-terminal domain comprising initial 77 amino acids of eEF1Bß, eEF1Bß(1-77), is a monomer in solution with increased hydrodynamic volume. This domain binds eEF1Bγ in equimolar ratio. The CD spectra reveal that the secondary structure of eEF1Bß(1-77) consists predominantly of α-helices and a portion of disordered region. Very rapid hydrogen/deuterium exchange for all eEF1Bß(1-77) peptides favors a flexible tertiary organization of eEF1Bß(1-77). Computational modeling of eEF1Bß(1-77) suggests several conformation states each composed of three α-helices connected by flexible linkers. Altogether, the data imply that the protein-binding domain of eEF1Bß shows flexible spatial organization which may be needed for interaction with eEF1Bγ or other protein partners.


Subject(s)
Guanine Nucleotide Exchange Factors/chemistry , Guanine Nucleotide Exchange Factors/metabolism , Peptide Elongation Factor 1/chemistry , Peptide Elongation Factor 1/metabolism , Guanine Nucleotide Exchange Factors/isolation & purification , Humans , Models, Molecular , Peptide Elongation Factor 1/isolation & purification , Peptides/chemistry , Protein Binding , Protein Conformation, alpha-Helical , Protein Domains , Recombinant Proteins/isolation & purification , Reproducibility of Results , Structure-Activity Relationship
6.
IUBMB Life ; 70(3): 192-196, 2018 03.
Article in English | MEDLINE | ID: mdl-29417736

ABSTRACT

The question of what governs the translation elongation rate in eukaryotes has not yet been completely answered. Earlier, different availability of different tRNAs was considered as a main factor involved, however, recent data revealed that the elongation rate does not always depend on tRNA availability. Here, we offer another, codon-independent approach to explain specific tRNA-dependence of the elongation rate in eukaryotes. We hypothesize that the exit rate of eukaryotic translation elongation factor 1A (eEF1A)*GDP from the 80S ribosome depends on the protein affinity to specific aminoacyl-tRNA remaining on the ribosome after GTP hydrolysis. Subsequently, a slower dissociation of eEF1A*GDP from certain aminoacyl-tRNAs in the ribosome can negatively influence the ribosomal elongation rate in a tRNA-dependent and mRNA-independent way. The specific tRNA-dependent departure rate of eEF1A*GDP from the ribosome is suggested to be a novel factor contributing to the overall translation elongation control in eukaryotic cells. © 2018 IUBMB Life, 70(3):192-196, 2018.


Subject(s)
Peptide Chain Elongation, Translational , Protein Biosynthesis/genetics , RNA, Transfer/genetics , Ribosomes/genetics , Codon , Eukaryotic Cells/metabolism , Guanosine Diphosphate/genetics , Peptide Elongation Factor 1/genetics , RNA, Messenger/genetics
7.
Talanta ; 175: 101-107, 2017 Dec 01.
Article in English | MEDLINE | ID: mdl-28841965

ABSTRACT

Nanostructured polymeric membranes for selective recognition of aflatoxin B1 were synthesized in situ and used as highly sensitive recognition elements in the developed fluorescent sensor. Artificial binding sites capable of selective recognition of aflatoxin B1 were formed in the structure of the polymeric membranes using the method of molecular imprinting. A composition of molecularly imprinted polymer (MIP) membranes was optimized using the method of computational modeling. The MIP membranes were synthesized using the non-toxic close structural analogue of aflatoxin B1, ethyl-2-oxocyclopentanecarboxylate as a dummy template. The MIP membranes with the optimized composition demonstrated extremely high selectivity towards aflatoxin B1 (AFB1). Negligible binding of close structural analogues of AFB1 - aflatoxins B2 (AFB2), aflatoxin G2 (AFG2), and ochratoxin A (OTA) was demonstrated. Binding of AFB1 by the MIP membranes was investigated as a function of both type and concentration of the functional monomer in the initial monomer composition used for the membranes' synthesis, as well as sample composition. The conditions of the solid-phase extraction of the mycotoxin using the MIP membrane as a stationary phase (pH, ionic strength, buffer concentration, volume of the solution, ratio between water and organic solvent, filtration rate) were optimized. The fluorescent sensor system based on the optimized MIP membranes provided a possibility of AFB1 detection within the range 14-500ngmL-1 demonstrating detection limit (3Ϭ) of 14ngmL-1. The developed technique was successfully applied for the analysis of model solutions and waste waters from bread-making plants.


Subject(s)
Aflatoxin B1/analysis , Fluorometry/methods , Molecular Imprinting/methods , Nanostructures/chemistry , Polymers/chemistry , Wastewater/analysis , Water Pollutants, Chemical/analysis , Membranes, Artificial , Models, Molecular , Solid Phase Extraction/methods
8.
Biol Chem ; 398(1): 113-124, 2017 01 01.
Article in English | MEDLINE | ID: mdl-27483363

ABSTRACT

The question as to why a protein exerts oncogenic properties is answered mainly by well-established ideas that these proteins interfere with cellular signaling pathways. However, the knowledge about structural and functional peculiarities of the oncoproteins causing these effects is far from comprehensive. The 97.5% homologous tissue-specific A1 and A2 isoforms of mammalian translation elongation factor eEF1A represent an interesting model to study a difference between protein variants of a family that differ in oncogenic potential. We propose that the different oncogenic impact of A1 and A2 might be explained by differences in their ability to communicate with their respective cellular partners. Here we probed this hypothesis by studying the interaction of eEF1A with two known partners - calmodulin and actin. Indeed, an inability of the A2 isoform to interact with calmodulin is shown, while calmodulin is capable of binding A1 and interferes with its tRNA-binding and actin-bundling activities in vitro. Both A1 and A2 variants revealed actin-bundling activity; however, the form of bundles formed in the presence of A1 or A2 was distinctly different. Thus, a potential inability of A2 to be controlled by Ca2+-mediated regulatory systems is revealed.


Subject(s)
Actins/metabolism , Calmodulin/metabolism , Mutation , Oncogenes/genetics , Peptide Elongation Factor 1/genetics , Peptide Elongation Factor 1/metabolism , Actin Cytoskeleton/metabolism , Animals , Calcium/metabolism , Models, Molecular , Peptide Elongation Factor 1/chemistry , Protein Binding , Protein Conformation , RNA, Transfer/metabolism , Rabbits
9.
FEBS J ; 283(3): 484-97, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26587907

ABSTRACT

Eukaryotic translation elongation factor 1Bα (eEF1Bα) is a functional homolog of the bacterial factor EF-Ts, and is a component of the macromolecular eEF1B complex. eEF1Bα functions as a catalyst of guanine nucleotide exchange on translation elongation factor 1A (eEF1A). The C-terminal domain of eEF1Bα is necessary and sufficient for its catalytic activity, whereas the N-terminal domain interacts with eukaryotic translation elongation factor 1Bγ (eEF1Bγ) to form a tight complex. However, eEF1Bγ has been shown to enhance the catalytic activity of eEF1Bα attributed to the C-terminal domain of eEF1Bα. This suggests that the N-terminal domain of eEF1Bα may in some way influence the guanine nucleotide exchange process. We have shown that full-length recombinant eEF1Bα and its truncated forms are non-globular proteins with elongated shapes. Truncation of the N-terminal domain of eEF1Bα, which is dispensable for catalytic activity, resulted in acceleration of the rate of guanine nucleotide exchange on eEF1A compared to full-length eEF1Bα. A similar effect on the catalytic activity of eEF1Bα was observed after its interaction with eEF1Bγ. We suggest that the non-catalytic N-terminal domain of eEF1Bα may interfere with eEF1A binding to the C-terminal catalytic domain, resulting in a decrease in the overall rate of the guanine nucleotide exchange reaction. Formation of a tight complex between the eEF1Bγ and eEF1Bα N-terminal domains abolishes this inhibitory effect.


Subject(s)
Guanine Nucleotide Exchange Factors/chemistry , Guanine Nucleotide Exchange Factors/metabolism , Nucleotides/metabolism , Peptide Elongation Factor 1/chemistry , Peptide Elongation Factor 1/metabolism , Amino Acid Sequence , Biocatalysis , Humans , Molecular Sequence Data , Nucleotides/chemistry , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Sequence Alignment
10.
Biochimie ; 119: 137-45, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26545799

ABSTRACT

Mammalian translation elongation factor eEF1A is involved in ribosomal polypeptide synthesis. Also, the protein fulfills many additional duties in an eukaryotic cell. Here, we identified a novel partner of the eEF1A1 isoform, namely Sgt1, a protein that possesses co-chaperon properties and participates in antiviral defense processes. By applying different methods, we demonstrated the interaction between eEF1A1 and Sgt1 using both purified proteins and cell lysates. We also found that the D2 and D3 domains of eEF1A1 and the TPR domain of Sgt1 are involved in complex formation. Modeling of the Sgt1-eEF1A1 complex suggested both shape and charge complementarities of the eEF1A1-Sgt1 interface stabilized by a number of salt bridges. As long as such interaction mode is typical more for protein-nucleic acid interaction we suggested a possibility that Sgt1 competes with viral RNA for binding to eEF1A and obtained in vitro evidence to this effect.


Subject(s)
Cell Cycle Proteins/metabolism , Hepatocytes/metabolism , Models, Molecular , Peptide Elongation Factor 1/metabolism , Animals , Binding, Competitive , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Glutathione Transferase/chemistry , Glutathione Transferase/genetics , Glutathione Transferase/metabolism , HEK293 Cells , Hepatocytes/cytology , Hepatocytes/enzymology , Humans , Ligands , Molecular Docking Simulation , Peptide Elongation Factor 1/chemistry , Peptide Elongation Factor 1/genetics , Peptide Elongation Factor 1/isolation & purification , Peptide Fragments , Protein Interaction Domains and Motifs , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Multimerization , Protein Stability , Protein Structure, Tertiary , RNA, Viral/chemistry , RNA, Viral/metabolism , Rabbits , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
11.
FEBS Lett ; 589(11): 1187-93, 2015 May 08.
Article in English | MEDLINE | ID: mdl-25862498

ABSTRACT

Translation elongation factor eEF1A is a G-protein which has a crucial role in the ribosomal polypeptide elongation and possesses a number of non-translational functions. Here, we show that the A,A(∗),A' helices segment of mammalian eEF1A is dispensable for the eEF1A*eEF1Bα complex formation. The A,A(∗),A' helices region did not interact with actin; however, its removal eliminates the actin bundling activity of eEF1A, probably due to the destruction of a dimeric structure of eEF1A. The translation function of monomers and the actin-bundling function of dimers of mammalian eEF1A is suggested.


Subject(s)
Amino Acid Sequence , Peptide Elongation Factor 1/chemistry , Protein Multimerization , Sequence Deletion , Actins/chemistry , Actins/genetics , Actins/metabolism , Animals , Peptide Elongation Factor 1/genetics , Peptide Elongation Factor 1/metabolism , Protein Structure, Quaternary , Protein Structure, Secondary , Rabbits
12.
BMC Cancer ; 14: 913, 2014 Dec 03.
Article in English | MEDLINE | ID: mdl-25472873

ABSTRACT

BACKGROUND: The constituents of stable multiprotein complexes are known to dissociate from the complex to play independent regulatory roles. The components of translation elongation complex eEF1H (eEF1A, eEF1Bα, eEF1Bß, eEF1Bγ) were found overexpressed in different cancers. To gain the knowledge about novel cancer-related translational mechanisms we intended to reveal whether eEF1H exists as a single unit or independent subunits in different human cancers. METHODS: The changes in the expression level of every subunit of eEF1H in the human non-small-cell lung cancer tissues were examined. The localization of eEF1H subunits was assessed by immunohistochemistry methods, subcellular fractionation and confocal microscopy. The possibility of the interaction between the subunits was estimated by co-immunoprecipitation. RESULTS: The level of eEF1Bß expression was increased more than two-fold in 36%, eEF1Bγ in 28%, eEF1A in 20% and eEF1Bα in 8% of tumor specimens. The cancer-induced alterations in the subunits level were found to be uncoordinated, therefore the increase in the level of at least one subunit of eEF1H was observed in 52% of samples. Nuclear localization of eEF1Bß in the cancer rather than distal normal looking tissues was found. In cancer tissue, eEF1A and eEF1Bα were not found in nuclei while all four subunits of eEF1H demonstrated both cytoplasmic and nuclear appearance in the lung carcinoma cell line A549. Unexpectedly, in the A549 nuclear fraction eEF1A lost the ability to interact with the eEF1B complex. CONCLUSIONS: The results suggest independent functioning of some fraction of the eEF1H subunits in human tumors. The absence of eEF1A and eEF1B interplay in nuclei of A549 cells is a first evidence for non-translational role of nuclear-localized subunits of eEF1B. We conclude the appearance of the individual eEF1B subunits in tumors is a more general phenomenon than appreciated before and thus is a novel signal of cancer-related changes in translation apparatus.


Subject(s)
Adenocarcinoma/chemistry , Carcinoma, Squamous Cell/chemistry , Guanine Nucleotide Exchange Factors/analysis , Lung Neoplasms/chemistry , Peptide Elongation Factor 1/analysis , Adenocarcinoma/genetics , Carcinoma, Squamous Cell/genetics , Cell Line, Tumor , Cell Nucleus/chemistry , Cytoplasm/chemistry , Guanine Nucleotide Exchange Factors/genetics , Humans , Lung Neoplasms/genetics , Peptide Elongation Factor 1/genetics , RNA, Messenger/analysis
13.
Nucleic Acids Res ; 42(20): 12939-48, 2014 Nov 10.
Article in English | MEDLINE | ID: mdl-25326326

ABSTRACT

Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis.


Subject(s)
Guanosine Diphosphate/chemistry , Guanosine Triphosphate/chemistry , Peptide Elongation Factor 1/chemistry , Animals , Crystallography, X-Ray , Guanosine Diphosphate/metabolism , Guanosine Triphosphate/metabolism , Magnesium/chemistry , Models, Molecular , Peptide Elongation Factor 1/metabolism , Protein Binding , Protein Conformation , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Rabbits
14.
Biochemistry ; 52(32): 5345-53, 2013 Aug 13.
Article in English | MEDLINE | ID: mdl-23859436

ABSTRACT

Translation elongation factor 1A (eEF1A) directs aminoacyl-tRNA to the A site of 80S ribosomes. In addition, more than 97% homologous variants of eEF1A, A1 and A2, whose expression in different tissues is mutually exclusive, may fulfill a number of independent moonlighting functions in the cell; for instance, the unusual appearance of A2 in an A1-expressing tissue was recently linked to the induction of carcinogenesis. The structural background explaining the different functional performance of the highly homologous proteins is unclear. Here, the main difference in the structural properties of these proteins was revealed to be the improved ability of A1 to self-associate, as demonstrated by synchrotron small-angle X-ray scattering (SAXS) and analytical ultracentrifugation. Besides, the SAXS measurements at different urea concentrations revealed the low resistance of the A1 protein to urea. Titration of the proteins by hydrophobic dye 8-anilino-1-naphthalenesulfonate showed that the A1 isoform is more hydrophobic than A2. As the different association properties, lipophilicity, and stability of the highly similar eEF1A variants did not influence considerably their translation functions, at least in vitro, we suggest this difference may indicate a structural background for isoform-specific moonlighting roles.


Subject(s)
Peptide Elongation Factor 1/chemistry , Amino Acid Sequence , Anilino Naphthalenesulfonates/chemistry , Anilino Naphthalenesulfonates/metabolism , Animals , Hydrophobic and Hydrophilic Interactions , Molecular Sequence Data , Peptide Elongation Factor 1/metabolism , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Protein Stability , Protein Structure, Tertiary , RNA, Transfer, Amino Acyl/metabolism , Rabbits , Ribosomes/metabolism , Scattering, Small Angle , Surface Properties
15.
Expert Rev Proteomics ; 9(1): 71-83, 2012.
Article in English | MEDLINE | ID: mdl-22292825

ABSTRACT

Phosphoproteomics is often aimed at deciphering the modified components of signaling pathways in certain organisms, tissues and pathologies. Phosphorylation of housekeeping proteins, albeit important, usually attracts less attention. Here, we provide targeted analysis of eukaryotic translation elongation factor 1A (eEF1A), which is the main element of peptide elongation machinery. There are 97% homologous A1 and A2 isoforms of eEF1A; their expression in mammalian tissues is mutually exclusive and differentially regulated in development. The A2 isoform reveals proto-oncogenic properties and specifically interacts with some cellular proteins. Several tyrosine residues shown experimentally to be phosphorylated in eEF1A1 are hardly solution accessible, so their phosphorylation could be linked with structural rearrangement of the protein molecule. The possible role of tyrosine phosphorylation in providing the background for structural differences between the 'extended' A1 isoform and the compact oncogenic A2 isoform is discussed. The 'road map' for targeted analysis of any protein of interest using phosphoproteomics data is presented.


Subject(s)
Eukaryotic Initiation Factors/metabolism , Neoplasm Proteins/metabolism , Nerve Tissue Proteins/metabolism , Phosphoproteins/metabolism , Proteomics , Eukaryotic Initiation Factors/chemistry , Humans , Neoplasm Proteins/chemistry , Nerve Tissue Proteins/chemistry , Phosphorylation , Receptors, Antigen, T-Cell/metabolism , Signal Transduction , Tyrosine/metabolism
16.
Eur J Clin Invest ; 41(3): 269-76, 2011 Mar.
Article in English | MEDLINE | ID: mdl-20964681

ABSTRACT

BACKGROUND: The signalling role of individual subunits released from some stable translation multi-molecular complexes under unfavourable circumstances is known. The disease-related role of the translation elongation factor 1 complex (eEF1) as a whole is never researched; however, its subunits possess apparent regulatory potency. Whether the individual eEF1 subunits can exist and function in cell beyond the complex is not known. MATERIALS AND METHODS: The protein and mRNA levels of the A1, Bα, Bß or Bγ subunits of eEF1 were analysed by Western and Northern blot techniques in the same specimens of cardioesophageal carcinoma and correspondingly paired normal tissues. Cancer-induced changes in localization patterns of the eEF1 subunits were examined immunohistochemically. RESULTS: Changes in different eEF1 subunits expression were found to be unbalanced, indicating cancer-related emergence of individual components of the eEF1 complex. Independent overexpression of at least one eEF1 component was observed in 72% clinical samples. Noncomplexed eEF1B subunits were also detected by immunohistochemical analysis. In the normal tissue, localization of the Bα, Bß and Bγ subunits was nuclear-cytoplasmic while in the cancer tissue the only Bγ subunit stayed in nucleus. CONCLUSIONS: Our data are first to indicate that the individual subunits can exist separately from the eEF1B complex in cancer tissues and that disintegration of eEF1B could be an important sign of cancer development. Nuclear localization of Bγ both in normal and in cancer tissues suggests its previously unknown nucleus-specific role in human cells.


Subject(s)
Carcinoma/genetics , Esophageal Neoplasms/genetics , Peptide Elongation Factor 1/genetics , Stomach Neoplasms/genetics , Adult , Aged , Blotting, Northern , Blotting, Western , Carcinoma/metabolism , Esophageal Neoplasms/metabolism , Female , Humans , Male , Middle Aged , Molecular Sequence Data , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Peptide Elongation Factor 1/metabolism , Signal Transduction , Stomach Neoplasms/metabolism , Tumor Cells, Cultured
17.
Nucleic Acids Res ; 37(7): e49, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19264796

ABSTRACT

COTRASIF is a web-based tool for the genome-wide search of evolutionary conserved regulatory regions (transcription factor-binding sites, TFBS) in eukaryotic gene promoters. Predictions are made using either a position-weight matrix search method, or a hidden Markov model search method, depending on the availability of the matrix and actual sequences of the target TFBS. COTRASIF is a fully integrated solution incorporating both a gene promoter database (based on the regular Ensembl genome annotation releases) and both JASPAR and TRANSFAC databases of TFBS matrices. To decrease the false-positives rate an integrated evolutionary conservation filter is available, which allows the selection of only those of the predicted TFBS that are present in the promoters of the related species' orthologous genes. COTRASIF is very easy to use, implements a regularly updated database of promoters and is a powerful solution for genome-wide TFBS searching. COTRASIF is freely available at http://biomed.org.ua/COTRASIF/.


Subject(s)
Promoter Regions, Genetic , Software , Transcription Factors/metabolism , Algorithms , Animals , Base Sequence , Binding Sites , Conserved Sequence , Genome , Internet , Markov Chains , Mice , Rats
18.
Nucleic Acids Res ; 36(14): 4736-44, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18632761

ABSTRACT

It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (P(i)), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (K(d) 30 microM and 1-2 microM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic.


Subject(s)
Protein Biosynthesis , Ribosome Subunits, Small, Eukaryotic/metabolism , Ribosomes/metabolism , Allosteric Regulation , Animals , Anti-Bacterial Agents/pharmacology , Bacteria/genetics , Peptide Chain Initiation, Translational , RNA, Messenger/metabolism , RNA, Transfer/metabolism , Rabbits , Ribosome Subunits, Large, Eukaryotic/metabolism , Ribosome Subunits, Small, Bacterial/metabolism , Ribosomes/chemistry , Ribosomes/drug effects , Tetracycline/pharmacology
19.
BMC Struct Biol ; 8: 4, 2008 Jan 25.
Article in English | MEDLINE | ID: mdl-18221514

ABSTRACT

BACKGROUND: Eukaryotic translation elongation factor eEF1A directs the correct aminoacyl-tRNA to ribosomal A-site. In addition, eEF1A is involved in carcinogenesis and apoptosis and can interact with large number of non-translational ligands. There are two isoforms of eEF1A, which are 98% similar. Despite the strong similarity, the isoforms differ in some properties. Importantly, the appearance of eEF1A2 in tissues in which the variant is not normally expressed can be coupled to cancer development.We reasoned that the background for the functional difference of eEF1A1 and eEF1A2 might lie in changes of dynamics of the isoforms. RESULTS: It has been determined by multiple MD simulation that eEF1A1 shows increased reciprocal flexibility of structural domains I and II and less average distance between the domains, while increased non-correlated diffusive atom motions within protein domains characterize eEF1A2. The divergence in the dynamic properties of eEF1A1 and eEF1A2 is caused by interactions of amino acid residues that differ between the two variants with neighboring residues and water environment. The main correlated motion of both protein isoforms is the change in proximity of domains I and II which can lead to disappearance of the gap between the domains and transition of the protein into a "closed" conformation. Such a transition is reversible and the protein can adopt an "open" conformation again. This finding is in line with our earlier experimental observation that the transition between "open" and "closed" conformations of eEF1A could be essential for binding of tRNA and/or other biological ligands. The putative calmodulin-binding region Asn311-Gly327 is less flexible in eEF1A1 implying its increased affinity for calmodulin. The ability of eEF1A1 rather than eEF1A2 to interact with Ca2+/calmodulin is shown experimentally in an ELISA-based test. CONCLUSION: We have found that reversible transitions between "open" and "close" conformations of eEF1A provide a molecular background for the earlier observation that the eEF1A molecule is able to change the shape upon interaction with tRNA. The ability of eEF1A1 rather than eEF1A2 to interact with calmodulin is predicted by MD analysis and showed experimentally. The differential ability of the eEF1A isoforms to interact with signaling molecules discovered in this study could be associated with cancer-related properties of eEF1A2.


Subject(s)
Calmodulin/metabolism , Peptide Elongation Factor 1/chemistry , Amino Acid Sequence , Binding Sites , Calcium/chemistry , Calmodulin/chemistry , Humans , Models, Molecular , Molecular Sequence Data , Peptide Elongation Factor 1/metabolism , Protein Conformation , Protein Isoforms/chemistry , Protein Structure, Tertiary , Sequence Alignment
20.
Int J Biochem Cell Biol ; 40(1): 63-71, 2008.
Article in English | MEDLINE | ID: mdl-17936057

ABSTRACT

The eEF1A1 and eEF1A2 isoforms of translation elongation factor 1A have 98% similarity and perform the same protein synthesis function catalyzing codon-dependent binding of aminoacyl-tRNA to 80S ribosome. However, the isoforms apparently play different non-canonical roles in apoptosis and cancer development which are awaiting further investigations. We hypothesize that the difference in non-translational functions could be caused, in particular, by differential ability of the isoforms to be involved in phosphotyrosine-mediated signalling. The ability of eEF1A1 and eEF1A2 to interact with SH2 and SH3 domains of different signalling molecules in vitro was compared. Indeed, contrary to eEF1A1, eEF1A2 was able to interact with SH2 domains of Grb2, RasGAP, Shc and C-terminal part of Shp2 as well as with SH3 domains of Crk, Fgr, Fyn and phospholipase C-gamma1. Interestingly, the interaction of both isoforms with Shp2 in vivo was found using stable cell lines expressing eEF1A1-His or eEF1A2-His. The formation of a complex between endogenous eEF1A and Shp2 was also shown. Importantly, a higher level of tyrosine phosphorylation of eEF1A2 as compared to eEF1A1 was demonstrated in several independent experiments and its importance for interaction of eEF1A2 with Shp2 in vitro was revealed. Thus, despite the fact that both isoforms of eEF1A could be involved in the phosphotyrosine-mediated processes, eEF1A2 apparently has greater potential to participate in such signalling pathways. Since tyrosine kinases/phosphatases play a prominent role in human cancerogenesis, our observations may gave a basis for recently found oncogenicity of the eEF1A2 isoform.


Subject(s)
Peptide Elongation Factor 1 , Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism , Signal Transduction , Animals , Cattle , Cell Line , Cell Transformation, Neoplastic , Humans , Peptide Elongation Factor 1/genetics , Peptide Elongation Factor 1/metabolism , Phosphorylation , Protein Biosynthesis , Protein Interaction Domains and Motifs/genetics , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics , Rabbits , Transfection , src Homology Domains/genetics
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