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1.
J Virol ; 96(1): e0150521, 2022 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-34613791

RESUMO

During evolution, viruses had to adapt to an increasingly complex environment of eukaryotic cells. Viral proteins that need to enter the cell nucleus or associate with nucleoli possess nuclear localization signals (NLSs) and nucleolar localization signals (NoLSs) for nuclear and nucleolar accumulation, respectively. As viral proteins are relatively small, acquisition of novel sequences seems to be a more complicated task for viruses than for eukaryotes. Here, we carried out a comprehensive analysis of the basic domain (BD) of HIV-1 Tat to show how viral proteins might evolve with NLSs and NoLSs without an increase in protein size. The HIV-1 Tat BD is involved in several functions, the most important being the transactivation of viral transcription. The BD also functions as an NLS, although it is substantially longer than a typical NLS. It seems that different regions in the BD could function as NLSs due to its enrichment with positively charged amino acids. Additionally, the high positive net charge inevitably causes the BD to function as an NoLS through a charge-specific mechanism. The integration of NLSs and NoLSs into functional domains enriched with positively charged amino acids might be a mechanism that allows the condensation of different functional sequences in small protein regions and, as a result, reduces protein size, influencing the origin and evolution of NLSs and NoLSs in viruses. IMPORTANCE Here, we investigated the molecular mechanism of nuclear localization signal (NLS) and nucleolar localization signal (NoLS) integration into the basic domain of HIV-1 Tat (49RKKRRQRRR57) and found that these two supplementary functions (i.e., function of NLS and function of NoLS) are embedded in the basic domain amino acid sequence. The integration of NLSs and NoLSs into functional domains of viral proteins enriched with positively charged amino acids is a mechanism that allows the concentration of different functions within small protein regions. Integration of NLS and NoLS into functional protein domains might have influenced the viral evolution, as this could prevent an increase in the protein size.


Assuntos
Regulação Viral da Expressão Gênica , Infecções por HIV/virologia , HIV-1/fisiologia , Sinais de Localização Nuclear , Domínios e Motivos de Interação entre Proteínas , Produtos do Gene tat do Vírus da Imunodeficiência Humana/química , Produtos do Gene tat do Vírus da Imunodeficiência Humana/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Nucléolo Celular/metabolismo , Núcleo Celular/metabolismo , Sequência Consenso , Evolução Molecular , Interações Hospedeiro-Patógeno , Modelos Moleculares , Ligação Proteica , Transporte Proteico , Relação Estrutura-Atividade , Proteínas Virais/metabolismo , Produtos do Gene tat do Vírus da Imunodeficiência Humana/genética
2.
Proc Natl Acad Sci U S A ; 117(37): 22841-22848, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32859757

RESUMO

Quantum mechanics/molecular mechanics (QM/MM) maturation of an immunoglobulin (Ig) powered by supercomputation delivers novel functionality to this catalytic template and facilitates artificial evolution of biocatalysts. We here employ density functional theory-based (DFT-b) tight binding and funnel metadynamics to advance our earlier QM/MM maturation of A17 Ig-paraoxonase (WTIgP) as a reactibody for organophosphorus toxins. It enables regulation of biocatalytic activity for tyrosine nucleophilic attack on phosphorus. The single amino acid substitution l-Leu47Lys results in 340-fold enhanced reactivity for paraoxon. The computed ground-state complex shows substrate-induced ionization of the nucleophilic l-Tyr37, now H-bonded to l-Lys47, resulting from repositioning of l-Lys47. Multiple antibody structural homologs, selected by phenylphosphonate covalent capture, show contrasting enantioselectivities for a P-chiral phenylphosphonate toxin. That is defined by crystallographic analysis of phenylphosphonylated reaction products for antibodies A5 and WTIgP. DFT-b analysis using QM regions based on these structures identifies transition states for the favored and disfavored reactions with surprising results. This stereoselection analysis is extended by funnel metadynamics to a range of WTIgP variants whose predicted stereoselectivity is endorsed by experimental analysis. The algorithms used here offer prospects for tailored design of highly evolved, genetically encoded organophosphorus scavengers and for broader functionalities of members of the Ig superfamily, including cell surface-exposed receptors.

3.
Int J Mol Sci ; 24(22)2023 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-38003521

RESUMO

Over the past decades, the problem of bacterial resistance to most antibiotics has become a serious threat to patients' survival. Nevertheless, antibiotics of a novel class have not been approved since the 1980s. The development of antibiotic potentiators is an appealing alternative to the challenging process of searching for new antimicrobials. Production of H2S-one of the leading defense mechanisms crucial for bacterial survival-can be influenced by the inhibition of relevant enzymes: bacterial cystathionine γ-lyase (bCSE), bacterial cystathionine ß-synthase (bCBS), or 3-mercaptopyruvate sulfurtransferase (MST). The first one makes the main contribution to H2S generation. Herein, we present data on the synthesis, in silico analyses, and enzymatic and microbiological assays of novel bCSE inhibitors. Combined molecular docking and molecular dynamics analyses revealed a novel binding mode of these ligands to bCSE. Lead compound 2a manifested strong potentiating activity when applied in combination with some commonly used antibiotics against multidrug-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus. The compound was found to have favorable in vitro absorption, distribution, metabolism, excretion, and toxicity parameters. The high effectiveness and safety of compound 2a makes it a promising candidate for enhancing the activity of antibiotics against high-priority pathogens.


Assuntos
Sulfeto de Hidrogênio , Staphylococcus aureus Resistente à Meticilina , Humanos , Antibacterianos/farmacologia , Sulfeto de Hidrogênio/metabolismo , Cistationina gama-Liase/metabolismo , Staphylococcus aureus Resistente à Meticilina/metabolismo , Pirróis/farmacologia , Simulação de Acoplamento Molecular , Bactérias/metabolismo , Indóis/farmacologia , Cistationina beta-Sintase/metabolismo
4.
Molecules ; 28(1)2022 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-36615487

RESUMO

Central nervous system tumors related to gliomas are of neuroectodermal origin and cover about 30% of all primary brain tumors. Glioma is not susceptible to any therapy and surgical attack remains one of the main approaches to its treatment. Preoperative tumor imaging methods, such as positron emission tomography (PET), are currently used to distinguish malignant tissue to increase the accuracy of glioma removal. However, PET is lacking a specific visualization of cells possessing certain molecular markers. Here, we report an application of aptamers to enhancing specificity in imaging tumor cells bearing the epidermal growth factor receptor (EGFR). Glioblastoma is characterized by increased EGFR expression, as well as mutations of this receptor associated with active division, migration, and adhesion of tumor cells. Since 2021, EGFR has been included into the WHO classification of gliomas as a molecular genetic marker. To obtain conjugates of aptamers GR20 and GOL1-specific to EGFR, a 4-[18F]fluorobenzylazide radiotracer was used as a synthon. For the production of the synthon, a method of automatic synthesis on an Eckert & Ziegler research module was adapted and modified using spirocyclic iodonium ylide as a precursor. Conjugation of 4-[18F]fluorobenzylazide and alkyne-modified aptamers was carried out using Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) with/without the TBTA ligand. As a result, it was possible to obtain 18F-labelled conjugates with 97% radiochemical purity for [18F]FB-GR20 and 98% for [18F]FB-GOL1. The obtained conjugates can be used for further studies in PET analysis on model animals with grafted glioblastoma.


Assuntos
Glioblastoma , Glioma , Animais , Radioisótopos de Flúor/química , Glioblastoma/diagnóstico por imagem , Tomografia por Emissão de Pósitrons/métodos , Compostos Radiofarmacêuticos/química , Receptores ErbB/metabolismo , Oligonucleotídeos , Glioma/diagnóstico por imagem
5.
Biochemistry (Mosc) ; 86(8): 1012-1024, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34488577

RESUMO

Conventional approaches for studying and molecular typing of tumors include PCR, blotting, omics, immunocytochemistry, and immunohistochemistry. The last two methods are the most used, as they enable detecting both tumor protein markers and their localizations within the cells. In this study, we have investigated a possibility of using RNA aptamers, in particular, 2'-F-pyrimidyl-RNA aptamer ME07 (48 nucleotides long), specific to the receptor of epidermal growth factor (EGFR, ErbB1, Her1), as an alternative to monoclonal antibodies for aptacytochemistry and aptahistochemistry for human glioblastoma multiforme (GBM). A specificity of binding of FAM-ME07 to the receptor on the tumor cells has been demonstrated by flow cytometry; an apparent dissociation constant for the complex of aptamer - EGFR on the cell has been determined; a number of EGFR molecules has been semi-quantitatively estimated for the tumor cell lines having different amount of EGFR: A431 (106 copies per cell), U87 (104 copies per cell), MCF7 (103 copies per cell), and ROZH, primary GBM cell culture derived from patient (104 copies per cell). According to fluorescence microscopy, FAM-ME07 interacts directly with the receptors on A431 cells, followed by its internalization into the cytoplasm and translocation to the nucleolus; this finding opens a possibility of ME07 application as an escort aptamer for a delivery of therapeutic agents into tumor cells. FAM-ME07 efficiently stains sections of GBM clinical specimens, which enables an identification of EGFR-positive clones within a heterogeneous tumor; and providing a potential for further studying animal models of GBM.


Assuntos
Aptâmeros de Nucleotídeos/química , Neoplasias Encefálicas/terapia , Glioblastoma/terapia , RNA/química , Anticorpos Monoclonais , Neoplasias Encefálicas/genética , Linhagem Celular Tumoral , Citoplasma/metabolismo , Ensaios de Seleção de Medicamentos Antitumorais , Fator de Crescimento Epidérmico/metabolismo , Receptores ErbB , Glioblastoma/genética , Humanos , Concentração Inibidora 50 , Células MCF-7 , Microscopia de Fluorescência , Oligonucleotídeos/química , Medicina de Precisão , Transporte Proteico
6.
Int J Mol Sci ; 22(22)2021 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-34830487

RESUMO

Neuronal calcium sensor-1 (NCS-1) is a four-EF-hand ubiquitous signaling protein modulating neuronal function and survival, which participates in neurodegeneration and carcinogenesis. NCS-1 recognizes specific sites on cellular membranes and regulates numerous targets, including G-protein coupled receptors and their kinases (GRKs). Here, with the use of cellular models and various biophysical and computational techniques, we demonstrate that NCS-1 is a redox-sensitive protein, which responds to oxidizing conditions by the formation of disulfide dimer (dNCS-1), involving its single, highly conservative cysteine C38. The dimer content is unaffected by the elevation of intracellular calcium levels but increases to 10-30% at high free zinc concentrations (characteristic of oxidative stress), which is accompanied by accumulation of the protein in punctual clusters in the perinuclear area. The formation of dNCS-1 represents a specific Zn2+-promoted process, requiring proper folding of the protein and occurring at redox potential values approaching apoptotic levels. The dimer binds Ca2+ only in one EF-hand per monomer, thereby representing a unique state, with decreased α-helicity and thermal stability, increased surface hydrophobicity, and markedly improved inhibitory activity against GRK1 due to 20-fold higher affinity towards the enzyme. Furthermore, dNCS-1 can coordinate zinc and, according to molecular modeling, has an asymmetrical structure and increased conformational flexibility of the subunits, which may underlie their enhanced target-binding properties. In HEK293 cells, dNCS-1 can be reduced by the thioredoxin system, otherwise accumulating as protein aggregates, which are degraded by the proteasome. Interestingly, NCS-1 silencing diminishes the susceptibility of Y79 cancer cells to oxidative stress-induced apoptosis, suggesting that NCS-1 may mediate redox-regulated pathways governing cell death/survival in response to oxidative conditions.


Assuntos
Sinalização do Cálcio/genética , Receptor Quinase 1 Acoplada a Proteína G/genética , Neoplasias/genética , Proteínas Sensoras de Cálcio Neuronal/genética , Neurônios/metabolismo , Neuropeptídeos/genética , Cálcio/metabolismo , Proteínas de Ligação ao Cálcio/genética , Linhagem Celular Tumoral , Dimerização , Dissulfetos/química , Motivos EF Hand/genética , Células HEK293 , Humanos , Cinética , Neoplasias/patologia , Proteínas Sensoras de Cálcio Neuronal/antagonistas & inibidores , Neurônios/química , Neuropeptídeos/antagonistas & inibidores , Oxirredução , Receptores Acoplados a Proteínas G/genética , Transdução de Sinais/genética , Zinco/metabolismo
7.
Nucleic Acids Res ; 46(3): 1102-1112, 2018 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-29267876

RESUMO

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.


Assuntos
DNA/química , Fator Neurotrófico Derivado de Linhagem de Célula Glial/genética , Simulação de Dinâmica Molecular , Pareamento de Bases , Sequência de Bases , Microscopia Crioeletrônica , DNA/genética , Fator Neurotrófico Derivado de Linhagem de Célula Glial/química , Humanos , Microscopia de Força Atômica , Conformação de Ácido Nucleico
8.
Int J Mol Sci ; 21(23)2020 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-33260324

RESUMO

Transactive response DNA and RNA binding protein 43 kDa (TDP-43) is a highly conserved heterogeneous nuclear ribonucleoprotein (hnRNP), which is involved in several steps of protein production including transcription and splicing. Its aggregates are frequently observed in motor neurons from amyotrophic lateral sclerosis patients and in the most common variant of frontotemporal lobar degeneration. Recently it was shown that TDP-43 is able to bind Zn2+ by its RRM domain. In this work, we have investigated Zn2+ binding to a short peptide 256-264 from C-terminus of RRM2 domain using isothermal titration calorimetry, electrospray ionization mass spectrometry, QM/MM simulations, and NMR spectroscopy. We have found that this peptide is able to bind zinc ions with a Ka equal to 1.6 × 105 M-1. Our findings suggest the existence of a zinc binding site in the C-terminal region of RRM2 domain. Together with the existing structure of the RRM2 domain of TDP-43 we propose a model of its complex with Zn2+ which illustrates how zinc might regulate DNA/RNA binding.


Assuntos
Proteínas de Ligação a DNA/química , Peptídeos/metabolismo , Zinco/metabolismo , Sequência de Aminoácidos , Simulação por Computador , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Peptídeos/química , Ligação Proteica , Conformação Proteica , Domínios Proteicos
9.
Photosynth Res ; 142(2): 229-240, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31302832

RESUMO

Mitochondria-targeted antioxidants (also known as 'Skulachev Ions' electrophoretically accumulated by mitochondria) exert anti-ageing and ROS-protecting effects well documented in animal and human cells. However, their effects on chloroplast in photosynthetic cells and corresponding mechanisms are scarcely known. For the first time, we describe a dramatic quenching effect of (10-(6-plastoquinonyl)decyl triphenylphosphonium (SkQ1) on chlorophyll fluorescence, apparently mediated by redox interaction of SkQ1 with Mn cluster in Photosystem II (PSII) of chlorophyte microalga Chlorella vulgaris and disabling the oxygen-evolving complex (OEC). Microalgal cells displayed a vigorous uptake of SkQ1 which internal concentration built up to a very high level. Using optical and EPR spectroscopy, as well as electron donors and in silico molecular simulation techniques, we found that SkQ1 molecule can interact with Mn atoms of the OEC in PSII. This stops water splitting giving rise to potent quencher(s), e.g. oxidized reaction centre of PSII. Other components of the photosynthetic apparatus proved to be mostly intact. This effect of the Skulachev ions might help to develop in vivo models of photosynthetic cells with impaired OEC function but essentially intact otherwise. The observed phenomenon suggests that SkQ1 can be applied to study stress-induced damages to OEC in photosynthetic organisms.


Assuntos
Antioxidantes/metabolismo , Manganês/metabolismo , Complexo de Proteína do Fotossistema II/metabolismo , Cátions , Chlorella vulgaris/efeitos dos fármacos , Chlorella vulgaris/metabolismo , Clorofila/metabolismo , Fluorescência , Interações Hidrofóbicas e Hidrofílicas , Cinética , Luz , Simulação de Acoplamento Molecular , Oxigênio/metabolismo , Plastoquinona/análogos & derivados , Plastoquinona/farmacologia
10.
Molecules ; 24(2)2019 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-30642123

RESUMO

Peptides are promising drug candidates due to high specificity and standout safety. Identification of bioactive peptides de novo using molecular docking is a widely used approach. However, current scoring functions are poorly optimized for peptide ligands. In this work, we present a novel algorithm PeptoGrid that rescores poses predicted by AutoDock Vina according to frequency information of ligand atoms with particular properties appearing at different positions in the target protein's ligand binding site. We explored the relevance of PeptoGrid ranking with a virtual screening of peptide libraries using angiotensin-converting enzyme and GABAB receptor as targets. A reasonable agreement between the computational and experimental data suggests that PeptoGrid is suitable for discovering functional leads.


Assuntos
Descoberta de Drogas , Simulação de Acoplamento Molecular , Biblioteca de Peptídeos , Peptídeos/química , Peptídeos/farmacologia , Algoritmos , Animais , Simulação por Computador , Simulação de Dinâmica Molecular , Reprodutibilidade dos Testes , Relação Estrutura-Atividade , Peixe-Zebra
11.
Int J Mol Sci ; 19(12)2018 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-30544979

RESUMO

Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model (HMMer) algorithm and Pfam database, comprehensive analysis of the T. aestivum genome revealed a large number of proteases (1544 in total) belonging to the five major protease families: serine, cysteine, threonine, aspartic, and metallo-proteases. Mass-spectrometry analysis revealed a 30% difference between degradomes of distinct wheat cultivars (Khakasskaya and Darya), and infection by biotrophic (Puccinia recondita Rob. ex Desm f. sp. tritici) or necrotrophic (Stagonospora nodorum) pathogens induced drastic changes in the presence of proteolytic enzymes. This study shows that an early immune response to biotic stress is associated with the same core of proteases from the C1, C48, C65, M24, M41, S10, S9, S8, and A1 families. Further liquid chromatography-mass spectrometry (LC-MS) analysis of the detected protease-derived peptides revealed that infection by both pathogens enhances overall proteolytic activity in wheat cells and leads to activation of proteolytic cascades. Moreover, sites of proteolysis were identified within the proteases, which probably represent targets of autocatalytic activation, or hydrolysis by another protease within the proteolytic cascades. Although predicted substrates of metacaspase-like and caspase-like proteases were similar in biotrophic and necrotrophic infections, proteolytic activation of proteases was not found to be associated with metacaspase-like and caspase-like activities. These findings indicate that the response of T. aestivum to biotic stress is regulated by unique mechanisms.


Assuntos
Caspases/metabolismo , Peptídeo Hidrolases/metabolismo , Doenças das Plantas/microbiologia , Proteômica/métodos , Ascomicetos/patogenicidade , Basidiomycota/patogenicidade , Doenças das Plantas/genética , Folhas de Planta/genética , Folhas de Planta/microbiologia , Subtilisinas/genética , Subtilisinas/metabolismo
12.
Biophys J ; 112(11): 2327-2335, 2017 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-28591605

RESUMO

Measurements of ion conductance through α-hemolysin pore in a bilayer lipid membrane revealed blocking of the ion channel by a series of rhodamine 19 and rhodamine B esters. The longest dwell closed time of the blocking was observed with rhodamine 19 butyl ester (C4R1), whereas the octyl ester (C8R1) was of poor effect. Voltage asymmetry in the binding kinetics indicated that rhodamine derivatives bound to the stem part of the aqueous pore lumen. The binding frequency was proportional to a quadratic function of rhodamine concentrations, thereby showing that the dominant binding species were rhodamine dimers. Two levels of the pore conductance and two dwell closed times of the pore were found. The dwell closed times lengthened as the voltage increased, suggesting impermeability of the channel for the ligands. Molecular docking analysis revealed two distinct binding sites within the lumen of the stem of the α-hemolysin pore for the C4R1 dimer, but only one binding site for the C8R1 dimer. The blocking of the α-hemolysin nanopore by rhodamines could be utilized in DNA sequencing as additional optical sensing owing to bright fluorescence of rhodamines if used for DNA labeling.


Assuntos
Toxinas Bacterianas/agonistas , Toxinas Bacterianas/química , Proteínas Hemolisinas/agonistas , Proteínas Hemolisinas/química , Rodaminas/química , Escherichia coli , Interações Hidrofóbicas e Hidrofílicas , Cinética , Bicamadas Lipídicas/química , Potenciais da Membrana , Simulação de Acoplamento Molecular , Multimerização Proteica , Staphylococcus aureus
13.
J Org Chem ; 82(19): 10015-10024, 2017 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-28856889

RESUMO

Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475-510 nm; Stokes shifts 125-160 nm or 7520-8960 cm-1) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold.

14.
Bioorg Med Chem ; 25(14): 3597-3605, 2017 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-28396019

RESUMO

Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.


Assuntos
Guanosina/análogos & derivados , Oligonucleotídeos/síntese química , Orbivirus/genética , Oxazinas/química , RNA Viral/metabolismo , Dicroísmo Circular , Exonucleases/metabolismo , Guanosina/metabolismo , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , Oligonucleotídeos/química , RNA de Cadeia Dupla/análise , RNA de Cadeia Dupla/genética , RNA de Cadeia Dupla/metabolismo , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real
15.
Nucleic Acids Res ; 39(22): 9789-802, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21893589

RESUMO

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.


Assuntos
Aptâmeros de Nucleotídeos/química , Cátions/química , Quadruplex G , Calorimetria , DNA/química , Simulação de Dinâmica Molecular , Potássio/química , Sódio/química
16.
Int J Biol Macromol ; 209(Pt A): 779-784, 2022 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-35421417

RESUMO

Tau protein has been extensively studied due to its key roles in microtubular cytoskeleton regulation and in the formation of aggregates found in some neurodegenerative diseases. Recently it has been shown that zinc is able to induce tau aggregation by interacting with several binding sites. However, the precise location of these sites and the molecular mechanism of zinc-induced aggregation remain unknown. Here we used Nuclear Magnetic Resonance (NMR) to identify zinc binding sites on tau. These experiments revealed three distinct zinc binding sites on tau, located in the N-terminal part, the repeat region and the C-terminal part. Further analysis enabled us to show that the N-terminal and the C-terminal sites are independent of each other. Using molecular simulations, we proposed a model of each site in a complex with zinc. Given the clinical importance of zinc in tau aggregation, our findings pave the way for designing potential therapies for tauopathies.


Assuntos
Tauopatias , Proteínas tau , Sítios de Ligação , Humanos , Microtúbulos/metabolismo , Ligação Proteica , Tauopatias/metabolismo , Zinco/metabolismo , Proteínas tau/química
17.
RNA ; 15(6): 1134-41, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19383770

RESUMO

Transfer RNA is highly modified. Nucleotide 37 of the anticodon loop is represented by various modified nucleotides. In Escherichia coli, the valine-specific tRNA (cmo(5)UAC) contains a unique modification, N(6)-methyladenosine, at position 37; however, the enzyme responsible for this modification is unknown. Here we demonstrate that the yfiC gene of E. coli encodes an enzyme responsible for the methylation of A37 in tRNA(1)(Val). Inactivation of yfiC gene abolishes m(6)A formation in tRNA(1)(Val), while expression of the yfiC gene from a plasmid restores the modification. Additionally, unmodified tRNA(1)(Val) can be methylated by recombinant YfiC protein in vitro. Although the methylation of m(6)A in tRNA(1)(Val) by YfiC has little influence on the cell growth under standard conditions, the yfiC gene confers a growth advantage under conditions of osmotic and oxidative stress.


Assuntos
Proteínas de Escherichia coli/genética , Escherichia coli/enzimologia , Genes Bacterianos , Metiltransferases/genética , RNA de Transferência de Valina/metabolismo , tRNA Metiltransferases/genética , Adenosina/análogos & derivados , Adenosina/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Metilação , Metiltransferases/metabolismo , Estresse Oxidativo , RNA de Transferência de Valina/genética , tRNA Metiltransferases/metabolismo
18.
RNA ; 15(12): 2312-20, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19861420

RESUMO

Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA-ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.


Assuntos
Escherichia coli/química , Conformação de Ácido Nucleico , RNA Bacteriano/química , RNA Mensageiro/química , RNA de Transferência/química , Ribossomos/química , Sequência de Bases , Microscopia Crioeletrônica , Escherichia coli/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Biossíntese de Proteínas , RNA Bacteriano/metabolismo , RNA Bacteriano/ultraestrutura , RNA Mensageiro/metabolismo , RNA Mensageiro/ultraestrutura , RNA de Transferência/metabolismo , RNA de Transferência/ultraestrutura , Ribossomos/metabolismo , Ribossomos/ultraestrutura
19.
Biomolecules ; 11(12)2021 12 03.
Artigo em Inglês | MEDLINE | ID: mdl-34944467

RESUMO

S100A1 is a member of the S100 family of small ubiquitous Ca2+-binding proteins, which participates in the regulation of cell differentiation, motility, and survival. It exists as homo- or heterodimers. S100A1 has also been shown to bind Zn2+, but the molecular mechanisms of this binding are not yet known. In this work, using ESI-MS and ITC, we demonstrate that S100A1 can coordinate 4 zinc ions per monomer, with two high affinity (KD~4 and 770 nm) and two low affinity sites. Using competitive binding experiments between Ca2+ and Zn2+ and QM/MM molecular modeling we conclude that Zn2+ high affinity sites are located in the EF-hand motifs of S100A1. In addition, two lower affinity sites can bind Zn2+ even when the EF-hands are saturated by Ca2+, resulting in a 2Ca2+:S100A1:2Zn2+ conformer. Finally, we show that, in contrast to calcium, an excess of Zn2+ produces a destabilizing effect on S100A1 structure and leads to its aggregation. We also determined a higher affinity to Ca2+ (KD~0.16 and 24 µm) than was previously reported for S100A1, which would allow this protein to function as a Ca2+/Zn2+-sensor both inside and outside cells, participating in diverse signaling pathways under normal and pathological conditions.


Assuntos
Cálcio/metabolismo , Proteínas S100/química , Proteínas S100/metabolismo , Zinco/metabolismo , Sítios de Ligação , Humanos , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Transdução de Sinais
20.
Front Neurosci ; 15: 705590, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34421525

RESUMO

The aim of the study was to develop better anxiolytics and antidepressants. We focused on GABA A receptors and the α2δ auxiliary subunit of V-gated Ca2+ channels as putative targets because they are established as mediators of efficacious anxiolytics, antidepressants, and anticonvulsants. We further focused on short peptides as candidate ligands because of their high safety and tolerability profiles. We employed a structural bioinformatics approach to develop novel tetrapeptides with predicted affinity to GABA A receptors and α2δ. In silico docking studies of one of these peptides, LCGA-17, showed a high binding score for both GABA A receptors and α2δ, combined with anxiolytic-like properties in a Danio rerio behavioral screen. LCGA-17 showed anxiolytic-like effects in the novel tank test, the light-dark box, and the social preference test, with efficacy comparable to fluvoxamine and diazepam. In binding assays using rat brain membranes, [3H]-LCGA-17 was competed more effectively by gabapentinoid ligands of α2δ than ligands of GABA A receptors, suggesting that α2δ represents a likely target for LCGA-17. [3H]-LCGA-17 binding to brain lysates was unaffected by competition with ligands for GABAB, glutamate, dopamine, serotonin, and other receptors, suggesting specific interaction with α2δ. Dose-finding studies in mice using acute administration of LCGA-17 (i.p.) demonstrated anxiolytic-like effects in the open field test, elevated plus maze, and marble burying tests, as well as antidepressant-like properties in the forced swim test. The anxiolytic effects were effectively blocked by bicuculline. Therefore, LCGA-17 is a novel candidate anxiolytic and antidepressant that may act through α2δ, with possible synergism by GABA A receptors.

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