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1.
J Cell Sci ; 137(20)2024 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-39404619

RESUMO

Ever since Robert Hooke's 17th century discovery of the cell using a humble compound microscope, light-matter interactions have continuously redefined our understanding of cell biology. Fluorescence microscopy has been particularly transformative and remains an indispensable tool for many cell biologists. The subcellular localization of biomolecules is now routinely visualized simply by manipulating the wavelength of light. Fluorescence polarization microscopy (FPM) extends these capabilities by exploiting another optical property - polarization - allowing researchers to measure not only the location of molecules, but also their organization or alignment within larger cellular structures. With only minor modifications to an existing fluorescence microscope, FPM can reveal the nanoscale architecture, orientational dynamics, conformational changes and interactions of fluorescently labeled molecules in their native cellular environments. Importantly, FPM excels at imaging systems that are challenging to study through traditional structural approaches, such as membranes, membrane proteins, cytoskeletal networks and large macromolecular complexes. In this Review, we discuss key discoveries enabled by FPM, compare and contrast the most common optical setups for FPM, and provide a theoretical and practical framework for researchers to apply this technique to their own research questions.


Assuntos
Polarização de Fluorescência , Microscopia de Fluorescência , Polarização de Fluorescência/métodos , Microscopia de Fluorescência/métodos , Humanos , Animais , Citoesqueleto/metabolismo
2.
J Biol Chem ; 300(8): 107528, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38960038

RESUMO

Therapeutic inhibition of the viral protein Nef is an intriguing direction of antiretroviral drug discovery-it may revitalize immune mechanisms to target, and potentially clear, HIV-1-infected cells. Of the many cellular functions of Nef, the most conserved is the downregulation of surface CD4, which takes place through Nef hijacking the clathrin adaptor protein complex 2 (AP2)-dependent endocytosis. Our recent crystal structure has unraveled the molecular details of the CD4-Nef-AP2 interaction. Guided by the new structural knowledge, we have developed a fluorescence polarization-based assay for inhibitor screening against Nef's activity on CD4. In our assay, AP2 is included along with Nef to facilitate the proper formation of the CD4-binding pocket and a fluorescently labeled CD4 cytoplasmic tail binds competently to the Nef-AP2 complex generating the desired polarization signal. The optimized assay has a good signal-to-noise ratio, excellent tolerance of dimethylsulfoxide and detergent, and the ability to detect competitive binding at the targeted Nef pocket, making it suitable for high-throughput screening.


Assuntos
Antígenos CD4 , Regulação para Baixo , Polarização de Fluorescência , HIV-1 , Ensaios de Triagem em Larga Escala , Produtos do Gene nef do Vírus da Imunodeficiência Humana , Produtos do Gene nef do Vírus da Imunodeficiência Humana/metabolismo , Produtos do Gene nef do Vírus da Imunodeficiência Humana/antagonistas & inibidores , Produtos do Gene nef do Vírus da Imunodeficiência Humana/química , Produtos do Gene nef do Vírus da Imunodeficiência Humana/genética , Antígenos CD4/metabolismo , Antígenos CD4/química , Humanos , Polarização de Fluorescência/métodos , HIV-1/metabolismo , HIV-1/efeitos dos fármacos , Ensaios de Triagem em Larga Escala/métodos , Regulação para Baixo/efeitos dos fármacos , Complexo 2 de Proteínas Adaptadoras/metabolismo , Fármacos Anti-HIV/farmacologia , Fármacos Anti-HIV/química , Ligação Proteica
3.
J Biol Chem ; 300(8): 107529, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38960039

RESUMO

The multifunctional, HIV-1 accessory protein Nef enables infected cells to evade host immunity and thus plays a key role in viral pathogenesis. One prominent function of Nef is the downregulation of major histocompatibility complex class I (MHC-I), which disrupts antigen presentation and thereby allows the infected cells to evade immune surveillance by the cytotoxic T cells. Therapeutic inhibition of this Nef function is a promising direction of antiretroviral drug discovery as it may revitalize cytotoxic T cells to identify, and potentially clear, hidden HIV-1 infections. Guided by the crystal structure of the protein complex formed between Nef, MHC-I, and the hijacked clathrin adaptor protein complex 1, we have developed a fluorescence polarization-based assay for inhibitor screening against Nef's activity on MHC-I. The optimized assay has a good signal-to-noise ratio, substantial tolerance of dimethylsulfoxide, and excellent ability to detect competitive inhibition, indicating that it is suitable for high-throughput screening.


Assuntos
Regulação para Baixo , Polarização de Fluorescência , HIV-1 , Ensaios de Triagem em Larga Escala , Antígenos de Histocompatibilidade Classe I , Produtos do Gene nef do Vírus da Imunodeficiência Humana , Produtos do Gene nef do Vírus da Imunodeficiência Humana/metabolismo , Produtos do Gene nef do Vírus da Imunodeficiência Humana/antagonistas & inibidores , Produtos do Gene nef do Vírus da Imunodeficiência Humana/genética , Produtos do Gene nef do Vírus da Imunodeficiência Humana/química , HIV-1/efeitos dos fármacos , HIV-1/metabolismo , Humanos , Polarização de Fluorescência/métodos , Ensaios de Triagem em Larga Escala/métodos , Regulação para Baixo/efeitos dos fármacos , Antígenos de Histocompatibilidade Classe I/metabolismo , Fármacos Anti-HIV/farmacologia , Fármacos Anti-HIV/química
4.
Bioorg Med Chem ; 100: 117614, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38340640

RESUMO

Ricin, a category-B agent for bioterrorism, and Shiga toxins (Stxs), which cause food poisoning bind to the ribosomal P-stalk to depurinate the sarcin/ricin loop. No effective therapy exists for ricin or Stx intoxication. Ribosome binding sites of the toxins have not been targeted by small molecules. We previously identified CC10501, which inhibits toxin activity by binding the P-stalk pocket of ricin toxin A subunit (RTA) remote from the catalytic site. Here, we developed a fluorescence polarization assay and identified a new class of compounds, which bind P-stalk pocket of RTA with higher affinity and inhibit catalytic activity with submicromolar potency. A lead compound, RU-NT-206, bound P-stalk pocket of RTA with similar affinity as a five-fold larger P-stalk peptide and protected cells against ricin and Stx2 holotoxins for the first time. These results validate the P-stalk binding site of RTA as a critical target for allosteric inhibition of the active site.


Assuntos
Ricina , Sítios de Ligação , Peptídeos/farmacologia , Ligação Proteica , Ribossomos/metabolismo , Ricina/antagonistas & inibidores , Ricina/metabolismo
5.
Arch Toxicol ; 2024 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-39167138

RESUMO

Transthyretin (TTR) and thyroxine-binding globulin (TBG) are two major thyroid hormone (TH) distributor proteins in human plasma, playing important roles in stabilizing the TH levels in plasma, delivery of TH to target tissues, and trans-barrier transport. Binding of xenobiotics to these distributor proteins can potentially affect all these three important roles of distributor proteins. Therefore, fast and cost-effective experimental methods are required for both TTR and TBG to screen both existing and new chemicals for their potential binding. In the present study, the TTR-binding assay was therefore simplified, optimized and pre-validated, while a new TBG-binding assay was developed based on fluorescence polarization as a readout. Seven model compounds (including positive and negative controls) were tested in the pre-validation study of the optimized TTR-binding assay and in the newly developed TBG-binding assay. The dissociation constants of the natural ligand (thyroxine, T4) and potential competitors were determined and compared between two distributor proteins, showing striking differences for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA).

6.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33674463

RESUMO

Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.


Assuntos
Citoesqueleto de Actina/metabolismo , Polarização de Fluorescência/métodos , Corantes Fluorescentes/metabolismo , Microscopia de Fluorescência/métodos , Microtúbulos/metabolismo , Imagem Molecular/métodos , Estrelas-do-Mar/embriologia , Animais , Embrião não Mamífero/citologia , Embrião não Mamífero/metabolismo , Proteínas de Fluorescência Verde/metabolismo , Células HeLa , Humanos , Células LLC-PK1 , Suínos
7.
Sensors (Basel) ; 24(10)2024 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-38794084

RESUMO

Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer-fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems.


Assuntos
Aflatoxina B1 , Aptâmeros de Nucleotídeos , Polarização de Fluorescência , Aflatoxina B1/análise , Aflatoxina B1/química , Aptâmeros de Nucleotídeos/química , Polarização de Fluorescência/métodos , Polieletrólitos/química , Técnicas Biossensoriais/métodos , Poliaminas/química , Limite de Detecção , Corantes Fluorescentes/química
8.
Int J Mol Sci ; 25(12)2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38928409

RESUMO

The beta-galactoside-binding mammalian lectin galectin-1 can bind, via its carbohydrate recognition domain (CRD), to various cell surface glycoproteins and has been implicated in a range of cancers. As a consequence of binding to sugar residues on cell surface receptors, it has been shown to have a pleiotropic effect across many cell types and mechanisms, resulting in immune system modulation and cancer progression. As a result, it has started to become a therapeutic target for both small and large molecules. In previous studies, we used fluorescence polarization (FP) assays to determine KD values to screen and triage small molecule glycomimetics that bind to the galectin-1 CRD. In this study, surface plasmon resonance (SPR) was used to compare human and mouse galectin-1 affinity measures with FP, as SPR has not been applied for compound screening against this galectin. Binding affinities for a selection of mono- and di-saccharides covering a 1000-fold range correlated well between FP and SPR assay formats for both human and mouse galectin-1. It was shown that slower dissociation drove the increased affinity at human galectin-1, whilst faster association was responsible for the effects in mouse galectin-1. This study demonstrates that SPR is a sound alternative to FP for early drug discovery screening and determining affinity estimates. Consequently, it also allows association and dissociation constants to be measured in a high-throughput manner for small molecule galectin-1 inhibitors.


Assuntos
Galectina 1 , Ligação Proteica , Ressonância de Plasmônio de Superfície , Galectina 1/metabolismo , Galectina 1/antagonistas & inibidores , Galectina 1/química , Ressonância de Plasmônio de Superfície/métodos , Humanos , Animais , Camundongos , Cinética , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/química , Polarização de Fluorescência/métodos
9.
Molecules ; 29(16)2024 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-39202926

RESUMO

The adenosine A2A receptor (A2AR) has been identified as a therapeutic target for treating neurodegenerative diseases and cancer. In recent years, we have highlighted the 2-aminoquinazoline heterocycle as an promising scaffold for designing new A2AR antagonists, exemplified by 6-bromo-4-(furan-2-yl)quinazolin-2-amine 1 (Ki (hA2AR) = 20 nM). Here, we report the synthesis of new 2-aminoquinazoline derivatives with substitutions at the C6- and C7-positions, and the introduction of aminoalkyl chains containing tertiary amines at the C2-position to enhance antagonist activity and solubility properties. Compound 5m showed a high affinity for hA2AR with a Ki value of 5 nM and demonstrated antagonist activity with an IC50 of 6 µM in a cyclic AMP assay. Introducing aminopentylpiperidine and 4-[(piperidin-1-yl)methyl]aniline substituents maintained the binding affinities (9x, Ki = 21 nM; 10d, Ki = 15 nM) and functional antagonist activities (9x, IC50 = 9 µM; 10d, IC50 = 5 µM) of the synthesized compounds while improving solubility. This study provides insights into the future development of A2AR antagonists for therapeutic applications.


Assuntos
Antagonistas do Receptor A2 de Adenosina , Quinazolinas , Receptor A2A de Adenosina , Quinazolinas/química , Quinazolinas/farmacologia , Quinazolinas/síntese química , Antagonistas do Receptor A2 de Adenosina/química , Antagonistas do Receptor A2 de Adenosina/síntese química , Antagonistas do Receptor A2 de Adenosina/farmacologia , Receptor A2A de Adenosina/metabolismo , Receptor A2A de Adenosina/química , Humanos , Relação Estrutura-Atividade , Estrutura Molecular , AMP Cíclico/metabolismo , Solubilidade , Ligação Proteica
10.
J Biol Chem ; 298(3): 101697, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35148989

RESUMO

Chaperones of the heat shock protein 70 (Hsp70) family engage in protein-protein interactions with many cochaperones. One "hotspot" for cochaperone binding is the EEVD motif, found at the extreme C terminus of cytoplasmic Hsp70s. This motif is known to bind tetratricopeptide repeat domain cochaperones, such as the E3 ubiquitin ligase CHIP. In addition, the EEVD motif also interacts with a structurally distinct domain that is present in class B J-domain proteins, such as DnaJB4. These observations suggest that CHIP and DnaJB4 might compete for binding to Hsp70's EEVD motif; however, the molecular determinants of such competition are not clear. Using a collection of EEVD-derived peptides, including mutations and truncations, we explored which residues are critical for binding to both CHIP and DnaJB4. These results revealed that some features, such as the C-terminal carboxylate, are important for both interactions. However, CHIP and DnaJB4 also had unique preferences, especially at the isoleucine position immediately adjacent to the EEVD. Finally, we show that competition between these cochaperones is important in vitro, as DnaJB4 limits the ubiquitination activity of the Hsp70-CHIP complex, whereas CHIP suppresses the client refolding activity of the Hsp70-DnaJB4 complex. Together, these data suggest that the EEVD motif has evolved to support diverse protein-protein interactions, such that competition between cochaperones may help guide whether Hsp70-bound proteins are folded or degraded.


Assuntos
Proteínas de Choque Térmico HSP70 , Chaperonas Moleculares , Proteínas de Choque Térmico HSP70/metabolismo , Humanos , Chaperonas Moleculares/metabolismo , Ligação Proteica , Dobramento de Proteína , Ubiquitina-Proteína Ligases/metabolismo
11.
Bioorg Med Chem ; 90: 117371, 2023 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-37339537

RESUMO

A proteolysis targeting chimera (PROTAC) is a bivalent molecule consisting of an E3 ligase ligand and a protein of interest ligand, which promotes the degradation of specific proteins by recruiting the ubiquitin-proteasome system. Although VHL and CRBN ligands have been extensively used in PROTAC development, the availability of small molecule E3 ligase ligands remains limited. Therefore, identifying novel E3 ligase ligands would expand the repertoire for PROTAC development. FEM1C, an E3 ligase that recognizes proteins with an R/K-X-R or R/K-X-X-R motif at the C-terminus, is a promising candidate for this purpose. In this study, we present the design and synthesis of a fluorescent probe ES148, exhibiting a Ki value of 1.6 ± 0.1 µM for FEM1C. Utilizing this fluorescent probe, we have established a robust fluorescence polarization (FP) based competition assay to characterize FEM1C ligands, with a Z' factor of 0.80 and a S/N ratio > 20 in a high-throughput format. Furthermore, we have validated binding affinities of FEM1C ligands using isothermal titration calorimetry, consistently corroborating the results from our FP assay. Thus, we anticipate that our FP competition assay will expedite the discovery of FEM1C ligands, offering new tools for PROTAC development.


Assuntos
Corantes Fluorescentes , Ubiquitina-Proteína Ligases , Ubiquitina-Proteína Ligases/metabolismo , Ligantes , Proteólise , Complexo de Endopeptidases do Proteassoma/metabolismo
12.
Bioorg Chem ; 141: 106929, 2023 12.
Artigo em Inglês | MEDLINE | ID: mdl-37879181

RESUMO

Compounds that mimic the biological properties of glycosaminoglycans (GAGs) and can be more easily prepared than the native GAG oligosaccharides are highly demanded. Here, we present the synthesis of sulfated oligosaccharides displaying a perfluorinated aliphatic tag at the reducing end as GAG mimetics. The preparation of these molecules was greatly facilitated by the presence of the fluorinated tail since the reaction intermediates were isolated by simple fluorous solid-phase extraction. Fluorescence polarization competition assays indicated that the synthesized oligosaccharides interacted with two heparin-binding growth factors, midkine (MK) and FGF-2, showing higher binding affinities than the natural oligosaccharides, and can be therefore considered as useful GAG mimetics. Moreover, NMR experiments showed that the 3D structure of these compounds is similar to that of the native sequences, in terms of sugar ring and glycosidic linkage conformations. Finally, we also demonstrated that these derivatives are able to block the MK-stimulating effect on NIH3T3 cells growth.


Assuntos
Peptídeos e Proteínas de Sinalização Intercelular , Sulfatos , Animais , Camundongos , Células NIH 3T3 , Glicosaminoglicanos , Oligossacarídeos/química
13.
Proc Natl Acad Sci U S A ; 117(31): 18431-18438, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32690700

RESUMO

Influenza hemagglutinin (HA) glycoprotein is the primary surface antigen targeted by the host immune response and a focus for development of novel vaccines, broadly neutralizing antibodies (bnAbs), and therapeutics. HA enables viral entry into host cells via receptor binding and membrane fusion and is a validated target for drug discovery. However, to date, only a very few bona fide small molecules have been reported against the HA. To identity new antiviral lead candidates against the highly conserved fusion machinery in the HA stem, we synthesized a fluorescence-polarization probe based on a recently described neutralizing cyclic peptide P7 derived from the complementarity-determining region loops of human bnAbs FI6v3 and CR9114 against the HA stem. We then designed a robust binding assay compatible with high-throughput screening to identify molecules with low micromolar to nanomolar affinity to influenza A group 1 HAs. Our simple, low-cost, and efficient in vitro assay was used to screen H1/Puerto Rico/8/1934 (H1/PR8) HA trimer against ∼72,000 compounds. The crystal structure of H1/PR8 HA in complex with our best hit compound F0045(S) confirmed that it binds to pockets in the HA stem similar to bnAbs FI6v3 and CR9114, cyclic peptide P7, and small-molecule inhibitor JNJ4796. F0045 is enantioselective against a panel of group 1 HAs and F0045(S) exhibits in vitro neutralization activity against multiple H1N1 and H5N1 strains. Our assay, compound characterization, and small-molecule candidate should further stimulate the discovery and development of new compounds with unique chemical scaffolds and enhanced influenza antiviral capabilities.


Assuntos
Antivirais/farmacologia , Avaliação Pré-Clínica de Medicamentos/métodos , Polarização de Fluorescência/métodos , Vírus da Influenza A Subtipo H1N1/efeitos dos fármacos , Virus da Influenza A Subtipo H5N1/efeitos dos fármacos , Influenza Humana/virologia , Bibliotecas de Moléculas Pequenas/farmacologia , Antivirais/química , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Glicoproteínas de Hemaglutininação de Vírus da Influenza/metabolismo , Humanos , Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H1N1/metabolismo , Virus da Influenza A Subtipo H5N1/genética , Virus da Influenza A Subtipo H5N1/metabolismo , Bibliotecas de Moléculas Pequenas/química
14.
Proc Natl Acad Sci U S A ; 117(28): 16313-16323, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32601209

RESUMO

Peroxiredoxins are central to cellular redox homeostasis and signaling. They serve as peroxide scavengers, sensors, signal transducers, and chaperones, depending on conditions and context. Typical 2-Cys peroxiredoxins are known to switch between different oligomeric states, depending on redox state, pH, posttranslational modifications, and other factors. Quaternary states and their changes are closely connected to peroxiredoxin activity and function but so far have been studied, almost exclusively, outside the context of the living cell. Here we introduce the use of homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization to monitor dynamic changes in peroxiredoxin quaternary structure inside the crowded environment of living cells. Using the approach, we confirm peroxide- and thioredoxin-related quaternary transitions to take place in cellulo and observe that the relationship between dimer-decamer transitions and intersubunit disulfide bond formation is more complex than previously thought. Furthermore, we demonstrate the use of the approach to compare different peroxiredoxin isoforms and to identify mutations and small molecules affecting the oligomeric state inside cells. Mutagenesis experiments reveal that the dimer-decamer equilibrium is delicately balanced and can be shifted by single-atom structural changes. We show how to use this insight to improve the design of peroxiredoxin-based redox biosensors.


Assuntos
Peroxirredoxinas/química , Linhagem Celular , Transferência Ressonante de Energia de Fluorescência , Proteínas de Homeodomínio/química , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Humanos , Peróxido de Hidrogênio/metabolismo , Peróxido de Hidrogênio/farmacologia , Proteínas Luminescentes/química , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Mutação , Peroxirredoxinas/genética , Peroxirredoxinas/metabolismo , Multimerização Proteica/efeitos dos fármacos , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo
15.
Int J Mol Sci ; 24(20)2023 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-37894874

RESUMO

In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide-nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.


Assuntos
Histonas , Nucleossomos , Histonas/metabolismo , Transferência Ressonante de Energia de Fluorescência , Cromatina , DNA/química , Simulação de Dinâmica Molecular , Peptídeos/metabolismo , Polarização de Fluorescência
16.
Molecules ; 28(7)2023 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-37049741

RESUMO

EPR imaging techniques are known to be successful tools for mapping living bodies, especially because of the high transparency of tissues in the microwave range. This technique assumes the presence of radicals whose in vivo transport is also controlled by serum albumins. Accordingly, in this study, the interactions between 3-hydroxymethyl-1-oxyl-4-(pyren-1-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrole radical and the human serum albumin molecules were investigated. To clarify the adsorption processes of this radical onto the surface of human serum albumin (HSA), the interaction of the OMe derivative of the radical was also examined parallel with the studies on the radical-HSA interactions. Considering the solubility issues and also to modulate the transport, inclusion complexes of the radical with a cavitand derivative were also studied. The latter interactions were observed through fluorescence spectroscopy, fluorescence polarization, and by EPR spectroscopy. As a double-sensor molecule, we found that the fluorophore nitroxide is a good candidate as it gave further information about host-guest interactions (fluorescence, fluorescence polarization, and EPR). We also found that in the presence of a cavitand, a complex with greater stability was formed between the sensor molecule and the human serum albumin. Based on these observations, we can conclude that applying this double-sensor (spin, fluorescent) molecule is useful in cases when different interactions can affect the EPR measurements.


Assuntos
Éteres Cíclicos , Resorcinóis , Humanos , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Albumina Sérica Humana , Radicais Livres , Marcadores de Spin
17.
Chembiochem ; 23(5): e202100609, 2022 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-34902208

RESUMO

Proline-rich antimicrobial peptides (PrAMPs) are promising candidates for the treatment of infections caused by high-priority human pathogens. Their mode of action consists of (I) passive diffusion across the outer membrane, (II) active transport through the inner membrane, and (III) inhibition of protein biosynthesis by blocking the exit tunnel of the 70S ribosome. We tested whether in vitro data on ribosomal binding and bacterial uptake could predict the antibacterial activity of PrAMPs against Gram-negative and Gram-positive bacteria. Ribosomal binding and bacterial uptake rates were measured for 47 derivatives of PrAMP Onc112 and compared to the minimal inhibitory concentrations (MIC) of each peptide. Ribosomal binding was evaluated for ribosome extracts from four Gram-negative bacteria. Bacterial uptake was assessed by quantifying each peptide in the supernatants of bacterial cultures. Oncocin analogues with a higher net positive charge appeared to be more active, although their ribosome binding and uptake rates were not necessarily better than for Onc112. The data suggest a complex mode of action influenced by further factors improving or reducing the antibacterial activity, including diffusion through membranes, transport mechanism, secondary targets, off-target binding, intracellular distribution, and membrane effects. Relying only on in vitro binding and uptake data may not be sufficient for the rational development of more active analogues.


Assuntos
Antibacterianos , Peptídeos Catiônicos Antimicrobianos , Ribossomos , Substituição de Aminoácidos , Antibacterianos/química , Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Testes de Sensibilidade Microbiana , Ribossomos/metabolismo
18.
Anal Biochem ; 646: 114626, 2022 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-35218735

RESUMO

Calcineurin is a Ca2+/calmodulin-dependent phosphatase. It is very important to study the affinity between calcineurin and its substrate or other interacting proteins. Two conserved motifs have been reported on the interactive proteins of calcineurin, namely, the PxIxIT motif and the LxVP motif. Here, we used 5(6)-carboxyfluorescein to fluorescently label the N-terminus of the short peptides derived from the two motifs and then determined the affinity between the protein and polypeptides. Microscale thermophoresis (MST) is very suitable for determining calcineurin with peptides containing the LxVP motif. The Kd values of the binding of calcineurin with NFATc1-YLAVP, NHE1-YLTVP, and A238L-FLCVK peptides were 6.72 ± 0.19 µM, 17.14 ± 0.35 µM, and 15.57 ± 0.10 µM, respectively. The GST pull-down results further confirmed the binding trend of the three peptides to calcineurin. However, fluorescently labeled PxIxIT polypeptides are not suitable for MST due to their own aggregation. We determined the binding affinity of the RCAN1-PSVVVH polypeptide to calcineurin by the fluorescence polarization (FP) method. MST and FP assays are fast and accurate in determining the affinity between protein-peptide interactions. Our research laid the foundation for screening the molecules that affect the binding between calcineurin and its substrates in the future.


Assuntos
Calcineurina , Calmodulina , Motivos de Aminoácidos , Calcineurina/química , Calmodulina/metabolismo , Polarização de Fluorescência , Ligação Proteica
19.
RNA Biol ; 19(1): 26-43, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34895045

RESUMO

Igf2bp1 is an oncofetal RNA binding protein whose expression in numerous types of cancers is associated with upregulation of key pro-oncogenic RNAs, poor prognosis, and reduced survival. Importantly, Igf2bp1 synergizes with mutations in Kras to enhance signalling and oncogenic activity, suggesting that molecules inhibiting Igf2bp1 could have therapeutic potential. Here, we isolate a small molecule that interacts with a hydrophobic surface at the boundary of Igf2bp1 KH3 and KH4 domains, and inhibits binding to Kras RNA. In cells, the compound reduces the level of Kras and other Igf2bp1 mRNA targets, lowers Kras protein, and inhibits downstream signalling, wound healing, and growth in soft agar, all in the absence of any toxicity. This work presents an avenue for improving the prognosis of Igf2bp1-expressing tumours in lung, and potentially other, cancer(s).


Assuntos
Antineoplásicos/farmacologia , Carcinogênese/efeitos dos fármacos , Proteínas Proto-Oncogênicas p21(ras)/antagonistas & inibidores , Proteínas de Ligação a RNA/antagonistas & inibidores , Linhagem Celular Tumoral , Ensaios de Seleção de Medicamentos Antitumorais , Ensaios de Triagem em Larga Escala , Humanos , Ligação Proteica/efeitos dos fármacos , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais/efeitos dos fármacos
20.
Anal Bioanal Chem ; 414(20): 6127-6137, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35804073

RESUMO

In order to address the widespread concerns with food safety such as adulteration and forgery in the edible oil field, this study developed a fluorescence polarization immunoassay (FPIA) based on a monoclonal antibody in a homogeneous solution system for determination of capsaicinoids in gutter cooking oil by using chemically stable capsaicinoids as an adulteration marker. The prepared fluoresceinthiocarbamyl ethylenediamine (EDF) was coupled with capsaicinoid hapten C, and the synthesized tracer was purified by thin-layer chromatography (TLC) and showed good binding to the monoclonal antibody CPC Ab-D8. The effects of concentration of tracer and recognition components, type and pH of buffer and incubation time on the performance of FPIA were studied. The linear range (IC20 to IC80) was 3.97-97.99 ng/mL, and the half maximal inhibitory concentration (IC50) was 19.73 ng/mL, and the limit of detection (LOD) was 1.56 ng/mL. The recovery rates of corn germ oil, soybean oil and peanut blend oil were in the range of 94.7-132.3%. The experimental results showed that the fluorescence polarization detection system could realize the rapid detection of capsaicinoids, and had the potential to realize on-site identification of gutter cooking oil. As a universal monoclonal antibody, CPC Ab-D8 can also specifically identify capsaicin and dihydrocapsaicin, so the proposed method can be used to quickly monitor for the presence of gutter cooking oil in normal cooking oil.


Assuntos
Culinária , Alimentos , Anticorpos Monoclonais , Imunoensaio de Fluorescência por Polarização/métodos , Limite de Detecção
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