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1.
Chem Rev ; 124(10): 6501-6542, 2024 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-38722769

RESUMEN

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.


Asunto(s)
Aminoácidos , Aminoácidos/química , Proteínas/química , Proteínas/metabolismo , Espectroscopía de Resonancia por Spin del Electrón/métodos , Microscopía/métodos , Espectroscopía de Resonancia Magnética/métodos , Humanos
2.
J Magn Reson ; 362: 107690, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38692250

RESUMEN

This research report describes a novel surface dielectric resonator (SDR) with a flexible connector for in vivo electron paramagnetic resonance (EPR) spectroscopy. Contrary to the conventional cavity or surface loop-gap resonators, the newly developed SDR is constructed from a ceramic dielectric material, and it is tuned to operate at the L-band frequency band (1.15 GHz) in continuous-wave mode. The SDR is designed to be critically coupled and capable of working with both very lossy samples, such as biological tissues, and non-lossy materials. The SDR was characterized using electromagnetic field simulations, assessed for sensitivity with a B1 field-perturbation method, and validated with tissue phantoms using EPR measurements. The results showed remarkably higher sensitivity in lossy tissue phantoms than the previously reported multisegment surface-loop resonators. The new SDR can provide potential new insights for advancements in the application of in vivo EPR spectroscopy for biological measurements, including clinical oximetry.


Asunto(s)
Campos Electromagnéticos , Diseño de Equipo , Fantasmas de Imagen , Espectroscopía de Resonancia por Spin del Electrón/métodos , Espectroscopía de Resonancia por Spin del Electrón/instrumentación , Reproducibilidad de los Resultados , Oximetría/instrumentación , Oximetría/métodos
3.
Nat Commun ; 15(1): 4041, 2024 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-38740794

RESUMEN

Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach. Both methods yield similar probability distributions that reveal the presence of at least four other species with different electronic structures in addition to the ground state E0. Two of these species were preliminary assigned to hydrogenated E2 states. In addition, advanced pulsed-EPR experiments are utilized to verify the incorporation of sulfur and selenium into the FeMo cofactor, and to assign hyperfine couplings of 33S and 77Se that directly couple to the FeMo cluster. With this analysis, we report selenium incorporation under turnover conditions as a straightforward approach to stabilize and analyze early intermediate states of the FeMo cofactor.


Asunto(s)
Azotobacter vinelandii , Molibdoferredoxina , Nitrogenasa , Selenio , Azufre , Espectroscopía de Resonancia por Spin del Electrón/métodos , Azotobacter vinelandii/enzimología , Azotobacter vinelandii/metabolismo , Nitrogenasa/metabolismo , Nitrogenasa/química , Molibdoferredoxina/metabolismo , Molibdoferredoxina/química , Selenio/metabolismo , Selenio/química , Azufre/metabolismo , Azufre/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química
4.
J Phys Chem B ; 128(14): 3350-3359, 2024 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-38564809

RESUMEN

Secondary coordination sphere (SCS) interactions have been shown to play important roles in tuning reduction potentials and electron transfer (ET) properties of the Type 1 copper proteins, but the precise roles of these interactions are not fully understood. In this work, we examined the influence of F114P, F114N, and N47S mutations in the SCS on the electronic structure of the T1 copper center in azurin (Az) by studying the hyperfine couplings of (i) histidine remote Nε nitrogens and (ii) the amide Np using the two-dimensional (2D) pulsed electron paramagnetic resonance (EPR) technique HYSCORE (hyperfine sublevel correlation) combined with quantum mechanics/molecular mechanics (QM/MM) and DLPNO-CCSD calculations. Our data show that some components of hyperfine tensor and isotropic coupling in N47SAz and F114PAz (but not F114NAz) deviate by up to ∼±20% from WTAz, indicating that these mutations significantly influence the spin density distribution between the CuII site and coordinating ligands. Furthermore, our calculations support the assignment of Np to the backbone amide of residue 47 (both in Asn and Ser variants). Since the spin density distributions play an important role in tuning the covalency of the Cu-Scys bond of Type 1 copper center that has been shown to be crucial in controlling the reduction potentials, this study provides additional insights into the electron spin factor in tuning the reduction potentials and ET properties.


Asunto(s)
Nativos Alasqueños , Azurina , Azurina/genética , Azurina/química , Cobre/química , Nitrógeno/química , Mutación , Espectroscopía de Resonancia por Spin del Electrón/métodos , Amidas
5.
Eur Biophys J ; 53(4): 171-181, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38597963

RESUMEN

Polymeric micelles are nanocarriers for drug, protein and gene delivery due to their unique core/shell structure, which encapsulates and protects therapeutic cargos with diverse physicochemical properties. However, information regarding the micellar nanoenvironment's fluidity can provide unique insight into their makeup. In this study, we used electron paramagnetic resonance (EPR) spectroscopy to study free radical spin probe (5-doxylstearate methyl ester, 5-MDS, and 16-doxylstearic acid, 16-DS) behaviour in methoxy-poly(ethylene oxide)-poly(α-benzyl carboxylate-ε-caprolactone) (PEO-PBCL) and methoxy-poly(ethylene oxide)-poly(ε-caprolactone) (PEO-PCL) polymeric micelles. Spin probes provided information about the spectroscopic rotational correlation time (τ, s) and the spectroscopic partition parameter F. We hypothesized that spin probes would partition into the polymeric micelles, and these parameters would be calculated. The results showed that both 5-MDS and 16-DS spectra were modulated in the presence of polymeric micelles. Based on τ values, 5-MDS revealed that PEO-PCL (τ = 3.92 ± 0.26 × 10-8 s) was more fluid than PEO-PBCL (τ = 7.15 ± 0.63 × 10-8 s). The F parameter, however, could not be calculated due to the rotational hindrance of the probe within the micelles. With 16-DS, more probe rotation was observed, and although the F parameter could be calculated, it was not helpful to distinguish the micelles' fluidity. Also, doxorubicin-loading interfered with the spin probes, particularly for 16-DS. However, using simulations, we could distinguish the hydrophilic and hydrophobic components of the 16-DS probe. The findings suggest that EPR spectroscopy is a valuable method for determining core fluidity in polymeric micelles.


Asunto(s)
Micelas , Espectroscopía de Resonancia por Spin del Electrón/métodos , Poliésteres/química , Polietilenglicoles/química , Marcadores de Spin , Polímeros/química
6.
Biochemistry ; 63(9): 1214-1224, 2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38679935

RESUMEN

A central goal of photoprotective energy dissipation processes is the regulation of singlet oxygen (1O2*) and reactive oxygen species in the photosynthetic apparatus. Despite the involvement of 1O2* in photodamage and cell signaling, few studies directly correlate 1O2* formation to nonphotochemical quenching (NPQ) or lack thereof. Here, we combine spin-trapping electron paramagnetic resonance (EPR) and time-resolved fluorescence spectroscopies to track in real time the involvement of 1O2* during photoprotection in plant thylakoid membranes. The EPR spin-trapping method for detection of 1O2* was first optimized for photosensitization in dye-based chemical systems and then used to establish methods for monitoring the temporal dynamics of 1O2* in chlorophyll-containing photosynthetic membranes. We find that the apparent 1O2* concentration in membranes changes throughout a 1 h period of continuous illumination. During an initial response to high light intensity, the concentration of 1O2* decreased in parallel with a decrease in the chlorophyll fluorescence lifetime via NPQ. Treatment of membranes with nigericin, an uncoupler of the transmembrane proton gradient, delayed the activation of NPQ and the associated quenching of 1O2* during high light. Upon saturation of NPQ, the concentration of 1O2* increased in both untreated and nigericin-treated membranes, reflecting the utility of excess energy dissipation in mitigating photooxidative stress in the short term (i.e., the initial ∼10 min of high light).


Asunto(s)
Fotosíntesis , Oxígeno Singlete , Tilacoides , Espectroscopía de Resonancia por Spin del Electrón/métodos , Oxígeno Singlete/metabolismo , Oxígeno Singlete/química , Tilacoides/metabolismo , Tilacoides/química , Detección de Spin/métodos , Clorofila/metabolismo , Clorofila/química , Spinacia oleracea/metabolismo , Spinacia oleracea/química , Luz
7.
Int J Mol Sci ; 25(8)2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38673758

RESUMEN

Animal tumors serve as reasonable models for human cancers. Both human and animal tumors often reveal triplet EPR signals of nitrosylhemoglobin (HbNO) as an effect of nitric oxide formation in tumor tissue, where NO is complexed by Hb. In search of factors determining the appearance of nitrosylhemoglobin (HbNO) in solid tumors, we compared the intensities of electron paramagnetic resonance (EPR) signals of various iron-nitrosyl complexes detectable in tumor tissues, in the presence and absence of excess exogenous iron(II) and diethyldithiocarbamate (DETC). Three types of murine tumors, namely, L5178Y lymphoma, amelanotic Cloudman S91 melanoma, and Ehrlich carcinoma (EC) growing in DBA/2 or Swiss mice, were used. The results were analyzed in the context of vascularization determined histochemically using antibodies to CD31. Strong HbNO EPR signals were found in melanoma, i.e., in the tumor with a vast amount of a hemorrhagic necrosis core. Strong Fe(DETC)2NO signals could be induced in poorly vascularized EC. In L5178Y, there was a correlation between both types of signals, and in addition, Fe(RS)2(NO)2 signals of non-heme iron-nitrosyl complexes could be detected. We postulate that HbNO EPR signals appear during active destruction of well-vascularized tumor tissue due to hemorrhagic necrosis. The presence of iron-nitrosyl complexes in tumor tissue is biologically meaningful and defines the evolution of complicated tumor-host interactions.


Asunto(s)
Ditiocarba , Hemoglobinas , Óxido Nítrico , Animales , Óxido Nítrico/metabolismo , Ditiocarba/farmacología , Ditiocarba/química , Ratones , Hemoglobinas/metabolismo , Hemoglobinas/química , Espectroscopía de Resonancia por Spin del Electrón/métodos , Detección de Spin/métodos , Neovascularización Patológica/metabolismo , Línea Celular Tumoral , Modelos Animales de Enfermedad , Ratones Endogámicos DBA , Compuestos Ferrosos/química
8.
Free Radic Biol Med ; 218: 57-67, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38574976

RESUMEN

Understanding the tumor redox status is important for efficient cancer treatment. Here, we noninvasively detected changes in the redox environment of tumors before and after cancer treatment in the same individuals using a novel compact and portable electron paramagnetic resonance imaging (EPRI) device and compared the results with glycolytic information obtained through autoradiography using 2-deoxy-2-[18F]fluoro-d-glucose ([18F]FDG). Human colon cancer HCT116 xenografts were used in the mice. We used 3-carbamoyl-PROXYL (3CP) as a paramagnetic and redox status probe for the EPRI of tumors. The first EPRI was followed by the intraperitoneal administration of buthionine sulfoximine (BSO), an inhibitor of glutathione synthesis, or X-ray irradiation of the tumor. A second EPRI was performed on the following day. Autoradiography was performed after the second EPRI. After imaging, the tumor sections were evaluated by histological analysis and the amount of reducing substances in the tumor was measured. BSO treatment and X-ray irradiation significantly decreased the rate of 3CP reduction in tumors. Redox maps of tumors obtained from EPRI can be compared with tissue sections of approximately the same cross section. BSO treatment reduced glutathione levels in tumors, whereas X-ray irradiation did not alter the levels of any of the reducing substances. Comparison of the redox map with the autoradiography of [18F]FDG revealed that regions with high reducing power in the tumor were active in glucose metabolism; however, this correlation disappeared after X-ray irradiation. These results suggest that the novel compact and portable EPRI device is suitable for multimodal imaging, which can be used to study tumor redox status and therapeutic efficacy in cancer, and for combined analysis with other imaging modalities.


Asunto(s)
Estudios de Factibilidad , Fluorodesoxiglucosa F18 , Glucosa , Imagen Multimodal , Oxidación-Reducción , Animales , Humanos , Ratones , Fluorodesoxiglucosa F18/metabolismo , Glucosa/metabolismo , Imagen Multimodal/métodos , Espectroscopía de Resonancia por Spin del Electrón/métodos , Butionina Sulfoximina/farmacología , Autorradiografía , Células HCT116 , Neoplasias del Colon/metabolismo , Neoplasias del Colon/diagnóstico por imagen , Neoplasias del Colon/patología , Radiofármacos/metabolismo , Tomografía de Emisión de Positrones/métodos , Ensayos Antitumor por Modelo de Xenoinjerto , Glutatión/metabolismo , Ratones Desnudos
9.
Yakugaku Zasshi ; 144(4): 339-344, 2024.
Artículo en Japonés | MEDLINE | ID: mdl-38556304

RESUMEN

Excessive production of reactive oxygen species (ROS) causes oxidative stress and is involved in the development and progression of a wide variety of diseases. Therefore, techniques for measuring oxidative stress are indispensable for analysis of the mechanisms of various diseases. The method involving ESR and the durable nitroxyl radical (ESR/spin probe method) is useful for this purpose, because the ESR signal intensity of the spin probe changes on reacting with ROS and other unstable radicals. In this review, the author's research applying the ESR/spin probe method to clarify disease mechanisms in vivo and in vitro is presented. The ESR signal of the probe injected into animals may decay through a few mechanisms besides reaction with ROS; thus, interpretation of the results is complicated. As the first approach to solving this problem, a probe resistant to enzymatic reduction by introducing a bulky group adjacent to the nitroxy group was created. The second approach was the use of a hydroxylamine probe which dominantly oxidized to nitroxyl radicals by reacting with superoxide anion radicals and oxidants. Using acyl-protected hydroxyl amine, it was demonstrated that sepsis model mice are under oxidative stress due to ROS production by activated phagocytes. On the other hand, it was shown in vitro that the UV-induced radical reaction of ketoprofen also occurs in lipid membranes, and that the reaction is related to ROS generation and membrane disruption. We believe that use of the ESR/spin probe method with ingenuity will clarify the mechanisms of various diseases.


Asunto(s)
Óxidos de Nitrógeno , Estrés Oxidativo , Ratones , Animales , Espectroscopía de Resonancia por Spin del Electrón/métodos , Especies Reactivas de Oxígeno , Radicales Libres
10.
Appl Radiat Isot ; 208: 111286, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38498957

RESUMEN

Dried figs were studied by Electron Paramagnetic Resonance (EPR) spectroscopy for identification of radiation treatment and dosage assessment. Gamma-irradiated samples show a multicomponent "sugar-like" EPR spectrum with line width of 6-8 mT, centered at g = 2.004. The investigation of the influence of the instrumental parameters microwave power and modulation amplitude on the EPR signal show saturation effect at microwave power above 2 mW and over modulation at modulation amplitude above 0.4 mT. Determination of the stability of radiation induced signals shows, that identification of previous radiation treatment is possible for a long time period after irradiation even more than one year. Dose-response curves of gamma-irradiated samples exhibits a linear response up to about 4 kGy and the saturation of the EPR signal at higher doses. A Single Aliquot Additive dosing method used to estimate the initial absorbed dose in irradiated dried fig flesh shows initial dose 0.25 kGy for the sample irradiated by 5 kGy and 3.7 kGy for those irradiated using 10 kGy. Taking into account the signal decay after 150 days of storage, the dose defined as initial should be 4.65 kGy for the 5 kGy irradiated sample and 8 kGy for that irradiated using 10 kGy.


Asunto(s)
Ficus , Espectroscopía de Resonancia por Spin del Electrón/métodos , Rayos gamma
11.
J Magn Reson ; 361: 107652, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38457937

RESUMEN

Precise radiation guided by oxygen images has demonstrated superiority over the traditional radiation methods. Electron paramagnetic resonance (EPR) imaging has proven to be the most advanced oxygen imaging modality. However, the main drawback of EPR imaging is the long scan time. For each projection, we usually need to collect the projection many times and then average them to achieve high signal-to-noise ratio (SNR). One approach to fast scan is to reduce the repeating time for each projection. While the projections would be noisy and thus the traditional commonly-use filtered backprojection (FBP) algorithm would not be capable of accurately reconstructing images. Optimization-based iterative algorithms may accurately reconstruct images from noisy projections for they may incorporate prior information into optimization models. Based on the total variation (TV) algorithms for EPR imaging, in this work, we propose a directional TV (DTV) algorithm to further improve the reconstruction accuracy. We construct the DTV constrained, data divergence minimization (DTVcDM) model, derive its Chambolle-Pock (CP) solving algorithm, validate the correctness of the whole algorithm, and perform evaluations via simulated and real data. The experimental results show that the DTV algorithm outperforms the existing TV and FBP algorithms in fast EPR imaging. Compared to the standard FBP algorithm, the proposed algorithm may achieve 10 times of acceleration.


Asunto(s)
Algoritmos , Imagenología Tridimensional , Espectroscopía de Resonancia por Spin del Electrón/métodos , Fantasmas de Imagen , Imagenología Tridimensional/métodos , Oxígeno , Procesamiento de Imagen Asistido por Computador/métodos
12.
Methods Mol Biol ; 2778: 237-257, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38478282

RESUMEN

Outer membrane proteins (OMPs) of Gram-negative bacteria are involved in many essential functions of the cell. They are tightly packed in the outer membrane, which is an asymmetric lipid bilayer. Electron spin resonance (ESR) spectroscopic techniques combined with site-directed spin labeling (SDSL) enable observation of structure and conformational dynamics of these proteins directly in their native environments. Here we depict a protocol for site-directed spin labeling of ß-barrel membrane proteins in isolated outer membranes and intact E. coli using nitroxide, triarylmethyl (trityl), and Gd3+-based spin tags. Furthermore, subsequent continuous wave (CW) and orthogonal pulsed electron-electron double resonance (PELDOR) measurements are described along with experimental setup at Q-band (34 GHz), the data analysis, and interpretation.


Asunto(s)
Escherichia coli , Proteínas de la Membrana , Espectroscopía de Resonancia por Spin del Electrón/métodos , Marcadores de Spin , Proteínas de la Membrana/metabolismo , Escherichia coli/metabolismo , Conformación Molecular
13.
Methods Mol Biol ; 2754: 55-75, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38512660

RESUMEN

Tau is a microtubule-associated protein that belongs to the Intrinsically Disordered Proteins (IDPs) family. IDPs or Intrinsically Disordered Regions (IDRs) play key roles in protein interaction networks and their dysfunctions are often related to severe diseases. Defined by their lack of stable secondary and tertiary structures in physiological conditions while being functional, these proteins use their inherent structural flexibility to adapt to and interact with various binding partners. Knowledges on the structural dynamics of IDPs and their different conformers are crucial to finely decipher fundamental biological processes controlled by mechanisms such as conformational adaptations or switches, induced fit, or conformational selection events. Different mechanisms of binding have been proposed: among them, the so-called folding-upon-binding in which the IDP adopts a certain conformation upon interacting with a partner protein, or the formation of a "fuzzy" complex in which the IDP partly keeps its dynamical character at the surface of its partner. The dynamical nature and physicochemical properties of unbound as well as bound IDPs make this class of proteins particularly difficult to characterize by classical bio-structural techniques and require specific approaches for the fine description of their inherent dynamics.Among other techniques, Site-Directed Spin Labeling combined with Electron Paramagnetic Resonance (SDSL-EPR) spectroscopy has gained much interest in this last decade for the study of IDPs. SDSL-EPR consists in grafting a paramagnetic label (mainly a nitroxide radical) at selected site(s) of the macromolecule under interest followed by its observation using and/or combining different EPR strategies. These nitroxide spin labels detected by continuous wave (cw) EPR spectroscopy are used as perfect reporters or "spy spins" of their local environment, being able to reveal structural transitions, folding/unfolding events, etc. Another approach is based on the measurement of inter-label distance distributions in the 1.5-8.0 nm range using pulsed dipolar EPR experiments, such as Double Electron-Electron Resonance (DEER) spectroscopy. The technique is then particularly well suited to study the behavior of Tau in its interaction with its physiological partner: microtubules (MTs). In this chapter we provide a detailed experimental protocol for the labeling of Tau protein and its EPR study while interacting with preformed (Paclitaxel-stabilized) MTs, or using Tau as MT inducer. We show how the choice of nitroxide label can be crucial to obtain functional information on Tau/tubulin complexes.


Asunto(s)
Proteínas Intrínsecamente Desordenadas , Óxidos de Nitrógeno , Proteínas tau , Espectroscopía de Resonancia por Spin del Electrón/métodos , Marcadores de Spin , Microtúbulos
14.
J Am Chem Soc ; 146(6): 3710-3720, 2024 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-38308759

RESUMEN

1/2H and 13C hyperfine coupling constants to 5'-deoxyadenosyl (5'-dAdo•) radical trapped within the active site of the radical S-adenosyl-l-methionine (SAM) enzyme, pyruvate formate lyase-activating enzyme (PFL-AE), both in the absence of substrate and the presence of a reactive peptide-model of the PFL substrate, are completely characteristic of a classical organic free radical whose unpaired electron is localized in the 2pπ orbital of the sp2 C5'-carbon (J. Am. Chem. Soc. 2019, 141, 12139-12146). However, prior electron-nuclear double resonance (ENDOR) measurements had indicated that this 5'-dAdo• free radical is never truly "free": tight van der Waals contact with its target partners and active-site residues guide it in carrying out the exquisitely precise, regioselective reactions that are hallmarks of RS enzymes. Here, our understanding of how the active site chaperones 5'-dAdo• is extended through the finding that this apparently unexceptional organic free radical has an anomalous g-tensor and exhibits significant 57Fe, 13C, 15N, and 2H hyperfine couplings to the adjacent, isotopically labeled, methionine-bound [4Fe-4S]2+ cluster cogenerated with 5'-dAdo• during homolytic cleavage of cluster-bound SAM. The origin of the 57Fe couplings through nonbonded radical-cluster contact is illuminated by a formal exchange-coupling model and broken symmetry-density functional theory computations. Incorporation of ENDOR-derived distances from C5'(dAdo•) to labeled-methionine as structural constraints yields a model for active-site positioning of 5'-dAdo• with a short, nonbonded C5'-Fe distance (∼3 Å). This distance involves substantial motion of 5'-dAdo• toward the unique Fe of the [4Fe-4S]2+ cluster upon S-C(5') bond-cleavage, plausibly an initial step toward formation of the Fe-C5' bond of the organometallic complex, Ω, the central intermediate in catalysis by radical-SAM enzymes.


Asunto(s)
Proteínas Hierro-Azufre , S-Adenosilmetionina , S-Adenosilmetionina/metabolismo , Metionina , Espectroscopía de Resonancia por Spin del Electrón/métodos , Dominio Catalítico , Racemetionina , Radicales Libres/química , Proteínas Hierro-Azufre/química
15.
Adv Sci (Weinh) ; 11(16): e2306710, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38419268

RESUMEN

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.


Asunto(s)
Cobre , ADN , Simulación de Dinámica Molecular , Cobre/química , Espectroscopía de Resonancia por Spin del Electrón/métodos , ADN/química , Conformación de Ácido Nucleico , División del ADN , ADN Catalítico/química , ADN Catalítico/metabolismo , Iones/química
16.
Protein Sci ; 33(3): e4903, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38358137

RESUMEN

The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.


Asunto(s)
Escherichia coli , Óxidos de Nitrógeno , Proteínas , Humanos , Espectroscopía de Resonancia por Spin del Electrón/métodos , Escherichia coli/genética , Escherichia coli/química , Células HeLa , Marcadores de Spin , Proteínas/química
17.
Phys Chem Chem Phys ; 26(8): 6806-6816, 2024 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-38324256

RESUMEN

The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.


Asunto(s)
Cobre , Proteínas , Marcadores de Spin , Cobre/química , Proteínas/química , Espectroscopía de Resonancia por Spin del Electrón/métodos , Simulación de Dinámica Molecular
18.
Eur J Pharm Biopharm ; 197: 114211, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38340877

RESUMEN

The concentration of air pollution is gradually increasing every year so that daily skin exposure is unavoidable. Dietary supplements and topical formulations currently represent the protective strategies to guard against the effects of air pollution on the body and the skin. Unfortunately, there are not yet enough methods available to measure the effectiveness of anti-pollution products on skin. Here, we present two ex vivo methods for measuring the protective effect against air pollution of different cream formulations on the skin: Electron paramagnetic resonance (EPR) spectroscopy and autofluorescence excited by 785 nm using a confocal Raman microspectrometer (CRM). Smoke from one cigarette was used as a model pollutant. EPR spectroscopy enables the direct measurement of free radicals in excised porcine skin after smoke exposure. The autofluorescence in the skin was measured ex vivo, which is an indicator of oxidative stress. Two antioxidants and a chelating agent in a base formulation and a commercial product containing an antioxidant mixture were investigated. The ex vivo studies show that the antioxidant epigallocatechin-3-gallate (EGCG) in the base cream formulation provided the best protection against oxidative stress from smoke exposure for both methods.


Asunto(s)
Antioxidantes , Piel , Animales , Porcinos , Antioxidantes/química , Espectroscopía de Resonancia por Spin del Electrón/métodos , Piel/metabolismo , Estrés Oxidativo , Radicales Libres/química
19.
J Pharm Biomed Anal ; 242: 116057, 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38422674

RESUMEN

Free radical formation in two diuretics: indapamide and torasemide was examined during UV irradiation and storage at higher temperatures using X-band (9.3 GHz) electron paramagnetic resonance spectroscopy (EPR). The aim of this study was to investigate the possibility of storing indapamide and torasemide under UV irradiation and at higher temperatures, which may occur during exposure to light. The diuretic samples were exposed to UVA irradiation for 15, 30 and 45 minutes, and stored at temperatures of 40 °C and 50 °C by 30 minutes. The EPR spectra were analyzed to determine the amplitudes (A), linewidths (ΔBpp), and integral intensities (I) and g factors. The concentrations of free radical (N) in the diuretic samples were also determined. The influence of microwave power on amplitudes, linewidths and the asymmetry parameter were evaluated. The result showed that the tested indapamide and torasemide samples exhibited high free radical concentrations in the range of 1018-1019 spin/g after UV irradiation and heat treatment. Therefore, due to the significant free radical formation indapamide and torasemide should not be stored under UV light and at temperatures of 40 °C and 50 °C. The complex character of free radical systems in the diuretic samples was proved as evidenced by the changes of the asymmetry parameters of the EPR lines with increasing microwave power. Fast spin-lattice relaxation processes were observed in all tested diuretic samples, regardless of the storage conditions. Electron paramagnetic resonance spectroscopy is proposed as a useful method in pharmacy to determine the appropriate storage conditions for diuretics.


Asunto(s)
Calor , Indapamida , Torasemida , Temperatura , Espectroscopía de Resonancia por Spin del Electrón/métodos , Rayos Ultravioleta , Radicales Libres/química , Diuréticos
20.
Phys Med Biol ; 69(5)2024 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-38306975

RESUMEN

Objective. Water-equivalent dosimeters are desirable for dosimetry in radiotherapy. The present work investigates basic characteristics of novel aqueous detector materials and presents a signal loss approach for electron paramagnetic resonance (EPR) dosimetry.Approach. The proposed principle is based on the radiation dose dependent annihilation of EPR active nitroxides (NO·) in aqueous solutions. Stable nitroxide radicals (3-Maleimido-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (MmP), 3-Carbamoyl-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (CmP)) in aqueous solutions containing dimethyl sulfoxide (DMSO) as an additive were filled in glass capillaries for irradiation and EPR readout. Radiation doses ranging from 1 to 64 Gy were applied with a clinical 6 MV flattening filter free photon beam. EPR readout was then performed with a X-band benchtop spectrometer. The dose response, temporal stability and reproducibility of the samples' EPR signal amplitudes as well as the influence of the nitroxide concentration between 10 and 160µM on the absolute signal loss were investigated using MmP. CmP was used to examine the dependence of the dose response on DMSO concentration between 0 and 10 vol%. An indirect effect model was fitted to the experimental data assuming irradiation induced radical reactions as the underlying mechanism.Main results. For an initial MmP concentration of 20µM, absolute EPR signal loss is linear up to a dose of 16 Gy with a yield G(-NO·) of approximately 0.4µmol J-1. Within five weeks upon sample irradiation to doses between 0 and 32 Gy relative EPR signal fluctuations were on average (126 readouts) below 1% (1σ). For c(MmP) ≥ 20µM, absolute signal loss is only weakly dependent on c(MmP), whereas it increases strongly with increasing c(DMSO) in the range 0-5 vol%. An indirect effect model is applicable to describe the reaction mechanism resulting in the observed dose response curve.Significance. Liquids consisting of nitroxides in aqueous solution and small amounts of DMSO (2 vol%) show promising basic characteristics for application as water-equivalent EPR dosimeter materials in radiotherapy. The EPR signal loss is based on an indirect effect mediated by diffusing radicals originating from the radiolysis of the water/DMSO mixture.


Asunto(s)
Dimetilsulfóxido , Óxidos de Nitrógeno , Radiometría , Espectroscopía de Resonancia por Spin del Electrón/métodos , Reproducibilidad de los Resultados , Radiometría/métodos , Agua
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