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1.
Small ; : e2401248, 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38639029

RESUMO

Chlorine has been supplied by the chlor-alkali process that deploys dimensionally stable anodes (DSAs) for the electrochemical chlorine evolution reaction (ClER). The paramount bottlenecks have been ascribed to an intensive usage of precious elements and inevitable competition with the oxygen evolution reaction. Herein, a unique case of Ru2+-O4 active motifs anchored on Magnéli Ti4O7 (Ru-Ti4O7) via a straightforward wet impregnation and mild annealing is reported. The Ru-Ti4O7 performs radically active ClER with minimal deployment of Ru (0.13 wt%), both in 5 m NaCl (pH 2.3) and 0.1 m NaCl (pH 6.5) electrolytes. Scanning electrochemical microscopy demonstrates superior ClER selectivity on Ru-Ti4O7 compared to the DSA. Operando X-ray absorption spectroscopy and density functional theory calculations reveal a universally active ClER (over a wide range of pH and [Cl-]), through a direct adsorption of Cl- on Ru2+-O4 sites as the most plausible pathway, together with stabilized ClO* at low [Cl-] and high pH.

2.
J Magn Reson ; 358: 107600, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38039655

RESUMO

We present a new program REDEN (Residual Decomposition of NMR peaks) designed to perform identification of peaks in NMR spectra. This integrated, cross-platform, open-source software visually assists with explicit peak picking through decomposition of NMR peaks on the frequency domain data. It provides a distinctive interactive workflow with iPick due to its integration with the POKY suite, providing users with a seamless and efficient experience. The decomposition of peaks operates in a chosen region of an NMR spectrum by multi-fitting simulated peaks with four lineshape fitting options as support, Gaussian, Lorentzian, a fast/optimized Lorentzian, and Pseudo-Voigt. Furthermore, REDEN provides a way to fine-tune for the users in two operating modes (Basic and Advanced). REDEN is pre-built in the POKY suite, which is available from https://poky.clas.ucdenver.edu.

3.
J Biomol NMR ; 78(1): 19-30, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38102490

RESUMO

A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15N-15N correlations on uniformly 15N-labeled GB1 powders. A major feature exploited in these 15N-15N correlations was AL FRESCO's remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15N-15N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15N spin-diffusion experiments. An indirect approach producing long-range 15N-15N correlations was also tested, relying on short (ms-long) 1HN-1HN mixings schemes while applying AL FRESCO chirped pulses along the 15N channel. These indirect mixing schemes produced numerous long-distance Ni-Ni±n (n = 2 - 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1HN-1HN counterparts.


Assuntos
Peptídeos , Proteínas , Ressonância Magnética Nuclear Biomolecular/métodos , Peptídeos/química , Espectroscopia de Ressonância Magnética/métodos , Proteínas/química , Imageamento por Ressonância Magnética , Prótons
4.
J Biomol NMR ; 77(5-6): 217-228, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37804349

RESUMO

Nuclear magnetic resonance is a crucial technique for studying biological complexes, as it provides precise structural and dynamic information at the atomic level. However, the process of assigning resonances can be time-consuming and challenging, particularly in cases where peaks overlap, or the data quality is poor. In this paper, we present TINTO (Two and three-dimensional Imaging for NMR sTrip Operation via CV/ML), an advanced semiautomatic toolset for NMR resonance assignment. TINTO comprises two separate tools, each tailored for either two-dimensional or three-dimensional imaging. The toolset utilizes a computer-vision approach and a machine learning approach, specifically structural similarity index and principal components analysis, to perform visual similarity searches of resonances and quickly locate similar strips, and in that way overcome the challenges associated with peak overlap without requiring peak picking. Our tool offers a user-friendly interface and has the potential to enhance the efficiency and accuracy of NMR resonance assignment, particularly in complex cases. This advancement holds promising implications for furthering our understanding of biological systems at the molecular level. TINTO is pre-installed in the POKY suite, which is available at https://poky.clas.ucdenver.edu .


Assuntos
Computadores , Proteínas , Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas/química , Espectroscopia de Ressonância Magnética , Imageamento por Ressonância Magnética , Algoritmos
5.
Antioxidants (Basel) ; 12(2)2023 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-36829815

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) has naturally aggressive characteristics including postoperative recurrence, resistance to conventional treatment, and metastasis. Surgical resection with chemotherapeutic agents has been conducted as the major treatment for PDAC. However, surgical treatment is ineffective in the case of advanced cancer, and conventional adjuvant chemotherapy, including gemcitabine and 5-fluorouracil, show low effectiveness due to the high drug resistance of PDAC to this type of treatment. Therefore, the development of innovative therapeutic drugs is crucial to solving the present limitation of conventional drugs. Glucotropaeolin (GT) is a glucosinolate that can be isolated from the Brassicaceae family. GT has exhibited a growth-inhibitory effect against liver and colon cancer cells; however, there is no study regarding the anticancer effect of GT on PDAC. In our study, we determined the antiproliferative effect of GT in PANC-1 and MIA PaCa-2, representative of PDAC. We revealed the intracellular mechanisms underlying the anticancer effect of GT with respect to cell viability, reactive oxygen species (ROS) accumulation, alteration of mitochondrial membrane potential (MMP), calcium dysregulation, cell migration, and the induction of apoptosis. Moreover, GT regulated the signaling pathways related to anticancer in PDAC cells. Finally, the silencing of the forkhead box protein M, a key factor regulating PDAC progression, contributes to the anticancer property of GT in terms of the induction of apoptosis and cell migration. Therefore, GT may be a potential therapeutic drug against PDAC.

6.
Environ Sci Technol ; 57(47): 18529-18537, 2023 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-36245147

RESUMO

This study valorized scanning electrochemical microscopy (SECM) for the detection of dissolved O3, which is increasingly in demand for water treatment. Au ultramicroelectrodes biased at 0.62 V RHE provided superior activity and selectivity for O3 reduction, compared to Pt analogues. It allowed quantitative in situ interrogation of ozone evolution reaction (OZER) electrocatalysts with unprecedented estimations on the OZER overpotential. The difference in onset potentials between the OZER and the competing oxygen evolution reaction (OER) primarily accounted for the OZER current efficiency (CE) on boron-doped diamond (BDD, 1.4% at 10 mA cm-2 in 0.5 M H2SO4), Ni-Sb-doped SnO2 (NSS, 10.8%), and SiOx-coated NSS (NSS/SiOx, 34.4%). SECM areal scans in tandem with elemental mapping perspicuously visualized the improved OZER activity by the SiOx overlayer on NSS. A shift in the charge transfer coefficient further rationalized the elevated OZER selectivity on NSS/SiOx, in association with the weakened Sn-O bond strength confirmed by valence band X-ray photoelectron spectra. The invigorated OZER on NSS/SiOx effectively accelerated the degradation of a model aqueous pollutant (4-chlorophenol).


Assuntos
Ozônio , Purificação da Água , Microscopia Eletroquímica de Varredura , Oxirredução , Estresse Oxidativo
7.
Sensors (Basel) ; 22(24)2022 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-36560269

RESUMO

Chemical agents are one of the major threats to soldiers in modern warfare, so it is so important to detect chemical agents rapidly and accurately on battlefields. Raman spectroscopy-based detectors are widely used but have many limitations. The Raman spectrum changes unpredictably due to various environmental factors, and it is hard for detectors to make appropriate judgments about new chemical substances without prior information. Thus, the existing detectors with inflexible techniques based on determined rules cannot deal with such problems flexibly and reactively. Artificial intelligence (AI)-based detection techniques can be good alternatives to the existing techniques for chemical agent detection. To build AI-based detection systems, sufficient amounts of data for training are required, but it is not easy to produce and handle fatal chemical agents, which causes difficulty in securing data in advance. To overcome the limitations, in this paper, we propose the distributed Raman spectrum data augmentation system that leverages federated learning (FL) with deep generative models, such as generative adversarial network (GAN) and autoencoder. Furthermore, the proposed system utilizes various additional techniques in combination to generate a large number of Raman spectrum data with reality along with diversity. We implemented the proposed system and conducted diverse experiments to evaluate the system. The evaluation results validated that the proposed system can train the models more quickly through cooperation among decentralized troops without exchanging raw data and generate realistic Raman spectrum data well. Moreover, we confirmed that the classification model on the proposed system performed learning much faster and outperformed the existing systems.


Assuntos
Inteligência Artificial , Aprendizagem , Redes de Comunicação de Computadores , Julgamento
8.
Antioxidants (Basel) ; 11(10)2022 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-36290616

RESUMO

Recent studies have identified obesity as one of the world's most serious chronic disorders. Adipogenesis, in which preadipocytes are differentiated into mature adipocytes, has a decisive role in establishing the number of adipocytes and determining the lipid storage capacity of adipose tissue and fat mass in adults. Fat accumulation in obesity is implicated with elevated oxidative stress in adipocytes induced by reactive oxygen species (ROS). Adipogenesis regulation by inhibiting adipogenic differentiation and ROS production has been selected as the strategy to treat obesity. The conventional anti-obesity drugs allowed by the U.S. Food and Drug Administration have severe adverse effects. Therefore, various natural products have been developed as a solution for obesity, suppressing adipogenic differentiation. Fraxetin is a major component extracted from the stem barks of Fraxinus rhynchophylla, with various bioactivities, including anti-inflammatory, anticancer, antioxidant, and antibacterial functions. However, the effect of fraxetin on adipogenesis is still not clearly understood. We studied the pharmacological functions of fraxetin in suppressing lipid accumulation and its underlying molecular mechanisms involving 3T3-L1 preadipocytes. Moreover, increased ROS production induced by a mixture of insulin, dexamethasone, and 3-isobutylmethylxanthine (MDI) in 3T3-L1 was attenuated by fraxetin during adipogenesis. These effects were regulated by mitogen-activated protein kinase (MAPK) signaling pathways. Therefore, our findings imply that fraxetin possesses inhibitory roles in adipogenesis and can be a potential anti-obesity drug.

10.
J Struct Biol X ; 6: 100073, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36081577

RESUMO

NMR spectroscopy provides structural and functional information about biomolecules and their complexes. The complexity of these systems can make the NMR data difficult to interpret, particularly for newer users of NMR technology, who may have limited understanding of the tools available and how they are used. To alleviate this problem, we have created software based on standardized workflows for both solution and solid-state NMR spectroscopy of proteins. These tools assist with manual and automated peak picking and with chemical shift assignment and validation. They provide users with an optimized path through spectral analysis that can help them perform the necessary tasks more efficiently.

11.
Antioxidants (Basel) ; 11(9)2022 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-36139787

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is a notoriously aggressive type of cancer with a high metastasis rate. It is conventionally treated by surgical resection and neoadjuvant chemotherapy. However, continuous chemotherapy leads to relapse in most PDAC patients due to chemical resistance. Therefore, novel anticancer agents need to be identified and developed. The antitumor activities of laminarin extracted from brown algae against hepatocarcinoma, lung, and colon cancer have been established. However, its effects on pancreatic cancer have remained obscure. Our study identified the anticancer effects of laminarin on pancreatic cancer cells and tried to explain its intracellular mechanisms. We assessed the cell viability of PANC-1 and MIA PaCa-2 cells using MTT assay. Hanging drop method was used for the spheroid formation. Flow cytometry was conducted to evaluate the several intracellular alterations including apoptosis, ROS production, mitochondrial membrane potential (MMP), and calcium concentration induced by laminarin. An invasion test was performed to assess the inhibitory effect of laminarin on cell migration and the invasive genes were evaluated by RT-qPCR. Signaling pathway related with anticancer effects of laminarin was analyzed by western blot. We report that inhibiting laminarin increased the proliferation and viability of the representative pancreatic cancer cell lines, MIA PaCa-2 and PANC-1. Laminarin triggered apoptosis and mitochondrial impairment as evidenced by depolarized mitochondrial membranes, disrupted calcium, and suppressed cell migration caused by reactive oxygen species production and related intracellular signaling pathways. Moreover, laminarin showed synergistic effects when combined with 5-FU, a standard anticancer agent for PDAC. The present study is the first to report that laminarin exerts anticancer effect through ROS production in pancreatic cancer cells. Laminarin shows potential to serve as a new anticancer agent for treating PDAC.

12.
Membranes (Basel) ; 12(9)2022 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-36135853

RESUMO

The heightened dipolar interactions in solids render solid-state NMR (ssNMR) spectra more difficult to interpret than solution NMR spectra. On the other hand, ssNMR does not suffer from severe molecular weight limitations like solution NMR. In recent years, ssNMR has undergone rapid technological developments that have enabled structure-function studies of increasingly larger biomolecules, including membrane proteins. Current methodology includes stable isotope labeling schemes, non-uniform sampling with spectral reconstruction, faster magic angle spinning, and innovative pulse sequences that capture different types of interactions among spins. However, computational tools for the analysis of complex ssNMR data from membrane proteins and other challenging protein systems have lagged behind those for solution NMR. Before a structure can be determined, thousands of signals from individual types of multidimensional ssNMR spectra of samples, which may have differing isotopic composition, must be recognized, correlated, categorized, and eventually assigned to atoms in the chemical structure. To address these tedious steps, we have developed an automated algorithm for ssNMR spectra called "ssPINE". The ssPINE software accepts the sequence of the protein plus peak lists from a variety of ssNMR experiments as inputs and offers automated backbone and side-chain assignments. The alpha version of ssPINE, which we describe here, is freely available through a web submission form.

13.
Nature ; 610(7930): 54-60, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36171286

RESUMO

Integrated photonics has profoundly affected a wide range of technologies underpinning modern society1-4. The ability to fabricate a complete optical system on a chip offers unrivalled scalability, weight, cost and power efficiency5,6. Over the last decade, the progression from pure III-V materials platforms to silicon photonics has significantly broadened the scope of integrated photonics, by combining integrated lasers with the high-volume, advanced fabrication capabilities of the commercial electronics industry7,8. Yet, despite remarkable manufacturing advantages, reliance on silicon-based waveguides currently limits the spectral window available to photonic integrated circuits (PICs). Here, we present a new generation of integrated photonics by directly uniting III-V materials with silicon nitride waveguides on Si wafers. Using this technology, we present a fully integrated PIC at photon energies greater than the bandgap of silicon, demonstrating essential photonic building blocks, including lasers, amplifiers, photodetectors, modulators and passives, all operating at submicrometre wavelengths. Using this platform, we achieve unprecedented coherence and tunability in an integrated laser at short wavelength. Furthermore, by making use of this higher photon energy, we demonstrate superb high-temperature performance and kHz-level fundamental linewidths at elevated temperatures. Given the many potential applications at short wavelengths, the success of this integration strategy unlocks a broad range of new integrated photonics applications.

14.
Pharmaceutics ; 14(8)2022 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-36015303

RESUMO

Triple-negative breast cancer (TNBC) does not express estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Because TNBC lacks the expression of commonly targeted receptors, it is challenging to develop a new imaging agent for this cancer subtype. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-protein complexes that have been linked to tumor development and progression. Considering the high expression of hnRNPA2B1, an hnRNP subtype, in TNBC MDA-MB-231 cells, this study aimed to develop a novel hnRNPA2B1 antibody-based nuclear imaging agent. The hnRNPA2B1-specific antibody was radiolabeled with 64Cu and evaluated in vitro and in vivo. The trans-cyclooctene (TCO) was functionalized on the antibody to obtain hnRNP-PEG4-TCO and reactive tetrazine (Tz) on the ultrastable bifunctional chelator PCB-TE2A-alkyne to yield PCB-TE2A-Tz for the inverse electron demand Diels-Alder reaction. The 64Cu-radiolabeled antibody was administered and imaged at 1-18 h time points for conventional imaging. Alternatively, the unlabeled antibody conjugate was administered, and 48 h later radiolabeled 64Cu-PCB-TE2A-Tz was administered to the same mice for the pretargeting strategy and imaged at the same time intervals for direct comparison. The tumor was successfully visualized in both strategies, and comparatively, pretargeting showed superior results. The 64Cu-PCB-TE2A-Tz was successfully clicked at the tumor site with hnRNP-PEG4-TCO and the non-clicked were concurrently eliminated. This led to increase the tumor uptake with extremely high tumor-to-background ratio manifested by positron emission tomography (PET) imaging and biodistribution studies.

15.
Sci Rep ; 12(1): 13360, 2022 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-35922534

RESUMO

While boron neutron capture therapy (BNCT) depends primarily on the short flight range of the alpha particles emitted by the boron neutron capture reaction, gadolinium neutron capture therapy (GdNCT) mainly relies on gamma rays and Auger electrons released by the gadolinium neutron capture reaction. BNCT and GdNCT can be complementary in tumor therapy. Here, we studied the combined effects of BNCT and GdNCT when boron and gadolinium compounds were co-injected, followed by thermal neutron irradiation, and compared these effects with those of the single therapies. In cytotoxicity studies, some additive effects (32‒43%) were observed when CT26 cells were treated with both boron- and gadolinium-encapsulated PEGylated liposomes (B- and Gd-liposomes) compared to the single treatments. The tumor-suppressive effect was greater when BNCT was followed by GdNCT at an interval of 10 days rather than vice versa. However, tumor suppression with co-injection of B- and Gd-liposomes into tumor-bearing mice followed by neutron beam irradiation was comparable to that observed with Gd-liposome-only treatment but lower than B-liposome-only injection. No additive effect was observed with the combination of BNCT and GdNCT, which could be due to the shielding effect of gadolinium against thermal neutrons because of its overwhelmingly large thermal neutron cross section.


Assuntos
Neoplasias , Terapia por Captura de Nêutron , Animais , Boro , Compostos de Boro , Modelos Animais de Doenças , Gadolínio , Lipossomos , Camundongos
16.
Mar Drugs ; 20(8)2022 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-35892941

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive types of cancer and exhibits a devastating 5-year survival rate. The most recent procedure for the treatment of PDAC is a combination of several conventional chemotherapeutic agents, termed FOLFIRINOX, that includes irinotecan, leucovorin, oxaliplatin, and 5-fluorouracil (5-FU). However, ongoing treatment using these agents is challenging due to their severe side effects and limitations on the range of patients available for PDAC. Therefore, safer and more innovative anticancer agents must be developed. The anticarcinoma activity of matairesinol that can be extracted from seagrass has been reported in various types of cancer, including prostate, breast, cervical, and pancreatic cancer. However, the molecular mechanism of effective anticancer activity of matairesinol against pancreatic cancer remains unclear. In the present study, we confirmed the inhibition of cell proliferation and progression induced by matairesinol in representative human pancreatic cancer cell lines (MIA PaCa-2 and PANC-1). Additionally, matairesinol triggers apoptosis and causes mitochondrial impairment as evidenced by the depolarization of the mitochondrial membrane, disruption of calcium, and suppression of cell migration and related intracellular signaling pathways. Finally, matairesinol exerts a synergistic effect with 5-FU, a standard anticancer agent for PDAC. These results demonstrate the therapeutic potential of matairesinol in the treatment of PDAC.


Assuntos
Antineoplásicos , Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Antineoplásicos/uso terapêutico , Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Carcinoma Ductal Pancreático/tratamento farmacológico , Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/patologia , Linhagem Celular Tumoral , Fluoruracila/farmacologia , Furanos , Humanos , Lignanas , Masculino , Mitocôndrias , Neoplasias Pancreáticas/patologia , Neoplasias Pancreáticas
17.
Eur J Nucl Med Mol Imaging ; 49(12): 4073-4087, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35680737

RESUMO

PURPOSE: Hydrogen sulfide (H2S) plays important roles in brain pathophysiology. However, nuclear imaging probes for the in vivo detection of brain H2S in living animals have not been developed. Here, we report the first nuclear imaging probe that enables in vivo imaging of endogenous H2S in the brain of live mice. METHODS: Utilizing a bis(thiosemicarbazone) backbone, a fluorescent ATSM-FITC conjugate was synthesized. Its copper complex, Cu(ATSM-FITC) was thoroughly tested as a biosensor for H2S. The same ATSM-FITC ligand was quantitatively labeled with [64Cu]CuCl2 to obtain a radioactive [64Cu][Cu(ATSM-FITC)] imaging probe. Biodistribution and positron emission tomography (PET) imaging studies were performed in healthy mice and neuroinflammation models. RESULTS: The Cu(ATSM-FITC) complex reacts instantly with H2S to release CuS and becomes fluorescent. It showed excellent reactivity, sensitivity, and selectivity to H2S. Endogenous H2S levels in living cells were successfully detected by fluorescence microscopy. Exceptionally high brain uptake of [64Cu][Cu(ATSM-FITC)] (> 9% ID/g) was observed in biodistribution and PET imaging studies. Subtle changes in brain H2S concentrations in live mice were accurately detected by quantitative PET imaging. Due to its dual modality feature, increased H2S levels in neuroinflammation models were characterized at the subcellular level by fluorescence imaging and at the whole-body scale by PET imaging. CONCLUSION: Our biosensor can be readily utilized to study brain H2S function in live animal models and shows great potential as a novel imaging agent for diagnosing brain diseases.


Assuntos
Complexos de Coordenação , Sulfeto de Hidrogênio , Compostos Organometálicos , Tiossemicarbazonas , Animais , Encéfalo/diagnóstico por imagem , Cobre , Fluoresceína-5-Isotiocianato , Corantes Fluorescentes , Ligantes , Camundongos , Doenças Neuroinflamatórias , Distribuição Tecidual
18.
J Magn Reson ; 339: 107214, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35490563

RESUMO

Proteins are the building blocks of life. The shape of the protein determines its functionality. This understanding of the 3D structure of proteins has applications in study of diseases, medicine, body functions, and other aspects of life. Nuclear magnetic resonance (NMR) has been a powerful tool for researchers to get insight into the metabolome of cells, tissues, biofluids, secretions, and overall etiology of the disease state. Solid-state NMR (ssNMR) spectroscopy is used for samples that have low solubility in common NMR solvents. The use of ssNMR for 3D structure determination of proteins has been on the rise in the recent years especially for such samples. Still, one of the challenges that researchers face in this area is a shortage of easy and user-friendly computational aids. To address this, we are introducing our comprehensive software solution by automating every step of the process and essentially transforming the task into a few clicks of the mouse. The workflow for 3D structure determination has been simplified down to only a few procedures. Starting with selection of an ssNMR spectrum, user can receive its 3D structure along with an abundance of statistical information and validation tools using our software. We have tested this toolset to test the usefulness and user-friendliness with different data sets available on biological magnetic resonance bank (BMRB).


Assuntos
Proteínas , Software , Espectroscopia de Ressonância Magnética , Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas/química , Fluxo de Trabalho
19.
Int J Mol Sci ; 23(6)2022 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-35328522

RESUMO

Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two ß sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.


Assuntos
Proteínas Arqueais , Sulfolobus solfataricus , Proteínas Arqueais/metabolismo , Biofísica , DNA de Cadeia Simples/metabolismo , Proteínas de Ligação a DNA/metabolismo , Ressonância Magnética Nuclear Biomolecular , Ligação Proteica , Sulfolobus solfataricus/metabolismo
20.
Protein Sci ; 31(5): e4282, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35137487

RESUMO

The bacterial pathogen Vibrio cholerae use a type III secretion system to inject effector proteins into a host cell. Recently, a putative Toxic GTPase Activating Protein (ToxGAP) called Vibrio outer protein E (VopE) was identified as a T3SS substrate and virulence factor that affected host mitochondrial dynamics and immune response. However, biophysical and structural characterization has been absent. Here, we describe solution NMR structure of the putative GTPase-activating protein (GAP) domain (73-204) of VopE. Using size exclusion chromatography coupled with small-angle x-ray scattering and residual dipolar coupling data, we restrained the MD process to efficiently determine the overall fold and improve the quality of the output calculated structures. Comparing the structure of VopE with other ToxGAP's revealed a similar overall fold with several features unique to VopE. Specifically, the "Bulge 1," α1 helix, and noteworthy "backside linker" elements on the N-terminus are dissimilar to the other ToxGAP's. By using NMR relaxation dispersion experiments, we demonstrate that these regions undergo motions on a > 6 s-1 timescale. Based on the disposition of these mobile regions relative to the putative catalytic arginine residue, we hypothesize that the protein may undergo structural changes to bind cognate GTPases.


Assuntos
Proteínas Ativadoras de GTPase , Vibrio , Proteínas Ativadoras de GTPase/química , Espalhamento a Baixo Ângulo , Fatores de Virulência/metabolismo , Difração de Raios X
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