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1.
Nano Lett ; 22(16): 6537-6544, 2022 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-35900218

RESUMO

Applying an electric-field (E-field) during antibody immobilization aligns the orientation of the antibody on the biosensor surface, thereby enhancing the binding probability between the antibody and antigen and maximizing the sensitivity of the biosensor. In this study, a biosensor with enhanced antibody-antigen binding probability was developed using the alignment of polar antibodies (immunoglobulin G [IgG]) under an E-field applied inside the interdigitated electrodes. The optimal alignment condition was first theoretically calculated and then experimentally confirmed by comparing the impedance change before and after the alignment of IgG (a purified anti-ß-amyloid antibody). With the optimized condition, the impedance change of the biosensor was maximized because of the alignment of IgG orientation on the sensor surface; the detection sensitivity of the antigen amyloid-beta 1-42 was also maximized. The E-field-based in-sensor alignment of antibodies is an easy and effective method for enhancing biosensor sensitivity.


Assuntos
Técnicas Biossensoriais , Técnicas Biossensoriais/métodos , Impedância Elétrica , Eletricidade , Eletrodos , Imunoglobulina G
2.
Anal Chem ; 94(21): 7449-7454, 2022 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-35583342

RESUMO

Nanopore sensors are a highly attractive platform for single-molecule sensing for sequencing, disease diagnostics, and drug screening. Outer membrane protein G (OmpG) nanopores have advantages for single-molecule sensing owing to their rigid monomeric structure, which comprises seven flexible loops, providing distinct gating patterns upon analyte binding. Blocking of the protein-protein interaction between B-cell lymphoma-extra-large (Bcl-xL) and the BH3 domain of Bcl-2 homologous antagonist/killer (Bak-BH3) has been reported as a promising strategy for anticancer therapy. Here, we characterized the interaction between Bcl-xL and Bak-BH3 as well as its inhibition by a small-molecule inhibitor using click chemistry-based Bak-BH3 peptide-conjugated OmpG nanopores. The binding of Bcl-xL to Bak-BH3 generated characteristic gating signals involving significant changes in the amplitudes of noise and gating parameters such as gating frequency, open probability, and durations of open and closed states. Notably, specific inhibition of Bcl-xL by the small-molecule antagonist, ABT-737, led to the recovery of the noise and gating parameters. Collectively, these results revealed that the chemically modified OmpG nanopore can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions, which are therapeutic targets for various diseases.


Assuntos
Proteínas de Escherichia coli , Nanoporos , Apoptose , Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/metabolismo , Nanotecnologia , Porinas/química , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Proteína bcl-X/metabolismo
3.
Biochem Biophys Res Commun ; 588: 97-103, 2022 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-34953212

RESUMO

Apoptosis plays an essential role in maintaining cellular homeostasis and preventing cancer progression. Bcl-xL, an anti-apoptotic protein, is an important modulator of the mitochondrial apoptosis pathway and is a promising target for anticancer therapy. In this study, we identified octenidine as a novel Bcl-xL inhibitor through structural feature-based deep learning and molecular docking from a library of approved drugs. The NMR experiments demonstrated that octenidine binds to the Bcl-2 homology 3 (BH3) domain-binding hydrophobic region that consists of the BH1, BH2, and BH3 domains in Bcl-xL. A structural model of the Bcl-xL/octenidine complex revealed that octenidine binds to Bcl-xL in a similar manner to that of the well-known Bcl-2 family protein antagonist ABT-737. Using the NanoBiT protein-protein interaction system, we confirmed that the interaction between Bcl-xL and Bak-BH3 domains within cells was inhibited by octenidine. Furthermore, octenidine inhibited the proliferation of MCF-7 breast and H1299 lung cancer cells by promoting apoptosis. Taken together, our results shed light on a novel mechanism in which octenidine directly targets anti-apoptotic Bcl-xL to trigger mitochondrial apoptosis in cancer cells.


Assuntos
Inteligência Artificial , Iminas/farmacologia , Piridinas/farmacologia , Proteína bcl-X/antagonistas & inibidores , Antineoplásicos/química , Antineoplásicos/farmacologia , Apoptose/efeitos dos fármacos , Linhagem Celular , Proliferação de Células/efeitos dos fármacos , Humanos , Iminas/química , Simulação de Acoplamento Molecular , Neoplasias/patologia , Ligação Proteica/efeitos dos fármacos , Piridinas/química , Proteína Killer-Antagonista Homóloga a bcl-2/química , Proteína Killer-Antagonista Homóloga a bcl-2/metabolismo , Proteína bcl-X/química
4.
Proc Natl Acad Sci U S A ; 116(36): 17775-17785, 2019 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-31431530

RESUMO

Legionella pneumophila causes a potentially fatal form of pneumonia by replicating within macrophages in the Legionella-containing vacuole (LCV). Bacterial survival and proliferation within the LCV rely on hundreds of secreted effector proteins comprising high functional redundancy. The vacuolar membrane-localized MavN, hypothesized to support iron transport, is unique among effectors because loss-of-function mutations result in severe intracellular growth defects. We show here an iron starvation response by L. pneumophila after infection of macrophages that was prematurely induced in the absence of MavN, consistent with MavN granting access to limiting cellular iron stores. MavN cysteine accessibilities to a membrane-impermeant label were determined during macrophage infections, revealing a topological pattern supporting multipass membrane transporter models. Mutations to several highly conserved residues that can take part in metal recognition and transport resulted in defective intracellular growth. Purified MavN and mutant derivatives were directly tested for transporter activity after heterologous purification and liposome reconstitution. Proteoliposomes harboring MavN exhibited robust transport of Fe2+, with the severity of defect of most mutants closely mimicking the magnitude of defects during intracellular growth. Surprisingly, MavN was equivalently proficient at transporting Fe2+, Mn2+, Co2+, or Zn2+ Consequently, flooding infected cells with either Mn2+ or Zn2+ allowed collaboration with iron to enhance intracellular growth of L. pneumophila ΔmavN strains, indicating a clear role for MavN in transporting each of these ions. These findings reveal that MavN is a transition-metal-ion transporter that plays a critical role in response to iron limitation during Legionella infection.


Assuntos
Proteínas de Bactérias , Proteínas de Transporte de Cátions , Legionella pneumophila , Metais/metabolismo , Vacúolos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Transporte de Cátions/genética , Proteínas de Transporte de Cátions/metabolismo , Humanos , Legionella pneumophila/genética , Legionella pneumophila/metabolismo , Doença dos Legionários/genética , Doença dos Legionários/metabolismo , Doença dos Legionários/patologia , Macrófagos/metabolismo , Macrófagos/microbiologia , Macrófagos/patologia , Células U937 , Vacúolos/genética , Vacúolos/metabolismo
5.
Ecotoxicol Environ Saf ; 228: 112964, 2021 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-34773844

RESUMO

Polypropylene (PP) is the second most highly produced plastic worldwide, and its microplastic forms are found in water and food matrices. However, the effects of PP microplastics on human health remain largely unknown. Here, we prepared 85.2 µm-sized weathered PP (w-PP) microplastics by sieving the microplastic particles after fragmentation and accelerated weathering processes. The prepared particles are irregular in shape and no chemical additives including phthalates and bisphenol A were not released in simulated body fluids. Then, the w-PP samples were gavaged to rats for acute and subacute toxicity testing in accordance to the Organization for Economic Co-operation and Development (OECD) test guidelines under good laboratory practice regulations. The highest dose for gavaging to rats was 25 mg/kg bw/day, which was the maximum feasible dose based on the dispersibility of microplastics. Both toxicity testings for w-PP microplastics showed no adverse effects and mutagenicity. Thus, the no observed adverse effect level (NOAEL) of w-PP microplastics is higher than 25 mg/kg bw/day. Furthermore, the w-PP microplastics did not show any skin or eye irritation potentials in the 3-dimensional reconstructed human skin or corneal culture model. The dose of 25 mg/kg of w-PP microplastics is roughly equal to 2.82 × 105 particles/kg, which suggests that human exposure to w-PP microplastics in a real-life situation may not have any adverse effects.

6.
Anal Chem ; 92(21): 14303-14308, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33138377

RESUMO

Neuraminidase (NA), one of the major surface glycoproteins of influenza A virus (IAV), is an important diagnostic biomarker and antiviral therapeutic target. Cytolysin A (ClyA) is a nanopore sensor with an internal constriction of 3.3 nm, enabling the detection of protein conformations at the single-molecule level. In this study, a nanopore-based approach is developed for analysis of the enzymatic activity of NA, which facilitates rapid and highly sensitive diagnosis of IAV. Current blockade analysis of the d-glucose/d-galactose-binding protein (GBP) trapped within a type I ClyA-AS (ClyA mutant) nanopore reveals that galactose cleaved from sialyl-galactose by NA of the influenza virus can be detected in real time and at the single-molecule level. Our results show that this nanopore sensor can quantitatively measure the activity of NA with 40-80-fold higher sensitivity than those previously reported. Furthermore, the inhibition of NA is monitored using small-molecule antiviral drugs, such as zanamivir. Taken together, our results reveal that the ClyA protein nanopore can be a valuable platform for the rapid and sensitive point-of-care diagnosis of influenza and for drug screening against the NA target.


Assuntos
Citotoxinas/metabolismo , Ensaios Enzimáticos/métodos , Vírus da Influenza A/enzimologia , Nanoporos , Neuraminidase/metabolismo , Citotoxinas/química , Modelos Moleculares , Neuraminidase/química , Conformação Proteica
7.
Regul Toxicol Pharmacol ; 117: 104725, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32768665

RESUMO

We conducted a me-too validation study to confirm the reproducibility, reliability, and predictive capacity of KeraSkin™ skin irritation test (SIT) as a me-too method of OECD TG 439. With 20 reference chemicals, within-laboratory reproducibility (WLR) of KeraSkin™ SIT in the decision of irritant or non-irritant was 100%, 100%, and 95% while between-laboratory reproducibility (BLR) was 100%, which met the criteria of performance standard (PS, WLR≥90%, BLR≥80%). WLR and BLR were further confirmed with intra-class correlation (ICC, coefficients >0.950). WLR and BLR in raw data (viability) were also shown with a scatter plot and Bland-Altman plot. Comparison with existing VRMs with Bland-Altman plot, ICC and kappa statistics confirmed the compatibility of KeraSkin™ SIT with OECD TG 439. The predictive capacity of KeraSkin™ SIT was estimated with 20 reference chemicals (the sensitivity of 98.9%, the specificity of 70%, and the accuracy of 84.4%) and additional 46 chemicals (for 66 chemicals [20 + 46 chemicals, the sensitivity, specificity and accuracy: 95.2%, 82.2% and 86.4%]). The receiver operating characteristic (ROC) analysis suggested a potential improvement of the predictive capacity, especially sensitivity, when changing cut-off (50% → 60-75%). Collectively, the me-too validation study demonstrated that KeraSkin™ SIT can be a new me-too method for OECD TG 439.


Assuntos
Epiderme/efeitos dos fármacos , Fidelidade a Diretrizes/normas , Irritantes/toxicidade , Modelos Biológicos , Organização para a Cooperação e Desenvolvimento Econômico/normas , Testes de Irritação da Pele/normas , Epiderme/metabolismo , Epiderme/patologia , Humanos , Irritantes/metabolismo , Testes de Irritação da Pele/métodos
8.
Sensors (Basel) ; 20(11)2020 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-32517305

RESUMO

Since separation of target biomolecules is a crucial step for highly sensitive and selective detection of biomolecules, hence, various technologies have been applied to separate biomolecules, such as deoxyribonucleic acid (DNA), protein, exosome, virus, etc. Among the various technologies, dielectrophoresis (DEP) has the significant advantage that the force can provide two different types of forces, attractive and repulsive DEP force, through simple adjustment in frequency or structure of microfluidic chips. Therefore, in this review, we focused on separation technologies based on DEP force and classified various separation technologies. First, the importance of biomolecules, general separation methods and various forces including DEP, electrophoresis (EP), electrothermal flow (ETF), electroosmosis (EO), magnetophoresis, acoustophoresis (ACP), hydrodynamic, etc., was described. Then, separating technologies applying only a single DEP force and dual force, moreover, applying other forces simultaneously with DEP force were categorized. In addition, advanced technologies applying more than two different kinds of forces, namely complex force, were introduced. Overall, we critically reviewed the state-of-the-art of converged various forces for detection of biomolecules with novelty of DEP.


Assuntos
Técnicas Eletroquímicas , Técnicas Analíticas Microfluídicas , DNA/isolamento & purificação , Eletroforese , Osmose , Proteínas/isolamento & purificação , Vírus/isolamento & purificação
9.
Sensors (Basel) ; 19(19)2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31557904

RESUMO

The concentration effect of dielectrophoresis (DEP) enables detection of biomolecules with high sensitivity. In this study, microstructures were patterned between the interdigitated microelectrodes (IMEs) to increase the concentration effect of DEP. The microstructures increased the electric field gradient ( ∇ | E 2 | ) between the IMEs to approximately 6.61-fold higher than in the bare IMEs with a gap of 10 µm, resulting in a decreased optimal voltage to concentrate amyloid beta 42 (Aß42, from 0.8 Vpp to 0.5 Vpp) and tau-441 (from 0.9 Vpp to 0.6 Vpp) between the IMEs. Due to the concentration effect of DEP, the impedance change in the optimal condition was higher than the values in the reference condition at 2.64-fold in Aß42 detection and at 1.59-fold in tau-441 detection. This concentration effect of DEP was also verified by counting the number of gold (Au) particles which conjugated with the secondary antibody. Finally, an enhanced concentration effect in the patterned IMEs was verified by measuring the impedance change depending on the concentration of Aß42 and tau-441. Our results suggest that microstructures increase the concentration effect of DEP, leading to enhanced sensitivity of the IMEs.

10.
Biochem Biophys Res Commun ; 504(2): 519-524, 2018 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-30197003

RESUMO

GSK3ß is a key kinase that plays a role in cellular signaling pathways. In Alzheimer's disease (AD), GSK3ß has been implicated in hyperphosphorylation of tau proteins in the neuron, which is a hallmark of AD. Morin, a flavonoid that is abundant in nature, was found as an inhibitor of GSK3ß that can reduce tau pathology in vivo and in vitro. In this study, we determined the crystal structure of GSK3ß in complex with morin. The structure revealed that morin inhibits GSK3ß by binding to the ATP binding pocket. Our findings augment the potential of morin as a functional food to help prevent AD, as well as to provide structural information to develop new therapeutics based on the morin skeleton.


Assuntos
Flavonoides/química , Glicogênio Sintase Quinase 3 beta/química , Animais , Cristalografia por Raios X , Humanos , Camundongos , Conformação Molecular , Ligação Proteica , Ressonância de Plasmônio de Superfície
11.
Proc Natl Acad Sci U S A ; 112(20): 6443-8, 2015 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-25931525

RESUMO

OxyR, a bacterial peroxide sensor, is a LysR-type transcriptional regulator (LTTR) that regulates the transcription of defense genes in response to a low level of cellular H2O2. Consisting of an N-terminal DNA-binding domain (DBD) and a C-terminal regulatory domain (RD), OxyR senses H2O2 with conserved cysteine residues in the RD. However, the precise mechanism of OxyR is not yet known due to the absence of the full-length (FL) protein structure. Here we determined the crystal structures of the FL protein and RD of Pseudomonas aeruginosa OxyR and its C199D mutant proteins. The FL crystal structures revealed that OxyR has a tetrameric arrangement assembled via two distinct dimerization interfaces. The C199D mutant structures suggested that new interactions that are mediated by cysteine hydroxylation induce a large conformational change, facilitating intramolecular disulfide-bond formation. More importantly, a bound H2O2 molecule was found near the Cys199 site, suggesting the H2O2-driven oxidation mechanism of OxyR. Combined with the crystal structures, a modeling study suggested that a large movement of the DBD is triggered by structural changes in the regulatory domains upon oxidation. Taken together, these findings provide novel concepts for answering key questions regarding OxyR in the H2O2-sensing and oxidation-dependent regulation of antioxidant genes.


Assuntos
Regulação Bacteriana da Expressão Gênica/fisiologia , Peróxido de Hidrogênio/metabolismo , Modelos Moleculares , Transativadores/química , Transativadores/metabolismo , Sítios de Ligação/genética , Cristalização , Regulação Bacteriana da Expressão Gênica/genética , Estrutura Molecular , Mutagênese Sítio-Dirigida , Oxirredução , Reação em Cadeia da Polimerase , Ligação Proteica , Conformação Proteica , Difração de Raios X
12.
Sensors (Basel) ; 18(2)2018 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-29389878

RESUMO

Faradaic electrochemical impedance spectroscopy (f-EIS) in the presence of redox reagent, e.g., [Fe(CN)6]3-/4-, is widely used in biosensors owing to its high sensitivity. However, in sensors detecting amyloid beta (Aß), the redox reagent can cause the aggregation of Aß, which is a disturbance factor in accurate detection. Here, we propose an interdigitated microelectrode (IME) based f-EIS technique that can alleviate the aggregation of Aß and achieve high sensitivity by buffer control. The proposed method was verified by analyzing three different EIS-based sensors: non-faradaic EIS (nf-EIS), f-EIS, and the proposed f-EIS with buffer control. We analyzed the equivalent circuits of nf-EIS and f-EIS sensors. The dominant factors of sensitivity were analyzed, and the impedance change rates via Aß reaction was compared. We measured the sensitivity of the IME sensors based on nf-EIS, f-EIS, and the proposed f-EIS. The results demonstrate that the proposed EIS-based IME sensor can detect Aß with a sensitivity of 7.40-fold and 10.93-fold higher than the nf-EIS and the f-EIS sensors, respectively.

13.
Sensors (Basel) ; 18(6)2018 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-29843431

RESUMO

Determination of the conformation (monomer, oligomer, or fibril) of amyloid peptide aggregates in the human brain is essential for the diagnosis and treatment of Alzheimer's disease (AD). Accordingly, systematic investigation of amyloid conformation using analytical tools is essential for precisely quantifying the relative amounts of the three conformations of amyloid peptide. Here, we developed a reduced graphene oxide (rGO) based multiplexing biosensor that could be used to monitor the relative amounts of the three conformations of various amyloid-ß 40 (Aß40) fluids. The electrical rGO biosensor was composed of a multichannel sensor array capable of individual detection of monomers, oligomers, and fibrils in a single amyloid fluid sample. From the performance test of each sensor, we showed that this method had good analytical sensitivity (1 pg/mL) and a fairly wide dynamic range (1 pg/mL to 10 ng/mL) for each conformation of Aß40. To verify whether the rGO biosensor could be used to evaluate the relative amounts of the three conformations, various amyloid solutions (monomeric Aß40, aggregated Aß40, and disaggregated Aß40 solutions) were employed. Notably, different trends in the relative amounts of the three conformations were observed in each amyloid solution, indicating that this information could serve as an important parameter in the clinical setting. Accordingly, our analytical tool could precisely detect the relative amounts of the three conformations of Aß40 and may have potential applications as a diagnostic system for AD.


Assuntos
Doença de Alzheimer/diagnóstico , Peptídeos beta-Amiloides/química , Técnicas Biossensoriais , Fragmentos de Peptídeos/química , Doença de Alzheimer/patologia , Peptídeos beta-Amiloides/isolamento & purificação , Grafite/química , Humanos , Óxidos/química , Conformação Proteica
14.
Biochem Biophys Res Commun ; 494(3-4): 668-673, 2017 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-29061301

RESUMO

The MacAB-TolC tripartite efflux pump is involved in resistance to macrolide antibiotics and secretion of protein toxins in many Gram-negative bacteria. The pump spans the entire cell envelope and operates by expelling substances to extracellular space. X-ray crystal and electron microscopic structures have revealed the funnel-like MacA hexamer in the periplasmic space and the cylindrical TolC trimer. Nonetheless, the inner membrane transporter MacB still remains ambiguous in terms of its oligomeric state in the functional complex. In this study, we purified a stable binary complex using a fusion protein of MacA and MacB of Escherichia coli, and then supplemented MacA to meet the correct stoichiometry between the two proteins. The result demonstrated that MacB is a homodimer in the complex, which is consistent with results from the recent complex structure using cryo-electron microscopy single particle analysis. Structural comparison with the previously reported MacB periplasmic domain structure suggests a molecular mechanism for regulation of the activity of MacB via an interaction between the MacB periplasmic domain and MacA. Our results provide a better understanding of the tripartite pumps at the molecular level.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/ultraestrutura , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/ultraestrutura , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/ultraestrutura , Proteínas de Membrana Transportadoras/química , Proteínas de Membrana Transportadoras/ultraestrutura , Sítios de Ligação , Simulação por Computador , Modelos Químicos , Modelos Moleculares , Ligação Proteica , Conformação Proteica
15.
Sensors (Basel) ; 17(4)2017 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-28425964

RESUMO

A lead zirconate titanate (PZT;Pb(Zr0.52Ti0.48)O3) layer embedded infrared (IR) detector decorated with wavelength-selective plasmonic crystals has been investigated for high-performance non-dispersive infrared (NDIR) spectroscopy. A plasmonic IR detector with an enhanced IR absorption band has been designed based on numerical simulations, fabricated by conventional microfabrication techniques, and characterized with a broadly tunable quantum cascade laser. The enhanced responsivity of the plasmonic IR detector at specific wavelength band has improved the performance of NDIR spectroscopy and pushed the limit of detection (LOD) by an order of magnitude. In this paper, a 13-fold enhancement in the LOD of a methane gas sensing using NDIR spectroscopy is demonstrated with the plasmonic IR detector.

16.
Sensors (Basel) ; 17(8)2017 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-28783132

RESUMO

A microsized slit-embedded cantilever sensor (slit cantilever) was fabricated and evaluated as a biosensing platform in a liquid environment. In order to minimize the degradation caused by viscous damping, a 300 × 100 µm² (length × width) sized cantilever was released by a 5 µm gap-surrounding and vibrated by an internal piezoelectric-driven self-actuator. Owing to the structure, when the single side of the slit cantilever was exposed to liquid a significant quality factor (Q = 35) could be achieved. To assess the sensing performance, the slit cantilever was exploited to study the biophysical kinetics related to Aß peptide. First, the quantification of Aß peptide with a concentration of 10 pg/mL to 1 µg/mL was performed. The resonant responses exhibited a dynamic range from 100 pg/mL to 100 ng/mL (-56.5 to -774 ΔHz) and a dissociation constant (KD) of binding affinity was calculated as 1.75 nM. Finally, the Aß self-aggregation associated with AD pathogenesis was monitored by adding monomeric Aß peptides. As the concentration of added analyte increased from 100 ng/mL to 10 µg/mL, both the frequency shift values (-813 to -1804 ΔHz) and associate time constant increased. These results showed the excellent sensing performance of the slit cantilever overcoming a major drawback in liquid environments to become a promising diagnostic tool candidate.


Assuntos
Doença de Alzheimer , Técnicas Biossensoriais , Cinética
17.
BMC Struct Biol ; 16: 3, 2016 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-26865045

RESUMO

BACKGROUND: The universal stress proteins (USP) family member UspE is a tandem-type USP that consists of two Usp domains. The UspE expression levels of the Escherichia coli (E. coli) become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. It has been shown that UspA family members are survival factors during cellular growth arrest. The structures and functions of the UspA family members control the growth of E. coli in animal hosts. While several UspA family members have known structures, the structure of E. coli UspE remains to be elucidated. RESULTS: To understand the biochemical function of UspE, we have determined the crystal structure of E. coli UspE at 3.2 Å resolution. The asymmetric unit contains two protomers related by a non-crystallographic symmetry, and each protomer contains two tandem Usp domains. The crystal structure shows that UspE is folded into a fan-shaped structure similar to that of the tandem-type Usp protein PMI1202 from Proteus mirabilis, and it has a hydrophobic cavity that binds its ligand. Structural analysis revealed that E. coli UspE has two metal ion binding sites, and isothermal titration calorimetry suggested the presence of two Cd(2+) binding sites with a Kd value of 38.3-242.7 µM. Structural analysis suggested that E. coli UspE has two Cd(2+) binding sites (Site I: His117, His 119; Site II: His193, His244). CONCLUSION: The results show that the UspE structure has a hydrophobic pocket. This pocket is strongly bound to an unidentified ligand. Combined with a previous study, the ligand is probably related to an intermediate in lipid A biosynthesis. Subsequently, sequence analysis found that UspE has an ATP binding motif (Gly(269)- X2-Gly(272)-X9-Gly(282)-Asn) in its C-terminal domain, which was confirmed by in vitro ATPase activity monitored using Kinase-Glo® Luminescent Kinase Assay. However, the residues constituting this motif were disordered in the crystal structure, reflecting their intrinsic flexibility. ITC experiments revealed that the UspE probably has two Cd(2+) binding sites. The His117, His 119, His193, and His244 residues within the ß-barrel domain are necessary for Cd(2+) binding to UspE protein. As mentioned above, USPs are associated with several functions, such as cadmium binding, ATPase function, and involvement in lipid A biosynthesis by some unknown way.


Assuntos
Proteínas de Escherichia coli/química , Escherichia coli/química , Proteínas de Choque Térmico/química , Cádmio/química , Cristalografia por Raios X , Escherichia coli/fisiologia , Proteínas de Escherichia coli/fisiologia , Proteínas de Choque Térmico/fisiologia , Ligantes , Conformação Proteica
18.
Biochem Biophys Res Commun ; 464(3): 869-74, 2015 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-26187666

RESUMO

CbsA from the thermophilic marine bacteria Thermotoga neapolitana is a chitinolyitc enzyme that can cleave a glycosidic bond of the polymer N-acetylglucosamine at the non-reducing end. This enzyme has particularly high activity on di-N-acetylchitobiose. CbsA consists of a family of 3 glycoside hydrolase (GH3)-type catalytic domains and a unique C-terminal domain. The C-terminal domain distinguishes CbsA from other GH3-type enzymes. Sequence analyses have suggested that CbsA has the Asp-His dyad as a general acid/base with the NagZ of Bacillus subtilis and the Salmonella enterica serovar Typhimurium. Here, we determined the crystal structure of CbsA from T. neapolitana at a resolution of 2.0 Å using the Zn-SAD method, revealing a unique homodimeric assembly facilitated by the C-terminal domains in the dimer. We observed that CbsA is strongly inhibited by ZnCl2, and two zinc ions were consistently bound in the active site. Our results can explain the zinc ion's inhibition mechanism in the subfamily of GH3 enzymes, and provide information on the structural diversity and substrate specificity of this hydrolase family.


Assuntos
Acetilglucosaminidase/química , Acetilglucosaminidase/metabolismo , Thermotoga neapolitana/enzimologia , Bacillus subtilis/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Domínio Catalítico , Cristalografia por Raios X , Modelos Moleculares , Conformação Proteica , Multimerização Proteica , Salmonella typhimurium/enzimologia , Especificidade por Substrato , Zinco/metabolismo
19.
Appl Environ Microbiol ; 81(15): 5266-77, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-26025888

RESUMO

The bacterial 2-nitroreductase NbaA is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-NBA), and its activity is controlled by posttranslational modifications. To date, the structure of NbaA remains to be elucidated. In this study, the crystal structure of a Cys194Ala NbaA mutant was determined to a 1.7-Å resolution. The substrate analog 2-NBA methyl ester was used to decipher the substrate binding site by inhibition of the wild-type NbaA protein. Tandem mass spectrometry showed that 2-NBA methyl ester produced a 2-NBA ester bond at the Tyr193 residue in the wild-type NbaA but not residues in the Tyr193Phe mutant. Moreover, covalent binding of the 2-NBA methyl ester to Tyr193 reduced the reactivity of the Cys194 residue on the peptide link. The Tyr193 hydroxyl group was shown to be essential for enzyme catalysis, as a Tyr193Phe mutant resulted in fast dissociation of flavin mononucleotide (FMN) from the protein with the reduced reactivity of Cys194. FMN binding to NbaA varied with solution NaCl concentration, which was related to the catalytic activity but not to cysteine reactivity. These observations suggest that the Cys194 reactivity is negatively affected by a posttranslational modification of the adjacent Tyr193 residue, which interacts with FMN and the substrate in the NbaA catalytic site.


Assuntos
Nitrobenzoatos/química , Nitrobenzoatos/metabolismo , Nitrorredutases/química , Nitrorredutases/metabolismo , Pseudomonas fluorescens/enzimologia , Sítios de Ligação , Cristalografia por Raios X , Modelos Moleculares , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Mutação de Sentido Incorreto , Ligação Proteica , Conformação Proteica , Processamento de Proteína Pós-Traducional , Cloreto de Sódio/metabolismo , Espectrometria de Massas em Tandem
20.
Sensors (Basel) ; 15(8): 18167-77, 2015 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-26213944

RESUMO

Preventing unexpected explosive attacks and tracing explosion-related molecules require the development of highly sensitive gas-vapor detection systems. For that purpose, a micromechanical cantilever-based olfactory sensing system including a sample preconcentrator was developed to detect 2,4-dinitrotoluene (2,4-DNT), which is a well-known by-product of the explosive molecule trinitrotoluene (TNT) and exists in concentrations on the order of parts per billion in the atmosphere at room temperature. A peptide receptor (His-Pro-Asn-Phe-Ser-Lys-Tyr-Ile-Leu-His-Gln-Arg) that has high binding affinity for 2,4-DNT was immobilized on the surface of the cantilever sensors to detect 2,4-DNT vapor for highly selective detection. A micro-preconcentrator (µPC) was developed using Tenax-TA adsorbent to produce higher concentrations of 2,4-DNT molecules. The preconcentration was achieved via adsorption and thermal desorption phenomena occurring between target molecules and the adsorbent. The µPC directly integrated with a cantilever sensor and enhanced the sensitivity of the cantilever sensor as a pretreatment tool for the target vapor. The response was rapidly saturated within 5 min and sustained for more than 10 min when the concentrated vapor was introduced. By calculating preconcentration factor values, we verified that the cantilever sensor provides up to an eightfold improvement in sensing performance.


Assuntos
Técnicas Biossensoriais/instrumentação , Dinitrobenzenos/análise , Gases/análise , Fenômenos Mecânicos , Microtecnologia/instrumentação , Olfato , Modelos Teóricos , Peptídeos/análise , Processamento de Sinais Assistido por Computador , Volatilização
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