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1.
Pestic Biochem Physiol ; 194: 105463, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37532308

RESUMO

Plant glutathione S-transferase (GST, EC 2.5.1.18) is an enzyme that detoxifies various electrophilic compounds including herbicides and organic pollutants by catalyzing the formation of conjugates with reduced glutathione (GSH). Although the structure and function of the GST subunits in rice, an important food in Asia, are not well understood, they are crucial for herbicide development. To investigate the role of active site residues in rice Phi-class GSTF3 (OsGSTF3), evolutionarily conserved serine residues were replaced with alanine using site-directed mutagenesis to obtain the mutants S13A, S38A, S69A, and S169A. These four mutants were expressed in Escherichia coli and purified to electrophoretic homogeneity using immobilized GSH affinity chromatography. Mutation of Ser13 to Ala resulted in substantial reductions in specific activities and kcat/Km values for the GSH-[1-chloro-2,4-dinitrobenzene (CDNB)] conjugation reaction. In contrast, mutations of Ser38, Ser69, and Ser169 to Ala had little effect on the activities and kinetic parameters. Additionally, the mutation of Ser13 to Ala significantly affected the KmGSH and I50 values of S-hexylglutathione and S-(2,4-dinitrophenyl)glutathione, which compete with GSH and the product of GSH-CDNB conjugation, respectively. A pH-log (kcat/KmCDNB) plot was used to estimate the pKa value of GSH in the enzyme-GSH complex of the wild-type enzyme, which was approximately 6.9. However, the pKa value of GSH in the enzyme-GSH complex of the S13A mutant was approximately 8.7, which was about 1.8 pK units higher than that of the wild-type enzyme. OsGSTF3 was also crystallized for crystallographic study, and the structure analyses revealed that Ser13 is located in the active site and that its side chain is in close proximity to the thiol group of glutathione bound in the enzyme. Based on these substitution effects on kinetic parameters, the dependence of kinetic parameters on the pH and 3-dimensional structure, it was suggested that Ser13 in rice OsGSTF3 is the residue responsible for catalytic activity by lowering the pKa of GSH in the enzyme-GSH complex and enhancing the nucleophilicity of the GSH thiol in the active site.


Assuntos
Oryza , Domínio Catalítico , Oryza/genética , Oryza/metabolismo , Glutationa Transferase/genética , Glutationa Transferase/metabolismo , Serina , Compostos de Sulfidrila/metabolismo , Cinética , Glutationa/metabolismo , Sítios de Ligação
2.
Biochem Biophys Res Commun ; 583: 178-183, 2021 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-34741988

RESUMO

Constant remodeling is necessary for bacterial cell growth and bacterial morphogenesis; peptidoglycan (PG) is a crucial component in this process. Murein DD-endopeptidase (MepS), initially annotated as Spr from E. coli K12, is a NlpC/P60 family endopeptidase, which cleaves the meso-diaminopimelate (DAP)-D-Ala peptide bond of PG. The Cys68, His119, His131 triad form the active site residues. MepS has autolytic activity, which is strictly regulated by a periplasmic degradation system comprising the NlpI/Prc protease complex. MepS is essential for maintaining the cell viability, and therefore, it is a potential target for developing antibiotics. This study aimed to understand the structural basis of substrate recognition and degradation. We determined the high-resolution structures of MepS, after mutating Cys68 to serine (MepS-C68S) to improve stability. We further found that citrate and L-malate molecules bind to the active site of MepS-C68S; this is in line with the recurrent observation of organic acids binding to PG endopeptidases. The presence of conserved residues on the surface revealed the potential peptide binding sites of MepS. We modelled a cross-linked peptide model of meso-DAP-D-Ala-meso-DAP, bound to the active site groove of MepS-C68S. Two conserved tyrosine residues, Tyr56 and Tyr147 appeared to be essential for the recognition of peptides. Our structural discoveries could provide insights for the design of novel antibiotics targeting MepS.

3.
Sensors (Basel) ; 21(20)2021 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-34696115

RESUMO

This paper addresses ground target tracking (GTT) for airborne radar. Digital terrain elevation data (DTED) are widely used for GTT as prior information under the premise that ground targets are constrained on terrain. Existing works fuse DTED to a tracking filter in a way that adopts only the assumption that the position of the target is constrained on the terrain. However, by kinematics, it is natural that the velocity of the moving ground target is constrained as well. Furthermore, DTED provides neither continuous nor accurate measurement of terrain elevation. To overcome such limitations, we propose a novel soft terrain constraint and a constraint-aided particle filter. To resolve the difficulties in applying the DTED to the GTT, first, we reconstruct the ground-truth terrain elevation using a Gaussian process and treat DTED as a noisy observation of it. Then, terrain constraint is formulated as joint soft constraints of position and velocity. Finally, we derive a Soft Terrain Constrained Particle Filter (STC-PF) that propagates particles while approximately satisfying the terrain constraint in the prediction step. In the numerical simulations, STC-PF outperforms the Smoothly Constrained Kalman Filter (SCKF) in terms of tracking performance because SCKF can only incorporate hard constraints.

4.
Int J Mol Sci ; 22(7)2021 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-33805050

RESUMO

Fatty acid synthesis is essential for bacterial viability. Thus, fatty acid synthases (FASs) represent effective targets for antibiotics. Nevertheless, multidrug-resistant bacteria, including the human opportunistic bacteria, Acinetobacter baumannii, are emerging threats. Meanwhile, the FAS pathway of A. baumannii is relatively unexplored. Considering that acyl carrier protein (ACP) has an important role in the delivery of fatty acyl intermediates to other FAS enzymes, we elucidated the solution structure of A. baumannii ACP (AbACP) and, using NMR spectroscopy, investigated its interactions with ß-ketoacyl ACP synthase III (AbKAS III), which initiates fatty acid elongation. The results show that AbACP comprises four helices, while Ca2+ reduces the electrostatic repulsion between acid residues, and the unconserved F47 plays a key role in thermal stability. Moreover, AbACP exhibits flexibility near the hydrophobic cavity entrance from D59 to T65, as well as in the α1α2 loop region. Further, F29 and A69 participate in slow exchanges, which may be related to shuttling of the growing acyl chain. Additionally, electrostatic interactions occur between the α2 and α3-helix of ACP and AbKAS III, while the hydrophobic interactions through the ACP α2-helix are seemingly important. Our study provides insights for development of potent antibiotics capable of inhibiting A. baumannii FAS protein-protein interactions.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/química , Acinetobacter baumannii/enzimologia , Acinetobacter baumannii/metabolismo , Proteína de Transporte de Acila/química , Antibacterianos/química , Sítios de Ligação , Cálcio/química , Dicroísmo Circular , Resistência Microbiana a Medicamentos , Ácidos Graxos/química , Interações Hidrofóbicas e Hidrofílicas , Espectroscopia de Ressonância Magnética , Metais/química , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica , Mapeamento de Interação de Proteínas , Eletricidade Estática
5.
Int J Mol Sci ; 21(7)2020 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-32283632

RESUMO

Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, we investigated the structure and dynamics of Tm-ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm-ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm-ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm-ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans.


Assuntos
Proteína de Transporte de Acila/química , Adaptação Biológica , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Modelos Moleculares , Temperatura , Thermotoga maritima/fisiologia , Proteína de Transporte de Acila/genética , Proteína de Transporte de Acila/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Conformação Proteica , Estabilidade Proteica , Desdobramento de Proteína , Relação Estrutura-Atividade , Temperatura de Transição
6.
Mol Microbiol ; 108(5): 567-577, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29528170

RESUMO

Originally annotated as the initiator of fatty acid synthesis (FAS), ß-ketoacyl-acyl carrier protein synthase III (KAS III) is a unique component of the bacterial FAS system. Novel variants of KAS III have been identified that promote the de novo use of additional extracellular fatty acids by FAS. These KAS III variants prefer longer acyl-groups, notably octanoyl-CoA. Acinetobacter baumannii, a clinically important nosocomial pathogen, contains such a multifunctional KAS III (AbKAS III). To characterize the structural basis of its substrate specificity, we determined the crystal structures of AbKAS III in the presence of different substrates. The acyl-group binding cavity of AbKAS III and co-crystal structure of AbKAS III and octanoyl-CoA confirmed that the cavity can accommodate acyl groups with longer alkyl chains. Interestingly, Cys264 formed a disulfide bond with residual CoA used in the crystallization, which distorted helices at the putative interface with acyl-carrier proteins. The crystal structure of KAS III in the alternate conformation can also be utilized for designing novel antibiotics.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/química , Acinetobacter baumannii/enzimologia , Sequência de Aminoácidos , Ácidos Graxos/biossíntese , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/genética , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/metabolismo , Acinetobacter baumannii/genética , Acinetobacter baumannii/patogenicidade , Acil Coenzima A/química , Acil Coenzima A/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cisteína/química , Cisteína/metabolismo , Modelos Moleculares , Conformação Proteica , Especificidade por Substrato , Difração de Raios X
7.
Biochem Biophys Res Commun ; 509(1): 322-328, 2019 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-30587339

RESUMO

Propionibacterium acnes is an anaerobic gram-positive bacterium found in the niche of the sebaceous glands in the human skin, and is a causal pathogen of inflammatory skin diseases as well as periprosthetic joint infection. To gain effective control of P. acnes, a deeper understanding of the cellular metabolism mechanism involved in its ability to reside in this unique environment is needed. P. acnes exhibits typical cell membrane features of gram-positive bacteria, such as control of membrane fluidity by branched-chain fatty acids (BCFAs). Branching at the iso- or anteiso-position is achieved by incorporation of isobutyryl- or 2-methyl-butyryl-CoA via ß-ketoacyl acyl carrier protein synthase (KAS III) from fatty acid synthesis. Here, we determined the crystal structure of P. acnes KAS III (PaKAS III) at the resolution of 1.9 Šfor the first time. Conformation-sensitive urea polyacrylamide gel electrophoresis and tryptophan fluorescence quenching experiments confirmed that PaKAS III prefers isobutyryl-CoA as the acetyl-CoA, and the unique shape of the active site cavity complies with incorporation of branched-short chain CoAs. The determined structure clearly illustrates how BCFA synthesis is achieved in P. acnes. Moreover, the unique shape of the cavity required for the branched-chain primer can be invaluable in designing novel inhibitors of PaKAS III and developing new specifically targeted antibiotics.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/metabolismo , Proteínas de Bactérias/metabolismo , Ácidos Graxos/metabolismo , Propionibacterium acnes/metabolismo , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/química , Acil Coenzima A/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Vias Biossintéticas , Cristalografia por Raios X , Ácidos Graxos/química , Modelos Moleculares , Propionibacterium acnes/química , Propionibacterium acnes/enzimologia , Conformação Proteica , Alinhamento de Sequência
8.
Sensors (Basel) ; 19(20)2019 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-31635128

RESUMO

This paper proposes a binary linear programming formulation for multiple target assignment of a radar network and demonstrates its applicability to obtain optimal solutions using an off-the-shelf mixed-integer linear programming solver. The goal of radar resource scheduling in this paper is to assign the maximum number of targets by handing over targets between networked radar systems to overcome physical limitations such as the detection range and simultaneous tracking capability of each radar. To achieve this, time windows are generated considering the relation between each radar and target considering incoming target information. Numerical experiments using a local-scale simulation were performed to verify the functionality of the formulation and a sensitivity analysis was conducted to identify the trend of the results with respect to several parameters. Additional experiments performed for a large-scale (battlefield) scenario confirmed that the proposed formulation is valid and applicable for hundreds of targets and corresponding radar network systems composed of five distributed radars. The performance of the scheduling solutions using the proposed formulation was better than that of the general greedy algorithm as a heuristic approach in terms of objective value as well as the number of handovers.

9.
Biochem Biophys Res Commun ; 505(1): 208-214, 2018 10 20.
Artigo em Inglês | MEDLINE | ID: mdl-30243724

RESUMO

Bacterial fatty acid synthesis (FAS) has been extensively studied as a potential target of antimicrobials. In FAS, FabD mediates transacylation of the malonyl group from malonyl-CoA to acyl-carrier protein (ACP). The mounting threat of nosocomial infection by multidrug-resistant Acinetobacter baumannii warrants a deeper understanding of its essential cellular mechanisms, which could lead to effective control of this highly competent pathogen. The molecular mechanisms involved in A. baumannii FAS are poorly understood, and recent research has suggested that Pseudomonas aeruginosa, a closely related nosocomial pathogen of A. baumannii, utilizes FAS to produce virulence factors. In this study, we solved the crystal structure of A. baumannii FabD (AbFabD) to provide a platform for the development of new antibacterial agents. Analysis of the structure of AbFabD confirmed the presence of highly conserved active site residues among bacterial homologs. Binding constants between AbFabD variants and A. baumannii ACP (AbACP) revealed critical conserved residues Lys195 and Lys200 involved in AbACP binding. Computational docking of a potential inhibitor, trifluoperazine, revealed a unique inhibitor-binding pocket near the substrate-binding site. The structural study presented herein will be useful for the structure-based design of potent AbFabD inhibitors.


Assuntos
Acinetobacter baumannii/genética , Proteína de Transporte de Acila S-Maloniltransferase/genética , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana Múltipla/genética , Ácido Graxo Sintase Tipo II/genética , Acinetobacter baumannii/enzimologia , Proteína de Transporte de Acila S-Maloniltransferase/química , Proteína de Transporte de Acila S-Maloniltransferase/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação/genética , Cristalografia por Raios X , Ácido Graxo Sintase Tipo II/química , Ácido Graxo Sintase Tipo II/metabolismo , Modelos Moleculares , Mutação , Domínios Proteicos , Homologia de Sequência de Aminoácidos
10.
Nucleic Acids Res ; 44(19): 9483-9493, 2016 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-27596595

RESUMO

GTP and branched-chain amino acids (BCAAs) are metabolic sensors that are indispensable for the determination of the metabolic status of cells. However, their molecular sensing mechanism remains unclear. CodY is a unique global transcription regulator that recognizes GTP and BCAAs as specific signals and affects expression of more than 100 genes associated with metabolism. Herein, we report the first crystal structures of the full-length CodY complex with sensing molecules and describe their functional states. We observed two different oligomeric states of CodY: a dimeric complex of CodY from Staphylococcus aureus with the two metabolites GTP and isoleucine, and a tetrameric form (apo) of CodY from Bacillus cereus Notably, the tetrameric state shows in an auto-inhibitory manner by blocking the GTP-binding site, whereas the binding sites of GTP and isoleucine are clearly visible in the dimeric state. The GTP is located at a hinge site between the long helical region and the metabolite-binding site. Together, data from structural and electrophoretic mobility shift assay analyses improve understanding of how CodY senses GTP and operates as a DNA-binding protein and a pleiotropic transcription regulator.


Assuntos
Proteínas de Bactérias/química , Guanosina Trifosfato/química , Modelos Moleculares , Proteínas Repressoras/química , Fatores de Transcrição/química , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Sítios de Ligação , DNA/química , DNA/metabolismo , Guanosina Trifosfato/metabolismo , Conformação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas Repressoras/metabolismo , Relação Estrutura-Atividade , Fatores de Transcrição/metabolismo
11.
Luminescence ; 33(6): 1081-1086, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29927536

RESUMO

Europium ion (Eu2+ ) doped Sr2 SiO4 phosphors with greenish-yellow emission were synthesized using microwave-assisted sintering. The phase structure and photoluminescence (PL) properties of the obtained phosphor samples were investigated. The PL excitation spectra of the Sr2 SiO4 :Eu2+ phosphors exhibited a broad band in the range of 260 nm to 485 nm with a maximum at 361 nm attributed to the 5f-4d allowed transition of the Eu2+ ions. Under an excitation at 361 nm, the Sr2 SiO4 :Eu2+ phosphor exhibited a greenish-yellow emission peak at 541 nm with an International-Commission-on-Illumination (CIE) chromaticity of (0.3064, 0.4772). The results suggest that the microwave-assisted sintering method is promising for the synthesis of phosphors owing to the decreased sintering time without the use of additional reductive agents.


Assuntos
Európio/química , Luminescência , Substâncias Luminescentes/química , Micro-Ondas , Silicatos/química , Estrôncio/química , Tamanho da Partícula , Processos Fotoquímicos , Propriedades de Superfície
12.
Proteins ; 85(6): 1171-1177, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28205250

RESUMO

The dibenzothiophene (DBT) sulfone monooxygenase BdsA from Bacillus subtilis WU-S2B catalyzes the conversion of DBT sulfone to 2'-hydroxybiphenyl 2-sulfinate. We report the crystal structures of BdsA at a resolution of 2.80 Å. BdsA exists as a homotetramer with a dimer-of-dimers configuration in the crystal, and the interaction between E288 and R296 in BdsA is important for tetramer formation. A structural comparison with homologous proteins shows that the orientation and location of the α9-α12 helices in BdsA are closer to those of the closed form than those of the open form in the EDTA monooxygenase EmoA. Proteins 2017; 85:1171-1177. © 2017 Wiley Periodicals, Inc.


Assuntos
Bacillus subtilis/química , Proteínas de Bactérias/química , Compostos de Bifenilo/química , Oxigenases/química , Subunidades Proteicas/química , Tiofenos/química , Sequência de Aminoácidos , Arginina/química , Arginina/metabolismo , Bacillus subtilis/enzimologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Compostos de Bifenilo/metabolismo , Clonagem Molecular , Cristalografia por Raios X , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Ácido Glutâmico/química , Ácido Glutâmico/metabolismo , Modelos Moleculares , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/química , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/genética , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Oxigenases/genética , Oxigenases/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia Estrutural de Proteína , Especificidade por Substrato , Tiofenos/metabolismo
13.
Biochem Biophys Res Commun ; 484(4): 787-793, 2017 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-28161633

RESUMO

Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75-80 °C and in the pH range of 6.8-7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 °C. We also determined the crystal structure of TthCP at 2.6 Å resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a Cα RMSD value of 2.2 Å; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with Cα RMSD values of 0.84 and 0.53 Å, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction.


Assuntos
Carboxipeptidases/química , Modelos Químicos , Simulação de Dinâmica Molecular , Thermus thermophilus/enzimologia , Sítios de Ligação , Ativação Enzimática , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , Especificidade por Substrato , Trometamina
14.
Bioorg Med Chem ; 25(1): 372-380, 2017 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-27840136

RESUMO

To discover potent antibiotics against the Gram-negative bacteria, we performed a structure-activity relationship (SAR) study of YKsa-6, which was the most potent inhibitor of Staphylococcus aureus ß-ketoacyl acyl carrier protein III in our previous study. We identified and selected 11 candidates, and finally screened two active compounds, YKab-4 (4-[(3-chloro-4-methylphenyl)aminoiminomethyl]benzene-1,3-diol) and YKab-6 (4-[[3-(trifluoromethyl)phenyl]aminoiminomethyl]phenol) as inhibitors of Acinetobacter baumannii KAS III (abKAS III). They showed potent antimicrobial activities at 2 or 8 µg/mL, specifically against Acinetobacter baumannii and a strong binding affinity for abKAS III. From the homology modeling, we defined the three-dimensional (3D) structure of abKAS III for the first time and found that it had an extra loop region compared with common Gram-negative bacteria derived KAS IIIs. The docking study revealed that the hydroxyl groups of inhibitors formed extensive hydrogen bonds and the complicated hydrophobic and cation-stacking interactions are important to binding with abKAS III. We confirmed that the hydrophobicity of these compounds might be the essential factor for their antimicrobial activities against Gram-negative bacteria as well as their structural rigidity, a cooperative feature for retaining the hydrophobic interactions between abKAS III and its inhibitors. This study may provide an insight developing strategies for potent antibiotics against A. baumannii.


Assuntos
Acinetobacter baumannii/efeitos dos fármacos , Antibacterianos/farmacologia , Avaliação Pré-Clínica de Medicamentos , Hidrazonas/farmacologia , Fenóis/farmacologia , Resorcinóis/farmacologia , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/antagonistas & inibidores , Animais , Antibacterianos/química , Anti-Inflamatórios não Esteroides/química , Anti-Inflamatórios não Esteroides/farmacologia , Linhagem Celular Tumoral , Hidrazonas/química , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Camundongos , Simulação de Acoplamento Molecular , Nitritos/metabolismo , Fenóis/química , RNA Mensageiro/metabolismo , Resorcinóis/química , Relação Estrutura-Atividade
15.
BMC Oral Health ; 17(1): 110, 2017 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-28697771

RESUMO

BACKGROUND: Although many studies have compared the properties of ultrasonic scaling instruments, it remains controversial as to which is most suitable for implant scaling. This study evaluated the safety and efficiency of novel metallic ultrasonic scaler tips made by the powder injection molding (PIM) technique on titanium surfaces. METHODS: Mechanical instrumentation was carried out using four types of metal scaler tips consisting of copper (CU), bronze (BR), 316 L stainless steel (316 L), and conventional stainless steel (SS) tips. The instrumented surface alteration image of samples was viewed with scanning electron microscope (SEM) and surface profile of the each sample was investigated with confocal laser scanning microscopy (CLSM). Arithmetic mean roughness (Ra) and maximum height roughness (Rmax) of titanium samples were measured and dissipated power of the scaler tip was estimated for scaling efficiency. RESULTS: The average Ra values caused by the 316 L and SS tip were about two times higher than those of the CU and BR tips (p < 0.05). The Rmax value showed similar results. The efficiency of the SS tip was about 3 times higher than that of CU tip, the 316 L tip is about 2.7 times higher than that of CU tip, and the BR tip is about 1.2 times higher than that of CU tip. CONCLUSIONS: Novel metallic bronze alloy ultrasonic scaler tip minimally damages titanium surfaces, similar to copper alloy tip. Therefore, this bronze alloy scaler tip may be promising instrument for implant maintenance therapy.


Assuntos
Implantes Dentários , Planejamento de Prótese Dentária/métodos , Planejamento de Prótese Dentária/instrumentação , Humanos , Microscopia Confocal , Microscopia Eletrônica de Varredura , Propriedades de Superfície , Titânio , Ultrassom
16.
Arch Biochem Biophys ; 606: 143-50, 2016 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-27495739

RESUMO

RNase H fold protein PF2046 of Pyrococcus furiosus is a 3'-5' ssDNA exonuclease that cleaves after the second nucleotide from the 3' end of ssDNA and prefers poly-dT over poly-dA as a substrate. In our crystal structure of PF2046 complexed with an oligonucleotide of four thymidine nucleotides (dT4), PF2046 accommodates dT4 tightly in a groove and imposes steric hindrance on dT4 mainly by Phe220 such that dT4 assumes the A-form. As poly-dA prefer B-form due to the stereochemical restrictions, the A-form ssDNA binding by PF2046 should disfavor the processing of poly-dA. Phe220 variants display reduced activity toward poly-dA and the A-form appears to be a prerequisite for the processing by PF2046.


Assuntos
Proteínas de Bactérias/química , DNA de Cadeia Simples/química , Pyrococcus furiosus/enzimologia , Ribonuclease H/química , Domínio Catalítico , Cristalização , Cristalografia por Raios X , Reparo do DNA , Exonucleases/química , Concentração de Íons de Hidrogênio , Mutação , Conformação de Ácido Nucleico , Oligodesoxirribonucleotídeos , Especificidade por Substrato , Difração de Raios X
17.
Biochem Biophys Res Commun ; 465(4): 817-24, 2015 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-26315269

RESUMO

The SET domain of LegAS4, a type IV secretion system effector of Legionella pneumophila, is a eukaryotic protein motif involved in histone methylation and epigenetic modulation. The SET domain of LegAS4 is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. Moreover, LegAS4 contains an ankyrin repeat domain of unknown function at its C-terminal region. Here, we report the crystal structure of LegAS4 in complex with S-adenosyl-l-methionine (SAM). Our data indicate that the ankyrin repeats interact extensively with the SET domain, especially with the SAM-binding amino acids, through conserved residues. Conserved surface analysis marks Glu159, Glu203, and Glu206 on the SET domain serve as candidate residues involved in interaction with the positively charged histone tail. Conserved surface residues on the ankyrin repeat domain surround a small pocket, which is suspected to serve as a binding site for an unknown ligand.


Assuntos
Proteínas de Bactérias/química , Legionella pneumophila/química , Sistemas de Secreção Tipo IV/química , Sequência de Aminoácidos , Repetição de Anquirina , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Histonas/genética , Histonas/metabolismo , Legionella pneumophila/genética , Legionella pneumophila/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , Homologia Estrutural de Proteína , Sistemas de Secreção Tipo IV/genética , Sistemas de Secreção Tipo IV/metabolismo
18.
Mediators Inflamm ; 2015: 385127, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26604431

RESUMO

Porphyromonas gingivalis is considered with inducing pulpal inflammation and has lipopolysaccharide (LPS) as an inflammatory stimulator. GV1001 peptide has anticancer and anti-inflammation activity due to inhibiting activation of signaling molecules after penetration into the various types of cells. Therefore, this study examined inhibitory effect of GV1001 on dental pulp cells (hDPCs) stimulated by P. gingivalis LPS. The intracellular distribution of GV1001 was analyzed by confocal microscopy. Real-time RT-PCR was performed to determine the expression levels of TNF-α and IL-6 cytokines. The role of signaling by MAP kinases (ERK and p38) was explored using Western blot analysis. The effect of GV1001 peptide on hDPCs viability was measured by MTT assay. GV1001 was predominantly located in hDPC cytoplasm. The peptide inhibited P. gingivalis LPS-induced TNF-α and IL-6 production in hDPCs without significant cytotoxicity. Furthermore, GV1001 treatment markedly inhibited the phosphorylation of MAP kinases (ERK and p38) in LPS-stimulated hDPCs. GV1001 may prevent P. gingivalis LPS-induced inflammation of apical tissue. Also, these findings provide mechanistic insight into how GV1001 peptide causes anti-inflammatory actions in LPS-stimulated pulpitis without significantly affecting cell viability.


Assuntos
Anti-Inflamatórios/farmacologia , Citocinas/biossíntese , Polpa Dentária/imunologia , Lipopolissacarídeos/farmacologia , Fragmentos de Peptídeos/farmacologia , Porphyromonas gingivalis/patogenicidade , Telomerase/farmacologia , Adolescente , Adulto , Polpa Dentária/citologia , MAP Quinases Reguladas por Sinal Extracelular/antagonistas & inibidores , Humanos , Interleucina-6/biossíntese , Telomerase/metabolismo , Receptores Toll-Like/fisiologia , Fator de Necrose Tumoral alfa/biossíntese , Proteínas Quinases p38 Ativadas por Mitógeno/antagonistas & inibidores
19.
Am J Dent ; 28(5): 303-8, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26714349

RESUMO

PURPOSE: To evaluate the effects of lasers (Nd:YAG and Er:YAG) and of topical desensitizing agents on dentin tubule occlusion by measuring real-time dentin fluid flow (DFF). METHODS: 32 molars were prepared with V-shape cavity at the cervical area, acid-etched, water rinsed, blotted dry, and treated with (1) Nd:YAG laser; (2) Er:YAG laser; (3) SuperSeal, a desensitizing agent; (4) ClinproXT, a resin-modified glass-ionomer (RMGI) varnish (n = 8 each). A real-time fluid flow measuring instrument (nano-Flow) was used to measure the DFF throughout the procedures. The DFF rates before and after the treatment were compared. Moreover, the surface topography of dentin tubules after each desensitizing method was examined using SEM. RESULTS: DFF varied among the groups. The DFF rate was significantly reduced after laser irradiation/application of the desensitizing agents (P < 0.05). ClinproXT showed the greatest reduction of DFF rate (71.9%), followed by the SuperSeal (34.8%) and laser groups (P< 0.05). However, there was no significant difference between the Nd:YAG (24.1%) and Er:YAG (20.6%) groups (P > 0.05). In SEM images, narrowed dentin tubules were observed in both lased groups and SuperSeal group. In the ClinproXT group, the occluded dentin tubules by the RMGI covering were observed.


Assuntos
Dessensibilizantes Dentinários/uso terapêutico , Dentina/ultraestrutura , Líquido Dentinal/fisiologia , Lasers de Estado Sólido/uso terapêutico , Condicionamento Ácido do Dente/métodos , Preparo da Cavidade Dentária/classificação , Dentina/efeitos dos fármacos , Dentina/efeitos da radiação , Sensibilidade da Dentina/fisiopatologia , Líquido Dentinal/efeitos dos fármacos , Líquido Dentinal/efeitos da radiação , Cimentos de Ionômeros de Vidro/química , Humanos , Hidrodinâmica , Microscopia Eletrônica de Varredura , Ácido Oxálico/uso terapêutico , Distribuição Aleatória , Cimentos de Resina/química , Colo do Dente/ultraestrutura
20.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 7): 1944-53, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25004971

RESUMO

Despite recent progress in research on the Hippo signalling pathway, the structural information available in this area is extremely limited. Intriguingly, the homodimeric and heterodimeric interactions of mammalian sterile 20-like (MST) kinases through the so-called `SARAH' (SAV/RASSF/HPO) domains play a critical role in cellular homeostasis, dictating the fate of the cell regarding cell proliferation or apoptosis. To understand the mechanism of the heterodimerization of SARAH domains, the three-dimensional structures of an MST1-RASSF5 SARAH heterodimer and an MST2 SARAH homodimer were determined by X-ray crystallography and were analysed together with that previously determined for the MST1 SARAH homodimer. While the structure of the MST2 homodimer resembled that of the MST1 homodimer, the MST1-RASSF5 heterodimer showed distinct structural features. Firstly, the six N-terminal residues (Asp432-Lys437), which correspond to the short N-terminal 310-helix h1 kinked from the h2 helix in the MST1 homodimer, were disordered. Furthermore, the MST1 SARAH domain in the MST1-RASSF5 complex showed a longer helical structure (Ser438-Lys480) than that in the MST1 homodimer (Val441-Lys480). Moreover, extensive polar and nonpolar contacts in the MST1-RASSF5 SARAH domain were identified which strengthen the interactions in the heterodimer in comparison to the interactions in the homodimer. Denaturation experiments performed using urea also indicated that the MST-RASSF heterodimers are substantially more stable than the MST homodimers. These findings provide structural insights into the role of the MST1-RASSF5 SARAH domain in apoptosis signalling.


Assuntos
MAP Quinase Quinase Quinases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transdução de Sinais , Sequência de Aminoácidos , Cristalografia por Raios X , Dimerização , Via de Sinalização Hippo , Humanos , Dados de Sequência Molecular , Conformação Proteica , Homologia de Sequência de Aminoácidos
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