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1.
J Biol Chem ; 299(1): 102763, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36463961

RESUMO

PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.


Assuntos
Pigmentos Biliares , Oxirredutases , Pigmentos Biliares/biossíntese , Pigmentos Biliares/química , Biliverdina/química , Catálise , Cristalografia , Oxirredutases/genética , Oxirredutases/química , Mutação
2.
Proc Natl Acad Sci U S A ; 118(20)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-33972439

RESUMO

Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a "bucket" consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen bonded in the ß-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the "leaky bucket" structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.


Assuntos
Proteínas de Bactérias/química , Pigmentos Biliares/química , Complexos de Proteínas Captadores de Luz/química , Fotorreceptores Microbianos/química , Fitocromo/química , Prótons , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Pigmentos Biliares/genética , Pigmentos Biliares/metabolismo , Sítios de Ligação , Clonagem Molecular , Cristalografia por Raios X , Cianobactérias/química , Cianobactérias/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Luz , Complexos de Proteínas Captadores de Luz/genética , Complexos de Proteínas Captadores de Luz/metabolismo , Simulação de Dinâmica Molecular , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/metabolismo , Fitocromo/genética , Fitocromo/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Pirróis/química , Pirróis/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
3.
Lasers Med Sci ; 38(1): 158, 2023 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-37421518

RESUMO

Nd:YAG laser is in common clinical use for the treatment of tissue incision, transpiration, and haemostasis in soft tissues. However, few studies have reported the effects of low-level laser therapy (LLLT) from Nd:YAG laser on bone healing. The aim of this study was to perform three-dimensional (3D) morphological evaluation of the photobiomodulation of Nd:YAG laser in bone defects in rat tibiae using micro-computed tomography CT (micro-CT) imaging. A bone defect was created in each tibia of 30 rats. The right side was treated with LLLT from Nd:YAG laser (LT group) daily until sacrifice and the left tibiae served as controls (control group). All tibiae underwent micro-CT imaging at 7, 14, and 21 days after the operation. Three-dimensional image analysis of bone volume (BV) and bone surface area (BS) of new bone formation in the defects was performed and histologic analysis was conducted for all tibiae. Tibial BV and BS values were highest in both groups at 7 days after the operation and decreased at 14 days after operation. BV and BS values were both significantly higher in the LT group than in the control group at 7 and 14 days. There was no significant difference between the groups for either metric at 21 days. The present findings demonstrate that Nd:YAG laser simulates bone formation during the early healing period.


Assuntos
Lasers de Estado Sólido , Osteogênese , Ratos , Animais , Lasers de Estado Sólido/uso terapêutico , Microtomografia por Raio-X , Tíbia/diagnóstico por imagem , Tíbia/cirurgia , Tíbia/patologia , Imageamento Tridimensional
4.
Mol Microbiol ; 115(4): 807-818, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33202070

RESUMO

IscU is a central component of the ISC machinery and serves as a scaffold for de novo assembly of Fe-S clusters. The dedicated chaperone system composed of the Hsp70-chaperone HscA and the J-protein cochaperone HscB synergistically interacts with IscU and facilitates cluster transfer from IscU to recipient apo-proteins. Here, we report that the otherwise essential roles of HscA and HscB can be bypassed in vivo by a number of single amino acid substitutions in IscU. CD spectroscopic studies of the variant IscU proteins capable of this bypass activity revealed dynamic interconversion between two conformations: the denatured (D) and the structured (S) state in the absence and presence of Zn2+ , respectively, which was far more prominent than interconversion observed in wild-type IscU. Furthermore, we found that neither the S-shifted (more structured) variants of IscU nor the perpetually denatured variants could perform their in vivo role regardless of whether the chaperone system was present or not. The present study thus provides for the first time evidence that an in vivo D-state of IscU exists and implies that conformational interconversion between the S- and D-states of the scaffolding protein is a fundamental requirement for the assembly and transfer of the Fe-S cluster.


Assuntos
Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Escherichia coli/fisiologia , Proteínas de Choque Térmico HSP70/metabolismo , Proteínas de Choque Térmico/metabolismo , Proteínas Ferro-Enxofre/metabolismo , Substituição de Aminoácidos , Escherichia coli/química , Proteínas de Escherichia coli/química , Proteínas de Choque Térmico HSP70/genética , Proteínas de Choque Térmico/genética , Proteínas Ferro-Enxofre/química , Proteínas Ferro-Enxofre/genética , Modelos Moleculares , Mutação , Fenótipo , Conformação Proteica , Desnaturação Proteica , Domínios e Motivos de Interação entre Proteínas , Zinco/química , Zinco/metabolismo
5.
Biochem J ; 478(5): 1023-1042, 2021 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-33600566

RESUMO

Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Šresolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.


Assuntos
Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Porfobilinogênio/metabolismo , Uroporfirinogênios/metabolismo , Catálise , Domínio Catalítico , Cristalografia por Raios X , Humanos , Simulação de Dinâmica Molecular , Conformação Proteica , Domínios Proteicos , Especificidade por Substrato
6.
J Biol Chem ; 295(3): 771-782, 2020 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-31822504

RESUMO

Phytochromobilin (PΦB) is a red/far-red light sensory pigment in plant phytochrome. PΦB synthase is a ferredoxin-dependent bilin reductase (FDBR) that catalyzes the site-specific reduction of bilins, which are sensory and photosynthesis pigments, and produces PΦB from biliverdin, a heme-derived linear tetrapyrrole pigment. Here, we determined the crystal structure of tomato PΦB synthase in complex with biliverdin at 1.95 Å resolution. The overall structure of tomato PΦB synthase was similar to those of other FDBRs, except for the addition of a long C-terminal loop and short helices. The structure further revealed that the C-terminal loop is part of the biliverdin-binding pocket and that two basic residues in the C-terminal loop form salt bridges with the propionate groups of biliverdin. This suggested that the C-terminal loop is involved in the interaction with ferredoxin and biliverdin. The configuration of biliverdin bound to tomato PΦB synthase differed from that of biliverdin bound to other FDBRs, and its orientation in PΦB synthase was inverted relative to its orientation in the other FDBRs. Structural and enzymatic analyses disclosed that two aspartic acid residues, Asp-123 and Asp-263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. On the basis of these observations and enzymatic assays with a V121A PΦB synthase variant, we propose the following mechanistic product release mechanism: PΦB synthase-catalyzed stereospecific reduction produces 2(R)-PΦB, which when bound to PΦB synthase collides with the side chain of Val-121, releasing 2(R)-PΦB from the synthase.


Assuntos
Biliverdina/química , Oxirredutases/química , Fitocromo/biossíntese , Conformação Proteica , Aminoácidos/química , Aminoácidos/genética , Pigmentos Biliares/biossíntese , Pigmentos Biliares/química , Biliverdina/genética , Catálise , Cristalografia por Raios X , Ligação de Hidrogênio , Solanum lycopersicum/enzimologia , Oxirredutases/genética , Oxirredutases/ultraestrutura , Fotossíntese/genética , Fitocromo/química , Fitocromo/genética , Estrutura Secundária de Proteína
7.
Mol Microbiol ; 112(6): 1769-1783, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31532036

RESUMO

IscU is a central component of the ISC machinery and serves as a scaffold for the de novo assembly of iron-sulfur (Fe-S) clusters prior to their delivery to target apo-Fe-S proteins. However, the molecular mechanism is not yet fully understood. In this study, we have conducted mutational analysis of E. coli IscU using the recently developed genetic complementation system of a mutant that can survive without Fe-S clusters. The Fe-S cluster ligands (C37, C63, H105, C106) and the proximal D39 and K103 residues are essential for in vivo function of IscU and could not be substituted with any other amino acids. Furthermore, we found that substitution of Y3, a strictly conserved residue among IscU homologs, abolished in vivo functions. Surprisingly, a second-site suppressor mutation in IscS (A349V) reverted the defect caused by IscU Y3 substitutions. Biochemical analysis revealed that IscU Y3 was crucial for functional interaction with IscS and sulfur transfer between the two proteins. Our findings suggest that the critical role of IscU Y3 is linked to the conformational dynamics of the flexible loop of IscS, which is required for the ingenious sulfur transfer to IscU.


Assuntos
Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/metabolismo , Aminoácidos/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/ultraestrutura , Ferro/metabolismo , Proteínas Ferro-Enxofre/ultraestrutura , Ligantes , Mutação/genética , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , Enxofre/metabolismo
8.
Biosci Biotechnol Biochem ; 84(3): 481-490, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31690227

RESUMO

ChlR is a MarR-type transcriptional regulator that activates the transcription of the chlAII-ho2-hemN operon in response to low oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803. Upon exposure to low oxygen conditions, ChlR activates transcription of the operon that encodes enzymes critical to tetrapyrrole biosynthesis under low oxygen conditions. We previously identified a super-activator variant, D35H, of ChlR that constitutively activates transcription of the operon. To gain insight into the low-oxygen induced activation of ChlR, we obtained eight additional super-activator variants of ChlR including D35H from pseudorevertants of a chlAI-disrupted mutant. Most substitutions were located in the N-terminal region of ChlR. Mapping of the substituted amino acid residues provided valuable structural insights that uncovered the activation mechanism of ChlR.


Assuntos
Proteínas de Bactérias/metabolismo , Cianobactérias/metabolismo , Oxigênio/metabolismo , Tetrapirróis/biossíntese , Fatores de Transcrição/metabolismo , Aerobiose , Proteínas de Bactérias/química , Cianobactérias/crescimento & desenvolvimento , Fatores de Transcrição/química
9.
J Am Chem Soc ; 139(22): 7533-7539, 2017 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-28510424

RESUMO

Telomeric repeat-containing RNA is a new noncoding RNA molecule that performs various biofunctions. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an RNA-binding protein involved in the telomere maintenance machinery. To date, little is known about how hnRNPA1 binds to telomeric RNA. In this study, we investigated the binding affinity and recognition mechanism of telomere RNA with the RNA recognition motif of hnRNPA1. Using the photochemical cross-linking method, we showed that the telomere RNA G-quadruplex with loops is important in the interaction of telomere RNA with hnRNPA1. Using small-molecule probes, we directly visualized the complex formed by the telomere RNA G-quadruplex and hnRNPA1 in vitro and in live cells. The results suggested that the structure-dependent binding of hnRNPA1 to telomere RNA regulates the telomere function. Therefore, our study provides new insights into the interactions between the RNA G-quadruplex and proteins at the telomere.


Assuntos
Quadruplex G , RNA/química , Telomerase/química , Reagentes de Ligações Cruzadas/química , Imunofluorescência , Células HeLa , Humanos , Espectroscopia de Ressonância Magnética , Microscopia de Fluorescência , Modelos Biológicos , Estrutura Molecular , Fotoquímica , Ligação Proteica , Bibliotecas de Moléculas Pequenas/química , Relação Estrutura-Atividade , Especificidade por Substrato
10.
Bioorg Med Chem Lett ; 27(21): 4920-4924, 2017 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-28985998

RESUMO

2-Amino-4-{[3-(carboxymethyl)phenoxy](methoxy)phosphoryl}butanoic acid (GGsTop) is a potent, highly selective, nontoxic, and irreversible inhibitor of γ-glutamyl transpeptidase (GGT). GGsTop has been widely used in academic and medicinal research, and also as an active ingredient (Nahlsgen) in commercial anti-aging cosmetics. GGsTop consists of four stereoisomers due to the presence of two stereogenic centers, i.e., the α-carbon atom of the glutamate mimic (l/d) and the phosphorus atom (RP/SP). In this study, each stereoisomer of GGsTop was synthesized stereoselectively and their inhibitory activity against human GGT was evaluated. The l- and d-configurations of each stereoisomer were determined by a combination of a chiral pool synthesis and chiral HPLC analysis. The synthesis of the four stereoisomers of GGsTop used chiral synthetic precursors that were separated by chiral HPLC on a preparative scale. With respect to the configuration of the α-carbon atom of the glutamate mimic, the l-isomer (kon=174M-1s-1) was ca. 8-fold more potent than the d-isomer (kon=21.5M-1s-1). In contrast, the configuration of the phosphorus atom is critical for GGT inhibitory activity. Based on a molecular modeling approach, the absolute configuration of the phosphorus atom of the active GGsTop isomers was postulated to be SP. The SP-isomers inhibited human GGT (kon=21.5-174M-1s-1), while the RP-isomers were inactive even at concentrations of 0.1mM.


Assuntos
Aminobutiratos/síntese química , Inibidores Enzimáticos/síntese química , Organofosfonatos/síntese química , gama-Glutamiltransferase/antagonistas & inibidores , Aminobutiratos/metabolismo , Sítios de Ligação , Inibidores Enzimáticos/metabolismo , Humanos , Cinética , Simulação de Acoplamento Molecular , Organofosfonatos/metabolismo , Ligação Proteica , Estereoisomerismo , gama-Glutamiltransferase/metabolismo
11.
Proc Natl Acad Sci U S A ; 111(7): 2524-9, 2014 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-24550278

RESUMO

NADPH-cytochrome P450 oxidoreductase (CPR) supplies electrons to various heme proteins including heme oxygenase (HO), which is a key enzyme for heme degradation. Electrons from NADPH flow first to flavin adenine dinucleotide, then to flavin mononucleotide (FMN), and finally to heme in the redox partner. For electron transfer from CPR to its redox partner, the ''closed-open transition'' of CPR is indispensable. Here, we demonstrate that a hinge-shortened CPR variant, which favors an open conformation, makes a stable complex with heme-HO-1 and can support the HO reaction, although its efficiency is extremely limited. Furthermore, we determined the crystal structure of the CPR variant in complex with heme-HO-1 at 4.3-Å resolution. The crystal structure of a complex of CPR and its redox partner was previously unidentified. The distance between heme and FMN in this complex (6 Å) implies direct electron transfer from FMN to heme.


Assuntos
Heme Oxigenase (Desciclizante)/metabolismo , Modelos Moleculares , Complexos Multiproteicos/metabolismo , NADPH-Ferri-Hemoproteína Redutase/metabolismo , Conformação Proteica , Western Blotting , Cromatografia em Gel , Cristalografia por Raios X , Transporte de Elétrons/fisiologia , Heme Oxigenase (Desciclizante)/química , Complexos Multiproteicos/química , NADPH-Ferri-Hemoproteína Redutase/química , Ressonância Magnética Nuclear Biomolecular , Espalhamento de Radiação
12.
J Biol Chem ; 290(50): 29717-31, 2015 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-26472926

RESUMO

ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas Ferro-Enxofre/biossíntese , Transportadores de Cassetes de Ligação de ATP/química , Sequência de Aminoácidos , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Modelos Moleculares , Dados de Sequência Molecular , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Difração de Raios X
13.
BMC Neurol ; 16: 82, 2016 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-27245327

RESUMO

BACKGROUND: It is extremely rare to see cerebrospinal fluid dissemination of intraventricular meningioma, particularly with the development of acute, progressive brainstem/cerebellar dysfunction with an absence of mass formation in the corresponding anatomical sites. CASE PRESENTATION: An 81-year-old man was admitted because of double vision, right facial nerve palsy and truncal ataxia. Brain magnetic resonance imaging showed normal findings except for a tumor mass in the left lateral ventricle, which had been noted over 6 months previously. The patient developed hiccups, hyperventilation, and drowsiness, which worsened progressively, and did not respond to corticosteroid or intraventricular immunoglobulin therapy. Cerebrospinal fluid study revealed a mild elevation of protein, and cytology was negative. The patient died and an autopsy was performed. Postmortem investigation disclosed a malignant transformation of benign fibroid meningioma with cerebrospinal fluid dissemination of the malignant cells, diversely involving the surface of brainstem, cerebellum, and spinal cords, secondarily resulting in extensive ischemia in the brain parenchyma by vessel occlusion. CONCLUSION: If a patient with an intraventricular tumor develops acute, progressive neurological symptoms, the possibility that it is be caused by cerebrospinal fluid dissemination of tumor cells, after malignant transformation, should be considered.


Assuntos
Encefalopatias/patologia , Doenças dos Nervos Cranianos/patologia , Neoplasias Meníngeas/patologia , Meningioma/patologia , Idoso de 80 Anos ou mais , Tronco Encefálico/patologia , Humanos , Imageamento por Ressonância Magnética , Masculino
14.
Bioorg Med Chem ; 24(21): 5340-5352, 2016 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-27622749

RESUMO

γ-Glutamyl transpeptidase (GGT, EC 2.3.2.2) that catalyzes the hydrolysis and transpeptidation of glutathione and its S-conjugates is involved in a number of physiological and pathological processes through glutathione metabolism and is an attractive pharmaceutical target. We report here the evaluation of a phosphonate-based irreversible inhibitor, 2-amino-4-{[3-(carboxymethyl)phenoxy](methoyl)phosphoryl}butanoic acid (GGsTop) and its analogues as a mechanism-based inhibitor of human GGT. GGsTop is a stable compound, but inactivated the human enzyme significantly faster than the other phosphonates, and importantly did not inhibit a glutamine amidotransferase. The structure-activity relationships, X-ray crystallography with Escherichia coli GGT, sequence alignment and site-directed mutagenesis of human GGT revealed a critical electrostatic interaction between the terminal carboxylate of GGsTop and the active-site residue Lys562 of human GGT for potent inhibition. GGsTop showed no cytotoxicity toward human fibroblasts and hepatic stellate cells up to 1mM. GGsTop serves as a non-toxic, selective and highly potent irreversible GGT inhibitor that could be used for various in vivo as well as in vitro biochemical studies.


Assuntos
Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Lisina/antagonistas & inibidores , Organofosfonatos/farmacologia , gama-Glutamiltransferase/antagonistas & inibidores , Domínio Catalítico/efeitos dos fármacos , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Lisina/metabolismo , Modelos Moleculares , Estrutura Molecular , Organofosfonatos/síntese química , Organofosfonatos/química , Eletricidade Estática , Relação Estrutura-Atividade , gama-Glutamiltransferase/química , gama-Glutamiltransferase/metabolismo
15.
J Am Chem Soc ; 137(16): 5452-60, 2015 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-25872660

RESUMO

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Biliverdina/metabolismo , Oxirredutases/química , Oxirredutases/metabolismo , Synechocystis/enzimologia , Cristalografia , Cristalografia por Raios X , Modelos Moleculares , Difração de Nêutrons , Prótons , Synechocystis/química , Synechocystis/metabolismo
16.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 2): 607-14, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24531494

RESUMO

γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Šresolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp2 hybridization to Thr403 Oγ, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.


Assuntos
Bacillus subtilis/química , Proteínas de Bactérias/química , Inibidores Enzimáticos/química , Isoxazóis/química , gama-Glutamiltransferase/química , Bacillus subtilis/enzimologia , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Domínio Catalítico , Cristalografia por Raios X , Escherichia coli/química , Escherichia coli/enzimologia , Ácido Glutâmico/química , Helicobacter pylori/química , Helicobacter pylori/enzimologia , Ligantes , Modelos Moleculares , Ligação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade por Substrato , gama-Glutamiltransferase/antagonistas & inibidores , gama-Glutamiltransferase/genética , gama-Glutamiltransferase/metabolismo
17.
Bioorg Med Chem ; 22(3): 1176-94, 2014 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-24411479

RESUMO

γ-Glutamyl transpeptidase (GGT) catalyzing the cleavage of γ-glutamyl bond of glutathione and its S-conjugates is involved in a number of physiological and pathological processes through glutathione homeostasis. Defining its Cys-Gly binding site is extremely important not only in defining the physiological function of GGT, but also in designing specific and effective inhibitors for pharmaceutical purposes. Here we report the synthesis and evaluation of a series of glutathione-analogous peptidyl phosphorus esters as mechanism-based inhibitors of human and Escherichia coli GGTs to probe the structural and stereochemical preferences in the Cys-Gly binding site. Both enzymes were inhibited strongly and irreversibly by the peptidyl phosphorus esters with a good leaving group (phenoxide). Human GGT was highly selective for l-aliphatic amino acid such as l-2-aminobutyrate (l-Cys mimic) at the Cys binding site, whereas E. coli GGT significantly preferred l-Phe mimic at this site. The C-terminal Gly and a l-amino acid analogue at the Cys binding site were necessary for inhibition, suggesting that human GGT was highly selective for glutathione (γ-Glu-l-Cys-Gly), whereas E. coli GGT are not selective for glutathione, but still retained the dipeptide (l-AA-Gly) binding site. The diastereoisomers with respect to the chiral phosphorus were separated. Both GGTs were inactivated by only one of the stereoisomers with the same stereochemistry at phosphorus. The strict recognition of phosphorus stereochemistry gave insights into the stereochemical course of the catalyzed reaction. Ion-spray mass analysis of the inhibited E. coli GGT confirmed the formation of a 1:1 covalent adduct with the catalytic subunit (small subunit) with concomitant loss of phenoxide, leaving the peptidyl moiety that presumably occupies the Cys-Gly binding site. The peptidyl phosphonate inhibitors are highly useful as a ligand for X-ray structural analysis of GGT for defining hitherto unidentified Cys-Gly binding site to design specific inhibitors.


Assuntos
Dipeptídeos/metabolismo , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Glutationa/análogos & derivados , Compostos de Fósforo/química , gama-Glutamiltransferase/antagonistas & inibidores , gama-Glutamiltransferase/metabolismo , Sítios de Ligação , Técnicas de Química Sintética , Inibidores Enzimáticos/síntese química , Proteínas de Escherichia coli/antagonistas & inibidores , Proteínas de Escherichia coli/metabolismo , Glutationa/metabolismo , Humanos , Espectrometria de Massas/métodos , Mimetismo Molecular , Estereoisomerismo , Especificidade por Substrato
18.
Biochem Biophys Res Commun ; 441(1): 13-7, 2013 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-24120497

RESUMO

A unique [Ni-Fe-S] cluster (C-cluster) constitutes the active center of Ni-containing carbon monoxide dehydrogenases (CODHs). His(261), which coordinates one of the Fe atoms with Cys(295), is suggested to be the only residue required for Ni coordination in the C-cluster. To evaluate the role of Cys(295), we constructed CODH-II variants. Ala substitution for the Cys(295) substitution resulted in the decrease of Ni content and didn't result in major change of Fe content. In addition, the substitution had no effect on the ability to assemble a full complement of [Fe-S] clusters. This strongly suggests Cys(295) indirectly and His(261) together affect Ni-coordination in the C-cluster.


Assuntos
Aldeído Oxirredutases/química , Aldeído Oxirredutases/metabolismo , Cisteína/metabolismo , Complexos Multienzimáticos/química , Complexos Multienzimáticos/metabolismo , Família Multigênica , Níquel/metabolismo , Peptococcaceae/enzimologia , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Filogenia , Homologia de Sequência de Aminoácidos , Espectrofotometria Ultravioleta , Relação Estrutura-Atividade
19.
Biosci Biotechnol Biochem ; 77(2): 409-12, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23391932

RESUMO

Heat-treated γ-glutamyltranspeptidase of Escherichia coli recovered enzymatic activity after incubation at 4 °C, while heat-treated γ-glutamyltranspeptidase of Bacillus subtilis did not. Fluorescent spectra, CD spectra, and native polyacrylamide gel electrophoresis analysis suggested that the dimer of E. coli γ-glutamyltranspeptidase was separated into protomers by heat-treatment, but was renatured by incubation at 4 °C.


Assuntos
Bacillus subtilis/enzimologia , Proteínas de Bactérias/química , Escherichia coli/enzimologia , Subunidades Proteicas/química , gama-Glutamiltransferase/química , Bacillus subtilis/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Desnaturação Proteica , Multimerização Proteica , Redobramento de Proteína , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Especificidade da Espécie , Temperatura , gama-Glutamiltransferase/genética , gama-Glutamiltransferase/metabolismo
20.
Leg Med (Tokyo) ; 64: 102278, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37276824

RESUMO

The Acetaminophen Detection Kit® (Kanto Chemical Company Co. Inc., Tokyo, Japan) is a colorimetric test based on an indophenol reaction. The test involves three reactions: deproteination of the sample, hydrolysis of acetaminophen to yield p-aminophenol, and coupling p-aminophenol with a derivative of phenol in alkali conditions to form a blue-colored indophenol dye. The kit was devised to accomplish these three reactions with only two reagents, allowing the prompt diagnosis of acetaminophen overdose in emergency medicine. In the user instructions included with the kit and in reports introducing the kit, the chemical composition of the two reagents was not disclosed. Details about the composition can be found in the Safety Data Sheet from the manufacturer; however, there is little explanation about the principle (mechanism) of the coupling reaction. This lack of information appears to have hampered the use of this kit in forensic medicine. In this report, we conducted the coupling reaction by successively adding the two reagents to a p-aminophenol (intermediate molecule) solution with the reaction vessel open to the air and under an anaerobic condition. Development of the blue color was inhibited in the absence of air but gradually developed when the reaction vessel was opened to air. Thus, the coupling reaction is an oxidation-reduction (redox) reaction that requires molecular oxygen (O2) dissolved from the air to act as an oxidant. This finding corroborates statements in previous reports and will hopefully facilitate the use of the kit for forensic purposes.


Assuntos
Acetaminofen , Indofenol , Humanos , Aminofenóis , Oxigênio
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