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1.
Cell ; 165(7): 1698-1707, 2016 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-27238019

RESUMO

Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.


Assuntos
Descoberta de Drogas , Glutamato Desidrogenase/ultraestrutura , Isocitrato Desidrogenase/ultraestrutura , L-Lactato Desidrogenase/ultraestrutura , Aminoquinolinas/química , Aminoquinolinas/farmacologia , Animais , Bovinos , Galinhas , Microscopia Crioeletrônica , Cristalografia por Raios X , Glutamato Desidrogenase/antagonistas & inibidores , Glutamato Desidrogenase/química , Humanos , Isocitrato Desidrogenase/antagonistas & inibidores , Isocitrato Desidrogenase/química , L-Lactato Desidrogenase/antagonistas & inibidores , L-Lactato Desidrogenase/química , Modelos Moleculares , Conformação Proteica , Sulfonamidas/química , Sulfonamidas/farmacologia
2.
Int J Mol Sci ; 25(8)2024 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-38673928

RESUMO

There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.


Assuntos
Evolução Molecular , Glutamato Desidrogenase , Processamento de Proteína Pós-Traducional , Animais , Humanos , Glutamato Desidrogenase/metabolismo , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/química , Ligantes , Mutação , Primatas/genética
3.
Physiol Plant ; 175(6): e14071, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38148220

RESUMO

In plants, glutamate dehydrogenase (GDH) is an ubiquitous enzyme that catalyzes the reversible amination of 2-oxoglutarate in glutamate. It contributes to both the amino acid homeostasis and the management of intracellular ammonium, and it is regarded as a key player at the junction of carbon and nitrogen assimilation pathways. To date, information about the GDH of terrestrial plants refers to a very few species only. We focused on selected species belonging to the division Marchantiophyta, providing the first panoramic overview of biochemical and functional features of GDH in liverworts. Native electrophoretic analyses showed an isoenzymatic profile less complex than what was reported for Arabidposis thaliana and other angiosperms: the presence of a single isoform corresponding to an α-homohexamer, differently prone to thermal inactivation on a species- and organ-basis, was found. Sequence analysis conducted on amino acid sequences confirmed a high similarity of GDH in modern liverworts with the GDH2 protein of A. thaliana, strengthening the hypothesis that the duplication event that gave origin to GDH1-homolog gene from GDH2 occurred after the evolutionary bifurcation that separated bryophytes and tracheophytes. Experiments conducted on Marchantia polymorpha and Calypogeia fissa grown in vitro and compared to A. thaliana demonstrated through in gel activity detection and monodimensional Western Blot that the aminating activity of GDH resulted in strongly enhanced responses to ammonium excess in liverworts as well, even if at a different extent compared to Arabidopsis and other vascular species. The comparative analysis by bi-dimensional Western Blot suggested that the regulation of the enzyme could be, at least partially, untied from the protein post-translational pattern. Finally, immuno-electron microscopy revealed that the GDH enzyme localizes at the subcellular level in both mitochondria and chloroplasts of parenchyma and is specifically associated to the endomembrane system in liverworts.


Assuntos
Compostos de Amônio , Arabidopsis , Hepatófitas , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/química , Glutamato Desidrogenase/metabolismo , Arabidopsis/metabolismo , Sequência de Aminoácidos , Hepatófitas/genética , Hepatófitas/metabolismo , Compostos de Amônio/metabolismo
4.
J Biol Chem ; 296: 100301, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33476647

RESUMO

ADP-ribosyltransferases (ARTs) are a widespread superfamily of enzymes frequently employed in pathogenic strategies of bacteria. Legionella pneumophila, the causative agent of a severe form of pneumonia known as Legionnaire's disease, has acquired over 330 translocated effectors that showcase remarkable biochemical and structural diversity. However, the ART effectors that influence L. pneumophila have not been well defined. Here, we took a bioinformatic approach to search the Legionella effector repertoire for additional divergent members of the ART superfamily and identified an ART domain in Legionella pneumophila gene0181, which we hereafter refer to as Legionella ADP-Ribosyltransferase 1 (Lart1) (Legionella ART 1). We show that L. pneumophila Lart1 targets a specific class of 120-kDa NAD+-dependent glutamate dehydrogenase (GDH) enzymes found in fungi and protists, including many natural hosts of Legionella. Lart1 targets a conserved arginine residue in the NAD+-binding pocket of GDH, thereby blocking oxidative deamination of glutamate. Therefore, Lart1 could be the first example of a Legionella effector which directly targets a host metabolic enzyme during infection.


Assuntos
ADP Ribose Transferases/química , Proteínas de Bactérias/química , Glutamato Desidrogenase/química , Legionella pneumophila/genética , ADP Ribose Transferases/genética , ADP Ribose Transferases/metabolismo , ADP-Ribosilação , Sequência de Aminoácidos , Amoeba/microbiologia , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Clonagem Molecular , Desaminação , Escherichia coli/genética , Escherichia coli/metabolismo , Fungos , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/metabolismo , Interações Hospedeiro-Patógeno , Cinética , Legionella pneumophila/enzimologia , Legionella pneumophila/patogenicidade , Modelos Moleculares , Oxirredução , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Especificidade por Substrato
5.
Bioorg Chem ; 120: 105601, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35033816

RESUMO

NADPH-dependent amino acid dehydrogenases (AADHs) are favorable enzymes to construct artificial biosynthetic pathways in whole-cell for high-value noncanonical amino acids (NcAAs) production. Glutamate dehydrogenases (GluDHs) represent attractive candidates for the development of novel NADPH-dependent AADHs. Here, we report the development of a novel NADPH-dependent phenylglycine dehydrogenase by combining active pocket engineering and hinge region engineering of a GluDH from Pseudomonas putida (PpGluDH). The active pocket of PpGluDH was firstly tailored to optimize its binding mode with bulky substrate α-oxobenzeneacetic acid (α-OA), and then, the hinge region was further engineered to tune the protein conformational dynamics, which finally resulted in a mutant M3 (T196A/T121I/L123D) with a 103-fold increase of catalytic efficiency (kcat/Km) toward α-OA. The M3 mutant exhibited high catalytic performance in both in vitro biocatalysis preparation and in vivo biosynthesis of l-phenylglycine, indicating its promising practical applications. Our results demonstrated that co-engineering of the active pocket and hinge region is an effective strategy for developing novel NADPH-dependent AADHs from GluDHs for NcAAs production.


Assuntos
Glutamato Desidrogenase , NADPH Desidrogenase , Aminoácido Oxirredutases/química , Aminoácido Oxirredutases/metabolismo , Aminoácidos/metabolismo , Glutamato Desidrogenase/química , Glutamato Desidrogenase/metabolismo , Cinética , NADP/metabolismo , NADPH Desidrogenase/metabolismo
6.
J Neurochem ; 157(3): 802-815, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33421122

RESUMO

INTRODUCTION: Mammalian glutamate dehydrogenase (hGDH1 in human cells) interconverts glutamate to α-ketoglutarate and ammonia while reducing NAD(P) to NAD(P)H. During primate evolution, humans and great apes have acquired hGDH2, an isoenzyme that underwent rapid evolutionary adaptation concomitantly with brain expansion, thereby acquiring unique catalytic and regulatory properties that permitted its function under conditions inhibitory to its ancestor hGDH1. Although the 3D-structures of GDHs, including hGDH1, have been determined, attempts to determine the hGDH2 structure were until recently unsuccessful. Comparison of the hGDH1/hGDH2 structures would enable a detailed understanding of their evolutionary differences. This work aimed at the determination of the hGDH2 crystal structure and the analysis of its functional implications. Recombinant hGDH2 was produced in the Spodoptera frugiperda ovarian cell line Sf21, using the Baculovirus expression system. Purification was achieved via a two-step chromatography procedure. hGDH2 was crystallized, X-ray diffraction data were collected using synchrotron radiation and the structure was determined by molecular replacement. The hGDH2 structure is reported at a resolution of 2.9 Å. The enzyme adopts a novel semi-closed conformation, which is an intermediate between known open and closed GDH1 conformations, differing from both. The structure enabled us to dissect previously reported biochemical findings and to structurally interpret the effects of evolutionary amino acid substitutions, including Arg470His, on ADP affinity. In conclusion, our data provide insights into the structural basis of hGDH2 properties, the functional evolution of hGDH isoenzymes, and open new prospects for drug design, especially for cancer therapeutics.


Assuntos
Encéfalo/enzimologia , Encéfalo/fisiologia , Glutamato Desidrogenase/fisiologia , Neoplasias/enzimologia , Neoplasias/fisiopatologia , Substituição de Aminoácidos , Animais , Linhagem Celular , Cristalização , Glutamato Desidrogenase/antagonistas & inibidores , Glutamato Desidrogenase/química , Humanos , Modelos Moleculares , Estrutura Molecular , Mutação , Conformação Proteica , Proteínas Recombinantes , Spodoptera , Difração de Raios X
7.
Biochem Biophys Res Commun ; 570: 15-20, 2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34271431

RESUMO

Glutamate dehydrogenase 3 from Candida albicans (CaGdh3) catalyzes the reversible oxidative deamination of l-glutamate, playing an important role in the yeast-to-hyphal transition of C. albicans. Here we report the crystal structures of CaGdh3 and its complex with α-ketoglutarate and NADPH. CaGdh3 exists as a hexamer, with each subunit containing two domains. The substrate and coenzyme bind in the cleft between the two domains and their binding induces a conformational change in CaGdh3. Our results will help to understand the catalytic mechanism of CaGdh3 and will provide a structural basis for the design of antifungal drugs targeting the CaGdh3 pathway.


Assuntos
Candida albicans/enzimologia , Proteínas Fúngicas/química , Glutamato Desidrogenase/química , Domínio Catalítico , Coenzimas/metabolismo , Cristalografia por Raios X , Modelos Moleculares , NADP/química , NADP/metabolismo , Conformação Proteica , Multimerização Proteica , Soluções , Especificidade por Substrato
8.
Hum Genomics ; 14(1): 9, 2020 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-32143698

RESUMO

BACKGROUND: Gain-of-function mutations in the GLUD1 gene, encoding for glutamate dehydrogenase (GDH), result in the hyperinsulinism/hyperammonemia HI/HA syndrome. HI/HA patients present with harmful hypoglycemia secondary to protein-induced HI and elevated plasma ammonia levels. These symptoms may be accompanied by seizures and mental retardation. GDH is a mitochondrial enzyme that catalyzes the oxidative deamination of glutamate to α-ketoglutarate, under allosteric regulations mediated by its inhibitor GTP and its activator ADP. The present study investigated the functional properties of the GDH-G446V variant (alias c.1496G > T, p.(Gly499Val) (NM_005271.4)) in patient-derived lymphoblastoid cells. RESULTS: The calculated energy barrier between the opened and closed state of the enzyme was 41% lower in GDH-G446V compared to wild-type GDH, pointing to altered allosteric regulation. Computational analysis indicated conformational changes of GDH-G446V in the antenna region that is crucial for allosteric regulators. Enzymatic activity measured in patient-derived lymphoblastoid cells showed impaired allosteric responses of GDH-G446V to both regulators GTP and ADP. In particular, as opposed to control lymphoblastoid cells, GDH-G446V cells were not responsive to GTP in the lower range of ADP concentrations. Assessment of the metabolic rate revealed higher mitochondrial respiration in response to GDH-dependent substrates in the GDH-G446V lymphoblastoid cells compared to control cells. This indicates a shift toward glutaminolysis for energy provision in cells carrying the GDH-G446V variant. CONCLUSIONS: Substitution of the small amino acid glycine for the hydrophobic branched-chain valine altered the allosteric sensitivity to both inhibitory action of GTP and activation by ADP, rendering cells metabolically responsive to glutamine.


Assuntos
Glutamato Desidrogenase/genética , Glutamato Desidrogenase/metabolismo , Guanosina Trifosfato/metabolismo , Hiperinsulinismo/patologia , Linfócitos/patologia , Mutação , Adulto , Regulação Alostérica , Estudos de Casos e Controles , Feminino , Glutamato Desidrogenase/química , Humanos , Hiperinsulinismo/genética , Recém-Nascido , Linfócitos/metabolismo , Masculino , Pessoa de Meia-Idade , Conformação Proteica
9.
Biosci Biotechnol Biochem ; 85(2): 262-271, 2021 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-33604622

RESUMO

Glutamate dehydrogenase (GDH) is an important enzyme in ammonium metabolism, the activity of which is regulated by multiple factors. In this study, we investigate the effects of ammonium and potassium on the activity of maize GDH. Our results show that both ammonium and potassium play multiple roles in regulating the activity of maize GDH, with the specific roles depending on the concentration of potassium. Together with the structural information of GDH, we propose models for the substrate inhibition of ammonium, and the elimination of substrate inhibition by potassium. These models are supported by the analysis of statistic thermodynamics. We also analyze the binding sites of ammonium and potassium on maize GDH, and the conformational changes of maize GDH. The findings provide insight into the regulation of maize GDH activity by ammonium and potassium and reveal the importance of the dose and ratio of nitrogen and potassium in crop cultivation.


Assuntos
Compostos de Amônio/farmacologia , Glutamato Desidrogenase/metabolismo , Potássio/farmacologia , Zea mays/enzimologia , Sequência de Aminoácidos , Relação Dose-Resposta a Droga , Glutamato Desidrogenase/química , Cinética , Modelos Moleculares , Conformação Proteica
10.
J Neurochem ; 153(1): 80-102, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31886885

RESUMO

Glutamate dehydrogenase (GDH) is essential for the brain function and highly regulated, according to its role in metabolism of the major excitatory neurotransmitter glutamate. Here we show a diurnal pattern of the GDH acetylation in rat brain, associated with specific regulation of GDH function. Mornings the acetylation levels of K84 (near the ADP site), K187 (near the active site), and K503 (GTP-binding) are highly correlated. Evenings the acetylation levels of K187 and K503 decrease, and the correlations disappear. These daily variations in the acetylation adjust the GDH responses to the enzyme regulators. The adjustment is changed when the acetylation of K187 and K503 shows no diurnal variations, as in the rats after a high dose of thiamine. The regulation of GDH function by acetylation is confirmed in a model system, where incubation of the rat brain GDH with acetyl-CoA changes the enzyme responses to GTP and ADP, decreasing the activity at subsaturating concentrations of substrates. Thus, the GDH acetylation may support cerebral homeostasis, stabilizing the enzyme function during diurnal oscillations of the brain metabolome. Daytime and thiamine interact upon the (de)acetylation of GDH in vitro. Evenings the acetylation of GDH from control animals increases both IC50GTP and EC50ADP . Mornings the acetylation of GDH from thiamine-treated animals increases the enzyme IC50GTP . Molecular mechanisms of the GDH regulation by acetylation of specific residues are proposed. For the first time, diurnal and thiamine-dependent changes in the allosteric regulation of the brain GDH due to the enzyme acetylation are shown.


Assuntos
Encéfalo/enzimologia , Ritmo Circadiano/fisiologia , Glutamato Desidrogenase/fisiologia , Tiamina/farmacologia , Acetilcoenzima A/farmacologia , Acetilação , Regulação Alostérica/efeitos dos fármacos , Animais , Córtex Cerebral/enzimologia , Glutamato Desidrogenase/antagonistas & inibidores , Glutamato Desidrogenase/química , Masculino , Mitocôndrias/enzimologia , NAD/farmacologia , Ratos , Ratos Wistar
11.
Anal Chem ; 92(9): 6622-6630, 2020 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-32250604

RESUMO

Native mass spectrometry (MS) provides the capacity to monitor membrane protein complexes and noncovalent binding of ligands and lipids to membrane proteins. The charge states produced by native MS of membrane proteins often result in gas-phase protein unfolding or loss of noncovalent interactions. In an effort to reduce the charge of membrane proteins, we examined the utility of alkali metal salts as a charge-reducing agent. Low concentrations of alkali metal salts caused marked charge reduction in the membrane protein, Erwinia ligand-gated ion channel (ELIC). The charge-reducing effect only occurred for membrane proteins and was detergent-dependent, being most pronounced in long polyethylene glycol (PEG)-based detergents such as C10E5 and C12E8. On the basis of these results, we propose a mechanism for alkali metal charge reduction of membrane proteins. Addition of low concentrations of alkali metals may provide an advantageous approach for charge reduction of detergent-solubilized membrane proteins by native MS.


Assuntos
Acetatos/química , Glutamato Desidrogenase/química , Proteínas de Membrana/química , Metais Alcalinos/química , Piruvato Quinase/química , Animais , Bovinos , Detergentes/química , Glutamato Desidrogenase/metabolismo , Espectrometria de Massas , Proteínas de Membrana/metabolismo , Oxirredução , Piruvato Quinase/metabolismo , Coelhos , Sais/química , Solubilidade
12.
J Biol Chem ; 293(17): 6241-6258, 2018 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-29540480

RESUMO

Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP+-dependent allosteric enzyme that is forward-inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (α-ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (α-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously reported. The AnGDH hexamers having subunits with different conformations indicated that its α-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp-154 and Gly-153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning α-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.


Assuntos
Amônia/química , Aspergillus niger/enzimologia , Proteínas Fúngicas/química , Glutamato Desidrogenase/química , Glutamatos/química , NADP/química , Regulação Alostérica , Aspergillus niger/genética , Domínio Catalítico , Cristalografia por Raios X , Relação Estrutura-Atividade
13.
Proteins ; 87(1): 41-50, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30367518

RESUMO

Mammalian glutamate dehydrogenase (GDH) has complex allosteric regulation and the loss of GTP inhibition causes the hyperinsulinism/hyperammonemia syndrome (HHS) where insulin is hypersecreted upon consumption of protein. The archetypical HHS lesion is H454Y and lies in the GTP binding pocket. To better understand the mechanism of HHS, we determined the crystal structure of H454Y. When the bovine GDH crystal structures were minimized to prepare for further computational analysis, unusually large deviations were found at the allosteric NADH binding site due to chemical sequence errors. Notably, 387 lies in an allosteric where several activators and inhibitors bind and should be lysine rather than asparagine. All structures were re-refined and the consequence of this sequence error on NADH binding was calculated using free energy perturbation. The binding free energy penalty going from the correct to incorrect sequence found is +5 kcal/mol per site and therefore has a significant impact on drug development. BROADER AUDIENCE ABSTRACT: Glutamate dehydrogenase is a key enzyme involved in amino acid catabolism. As such, it is heavily regulated in animals by a wide array of metabolites. The importance of this regulation is most apparent in a genetic disorder called hyperinsulinism/hyperammonemia (HHS) where patients hypersecrete insulin upon the consumption of protein. We determined the atomic structure of one of these HHS mutants to better understand the disease and also analyzed an allosteric regulatory site.


Assuntos
Glutamato Desidrogenase/química , Guanosina Trifosfato/metabolismo , Hiperinsulinismo/genética , Hipoglicemia/genética , Proteínas Mutantes/química , Mutação , Regulação Alostérica , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/metabolismo , Humanos , Hiperinsulinismo/enzimologia , Hipoglicemia/enzimologia , Modelos Moleculares , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Conformação Proteica
14.
Biochem Biophys Res Commun ; 509(1): 262-267, 2019 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-30583861

RESUMO

High levels of glutamate dehydrogenase (GDH) activity are associated with hypoglycemia, cancer, and Parkinson's disease. Propylselen was synthesized to investigate its mechanism of GDH inhibition in comparison with Ebselen and Epigallocatechin gallate (EGCG). Because Ebselen was found to crosslink with the peptide (AA299-341) at the active site of E.coli GDH, the Cys, Pro, and Lys residues of the corresponding peptide were mutagenized to Ala residues. Using enzyme kinetics and biomolecular interaction assays, we found that the conserved GDH P320 residue is important for propylselen binding, C321 for Ebselen binding, and K341 for EGCG binding. In addition, these 3 mutations abolished NADP+ binding to E. coli GDH in the absence of glutamate substrate, but in the presence of glutamate, the catalytic activity of the mutants was reduced only by 2-4 fold, indicating that a substrate-induced fit mechanism exists in E. coli GDH. Furthermore, biochemical analysis showed that NADP+ had high affinity (Kd of 77 nM) for GDH; by targeting the NADP binding site, propylselen effectively inhibited both E. coli and human GDH activity and improved anticancer activity.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Azóis/química , Azóis/farmacologia , Proliferação de Células/efeitos dos fármacos , Glutamato Desidrogenase/antagonistas & inibidores , Compostos Organosselênicos/química , Compostos Organosselênicos/farmacologia , Sítios de Ligação/efeitos dos fármacos , Linhagem Celular Tumoral , Escherichia coli/enzimologia , Glutamato Desidrogenase/química , Glutamato Desidrogenase/metabolismo , Humanos , Isoindóis , Simulação de Acoplamento Molecular , NADP/metabolismo , Neoplasias/tratamento farmacológico , Neoplasias/enzimologia
15.
Neurochem Res ; 44(1): 154-169, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29777493

RESUMO

Human evolution is characterized by brain expansion and up-regulation of genes involved in energy metabolism and synaptic transmission, including the glutamate signaling pathway. Glutamate is the excitatory transmitter of neural circuits sub-serving cognitive functions, with glutamate-modulation of synaptic plasticity being central to learning and memory. GLUD2 is a novel positively-selected human gene involved in glutamatergic transmission and energy metabolism that underwent rapid evolutionary adaptation concomitantly with prefrontal cortex enlargement. Two evolutionary replacements (Gly456Ala and Arg443Ser) made hGDH2 resistant to GTP inhibition and allowed distinct regulation, enabling enhanced enzyme function under high glutamatergic system demands. GLUD2 adaptation may have contributed to unique human traits, but evidence for this is lacking. GLUD2 arose through retro-positioning of a processed GLUD1 mRNA to the X chromosome, a DNA replication mechanism that typically generates pseudogenes. However, by finding a suitable promoter, GLUD2 is thought to have gained expression in nerve and other tissues, where it adapted to their particular needs. Here we generated GLUD2 transgenic (Tg) mice by inserting in their genome a segment of the human X chromosome, containing the GLUD2 gene and its putative promoter. Double IF studies of Tg mouse brain revealed that the human gene is expressed in the host mouse brain in a pattern similar to that observed in human brain, thus providing credence to the above hypothesis. This expressional adaptation may have conferred novel role(s) on GLUD2 in human brain. Previous observations, also in GLUD2 Tg mice, generated and studied independently, showed that the non-redundant function of hGDH2 is markedly activated during early post-natal brain development, contributing to developmental changes in prefrontal cortex similar to those attributed to human divergence. Hence, GLUD2 adaptation may have influenced the evolutionary course taken by the human brain, but understanding the mechanism(s) involved remains challenging.


Assuntos
Adaptação Fisiológica/fisiologia , Encéfalo/fisiologia , Evolução Molecular , Glutamato Desidrogenase/biossíntese , Heterozigoto , Animais , Expressão Gênica , Glutamato Desidrogenase/química , Glutamato Desidrogenase/genética , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos CBA , Camundongos Transgênicos , Estrutura Secundária de Proteína , Cromossomo X/genética
16.
Neurochem Res ; 44(1): 117-132, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29079932

RESUMO

In-vitro, glutamate dehydrogenase (GDH) catalyzes the reversible oxidative deamination of glutamate to α-ketoglutarate (α-KG). GDH is found in all organisms, but in animals is allosterically regulated by a wide array of metabolites. For many years, it was not at all clear why animals required such complex control. Further, in both standard textbooks and some research publications, there has been some controversy as to the directionality of the reaction. Here we review recent work demonstrating that GDH operates mainly in the catabolic direction in-vivo and that the finely tuned network of allosteric regulators allows GDH to meet the varied needs in a wide range of tissues in animals. Finally, we review the progress in using pharmacological agents to activate or inhibit GDH that could impact a wide range of pathologies from insulin disorders to tumor growth.


Assuntos
Metabolismo Energético/fisiologia , Glutamato Desidrogenase/química , Glutamato Desidrogenase/metabolismo , Ácido Glutâmico/química , Ácido Glutâmico/metabolismo , Animais , Inibidores Enzimáticos/administração & dosagem , Inibidores Enzimáticos/metabolismo , Glutamato Desidrogenase/antagonistas & inibidores , Humanos , Doenças Metabólicas/tratamento farmacológico , Doenças Metabólicas/metabolismo , Ligação Proteica/fisiologia , Estrutura Secundária de Proteína
17.
Anal Chem ; 90(24): 14121-14125, 2018 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-30462475

RESUMO

This work has looked to explore an innovative and powerful visible fluorescence immunoassay method through wet NH3-triggered structural change of NH2-MIL-125(Ti) impregnated on paper for the detection of carcinoembryonic antigen (CEA). Gold nanoparticles heavily functionalized with glutamate dehydrogenase (GDH) and secondary antibody were used for generation of wet NH3 with a sandwiched immunoassay format. Paper-based analytical device (PAD) coated with NH2-MIL-125(Ti) exhibited good visible fluorescence intensity through wet NH3-triggeried structural change with high accuracy and reproducibility. Moreover, NH2-MIL-125(Ti)-based PAD displayed two visual modes of fluorescence color and physical color with the naked eye and allowed the detection of CEA at a concentration as low as 0.041 ng mL-1. Importantly, the PAD-based assay provides promise for use in the mass production of miniaturized devices and opens new opportunities for protein diagnostics and biosecurity.


Assuntos
Amônia/síntese química , Antígeno Carcinoembrionário/análise , Imunoensaio/métodos , Estruturas Metalorgânicas/química , Papel , Amônia/química , Amônia/metabolismo , Glutamato Desidrogenase/química , Glutamato Desidrogenase/metabolismo , Ouro/química , Limite de Detecção , Medições Luminescentes , Nanopartículas Metálicas/química
18.
J Proteome Res ; 16(7): 2457-2471, 2017 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-28516784

RESUMO

Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram-positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique interprotein cross-linked peptides with <1% false discovery rate by mass spectrometry and genome-wide database searching. Nearly 60% of the interprotein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and ß' subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth. Data are available via ProteomeXchange with identifier PXD006287.


Assuntos
Bacillus subtilis/metabolismo , Proteínas de Bactérias/metabolismo , Glutaratos/química , Mapeamento de Interação de Proteínas/métodos , Succinimidas/química , Sequência de Aminoácidos , Bacillus subtilis/química , Bacillus subtilis/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Reagentes de Ligações Cruzadas/química , Meios de Cultura/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , RNA Polimerases Dirigidas por DNA/química , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Escherichia coli/química , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Glutamato Desidrogenase/química , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/metabolismo , Biogênese de Organelas , Ligação Proteica , Subunidades Proteicas/química , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Ribossomos/genética , Ribossomos/metabolismo , Especificidade da Espécie , Fatores de Elongação da Transcrição/química , Fatores de Elongação da Transcrição/genética , Fatores de Elongação da Transcrição/metabolismo
19.
Proteins ; 85(8): 1422-1434, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28383162

RESUMO

It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with » of the residues increasing in their mobilities and » having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422-1434. © 2017 Wiley Periodicals, Inc.


Assuntos
Arginase/química , D-Aminoácido Oxidase/química , Glutamato Desidrogenase/química , Glicina N-Metiltransferase/química , Multimerização Proteica , Triose-Fosfato Isomerase/química , Motivos de Aminoácidos , Animais , Sítios de Ligação , Biocatálise , Domínio Catalítico , Cristalografia por Raios X , Humanos , Camundongos , Modelos Moleculares , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Especificidade por Substrato , Termodinâmica
20.
Arch Biochem Biophys ; 636: 90-99, 2017 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-29056417

RESUMO

Glutamate dehydrogenase (GDH) represents a critical enzyme catalyzing the reaction spanning amino acid catabolism, the Krebs cycle, and urea production in the wood frog. GDH breaks down glutamate and NAD+ to generate α-ketoglutaric acid (α-KG), NADH and ammonium that can be metabolized to form urea. Purification of GDH from control and frozen male wood frog livers was performed using a two-step column chromatography procedure with a cation exchange column and a GTP-agarose affinity column. Analysis of kinetic parameters of the purified GDH showed several notable differences between the control and stress. Under standard assay conditions, the affinity of GDH for its substrates was significantly higher for the freeze-exposed enzyme than for the control (glutamate Km: 41% decrease, NAD+ Km: 40% decrease). The maximal activity for the control enzyme was also noted to be lower than the frozen. This suggests that the frozen form of the GDH was activated relative to the control form. Western blot analysis of common posttranslational modifications indicated that the frozen enzyme had a lower degree of acetylation and ADP-ribosylation than its control counterpart. These results suggest that GDH is regulated in the wood frog liver by means of altering post-translational modifications in response to freezing.


Assuntos
ADP-Ribosilação , Proteínas de Anfíbios/metabolismo , Congelamento , Glutamato Desidrogenase/metabolismo , Fígado/enzimologia , Acetilação , Proteínas de Anfíbios/química , Animais , Glutamato Desidrogenase/química , Fígado/química , Ranidae
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