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1.
Biomolecules ; 10(12)2020 12 08.
Artículo en Inglés | MEDLINE | ID: mdl-33302546

RESUMEN

Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants.


Asunto(s)
Proteínas Arqueales/química , ADN Polimerasa beta/química , ADN de Archaea/química , Hexosafosfatos/química , Nucleótidos/química , ARN de Archaea/química , Thermococcus/química , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Sitios de Unión , Clonación Molecular , Cristalografía por Rayos X , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , ADN de Archaea/genética , ADN de Archaea/metabolismo , Evolución Molecular Dirigida/métodos , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Hexosafosfatos/metabolismo , Cinética , Simulación de Dinámica Molecular , Mutación , Conformación de Ácido Nucleico , Nucleótidos/genética , Nucleótidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Ingeniería de Proteínas/métodos , Dominios y Motivos de Interacción de Proteínas , ARN de Archaea/genética , ARN de Archaea/metabolismo , Especificidad por Sustrato , Thermococcus/enzimología
2.
Acta Crystallogr F Struct Biol Commun ; 72(Pt 11): 831-839, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27827354

RESUMEN

Fuculose-1-phosphate aldolase (FucA) catalyses the reversible cleavage of L-fuculose 1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. This enzyme from mesophiles and thermophiles has been extensively studied; however, there is no report on this enzyme from a psychrophile. In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1.34 Šresolution. The overall architecture of GaFucA and its catalytically essential histidine triad are highly conserved among other fuculose aldolases. Comparisons of structural features between GaFucA and its mesophilic and thermophilic homologues revealed that the enzyme has typical psychrophilic attributes, indicated by the presence of a high number of nonpolar residues at the surface and a lower number of arginine residues.


Asunto(s)
Aldehído-Liasas/química , Dihidroxiacetona Fosfato/química , Proteínas Fúngicas/química , Hexosafosfatos/química , Saccharomycetales/química , Aldehído-Liasas/genética , Aldehído-Liasas/metabolismo , Secuencia de Aminoácidos , Regiones Antárticas , Sitios de Unión , Dominio Catalítico , Clonación Molecular , Cristalografía por Rayos X , Dihidroxiacetona Fosfato/metabolismo , Estabilidad de Enzimas , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Expresión Génica , Hexosafosfatos/metabolismo , Modelos Moleculares , Plásmidos/química , Plásmidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomycetales/enzimología , Alineación de Secuencia , Homología de Secuencia de Aminoácido
3.
Acta Crystallogr D Struct Biol ; 72(Pt 4): 467-76, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-27050126

RESUMEN

Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) from Escherichia coli are C-C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B from E. coli. The crystal structure of the variant TalB(F178Y) with bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalently via its C2 atom to the ℇ-NH2 group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to ß-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formed via a Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid-base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalB(E96Q) formed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.


Asunto(s)
Proteínas de Escherichia coli/antagonistas & inhibidores , Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Hexosafosfatos/química , Transaldolasa/antagonistas & inhibidores , Transaldolasa/química , Sustitución de Aminoácidos , Dominio Catalítico , Cristalografía por Rayos X , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Mutación Missense , Transaldolasa/genética
4.
Int J Biol Macromol ; 88: 578-85, 2016 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-27083849

RESUMEN

Fine structure of the O-polysaccharide chain of the lipopolysaccharide (O-antigen) defines the serospecificity of bacterial cells, which is the basis for O-serotyping of medically and agriculturally important gram-negative bacteria including Escherichia coli. In order to obtain the O-polysaccharide for structural analysis, the lipopolysaccharide was isolated from cells of E. coli O84a by phenol/water extraction and degraded with mild acid. However, the O-polysaccharide was cleaved at a highly acid-labile ß-l-fucopyranosyl phosphate (ß-l-Fucp-1-P) linkage to give mainly a pentasaccharide that corresponded to the O-polysaccharide repeat. Therefore, the lipopolysaccharide and the pentasaccharide as well as their O-deacylated derivatives were studied using sugar analysis, NMR spectroscopy, and (for oligosaccharides) ESI HR MS, and the O84-polysaccharide structure was established. The O-polysaccharide is distinguished by the presence of ß-l-Fucp-1-P and randomly di-O-acetylated 6-deoxy-d-talose, which are found for the first time in natural carbohydrates. The gene cluster for the O84-antigen biosynthesis was analysed and its content was found to be consistent with the O-polysaccharide structure.


Asunto(s)
Escherichia coli/química , Lipopolisacáridos/química , Antígenos O/química , Relación Estructura-Actividad , Secuencia de Carbohidratos , Fucosa/análogos & derivados , Fucosa/química , Hexosafosfatos/química , Lipopolisacáridos/aislamiento & purificación , Espectroscopía de Resonancia Magnética , Antígenos O/aislamiento & purificación
5.
J Biomol Screen ; 19(7): 1014-23, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-24717911

RESUMEN

In the nuclei of hepatocytes, glucokinase regulatory protein (GKRP) modulates the activity of glucokinase (GK), a key regulator of glucose homeostasis. Currently, direct activators of GK (GKAs) are in development for the treatment of type 2 diabetes. However, this approach is generally associated with a risk of hypoglycemia. To mitigate such risk, we target the GKRP regulation, which indirectly restores GK activity. Here we describe a screening strategy to look specifically for GKRP modulators, in addition to traditional GKAs. Two high-throughput screening campaigns were performed with our compound libraries using a luminescence assay format, one with GK alone and the other with a GK/GKRP complex in the presence of sorbitol-6-phosphate (S6P). By a subtraction method in the hit triage process of these campaigns, we discovered two close analogs that bind GKRP specifically with sub-µM potency to a site distinct from where fructose-1-phosphate binds. These small molecules are first-in-class allosteric modulators of the GK/GKRP interaction and are fully active even in the presence of S6P. Activation of GK by this particular mechanism, without altering the enzymatic profile, represents a novel pharmacologic modality of intervention in the GK/GKRP pathway.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/química , Descubrimiento de Drogas/métodos , Glucoquinasa/química , Adenosina Trifosfato/química , Regulación Alostérica , Animales , Glucemia/análisis , Calorimetría , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Fluorescencia , Fluorometría , Fructosafosfatos/química , Hepatocitos/metabolismo , Hexosafosfatos/química , Homeostasis , Humanos , Hipoglucemia/prevención & control , Concentración 50 Inhibidora , Luminiscencia , Unión Proteica , Conformación Proteica , Mapeo de Interacción de Proteínas , Ratas , Resonancia por Plasmón de Superficie
6.
PLoS One ; 8(8): e72902, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24015281

RESUMEN

D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26), which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD), catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi). Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αßα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays.


Asunto(s)
Isomerasas Aldosa-Cetosa/química , Hexosafosfatos/química , Lacticaseibacillus rhamnosus/enzimología , Pliegue de Proteína , Isomerasas Aldosa-Cetosa/genética , Isomerasas Aldosa-Cetosa/metabolismo , Dominio Catalítico/fisiología , Cristalografía por Rayos X , Fructosa/química , Fructosa/genética , Fructosa/metabolismo , Hexosafosfatos/genética , Hexosafosfatos/metabolismo , Lacticaseibacillus rhamnosus/genética , Pentosas/química , Pentosas/genética , Pentosas/metabolismo , Estructura Cuaternaria de Proteína , Estructura Secundaria de Proteína , Relación Estructura-Actividad
7.
Anal Biochem ; 417(2): 295-7, 2011 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-21745456

RESUMEN

In a (13)C experiment for metabolic flux analysis ((13)C MFA), we examined isotope discrimination by measuring the labeling of glucose, amino acids, and hexose monophosphates via mass spectrometry. When Escherichia coli grew in a mix of 20% fully labeled and 80% naturally labeled glucose medium, the cell metabolism favored light isotopes and the measured isotopic ratios (δ(13)C) were in the range of -35 to -92. Glucose transporters might play an important role in such isotopic fractionation. Flux analysis showed that both isotopic discrimination and isotopic impurities in labeled substrates could affect the solution of (13)C MFA.


Asunto(s)
Aminoácidos/metabolismo , Ciclo del Carbono , Glucosa/metabolismo , Aminoácidos/química , Isótopos de Carbono/análisis , Isótopos de Carbono/metabolismo , Escherichia coli/química , Escherichia coli/metabolismo , Glucosa/química , Hexosafosfatos/química , Espectrometría de Masas
8.
Carbohydr Res ; 343(5): 865-74, 2008 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-18299123

RESUMEN

As Leloir glycosyltransferases are increasingly being used to prepare oligosaccharides, glycoconjugates, and glycosylated natural products, efficient access to stereopure sugar nucleotide donor substrates is required. Herein, the rapid synthesis and purification of eight sugar nucleotides is described by a facile 30 min activation of nucleoside 5'-monophosphates bearing purine and pyrimidine bases with trifluoroacetic anhydride and N-methylimidazole, followed by a 2 h coupling with stereospecifically prepared sugar-1-phosphates. Tributylammonium bicarbonate and tributylammonium acetate were the ion-pair reagents of choice for the C18 reversed-phase purification of 6-deoxysugar nucleotides, and hexose or pentose-derived sugar nucleotides, respectively.


Asunto(s)
Nucleótidos/síntesis química , Fosfatos de Azúcar/síntesis química , Nucleótidos de Adenina/síntesis química , Nucleótidos de Adenina/química , Cromatografía Liquida/métodos , Fucosa/análogos & derivados , Fucosa/síntesis química , Fucosa/química , Hexosafosfatos/síntesis química , Hexosafosfatos/química , Espectroscopía de Resonancia Magnética , Microscopía Ultravioleta , Estructura Molecular , Nucleótidos/química , Ramnosa/química , Estereoisomerismo , Fosfatos de Azúcar/química , Nucleótidos de Uracilo/síntesis química , Nucleótidos de Uracilo/química
9.
J Biochem Mol Biol ; 40(5): 801-4, 2007 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-17927915

RESUMEN

The products of reactions catalyzed by Methanococcus. jannaschii (Mj) aldolase using various substrates were identified by gas chromatography (GC). Although Mj aldolase is considered a fuculose-1-phosphate aldolase based on homology searching after gene sequencing, it has not been proven to be a fuculose-1-phosphate aldolase based on its reaction products. Mj aldolase was found to catalyze reactions between glycoaldehyde or D, L-glyceraldehyde and DHAP (dihydroxyacetone phosphate). Before performing GC the ketoses produced were converted into peracetylated alditol derivatives by sequential reactions, i.e., dephosphorylation, NaBH(4) reduction, and acetylation. By comparing the GC data of final products with those of standard alditol samples, it was found that the enzymatic reactions with glycoaldehyde, D-glyceraldehyde, and D, L-glyceraldehyde produced D-ribulose-1-phosphate, D-psicose-1-phosphate, and a mixture of D-psicose and L-tagatose-1-phosphate, respectively. These results provide direct evidence that Mj aldolase is a fuculose-1-phosphate aldolase.


Asunto(s)
Cromatografía de Gases/métodos , Fructosa-Bifosfato Aldolasa/química , Fructosa-Bifosfato Aldolasa/metabolismo , Methanococcus/enzimología , Hexosafosfatos/química , Hexosafosfatos/metabolismo , Estructura Molecular , Pentosas/química , Pentosas/metabolismo , Especificidad por Sustrato
10.
J Bacteriol ; 189(11): 4108-19, 2007 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-17400748

RESUMEN

Ignicoccus hospitalis is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon, Nanoarchaeum equitans. In this study, the biosynthetic pathways of I. hospitalis were investigated by in vitro enzymatic analyses, in vivo (13)C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO(2) fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO(2) acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvate-ferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarate-oxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the alpha-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of I. hospitalis revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.


Asunto(s)
Archaea/metabolismo , Procesos Autotróficos , Carbono/metabolismo , Ácido 2-Aminoadípico/química , Ácido 2-Aminoadípico/metabolismo , Acetilcoenzima A/metabolismo , Dióxido de Carbono/metabolismo , Isótopos de Carbono/metabolismo , Citrato (si)-Sintasa/metabolismo , Ácido Cítrico/química , Ácido Cítrico/metabolismo , Fructosa-Bifosfato Aldolasa/química , Fructosa-Bifosfato Aldolasa/metabolismo , Gluconeogénesis , Glucólisis , Hexosafosfatos/química , Hexosafosfatos/metabolismo , Isoleucina/metabolismo , Lisina/metabolismo , Espectroscopía de Resonancia Magnética , Malatos/química , Malatos/metabolismo , Modelos Biológicos , Estructura Molecular , Ácido Oxaloacético/química , Ácido Oxaloacético/metabolismo , Pentosafosfatos/química , Pentosafosfatos/metabolismo , Fosfoenolpiruvato/química , Fosfoenolpiruvato/metabolismo , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Piruvato-Sintasa/metabolismo , Piruvatos/química , Piruvatos/metabolismo
11.
J Biol Chem ; 281(40): 30175-85, 2006 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-16857670

RESUMEN

Despite the generation of a large amount of sequence information over the last decade, more than 40% of well characterized enzymatic functions still lack associated protein sequences. Assigning protein sequences to documented biochemical functions is an interesting challenge. We illustrate here that structural genomics may be a reasonable approach in addressing these questions. We present the crystal structure of the Saccharomyces cerevisiae YMR099cp, a protein of unknown function. YMR099cp adopts the same fold as galactose mutarotase and shares the same catalytic machinery necessary for the interconversion of the alpha and beta anomers of galactose. The structure revealed the presence in the active site of a sulfate ion attached by an arginine clamp made by the side chain from two strictly conserved arginine residues. This sulfate is ideally positioned to mimic the phosphate group of hexose 6-phosphate. We have subsequently successfully demonstrated that YMR099cp is a hexose-6-phosphate mutarotase with broad substrate specificity. We solved high resolution structures of some substrate enzyme complexes, further confirming our functional hypothesis. The metabolic role of a hexose-6-phosphate mutarotase is discussed. This work illustrates that structural information has been crucial to assign YMR099cp to the orphan EC activity: hexose-phosphate mutarotase.


Asunto(s)
Carbohidrato Epimerasas/genética , Hexosafosfatos/química , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Secuencia de Aminoácidos , Carbohidrato Epimerasas/química , Carbohidrato Epimerasas/metabolismo , Dominio Catalítico , Cristalografía por Rayos X , Hexosafosfatos/metabolismo , Datos de Secuencia Molecular , Pliegue de Proteína , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato/genética
12.
Protein Sci ; 14(3): 727-34, 2005 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-15689508

RESUMEN

Phosphoglucose isomerase (PGI) catalyzes the isomerization of D-glucose-6-phosphate (G6P) and D-fructose-6-phosphate (F6P) in glycolysis and gluconeogenesis. Analysis of previously reported X-ray crystal structures of PGI without ligand, with the cyclic form of F6P, or with inhibitors that mimic the cis-enediol intermediate led to proposed mechanisms for the ring opening and isomerization steps in the multistep catalytic mechanism. To help complete our model of the overall mechanism, information is needed about the state of PGI between the ring opening and isomerization steps, in other words, a structure of the enzyme complexed with the open form of a substrate or an analog. Here, we report the crystal structure of rabbit PGI complexed with D-sorbitol-6-phosphate (S6P), an analog of the open chain form of G6P, at 2.0 A resolution. As was seen in the PGI/F6P structure, a helix containing amino acid residues 512-520 is found in the "out" position, which provides sufficient space in the active site for a substrate in its cyclic form and which is probably the location of that helix just after ring opening (or just before ring closure). However, the S6P ligand is in an extended conformation, as was seen previously with ligands that mimic the cis-enediol intermediate. The extended conformation enables the ligand to interact with Glu357, which transfers a proton during the isomerization step. The PGI/S6P structure represents the conformation of the enzyme and substrate between the ring opening (or ring closing) step and the isomerization step and helps to complete the model for PGI's catalytic mechanism.


Asunto(s)
Glucosa-6-Fosfato Isomerasa/química , Glucosa-6-Fosfato/análogos & derivados , Hexosafosfatos/química , Animales , Dominio Catalítico , Cristalografía por Rayos X , Glucosa-6-Fosfato Isomerasa/metabolismo , Hexosafosfatos/metabolismo , Modelos Moleculares , Estructura Terciaria de Proteína , Conejos
13.
J Fluoresc ; 14(5): 569-84, 2004 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-15617264

RESUMEN

This review provides a chronological survey of over fifty fluorescent chemosensors for carbohydrates from the period between 1992 to the present. The survey contains only those sensors that are synthetic or chemosensory, utilize boronic acids and display a fluorescence response in the form of intensity changes or shifts in wavelength. With each compound listed, a description of the saccharide probe is given with regard to concentration, excitation and emission wavelengths, pH and solvent mixture proportions. In addition, the selectivity of each chemosensor is provided as well as the trends in binding constants. Where possible, a description of the fluorescence signaling mechanism is given as well as commentary on the probe's unique features within this class of sensors.


Asunto(s)
Ácidos Borónicos/química , Carbohidratos/análisis , Colorantes Fluorescentes/química , Carbohidratos/química , Disacáridos/análisis , Disacáridos/química , Glicoles/análisis , Glicoles/química , Hexosaminas/análisis , Hexosaminas/química , Hexosafosfatos/análisis , Hexosafosfatos/química , Concentración de Iones de Hidrógeno , Monosacáridos/análisis , Monosacáridos/química , Solventes , Espectrometría de Fluorescencia , Azúcares Ácidos/análisis , Azúcares Ácidos/química
14.
Curr Protoc Nucleic Acid Chem ; Chapter 1: Unit 1.9, 2003 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-18428902

RESUMEN

This unit describes in detail, the optimized preparations of 1,5-anhydrohexitol and the 1,5-anhydrohexitol building blocks for oligonucleotide synthesis (hG, hA, hC, hT).


Asunto(s)
Hexosafosfatos/síntesis química , Oligonucleótidos/síntesis química , Alcoholes del Azúcar/síntesis química , Técnicas de Laboratorio Clínico , Hexosafosfatos/química , Modelos Biológicos
15.
J Am Chem Soc ; 124(6): 928-33, 2002 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-11829600

RESUMEN

A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.


Asunto(s)
Hexosafosfatos/química , ADN/química , Modelos Moleculares , Conformación de Ácido Nucleico , Ácidos Nucleicos/química , ARN/química
16.
Nucleic Acids Res ; 29(15): 3154-63, 2001 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-11470872

RESUMEN

Several reverse transcriptases were studied for their ability to accept anhydrohexitol triphosphates, having a conformationally restricted six-membered ring, as substrate for template-directed synthesis of HNA. It was found that AMV, M-MLV, M-MLV (H(-)), RAV2 and HIV-1 reverse transcriptases were able to recognise the anhydrohexitol triphosphate as substrate and to efficiently catalyse the incorporation of one non-natural anhydrohexitol nucleotide opposite a natural complementary nucleotide. However, only the dimeric enzymes, the RAV2 and HIV-1 reverse transcriptases, seemed to be able to further extend the primer with another anhydrohexitol building block. Subsequently, several HIV-1 mutants (4xAZT, 4xAZT/L100I, L74V, M184V and K65A) were likewise analysed, resulting in selection of K65A and, in particular, M184V as the most succesful mutant HIV-1 reverse transcriptases capable of elongating a DNA primer with several 1,5-anhydrohexitol adenines in an efficient way. Results of kinetic experiments in the presence of this enzyme revealed that incorporation of one anhydrohexitol nucleotide of adenine or thymine gave an increased (for 1,5-anhydrohexitol-ATP) and a slightly decreased (for 1,5-anhydrohexitol-TTP) K(m) value in comparison to that of their natural counterparts. However, no more than four analogues could be inserted under the experimental conditions required for selective incorporation. Investigation of incorporation of the altritol anhydrohexitol nucleotide of adenine in the presence of M184V and Vent (exo(-)) DNA polymerase proved that an adjacent hydroxyl group on C3 of 1,5-anhydrohexitol-ATP has a detrimental effect on the substrate activity of the six-ring analogue. These results could be rationalised based on the X-ray structure of HIV-1 reverse transcriptase.


Asunto(s)
ADN/metabolismo , Transcriptasa Inversa del VIH/metabolismo , VIH-1/enzimología , Hexosafosfatos/metabolismo , Nucleótidos/metabolismo , Transcripción Genética , Adenosina Trifosfato/análogos & derivados , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Sustitución de Aminoácidos/genética , Secuencia de Bases , ADN/biosíntesis , ADN/química , ADN/genética , ADN Polimerasa Dirigida por ADN/metabolismo , Transcriptasa Inversa del VIH/química , Transcriptasa Inversa del VIH/genética , Hexosafosfatos/química , Cinética , Modelos Moleculares , Mutación/genética , Conformación de Ácido Nucleico , Nucleótidos/química , Conformación Proteica , Moldes Genéticos , Nucleótidos de Timina/química , Nucleótidos de Timina/metabolismo
17.
Biochemistry ; 39(42): 12757-65, 2000 Oct 24.
Artículo en Inglés | MEDLINE | ID: mdl-11041840

RESUMEN

The ability of several DNA polymerases to catalyze the template-directed synthesis of duplex oligonucleotides containing a base pair between a nucleotide with anhydrohexitol ring and its natural complement has been investigated. All DNA polymerases were able to accept the chemically synthesized anhydrohexitol triphosphate as substrate and to catalyze the incorporation of one anhydrohexitol nucleotide. However, only family B DNA polymerases succeeded in elongating the primer after the incorporation of an anhydrohexitol nucleotide. In this family, Vent (exo(-)) DNA polymerase is the most successful one and was therefore selected for further investigation. Results revealed that at high enzyme concentrations six hATPs could be incorporated; however, a selective incorporation proved only feasible under experimental conditions where no more than two analogues could be inserted. Also the synthesis of a mixed HNA-DNA sequence was examined. Kinetic parameters for incorporation of one anhydrohexitol adenine nucleoside were similar to those of its natural analogue.


Asunto(s)
ADN Polimerasa Dirigida por ADN/química , ADN/química , Nucleósidos/química , Alcoholes del Azúcar/química , Cromatografía Líquida de Alta Presión , Cartilla de ADN/química , Nucleótidos de Desoxiadenina/síntesis química , Nucleótidos de Desoxiadenina/química , Nucleótidos de Desoxiadenina/aislamiento & purificación , Hexosafosfatos/química , Cinética , Oligodesoxirribonucleótidos/química , Moldes Genéticos
18.
Biochim Biophys Acta ; 1362(2-3): 232-42, 1997 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-9540854

RESUMEN

Diabetes, diarrhoea, renal failure and glucocorticoid therapy have all been identified as independent risk factors for cataract. Increased post-translational modification of proteins, leading to inactivation of enzymes and induction of conformational changes within proteins could result in lens opacification and cataract. Aspirin has been associated with many beneficial effects, including protection against cataract, in-vivo. alpha-Crystallin has been shown to act as a molecular chaperone in-vitro. This lenticular protein prevented the thermal aggregation of other lens proteins in-vitro and has sequence and functional homology with the small heat shock proteins. Glyceraldehyde 3-phosphate dehydrogenase (GAP-DH) is constitutively expressed in tissues and is susceptible to chemical modification in-vivo. In-vitro incubations of GAP-DH with sugars, cyanate and prednisolone-21-hemisuccinate, all led to significant loss of enzyme activity with time in two buffer systems. Rapid inactivation occurred when GAP-DH was incubated with fructose 6-phosphate or prednisolone-21-hemisuccinate. Slower inactivation was observed when GAP-DH was incubated with fructose, glucose 6-phosphate or potassium cyanate. Glucose did not inactivate GAP-DH under the conditions of our experiments. Aspirin and ibuprofen were shown to inactivate GAP-DH very rapidly in-vitro. Bovine lenticular alpha-crystallin conferred no protection against GAP-DH inactivation. This is the first occasion that alpha-crystallin has been demonstrated to be unable to protect against inactivation in our chemical enzyme inactivation system. This may have implications for the susceptibility of lenticular GAP-DH to post-translational inactivation.


Asunto(s)
Gliceraldehído-3-Fosfato Deshidrogenasas/química , Animales , Antiinflamatorios no Esteroideos/química , Tampones (Química) , Carbohidratos/química , Bovinos , Sistema Libre de Células , Cristalinas/química , Cianatos/química , Hexosafosfatos/química , Oxidación-Reducción , Prednisolona/análogos & derivados , Prednisolona/química , Temperatura
19.
Protein Sci ; 5(8): 1541-53, 1996 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-8844845

RESUMEN

The active site of pig kidney fructose-1,6-bisphosphatase (EC 3.1.3.11) is shared between subunits, Arg-243 of one chain interacting with fructose-1,6-bisphosphate or fructose-2,6-bisphosphate in the active site of an adjacent chain. In this study, we present the X-ray structures of the mutant version of the enzyme with Arg-243 replaced by alanine, crystallized in both T and R allosteric states. Kinetic characteristics of the altered enzyme showed the magnesium binding and inhibition by AMP differed slightly; affinity for the substrate fructose-1,6-bisphosphate was reduced 10-fold and affinity for the inhibitor fructose-2,6-bisphosphate was reduced 1,000-fold (Giroux E, Williams MK, Kantrowitz ER, 1994, J Biol Chem 269:31404-31409). The X-ray structures show no major changes in the organization of the active site compared with wild-type enzyme, and the structures confirm predictions of molecular dynamics simulations involving Lys-269 and Lys-274. Comparison of two independent models of the T form structures have revealed small but significant changes in the conformation of the bound AMP molecules and small reorganization of the active site correlated with the presence of the inhibitor. The differences in kinetic properties of the mutant enzyme indicate the key importance of Arg-243 in the function of fructose-1,6-bisphosphatase. Calculations using the X-ray structures of the Arg-243-->Ala enzyme suggest that the role of Arg-243 in the wild-type enzyme is predominantly electrostatic in nature.


Asunto(s)
Fructosa-Bifosfatasa/química , Estructura Terciaria de Proteína , Adenosina Monofosfato/química , Regulación Alostérica , Animales , Arginina/química , Arginina/genética , Sitios de Unión , Cristalización , Cristalografía por Rayos X , Electroquímica , Escherichia coli/genética , Fructosa-Bifosfatasa/antagonistas & inhibidores , Fructosa-Bifosfatasa/genética , Fructosa-Bifosfatasa/metabolismo , Hexosafosfatos/química , Hexosafosfatos/metabolismo , Enlace de Hidrógeno , Riñón/enzimología , Mutagénesis Sitio-Dirigida , Proteínas Recombinantes/antagonistas & inhibidores , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Estereoisomerismo , Porcinos
20.
Proc Natl Acad Sci U S A ; 92(19): 8916-20, 1995 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-7568043

RESUMEN

Fructose-1,6-bisphosphatase (Fru-1,6-Pase; D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11) requires two divalent metal ions to hydrolyze alpha-D-fructose 1,6-bisphosphate. Although not required for catalysis, monovalent cations modify the enzyme activity; K+ and Tl+ ions are activators, whereas Li+ ions are inhibitors. Their mechanisms of action are still unknown. We report here crystallographic structures of pig kidney Fru-1,6-Pase complexed with K+, Tl+, or both Tl+ and Li+. In the T form Fru-1,6-Pase complexed with the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2) and Tl+ or K+ ions, three Tl+ or K+ binding sites are found. Site 1 is defined by Glu-97, Asp-118, Asp-121, Glu-280, and a 1-phosphate oxygen of AhG-1,6-P2; site 2 is defined by Glu-97, Glu-98, Asp-118, and Leu-120. Finally, site 3 is defined by Arg-276, Glu-280, and the 1-phosphate group of AhG-1,6-P2. The Tl+ or K+ ions at sites 1 and 2 are very close to the positions previously identified for the divalent metal ions. Site 3 is specific to K+ or Tl+. In the divalent metal ion complexes, site 3 is occupied by the guanidinium group of Arg-276. These observations suggest that Tl+ or K+ ions can substitute for Arg-276 in the active site and polarize the 1-phosphate group, thus facilitating nucleophilic attack on the phosphorus center. In the T form complexed with both Tl+ and Li+ ions, Li+ replaces Tl+ at metal site 1. Inhibition by lithium very likely occurs as it binds to this site, thus retarding turnover or phosphate release. The present study provides a structural basis for a similar mechanism of inhibition for inositol monophosphatase, one of the potential targets of lithium ions in the treatment of manic depression.


Asunto(s)
Litio/química , Potasio/química , Talio/química , Regulación Alostérica , Animales , Sitios de Unión , Cristalografía por Rayos X , Fructosa-Bifosfatasa/antagonistas & inhibidores , Fructosa-Bifosfatasa/química , Fructosa-Bifosfatasa/efectos de los fármacos , Hexosafosfatos/química , Riñón/enzimología , Litio/farmacología , Modelos Químicos , Modelos Moleculares , Monoéster Fosfórico Hidrolasas/antagonistas & inhibidores , Potasio/farmacología , Conformación Proteica , Porcinos , Talio/farmacología
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