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1.
Nature ; 604(7905): 371-376, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35388216

RESUMEN

The outer membrane of Gram-negative bacteria has an external leaflet that is largely composed of lipopolysaccharide, which provides a selective permeation barrier, particularly against antimicrobials1. The final and crucial step in the biosynthesis of lipopolysaccharide is the addition of a species-dependent O-antigen to the lipid A core oligosaccharide, which is catalysed by the O-antigen ligase WaaL2. Here we present structures of WaaL from Cupriavidus metallidurans, both in the apo state and in complex with its lipid carrier undecaprenyl pyrophosphate, determined by single-particle cryo-electron microscopy. The structures reveal that WaaL comprises 12 transmembrane helices and a predominantly α-helical periplasmic region, which we show contains many of the conserved residues that are required for catalysis. We observe a conserved fold within the GT-C family of glycosyltransferases and hypothesize that they have a common mechanism for shuttling the undecaprenyl-based carrier to and from the active site. The structures, combined with genetic, biochemical, bioinformatics and molecular dynamics simulation experiments, offer molecular details on how the ligands come in apposition, and allows us to propose a mechanistic model for catalysis. Together, our work provides a structural basis for lipopolysaccharide maturation in a member of the GT-C superfamily of glycosyltransferases.


Asunto(s)
Ligasas , Lipopolisacáridos , Antígenos O , Proteínas Bacterianas/química , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Microscopía por Crioelectrón , Glicosiltransferasas , Bacterias Gramnegativas , Lipopolisacáridos/química , Lipopolisacáridos/metabolismo
2.
Annu Rev Biochem ; 89: 741-768, 2020 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-32569526

RESUMEN

Complex carbohydrates are essential for many biological processes, from protein quality control to cell recognition, energy storage, and cell wall formation. Many of these processes are performed in topologically extracellular compartments or on the cell surface; hence, diverse secretion systems evolved to transport the hydrophilic molecules to their sites of action. Polyprenyl lipids serve as ubiquitous anchors and facilitators of these transport processes. Here, we summarize and compare bacterial biosynthesis pathways relying on the recognition and transport of lipid-linked complex carbohydrates. In particular, we compare transporters implicated in O antigen and capsular polysaccharide biosyntheses with those facilitating teichoic acid and N-linked glycan transport. Further, we discuss recent insights into the generation, recognition, and recycling of polyprenyl lipids.


Asunto(s)
Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Glucolípidos/biosíntesis , Antígenos O/biosíntesis , Poliprenoles/metabolismo , Transferasas (Grupos de Otros Fosfatos Sustitutos)/química , Transportadoras de Casetes de Unión a ATP/química , Transportadoras de Casetes de Unión a ATP/genética , Transportadoras de Casetes de Unión a ATP/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Transporte Biológico , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Ligasas de Carbono-Oxígeno/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Glicosiltransferasas/química , Glicosiltransferasas/genética , Glicosiltransferasas/metabolismo , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/metabolismo , Proteínas de Transporte de Membrana/química , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/metabolismo , Modelos Moleculares , Estructura Secundaria de Proteína , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Ácidos Teicoicos/metabolismo , Transferasas (Grupos de Otros Fosfatos Sustitutos)/genética , Transferasas (Grupos de Otros Fosfatos Sustitutos)/metabolismo
3.
Mol Microbiol ; 110(1): 95-113, 2018 10.
Artículo en Inglés | MEDLINE | ID: mdl-30047569

RESUMEN

WaaL is an inner membrane glycosyltransferase that catalyzes the transfer of O-antigen polysaccharide from its lipid-linked intermediate to a terminal sugar of the lipid A-core oligosaccharide, a conserved step in lipopolysaccharide biosynthesis. Ligation occurs at the periplasmic side of the bacterial cell membrane, suggesting the catalytic region of WaaL faces the periplasm. Establishing the membrane topology of the WaaL protein family will enable understanding its mechanism and exploit it as a potential antimicrobial target. Applying oxidative labeling of native methionine/cysteine residues, we previously validated a topological model for Escherichia coli WaaL, which differs substantially from the reported topology of the Pseudomonas aeruginosa WaaL, derived from the analysis of truncated protein reporter fusions. Here, we examined the topology of intact E. coli and P. aeruginosa WaaL proteins by labeling engineered cysteine residues with the membrane-impermeable sulfhydryl reagent polyethylene glycol maleimide (PEG-Mal). The accessibility of PEG-Mal to targeted engineered cysteine residues in both E. coli and P. aeruginosa WaaL proteins demonstrates that both ligases share similar membrane topology. Further, we also demonstrate that P. aeruginosa WaaL shares similar functional properties with E. coli WaaL and that E. coli WaaL may adopt a functional dimer conformation.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Antígenos O/metabolismo , Pseudomonas aeruginosa/enzimología , Alanina/genética , Proteínas Bacterianas/química , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Membrana Celular/metabolismo , Cisteína/genética , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Lípido A/metabolismo , Maleimidas/química , Maleimidas/metabolismo , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Periplasma/metabolismo , Polietilenglicoles/química , Polietilenglicoles/metabolismo , Pseudomonas aeruginosa/genética
4.
J Chem Inf Model ; 56(9): 1762-75, 2016 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-27579990

RESUMEN

The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called "ω-loop", so that the substrates can enter the active site. Here, the conformational landscape of VanA is explored by an enhanced sampling approach: the temperature-accelerated molecular dynamics (TAMD). Analysis of the molecular dynamics (MD) and TAMD trajectories recorded on VanA permits a graphical description of the structural and kinetics aspects of the conformational space of VanA, where the internal mobility and various opening modes of the ω-loop play a major role. The other important feature is the correlation of the ω-loop motion with the movements of the opposite domain, defined as containing the residues A149-Q208. Conformational and kinetic clusters have been determined and a path describing the ω-loop opening was extracted from these clusters. The determination of this opening path, as well as the relative importance of hydrogen bonds along the path, permit one to propose some key residue interactions for the kinetics of the ω-loop opening.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/metabolismo , Simulación de Dinámica Molecular , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Ligasas de Carbono-Oxígeno/química , Gráficos por Computador , Cinética , Ligandos , Simulación del Acoplamiento Molecular , Conformación Proteica , Temperatura
5.
Biochim Biophys Acta ; 1857(9): 1430-1439, 2016 09.
Artículo en Inglés | MEDLINE | ID: mdl-27133505

RESUMEN

Chl synthase (ChlG) is an important enzyme of the Chl biosynthetic pathway catalyzing attachment of phytol/geranylgeraniol tail to the chlorophyllide molecule. Here we have investigated the Flag-tagged ChlG (f.ChlG) in a complex with two different high-light inducible proteins (Hlips) HliD and HliC. The f.ChlG-Hlips complex binds a Chl a and three different carotenoids, ß-carotene, zeaxanthin and myxoxanthophyll. Application of ultrafast time-resolved absorption spectroscopy performed at room and cryogenic temperatures revealed excited-state dynamics of complex-bound pigments. After excitation of Chl a in the complex, excited Chl a is efficiently quenched by a nearby carotenoid molecule via energy transfer from the Chl a Qy state to the carotenoid S1 state. The kinetic analysis of the spectroscopic data revealed that quenching occurs with a time constant of ~2ps and its efficiency is temperature independent. Even though due to its long conjugation myxoxanthophyll appears to be energetically best suited for role of Chl a quencher, based on comparative analysis and spectroscopic data we propose that ß-carotene bound to Hlips acts as the quencher rather than myxoxanthophyll and zeaxanthin, which are bound at the f.ChlG and Hlips interface. The S1 state lifetime of the quencher has been determined to be 13ps at room temperature and 21ps at 77K. These results demonstrate that Hlips act as a conserved functional module that prevents photodamage of protein complexes during photosystem assembly or Chl biosynthesis.


Asunto(s)
Proteínas Bacterianas/química , Ligasas de Carbono-Oxígeno/química , Carotenoides/farmacología , Cianobacterias/enzimología , Complejos de Proteína Captadores de Luz/química , Fotólisis
6.
J Biol Chem ; 291(4): 1735-1750, 2016 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-26586916

RESUMEN

We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its "enzymatic activity" and (ii) subsequent "chemical" S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed.


Asunto(s)
Bacillus subtilis/enzimología , Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/metabolismo , Péptidos/metabolismo , Bacillus subtilis/química , Bacillus subtilis/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Sitios de Unión , Biocatálisis , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Especificidad por Sustrato
7.
Biochemistry ; 54(32): 4998-5005, 2015 Aug 18.
Artículo en Inglés | MEDLINE | ID: mdl-26258685

RESUMEN

The activity of an enzyme encoded by the CT1610 gene in the green sulfur photosynthetic bacterium Chlorobaculum tepidum, which was annotated as bacteriochlorophyll (BChl) a synthase, BchG (denoted as tepBchG), was examined in vitro using the lysates of Escherichia coli containing the heterologously expressed enzyme. BChl a possessing a geranylgeranyl group at the 17-propionate residue (BChl aGG) was produced from bacteriochlorophyllide (BChlide) a and geranylgeranyl pyrophosphate in the presence of tepBchG. Surprisingly, tepBchG catalyzed the formation of BChl a bearing a farnesyl group (BChl aF) as in the enzymatic production of BChl aGG, indicating loose recognition of isoprenoid pyrophosphates in tepBchG. In contrast to such loose recognition of isoprenoid substrates, BChlide c and chlorophyllide a gave no esterifying product upon being incubated with geranylgeranyl or farnesyl pyrophosphate in the presence of tepBchG. These results confirm that tepBchG undoubtedly acts as the BChl a synthase in Cba. tepidum. The enzymatic activity of tepBchG was higher than that of BchG of Rhodobacter sphaeroides at 45 °C, although the former activity was lower than the latter below 35 °C.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/metabolismo , Chlorobi/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Bacterioclorofila A/biosíntesis , Bacterioclorofila A/química , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Chlorobi/genética , Genes Bacterianos , Estructura Molecular , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Rhodobacter sphaeroides/enzimología , Especificidad de la Especie , Especificidad por Sustrato
8.
PLoS One ; 10(3): e0120844, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25790471

RESUMEN

The Trypanosoma brucei parasite causes the vector-borne disease African sleeping sickness. Mitochondrial mRNAs of T. brucei undergo posttranscriptional RNA editing to make mature, functional mRNAs. The final step of this process is catalyzed by the essential ligase, T. brucei RNA Editing Ligase 1 (TbREL1) and the closely related T. brucei RNA Editing Ligase 2 (TbREL2). While other ligases such as T7 DNA ligase have both a catalytic and an oligonucleotide/oligosaccharide-binding (OB)-fold domain, T. brucei RNA editing ligases contain only the catalytic domain. The OB-fold domain, which is required for interaction with the substrate RNA, is provided in trans by KREPA2 (for TbREL1) and KREPA1 (for TbREL2). KREPA2 enhancement of TbREL1 ligase activity is presumed to occur via an OB-fold-mediated increase in substrate specificity and catalysis. We characterized the interaction between TbREL1 and KREPA2 in vitro using full-length, truncated, and point-mutated ligases. As previously shown, our data indicate strong, specific stimulation of TbREL1 catalytic activity by KREPA2. We narrowed the region of contact to the final 59 C-terminal residues of TbREL1. Specifically, the TbREL1 C-terminal KWKE (441-444) sequence appear to coordinate the KREPA2-mediated enhancement of TbREL1 activities. N-terminal residues F206, T264 and Y275 are crucial for the overall activity of TbREL1, particularly for F206, a mutation of this residue also disrupts KREPA2 interaction. Thus, we have identified the critical TbREL1 regions and amino acids that mediate the KREPA2 interaction.


Asunto(s)
Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/metabolismo , Mutagénesis/genética , Edición de ARN , Trypanosoma brucei brucei/enzimología , Secuencia de Aminoácidos , Ligasas de Carbono-Oxígeno/genética , Datos de Secuencia Molecular , Mutación Puntual , Unión Proteica , Eliminación de Secuencia , Relación Estructura-Actividad , Trypanosoma brucei brucei/genética
9.
Methods Mol Biol ; 1215: 445-69, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25330975

RESUMEN

It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual screening protocols used for drug discovery remains a significant challenge. Here, stepwise methodologies are described to generate and select relevant protein conformations for virtual screening in the context of the relaxed complex scheme (RCS), to design small molecule libraries for docking, and to perform statistical analyses on the virtual screening results. Methods include equidistant spacing, RMSD-based clustering, and QR factorization protocols for ensemble generation and ROC analysis for ensemble selection.


Asunto(s)
Evaluación Preclínica de Medicamentos , Simulación del Acoplamiento Molecular/métodos , Adenosina Trifosfato/metabolismo , Algoritmos , Área Bajo la Curva , Ligasas de Carbono-Oxígeno/química , Cristalografía por Rayos X , Ligandos , Proteínas Mitocondriales/química , Probabilidad , Termodinámica , Interfaz Usuario-Computador
10.
Annu Rev Biochem ; 83: 317-40, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24635479

RESUMEN

Chlorophylls are magnesium-tetrapyrrole molecules that play essential roles in photosynthesis. All chlorophylls have similar five-membered ring structures, with variations in the side chains and/or reduction states. Formyl group substitutions on the side chains of chlorophyll a result in the different absorption properties of chlorophyll b, chlorophyll d, and chlorophyll f. These formyl substitution derivatives exhibit different spectral shifts according to the formyl substitution position. Not only does the presence of various types of chlorophylls allow the photosynthetic organism to harvest sunlight at different wavelengths to enhance light energy input, but the pigment composition of oxygenic photosynthetic organisms also reflects the spectral properties on the surface of the Earth. Two major environmental influencing factors are light and oxygen levels, which may play central roles in the regulatory pathways leading to the different chlorophylls. I review the biochemical processes of chlorophyll biosynthesis and their regulatory mechanisms.


Asunto(s)
Clorofila/química , Oxígeno/química , Fotosíntesis , Fenómenos Fisiológicos de las Plantas , Ligasas de Carbono-Oxígeno/química , Clorofila/análogos & derivados , Clorofila A , Luz , Liasas/química , Magnesio/química , Protoporfirinas/química
11.
J Chem Inf Model ; 54(1): 289-301, 2014 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-24397493

RESUMEN

The VanA D-Ala:D-Lac ligase is a key enzyme in the emergence of high level resistance to vancomycin in Enterococcus species and methicillin-resistant Staphylococcus aureus. It catalyzes the formation of D-Ala-D-Lac instead of the vancomycin target, D-Ala-D-Ala, leading to the production of modified, low vancomycin binding affinity peptidoglycan precursors. Therefore, VanA appears as an attractive target for the design of new antibacterials to overcome resistance. The catalytic site of VanA is delimited by three domains and closed by an ω-loop upon enzymatic reaction. The aim of the present work was (i) to investigate the conformational transition of VanA associated with the opening of its ω-loop and of a part of its central domain and (ii) to relate this transition with the substrate or product binding propensities. Molecular dynamics trajectories of the VanA ligase of Enterococcus faecium with or without a disulfide bridge distant from the catalytic site revealed differences in the catalytic site conformations with a slight opening. Conformations were clustered with an original machine learning method, based on self-organizing maps (SOM), which revealed four distinct conformational basins. Several ligands related to substrates, intermediates, or products were docked to SOM representative conformations with the DOCK 6.5 program. Classification of ligand docking poses, also performed with SOM, clearly distinguished ligand functional classes: substrates, reaction intermediates, and product. This result illustrates the acuity of the SOM classification and supports the quality of the DOCK program poses. The protein-ligand interaction features for the different classes of poses will guide the search and design of novel inhibitors.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/metabolismo , Modelos Moleculares , Inteligencia Artificial , Dominio Catalítico , Biología Computacional , Cristalografía por Rayos X , Diseño de Fármacos , Enterococcus faecium/enzimología , Ligandos , Simulación de Dinámica Molecular , Conformación Proteica , Programas Informáticos , Resistencia a la Vancomicina
12.
Elife ; 3: e05334, 2014 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-25551294

RESUMEN

The lipopolysaccharide (LPS) forms the surface-exposed leaflet of the outer membrane (OM) of Gram-negative bacteria, an organelle that shields the underlying peptidoglycan (PG) cell wall. Both LPS and PG are essential cell envelope components that are synthesized independently and assembled by dedicated transenvelope multiprotein complexes. We have identified a point-mutation in the gene for O-antigen ligase (WaaL) in Escherichia coli that causes LPS to be modified with PG subunits, intersecting these two pathways. Synthesis of the PG-modified LPS (LPS*) requires ready access to the small PG precursor pool but does not weaken cell wall integrity, challenging models of precursor sequestration at PG assembly machinery. LPS* is efficiently transported to the cell surface without impairing OM function. Because LPS* contains the canonical vancomycin binding site, these surface-exposed molecules confer increased vancomycin-resistance by functioning as molecular decoys that titrate the antibiotic away from its intracellular target. This unexpected LPS glycosylation fuses two potent pathogen-associated molecular patterns (PAMPs).


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/genética , Ligasas de Carbono-Oxígeno/genética , Pared Celular/química , Proteínas de Escherichia coli/genética , Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Lipopolisacáridos/metabolismo , Peptidoglicano/metabolismo , Antibacterianos/farmacología , Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/metabolismo , Sitios de Unión , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/metabolismo , Pared Celular/efectos de los fármacos , Pared Celular/metabolismo , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Glicosilación , Lipopolisacáridos/química , Mutación , Peptidoglicano/química , Vancomicina/farmacología , Resistencia a la Vancomicina/genética
13.
Methods Mol Biol ; 993: 231-43, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23568474

RESUMEN

Computational simulations of essential biological systems in pathogenic organisms are increasingly being used to reveal structural and dynamical features for targets of interest. At the same time, increased research efforts, especially from academia, have been directed toward drug discovery for neglected tropical diseases. Although these diseases cripple large populations in less fortunate parts of the world, either very few new drugs are being developed or the available treatments for them have severe side effects, including death. This chapter walks readers through a computational investigation used to find novel inhibitors to target one of these neglected diseases, African sleeping sickness (human African trypanosomiasis). Such studies may suggest novel small-molecule compounds that could be considered as part of an early-stage drug discovery effort. As an example target protein of interest, we focus on the essential protein RNA-editing ligase 1 (REL1) in Trypanosoma brucei, the causative agent of human African trypanosomiasis.


Asunto(s)
Diseño de Fármacos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Tripanocidas/farmacología , Trypanosoma brucei brucei/efectos de los fármacos , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/metabolismo , Humanos , Proteínas Mitocondriales/química , Proteínas Mitocondriales/metabolismo , Conformación Proteica , Tripanocidas/metabolismo
14.
Water Res ; 47(1): 130-40, 2013 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-23089359

RESUMEN

Recent studies have demonstrated that wastewater treatment plants (WWTPs) significantly alter the magnitude and distribution of antibiotic resistance genes (ARGs) in receiving environments, indicating that wastewater treatment represents an important node for limiting ARG dissemination. This study examined the potential for membrane treatment of microconstituent ARGs and the effect of native wastewater colloids on the extent of their removal. Plasmids containing vanA (vancomycin) and bla(TEM) (ß-lactam) ARGs were spiked into three representative WWTP effluents versus a control buffer and tracked by quantitative polymerase chain reaction through a cascade of microfiltration and ultrafiltration steps ranging from 0.45 µm to 1 kDa. Significant removal of ARGs was achieved by membranes of 100 kDa and smaller, and presence of wastewater colloids resulted in enhanced removal by 10 kDa and 1 kDa membranes. ARG removal was observed to correlate significantly with the corresponding protein, polysaccharide, and total organic carbon colloidal fractions. Alumina membranes removed ARGs to a greater extent than polyvinylidene fluoride membranes of the same pore size (0.1 µm), but only in the presence of wastewater material. Control studies confirmed that membrane treatment was the primary mechanism of ARG removal, versus other potential sources of loss. This study suggests that advanced membrane treatment technology is promising for managing public health risks of ARGs in wastewater effluents and that removal may even be enhanced by colloids in real-world wastewaters.


Asunto(s)
Antibacterianos/farmacología , Proteínas Bacterianas/química , Ligasas de Carbono-Oxígeno/química , Coloides/química , ADN Bacteriano/química , Eliminación de Residuos Líquidos/métodos , beta-Lactamasas/química , Genes Bacterianos , Membranas Artificiales , Plásmidos/química , Microbiología del Agua , Contaminantes Químicos del Agua
15.
J Biol Chem ; 287(45): 37583-92, 2012 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-22969085

RESUMEN

d-Alanyl:d-lactate (d-Ala:d-Lac) and d-alanyl:d-serine ligases are key enzymes in vancomycin resistance of Gram-positive cocci. They catalyze a critical step in the synthesis of modified peptidoglycan precursors that are low binding affinity targets for vancomycin. The structure of the d-Ala:d-Lac ligase VanA led to the understanding of the molecular basis for its specificity, but that of d-Ala:d-Ser ligases had not been determined. We have investigated the enzymatic kinetics of the d-Ala:d-Ser ligase VanG from Enterococcus faecalis and solved its crystal structure in complex with ADP. The overall structure of VanG is similar to that of VanA but has significant differences mainly in the N-terminal and central domains. Based on reported mutagenesis data and comparison of the VanG and VanA structures, we show that residues Asp-243, Phe-252, and Arg-324 are molecular determinants for d-Ser selectivity. These residues are conserved in both enzymes and explain why VanA also displays d-Ala:d-Ser ligase activity, albeit with low catalytic efficiency in comparison with VanG. These observations suggest that d-Ala:d-Lac and d-Ala:d-Ser enzymes have evolved from a common ancestral d-Ala:d-X ligase. The crystal structure of VanG showed an unusual interaction between two dimers involving residues of the omega loop that are deeply anchored in the active site. We constructed an octapeptide mimicking the omega loop and found that it selectively inhibits VanG and VanA but not Staphylococcus aureus d-Ala:d-Ala ligase. This study provides additional insight into the molecular evolution of d-Ala:d-X ligases and could contribute to the development of new structure-based inhibitors of vancomycin resistance enzymes.


Asunto(s)
Proteínas Bacterianas/química , Enterococcus faecalis/enzimología , Estructura Terciaria de Proteína , Resistencia a la Vancomicina , Adenosina Difosfato/química , Adenosina Difosfato/metabolismo , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Arginina/química , Arginina/genética , Arginina/metabolismo , Ácido Aspártico/química , Ácido Aspártico/genética , Ácido Aspártico/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión/genética , Biocatálisis/efectos de los fármacos , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Ligasas de Carbono-Oxígeno/metabolismo , Cristalografía por Rayos X , Farmacorresistencia Microbiana/genética , Enterococcus faecalis/genética , Cinética , Modelos Moleculares , Mutación , Oligopéptidos/farmacología , Fenilalanina/química , Fenilalanina/genética , Fenilalanina/metabolismo , Filogenia , Unión Proteica , Multimerización de Proteína , Especificidad por Sustrato
16.
Nucleic Acids Res ; 40(14): 6966-77, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22561373

RESUMEN

Trypanosomatids, such as the sleeping sickness parasite Trypanosoma brucei, contain a ∼ 20S RNA-editing complex, also called the editosome, which is required for U-insertion/deletion editing of mitochondrial mRNAs. The editosome contains a core of 12 proteins including the large interaction protein A1, the small interaction protein A6, and the editing RNA ligase L2. Using biochemical and structural data, we identified distinct domains of T. brucei A1 which specifically recognize A6 and L2. We provide evidence that an N-terminal domain of A1 interacts with the C-terminal domain of L2. The C-terminal domain of A1 appears to be required for the interaction with A6 and also plays a key role in RNA binding by the RNA-editing ligase L2 in trans. Three crystal structures of the C-terminal domain of A1 have been elucidated, each in complex with a nanobody as a crystallization chaperone. These structures permitted the identification of putative dsRNA recognition sites. Mutational analysis of conserved residues of the C-terminal domain identified Arg703, Arg731 and Arg734 as key requirements for RNA binding. The data show that the editing RNA ligase activity is modulated by a novel mechanism, i.e. by the trans-acting RNA binding C-terminal domain of A1.


Asunto(s)
Ligasas de Carbono-Oxígeno/química , Proteínas Mitocondriales/química , Proteínas Protozoarias/química , Trypanosoma brucei brucei , Sitios de Unión , Ligasas de Carbono-Oxígeno/metabolismo , Proteínas Mitocondriales/metabolismo , Modelos Moleculares , Dominios y Motivos de Interacción de Proteínas , Proteínas Protozoarias/metabolismo , Edición de ARN , ARN Bicatenario/metabolismo , Trypanosoma brucei brucei/genética
17.
J Am Soc Mass Spectrom ; 23(5): 889-98, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22410873

RESUMEN

Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ·OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008, 70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ·OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms.


Asunto(s)
Espectrometría de Masas/métodos , Proteínas de la Membrana/química , Mapeo Peptídico/métodos , Algoritmos , Secuencia de Aminoácidos , Ligasas de Carbono-Oxígeno/química , Biología Computacional , Proteínas de Escherichia coli/química , Lipopolisacáridos , Metionina/química , Modelos Moleculares , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Oxidación-Reducción , Fragmentos de Péptidos/química , Conformación Proteica , Reproducibilidad de los Resultados
18.
J Biol Chem ; 287(8): 5357-65, 2012 Feb 17.
Artículo en Inglés | MEDLINE | ID: mdl-22158874

RESUMEN

The WaaL-mediated ligation of O-antigen onto the core region of the lipid A-core block is an important step in the lipopolysaccharide (LPS) biosynthetic pathway. Although the LPS biosynthesis has been largely characterized, only a limited amount of in vitro biochemical evidence has been established for the ligation reaction. Such limitations have primarily resulted from the barriers in purifying WaaL homologues and obtaining chemically defined substrates. Accordingly, we describe herein a chemical biology approach that enabled the reconstitution of this ligation reaction. The O-antigen repeating unit (O-unit) of Escherichia coli O86 was first enzymatically assembled via sequential enzymatic glycosylation of a chemically synthesized GalNAc-pyrophosphate-undecaprenyl precursor. Subsequent expression of WaaL through use of a chaperone co-expression system then enabled the demonstration of the in vitro ligation between the synthesized donor (O-unit-pyrophosphate-undecaprenyl) and the isolated lipid A-core acceptor. The previously reported ATP and divalent metal cation dependence were not observed using this system. Further analyses of other donor substrates revealed that WaaL possesses a highly relaxed specificity toward both the lipid moiety and the glycan moiety of the donor. Lastly, three conserved amino acid residues identified by sequence alignment were found essential for the WaaL activity. Taken together, the present work represents an in vitro systematic investigation of the WaaL function using a chemical biology approach, providing a system that could facilitate the elucidation of the mechanism of WaaL-catalyzed ligation reaction.


Asunto(s)
Ligasas de Carbono-Oxígeno/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Antígenos O/química , Antígenos O/metabolismo , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/genética , Ligasas de Carbono-Oxígeno/aislamiento & purificación , Membrana Celular/metabolismo , Difosfatos/química , Difosfatos/metabolismo , Escherichia coli/citología , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/aislamiento & purificación , Mutación , Especificidad por Sustrato
19.
Glycobiology ; 22(2): 288-99, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21983211

RESUMEN

WaaL is a membrane enzyme that catalyzes a key step in lipopolysaccharide (LPS) synthesis: the glycosidic bonding of a sugar at the proximal end of the undecaprenyl-diphosphate (Und-PP) O-antigen with a terminal sugar of the lipid A-core oligosaccharide (OS). Utilizing an in vitro assay, we demonstrate here that ligation with purified Escherichia coli WaaL occurs without adenosine-5'-triphosphate (ATP) and magnesium ions. Furthermore, E. coli and Pseudomonas aeruginosa WaaL proteins cannot catalyze ATP hydrolysis in vitro. We also show that a lysine substitution of the arginine (Arg)-215 residue renders an active protein, whereas WaaL mutants with alanine replacements in the periplasmic-exposed residues Arg-215, Arg-288 and histidine (His)-338 and also the membrane-embedded aspartic acid-389 are nonfunctional. An in silico approach, combining predicted topological information with the analysis of sequence conservation, confirms the importance of a positive charge at the small periplasmic loop of WaaL, since an Arg corresponding to Arg-215 was found at a similar position in all the WaaL homologs. Also, a universally conserved H[NSQ]X(9)GXX[GTY] motif spanning the C-terminal end of the predicted large periplasmic loop and the membrane boundary of the transmembrane helix was identified. The His residue in this motif corresponds to His-338. A survey of LPS structures in which the linkage between O-antigen and lipid A-core OS was elucidated reveals that it is always in the ß-configuration, whereas the sugars bound to Und-PP are in the α-configuration. Together, our biochemical and in silico data argue that WaaL proteins use a common reaction mechanism and share features of metal ion-independent inverting glycosyltransferases.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ligasas de Carbono-Oxígeno/metabolismo , Glicosiltransferasas/metabolismo , Iones/metabolismo , Ligasas/metabolismo , Lipopolisacáridos/metabolismo , Magnesio/metabolismo , Antígenos O/metabolismo , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/aislamiento & purificación , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/aislamiento & purificación , Secuencia Conservada , Escherichia coli/química , Escherichia coli/metabolismo , Glicosiltransferasas/química , Glicosiltransferasas/aislamiento & purificación , Hexosiltransferasas/química , Hexosiltransferasas/metabolismo , Iones/química , Ligasas/química , Lipopolisacáridos/química , Magnesio/química , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Datos de Secuencia Molecular , Antígenos O/química , Pseudomonas aeruginosa/química , Pseudomonas aeruginosa/metabolismo
20.
BMC Pharmacol ; 11: 9, 2011 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-21878090

RESUMEN

BACKGROUND: Trypanosoma brucei (T. brucei) is an infectious agent for which drug development has been largely neglected. We here use a recently developed computer program called AutoGrow to add interacting molecular fragments to S5, a known inhibitor of the validated T. brucei drug target RNA editing ligase 1, in order to improve its predicted binding affinity. RESULTS: The proposed binding modes of the resulting compounds mimic that of ATP, the native substrate, and provide insights into novel protein-ligand interactions that may be exploited in future drug-discovery projects. CONCLUSIONS: We are hopeful that these new predicted inhibitors will aid medicinal chemists in developing novel therapeutics to fight human African trypanosomiasis.


Asunto(s)
Ligasas de Carbono-Oxígeno/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Proteínas Mitocondriales/antagonistas & inhibidores , Trypanosoma brucei brucei/efectos de los fármacos , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Animales , Sitios de Unión , Ligasas de Carbono-Oxígeno/química , Ligasas de Carbono-Oxígeno/metabolismo , Dominio Catalítico , Cristalografía por Rayos X , Diseño de Fármacos , Descubrimiento de Drogas/métodos , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/metabolismo , Humanos , Proteínas Mitocondriales/química , Proteínas Mitocondriales/metabolismo , Modelos Moleculares , Estructura Molecular , Unión Proteica , Estructura Terciaria de Proteína , Edición de ARN , Programas Informáticos , Trypanosoma brucei brucei/enzimología , Trypanosoma brucei brucei/genética , Tripanosomiasis Africana/tratamiento farmacológico , Tripanosomiasis Africana/parasitología
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