Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 27
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Sci Adv ; 10(1): eadi7965, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-38170770

RESUMO

Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.


Assuntos
Populus , Celulose , Espectroscopia de Ressonância Magnética , Biopolímeros , Plantas , Parede Celular
2.
J Inorg Biochem ; 251: 112428, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38008043

RESUMO

Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron­sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2×[4Fe4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 ± 9 mV and - 516 ± 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.


Assuntos
Ferredoxinas , Synechocystis , Ferredoxinas/metabolismo , Transporte de Elétrons , Ferro/química , Enxofre/metabolismo
3.
Essays Biochem ; 67(3): 639-652, 2023 04 14.
Artigo em Inglês | MEDLINE | ID: mdl-36960794

RESUMO

Glycosyltransferases (GTs) are carbohydrate-active enzymes that are encoded by the genomes of organisms spanning all domains of life. GTs catalyze glycosidic bond formation, transferring a sugar monomer from an activated donor to an acceptor substrate, often another saccharide. GTs from family 47 (GT47, PF03016) are involved in the synthesis of complex glycoproteins in mammals and insects and play a major role in the synthesis of almost every class of polysaccharide in plants, with the exception of cellulose, callose, and mixed linkage ß-1,3/1,4-glucan. GT47 enzymes adopt a GT-B fold and catalyze the formation of glycosidic bonds through an inverting mechanism. Unlike animal genomes, which encode few GT47 enzymes, plant genomes contain 30 or more diverse GT47 coding sequences. Our current knowledge of the GT47 family across plant species brings us an interesting view, showcasing how members exhibit a great diversity in both donor and acceptor substrate specificity, even for members that are classified in the same phylogenetic clade. Thus, we discuss how plant GT47 family members represent a great case to study the relationship between substrate specificity, protein structure, and protein evolution. Most of the plant GT47 enzymes that are identified to date are involved in biosynthesis of plant cell wall polysaccharides, including xyloglucan, xylan, mannan, and pectins. This indicates unique and crucial roles of plant GT47 enzymes in cell wall formation. The aim of this review is to summarize findings about GT47 enzymes and highlight new challenges and approaches on the horizon to study this family.


Assuntos
Glicosiltransferases , Plantas , Animais , Glicosiltransferases/genética , Glicosiltransferases/metabolismo , Filogenia , Plantas/metabolismo , Proteínas de Plantas/metabolismo , Genoma de Planta , Especificidade por Substrato , Mamíferos/metabolismo
4.
Nat Plants ; 9(3): 486-500, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36849618

RESUMO

Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the ß-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.


Assuntos
Galactanos , Glicosiltransferases , Galactanos/metabolismo , Glicosiltransferases/metabolismo
5.
Front Microbiol ; 13: 903951, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36246213

RESUMO

The [FeFe]-hydrogenases are enzymes that catalyze the reversible activation of H2 coupled to the reduction-oxidation of electron carriers. Members of the different taxonomic groups of [FeFe]-hydrogenases display a wide range of preference, or bias, for H2 oxidation or H2 production reactions, despite sharing a common catalytic cofactor, or H-cluster. Identifying the properties that control reactivity remains an active area of investigation, and models have emerged that include diversity in the catalytic site coordination environments and compositions of electron transfer chains. The kinetics of proton-coupled electron transfer at the H-cluster might be expected to be a point of control of reactivity. To test this hypothesis, systematic changes were made to the conserved cysteine residue that functions in proton exchange with the H-cluster in the three model enzymes: CaI, CpII, and CrHydA1. CaI and CpII both employ electron transfer accessory clusters but differ in bias, whereas CrHydA1 lacks accessory clusters having only the H-cluster. Changing from cysteine to either serine (more basic) or aspartate (more acidic) modifies the sidechain pKa and thus the barrier for the proton exchange step. The reaction rates for H2 oxidation or H2 evolution were surveyed and measured for model [FeFe]-hydrogenases, and the results show that the initial proton-transfer step in [FeFe]-hydrogenase is tightly coupled to the control of reactivity; a change from cysteine to more basic serine favored H2 oxidation in all enzymes, whereas a change to more acidic aspartate caused a shift in preference toward H2 evolution. Overall, the changes in reactivity profiles were profound, spanning 105 in ratio of the H2 oxidation-to-H2 evolution rates. The fact that the change in reactivity follows a common trend implies that the effect of changing the proton-transfer residue pKa may also be framed as an effect on the scaling relationship between the H-cluster di(thiolmethyl)amine (DTMA) ligand pKa and E m values of the H-cluster. Experimental observations that support this relationship, and how it relates to catalytic function in [FeFe]-hydrogenases, are discussed.

6.
Chem Sci ; 13(16): 4581-4588, 2022 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-35656134

RESUMO

One of the many functions of reduction-oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe-4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe-4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor-acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe-4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron-sulfur cluster relay for coupling to reversible H2 activation at the catalytic site.

7.
Carbohydr Polym ; 273: 118564, 2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34560975

RESUMO

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.


Assuntos
Acetiltransferases/metabolismo , Proteínas de Arabidopsis/metabolismo , Proteínas de Membrana/metabolismo , Xilanos/metabolismo , Acetilação , Acetiltransferases/química , Acetiltransferases/genética , Arabidopsis/enzimologia , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Domínio Catalítico , Proteínas de Membrana/química , Proteínas de Membrana/genética , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Mutação , Ligação Proteica , Xilanos/química
8.
Front Mol Biosci ; 8: 756219, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35141275

RESUMO

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure-spectra relationships of apio-borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional-basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13C shifts and yield predictions that are, on average, within 1.50 ppm for 13C and 0.12 ppm for 1H shifts for apio-borate compounds.

9.
J Phys Chem B ; 124(45): 10117-10125, 2020 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-33112619

RESUMO

Rhamnogalacturonan II (RG-II)-the most complex polysaccharide known in nature-exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II's side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.


Assuntos
Ácidos Bóricos , Pectinas , Parede Celular , Pentoses
10.
J Phys Chem B ; 124(44): 9870-9883, 2020 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-33091304

RESUMO

Two-dimensional (2D) and 3D through-space 13C-13C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13C-13C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13C-13C spin-diffusion methods described here apply in select cases in which the 1D 13C solid-state NMR spectrum displays chemical shift-resolved moieties. This is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13C-13C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13C-13C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ∼0.45-0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks.


Assuntos
Parede Celular , Seda , Animais , Lignina , Espectroscopia de Ressonância Magnética , Ressonância Magnética Nuclear Biomolecular , Peptídeos , Plantas , Aranhas
11.
SLAS Technol ; 25(4): 329-344, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32468908

RESUMO

Rhamnogalacturonan II (RG-II) is a structurally complex pectic polysaccharide that exists as a borate ester cross-linked dimer in the cell walls of all vascular plants. The glycosyl sequence of RG-II is largely conserved, but there is evidence that galacturonic acid (GalA) methyl etherification and glucuronic acid (GlcA) methyl esterification vary in the A sidechain across plant species. Methyl esterification of the galacturonan backbone has also been reported but not confirmed. Here we describe a new procedure, utilizing aq. sodium borodeuteride (NaBD4)-reduced RG-II, to identify the methyl esterification status of backbone GalAs. Our data suggest that up to two different GalAs are esterified in the RG-II backbone. We also adapted a procedure based on methanolysis and NaBD4 reduction to identify 3-, 4-, and 3,4-O-methyl GalA in RG-II. These data, together with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) MS analysis of sidechain A generated from selected RG-IIs and their NaBD4-reduced counterparts, suggest that methyl etherification of the ß-linked GalA and methyl esterification of the GlcA are widespread. Nevertheless, the extent of these modifications varies between plant species. Our analysis of the sidechain B glycoforms in RG-II from different dicots and nonpoalean monocots suggests that this sidechain has a minimum structure of an O-acetylated hexasaccharide (Ara-[MeFuc]-Gal-AceA-Rha-Api-). To complement these studies, we provide further evidence showing that dimer formation and stability in vitro is cation and borate dependent. Taken together, our data further refine the primary sequence and sequence variation of RG-II and provide additional insight into dimer stability and factors controlling dimer self-assembly.


Assuntos
Parede Celular/química , Pectinas/metabolismo , Células Vegetais/metabolismo , Ácidos Urônicos/metabolismo , Cátions , Dimerização , Esterificação , Metilação , Pectinas/química , Temperatura , Ácidos Urônicos/química
12.
Plant Cell ; 32(7): 2367-2382, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32354790

RESUMO

Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the α/ß/α topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac-Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Polissacarídeos/metabolismo , Acetilação , Acetiltransferases/química , Acetiltransferases/genética , Acetiltransferases/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Arginina/metabolismo , Catálise , Domínio Catalítico , Cristalografia por Raios X , Células HEK293 , Humanos , Espectroscopia de Ressonância Magnética , Proteínas de Membrana , Modelos Moleculares , Mutação , Conformação Proteica , Xilanos/metabolismo
14.
J Biol Chem ; 295(14): 4477-4487, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32054684

RESUMO

Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall-modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the -1 to +1 subsites is currently lacking. Here we constructed and validated a putative Michaelis complex in silico and used it to elucidate the hydrolytic mechanism in a GH45, Cel45A from the fungus Humicola insolens, via unbiased simulation approaches. These molecular simulations revealed that the solvent-exposed active-site architecture results in lack of coordination for the hydroxymethyl group of the substrate at the -1 subsite. This lack of coordination imparted mobility to the hydroxymethyl group and enabled a crucial hydrogen bond with the catalytic acid during and after the reaction. This suggests the possibility of a nonhydrolytic reaction mechanism when the catalytic base aspartic acid is missing, as is the case in some LTs (murein transglycosylase A) and expansins. We calculated reaction free energies and demonstrate the thermodynamic feasibility of the hydrolytic and nonhydrolytic reaction mechanisms. Our results provide molecular insights into the hydrolysis mechanism in HiCel45A, with possible implications for elucidating the elusive catalytic mechanism in LTs and expansins.


Assuntos
Celulase/metabolismo , Proteínas Fúngicas/metabolismo , Domínio Catalítico , Celulase/química , Celulase/genética , Gênero de Fungos Humicola/enzimologia , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Glicosiltransferases/metabolismo , Hidrólise , Cinética , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Estrutura Terciária de Proteína , Teoria Quântica , Especificidade por Substrato
15.
Proc Natl Acad Sci U S A ; 116(20): 9825-9830, 2019 05 14.
Artigo em Inglês | MEDLINE | ID: mdl-31036649

RESUMO

Technologies surrounding utilization of cellulosic materials have been integral to human society for millennia. In many materials, controlled introduction of defects provides a means to tailor properties, introduce reactivity, and modulate functionality for various applications. The importance of defects in defining the behavior of cellulose is becoming increasingly recognized. However, fully exploiting defects in cellulose to benefit biobased materials and conversion applications will require an improved understanding of the mechanisms of defect induction and corresponding molecular-level consequences. We have identified a fundamental relationship between the macromolecular structure and mechanical behavior of cellulose nanofibrils whereby molecular defects may be induced when the fibrils are subjected to bending stress exceeding a certain threshold. By nanomanipulation, imaging, and molecular modeling, we demonstrate that cellulose nanofibrils tend to form kink defects in response to bending stress, and that these macromolecular features are often accompanied by breakages in the glucan chains. Direct observation of deformed cellulose fibrils following partial enzymatic digestion reveals that processive cellulases exploit these defects as initiation sites for hydrolysis. Collectively, our findings provide a refined understanding of the interplay between the structure, mechanics, and reactivity of cellulose assemblies.


Assuntos
Celulose/química , Nanoestruturas
16.
Sci Rep ; 8(1): 12826, 2018 08 27.
Artigo em Inglês | MEDLINE | ID: mdl-30150737

RESUMO

Biological routes to the production of fuels from renewable feedstocks hold significant promise in our efforts towards a sustainable future. The fatty acid decarboxylase enzyme (OleTJE) is a cytochrome P450 enzyme that converts long and medium chain fatty acids to terminal alkenes and shares significant similarities in terms of structure, substrate scope and mechanism with the hydroxylase cytochrome P450 (P450BSß). Recent reports have demonstrated that catalytic pathways in these enzymes bifurcate when the heme is in its iron-hydroxo (compound II) state. In spite of significant similarities, the fundamental underpinnings of their different characteristic wild-type reactivities remain ambiguous. Here, we develop point charges, modified parameters and report molecular simulations of this crucial intermediate step. Water occupancies and substrate mobility at the active site are observed to be vital differentiating aspects between the two enzymes in the compound II state and corroborate recent experimental hypotheses. Apart from increased substrate mobility in the hydroxylase, which could have implications for enabling the rebound mechanism for hydroxylation, OleTJE is characterized by much stronger binding of the substrate carboxylate group to the active site arginine, implicating it as an important enabling actor for decarboxylation.


Assuntos
Carboxiliases/química , Carboxiliases/metabolismo , Sistema Enzimático do Citocromo P-450/química , Sistema Enzimático do Citocromo P-450/metabolismo , Oxigenases de Função Mista/química , Oxigenases de Função Mista/metabolismo , Arginina/química , Sítios de Ligação , Catálise , Domínio Catalítico , Descarboxilação , Hidroxilação , Modelos Moleculares , Conformação Molecular , Estrutura Molecular , Ligação Proteica , Especificidade por Substrato
17.
Angew Chem Int Ed Engl ; 57(38): 12385-12389, 2018 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-30089191

RESUMO

Making cells magnetic is a long-standing goal of chemical biology, aiming to enable the separation of cells from complex biological samples and their visualization in vivo using magnetic resonance imaging (MRI). Previous efforts towards this goal, focused on engineering cells to biomineralize superparamagnetic or ferromagnetic iron oxides, have been largely unsuccessful due to the stringent required chemical conditions. Here, we introduce an alternative approach to making cells magnetic, focused on biochemically maximizing cellular paramagnetism. We show that a novel genetic construct combining the functions of ferroxidation and iron chelation enables engineered bacterial cells to accumulate iron in "ultraparamagnetic" macromolecular complexes, allowing these cells to be trapped with magnetic fields and imaged with MRI in vitro and in vivo. We characterize the properties of these cells and complexes using magnetometry, nuclear magnetic resonance, biochemical assays, and computational modeling to elucidate the unique mechanisms and capabilities of this paramagnetic concept.


Assuntos
Quelantes/química , Compostos Férricos/química , Magnetismo , Animais , Proteínas de Transporte de Cátions/genética , Ceruloplasmina/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Imageamento por Ressonância Magnética , Camundongos , Camundongos Endogâmicos BALB C , Oxirredução , Peptídeos/genética , Plasmídeos/genética , Plasmídeos/metabolismo
18.
Phys Chem Chem Phys ; 20(14): 9671, 2018 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-29616253

RESUMO

Correction for 'Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism - a gas-phase ab initio study' by Vivek S. Bharadwaj et al., Phys. Chem. Chem. Phys., 2015, 17, 4054-4066.

19.
Plant J ; 91(6): 931-949, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28670741

RESUMO

The mechanistic underpinnings of the complex process of plant polysaccharide biosynthesis are poorly understood, largely because of the resistance of glycosyltransferase (GT) enzymes to structural characterization. In Arabidopsis thaliana, a glycosyl transferase family 37 (GT37) fucosyltransferase 1 (AtFUT1) catalyzes the regiospecific transfer of terminal 1,2-fucosyl residues to xyloglucan side chains - a key step in the biosynthesis of fucosylated sidechains of galactoxyloglucan. We unravel the mechanistic basis for fucosylation by AtFUT1 with a multipronged approach involving protein expression, X-ray crystallography, mutagenesis experiments and molecular simulations. Mammalian cell culture expressions enable the sufficient production of the enzyme for X-ray crystallography, which reveals the structural architecture of AtFUT1 in complex with bound donor and acceptor substrate analogs. The lack of an appropriately positioned active site residue as a catalytic base leads us to propose an atypical water-mediated fucosylation mechanism facilitated by an H-bonded network, which is corroborated by mutagenesis experiments as well as detailed atomistic simulations.


Assuntos
Arabidopsis/enzimologia , Fucosiltransferases/química , Glucanos/química , Modelos Estruturais , Xilanos/química , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cristalografia por Raios X , Fucosiltransferases/genética , Fucosiltransferases/metabolismo , Glicosilação , Simulação de Dinâmica Molecular , Mutagênese , Água/metabolismo , Galactosídeo 2-alfa-L-Fucosiltransferase
20.
J Phys Chem B ; 121(4): 843-853, 2017 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-28072540

RESUMO

Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the IL's viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes. Additionally, the use of cosolvents to mitigate the cost and unfavorable traits of ILs is an area of growing interest with particular attention on water as the presence of water in biomass processes is inevitable. Through the use of biased and unbiased molecular dynamics (MD) simulations, this study provides a molecular-level perspective of the various solvent-solvent and solvent-solute interactions in binary mixtures of water and 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM+] [OAc-]) in the presence of model cellulose compounds (i.e., glucose and cellobiose). It is observed that at ∼75% w/w IL and water a transition in the nanostructure of the solvent occurs between water-like and IL-like solvation characteristics. It is shown that H-bonding interactions between the anion and water are a major driving force that significantly impacts the solvent properties of the IL as well as conformational preferences of the cellulosic model compound. In addition, it is found that the oligo(ethoxy) cation tail is responsible for the reduction in the propensity for tail aggregation as compared to alkyl tails of similar length, which, combined with increased ionic shielding, results in increased diffusion and enhanced water-like solvation characteristics.


Assuntos
Imidazóis/química , Líquidos Iônicos/química , Simulação de Dinâmica Molecular , Solventes/química , Biomassa , Solubilidade , Água/química
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...