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The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.
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Receptores ErbB/química , Receptores ErbB/metabolismo , Línea Celular Tumoral , Factor de Crecimiento Epidérmico/metabolismo , Receptores ErbB/aislamiento & purificación , Humanos , Membranas Intracelulares/química , Resonancia Magnética Nuclear Biomolecular , Multimerización de Proteína , Termodinámica , Vesículas Transportadoras/químicaRESUMEN
High-throughput analysis in fields such as industrial biotechnology, combinatorial chemistry, and life sciences is becoming increasingly important. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique providing exhaustive molecular information on complex samples. Flow NMR in particular is a cost- and time-efficient method for large screenings. In this study, we have developed a novel 3.0 mm inner diameter polychlorotrifluoroethylene (PCTFE) flow cell for a segmented-flow analysis (SFA) - NMR automated platform. The platform uses FC-72 fluorinated oil and fluoropolymer components to achieve a fully fluorinated flow path. Samples were repeatably transferred from 96-deepwell plates to the flow cell by displacing a fixed volume of oil, with a transfer time of 42 s. 1H spectra were acquired fully automated with 500 and 600 MHz NMR spectrometers. The spectral performance of the novel PCTFE cell was equal to that of commercial glass cells. Peak area repeatability was excellent with a relative standard deviation of 0.1-0.5% for standard samples, and carryover was below 0.2% without intermediate washing. The sample temperature was conditioned by using a thermostated transfer line in order to reduce the equilibration time in the probe and increase the throughput. Finally, analysis of urine samples demonstrated the applicability of this platform for screening complex matrices.
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Ensayos Analíticos de Alto Rendimiento , Imagen por Resonancia Magnética , Espectroscopía de Resonancia Magnética/métodosRESUMEN
Increasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane-protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein-protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein-ligand and protein-protein interactions that underlie essential biological functions in cellular membranes.
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Zeolite activity and selectivity is often determined by the underlying proton and hydrogen-transfer reaction pathways. For the first time, we use single-molecule fluorescence microscopy to directly follow the real-time behavior of individual styrene-derived carbocationic species formed within zeolite ZSM-5. We find that intermittent fluorescence and remarkable photostability of carbocationic intermediates strongly depend on the local chemical environment imposed by zeolite framework and guest solvent molecules. The carbocationic stability can be additionally altered by changing para-substituent on the styrene moiety, as suggested by DFT calculations. Thermodynamically unstable carbocations are more likely to switch between fluorescent (carbocationic) and dark (neutral) states. However, the rate constants of this reversible change can significantly differ among individual carbocations, depending on their exact location in the zeolite framework. The lifetimes of fluorescent states and reversibility of the process can be additionally altered by changing the interaction between dimeric carbocations and solvated Brønsted acid sites in the MFI framework. Advanced multidimensional magic angle spinning solid-state NMR spectroscopy has been employed for the accurate structural elucidation of the reaction products during the zeolite-catalyzed dimerization of styrene in order to corroborate the single-molecule fluorescence microscopy data. This complementary approach of single-molecule fluorescence microscopy, NMR, and DFT collectively indicates that the relative stability of the carbocationic and the neutral states largely depends on the substituent and the local position of the Brønsted acid site within the zeolite framework. As a consequence, new insights into the host-guest chemistry between the zeolite and aromatics, in terms of their surface mobility and reactivity, have been obtained.
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Understanding the 3-D distribution and nature of active sites in heterogeneous catalysts is critical to developing structure-function relationships. However, this is difficult to achieve in microporous materials as there is little relative z-contrast between active and inactive framework elements (e.g., Al, O, P, and Si), making them difficult to differentiate with electron microscopies. We have applied atom probe tomography (APT), currently the only nanometer-scale 3-D microscopy to offer routine light element contrast, to the methanol-to-hydrocarbons (MTH) catalyst SAPO-34, with Si as the active site, which may be present in the framework as either isolated Si species or clusters (islands) of Si atoms. 29Si solid-state NMR data on isotopically enriched and natural abundance materials are consistent with the presence of Si islands, and the APT results have been complemented with simulations to show the smallest detectable cluster size as a function of instrument spatial resolution and detector efficiency. We have identified significant Si-Si affinity in the materials, as well as clustering of coke deposited by the MTH reaction (13CH3OH used) and an affinity between Brønsted acid sites and coke. A comparison with simulations shows that the ultimate spatial resolution that can be attained by APT applied to molecular sieves is 0.5-1 nm. Finally, the observed 13C clusters are consistent with hydrocarbon pool mechanism intermediates that are preferentially located in regions of increased Brønsted acidity.
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The average and the local structure of phosphorus-treated HZSM-5 zeolites were investigated by means of atom probe tomography, powder X-ray diffraction (at ambient and cryogenic temperatures) and 1H, 29Si, 27Al, and 31P magic angle spinning (MAS) solid state nuclear magnetic resonance (NMR) spectroscopy. Phosphatation to yield a product with P/Al ≤ 1 followed by thermal treatment leads to breaking of the Si-OH-Al bridging groups, and subsequent partial dealumination of the zeolite framework, as shown by the contraction of the orthorhombic unit-cell volume and by the loss of tetrahedral framework Al, as observed in the 27Al Multiple Quantum (MQ) MAS NMR spectrum. Most of the framework Al is present in an electronic environment distorted by the presence of phosphorus and appears not to be involved in classic Si-OH-Al Brønsted acid sites. The 31P MAS NMR signals indicate that phosphorus interacts with the zeolitic framework to locally form silico-aluminophosphate (SAPO) domains and the presence of a new kind of acidic site was confirmed by the resonance at â¼8.6 ppm in the 1H MAS NMR spectra, attributed to P-OH groups. Increasing the phosphorus loading (P/Al â« 1) promotes further dealumination of the framework and cross-dehydroxylation between P-OH and Si-OH species, leading to the formation of a crystalline silicon orthophosphate phase. With decreasing Al content, the monoclinic HZSM-5 structure becomes preferred, especially at 85 K where the strain relaxation is higher. However, the presence of a higher amount of silicophosphate impurities hinders the low-temperature strain release of the framework, indicating that some of these species are localized in the zeolite pores and contribute to the strain build up.
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After a prolonged effort over many years, the route for the formation of a direct carbon-carbon (C-C) bond during the methanol-to-hydrocarbon (MTH) process has very recently been unveiled. However, the relevance of the "direct mechanism"-derived molecules (that is, methyl acetate) during MTH, and subsequent transformation routes to the conventional hydrocarbon pool (HCP) species, are yet to be established. This important piece of the MTH chemistry puzzle is not only essential from a fundamental perspective, but is also important to maximize catalytic performance. The MTH process was probed over a commercially relevant H-SAPO-34 catalyst, using a combination of advanced solid-state NMR spectroscopy and operando UV/Vis diffuse reflectance spectroscopy coupled to an on-line mass spectrometer. Spectroscopic evidence is provided for the formation of (olefinic and aromatic) HCP species, which are indeed derived exclusively from the direct C-C bond-containing acetyl group of methyl acetate. New mechanistic insights have been obtained from the MTH process, including the identification of hydrocarbon-based co-catalytic organic reaction centers.
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Chromatin function depends on a dense network of interactions between nucleosomes and a wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Herein, we show that the structure, dynamics, and interactions of nucleosomes can be interrogated in a residue-specific manner by using state-of-the-art solid-state NMR spectroscopy. Using sedimented nucleosomes, high-resolution spectra were obtained for both flexible histone tails and the non-mobile histone core. Through co-sedimentation of a nucleosome-binding peptide, we demonstrate that protein-binding sites on the nucleosome surface can be determined. We believe that this approach holds great promise as it is generally applicable, extendable to include the structure and dynamics of the bound proteins, and scalable to interactions of proteins with higher-order chromatin structures, including isolated and cellular chromatin.
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Cromatina/química , Resonancia Magnética Nuclear Biomolecular , Nucleosomas/química , Sitios de Unión , Modelos Moleculares , Conformación de Ácido NucleicoRESUMEN
1 H detection can significantly improve solid-state NMR spectral sensitivity and thereby allows studying more complex proteins. However, the common prerequisite for 1 Hâ detection is the introduction of exchangeable protons in otherwise deuterated proteins, which has thus far significantly hampered studies of partly water-inaccessible proteins, such as membrane proteins. Herein, we present an approach that enables high-resolution 1 H-detected solid-state NMR (ssNMR) studies of water-inaccessible proteins, and that even works in highly complex environments such as cellular surfaces. In particular, the method was applied to study the K+ channel KcsA in liposomes and inâ situ in native bacterial cell membranes. We used our data for a dynamic analysis, and we show that the selectivity filter, which is responsible for ion conduction and highly conserved in K+ channels, undergoes pronounced molecular motion. We expect this approach to open new avenues for biomolecular ssNMR.
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Proteínas Bacterianas/química , Canales de Potasio/química , Agua/química , Membrana Celular/química , Liposomas/química , Espectroscopía de Protones por Resonancia MagnéticaRESUMEN
Methanol-to-olefin (MTO) catalysis is a very active field of research because there is a wide variety of sometimes conflicting mechanistic proposals. An example is the ongoing discussion on the initial C-C bond formation from methanol during the induction period of the MTO process. By employing a combination of solid-state NMR spectroscopy with UV/Vis diffuse reflectance spectroscopy and mass spectrometry on an active H-SAPO-34 catalyst, we provide spectroscopic evidence for the formation of surface acetate and methyl acetate, as well as dimethoxymethane during the MTO process. As a consequence, new insights in the formation of the first C-C bond are provided, suggesting a direct mechanism may be operative, at least in the early stages of the MTO reaction.
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The ß-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a "divide and conquer" approach in which we first obtained resonance assignments for BamA's periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.
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Proteínas de la Membrana Bacteriana Externa/ultraestructura , Proteínas de Escherichia coli/ultraestructura , Resonancia Magnética Nuclear Biomolecular/métodos , Estructura Terciaria de Proteína/genética , Secuencia de Aminoácidos , Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Modelos Moleculares , Datos de Secuencia Molecular , Pliegue de Proteína , Alineación de SecuenciaRESUMEN
(1) H-detection can greatly improve spectral sensitivity in biological solid-state NMR (ssNMR), thus allowing the study of larger and more complex proteins. However, the general requirement to perdeuterate proteins critically curtails the potential of (1) H-detection by the loss of aliphatic side-chain protons, which are important probes for protein structure and function. Introduced herein is a labelling scheme for (1) H-detected ssNMR, and it gives high quality spectra for both side-chain and backbone protons, and allows quantitative assignments and aids in probing interresidual contacts. Excellent (1) H resolution in membrane proteins is obtained, the topology and dynamics of an ion channel were studied. This labelling scheme will open new avenues for the study of challenging proteins by ssNMR.
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Humins, (side-)products of the acid-catalysed dehydration of carbohydrates, will be produced in substantial quantities with the development of industrial biorefining processes. Most structural knowledge about such humins is based on synthetic model humins prepared at lab-scale from typical carbohydrate(-derived) compounds. Here, we report the first extensive characterisation study of an industrial humin. The soluble humin was generated from pilot plant-scale methanolic cyclodehydration of D-fructose to 5-methoxymethyl-2-furfural (MMF), as part of the Avantium YXY® process to produce FDCA. Purification of the industrial humin followed by fractionation allowed isolation of a water-insoluble, high molecular weight fraction (WIPIH) and a water-soluble, low-to-middle molecular weight soluble fraction (WES). Characterisation by elemental analysis, thermogravimetry, IR and NMR spectroscopy and size exclusion chromatography provided a detailed picture of the humin structure in both fractions. Aided by a comprehensive NMR spectral library of furanic model compounds, we identified the main furanic building blocks and inter-unit linkages and propose a structure for this industrial humin sample. The WIPIH and WES fractions were found to be composed of furanic rings interconnected by short aliphatic chains containing a wide range of functionalities including alcohols, ethers, carboxylic acids, esters, aldehydes and ketones. The low level of crosslinking and high functional group content of the industrial humin differ from the more extensively studied, (highly over-)condensed synthetic model humins, towards which they can be considered intermediates. The structural and compositional insights into the nature of an actual industrial humin open up a broad spectrum of valorisation opportunities.
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Cell walls are essential in the interaction of fungi with the (a)biotic environment and are also key to hyphal morphogenesis and mechanical strength. Here, we used solid-state NMR (ssNMR) spectroscopy combined with HPLC and GC-MS to study the structural organization of the cell wall of a representative of the Basidiomycota, one of the two main phyla of fungi. Based on the data we propose a refined model for the cell wall of a basidiomycete. In this model, the rigid core is built from α- and ß-(1,3)-glucan, ß-(1,3)-(1,6)-glucan, highly branched and single stranded ß-(1,4)-chitin as well as polymeric fucose. The mobile fraction of the cell wall is composed of ß-(1,3)-glucan, ß-(1,3)-(1,6)-glucan, ß-(1,6)-glucan, α-linked reducing and non-reducing ends and polymeric mannose. Together, these findings provide novel insights into the structural organization of the cell wall of the model basidiomycete S. commune that was previously based on destructive chemical and enzymatic analysis.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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The aim of this study is to develop polymeric chemisorbents with a high density of ninhydrin groups, able to covalently bind urea under physiological conditions and thus potentially suitable for use in a wearable artificial kidney. Macroporous beads are prepared by suspension polymerization of 5-vinyl-1-indanone (vinylindanone) using a 90:10 (v/v) mixture of toluene and nitrobenzene as a porogen. The indanone groups are subsequently oxidized in a one-step procedure into ninhydrin groups. Their urea absorption kinetics are evaluated under both static and dynamic conditions at 37 °C in simulated dialysate (urea in phosphate buffered saline). Under static conditions and at a 1:1 molar ratio of ninhydrin: urea the sorbent beads remove ≈0.6-0.7 mmol g-1 and under dynamic conditions and at a 2:1 molar excess of ninhydrin ≈0.6 mmol urea g-1 sorbent in 8 h at 37 °C, which is a step toward a wearable artificial kidney.
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Riñones Artificiales , Ninhidrina/química , Urea/química , Dispositivos Electrónicos Vestibles , Adsorción , HumanosRESUMEN
A significant fraction of proteins coded in the human proteome do not fold into stable three-dimensional structures but are either partially or completely unfolded. A key feature of this family of proteins is their proposed capacity to undergo a disorder-to-order transition upon interaction with a physiological partner. The mechanisms governing protein folding upon interaction, in particular the extent to which recognition elements are preconfigured prior to formation of molecular complexes, can prove difficult to resolve in highly flexible systems. Here, we develop a conformational model of this type of protein, using an explicit description of the unfolded state, specifically modified to allow for the presence of transient secondary structure, and combining this with extensive measurement of residual dipolar couplings throughout the chain. This combination of techniques allows us to quantitatively analyze the level and nature of helical sampling present in the interaction site of the partially folded C-terminal domain of Sendai virus nucleoprotein (N(TAIL)). Rather than fraying randomly, the molecular recognition element of N(TAIL) preferentially populates three specific overlapping helical conformers, each stabilized by an N-capping interaction. The unfolded strands adjacent to the helix are thereby projected in the direction of the partner protein, identifying a mechanism by which they could achieve nonspecific encounter interactions prior to binding. This study provides experimental evidence for the molecular basis of helix formation in partially folded peptide chains, carrying clear implications for understanding early steps of protein folding.
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Nucleoproteínas/química , Virus Sendai/química , Secuencia de Aminoácidos , Sitios de Unión , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Pliegue de ProteínaRESUMEN
Resonance assignment of NMR spectra of unstructured proteins is made difficult by severe overlap due to the lack of secondary structure. Fortunately, this drawback is partially counterbalanced by the narrow line-widths due to the internal flexibility. Alternate sampling schemes can be used to achieve better resolution in less experimental time. Deterministic schemes (such as radial sampling) suffer however from the presence of systematic artifacts. Random acquisition patterns can alleviate this problem by randomizing the artifacts. We show in this communication that quantitative well-resolved spectra can be obtained, provided that the data points are properly weighted before FT. These weights can be evaluated using the concept of Voronoi cells associated with the data points. The introduced artifacts do not affect the direct surrounding of the peaks and thus do not alter the amplitude and frequency of the signals. This procedure is illustrated on 60-residue viral protein, which lacks any persistent secondary structure and thus exhibits major signal overlap.
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Algoritmos , Cristalografía/métodos , Imagenología Tridimensional/métodos , Espectroscopía de Resonancia Magnética/métodos , Modelos Químicos , Proteínas/química , Proteínas/ultraestructura , Simulación por Computador , Conformación Proteica , Pliegue de Proteína , Tamaño de la Muestra , Procesamiento de Señales Asistido por ComputadorRESUMEN
The N-terminally truncated variant of photoactive yellow protein (Delta25-PYP) undergoes a very similar photocycle as the corresponding wild-type protein (WT-PYP), although the lifetime of its light-illuminated (pB) state is much longer. This has allowed determination of the structure of both its dark- (pG) as well as its pB-state in solution by nuclear magnetic resonance (NMR) spectroscopy. The pG structure shows a well-defined fold, similar to WT-PYP and the X-ray structure of the pG state of Delta25-PYP. In the long-lived photocycle intermediate pB, the central beta sheet is still intact, as well as a small part of one alpha helix. The remainder of pB is unfolded and highly flexible, as evidenced by results from proton-deuterium exchange and NMR relaxation studies. Thus, the partially unfolded nature of the presumed signaling state of PYP in solution, as suggested previously, has now been structurally demonstrated.
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Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/genética , Cristalografía por Rayos X , Halorhodospira halophila/metabolismo , Luz , Espectroscopía de Resonancia Magnética , Modelos Químicos , Modelos Moleculares , Modelos Estadísticos , Conformación Proteica , Pliegue de Proteína , Estructura Terciaria de Proteína , Protones , Transducción de Señal , Rayos XRESUMEN
CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface. In vitro reconstitution assays combined with high-resolution fluorescence microscopy and cryo-electron tomography suggested that CKK preferentially associates with the transition zone between curved protofilaments and the regular microtubule lattice. We propose that minus-end-specific features of the interprotofilament interface at this site serve as the basis for CKK's minus-end preference. The steric clash between microtubule-bound CKK and kinesin motors explains how CKK protects microtubule minus ends against kinesin-13-induced depolymerization and thus controls the stability of free microtubule minus ends.