Stopped-flow NMR Research Articles

Development of stopped-flow hyper-CEST NMR method on recirculating hyperpolarization system as applied to void space analysis in polymers.

129Xe NMR spectroscopy of polymers can provide important information on void spaces, sometimes called free volume, in polymers. Unfortunately, the spectroscopy's low sensitivity has limited its widespread use in both academic and industrial research. In order to overcome such a difficult situation, hyper-CEST method which employs hyperpolarization and CEST techniques, is examined after the introduction of recirculation and subtraction modes. Alongside the incorporated stopped-flow technique, these modes were very efficient in detecting very weak hidden signals from cellulose nanofiber (CNF) and silk fibroin (SF) films and in discussing the void space in these polymers. From the analysis of detailed saturation frequency dependence in the increment of 100Hz, the chemical shifts of hidden peaks were successfully determined to give reasonable values for the size of void space in CNF and SF. Application on thermoplastic polyurethane film also supported our method of analysis. The subtraction mode was very efficient in judging the presence or absence of any peak at a fixed saturation frequency. These facts support that the mode will surely be useful in the future exploratory study of very weak hidden signals.

Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα)8-Barrel Enzyme of Histidine Biosynthesis HisF.

The overall significance of loop motions for enzymatic activity is generally accepted. However, it has largely remained unclear whether and how such motions can control different steps of catalysis. We have studied this problem on the example of the mobile active site β1α1-loop (loop1) of the (βα)8-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 variants containing single mutations of conserved amino acids showed drastically reduced rates for the turnover of the substrates N'-[(5'-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) and ammonia to the products imidazole glycerol phosphate (ImGP) and 5-aminoimidazole-4-carboxamide-ribotide (AICAR). A comprehensive mechanistic analysis including stopped-flow kinetics, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations detected three conformations of loop1 (open, detached, closed) whose populations differed between wild-type HisF and functionally affected loop1 variants. Transient stopped-flow kinetic experiments demonstrated that wt-HisF binds PrFAR by an induced-fit mechanism whereas catalytically impaired loop1 variants bind PrFAR by a simple two-state mechanism. Our findings suggest that PrFAR-induced formation of the closed conformation of loop1 brings active site residues in a productive orientation for chemical turnover, which we show to be the rate-limiting step of HisF catalysis. After the cyclase reaction, the closed loop conformation is destabilized, which favors the formation of detached and open conformations and hence facilitates the release of the products ImGP and AICAR. Our data demonstrate how different conformations of active site loops contribute to different catalytic steps, a finding that is presumably of broad relevance for the reaction mechanisms of (βα)8-barrel enzymes and beyond.

Quantitative and convenient real-time reaction monitoring using stopped-flow benchtop NMR

We present a stopped-flow benchtop NMR system (composed of commercially available hardware components) that allows for quantitative reaction monitoring to be completed with relative ease, even with experimentally complex reaction systems.

Protodeboronation of (Hetero)Arylboronic Esters: Direct versus Prehydrolytic Pathways and Self-/Auto-Catalysis.

The kinetics and mechanism of the base-catalyzed hydrolysis (ArB(OR)2 → ArB(OH)2) and protodeboronation (ArB(OR)2 → ArH) of a series of boronic esters, encompassing eight different polyols and 10 polyfluoroaryl and heteroaryl moieties, have been investigated by in situ and stopped-flow NMR spectroscopy (19F, 1H, and 11B), pH-rate dependence, isotope entrainment, 2H KIEs, and KS-DFT computations. The study reveals the phenomenological stability of boronic esters under basic aqueous-organic conditions to be highly nuanced. In contrast to common assumption, esterification does not necessarily impart greater stability compared to the corresponding boronic acid. Moreover, hydrolysis of the ester to the boronic acid can be a dominant component of the overall protodeboronation process, augmented by self-, auto-, and oxidative (phenolic) catalysis when the pH is close to the pKa of the boronic acid/ester.

Mechanism of Anion-Catalyzed C–H Silylation Using TMSCF3: Kinetically-Controlled CF3-Anionoid Partitioning As a Key Parameter

The mechanism of anion-catalyzed C–H silylation by R3SiCF3 reagents has been investigated using homogeneous TBAT-initiation, in situ and stopped-flow 19F NMR spectroscopy 2H-KIE, LFER, deuterium-la...

Anion-Initiated Trifluoromethylation by TMSCF3: Deconvolution of the Siliconate-Carbanion Dichotomy by Stopped-Flow NMR/IR.

The mechanism of CF3 transfer from R3SiCF3 (R = Me, Et, iPr) to ketones and aldehydes, initiated by M+X– (<0.004 to 10 mol %), has been investigated by analysis of kinetics (variable-ratio stopped-flow NMR and IR), 13C/2H KIEs, LFER, addition of ligands (18-c-6, crypt-222), and density functional theory calculations. The kinetics, reaction orders, and selectivity vary substantially with reagent (R3SiCF3) and initiator (M+X–). Traces of exogenous inhibitors present in the R3SiCF3 reagents, which vary substantially in proportion and identity between batches and suppliers, also affect the kinetics. Some reactions are complete in milliseconds, others take hours, and others stall before completion. Despite these differences, a general mechanism has been elucidated in which the product alkoxide and CF3– anion act as chain carriers in an anionic chain reaction. Silyl enol ether generation competes with 1,2-addition and involves protonation of CF3– by the α-C–H of the ketone and the OH of the enol. The overarching mechanism for trifluoromethylation by R3SiCF3, in which pentacoordinate siliconate intermediates are unable to directly transfer CF3– as a nucleophile or base, rationalizes why the turnover rate (per M+X– initiator) depends on the initial concentration (but not identity) of X–, the identity (but not concentration) of M+, the identity of the R3SiCF3 reagent, and the carbonyl/R3SiCF3 ratio. It also rationalizes which R3SiCF3 reagent effects the most rapid trifluoromethylation, for a specific M+X– initiator.

A Catalyst-Free Amination of Functional Organolithium Reagents by Flow Chemistry.

Reported is the electrophilic amination of functional organolithium intermediates with well-designed aminating reagents under mild reaction conditions using flow microreactors. The aminating reagents were optimized to achieve efficient C-N bond formation without using any catalyst. The electrophilic amination reactions of functionalized aryllithiums were successfully conducted under mild reaction conditions, within 1 minute, by using flow microreactors. The aminating reagent was also prepared by the flow method. Based on stopped-flow NMR analysis, the reaction time for the preparation of the aminating reagent was quickly optimized without the necessity of work-up. Integrated one-flow synthesis consisting of the generation of an aryllithium, the preparation of an aminating reagent, and their combined reaction was successfully achieved to give the desired amine within 5 minutes of total reaction time.

New insights into the membrane association mechanism of the glycosyltransferase WaaG from Escherichia coli

Monotopic glycosyltransferases (GTs) interact with membranes via electrostatic interactions. The N-terminal domain is permanently anchored to the membrane while the membrane interaction of the C-terminal domain is believed to be weaker so that it undergoes a functionally relevant conformational change upon donor or acceptor binding. Here, we studied the applicability of this model to the glycosyltransferase WaaG. WaaG is involved in the synthesis of lipopolysaccharides (LPS) in Gram-negative bacteria and was previously categorized as a monotopic GT. We analyzed the binding of WaaG to membranes by stopped-flow fluorescence and NMR diffusion experiments. We find that electrostatic interactions are required to bind WaaG to membranes while mere hydrophobic interactions are not sufficient. WaaG senses the membrane's surface charge density but there is no preferential binding to specific anionic lipids. However, the binding is weaker than expected for monotopic GTs but similar to peripheral GTs. Therefore, WaaG may be a peripheral GT and this could be of functional relevance in vivo since LPS synthesis occurs only when WaaG is membrane-bound. We could not observe a C-terminal domain movement under our experimental conditions.

Rapid Hydrogen-Deuterium Exchange in Liquid Droplets.

The rate of hydrogen-deuterium exchange (HDX) in aqueous droplets of phenethylamine has been determined with submillisecond temporal resolution by mass spectrometry using nanoelectrospray ionization with a theta-capillary. The average speed of the microdroplets is measured using microparticle image velocimetry. The droplet travel time is varied from 20 to 320 μs by changing the distance between the emitter and the heated inlet to the mass spectrometer and the voltage applied to the emitter source. The droplets were found to accelerate by ∼30% during their observable travel time. Our droplet imaging shows that the theta-capillary produces two Taylor cone-jets (one per channel), causing mixing to take place from droplet fusion in the Taylor spray zone. Phenethylamine (ϕCH2CH2NH2) was chosen to study because it has only one functional group (-NH2) that undergoes rapid HDX. We model the HDX with a system of ordinary differential equations. The rate constant for the formation of -NH2D+ from -NH3+ is 3660 ± 290 s-1, and the rate constant for the formation of -NHD2+ from -NH2D+ is 3330 ± 270 s-1. The observed rates are about 3 times faster than what has been reported for rapidly exchangeable peptide side-chain groups in bulk measurements using stopped-flow kinetics and NMR spectroscopy. We also applied this technique to determine the HDX rates for a small 10-residue peptide, angiotensin I, in aqueous droplets, from which we found a 7-fold acceleration of HDX in the droplet compared to that in bulk solution.

Stopped-Flow NMR and Quantitative GPC Reveal Unexpected Complexities for the Mechanism of NHC-Catalyzed Lactide Polymerization

Stopped-flow NMR spectroscopy provides the first direct, in situ observation of lactide epimerization during polymerization with the N-heterocyclic carbene organocatalyst 1,3-dimesitylimidazol-2-ylidene (IMes). Hexad analysis of the polymer microstructure using 13C NMR spectroscopy supports a chain-end-controlled mechanism for stereocontrol of the lactide polymerization. Data for both monomer consumption and molecular weight distribution (MWD) as a function of time have been examined using more than one dozen kinetic models. The most successful models feature reversible, unimolecular termination, first-order propagation in monomer, no backbiting term, and include a first-order catalyst death term. The developed modeling method allows insight into a challenging mechanistic problem by successfully modeling MWD evolution and monomer concentration with time.

Progress toward reaction monitoring at variable temperatures: a new stopped‐flow NMR probe design

A stopped-flow NMR probe is described that enables fast flow rates, short transfer times, and equilibration of the reactant magnetization and temperature prior to reaction. The capabilities of the probe are demonstrated by monitoring the polymerization of lactide as catalyzed by the air-sensitive catalyst 1,3-dimesitylimidazol-2-ylidene (IMes) over the temperature range of -30 to 40 °C. The incorporation of stopped-flow capabilities into an NMR probe permits the rich information content of NMR to be accessed during the first few seconds of a fast reaction. Copyright © 2016 John Wiley & Sons, Ltd.

Deciphering the unconventional peptide binding to the PDZ domain of MAST2.

Phosphatase and tensin homologue (PTEN) and microtubule-associated serine threonine kinase 2 (MAST2) are key negative regulators of survival pathways in neuronal cells. The two proteins interact via the PDZ (PSD-95, Dlg1, Zo-1) domain of MAST2 (MAST2-PDZ). During infection by rabies virus, the viral glycoprotein competes with PTEN for interaction with MAST2-PDZ and promotes neuronal survival. The C-terminal PDZ-binding motifs (PBMs) of the two proteins bind similarly to MAST2-PDZ through an unconventional network of connectivity involving two anchor points. Combining stopped-flow fluorescence, analytical ultracentrifugation (AUC), microcalorimetry and NMR, we document the kinetics of interaction between endogenous and viral ligands to MAST2-PDZ as well as the dynamic and structural effects of these interactions. Viral and PTEN peptide interactions to MAST2-PDZ occur via a unique kinetic step which involves both canonical C-terminal PBM binding and N-terminal anchoring. Indirect effects induced by the PBM binding include modifications to the structure and dynamics of the PDZ dimerization surface which prevent MAST2-PDZ auto-association. Such an energetic communication between binding sites and distal surfaces in PDZ domains provides interesting clues for protein regulation overall.

Fresh Surprises from the old Cofactor NAD(P)H

About 16% of all characterized enzymes use the pyridine nucleotides NADH or NADPH as hydride donors or acceptors during catalysis. The textbook mechanism for these cofactors is a direct hydride transfer between NAD(P)H and the corresponding substrate. This long-standing mechanistic hypothesis was recently challenged by the surprising discovery of an intermediate during catalysis of two NADPH-dependent enzymes of the middle chain dehydrogenase reductase superfamily (Rosenthal et al. Nature Chem. Biol. 2014). Stopped-flow spectroscopy, NMR and high resolution MS revealed that the intermediate in these enyzmes is a covalent ene-adduct between the substrate crotonyl-CoA and the NADPH-cofactor. These observations provide -for the first time- evidence that NAD(P)H-dependent enzymes can react through an ene-mechanism instead of the commonly assumed direct hydride transfer. Subsequent experiments allowed us to isolate the catalytic intermediate and use it as a novel tool to dissect the individual steps of catalysis. With this strategy we could directly study the protonation half-reaction of fatty acid reductases and identify the long-sought enigmatic proton donor in these enzymes. Having understood the structure function relationships in the active site we could engineer the enzyme to have an altered stereochemistry (Rosenthal et al. submitted). These results have implications for our fundamental understanding of Nature's most abundant redox cofactor and for enzyme engineering efforts in controlling stereo chemistry of reduction reactions.

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space.

Dissimilatory metal reducing organisms play key roles in the biogeochemical cycle of metals as well as in the durability of submerged and buried metallic structures. The molecular mechanisms that support electron transfer across the microbe-metal interface in these organisms remain poorly explored. It is known that outer membrane proteins, in particular multiheme cytochromes, are essential for this type of metabolism, being responsible for direct and indirect, via electron shuttles, interaction with the insoluble electron acceptors. Soluble electron shuttles such as flavins, phenazines, and humic acids are known to enhance extracellular electron transfer. In this work, this phenomenon was explored. All known outer membrane decaheme cytochromes from Shewanella oneidensis MR-1 with known metal terminal reductase activity and a undecaheme cytochrome from Shewanella sp. HRCR-6 were expressed and purified. Their interactions with soluble electron shuttles were studied using stopped-flow kinetics, NMR spectroscopy, and molecular simulations. The results show that despite the structural similarities, expected from the available structural data and sequence homology, the detailed characteristics of their interactions with soluble electron shuttles are different. MtrC and OmcA appear to interact with a variety of different electron shuttles in the close vicinity of some of their hemes, and with affinities that are biologically relevant for the concentrations typical found in the medium for this type of compounds. All data support a view of a distant interaction between the hemes of MtrF and the electron shuttles. For UndA a clear structural characterization was achieved for the interaction with AQDS a humic acid analog. These results provide guidance for future work of the manipulation of these proteins toward modulation of their role in metal attachment and reduction.

Rapid Formation of a Preoligomeric Peptide–Metal–Peptide Complex Following Copper(II) Binding to Amyloid β Peptides

CuII connects peptides: The mechanism of binding of CuII to amyloid β peptides (Aβ) implicated in Alzheimer's disease was elucidated by stopped-flow spectroscopy, NMR relaxation, and simulation of the kinetics on the millisecond timescale. Two monomeric Cu–Aβ species and a dimeric Aβ–Cu–Aβ species were identified (see picture). Aberrant aggregation apparently occurs from the monomeric species. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Detection of a ternary complex of NF-κB and IκBα with DNA provides insights into how IκBα removes NF-κB from transcription sites

It has been axiomatic in the field of NF-κB signaling that the formation of a stable complex between NF-κB and the ankyrin repeat protein IκBα precludes the interaction of NF-κB with DNA. Contradicting this assumption, we present stopped-flow fluorescence and NMR experiments that give unequivocal evidence for the presence of a ternary DNA-NF-κB-IκBα complex in solution. Stepwise addition of a DNA fragment containing the κB binding sequence to the IκBα-NF-κB complex results in changes in the IκBα NMR spectrum that are consistent with dissociation of the region rich in proline, glutamate, serine, and threonine (PEST) and C-terminal ankyrin repeat sequences of IκBα from the complex. However, even at high concentrations of DNA, IκBα remains associated with NF-κB, indicated by the absence of resonances of the free N-terminal ankyrin repeats of IκBα. The IκBα-mediated release of NF-κB from its DNA-bound state may be envisioned as the reverse of this process. The initial step would consist of the coupled folding and binding of the intrinsically disordered nuclear localization sequence of the p65 subunit of NF-κB to the well-structured N-terminal ankyrin repeats of IκBα. Subsequently the poorly folded C-terminal ankyrin repeats of IκBα would fold upon binding to the p50 and p65 dimerization domains of NF-κB, permitting the negatively charged C-terminal PEST sequence of IκBα to displace the bound DNA through a process of local mass action.

A Peek at Polymerization

Chemistry The properties of plastics depend intimately on the dynamics of the polymerization reactions used to produce them. Because the reactions are often quite rapid, though, they can prove hard to track. Christianson et al. have adapted a nuclear magnetic resonance (NMR) spectrometer in order to monitor polymerization reactions on a millisecond time scale. Using a stopped-flow approach more common in optical spectroscopy, they set up the probe to acquire data just after pneumatically driven mixing of a catalyst solution stream with a stream of reactive monomer. With this system in hand, they examined the room-temperature polymerization of 1-hexene by a borane-activated zirconium catalyst. They were able to observe initiation and chain propagation steps directly, and also monitor buildup of a transiently deactivated form of the catalyst, resulting from borane binding to a zirconium hydride ligand after chain elimination from the metal center. The results bolster previous mechanistic hypotheses surrounding this catalyst's behavior and highlight the utility of stopped-flow NMR. J. Am. Chem. Soc. 132 , 10.1021/ja105107y (2010).

Stopped-Flow NMR: Determining the Kinetics of [rac-(C2H4(1-indenyl)2)ZrMe][MeB(C6F5)3]-Catalyzed Polymerization of 1-Hexene by Direct Observation

Stopped-flow NMR measurements suitable for determination of reaction kinetics on time scales of 100 ms or longer have been achieved by adaptation of a commercial NMR flow probe with a high-efficiency mixer and drive system. Studies of metallocene-catalyzed alkene polymerization at room temperature have been complicated by high rates, imprecise knowledge of the distribution of different catalyst species with time, and the high sensitivity of the catalysts to low concentrations of impurities. Application of the stopped-flow NMR method to the study of the kinetics of 1-hexene polymerization in the presence of (EBI)ZrMe[MeB(C(6)F(5))(3)] demonstrates that NMR spectroscopy provides an efficient method for direct and simultaneous measurement of substrate consumption and catalyst speciation as a function of time. Kinetic modeling of the catalyst and substrate concentration time courses reveal efficient determination of initiation, propagation, and termination rate constants. As first suggested by Collins and co-workers (Polyhedron 2005, 24, 1234-1249), a kinetic model in which Zr-HB(C(6)F(5))(3) forms rapidly upon beta-hydride elimination but reacts relatively slowly with alkene to reinitiate chain growth is supported by these data.

Capillary scale NMR flow mapping

Stopped-flow NMR at capillary scale has many advantages over traditional methods of introducing the sample into the probe, particularly when large numbers of samples must be examined. This work describes application of a simple method for direct visualization of a sample inside the flow cell of flow NMR systems to capillary scale analysis. We describe the details of the method and show how it can be used to measure the optimum flow rate for a capillary NMR system and how to determine the optimum sampling efficiency for small samples.

The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection

To illuminate the evolutionary pressure acting on the folding free energy landscapes of naturally occurring proteins, we have systematically characterized the folding free energy landscape of Top7, a computationally designed protein lacking an evolutionary history. Stopped-flow kinetics, circular dichroism, and NMR experiments reveal that there are at least three distinct phases in the folding of Top7, that a nonnative conformation is stable at equilibrium, and that multiple fragments of Top7 are stable in isolation. These results indicate that the folding of Top7 is significantly less cooperative than the folding of similarly sized naturally occurring proteins, suggesting that the cooperative folding and smooth free energy landscapes observed for small naturally occurring proteins are not general properties of polypeptide chains that fold to unique stable structures but are instead a product of natural selection.