Fast Exchange Rate Research Articles

Rab29 Fast Exchange Mutants: Characterization of a Challenging Rab GTPase.

Rab29 has been implicated in multiple membrane trafficking processes with no described effectors or regulating proteins. Its fast nucleotide exchange rate and inability to bind GDI in cytosol make it a unique and poorly understood Rab. Because the conventional, "GTP-locked" Rab mutation does not have the desired effect in Rab29, we present here the use of a fluorescence-based assay to characterize novel Rab29 mutants (I64T and V156G) that display faster nucleotide exchange rates, allowing for GEF-independent Rab29 activation.

Self‐organization Properties of a GPCR‐Binding Peptide with a Fluorinated Tail Studied by Fluorine NMR Spectroscopy

Conjugation of the bioactive apelin-17 peptide with a fluorocarbon chain results in self-organization of the peptide into micelles. Fluorine NMR spectroscopy studies show that the fluoropeptide's micelles are monodisperse, while proton NMR indicates that the peptide moiety remains largely disordered despite micellization. A very fast exchange rate is measured between the free and micellar states of the peptide which enables the number of molecules present in the micelle to be estimated as 200, in agreement with values found by dynamic light scattering measurements.

In-situ synthesis TiO2 nanosheets@rGO for ultrafast sodium ion storage at both room and low temperatures

Abstract Sodium ion (Na+) storage has attracted wide attention as an advanced large-scale energy storage system for our modern society. Due to the larger radius of Na+ than lithium ion, finding a suitable anode material for sodium ion batteries (SIBs) is a big challenge especially at low temperature. Here, an in-situ method which simultaneous reduction of graphene and oxidation of Ti3+ was used to synthesize a 3 dimensional (3D) TiO2@ reduced graphene oxide (TiO2@rGO) structure. The special 3D structure built with the basic structure units of TiO2@rGO heterojunctions could offer fast ion insertion/deinsertion, short diffusion distance, and lower diffusion energy barrier as well, thus enhance the Na+ intercalation pseudocapacitive process. The enhanced pseudocapacitive process could increase the kinetic reaction of the cell especially at the high current densities. The synthesized TiO2@rGO sample exhibits an outstanding electrochemistry performance as an anode material for SIBs with superior cycling and rate performance. At a current density of 7 A g−1, it showed a high capacity retention of above 90% and with a capacity decay of 0.0003% per cycle. Most importantly, owning to the fast electron exchange rate in the system, the cell shows an outstanding electrochemical performance at an ultra-low temperature of −40 °C.

Towards an Improved Design of MRI Contrast Agents: Synthesis and Relaxometric Characterisation of Gd-HPDO3A Analogues.

The properties of LnIII -HPDO3A complexes as relaxation enhancers and paraCEST agents are essentially related to the hydroxylpropyl moiety. A series of three HPDO3A derivatives, with small modifications to the hydroxyl arm, were herein investigated to understand how heightened control can be gained over the parameters involved in the design of these agents. A full 1 H and 17 O-NMR relaxometric analysis was conducted and demonstrated that increasing the length of the OH group from the lanthanide centre significantly enhanced the water exchange rate of the gadolinium complex, but with a subsequent reduction in kinetic stability. Alternatively, the introduction of an additional methyl group, which increased the steric bulk around the OH moiety, resulted in the formation of almost exclusively the TSAP isomer (95 %) as identified by 1 H-NMR of the europium complex. The gadolinium analogue of this complex also exhibited a very fast water exchange rate, but with no detectable loss of kinetic stability. This complex therefore demonstrates a notable improvement over Gd-HPDO3A.

Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates.

Determining hydrogen exchange kinetics in proteins can shed light on their structure and dynamics. Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique to determine exchange rates. In this chapter, we describe a new method (Paris-DÉCOR) to determine fast protein amide backbone hydrogen exchange rates in the range 10 to 104s-1. Measuring fast exchange rates is particularly important for the study of intrinsically disordered proteins, where there is very little protection from exchange to the solvent by the formation of persistent structure. We provide a protocol to set up the experiment as well as MATLAB scripts for numerical simulation that is needed to determine the exchange rates.

Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus

Although the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan composed of the following structure [l-Fucp4(SO3−)-α(1-3)-l-Fucp2,4(SO3−)-α(1-3)-l-Fucp2(SO3−)-α(1-3)-l-Fucp2(SO3−)] and the composing monosaccharide unit Fucp, primarily by nuclear magnetic resonance (NMR) experiments performed at very low temperatures and using H2O as the solvent for the sugars rather than using the conventional deuterium oxide. By slowing down the fast chemical exchange rates and forcing the protonation of labile sites, we increased the number of through-space 1H–1H distances that could be measured by NMR spectroscopy. Following this strategy, additional conformational details of the tetrasaccharide and l-Fucp in solution were obtained. Computational molecular dynamics was performed to complement and validate the NMR-based measurements. A model of the NMR-restrained 3D structure is offered for the tetrasaccharide.

Chemical exchange saturation transfer magnetic resonance imaging and its main and potential applications in pre-clinical and clinical studies.

Chemical exchange saturation transfer (CEST) imaging is a novel contrast mechanism, relying on the exchange between mobile protons in amide (-NH), amine (-NH2) and hydroxyl (-OH) groups and bulk water. Due to the targeted protons present in endogenous molecules or exogenous compounds applied externally, CEST imaging can respectively, generate endogenous or exogenous contrast. Nowadays, CEST imaging for endogenous contrast has been explored in pre-clinical and clinical studies. Amide CEST, also called amide proton transfer weighted (APT) imaging, generates CEST effect at 3.5 ppm away from the water signal and has been widely investigated. Given the sensitivity to amide proton concentration and pH level, APT imaging has shown robust performance in the assessment of ischemia, brain tumors, breast and prostate cancer as well as neurodegenerative diseases. With advanced methods proposed, pure APT and Nuclear Overhauser Effect (NOE) mediated CEST effects were separately fitted from original APT signal. Using both effects, early but promising results were obtained for glioma patients in the evaluation of tumor response to therapy and patient survival. Compared to amide CEST, amine CEST is also mobile proton concentration and pH dependent, but has a faster exchange rate between amine protons and water. The resultant CEST effect is usually introduced at 1.8-3 ppm. Glutamate and creatine, as two main metabolites with amine groups for CEST imaging, have been applied to quantitatively assess diseases in the central nervous system and muscle system, respectively. Glycosaminoglycan (Gag) as a representative metabolite with hydroxyl groups has also been measured to evaluate the cartilage of knee or intervertebral discs in CEST MRI. Due to limited frequency difference between hydroxyl protons and water, 7T for better spectral separation is preferred over 3T for GagCEST measurement. The applications of CEST MRI with exogenous contrast agents are still quite limited in clinic. While certain diamagnetic CEST agents, such as dynamic-glucose, have been tried in human for brain tumor or neck cancer assessment, most exogenous agents, i.e., paramagnetic CEST agents, are still tested in the pre-clinical stage, mainly due to potential toxicity. Engineered tissues for tissue regeneration and drug delivery have also shown a great potential in CEST imaging, as many of them, such as hydrogel and polyamide materials, contain mobile protons or can be incorporated with CEST specific chemical compounds. These engineered tissues can thus generate CEST effect in vivo, allowing a possibility to understand the fate of them in vivo longitudinally. Although the CEST MRI with engineered tissues has only been established in early stage, the obtained first evidence is crucial for further optimizing these biomaterials and finally accomplishing the translation into clinical use.

Self-Healable Dielectric Polydimethylsiloxane Composite Based on Zinc-Imidazole Coordination Bond

Self-healing material has been intensively studied in the last decade due to its capability of improving materials’ lifetime and safety. Among the numerous proposed self-healing mechanisms, reversible metal-ligand coordination bond is considered as a strong candidate for a healing moiety because of its high tunability of mechanical properties based on the thermodynamic characteristics and kinetic parameters of metal ions or ligands. Furthermore, the dipolar nature of coordination bond can enhance the dielectric property of the material. Herein, zinc-imidazole coordination bond, having a fast ligand exchange rate in ambient condition, was employed as a healing moiety to synthesize room temperature self-healable polydimethylsiloxane (PDMS). Imidazole modified PDMS cross-linked by ligand and zinc ratio 4.5 (IMZ-PDMS-1100 L/Z 4.5) exhibited ultimate tensile strength (UT) of 60.73 kPa with ultimate extensibility (UE) of 211%. These mechanical properties could be adjusted by varying L/Z ratio and IMZ content. In comparison with previously reported metal-ligand based self-healing PDMS, IMZ-PDMS-1100 L/Z 4.5 showed faster healing rate that recovered 98% of UT and UE after 31 h healing and even faster healing rate was achieved with higher IMZ content. Moreover, cross-linked IMZ-PDMS displayed high dielectric constant of 8.30±0.74 at 1 MHz, which was 2.7 times higher than conventional PDMS.

Green solvent assisted synthesis of cesium bismuth halide perovskite nanocrystals and the influences of slow and fast anion exchange rates.

Replacing lead in halide perovskites to address the concerns of their toxicity and stability has driven a recent surge in research toward alternative lead-free perovskite materials. Lead-free all inorganic cesium bismuth halide (Cs3Bi2X9) perovskite nanocrystals have attracted attention in recent years due to the air-stability and non-toxic nature of bismuth. Herein, we demonstrate a facile sonication-assisted approach for the preparation of all-inorganic cesium bismuth iodide (Cs3Bi2I9) perovskite nanocrystals (NCs) using propylene carbonate as a green, alternative solvent. The photoluminescence (PL) spectra of the Cs3Bi2X9 NCs have a peak emission that can be tuned from 410 to 550 nm by controlling the composition of the NCs through an anion exchange reaction using tetraalkylammonium halides as a source of halide ions. The rate of this anion exchange reaction is demonstrated to have a significant influence on the dimensions of the NCs obtained from the parent Cs3Bi2I9 NCs. The PL emission of these nanocrystals is predominately due to exciton recombination processes. The NCs also exhibit air-stability for at least 150 days.

Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy.

NMR spectroscopy is a pivotal technique to measure hydrogen exchange rates in proteins. However, currently available NMR methods to measure backbone exchange are limited to rates of up to a few per second. To raise this limit, we have developed an approach that is capable of measuring proton exchange rates up to approximately 104 s-1 . Our method relies on the detection of signal loss due to the decorrelation of antiphase operators 2Nx Hz by exchange events that occur during a series of pi pulses on the 15 N channel. In practice, signal attenuation was monitored in a series of 2D H(CACO)N spectra, recorded with varying pi-pulse spacing, and the exchange rate was obtained by numerical fitting to the evolution of the density matrix. The method was applied to the small calcium-binding protein Calbindin D9k , where exchange rates up to 600 s-1 were measured for amides, where no signal was detectable in 15 N-1 H HSQC spectra. A temperature variation study allowed us to determine apparent activation energies in the range 47-69 kJ mol-1 for these fast exchanging amide protons, consistent with hydroxide-catalyzed exchange.

Supramolecular assemblies based on amphiphilic Mn2+-complexes as high relaxivity MRI probes.

In the research field of MRI contrast agents (CAs), amphiphilic paramagnetic complexes are typically sought for the increased plasmatic half-life and high relaxivity values, but limited examples of amphiphilic Mn2+-based CAs have been reported to date. In this work the Mn2+-complexes of six original amphiphilic ligands (three EDTA-like ligands and three 1,4-DO2A derivatives) embodying one or two aliphatic chains were evaluated as potential MRI contrast agents and compared. Strong self-association into micelles resulted in a relaxivity (r1) enhancement (ca. 80% with respect to MnEDTA) as a consequence of the increased molecular tumbling rate of the supramolecular aggregate. In the case of bis-substituted systems the r1 gain is much higher due to the restricted local rotation of the chelates about the pendant aliphatic chains (r1 in the range 12.6-18.4 mM-1 s-1, 2-3 times higher than for the micelles obtained with single-chain EDTA systems). Furthermore, these amphiphilic chelates tightly bind to human serum albumin (HSA) with association constants KA in the range 104-105 M-1. The resulting supramolecular adducts achieve remarkable relaxivity values, in the range 50-60 mM-1 s-1 for the MnEDTA-like chelates and 27-30 mM-1 s-1 for the 1,4-DO2A-like systems (at 298 K and 20 MHz), thanks to their fast water exchange rate.

Stepwise Synthesis of Metal-Organic Frameworks.

Metal-organic frameworks (MOFs) are a category of porous materials that offer unparalleled control over their surface areas (demonstrated as higher than for any other material), pore characteristics, and functionalization. This allows them to be customized for exceptional performance in a wide variety of applications, most commonly including gas storage and separation, drug delivery, luminescence, or heterogeneous catalysis. In order to optimize biomimicry, controlled separations and storage of small molecules, and detailed testing of structure-property relationships, one major goal of MOF research is "rational design" or "pore engineering", or precise control of the placement of multiple functional groups in pores of chosen sizes and shapes. MOF crystal growth can be controlled through judicious design of stepwise synthetic routes, which can also allow functionalization of MOFs in ways that were previously synthetically inaccessible. Organic chemists have developed a library of powerful techniques over the last century, allowing the total synthesis and detailed customization of complex molecules. Our hypothesis is that total synthesis is also possible for customized porous materials, through the development of similar multistep techniques. This will enable the rational design of MOFs, which is a major goal of many researchers in the field. We have begun developing a library of stepwise synthetic techniques for MOFs, allowing the synthesis of ultrastable MOFs with multiple crystallographically ordered and customizable functional groups at controlled locations within the pores. In order to design MOFs with precise control over pore size and shape, stability, and the placement of multiple different functional groups within the pores at tunable distances from one another, we have concentrated on methods which allow us to circumvent the lack of control inherent to one-pot MOF crystallization. Kinetically tuned dimensional augmentation (KTDA) is an approach using preformed metal clusters as starting materials and monotopic carboxylates as equilibrium shifting agents to make single crystals of ultrastable MOFs. Postsynthetic metathesis and oxidation (PSMO) takes advantage of the fast ligand exchange rate of a metal ion at the low oxidation state as well as the kinetic inertness of the same metal at high oxidation state to make ultrastable and highly crystalline MOFs. Multiple similar strategies have been successful for the metathesis of Fe-based MOFs to Cr3+. Several highly crystalline Ti-MOFs have also been prepared. Kinetically controlled linker installation and cluster metalation methods utilize a stable MOF with inherent coordinatively unsaturated sites as matrix and postsynthetically install linkers or grow clusters on the matrix, so that a robust MOF with precisely placed functionalities is realized. This method has diverse applications especially when specific functional groups or metals having synergistic effects are desired in the proper proximity. Exceptional porosity and stability are required for many potential applications. We have demonstrated several of these, including entrapment of nanoscaled functional moieties such as enzymes. We have developed a series of metal-organic frameworks (PCN-333) with rationally designed ultralarge mesoporous cages as single-molecule traps for enzyme encapsulation. We successfully incorporated metalloporphyrins, well-known biofunctional moieties, into robust MOFs for biomimetic catalytic applications. By rationally tuning the synthetic conditions, we obtained several different porphyrinic Zr-, Fe-, and Ti-MOFs with distinct pore size and concentrated acid or base stability, which offer eligible candidates for different applications. These and other stepwise kinetic tuning and catalyst incorporation methods are small steps toward achieving the grand challenge of detailed control of the placement of matter on an atomic and molecular level.

On coupling fluid plasma and kinetic neutral physics models

The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that they scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.

Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime

NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17O NMR of solid NaNO3 in which the NO3− ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO3 acquired in the temperature range of 173–413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO3− ion jumps span eight orders of magnitude (102–1010s−1) covering both transitions of the dynamic 17O line shape.

QUESPOWR MRI: QUantification of Exchange as a function of Saturation Power On the Water Resonance

QUantification of Exchange as a function of Saturation Power On the Water Resonance (QUESPOWR) MRI is a new method that can estimate chemical exchange rates. This method acquires a series of OPARACHEE MRI acquisitions with a range of RF powers for the WALTZ16∗ pulse train, which are applied on the water resonance. A QUESPOWR plot can be generated from the power dependence of the % water signal, which is similar to a QUESP plot that is generated from CEST MRI acquisition methods with RF saturation applied off-resonance from water. A QUESPOWR plot can be quantitatively analyzed using linear fitting methods to provide estimates of average chemical exchange rates. Analyses of the shapes of QUESPOWR plots can also be used to estimate relative differences in average chemical exchange rates and concentrations of biomolecules. The performance of QUESPOWR MRI was assessed via simulations, an in vitro study with iopamidol, and an in vivo study with a mouse model of mammary carcinoma. The results showed that QUESPOWR MRI is especially sensitive to chemical exchange between water and biomolecules that have intermediate to fast chemical exchange rates and chemical shifts that are close to water, which are notoriously difficult to assess with other CEST MRI methods. In addition, in vivo QUESPOWR MRI detected acidic tumor tissues relative to normal tissues that are pH-neutral, and therefore may be a new paradigm for tumor detection with MRI.

XANES Reveals the Flexible Nature of Hydrated Strontium in Aqueous Solution.

X-ray absorption near-edge structure (XANES) spectroscopy has been used to determine the structure of the hydrated strontium in aqueous solution. The XANES analysis has been carried out using solid [Sr(H2O)8](OH)2 as reference model. Classical and Car-Parrinello molecular dynamics (MD) simulations have been carried out and in the former case two different sets of Lennard-Jones parameters have been used for the Sr(2+) ion. The best performing theoretical approach has been chosen on the basis of the experimental results. XANES spectra have been calculated starting from MD trajectories, without carrying out any minimization of the structural parameters. This procedure allowed us to properly account for thermal and structural fluctuations occurring in the aqueous solution in the analysis of the experimental spectrum. A deconvolution procedure has been applied to the raw absorption data thus increasing the sensitivity of XANES spectroscopy. One of the classical MD simulations has been found to provide a XANES theoretical spectrum in better agreement with the experimental data. An 8-fold hydration complex with a Sr-O distance of 2.60 Å has been found to be compatible with the XANES data, in agreement with previous findings. However, the hydration shells of the strontium ions have been found to have a flexible nature with a fast ligand exchange rate between the first and second hydration shell occurring in the picosecond time scale.

A biomarker-responsive T2ex MRI contrast agent.

This study investigated a fundamentally new type of responsive MRI contrast agent for molecular imaging that alters T2 exchange (T2ex ) properties after interacting with a molecular biomarker. The contrast agent Tm-DO3A-oAA was treated with nitric oxide (NO) and O2 . The R1 and R2 relaxation rates of the reactant and product were measured with respect to concentration, temperature, and pH. Chemical exchange saturation transfer (CEST) spectra of the reactant and product were acquired using a 7 Tesla (T) MRI scanner and analyzed to estimate the chemical exchange rates and r2ex relaxivities. The reaction of Tm-DO3A-oAA with NO and O2 caused a 6.4-fold increase in the r2 relaxivity of the agent, whereas r1 relaxivity remained unchanged, which demonstrated that Tm-DO3A-oAA is a responsive T2ex agent. The effects of pH and temperature on the r2 relaxivities of the reactant and product supported the conclusion that the product's benzimidazole ligand caused the agent to have a fast chemical exchange rate relative to the slow exchange rate of the reactant's ortho-aminoanilide ligand. T2ex MRI contrast agents are a new type of responsive agent that have good detection sensitivity and specificity for detecting a biomarker, which can serve as a new tool for molecular imaging. Magn Reson Med 77:1665-1670, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Oxidative Conversion of a Europium(II)-Based T1 Agent into a Europium(III)-Based paraCEST Agent that can be Detected In Vivo by Magnetic Resonance Imaging.

The Eu(II) complex of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) tetra(glycinate) has a higher reduction potential than most Eu(II) chelates reported to date. The reduced Eu(II) form acts as an efficient water proton T1 relaxation reagent, while the Eu(III) form acts as a water-based chemical exchange saturation transfer (CEST) agent. The complex has extremely fast water exchange rate. Oxidation to the corresponding Eu(III) complex yields a well-defined signal from the paraCEST agent. The time course of oxidation was studied in vitro and in vivo by T1-weighted and CEST imaging.

Oxidative Conversion of a Europium(II)‐Based T1 Agent into a Europium(III)‐Based paraCEST Agent that can be Detected In Vivo by Magnetic Resonance Imaging

AbstractThe EuII complex of 1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) tetra(glycinate) has a higher reduction potential than most EuII chelates reported to date. The reduced EuII form acts as an efficient water proton T1 relaxation reagent, while the EuIII form acts as a water‐based chemical exchange saturation transfer (CEST) agent. The complex has extremely fast water exchange rate. Oxidation to the corresponding EuIII complex yields a well‐defined signal from the paraCEST agent. The time course of oxidation was studied in vitro and in vivo by T1‐weighted and CEST imaging.

Simultaneous optimization of power and duration of radio-frequency pulse in PARACEST MRI

Chemical exchange saturation transfer (CEST) MRI is increasingly used to probe mobile proteins and microenvironment properties, and shows great promise for tumor and stroke diagnosis. The CEST effect is complex and depends not only on the CEST agent concentration, exchange rates, the characteristic of the magnetization transfer (MT), and the relaxation properties of the tissue, but also varies with the experimental conditions such as radio-frequency (RF) pulse power and duration. The RF pulse is one of the most important factors that promote the CEST effect for biological properties such as pH, temperature and protein content, especially for contrast agents with intermediate to fast exchange rates. The CEST effect is susceptible to the RF duration and power. The present study aims at determining the optimal power and the corresponding optimal duration (that maximize the CEST effect) using an off-resonance scheme through a new definition of the CEST effect. This definition is formulated by solving the Bloch-McConnell equation through the R1ρ method (based on the eigenspace solution) for both of the MT and CEST effects as well as their interactions. The proposed formulations of the optimal RF pulse power and duration are the first formulations in which the MT effect is considered. The extracted optimal RF pulse duration and power are compared with those of the MTR asymmetry model in two- and three-pool systems, using synthetic data that are similar to the muscle tissue. To validate them further, the formulations are compared with the empirical formulation of the CEST effect and other findings of the previous researches. By extending our formulations, the optimal power and the corresponding optimal duration (in the biological systems with many chemical exchange sites) can be determined.