Friday, July 29, 2016

bcTol: a highly water-soluble biradical for efficient dynamic nuclear polarization of biomolecules


Jagtap, A.P., et al., bcTol: a highly water-soluble biradical for efficient dynamic nuclear polarization of biomolecules. Chem Commun (Camb), 2016. 52(43): p. 7020-3.


Dynamic nuclear polarization (DNP) is an efficient method to overcome the inherent low sensitivity of magic-angle spinning (MAS) solid-state NMR. We report a new polarizing agent (), designed for biological applications, that yielded an enhancement value of 244 in a microcrystalline SH3 domain sample at 110 K.

Wednesday, July 27, 2016

Creating a hyperpolarised pseudo singlet state through polarisation transfer from parahydrogen under SABRE


Olaru, A.M., et al., Creating a hyperpolarised pseudo singlet state through polarisation transfer from parahydrogen under SABRE. Chem Commun (Camb), 2016. 52(50): p. 7842-5.


The creation of magnetic states that have long lifetimes has been the subject of intense investigation, in part because of their potential to survive the time taken to travel from the point of injection in a patient to the point where a clinically diagnostic MRI trace is collected. We show here that it is possible to harness the signal amplification by reversible exchange (SABRE) process to create such states in a hyperpolarised form that improves their detectability in seconds without the need for any chemical change by reference to the model substrate 2-aminothiazole. We achieve this by transferring Zeeman derived polarisation that is 1500 times larger than that normally available at 400 MHz with greater than 90% efficiency into the new state, which in this case has a 27 second lifetime.

Tuesday, July 26, 2016

[NMR] Research Associate in Dynamic Nuclear Polarisation NMR - Nottingham # DNPNMR

From the Ampere Magnetic Resonance List



Research Associate/Fellow in Magnetic Resonance / Dynamic Nuclear Polarisation

Reference: SCI202816E

Closing Date: Tuesday, 16th August 2016

Department: Physics & Astronomy

Salary: £25769 to £30738 per annum, depending on skills and experience (minimum £28,982 with relevant PhD)

Applications are invited for the above post based in the Sir Peter Mansfield Magnetic Resonance Centre (SPMMRC) which is part of the School of Physics and Astronomy.

It is expected that the successful candidate will work in a theory-led project in collaboration with NMR theorists and theoretical physicists on the development of a theoretical frame work for dynamic nuclear polarisation (DNP) NMR and its experimental verification. The SPMMRC houses a 600MHz/395GHz DNP MAS NMR spectrometer, a pulsed W-band EPR spectrometer, several dissolution DNP NMR systems including a clinical system and a unique DNP NMR spectrometer based on a dual isocentre magnet. The project is motivated by recent progress in simulating the polarisation dynamics in large nuclear spin ensembles (see 1) and will focus on the experimental verification of some of the theoretical predictions. This is an EPSRC funded project that involves close collaboration between theoretical physicists and NMR experimentalists as well as input from synthetic chemists. 

Candidates should have a PhD (or equivalent), or near completion in physics or a related discipline and have comprehensive experience in magnetic resonance experimentation and the use of magnetic resonance instruments. In particular, experiences with either low temperature DNP or the use electron resonance spectrometers are desirable. They should have good communication skills and enjoy working with a variety of different people across discipline boundaries.

This full-time post will be initially offered on a fixed-term contract for a period of 2 years with a possibility for extension.

Informal enquiries should be addressed to Walter Köckenberger, Email: walter.kockenberger@nottingham.ac.uk. Please note that applications sent directly to this email address will not be accepted.

Instructions for how to apply can be found on http://www.nottingham.ac.uk/jobs/howtoapply/index.aspx

The University of Nottingham is an equal opportunities employer and welcomes applications from all sections of the community.



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Monday, July 25, 2016

Analysis of the SABRE (Signal Amplification by Reversible Exchange) Effect at High Magnetic Fields


Pravdivtsev, A.N., et al., Analysis of the SABRE (Signal Amplification by Reversible Exchange) Effect at High Magnetic Fields. Appl. Magn. Reson., 2016. 47(7): p. 711-725.


A detailed study of the Signal Amplification By Reversible Exchange (SABRE) effect at high magnetic fields is performed. SABRE is formed by spin order transfer from parahydrogen to a substrate in a transient organometallic complex. Typically, such a transfer is efficient at low magnetic fields; at high fields it requires radio-frequency (RF) excitation of spins in the SABRE complex. However, recently it has been shown (Barskiy et al. in J. Am. Chem. Soc. 136:3322–3325, 2014) that high-field SABRE is also feasible due to “spontaneous” spin order transfer (i.e., transfer in the absence of RF excitation) although the transfer efficiency is low. Here, we studied the SABRE field dependence for protons in the field range 1.0–16.4 T and found an increase of polarization with the field; further optimization of proton polarization can be achieved by varying the viscosity of the solvent. As previously, polarization transfer is attributed to cross-relaxation; this conclusion is supported by additional experiments. For spin-½ hetero-nuclei, such as 15N and 31P, spontaneous spin order transfer is also feasible; however, in contrast to protons, it is based on a coherent mechanism. Consequently, higher transfer efficiency is achieved; moreover the 15N and 31P spectral patterns are remarkably different from that for protons: multiplet (anti-phase) polarization is seen for hetero-nuclei. Our study is of importance for enhancing weak nuclear magnetic resonance (NMR) signals by exploiting non-thermally polarized spins. Although the efficiency of high-field SABRE is lower than that of low-field SABRE; the high-field SABRE experiment is easy to implement for improving the sensitivity of NMR methods.

Friday, July 22, 2016

Immobilization of soluble protein complexes in MAS solid-state NMR: Sedimentation versus viscosity


Sarkar, R., et al., Immobilization of soluble protein complexes in MAS solid-state NMR: Sedimentation versus viscosity. Solid State Nucl Magn Reson, 2016. 76-77: p. 7-14.


In recent years, MAS solid-state NMR has emerged as a technique for the investigation of soluble protein complexes. It was found that high molecular weight complexes do not need to be crystallized in order to obtain an immobilized sample for solid-state NMR investigations. Sedimentation induced by sample rotation impairs rotational diffusion of proteins and enables efficient dipolar coupling based cross polarization transfers. In addition, viscosity contributes to the immobilization of the molecules in the sample. Natural Deep Eutectic Solvents (NADES) have very high viscosities, and can replace water in living organisms. We observe a considerable amount of cross polarization transfers for NADES solvents, even though their molecular weight is too low to yield significant sedimentation. We discuss how viscosity and sedimentation both affect the quality of the obtained experimental spectra. The FROSTY/sedNMR approach holds the potential to study large protein complexes, which are otherwise not amenable for a structural characterization using NMR. We show that using this method, backbone assignments of the symmetric proteasome activator complex (1.1MDa), and high quality correlation spectra of non-symmetric protein complexes such as the prokaryotic ribosome 50S large subunit binding to trigger factor (1.4MDa) are obtained.

Wednesday, July 20, 2016

Do twisted laser beams evoke nuclear hyperpolarization?


Schmidt, A.B., et al., Do twisted laser beams evoke nuclear hyperpolarization? J Magn Reson, 2016. 268: p. 58-67.


The hyperpolarization of nuclear spins promises great advances in chemical analysis and medical diagnosis by substantially increasing the sensitivity of nuclear magnetic resonance (NMR). Current methods to produce a hyperpolarized sample, however, are arduous, time-consuming or costly and require elaborate equipment. Recently, a much simpler approach was introduced that holds the potential, if harnessed appropriately, to revolutionize the production of hyperpolarized spins. It was reported that high levels of hyperpolarization in nuclear spins can be created by irradiation with a laser beam carrying orbital angular momentum (twisted light). Aside from these initial reports however, no further experimental verification has been presented. In addition, this effect has so far evaded a critical theoretical examination. In this contribution, we present the first independent attempt to reproduce the effect. We exposed a sample of immersion oil or a fluorocarbon liquid that was placed within a low-field NMR spectrometer to Laguerre-Gaussian and Bessel laser beams at a wavelength of 514.5nm and various topological charges. We acquired (1)H and (19)F NMR free induction decay data, either during or alternating with the irradiation that was parallel to B0. We observed an irregular increase in NMR signal in experiments where the sample was exposed to beams with higher values of the topological charge. However, at no time did the effect reach statistical significance of 95%. Given the measured sensitivity of our setup, we estimate that a possible effect did not exceed a hyperpolarization (at 5mT) of 0.14-6%, depending on the assumed hyperpolarized volume. It should be noted though, that there were some differences between our setup and the previous implementation of the experiment, which may have inhibited the full incidence of this effect. To approach a theoretical description of this effect, we considered the interaction of an electron with a plane wave, which is known to be able to induce electronic (e.g. in rubidium) and subsequent nuclear hyperpolarization. Compared to the plane wave, the additional transitions caused by a twisted wave are of the order of 10(-3) less. This suggests that the twist of the laser is unlikely to be responsible for the hyperpolarization of nuclear spins, unless a new mechanism of momentum transfer is identified.

Monday, July 18, 2016

Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR


Geiger, Y., et al., Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR. J Am Chem Soc, 2016. 138(17): p. 5561-7.


Smart materials are created in nature at interfaces between biomolecules and solid materials. The ability to probe the structure of functional peptides that engineer biogenic materials at this heterogeneous setting can be facilitated tremendously by use of DNP-enhanced solid-state NMR spectroscopy. This sensitive NMR technique allows simple and quick measurements, often without the need for isotope enrichment. Here, it is used to characterize a pentalysine peptide, derived from a diatom's silaffin protein. The peptide accelerates the formation of bioinspired silica and gets embedded inside the material as it is formed. Two-dimensional DNP MAS NMR of the silica-bound peptide and solution NMR of the free peptide are used to derive its secondary structure in the two states and to pinpoint some subtle conformational changes that the peptide undergoes in order to adapt to the silica environment. In addition, interactions between abundant lysine residues and silica surface are identified, and proximity of other side chains to silica and to neighboring peptide molecules is discussed.

Friday, July 15, 2016

Towards Overhauser DNP in supercritical CO2


van Meerten, S.G., et al., Towards Overhauser DNP in supercritical CO2. J Magn Reson, 2016. 267: p. 30-6.


Overhauser Dynamic Nuclear Polarization (ODNP) is a well known technique to improve NMR sensitivity in the liquid state, where the large polarization of an electron spin is transferred to a nucleus of interest by cross-relaxation. The efficiency of the Overhauser mechanism for dipolar interactions depends critically on fast local translational dynamics at the timescale of the inverse electron Larmor frequency. The maximum polarization enhancement that can be achieved for (1)H at high magnetic fields benefits from a low viscosity solvent. In this paper we investigate the option to use supercritical CO2 as a solvent for Overhauser DNP. We have investigated the diffusion constants and longitudinal nuclear relaxation rates of toluene in high pressure CO2. The change in (1)H T1 by addition of TEMPO radical was analyzed to determine the Overhauser cross-relaxation in such a mixture, and is compared with calculations based on the Force Free Hard Sphere (FFHS) model. By analyzing the relaxation data within this model we find translational correlation times in the range of 2-4ps, depending on temperature, pressure and toluene concentration. Such short correlation times may be instrumental for future Overhauser DNP applications at high magnetic fields, as are commonly used in NMR. Preliminary DNP experiments have been performed at 3.4T on high pressure superheated water and model systems such as toluene in high pressure CO2.

Wednesday, July 13, 2016

Correlating Synthetic Methods, Morphology, Atomic-Level Structure, and Catalytic Activity of Sn-β Catalysts


Wolf, P., et al., Correlating Synthetic Methods, Morphology, Atomic-Level Structure, and Catalytic Activity of Sn-β Catalysts. ACS Catalysis, 2016. 6(7): p. 4047-4063.


Sn-β zeolites prepared using different recipes feature very different catalytic activities for aqueous phase glucose isomerization, suggesting the presence of different active sites. A systematic study of the morphology and atomic-level structure of the materials using DNP NMR spectroscopy in combination with first-principles calculations allows for the discrimination between potential sites and leads to a proposal of specific structural features that are important for high activity. The results indicate that the materials showing the highest activity possess a highly hydrophobic, defect-free zeolite framework. Those materials show so-called closed and associated partially hydrolyzed Sn(IV) sites in the T6 and T5/T7 lattice positions. On the other hand, postsynthetically synthesized Sn-β samples prepared in two steps via dealumination and subsequent solid-state ion exchange from Al-β show significantly lower activity, which is associated with a hydrophilic framework and/or a lower accessibility and different lattice position of the Sn sites in the zeolite crystal. Further, we provide a method to distinguish between different Sn sites on the basis of NMR cartography using chemical shift and chemical shift anisotropy as readily measurable parameters. This cartography allows identifying not only the nature of the active sites (closed, defect-open, and hydrolyzed-open) but also their position within the BEA framework.

Monday, July 11, 2016

High-field dissolution dynamic nuclear polarization of [1-(13)C]pyruvic acid


Yoshihara, H.A., et al., High-field dissolution dynamic nuclear polarization of [1-(13)C]pyruvic acid. Phys Chem Chem Phys, 2016. 18(18): p. 12409-13.


[1-(13)C]pyruvate is the most widely used hyperpolarized metabolic magnetic resonance imaging agent. Using a custom-built 7.0 T polarizer operating at 1.0 K and trityl radical-doped [1-(13)C]pyruvic acid, unextrapolated solution-state (13)C polarization greater than 60% was measured after dissolution and rapid transfer to a spectrometer magnet, demonstrating the signal enhancement attainable using optimized hardware. Slower rates of polarization under these conditions can be largely overcome with higher radical concentrations.

Friday, July 8, 2016

Tailoring of Polarizing Agents in the bTurea Series for Cross-Effect Dynamic Nuclear Polarization in Aqueous Media


Sauvee, C., et al., Tailoring of Polarizing Agents in the bTurea Series for Cross-Effect Dynamic Nuclear Polarization in Aqueous Media. Chemistry, 2016. 22(16): p. 5598-606.


A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors varepsilon ((1) H) in cross-effect dynamic nuclear polarization (CE DNP) NMR experiments at 9.4 and 14.1 T and 100 K in a DNP-optimized glycerol/water matrix ("DNP juice") have been studied. We observe that varepsilon ((1) H) is strongly correlated with the substituents on the polarizing agents, and its trend is discussed in terms of different molecular parameters: solubility, average e-e distance, relative orientation of the nitroxide moieties, and electron spin relaxation times. We show that too short an e-e distance or too long a T1e can dramatically limit varepsilon ((1) H). Our study also shows that the molecular structure of AMUPol is not optimal and its varepsilon ((1) H) could be further improved through stronger interaction with the glassy matrix and a better orientation of the TEMPO moieties. A new AMUPol derivative introduced here provides a better varepsilon ((1) H) than AMUPol itself (by a factor of ca. 1.2).

Wednesday, July 6, 2016

Further Characterization of 394-GHz Gyrotron FU CW GII with Additional PID Control System for 600-MHz DNP-SSNMR Spectroscopy #DNPNMR


Ueda, K., et al., Further Characterization of 394-GHz Gyrotron FU CW GII with Additional PID Control System for 600-MHz DNP-SSNMR Spectroscopy. J Infrared Milli Terahz Waves, 2016: p. 1-12.


A 394-GHz gyrotron, FU CW GII, has been designed at the University of Fukui, Japan, for dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (SSNMR) experiments at 600-MHz 1H resonant frequency. After installation at the Institute for Protein Research (IPR), Osaka University, Japan, a PID feedback control system was equipped to regulate the electron gun heater current for stabilization of the electron beam current, which ultimately achieved stabilization of output power when operating in continuous wave (CW) mode. During exploration to further optimize operating conditions, a continuous tuning bandwidth of approximately 1 GHz was observed by varying the operating voltage at a fixed magnetic field. In the frequency range required for positive DNP enhancement, the output power was improved by increasing the magnetic field and the operating voltage from their initial operational settings. In addition, fine tuning of output frequency by varying the cavity cooling water temperature was demonstrated. These operating conditions and ancillary enhancements are expected to contribute to further enhancement of SSNMR signal.

[NMR] Postdoctoral position in biological MAS ssNMR #NMR #SSNMR

From the Ampere Magnetic Resonance List



Postdoctoral position in biological MAS ssNMR

The Van der Wel lab is looking for potential postdoctoral researchers with a background and/or interest in advanced magic-angle-spinning solid-state NMR. As described below, there are two different NIH-funded research projects available, focused either on protein aggregation and amyloid formation, or on mitochondrial protein-lipid interactions. Applications are sought from individuals with expertise in biological solid-state NMR (preferred), or in biomolecular solution NMR. Highly qualified individuals with a strong track record in biophysical or biochemical studies of protein aggregation/membrane proteins may also be suitable.

Potentially interested parties are encouraged to contact me with (informal) inquiries by email at vanderwel@pitt.edu. I will also be available to discuss things in person at either EUROMAR or the Rocky Mountain ssNMR conference.

Best wishes,
Patrick van der Wel

-----------------------------------

Postdoctoral opportunities in biomolecular solid-state NMR

One or more postdoctoral position(s) are available in the Van der Wel solid-state NMR research group in the Department of Structural Biology of the University of Pittsburgh School of Medicine.

Research topics:

The researcher(s) will join the Van der Wel lab to contribute to our NIH-funded research projects. The first project is focused on the structural and mechanistic studies of amyloid formation and protein aggregation, with a particular focus on polyglutamine-expanded proteins implicated in Huntington’s Disease. The second project studies mitochondrial protein- lipid interactions critical to the early stages of apoptosis, with implications for neurodegenerative disease and cancer research. Common to both projects, and most of our research, is a central use of advanced magic-angle-spinning (MAS) solid-state NMR spectroscopy. Crucial biological insights regarding the structure and dynamics of aggregated and membrane-bound proteins are obtained via state-of-the-art ssNMR measurements of relaxation rates, dipolar order parameters, intra- and intermolecular distance constraints, and backbone and side-chain torsion angles.

Related recent publications: 
Hoop et al. (2016) Huntingtin exon 1 fibrils feature an interdigitated β-hairpin-based polyglutamine core. PNAS 113(6); 1546. 
Mandal et al. (2015) Structural changes and pro-apoptotic peroxidase activity of cardiolipin-bound mitochondrial cytochrome c. Biophys. J. 109(9): 1873. 

Resources & Location:

The Van der Wel lab uses departmental wide-bore 600MHz and 750MHz Bruker ssNMR spectrometers outfitted with 3.2, 1.9, and 1.3 mm CP/MAS as well as static ssNMR probes. Departmental facilities offer state-of-the-art EM, X-ray and solution NMR instrumentation, with the latter including 700, 800, and 900 MHz spectrometers. Excellent resources are available for protein production, biophysical and computational studies. The lab is housed in the interdisciplinary Dept of Structural Biology, one of the basic science departments of the University of Pittsburgh School of Medicine. The department and the school of medicine are located in walking distance of the main campuses of both the University of Pittsburgh and Carnegie Mellon University, providing a fertile collaborative research environment.

Candidate:

A strong preference is given to candidates with experience with biomolecular multidimensional ssNMR techniques. A strong interest or experience in the areas of disease-associated protein aggregation and/or membrane-protein structure and function is a bonus. Highly qualified candidates who have a background in solution-state NMR or other structural biology methods, and have in interest in the above topics, are also encouraged to apply.

More Information?

For more detailed information on these projects, links to related publications, and other useful information please visit the lab website at http://www.vanderwellab.org. To apply, or to obtain more information, please contact Patrick van der Wel by email at vanderwel@pitt.edu. Applications are expected to include a cover letter (or “cover email”) explaining specific research interests, a CV, and the names and contact information for three reference writers. 


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Monday, July 4, 2016

Solid Effect DNP in a Rapid-melt setup #DNPNMR


van Bentum, P.J.M., et al., Solid Effect DNP in a Rapid-melt setup. J. Magn. Reson., 2016. 263: p. 126-135.


Dynamic Nuclear Polarization (DNP) has become a key element in nuclear magnetic resonance (NMR). Recently, we developed a novel approach to DNP enhanced liquid-state NMR based on rapid melting of a solid hyperpolarized sample followed by ‘in situ’ liquid-state NMR detection. This method allows 1 H detection with fast cycling options for signal averaging. In nonpolar solvents, doped with BDPA radicals, proton enhancement factors were achieved of up to 400. A short recycling delay of about 5 s allows for a fast determination of the hyper-polarization dynamics as function of the microwave frequency and power. Here, we use the rapid melt dnp method to study the mechanisms for DNP in the solid phase in more detail. Solid Effect, Cross Effect, Solid Overhauser and Liquid-state (supercritical) Overhauser DNP enhancement can be observed in the same setup. In this paper, we concentrate on Solid Effect DNP observed with both homogeneous narrow line radicals such as BDPA and with wide line anisotropic nitroxide radicals such as TEMPOL. We find indications that BDPA protons play an important role in Solid Effect DNP with this radical. A simplified spin diffusion model for BDPA can give a semi-quantitative description of the enhancements as function of the microwave power and as function of the proton concentration in the solid solution. For aqueous frozen samples we observe a similar Solid Effect DNP enhancement, which is analyzed within the simplified spin diffusion model.

Friday, July 1, 2016

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods


Segawa, T.F., et al., Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods. J Chem Phys, 2016. 144(19): p. 194201.


Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic alpha-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 muM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter , being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.