Friday, August 29, 2014

Recent advances in magic angle spinning solid state NMR of membrane proteins


Wang, S. and V. Ladizhansky, Recent advances in magic angle spinning solid state NMR of membrane proteins. Prog. NMR. Spec., 2014. 82(0): p. 1-26.


Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.

Wednesday, August 27, 2014

Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature

Solid-state DNP-NMR are typically performed at cryogenic temperatures and samples, especially bio-macromolecules often require cryo-protection. This is a recent review about sample preparation and cryo-protecting samples to preserve the spectral resolution.

Lee, M. and M. Hong, Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature. J Biomol NMR, 2014. 59(4): p. 263-277.


Solid-state NMR spectra of membrane proteins often show significant line broadening at cryogenic temperatures. Here we investigate the effects of several cryoprotectants to preserve the spectral resolution of lipid membranes and membrane peptides at temperatures down to ~200 K. Trehalose, glycerol, dimethylsulfoxide (DMSO), dimethylformamide (DMF), and polyethylene glycol (PEG), were chosen. These compounds are commonly used in protein crystallography and cryobiology. 13C and 1H magic-angle-spinning spectra of several types of lipid membranes show that DMSO provides the best resolution enhancement over unprotected membranes and also best retards ice formation at low temperature. DMF and PEG-400 show slightly weaker cryoprotection, while glycerol and trehalose neither prevent membrane line broadening nor prevent ice formation under the conditions of our study. Neutral saturated-chain phospholipids are the most amenable to cryoprotection, whereas negatively charged and unsaturated lipids attenuate cryoprotection. 13C-1H dipolar couplings and 31P chemical shift anisotropies indicate that high spectral resolution at low temperature is correlated with stronger immobilization of the lipids at high temperature, indicating that line narrowing results from reduction of the conformational space sampled by the lipid molecules at high temperature. DMSO selectively narrowed the linewidths of the most disordered residues in the influenza M2 transmembrane peptide, while residues that exhibit narrow linewidths in the unprotected membrane are less impacted. A relatively rigid beta-hairpin antimicrobial peptide, PG-1, showed a linewidth increase of ~0.5 ppm over a ~70 K temperature drop both with and without cryoprotection. Finally, a short-chain saturated lipid, DLPE, exhibits excellent linewidths, suggesting that it may be a good medium for membrane protein structure determination. The three best cryoprotectants found in this work-DMSO, PEG, and DMF-should be useful for low-temperature membrane-protein structural studies by SSNMR without compromising spectral resolution.

Monday, August 25, 2014

John Waugh, Institute Professor emeritus, dies at 85

No DNP blog post today, but rather sad news.



John Waugh, Institute Professor emeritus, dies at 85

Chemist pioneered development of NMR spectroscopy, allowing study of molecular structures of solids.

Anne Trafton | MIT News Office 
August 22, 2014

John S. Waugh, an MIT Institute Professor emeritus and professor emeritus in the Department of Chemistry, died Friday, Aug. 22, at the age of 85. Waugh was an authority in chemical physics, known internationally for his work in magnetic resonance.

Waugh’s pioneering work in nuclear magnetic resonance (NMR) made it possible to study the molecular structures of proteins involved in Alzheimer’s and Parkinson’s diseases, diabetes, and many other disorders. NMR uses the magnetic properties of atomic nuclei to unravel the structures and dynamics of substances containing those nuclei. In NMR, the magnetic moments of atomic nuclei are stimulated with static and radiofrequency magnetic fields, and give rise to signals useful in a variety of applications — from medical imaging to spectroscopy.

“He was an extremely humble giant in the development of solid-state nuclear magnetic resonance spectroscopy,” says Sylvia Ceyer, head of MIT’s Department of Chemistry. “His keen wit, razor-sharp intellect, and extraordinary sense of humor made him a treasured jewel amongst his colleagues.”

Friday, August 22, 2014

Cross Polarization for Dissolution Dynamic Nuclear Polarization


Batel, M., et al., Cross Polarization for Dissolution Dynamic Nuclear Polarization. Phys. Chem. Chem. Phys., 2014.


Dynamic nuclear polarization (DNP) in combination with subsequent dissolution of the sample allows the detection of low-???? nuclei in solution state with a signal gain of tens of thousands compared to experiments starting from Boltzmann conditions. The long polarization build-up times of typically more than one hour are a drawback of this technique. The combination of dissolution DNP with crosspolarization (CP) in the solid state was shown to have the potential to overcome this disadvantage. In this article we discuss the cross-polarization step under dissolution DNP conditions in more detail. We show that adiabatic half-passage pulses allow us to enhance the CP efficiency in power-limited DNP probes. As a low-power alternative to Hartmann-Hahn CP we also demonstrate the applicability of frequency-swept de- and re-magnetization pulses for polarization transfer via dipolar order. We investigate implications and restrictions of the common solid-state DNP mechanisms to the DNP-CP technique and apply a spin-thermodynamic model based on the thermal-mixing mechanism. The model allows us to investigate the dynamics of the polarization levels in a system with two nuclear Zeeman reservoirs and explains the enhanced DNP efficiency upon solvent deuteration within a spinthermodynamic picture.

Wednesday, August 20, 2014

Exploiting level anti-crossings (LACs) in the rotating frame for transferring spin hyperpolarization


Pravdivtsev, A.N., et al., Exploiting level anti-crossings (LACs) in the rotating frame for transferring spin hyperpolarization. Phys Chem Chem Phys, 2014. 16(35): p. 18707-19.


A method of transferring hyperpolarization among scalar-coupled nuclear spins is proposed, which is based on spin mixing at energy Level Anti-Crossing (LAC) regions. To fulfill LAC conditions a resonant RF-field was applied with properly set frequency and amplitude. In this situation LACs occur between the nuclear spin levels in the rotating doubly tilted reference frame. The validity of the approach is demonstrated by taking as an example the transfer of para-hydrogen induced polarization in a symmetric molecule, whose coupled spin network can be modeled as a four-spin AA'MM'-system with two pairs of 'isochronous' spins. For this spin system LAC positions have been identified; rules for the sign of spin polarization have been established. The dependence of the polarization transfer efficiency on the RF-field parameters and on the time profile of switching off the RF-field has been studied in detail; experimental results are in excellent agreement with the theory developed. In general, exploiting LACs in the rotating doubly tilted frame is a powerful tool for manipulating hyperpolarization in multispin systems.

Tuesday, August 19, 2014

Position at MIT

From the AMPERE Magnetic Resonance List


MIT-Harvard Center for Magnetic Resonance


JOB DESCRIPTION:

A position is available at the MIT-Harvard Center for Magnetic Research (CMR) located at the Francis Bitter Magnet Laboratory at MIT. Duties require assisting with the management of the day-to-day operations of the CMR, and carries responsibilities for training and advising users. The candidate is expected to improve laboratory operations, evaluate and test new methods of data collection, assist in the administration and maintenance of a cluster of Linux computers, maintain records of laboratory use, and perform routine and non-routine maintenance. In addition, the position requires supervision of the CMR infrastructure that includes compressed air, chilled water, nitrogen purification, and in the near future, a helium recovery and liquefier system. In addition, it is required that the candidate actively participate in the ample research opportunities of the CMR in solution, solid state and DNP NMR and/or high frequency EPR.

Qualifications:

Interested parties are required to have a PhD and established record of accomplishment in magnetic resonance. Experience with custom-built magnetic resonance instruments, NMR probe design, high frequency microwave instrumentation and/or commercial spectrometers would be a distinct advantage.


Please e-mail a resume, list of publications, and the names and e-mail addresses of three references to :

Prof. Robert G. Griffin
Francis Bitter Magnet Laboratory
Mass. Institute of Technology
NW14-3220, 77 Mass. Avenue
Cambridge, MA 02139-4703
USA

Email: rgg@mit.edu
Voice: 617-253-5597
Fax : 617-253-5405


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Monday, August 18, 2014

The role of level anti-crossings in nuclear spin hyperpolarization


Ivanov, K.L., et al., The role of level anti-crossings in nuclear spin hyperpolarization. Prog. NMR. Spec., 2014. 81(0): p. 1-36.


Nuclear spin hyperpolarization is an important resource for increasing the sensitivity of NMR spectroscopy and MRI. Signal enhancements can be as large as 3–4 orders of magnitude. In hyperpolarization experiments, it is often desirable to transfer the initial polarization to other nuclei of choice, either protons or insensitive nuclei such as 13C and 15N. This situation arises primarily in Chemically Induced Dynamic Nuclear Polarization (CIDNP), Para-Hydrogen Induced Polarization (PHIP), and the related Signal Amplification By Reversible Exchange (SABRE). Here we review the recent literature on polarization transfer mechanisms, in particular focusing on the role of Level Anti-Crossings (LACs) therein. So-called “spontaneous” polarization transfer may occur both at low and high magnetic fields. In addition, transfer of spin polarization can be accomplished by using especially designed pulse sequences. It is now clear that at low field spontaneous polarization transfer is primarily due to coherent spin-state mixing under strong coupling conditions. However, thus far the important role of LACs in this process has not received much attention. At high magnetic field, polarization may be transferred by cross-relaxation effects. Another promising high-field technique is to generate the strong coupling condition by spin locking using strong radio-frequency fields. Here, an analysis of polarization transfer in terms of LACs in the rotating frame is very useful to predict which spin orders are transferred depending on the strength and frequency of the B1 field. Finally, we will examine the role of strong coupling and LACs in magnetic-field dependent nuclear spin relaxation and the related topic of long-lived spin-states.

Friday, August 15, 2014

The C solid DNP mechanisms with perchlorotriphenylmethyl radicals - the role of Cl


Vigier, F.M., et al., The C solid DNP mechanisms with perchlorotriphenylmethyl radicals - the role of Cl. Phys Chem Chem Phys, 2014.


The microwave frequency swept DNP enhancement, referred to as the DNP spectrum, is strongly dependent on the EPR spectrum of the polarizing radical and it reveals the underlying DNP mechanisms. Here we focus on two chlorinated trityl radicals that feature axially symmetric powder patterns at 95 GHz, the width of which are narrower than those of TEMPOL or TOTAPOL but broader than that of the trityl derivative OX63. The static DNP lineshapes of these commonly used radicals in DNP, have been recently analyzed in terms of a superposition of basic Solid Effect (SE) and Cross Effect (CE)-DNP lineshapes, with their relative contributions as a fit parameter. To substantiate the generality of this approach and further investigate an earlier suggestion that a 35,37Cl-13C polarization transfer pathway, termed "hetero-nuclear assisted DNP", may be in effect in the chlorinated radicals (C. Gabellieri et al., Angew. Chem., Int. Ed., 2010, 49, 3360-3362), we measured the static 13C-glycerol DNP spectra of solutions of ca. approximately 10 mM of the two chlorinated trityl radicals as a function of temperature (10-50 K) and microwave power. Analysis of the DNP lineshapes was first done in terms of the SE/CE superposition model calculated assuming a direct e-13C polarization transfer. The CE was found to prevail at the high temperature range (40-50 K), whereas at the low temperature end (10-20 K) the SE dominates, as was observed earlier for 13C DNP with OX63 and 1H DNP with TEMPOL and TOTAPOL, thus indicating that this is rather general behavior. Furthermore, it was found that at low temperatures it is possible to suppress the SE, and increase the CE by merely lowering the microwave power. While this analysis gave a good agreement between experimental and calculated lineshapes when the CE dominates, some significant discrepancies were observed at low temperatures, where the SE dominates. We show that by explicitly taking into account the presence of 35/37Cl nuclei through a e-35,37Cl-13C polarization pathway in the SE-DNP lineshape calculations, as proposed earlier, we can improve the fit significantly, thus supporting the existence of the "hetero-nuclear assisted DNP" pathway.

Wednesday, August 13, 2014

High-field liquid state NMR hyperpolarization: a combined DNP/NMRD approach


Neugebauer, P., et al., High-field liquid state NMR hyperpolarization: a combined DNP/NMRD approach. Phys Chem Chem Phys, 2014. 16(35): p. 18781-18787.


Here we show how fast dynamics between radicals and solvent molecules in liquid solutions can be detected by comparison of coupling factors determined by nuclear magnetic relaxation dispersion (NMRD) measurements and dynamic nuclear polarization (DNP) enhancement measurements at high magnetic field (9.2 T). This is important for a theoretical understanding of the Overhauser DNP mechanism at high magnetic fields and thus for optimization of the DNP agent/target system for high resolution liquid state NMR applications. Mixtures of the solution of TEMPOL radicals in water, toluene, acetone and DMSO have been investigated. The results are compared to the classical hard-sphere model and molecular dynamic simulations. Our results clearly indicate that fast sub-ps dynamics, which are not related to classical rotational or translational motion of the molecules, significantly contribute to the Overhauser DNP mechanism at high magnetic fields.

Monday, August 11, 2014

Dynamic Nuclear Polarization of 1H, 13C, and 59Co in a Tris(ethylenediamine)cobalt(III) Crystalline Lattice Doped with Cr(III)


Corzilius, B., et al., Dynamic Nuclear Polarization of H, C, and Co in a Tris(ethylenediamine)cobalt(III) Crystalline Lattice Doped with Cr(III). J Am Chem Soc, 2014.


The study of inorganic crystalline materials by solid-state NMR spectroscopy is often complicated by the low sensitivity of heavy nuclei. However, these materials often contain or can be prepared with paramagnetic dopants without significantly affecting the structure of the crystalline host. Dynamic nuclear polarization (DNP) is generally capable of enhancing NMR signals by transferring the magnetization of unpaired electrons to the nuclei. Therefore, the NMR sensitivity in these paramagnetically doped crystals might be increased by DNP. In this paper we demonstrate the possibility of efficient DNP transfer in polycrystalline samples of [Co(en)3Cl3]2.NaCl.6H2O (en = ethylenediamine, C2H8N2) doped with Cr(III) in varying concentrations between 0.1 and 3 mol %. We demonstrate that 1H, 13C, and 59Co can be polarized by irradiation of Cr(III) with 140 GHz microwaves at a magnetic field of 5 T. We further explain our findings on the basis of electron paramagnetic resonance spectroscopy of the Cr(III) site and analysis of its temperature-dependent zero-field splitting, as well as the dependence of the DNP enhancement factor on the external magnetic field and microwave power. This first demonstration of DNP transfer from one paramagnetic metal ion to its diamagnetic host metal ion will pave the way for future applications of DNP in paramagnetically doped materials or metalloproteins.

Friday, August 8, 2014

Dynamic nuclear polarisation NMR of nanosized zirconium phosphate polymer fillers


Ziarelli, F., et al., Dynamic nuclear polarisation NMR of nanosized zirconium phosphate polymer fillers. Chemical Communications, 2014. 50(70): p. 10137-10139.


Surface functionalisation with organic modifiers of multi-layered zirconium phosphate (ZrP) nanoparticles used as polymer fillers can be directly probed by dynamic nuclear polarisation NMR, which provides unambiguous evidence of the presence of P-O-C chemical bonds at the surface of the ZrP layers, thereby confirming successful functionalisation.

Wednesday, August 6, 2014

Silica-surface reorganization during organotin grafting evidenced by 119Sn DNP SENS: a tandem reaction of gem-silanols and strained siloxane bridges


Conley, M.P., et al., Silica-surface reorganization during organotin grafting evidenced by 119Sn DNP SENS: a tandem reaction of gem-silanols and strained siloxane bridges. Phys. Chem. Chem. Phys., 2014. 16(33): p. 17822-17827.

http://dx.doi.org/10.1039/C4CP01973C

Grafting reactive molecular complexes on dehydroxylated amorphous silica is a strategy to develop "single-site" heterogeneous catalysts. In general, only the reactivity of isolated silanols is invoked for silica dehydroxylated at 700 [degree]C ([SiO2-700]), though ca. 10% of the surface silanols are in fact geminal Q2-silanols. Here we report the reaction of allyltributylstannane with [SiO2-700] and find that the geminal Q2-silanols react to form products that would formally arise from vicinal Q3-silanols that are not present on [SiO2-700], indicating that a surface rearrangement occurs. The reorganization of the silica surface is unique to silica dehydroxylated at 700 [degree]C or above. The findings were identified using Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) combined with DFT calculations.

Tuesday, August 5, 2014

Postdoctoral Position Available at the National High Magnetic Field Laboratory (NHMFL) on Magic-Angle Spinning Dynamic Nuclear Polarization (MAS-DNP)

From the Ampere Magnetic Resonance List


Postdoctoral Position Available at the National High Magnetic Field Laboratory (NHMFL) on Magic-Angle Spinning Dynamic Nuclear Polarization (MAS-DNP)

A postdoctoral position is available immediately at the NHMFL in Tallahassee Florida working on magic-angle spinning DNP. The NHMFL just received a 600MHz MAS DNP system. The candidate will develop applications utilizing the state-of-art equipment for bio-solids, materials/surface and small molecules and collaborate with users of NHMFL facilities and the DNP system. The candidate will join other scientists and engineers in a lab-wide initiative which also includes dissolution DNP and solution Overhauser DNP. Minority and female candidates are encouraged to apply. Please send applications to Zhehong Gan at gan@magnet.fsu.edu.

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Monday, August 4, 2014

High-field ELDOR-detected NMR study of a nitroxide radical in disordered solids: Towards characterization of heterogeneity of microenvironments in spin-labeled systems

With nitroxides one of the most popular polarizing agents for DNP-NMR spectroscopy, this article gives more insights into the precise interactions (hyperfine, quadrupolar, g anisotropy ...) at high magnetic fields.


Nalepa, A., et al., High-field ELDOR-detected NMR study of a nitroxide radical in disordered solids: Towards characterization of heterogeneity of microenvironments in spin-labeled systems. J. Magn. Reson., 2014. 242(0): p. 203-213.


The combination of high-field EPR with site-directed spin-labeling (SDSL) techniques employing nitroxide radicals has turned out to be particularly powerful in probing the polarity and proticity characteristics of protein/matrix systems. This information is concluded from the principal components of the nitroxide Zeeman (g), nitrogen hyperfine (A) and quadrupole (P) tensors of the spin labels attached to specific sites. Recent multi-frequency high-field EPR studies underlined the complexity of the problem to treat the nitroxide microenvironment in proteins adequately due to inherent heterogeneities which result in several principal x-components of the nitroxide g-tensor. Concomitant, but distinctly different nitrogen hyperfine components could, however, not be determined from high-field cw EPR experiments owing to the large intrinsic EPR linewidth in fully protonated guest/host systems. It is shown in this work that, using the W-band (95 GHz) ELDOR- (electron–electron double resonance) detected NMR (EDNMR) method, different principal nitrogen hyperfine, Azz, and quadrupole, Pzz, tensor values of a nitroxide radical in glassy 2-propanol matrix can be measured with high accuracy. They belong to nitroxides with different hydrogen-bond situations. The satisfactory resolution and superior sensitivity of EDNMR as compared to the standard ENDOR (electron–nuclear double resonance) method are demonstrated.

Friday, August 1, 2014

Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research

With DNP becoming an important technique in the material science community it is good to take a look every now and then at the progress that the field of solid-state NMR spectroscopy is making in the area of material science.


Goobes, G., Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research. Israel Journal of Chemistry, 2014. 54(1-2): p. 113-124.

http://dx.doi.org/10.1002/ijch.201300113

Many cellular events involve attachment of proteins to the surfaces of rigid or semi-rigid solid materials, such as the inorganic materials in the extracellular matrix of hard tissue, and the macromolecular scaffolds made of actin and tubulin filaments in the cytoskeleton. Understanding these processes on a fundamental level will have far-reaching repercussions for the design of biomaterials, biomedical research, and biomineralization. Numerous studies have reported structural changes experienced by proteins as they adhere to surfaces, yet there are only a few examples in which detailed views of protein conformation and alignment on surfaces were measured. Modern multidimensional solid-state NMR spectroscopy is timely situated to unveil molecular details of these processes and shed light on many fundamental questions related to recognition of surfaces by biomolecules. Targeting these questions is currently at the focal point of many research fields and can lead to insights and breakthroughs in biotechnology and in biomimetic material design.