Category Archives: Review

Overhauser Dynamic Nuclear Polarization: A Tool for Building Maps of Hydration Water #DNPNMR #ODNP #Review

Franck, John M. “Overhauser Dynamic Nuclear Polarization: A Tool for Building Maps of Hydration Water.” Biophysical Journal 118, no. 3, Supplement 1 (February 7, 2020): 487a.

https://doi.org/10.1016/j.bpj.2019.11.2695

Coating the surface of every macromolecule or macromolecular assembly, one finds a hydration layer composed of water molecules that move typically between 3× and 10× slower than water molecules in bulk water. The interaction between the water molecules in the hydration layer and the macromolecules contributes to the structural stability and sometimes the function of, e.g., proteins and lipid bilayers. Overhauser Dynamic Nuclear Polarization (ODNP) is an emerging electron-spin nuclear-spin (EPR-NMR) double-resonance tool that has demonstrated a capability of measuring the translational dynamics of water in the hydration layer. Here we discuss our efforts on two fronts: First, we design a scheme for measuring the thickness of the hydration layer and the effect of confinement on translational dynamics, as measured by ODNP, with controlled, appropriately labeled reverse micelle systems. Second, we describe the development of an a priori technique for converting ODNP measurements into a 3D “map” of hydration layer properties in dynamic room temperature samples that explore an ensemble of structures. This latter effort focuses on transmembrane model systems and utilizes the modern structure-prediction tool Rosetta in a fashion analogous to successful efforts to predict NMR order parameters. Particular focus is given to improving the quality and automation of the ODNP measurement, as well as validating predicted ensemble structures against both continuous wave EPR and NMR Paramagnetic Relaxation Enhancement (PRE) data.

Dynamic Nuclear Polarization Enhanced Neutron Crystallography: Amplifying Hydrogen in Biological Crystals #DNPNMR

Pierce, Joshua, Matthew J. Cuneo, Anna Jennings, Le Li, Flora Meilleur, Jinkui Zhao, and Dean A.A. Myles. “Dynamic Nuclear Polarization Enhanced Neutron Crystallography: Amplifying Hydrogen in Biological Crystals.” In Methods in Enzymology, 634:153–75. Elsevier, 2020. 

https://doi.org/10.1016/bs.mie.2019.11.018

Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10–100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.

Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals #DNPNMR

Pierce, Joshua, Matthew J. Cuneo, Anna Jennings, Le Li, Flora Meilleur, Jinkui Zhao, and Dean A. A. Myles. “Chapter Eight – Dynamic Nuclear Polarization Enhanced Neutron Crystallography: Amplifying Hydrogen in Biological Crystals.” In Methods in Enzymology, edited by Peter C. E. Moody, 634:153–75. Neutron Crystallography in Structural Biology. Academic Press, 2020.

https://doi.org/10.1016/bs.mie.2019.11.018

Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10–100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.

Pulsed Dynamic Nuclear Polarization #DNPNMR

Tan, Kong Ooi, Sudheer Jawla, Richard J Temkin, and Robert G Griffin. “Pulsed Dynamic Nuclear Polarization,” 8:14, 2019.

https://doi.org/10.1002/9780470034590.emrstm1558

In the last two decades continuous-wave (CW) microwave irradiation obtained from gyrotron microwave sources has been utilized extensively in the development and applications of new experimental approaches to high frequency dynamic nuclear polarization (DNP). Despite the abundant successes of this approach, it is well established experimentally and understood theoretically that at higher magnetic fields, where the resolution of the NMR spectra is optimal, the enhancement factors in CW DNP experiments decrease. Potentially this issue can be mitigated by using time domain or pulsed DNP techniques, which theoretically have field-independent enhancement factors. In this contribution, we discuss the pulsed DNP experiments that have been developed to date, along with the theory and the applicability of the sequences. As we will see pulsed techniques are fundamentally different from the CW-DNP methodology and require a different array of instrumentation, spin physics, and radicals. Hence, in addition to the underlying theory, we discuss the specifications of the microwave sources, DNP probes, and optimal radicals for pulsed DNP. The review ends with a summary of the current and future applications of pulsed DNP and conjectures as to the development of the pulsed methods for experiments at increasingly higher magnetic fields.

DNP and Cellular Solid-state NMR #DNPNMR

Paioni, Alessandra Lucini, Marie A M Renault, and Marc Baldus. “DNP and Cellular Solid-State NMR,” 7:12, 2018.

https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470034590.emrstm1561.

Solid‐state nuclear magnetic resonance (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments, largely irrespective of solubility or crystallinity. Revolutionary developments in the field of dynamic nuclear polarization (DNP) have greatly enhanced ssNMR sensitivity. In this article, we discuss ssNMR concepts and applications that make use of these advancements and enable the study of complex biomolecular and even cellular systems at unprecedented structural resolution and molecular detail.

Cryogenic Platforms and Optimized DNP Sensitivity #DNPNMR

Matsuki, Yoh, and Toshimichi Fujiwara. “Cryogenic Platforms and Optimized DNP Sensitivity,” 7:16, 2018.

https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470034590.emrstm1553

Modern high-field DNP NMR spectrometers are typically based on a cryogenic magic-angle sample spinning (MAS) capability. Conventionally, sample temperatures of T ∼100 K have been widely used, enabling substantial NMR signal enhancement with DNP at high external field conditions such as B0 =9.4 T. Today, however, the need for performing MAS DNP at much lower temperatures (T ≪100 K) is receiving growing attention for its ability to recover the rapidly degrading efficiency of the cross-effect (CE)-based DNP at even higher magnetic fields, B0 >10 T. In this article, we describe three contemporary cryogenic DNP MAS NMR probe systems: one is N2 based for T ∼100 K, and the other two are helium based for T ≪100 K. Principal requirements important in designing the cryogenic MAS NMR systems include long-term stability, cost efficiency, and readiness of operation. All the described setups incorporated various modifications and novel features to meet these challenges. In particular, the novel closed-cycle helium MAS system realizes all the requirements to a high standard, establishing an efficient and practical platform for ultralow sample temperature (T ∼30 K) MAS DNP. The resulting dramatic increase in sensitivity gain suggests the regained promise for the CE-based DNP at very high-field conditions (B0 >10 T). The experimental DNP data and effective sensitivity gain obtained with the described systems operating at 14.1 and 16.4 T are also discussed.

Versatile Dynamic Nuclear Polarization Hardware with Integrated Electron Paramagnetic Resonance Capabilities #DNPNMR

Leavesley, Alisa, Ilia Kaminker, and Songi Han. “Versatile Dynamic Nuclear Polarization Hardware with Integrated Electron Paramagnetic Resonance Capabilities,” 7:22, 2018.

https://doi.org/10.1002/9780470034590.emrstm1564

Successful application of dynamic nuclear polarization (DNP) often relies on procedures and sample formulations that are empirically optimized. In order to expand the scope of DNP to a wider range of sample systems and applications, a better understanding of the underlying DNP mechanism and spin dynamics is required. An aspect of DNP spin dynamics that is understudied is the electron spins, which can be attributed to high-field EPR capabilities not being commonly available under DNP conditions. Here, we present a combined and versatile DNP/EPR instrument that allows us to simultaneously follow the electron and nuclear spin dynamics during the course of the DNP experiment. A modular design ensures the versatility of such an instrument, where a solid-state microwave (μw) source permits high agility for electron spin manipulation. This article presents a detailed description of the DNP/EPR instrument, including the discussion of the components required for a dual DNP/EPR instrument, the integration of arbitrary waveform generation for shape μw pulses, and a two-source quasi-optical configuration that enables artifact-free electron–electron double resonance experiments at 200 GHz. We conclude by providing select examples in which the evaluation of electron spin dynamics was necessary to elucidate the underlying DNP mechanism.

Dissolution Dynamic Nuclear Polarization Methodology and Instrumentation #DNPNMR

Kurzbach, Dennis, and Sami Jannin. “Dissolution Dynamic Nuclear Polarization Methodology and Instrumentation,” 7:16, 2018. 

https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470034590.emrstm1563

Dissolution dynamic nuclear polarization (d-DNP) denotes a method to enhance signals in nuclear magnetic resonance (NMR) spectroscopy by hyperpolarization of nuclear spins at cryogenic temperature in the solid state prior to a rapid dissolution, transfer of a sample to a conventional NMR spectrometer, and detection at ambient temperatures in the liquid state. The purpose of this chapter is to review the general methodology behind d-DNP, and instrumentational aspects going from basic tasks, such as sample preparation, over operational aspects, such as the use of crosspolarization techniques, magnetic tunnels, and the removal of polarization agents, to future perspectives, such as the long-distance transport of hyperpolarized substrates.

Paramagnetic Metal Ions for Dynamic Nuclear Polarization #DNPNMR

Corzilius, Björn. “Paramagnetic Metal Ions for Dynamic Nuclear Polarization,” 7:16, 2018.

https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470034590.emrstm1593

Paramagnetic metal ions have been utilized as polarizing agents already in the early days of dynamic nuclear polarization (DNP) and have been more recently introduced for magic-angle spinning (MAS) DNP at high magnetic field. In this article, a comprehensive overview is given about the concepts relevant to DNP with high-spin metal ions. The theoretical basis covering the peculiar electron spin dynamics including spin-orbit coupling and zero-field splitting is reviewed, and prerequisites for efficient DNP are introduced. Subsequently, special considerations about the relevant DNP mechanisms (i.e., solid effect and cross effect) are derived. The practical aspects particular to high-spin metal ion DNP are discussed, focusing on differences with respect to conventional (i.e., radical) polarizing agents. In the final section, several demonstrations of MAS DNP on model systems as well as samples relevant to structural biology and materials research are presented. At last, an outlook is given about the prospects of metal ion DNP in light of recent and future advances in modern DNP.

Electron Paramagnetic Resonance Instrumentation #DNPNMR

Instrumentation for DNP-NMR spectroscopy has many similar components to instrumentation for EPR spectroscopy. This is a comprehensive review of the current state-of-the-art in EPR instrumentation, covering all aspects from magnet technology, pulse generation, detection and resonator design.

Reijerse, Edward, and Anton Savitsky. “Electron Paramagnetic Resonance Instrumentation.” In EMagRes, edited by Robin K. Harris and Roderick L. Wasylishen, 187–206. Chichester, UK: John Wiley & Sons, Ltd, 2017.

https://doi.org/10.1002/9780470034590.emrstm1511

The article gives a general overview of instrumentation commonly used in electron paramagnetic resonance. It includes magnet systems, microwave bridge configurations, and sample cryostats. A special focus has been placed on the discussion of various resonator and sample probe designs used in CW as well as pulsed EPR. Specialized EPR applications such as very high frequency EPR, electrochemistry, stopped flow, and the application to volume limited samples are briefly discussed.

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