Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic-level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental ¹³C/¹⁵N chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.

19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies

We report remarkably high, up to 100-fold, signal enhancements in 19F dynamic nuclear polarization (DNP) magic angle spinning (MAS) spectra at 14.1 T on HIV-1 capsid protein (CA) assemblies. These enhancements correspond to absolute sensitivity ratios of 12-29 and are of similar magnitude to those seen for 1H signals in the same samples. At MAS frequencies above 20 kHz, it was possible to record 2D 19F-13C HETCOR spectra, which contain long-range intra- and intermolecular correlations. Such correlations provide unique distance restraints, inaccessible in conventional experiments without DNP, for protein structure determination. Furthermore, systematic quantification of the DNP enhancements as a function of biradical concentration, MAS frequency, temperature, and microwave power is reported. Our work establishes the power of DNP-enhanced 19F MAS NMR spectroscopy for structural characterization of HIV-1 CA assemblies, and this approach is anticipated to be applicable to a wide range of large biomolecular systems.

Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies

19 F NMR spectroscopy is an attractive and growing area of research with broad applications in biochemistry, chemical biology, medicinal chemistry, and materials science. We have explored fast magic angle spinning (MAS) 19 F solid-state NMR spectroscopy in assemblies of HIV-1 capsid protein. Tryptophan residues with fluorine substitution at the 5-position of the indole ring were used as the reporters. The 19 F chemical shifts for the five tryptophan residues are distinct, reflecting differences in their local environment. Spin-diffusion and radio-frequency-driven-recoupling experiments were performed at MAS frequencies of 35 kHz and 40-60 kHz, respectively. Fast MAS frequencies of 40-60 kHz are essential for consistently establishing 19 F-19 F correlations, yielding interatomic distances of the order of 20 Å. Our results demonstrate the potential of fast MAS 19 F NMR spectroscopy for structural analysis in large biological assemblies.

19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors

The ¹⁹F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the ¹⁹F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the ¹⁹F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of ¹⁹F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for ¹⁹F-based MAS NMR structural analysis of proteins and protein assemblies.

19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors

The ¹⁹F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the ¹⁹F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the ¹⁹F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of ¹⁹F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for ¹⁹F-based MAS NMR structural analysis of proteins and protein assemblies.

Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz

The recent breakthroughs in NMR probe technologies resulted in the development of MAS NMR probes with rotation frequencies exceeding 100 kHz. Herein, we explore dramatic increases in sensitivity and resolution observed at MAS frequencies of 110-111 kHz in a novel 0.7 mm HCND probe that enable structural analysis of fully protonated biological systems. Proton- detected 2D and 3D correlation spectroscopy under such conditions requires only 0.1-0.5 mg of sample and a fraction of time compared to conventional ¹³C-detected experiments. We discuss the performance of several proton- and heteronuclear- (¹³C-,¹⁵N-) based correlation experiments in terms of sensitivity and resolution, using a model microcrystalline fMLF tripeptide. We demonstrate the applications of ultrafast MAS to a large, fully protonated protein assembly of the 231-residue HIV-1 CA capsid protein. Resonance assignments of protons and heteronuclei, as well as ¹H-¹⁵N dipolar and ¹H^N CSA tensors are readily obtained from the high sensitivity and resolution proton-detected 3D experiments. The approach demonstrated here is expected to enable the determination of atomic-resolution structures of large protein assemblies, inaccessible by current methodologies.

Towards single egg toxicity screening using microcoil NMR

Planar NMR microcoils are evaluated, their application to single eggs is demonstrated, and their potential for studying smaller single cells is discussed.

DBTDL Replacement in High Resilience Slabstock Foams

Over the last two years, serious concerns have been expressed in the press about human exposures to trace amounts of alkyl tin moieties such as tributyltin (TBT). Organostannic compounds are commonly used as catalysts in polyurethane chemistry. Whereas stannous octoate (SNOCT) exhibits a TBT content below the detection limit of most analysis equipment (< 0.01%), TBT levels as high as 0.6% have been measured in dibutyltin dilaurate (DBTDL). Although DBTDL manufacturers are currentlyoptimising their process to lower the TBT content in DBTDL, the (chemo) pressure exerted on polyurethane foamers is such that DBTDL-free formulations are being activelylooked for.

High resilience (HR) foams based on various polymer polyols–particularly polyols made with pure polystyrene (POSTech*) or poly(styrene–acrylonitrile)–have been developed using DBTDL as the gel catalyst. The direct replacement of DBTDL is not straightforward, as foam block dimensional stabilityissues (often referred to as “cold flow”) are encountered when other catalyst (i.e., SNOCT) are used.

This “cold flow” phenomenon is verymuch dependent on the size and the weight of the foam block produced, making all small scale laboratory experiments unsuitable for developing novel stable HR foam formulations.

The present research has shown that properties derived from small scale experiments can nevertheless be related to the “cold flowability” of HR formulations. Amongst the various tests investigated, the variation in sag factor from top to bottom of the foam block was found to be the most relevant test method to assess the dimensional stability. Sag factor is here defined as the force exerted bythe foam compressed to 65% of the original thickness divided by that exerted at 25% compression during the compression load deflection (CLD) test. The test method based on this variation in sag factor through the foam block (vSag) made possible the laboratoryexamination of formulation parameters for their impact on foam block stability. It also allowed us to develop a wide density range of POSTech-based DBTDL-free HR slabstock foams that are dimensionallystable.

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

A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors ɛ ((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 ɛ ((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 ɛ ((1)H). Our study also shows that the molecular structure of AMUPol is not optimal and its ɛ ((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 ɛ ((1)H) than AMUPol itself (by a factor of ca. 1.2).

Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies

Mature infectious HIV-1 virions contain conical capsids composed of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20-64-fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar-based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4-18.8 T) and temperature (109-180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of the temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine side-chain conformers; unique intermolecular correlations across two CA molecules; and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR spectroscopy as an excellent tool for the characterization of HIV-1 assemblies.

High-resolution two-field nuclear magnetic resonance spectroscopy

Two-field NMR provides correlations of nuclear spins at the most favourable magnetic fields in a single experiment.

Rapid parameter optimization of low signal-to-noise samples in NMR spectroscopy using rapid CPMG pulsing during acquisition: application to recycle delays

A method is presented that combines Carr-Purcell-Meiboom-Gill (CPMG) during acquisition with either selective or nonselective excitation to produce a considerable intensity enhancement and a simultaneous loss in chemical shift information. A range of parameters can theoretically be optimized very rapidly on the basis of the signal from the entire sample (hard excitation) or spectral subregion (soft excitation) and should prove useful for biological, environmental, and polymer samples that often exhibit highly dispersed and broad spectral profiles. To demonstrate the concept, we focus on the application of our method to T(1) determination, specifically for the slowest relaxing components in a sample, which ultimately determines the optimal recycle delay in quantitative NMR. The traditional inversion recovery (IR) pulse program is combined with a CPMG sequence during acquisition. The slowest relaxing components are selected with a shaped pulse, and then, low-power CPMG echoes are applied during acquisition with intervals shorter than chemical shift evolution (RCPMG) thus producing a single peak with an SNR commensurate with the sum of the signal integrals in the selected region. A traditional (13)C IR experiment is compared with the selective (13)C IR-RCPMG sequence and yields the same T(1) values for samples of lysozyme and riverine dissolved organic matter within error. For lysozyme, the RCPMG approach is ~70 times faster, and in the case of dissolved organic matter is over 600 times faster. This approach can be adapted for the optimization of a host of parameters where chemical shift information is not necessary, such as cross-polarization/mixing times and pulse lengths.

Rapid estimation of nuclear magnetic resonance experiment time in low-concentration environmental samples

Nuclear magnetic resonance (NMR) spectroscopy is an essential tool for studying environmental samples but is often hindered by low sensitivity, especially for the direct detection of nuclei such as(13) C. In very heterogeneous samples with NMR nuclei at low abundance, such as soils, sediments, and air particulates, it can take days to acquire a conventional(13) C spectrum. The present study describes a prescreening method that permits the rapid prediction of experimental run time in natural samples. The approach focuses the NMR chemical shift dispersion into a single spike, and, even in samples with extremely low carbon content, the spike can be observed in two to three minutes, or less. The intensity of the spike is directly proportional to the total concentration of nuclei of interest in the sample. Consequently, the spike intensity can be used as a powerful prescreening method that answers two key questions: (1) Will this sample produce a conventional NMR spectrum? (2) How much instrument time is required to record a spectrum with a specific signal-to-noise (S/N) ratio? The approach identifies samples to avoid (or pretreat) and permits additional NMR experiments to be performed on samples producing high-quality NMR data. Applications in solid- and liquid-state(13) C NMR are demonstrated, and it is shown that the technique is applicable to a range of nuclei.

Biological solid-state NMR at ETH Zurich

Solid-state Magnetic Resonance has been greatly developed over the past decade. Higher field spectrometers and other technical developments are expected to lead to further significant improvements.

[Safety in intensive care medicine. Can we learn from aviation?]

Safety is of extraordinary value in commercial aviation. Therefore, sophisticated and complex systems have been developed to ensure safe operation. Within this system, the pilots are of specific concern: they form the human-machine interface and have a special responsibility in controlling and monitoring all aircraft systems. In order to prepare pilots for their challenging task, specific selection of suitable candidates is crucial. In addition, for every commercial pilot regulatory requirements demand a certain number of simulator training sessions and check flights to be completed at prespecified intervals. In contrast, career choice for intensive care medicine most likely depends on personal reasons rather than eligibility or aptitude. In intensive care medicine, auditing, licensing, or mandatory training are largely nonexistent. Although knowledge of risk management and safety culture in aviation can be transferred to the intensive care unit, the diversity of corporate culture and tradition of leadership and training will represent a barrier for the direct transfer of standards or procedures. To accomplish this challenging task, the analysis of appropriate fields of action with regard to structural requirements and the process of change are essential.

Identifying components in dissolved humic acid that bind organofluorine contaminants using (1)H{(19)F} reverse heteronuclear saturation transfer difference NMR spectroscopy

Interactions between dissolved peat humic acid and two structurally dissimilar organofluorine compounds, perfluoro-2-naphthol and perfluoro-octanoic acid, are probed using a novel (1)H{(19)F} Nuclear Magnetic Resonance (NMR) Spectroscopy technique based on the Saturation Transfer Difference (STD) experiment. This technique is used here to show selectively only those regions of the (1)H NMR spectrum of humic acid that arise from chemical constituents interacting with perfluorinated organic compounds. This approach provides a tool for high-resolution analysis of interactions between contaminants and soil organic matter (SOM) directly at the molecular level. Soil organic matter is a chemically heterogeneous mixture, and traditional techniques used to study sorption or binding phenomenon are unable to resolve multiple processes occurring simultaneously at distinct chemical moieties. Here, multiple interaction domains are identified based on known chemical constituents of humic acid, most notably from lignin- and protein-derived material. Specifically, perfluoro-2-naphthol is shown to interact with lignin, protein, and aliphatic material; however, preference is exhibited for lignin-derived domains, while perfluoro-octanoic acid exhibits near exclusive preference for the protein-derived domains of humic acid.

Proton assisted recoupling at high spinning frequencies

We demonstrate the successful application of (13)C-(13)C proton assisted recoupling (PAR) on [U-(13)C,(15)N] N-f-MLF-OH and [U-(13)C,(15)N] protein GB1 at high magic angle spinning (MAS) frequencies (omega(r)/2pi = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (omega(1H)/2pi approximately 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range (13)C-(13)C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power (1)H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.

Creativity in biological research

During the past century, several biologists have studied the mental processes involved in creativity. In recent years psychologists have approached the subject experimentally. In one such study (Carson, Peterson, and Higgins 2003), creativity has been shown to originate in the subconscious mind and to be transmitted to the conscious mind as a result of a decrease in latent inhibition, an ordinarily strong cognitive barrier between the conscious mind and the subconscious. In my scientific work I have found evidence for creativity in the design of experiments, in which the addition of apparently superfluous controls has led to important discoveries.

Wavelength-selective photodenitrogenation of azoalkanes to high-spin polyradicals with cyclopentane-1,3-diyl spin-carrying units and their photobleaching: EPR/UV spectroscopy and product studies of the matrix-isolated species

The photolysis of the mono-, bis-, and trisazoalkanes 1, 2, and 3 in a toluene matrix at 77 K has been studied by EPR and UV spectroscopy. The purpose was to find the optimal conditions for the generation of the corresponding organic high-spin polyradicals (the triplet diradicals D-1, D-2, and D-3, the tetraradicals T-2 and T-3, and the hexaradical H-3) all with localized cyclopentane-1,3-diyl spin-carrying units, connected by m-phenylene (except D-1) as ferromagnetic coupler. Irradiation of these azoalkanes at 333, 351, or 364 nm gave different polyradical compositions. This observed wavelength dependence is due to the secondary photoreaction (photobleaching) of the polyradical intermediate. The photobleaching process has been examined in detail for the triplet diradical D-1, for which pi,pi excitation affords the cyclopentenes 5 instead of the housane 4 (the usual product of the diradical D-1 on warm-up of the matrix). The pi,pi-excited diradical D-1 fragments into a pair of allyl and methyl radicals (the latter was observed by EPR spectroscopy of a photobleached sample), and recombination affords the cyclopentene. Similar photochemical events are proposed for the photobleaching of the tetraradical T-2 and hexaradical H-3, derived from the respective azoalkanes 2 and 3. Thus, photobleaching of the polyradicals competes effectively with their photogeneration from the azoalkane. This unavoidable event is the consequence of spectral overlap between the cumyl-radical pi,pi chromophore of the polyradical and the n,pi chromophore of the azoalkane at the wavelength (364 nm), at which the latter is photoactive for the required extrusion of molecular nitrogen.

Early detection of speech and language delays in the Netherlands. The case for integrating primary and secondary prevention

The early detection of speech and language delays has been an important feature of the child health services in the Netherlands for some 15 years. During this period ideas about both the purpose of screening and the methods themselves have changed considerably. There are four key outstanding issues: What is the best age to identify children? What screening measures are available? How can we detect speech and language delays in multilingual children? Which groups are best able to detect speech and language difficulties: parents, teachers, playgroup leaders, doctors, nurses, or speech and language therapists? These questions are influenced by social, demographic developments and an increase in the understanding of language delay. This article examines the Dutch solutions to these problems. The conclusion reached is that early language screening can only be part of the answer to early detection both because the available measures are not yet sufficiently accurate and because the growing group of multilingual children (e.g. in Amsterdam more than 50% of the children under the age of 4 years are multilingual) makes the application of specific measures at a population level unworkable. An alternative method is suggested, namely primary prevention by giving information and support to parents, playgroup leaders, doctors, etc.

Stable ribonucleic acid synthesis in stringent (rel+) and relaxed (rel-) polyamine auxotrophs of Escherichia coli K-12

The relationship of polyamines to stable ribonucleic acid (RNA) synthesis under conditions of amino acid withdrawal or chloramphenicol treatment was examined with the use of a closely related rel(+), rel(-) pair conditionally incapable of synthesizing putrescine. Under conditions of polyamine starvation, the cellular sperimidine level fell to one-third to one-half of the value observed in putrescine-supplemented cultures and putrescine became undetectable; cadaverine was synthesized by both strains, but the relaxed strain, MA 252, accumulated less cadaverine per cell than its stringent twin, MA 254. Upon amino acid withdrawal, the stringent strain remained stringent whether starved of or supplemented with polyamines. Similarly, the relaxed strain was capable of making RNA either with or without polyamine starvation. On the addition of chloramphenicol or upon amino acid withdrawal in the relaxed strain, supplementation with spermidine had no effect on the initial rate of RNA synthesis, although RNA accumulation was greater in the presence of added spermidine. Spermidine added at the conclusion of RNA synthesis prompted additional synthesis, although preincubation with spermidine again had no effect on the initial rate. All forms of stable RNA species were made with polyamine supplementation. The present data appear to rule out the possibility that polyamines are primary causative agents in stimulating RNA synthesis, but rather suggest an indirect or secondary role for spermidine in which the polyamines "stimulate" stable RNA synthesis probably by relieving RNA product inhibition of RNA synthesis.