Baltijas universitāšu bibliotēku speciālisti diskutē par atvērto zinātni un atvērto universitāti

Latvijas Universitātē (LU) no 2017.gada 25. līdz 26. maijam norisinājās LU Bibliotēkas organizētā Baltijas universitāšu bibliotēku speciālistu tikšanās “Atvērta zinātne, atvērta universitāte un atvērts prāts” (Open Science, Open University and Open Mind). Rakstā sniegta informācija par notikušo pasākumu

Baltijas universitāšu bibliotēku speciālisti diskutē par atvērto zinātni un atvērto universitāti

Latvijas Universitātē (LU) no 2017.gada 25. līdz 26. maijam norisinājās LU Bibliotēkas organizētā Baltijas universitāšu bibliotēku speciālistu tikšanās “Atvērta zinātne, atvērta universitāte un atvērts prāts” (Open Science, Open University and Open Mind). Rakstā sniegta informācija par notikušo pasākumu

Heteronuclear Decoupling by Multiple Rotating Frame Technique

The paper describes the multiple rotating frame technique for designing modulated rf-fields, that perform broadband heteronuclear decoupling in solution NMR spectroscopy. The decoupling is understood by performing a sequence of coordinate transformations, each of which demodulates a component of the Rf-field to a static component, that progressively averages the chemical shift and dipolar interaction. We show that by increasing the number of modulations in the decoupling field, the ratio of dispersion in the chemical shift to the strength of the rf-field is successively reduced in progressive frames. The known decoupling methods like continuous wave decoupling, TPPM etc, are special cases of this method and their performance improves by adding additional modulations in the decoupling field. The technique is also expected to find use in designing decoupling pulse sequences in Solid State NMR spectroscopy and design of various excitation, inversion and mixing sequences.Comment: 18 pages , 5 figure

Broadband 180 degree universal rotation pulses for NMR spectroscopy designed by optimal control

Broadband inversion pulses that rotate all magnetization components 180 degrees about a given fixed axis are necessary for refocusing and mixing in high-resolution NMR spectroscopy. The relative merits of various methodologies for generating pulses suitable for broadband refocusing are considered. The de novo design of 180 degree universal rotation pulses using optimal control can provide improved performance compared to schemes which construct refocusing pulses as composites of existing pulses. The advantages of broadband universal rotation by optimized pulses (BURBOP) are most evident for pulse design that includes tolerance to RF inhomogeneity or miscalibration. We present new modifications of the optimal control algorithm that incorporate symmetry principles and relax conservative limits on peak RF pulse amplitude for short time periods that pose no threat to the probe. We apply them to generate a set of pulses suitable for widespread use in Carbon-13 spectroscopy on the majority of available probes

Hadamard magnetization transfers achieve dramatic sensitivity enhancements in homonuclear multidimensional NMR correlations of labile sites in proteins, polysaccharides and nucleic acids

EXSY, TOCSY and NOESY lie at the foundation of homonuclear NMR experiments in organic and pharmaceutical chemistry, as well as in structural biology. Limited magnetization transfer efficiency is an intrinsic downside of these methods, particularly when targeting rapidly exchanging species such as labile protons ubiquitous in polysaccharides, sidechains and backbones of proteins, and in bases and sugars of nucleic acids: the fast decoherence imparted on these protons through solvent exchanges, greatly reduces their involvement in homonuclear correlation experiments. We have recently discussed how these decoherences can be visualized as an Anti-Zeno Effect, that can be harnessed to enhance the efficiency of homonuclear transfers within Looped PROjected SpectroscopY (L-PROSY) leading to 200-300% enhancements in NOESY and TOCSY cross-peaks for amide groups in biomolecules. This study demonstrates that even larger sensitivity gains per unit time, equivalent to reductions by several hundred-folds in the duration of experiments, can be achieved by looping inversion or using saturation procedures. In the ensuing experiments a priori selected frequencies are encoded according to Hadamard recipes, and subsequently resolved along the indirect dimension via linear combinations. Magnetization-transfer (MT) processes reminiscent of those occurring in CEST provide significant enhancements in the resulting cross-peaks, in only a fraction of acquisition time of a normal 2D experiment. The effectiveness of the ensuing three-way polarization transfer interplay between water, labile and non-labile protons was corroborated experimentally for proteins, homo-oligosaccharides and nucleic acids. In all cases, cross-peaks barely detectable in conventional 2D NMR counterparts, were measured ca. 10-fold faster and with 200-600% signal enhancements by the Hadamard MT counterparts

Multiplexing experiments in NMR and multi-nuclear MRI

Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid-and solidstate NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solidstate NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements. (c) 2021 Elsevier B.V. All rights reserved

Long-lived States in an intrinsically disordered protein domain

Long-lived states (LLS) are relaxation-favoured eigenstates of J-coupled magnetic nuclei. LLS were measured, along with classical 1H and 15 N relaxation rate constants, in aminoacids of the N-terminal Unique domain of the c-Src kinase (USrc), which is disordered in vitro under physiological conditions. The relaxation rates of LLS are a probe for motions and interactions in biomolecules. LLS of the aliphatic protons of glycines, with lifetimes ca. four times longer than their spin-lattice relaxation times, are reported for the first time in an intrinsically disordered protein domain (IDP). LLS relaxation experiments were integrated with 2D spectroscopy methods, further adapting them for studies on proteins

NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F 1 F 0 -ATPase

Bz-423 is an inhibitor of the mitochondrial F 1 F 0 -ATPase, with therapeutic properties in murine models of immune diseases. Here, we study the binding of a water-soluble Bz-423 analog (5-(3-(aminomethyl)phenyl)-7-chloro- 1-methyl-3-(naphthalen-2-ylmethyl)-1 H -benzo][ e ][1,4]diazepin-2(3 H )-one); (1) to its target subunit on the enzyme, the oligomycin sensitivity conferring protein (OSCP), by NMR spectroscopy using chemical shift perturbation and cross-relaxation experiments. Titration experiments with constructs representing residues 1–120 or 1–145 of the OSCP reveals that (a) 1 binds to a region of the protein, at the minimum, comprising residues M51, L56, K65, V66, K75, K77, and N92, and (b) binding of 1 induces conformational changes in the OSCP. Control experiments employing a variant of 1 in which a key binding element on the small molecule was deleted; it had no perturbational effect on the spectra of the OSCP, which indicates that the observed changes with 1 represent specific binding interactions. Collectively, these data suggest that 1 might inhibit the enzyme through an allosteric mechanism where binding results in conformational changes that perturb the OSCP-F 1 interface resulting in disrupted communication between the peripheral stalk and the F 1 -domain of the enzyme. © 2009 Wiley Periodicals, Inc. Biopolymers 29: 85–92, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64305/1/21306_ftp.pd