Experimental Magnetic Resonance Data Research Articles

Structural and dynamics characterization of the Zika virus NS2B using nuclear magnetic resonance and RosettaMP: A challenge for transmembrane protein studies

Zika virus (ZIKV) is an emergent flavivirus that represents a global public health concern due to its association with severe neurological disorders. NS2B is a multifunctional viral membrane protein primarily used to regulate viral protease activity and is crucial for virus replication, making it an appealing target for antiviral drugs. This study presents the structural elucidation of full-length ZIKV NS2B in sodium dodecyl sulfate (SDS) micelles using solution nuclear magnetic resonance experimental data and RosettaMP. The protein structure has four transmembrane α-helices, two amphipathic α-helices, and a β-hairpin in the hydrophilic region. NS2B presented secondary and tertiary stability in different concentrations of SDS. Furthermore, we studied the dynamics of NS2B in SDS micelles through relaxation parameters and paramagnetic relaxation enhancement experiments. The findings were consistent with the structural calculations. Our work will be essential in understanding the role of NS2B in viral replication and screening for inhibitors against ZIKV.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

BackgroundThe nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases.FindingsTo enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes.ConclusionsWe have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.Electronic supplementary materialThe online version of this article (doi:10.1186/s13326-016-0057-1) contains supplementary material, which is available to authorized users.

Gilbert ferromagnetic damping theory and the fluctuation-dissipation theorem

The phenomenological Gilbert–Landau–Lifshitz theory of magnetic damping in ordered magnetic materials has long served as the central model employed in the analysis of considerable experimental magnetic resonance data. The problem undertaken here is to formulate the microscopic basis of the model in terms of usual theory of irreversible transport embodied in the fluctuation-dissipation-response theorems. As an application of the general method we establish a rigorous relationship between magnetic damping and acoustic damping implicit in magnetoelastic models.

Magnetic and resonance properties of the two-dimensional S=1 compound Ni5(TeO3)4Cl2 with frustrated geometry

The magnetic and magnetoresonance properties of a new single-crystal compound Ni5(TeO3)4Cl2 are studied. Measurements of the magnetization and magnetic susceptibility of the crystal in a wide temperature range (5–300K) make it possible to conclude that Ni5(TeO3)4Cl2 is a quasi-two-dimensional antiferromagnet with the easy magnetization axis a* directed perpendicular to the crystallographic plane bc and a magnetic ordering temperature TN≈21K. Resonance measurements at 4.2K in wide range of frequencies (25–105GHz) and magnetic field (up to 200kOe) permit us to obtain the frequency-field dependence of the AFMR spectrum for a field applied along the easy magnetization axis a*. It is shown that a magnetic field directed along the antiferromagnetic axis (H∥a*) induces a magnetic phase transition of the spin-flop type, which is found to occur at Hsf≈120kOe. The magnetic resonance experimental data are described qualitatively in the model of a biaxial antiferromagnet.

Automatic estimation of the noise variance from the histogram of a magnetic resonance image

Estimation of the noise variance of a magnetic resonance (MR) image is important for various post-processing tasks. In the literature, various methods for noise variance estimation from MR images are available, most of which however require user interaction and/or multiple (perfectly aligned) images. In this paper, we focus on automatic histogram-based noise variance estimation techniques. Previously described methods are reviewed and a new method based on the maximum likelihood (ML) principle is presented. Using Monte Carlo simulation experiments as well as experimental MR data sets, the noise variance estimation methods are compared in terms of the root mean squared error (RMSE). The results show that the newly proposed method is superior in terms of the RMSE.

Theory of hyperfine interactions for iron-acceptor pairs in silicon based on ab initio calculations

We present theoretical calculations of the Zeeman g-factor and of hyperfine interactions for trigonal and orthorhombic (-) pairs. Our calculations are based on magnetization densities obtained from ab initio local spin density calculations, making use of two fitting parameters for those values that cannot be extracted from our ab initio results. We show by a comparison with experimental magnetic resonance data that the large spread of absolute values and anisotropies of the experimental data can naturally be accounted for.

Collapse of the spin gap with pressure in spin-ladder compounds

We introduce a model of weakly coupled spin ladders using a decomposition into triplet and singlet Majorana fermions. We show that a weak coupling between the ladders causes the triplet gap to vanish. Assuming that pressure enhances the interladder coupling, we find that the triplet gap vanishes with increased pressure. We suggest that this is the explanation of recent nuclear magnetic resonance experimental data in superconducting spin-ladder compounds such as Sr{sub 2}Ca{sub 12}Cu{sub 24}O{sub 41}. {copyright} {ital 1998} {ital The American Physical Society}

Solvent effect on previtamin D conformational equilibrium and photoreactions

The effect of solvent polarity on the conformational equilibrium of previtamin D has been discussed in terms of the abundance (5) of its conformers calculated by molecular mechanics in conjunction with nuclear magnetic resonance experimental data available in the literature. It has been assumed that polar reaction media shift the conformational equilibrium towards the most non-strained cZc conformations with the OH group in pseudo-equatorial orientation. 7-Dehydrocholesterol (provitamin D) photoisomerization on irradiation at λ = 254 nm has been studied in ethanol and hexane by UV spectroscopy. A consideration of the observed differences in combination with the calculations of the reaction kinetics provides an estimation of the quantum yields of previtamin D cis-trans isomerization and additional experimental evidence for the solvent-induced changes in the conformational equilibrium of previtamin D in favour of cZc forms in polar environments.

Selection of the ground state in CsCuCl3 by quantum fluctuations

The Heisenberg triangular antiferromagnet is a model widely studied by analytic low-temperature expansion and Monte Carlo simulation. The classical version of the model is characterized by infinitely many minimum energy configurations even if an in-plane external magnetic field is turned on. This degeneracy is lifted by thermal fluctuations and the same effect is found when quantum fluctuations are accounted for. We find an analogous scenario in the 3D hexagonal model where the intrachain coupling is ferromagnetic and the interchain one is antiferromagnetic. Such a model is suitable to describe some hexagonal ABX3 compounds. We are interested, in particular, in CsCuCl3, where our theoretical results compare favorably with magnetic resonance experimental data and with magnetization measurements as a function of the external magnetic field. The role of quantum and thermal fluctuations in the selection of a particular spin pattern out of the infinitely many configurations that minimize the classical energy of the model is discussed.

High-resolution inversion of finite Fourier transform data through a localised polynomial approximation

The authors address the problem of high-resolution inversion of finite Fourier transform data, which is frequently encountered in tomographic image reconstruction. A new parametric modelling approach, which uses an adaptive localised polynomial approximation model of the object function, is proposed to overcome the Gibbs artifact and the limited-resolution problem associated with conventional FFT methods. An algorithm for finding the model parameters is given which makes use of linear prediction theory, singular-value decomposition and least-squares fitting methods. Reconstruction results from simulated and real magnetic resonance experimental data are also presented to demonstrate its capability for Gibbs ringing reduction and resolution enhancement.