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Analysis of 31P MAS NMR spectra and transversal relaxation of bacteriophage M13 and tobacco mosaic virus.
No full textPhosphorus magic angle spinning nuclear magnetic resonance (NMR) spectra and transversal relaxation of M13 and TMV are analyzed by use of a model, which includes both local backbone motions of the encapsulated nucleic acid molecules and overall rotational diffusion of the rod-shaped virions about their length axis. Backbone motions influence the sideband intensities by causing a fast restricted reorientation of the phosphodiesters. To evaluate their influence on the observed sideband patterns, we extend the model that we used previously to analyze nonspinning 31P NMR lineshapes (Magusin, P.C.M.M., and M. A. Hemminga. 1993a. Biophys. J. 64:1861–1868) to magic angle spinning NMR experiments. Backbone motions also influence the conformation of the phosphodiesters, causing conformational averaging of the isotropic chemical shift, which offers a possible explanation for the various linewidths of the centerband and the sidebands observed for M13 gels under various conditions. The change of the experimental lineshape of M13 as a function of temperature and hydration is interpreted in terms of fast restricted fluctuation of the dihedral angles between the POC and the OCH planes on both sides of the 31P nucleus in the nucleic acid backbone. Backbone motions also seem to be the main cause of transversal relaxation measured at spinning rates of 4 kHz or higher. At spinning rates less than 2 kHz, transversal relaxation is significantly faster. This effect is assigned to slow, overall rotation of the rod-shaped M13 phage about its length axis. Equations are derived to simulate the observed dependence of T2e on the spinning rate
Solid-state 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus
No full textIn this thesis, the results of various 31P NMR experiments observed for intact virus particles of bacteriophage M13 and Tobacco Mosaic Virus (TMV), are presented. To explain the results in a consistent way, models are developed and tested. 31P nuclei in M13 and TMV are only present in the phosphodiesters of the encapsulated nucleic acid molecule. Therefore, 31P NMR spectroscopy reveals structural and dynamic properties of the nucleic acid backbone selectively without isotope labeling, even though the virus particles largely consist of coat proteins. In the Introduction (Chapter 1), it is discussed that the 31P chemical shift is sensitive to local nucleic acid backbone geometry and that the 31P NMR relaxation is dependent on the isolated and collective backbone motions. As shown in Chapter 3, high-power 1H-decoupled one-dimensional 31P NMR spectra observed for nonspinning samples of M13 and TMV contain a single, broad line dominated by the 31P chemical shift anisotropy (CSA), which masks any structural inequivalence among the encapsulated phosphodiesters. However, these spectra do contain interesting mobility information. On the one hand, they show that the nucleic acid molecule in each of the viruses is strongly immobilized in comparison to free nucleic acids in solution, as a result of interactions with the protein coat. On the other hand, the 31P resonance lineshapes; show clear signs of motional narrowing, which is indicative for (restricted) motion with frequencies in the order of the static linewidth or larger (≥10 4Hz). In contrast, the nonspinning 31P transversal relaxation measured for M13 indicates motion in the slow or intermediate frequency region as compared to the static linewidth (≤10 4Hz), because T 2e becomes shorter as the viscosity of the gel decreasesTo analyze the results in a more quantitative manner, three different rotational diffusion models for the phosphorus motion are developed in Chapter 2. These models are first tested at a theoretical level to get a feeling for their accuracy and to check their correspondence with standard theories under appropriate limiting conditions. Simulations show that a clear distinction between the effect of motional amplitude and frequency cannot be made within experimental error on the basis of one-dimensional spectra or transversal relaxation alone. However, these parameters can be extracted from the combined data. For fast motions, the transversal 31P NMR relaxation predicted by our models is consistent with standard Redfield relaxation theory. The relaxation effects caused by ultraslow rotational diffusion closely resemble the effects of translational diffusion of water protons in an inhomogeneous magnetic-field gradient. It is discussed in Chapter 3, that simple models, like isotropic and rigid-rod diffusion cannot reproduce the experimental data. Instead, a consistent description is offered by a combined diffusion model, in which the 31P NMR lineshape is dominated by fast internal DNA or RNA motions, and transversal relaxation reflects slow overall rotation of the rod-shaped virions about their length axis.To obtain more specific structural information, magic angle spinning (MAS) NMR spectroscopy is employed, which breaks up the broad 31P NMR lineshape into a sharp centerband at the isotropic chemical shift position flanked by rotational sidebands (Chapter 4). MAS 31P NMR spectra of TMV show two resolved sideband patterns with an overall intensity ratio of approximately 2, which are assigned to the three types of phosphodiesters in TMV on the basis of RO-P-OR' bondangles and supposed arginine bonding effects. In contrast, MAS 31P NMR spectra of M13, only contain a single, relatively broad centerband flanked by sidebands, indicating that a continuous distribution of phosphodiester conformations, rather than a few distinguishable, exists within the phage. The observed decrease of inhomogeneous linewidth at increasing temperature and hydration could perhaps be caused by some sort of "conformational averaging" as a consequence of nucleic acid backbone motion. This is illustrated by use of a simple model, which shows the lineshape effects caused by fast restricted fluctuation of the dihedral angles between the POC and the OCH planes on both sides of the 31P nucleus in the nucleic acid backbone. The presence of internal phosphodiester motions with frequencies ≥10 5Hz, as concluded from the motional narrowing of nonspinning 31P NMR lineshapes in Chapter 3, is confirmed by the deviation of sideband intensities in MAS 31P NMR spectra of dilute M13 gels from the theoretical values for solid powders. No dramatic broadening of the sidebands is observed, indicating that motions with frequencies in the order of the spinning rates applied (10 3Hz) are absent. Backbone motions also seem to be the main cause of transversal relaxation measured at spinning rates of 4 kHz or higher. At spinning rates below 2 kHz, transversal relaxation is significantly faster. This dependence of T 2e on the spinning rate is assigned to slow, overall rotation of the rod-shaped M13 phage about its length axis.Both nonspinning and MAS 31P NMR spectra are analyzed in Chapter 2 and 3, respectively, to study possible mobility differences among the phosphodiesters in M13 and TMV. The nonspinning lineshape of 30% TMV is best simulated, if it is assumed that one of the three binding sites is more mobile than the other two. It is shown that this is compatible with the reduced CSA reflected by the major sideband pattern in MAS spectra of TMV as compared to the minor one. A large mobility of one of the three binding sites would agree with structural models based on x-ray diffraction data, in which two of the binding sites are interacting with arginine residues, whereas no arginine is close to the third one. Two-component analysis of the nonspinning 31P NMR data of 30% M13 suggests that the encapsulated DNA molecule perhaps contains 83% immobile and 17% mobile phosphodiesters. This would shed new light on the nonintegral ratio 2.4:1 between the number of nucleotides and protein coat subunits in the phage: if 83% of the viral DNA is less mobile, the binding of the DNA molecule to the protein coat would actually occur at the integral ratio of two nucleotides per protein subunit. However, MAS NMR spectra provide no additional evidence for such a two-component model.Finally, in Chapter 5, the slow overall motion of M13 and TMV is investigated using 2D-exchange 31P NMR spectroscopy. 2D-exchange 31P NMR spectra recorded for TMV with mixing times t m ≤1 sec do not show any offdiagonal broadening indicating that the value of 3 Hz for the overall motion of TMV determined in Chapter 3 from nonspinning transversal relaxation, is an overestimation. For 30% M13, a log-Gaussian distribution around 25 Hz of coefficients mainly spread between 1 and 10 3Hz must be introduced to reproduce the 2D-exchange spectra recorded at various mixing times in a consistent way. Motional inhomogeneity in gels of M13 is probably caused by the tendency of the bacteriophages in solutions to form variously sized aggregates. Taking the same coefficient distribution and a minor relaxation contribution caused by fast backbone motion into account, nonspinning transversal relaxation can even be better simulated for inhomogeneous overall motion, than it was done for homogeneous motion in Chapter 3. The shrinking of the σ 22 -discontinuity on the diagonal with respect to the lineshape as a whole for t m ≥0.1 sec, cannot be explained by slow overall motion, but seems to be caused by restricted spindiffusion between 31P nuclei with chemical shifts that differ less than 1 ppm
Coherent Cross-Polarization Theory for a Spin-½ Coupled to a General Object
No full textZero-order average-Hamiltonian theory is used to extend the product-operator description of coherent spin–spin cross-polarization to the case of a spin-½ coupled to a general object, like a molecular rotor or a quantum oscillator. The object, which is not necessarily in a Boltzmann equilibrium state, is assumed to have no interaction with the lattice and no internal relaxation capacity. The Bloch–Wangsness–Redfield (BWR) theory for incoherent processes like spin–lattice relaxation does not apply for such an isolated spin– object pair. Nevertheless spectral density at the Larmor frequency, of key importance in BWR theory, also plays a central role in object-induced spin polarization. Spectral density in our theory is represented by quantum operators J2 and J1. If J2 and J1 do not commute, the spin– object coupling may cause spin polarization in an initially saturated spin system. This represents a coherent mechanism for spin cooling, which in specific cases may lead to enhanced spin polarization above the thermal equilibrium value. A master equation is derived for general spin– object crosspolarization, and applied to the case of a spin pair inside a uniaxial rotor, and a spin coupled to a microelectronic LC circuit
Brownian motion in a deformable medium
No full textDiffusion in a deformable medium shows a remarkable transition at the onset of concerted particle-medium motions. This is derived for Brownian motion in a periodic potential coupled to a broad phonon spectrum, and obsd. for rotation of org. mols. inside zeolite cavities. Interactions between the particle and local overdamped phonons in the potential wells cause residence-time dependent lattice deformations, which, in our model, decrease the energy barriers. The model explains the non-Arrhenius type of rotational motion of pentane inside zeolite ZK-5 obsd. with 1H-13C NMR relaxometry
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
2D Exchange 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus.
No full textTwo-dimensional (2D) exchange 31P nuclear magnetic resonance spectroscopy is used to study the slow overall motion of the rod-shaped viruses M13 and tobacco mosaic virus in concentrated gels. Even for short mixing times, observed diagonal spectra differ remarkably from projection spectra and one-dimensional spectra. Our model readily explains this to be a consequence of the T2e anisotropy caused by slow overall rotation of the viruses about their length axis. 2D exchange spectra recorded for 30% (w/w) tobacco mosaic virus with mixing times < 1 s do not show any off-diagonal broadening, indicating that its overall motion occurs in the sub-Hz frequency range. In contrast, the exchange spectra obtained for 30% M13 show significant off-diagonal intensity for mixing times of 0.01 s and higher. A log-gaussian distribution around 25 Hz of overall diffusion coefficients mainly spread between 1 and 10(3) Hz faithfully reproduces the 2D exchange spectra of 30% M13 recorded at various mixing times in a consistent way. A small but notable change in diagonal spectra at increasing mixing time is not well accounted for by our model and is probably caused by 31P spin diffusion
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
A theoretical study of rotational diffusion models for rod-shaped viruses. The influence of motion on 31P nuclear magnetic resonance lineshapes and transversal relaxation.
No full textInformation about the interaction between nucleic acids and coat proteins in intact virus particles may be obtained by studying the restricted backbone dynamics of the incapsulated nucleic acids using 31P nuclear magnetic resonance (NMR) spectroscopy. In this article, simulations are carried out to investigate how reorientation of a rod-shaped virus particle as a whole and isolated nucleic acid motions within the virion influence the 31P NMR lineshape and transversal relaxation dominated by the phosphorus chemical shift anisotropy. Two opposite cases are considered on a theoretical level. First, isotropic rotational diffusion is used as a model for mobile nucleic acids that are loosely or partially bound to the protein coat. The effect of this type of diffusion on lineshape and transversal relaxation is calculated by solving the stochastic Liouville equation by an expansion in spherical functions. Next, uniaxial rotational diffusion is assumed to represent the mobility of phosphorus in a virion that rotates as a rigid rod about its length axis. This type of diffusion is approximated by an exchange process among discrete sites. As turns out from these simulations, the amplitude and the frequency of the motion can only be unequivocally determined from experimental data by a combined analysis of the lineshape and the transversal relaxation. In the fast motional region both the isotropic and the uniaxial diffusion model predict the same transversal relaxation as the Redfield theory. For very slow motion, transversal relaxation resembles the nonexponential relaxation as observed for water molecules undergoing translational diffusion in a magnetic field gradient. In this frequency region T2e is inversely proportional to the cube root of the diffusion coefficient. In addition to the isotropic and uniaxial diffusion models, a third model is presented, in which fast restricted nucleic acid backbone motions dominating the lineshape are superimposed on a slow rotation of the virion about its length axis, dominating transversal relaxation. In an accompanying article the models are applied to the 31P NMR results obtained for bacteriophage M13 and tobacco mosaic virus
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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