1,721,052 research outputs found
Applications for measuring scalar and residual dipolar couplings in proteins
Full text linkAbstractNuclear magnetic resonance spectroscopic structure determination of proteins has been under rapid development during the last decade. The size limitation impeding structural studies of biological macromolecules in solution has increased from 10 kDa to 30 kDa thanks to exploitation of 15N/13C enrichment. Perdeuteration of non-exchangeable protons has pushed this limit even further, allowing backbone resonance assignment of 40 to 50 kDa proteins. Most recently, transverse relaxation optimized spectroscopy (TROSY) has been demonstrated to lengthen 15N and 1HN spin transverse relaxation times significantly, especially in large perdeuterated proteins, thus extending the size limit beyond 100 kDa systems. However, determination of structurally important nuclear Overhauser enhancements (NOE) suffers from perdeuteration, due to the lower density of proton spins available, eventually leading to imprecise protein structures. Very recently, residual dipolar couplings have been used to supplement NOE information, enabling accurate molecular structures to also be obtained with perdeuterated proteins. This thesis focuses on the measurement of the structurally important 3J-coupling between 1HN and 1Hα spins, and determination of residual dipolar couplings by utilizing the novel spin-state-selective subspectral editing together with the TROSY methodology. This approach allows precise measurement of a large number of ipolar couplings in larger protonated or perdeuterated proteins.Academic Dissertation to be presented with the assent of the Faculty of Science, University of Oulu, for public discussion in Raahensali (Auditorium L10), Linnanmaa, on November 25th, 2000, at 12 noon.Abstract
Nuclear magnetic resonance spectroscopic structure determination of proteins has been under rapid development during the last decade. The size limitation impeding structural studies of biological macromolecules in solution has increased from 10 kDa to 30 kDa thanks to exploitation of 15N/13C enrichment. Perdeuteration of non-exchangeable protons has pushed this limit even further, allowing backbone resonance assignment of 40 to 50 kDa proteins. Most recently, transverse relaxation optimized spectroscopy (TROSY) has been demonstrated to lengthen 15N and 1HN spin transverse relaxation times significantly, especially in large perdeuterated proteins, thus extending the size limit beyond 100 kDa systems. However, determination of structurally important nuclear Overhauser enhancements (NOE) suffers from perdeuteration, due to the lower density of proton spins available, eventually leading to imprecise protein structures. Very recently, residual dipolar couplings have been used to supplement NOE information, enabling accurate molecular structures to also be obtained with perdeuterated proteins. This thesis focuses on the measurement of the structurally important 3J-coupling between 1HN and 1Hα spins, and determination of residual dipolar couplings by utilizing the novel spin-state-selective subspectral editing together with the TROSY methodology. This approach allows precise measurement of a large number of ipolar couplings in larger protonated or perdeuterated proteins
Transverse relaxation optimised spin-state selective NMR experiments for measurement of residual dipolar couplings
No full textThree transverse relaxation optimised NMR experiments (TROSY) for the measurement of scalar and dipolar couplings suitable for proteins dissolved in aqueous iso- and anisotropic solutions are described. The triple-spin-state-selective experiments yield couplings between 1HN-13Cα, 15N-13Cα, 1HN-13Cαi−1, 15N-13Cαi−1, 1HN-13C′i−1, 15N-13C′i−1, and 13C′i−1-13Cαi−1 without introducing nonessential spectral crowding compared with an ordinary two-dimensional 15N-1H correlation spectrum and without requiring explicit knowledge of carbon assignments. This set of α/β-J-TROSY experiments is most useful for perdeuterated proteins in studies of structure–activity relationships by NMR to observe, in addition to epitopes for ligands, also conformational changes induced by binding of ligands.</p
Sequential resonance assignment from two-dimensional inter- and intra-residue <sup>15</sup>N-<sup>1</sup>H correlation spectra
No full textSequential assignment of amide resonances in proteins and peptides can conveniently be derived from twodimensional inter-residue 15Ni –1HN(i−1) and intra-residue 15Ni –1HNi correlation spectra. The inter-residue 15Ni –1HN(i−1)correlation spectrum is generated by recording the 15Ni frequency evolution indirectly and subsequently transferring the magnetization to 1HN(i−1) of the preceding residue for direct detection. The flow of coherence is established by the (H)N(COCAHA)-TOCSY pulse sequence. Following the path from intra-residue correlation via inter-residue correlation to the next intra-residue correlation results in sequential assignment in two dimensions. This kind of assignment protocol is most amenable to re-establishing sequential assignments of target proteins perturbed by binding of ligands or alternatively signals of peptide ligands can be traced in studies of structure–function relationships by NMR
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
A new approach for obtaining sequential assignment of large proteins
No full textA novel NMR experiment for obtaining sequential assignment of large proteins and protein complexes is described. The proposed method takes full advantage of transverse relaxation optimized spectroscopy (TROSY) and utilizes spin-state-selection to distinguish between intraresidual and sequential connectivities in the HNCA-TROSY-type correlation experiment. Thus, the intra- and interresidual cross peaks can be identified without relaying magnetization via carbonyl carbon, which relaxes very rapidly at the high magnetic fields where TROSY is most efficient. In addition, the presented method enables measurement of several scalar and residual dipolar couplings, which can potentially be used for structure determination of large proteins
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
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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