1,721,000 research outputs found
Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead
No full textInternal motions in the microsecond timescale have been proposed to play an active part in a protein's biological function. Nuclear magnetic resonance (NMR) relaxation dispersion is a robust method sensitive to this timescale with atomic resolution. However, due to technical limitations, the observation of motions faster than similar to 40 mu s for N-15 nuclei was not possible. We show that with a cryogenically cooled NMR probehead, a high spin-lock field strength can be generated that is able to detect motions as fast as 25 mu s. We apply this high spin-lock field strength in an NMR experiment used for characterizing dynamical processes. An on-resonance rotating-frame transverse relaxation experiment was implemented that allows for the detection of a 25 mu s process from a dispersion curve, and transverse relaxation rates were compared at low and high spin-lock field strengths showing that at high field strengths contributions from chemical exchange with lifetimes up to 25 mu s can be removed. Due to the increase in sensitivity towards fast motion, relaxation dispersion for a residue that undergoes smaller chemical shift variations due to dynamics was identified. This technique reduces the previously inaccessible window between the correlation time and the relaxation dispersion window that covers four orders of magnitude by a factor of 2. (C) 2012 Elsevier Inc. All rights reserved
Improved NMR experiments with 13C-isotropic mixing for assignment of aromatic and aliphatic side chains in labelled proteins
No full textThree improved 13C-13C-spinlock experiments for side chain assignments of isotope labelled proteins in liquid state are presented. These are based on wide bandwidth spinlock techniques that have become possible with contemporary cryogenic probes. The first application, the H(CaliCaro)H-TOCSY, is an HCCH-TOCSY in which all CHn moieties of a protein are detected in a single experiment, including the aromatic ones. This enables unambiguous assignment of aromatic amino acids in a single, highly sensitive experiment. In the second application, the 13C-detected Call-TOCSY, magnetization transfer comprises all carbons – aliphatic, aromatic as well as the carbonyl carbons – making the complete carbon assignment possible using one spectrum only. Thirdly, in the frequently used HC(CCO)NH experiment the long C-carbonyl refocused INEPT step is replaced by direct 13C-13C-TOCSY magnetization transfer from side chain carbons to the backbone carbonyls. The resulting HC(CCO)NH experiment minimizes relaxation losses because it is shorter and represents a more sensitive alternative particularly for larger proteins
NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules.
No full textIn this review, we cover NMR methods for identification and validation of ligands that interact with a biological macromolecule. Validation means making sure that the interaction is true, and initial binding effects from biophysical assays or activity readouts from biochemical assays were not just observed due to an experimental artifact. Out of scope of this review are methods for subsequent characterization of the interaction by quantitative KD determination, binding mode analysis, structure determination etc.
A plethora of NMR experiments is available for identification and validation of molecular interactions. We will focus on how to choose between different experiments and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Variations on the Author
Get PDF“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
Get PDFWe 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
Get PDFWe 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
- …
