bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histidine and not tyrosine is required for the Peroxide‐induced formation of haem to protein cross‐linked myoglobin
Authors: Reeder Brandon J. , Cutruzzolà Francesca , Bigotti Maria Giulia , Watmough Nicholas J. , Wilson Michael T. 
Published: August 2007

AbstractPeroxide‐induced oxidative modifications of haem proteins such as myoglobin and haemoglobin can lead to the formation of a covalent bond between the haem and globin. These haem to protein cross‐linked forms of myoglobin and haemoglobin are cytotoxic and have been identified in pathological conditions in vivo. An understanding of the mechanism of haem to protein cross‐link formation could provide important information on the mechanisms of the oxidative processes that lead to pathological complications associated with the formation of these altered myoglobins and haemoglobins. We have re‐examined the mechanism of the formation of haem to protein cross‐link to test the previously reported hypothesis that the haem forms a covalent bond to the protein via the tyrosine 103 residue (Catalano, C. E., Choe, Y. S., Ortiz de Montellano, P. R., J. Biol. Chem. 1989, 10534 ‐ 10541). Comparison of native horse myoglobin, recombinant sperm whale myoglobin and Tyr103 → Phe sperm whale mutant shows that, contrary to the previously proposed mechanism of haem to protein cross‐link formation, the absence of tyrosine 103 has no impact on the formation of haem to protein cross‐links. In contrast, we have found that engineered myoglobins that lack the distal histidine residue either cannot generate haem to protein cross‐links or show greatly suppressed levels of modified protein. Moreover, addition of a distal histidine to myoglobin from Aplysia limacina, that naturally lacks this histidine, restores the haem protein's capacity to generate haem to protein cross‐links. The distal histidine is, therefore, vital for the formation of haem to protein cross‐link and we explore this outcome.
Searching for Neuroglobin's role in the brain
Authors: Nienhaus Karin , Nienhaus G. Ulrich 
Published: August 2007

AbstractNeuroglobin is a small globin that plays an important role in the protection of brain neurons from ischemic and hypoxic injuries. The molecular mechanisms by which Ngb performs its physiological function are still under debate. Suggestions include oxygen storage and delivery, scavenging of NO and/or reactive oxygen species, oxygen sensing and signal transduction. In recent years, the molecular structures of Ngb with carbon monoxide bound to the heme iron and without an exogenous ligand have been solved, and interesting structural changes have been noticed upon ligand binding. Moreover, equilibrium and kinetic properties of the reactions with ligands have been examined in great detail. Here we summarize the molecular properties of Ngb and discuss them in relation to the potential physiological functions.
Allosteric effects on oxidative and nitrosative reactions of cell‐free hemoglobins
Authors: Bonaventura Celia , Henkens Robert , Alayash Abdu I. , Crumbliss Alvin L. 
Published: August 2007

AbstractA review of the oxidative and nitrosative reactions of cell‐free hemoglobin‐based oxygen carriers (HBOCs) shows that these reactions are intimately linked and are subject to allosteric control. Cross‐linking reactions used to produce HBOCs introduce conformational constraints and result in Hbs with reduced responses to heterotropic and homotropic allosteric effectors. The Nernst plots of heme oxidation of cross‐linked HBOCs are shifted to higher potentials relative to unmodified Hb in the absence of allosteric effectors, in accord with their T‐state stabilization and right‐shifted Hill plots of O2 binding. They exhibit enhanced rates of autoxidation and nitrite‐induced oxidation, features that appear due to their having more solvent‐accessible heme pockets. The stability of their NO‐Hb derivatives varies as a result of allosteric effects on the extent of formation of pentacoordinate NO‐heme geometry by α chains and subsequent oxidation of partner β chains. The physiological implications of these findings on the safety, efficacy and design of second generation HBOCs are discussed in the framework of a reaction scheme showing linkages between Hb‐mediated redox reactions. These redox reactions can drive formation of SNO‐Hb and other reactive species and are of significance for the use of cell‐free Hbs in vivo.
Protein dynamics and function: Insights from the energy landscape and solvent slaving
Authors: Frauenfelder Hans , Fenimore Paul W. , Young Robert D. 
Published: August 2007

AbstractProtein motions are complex and a good way to describe them is in terms of a very high‐dimensional conformation space. We give here a simple explanation of the conformation space and the energy landscape, the conformational motions and protein reactions, based on an analogy to a traffic problem. The analogy provides insight into the slaving of protein processes to bulk solvent fluctuations, in both the native and unfolded states.
Common dynamics of globin family proteins
Authors: Laberge Monique , Yonetani Takashi 
Published: August 2007

AbstractThe recently discovered new members of the globin family, neurogobin and cytoglobin, are the object of sustained structural and functional studies aimed at understanding their physiological role and elucidating the impact of their bis‐his heme hexacoordination. However, no studies have yet considered the dynamics of this protein family, an essential link between structure and function. In this communication, we present normal mode analysis results for neuroglobin, cytoglobin, hemoglobin and myoglobin to provide exploratory insights into globin characteristic motions. Our results show a clear correlation in the protein dynamics of this family. All four globins exhibit a high degree of correlated displacements involving residues in the C, E and F helices and link regions. They suggest that these motions play an important role in the reversible oxygen binding function of these proteins. Further, our results may help rationalize some functional features of the 6c‐globins in that they alone exhibit correlated displacements of the G‐helix region.
Protein structure in the truncated (2/2) hemoglobin family
Authors: Pesce Alessandra , Nardini Marco , Milani Mario , Bolognesi Martino 
Published: August 2007

AbstractThe discovery of protein sequences belonging to the widespread 'truncated hemoglobin' family has been followed in the last few years by extensive analyses of their three‐dimensional structures. Truncated hemoglobins can be classified in three main groups, in light of their overall structural properties. The three groups adopt a 2‐on‐2 α‐helical sandwich fold, based on four main α‐helices of the classical 3‐on‐3 α‐helical sandwich found in vertebrate and invertebrate globins. Each of the three groups displays sequence and structure specific features. Among these, a protein matrix tunnel system is typical of group I, a Trp residue at the G8 topological site is conserved in groups II and III, and residue TyrB10 is almost invariant in the three groups. Despite sequence variability in the heme distal site region, a strongly intertwined, but varied, network of hydrogen bonds stabilizes the heme ligand in the three protein groups. Fine mechanisms of ligand recognition and stabilization may vary based on group‐specific distal site residues and on differing ligand diffusion pathways to the heme. Taken together, the structural considerations here presented underline that 'truncated hemoglobins' result from careful editing of the 3‐on‐3 α‐helical globin sandwich fold, rather than from simple 'truncation' events. Thus, '2/2Hb' appears the most proper term to concisely address this protein family.
Ligand pathways in myoglobin: A review of trp cavity mutations
Authors: Olson J. S. , Soman J. , Phillips G. N. 
Published: August 2007

AbstractThe pathways for ligand entry and exit in myoglobin have now been well established by a wide variety of experimental results, including pico‐ to nano‐ to microsecond transient absorbance measurements and time‐resolved X‐ray crystallographic measurements. Trp insertions have been used to block, one at a time, the three major cavities occupied by photodissociated ligands. In this work, we review the effects of the L29(B10)W mutation, which places a large indole ring in the initial 'docking site' for photodissociated ligands. Then, the effects of blocking the Xe4 site with I28W, V68W, and I107W mutations and the Xe1 cavity with L89W, L104W, and F138W mutations are described. The structures of four of these mutants are shown for the first time (Trp28, Trp68, Trp107, and Trp 138 sperm whale metMb). All available results support a 'side path' mechanism in which ligands move into and out of myoglobin by outward rotation of the HisE7 side chain, but after entry can migrate into internal cavities, including the distal Xe4 and proximal Xe1 binding sites. The distal cavities act like the pocket of a baseball glove, catching the ligand and holding it long enough for the histidine gate to close and facilitate internal coordination with the heme iron atom. The physiological role of the proximal Xe1 site is less clear because changes in the size of this cavity have minimal effects on overall O2 binding parameters.
Electron transfer kinetics of soluble fragments indicate a direct interaction between complex III and the caa3 oxidase in Thermus thermophilus
Authors: Janzon Julia , Ludwig Bernd , Malatesta Francesco 
Published: August 2007

AbstractThe extremely thermophilic bacterium Thermus thermophilus expresses an aerobic respiratory chain resembling that of mitochondria and many mesophilic prokaryotes. Yet, interaction modes between redox partners differ between the thermophilic and mesophilic electron transport chains. While electron transfer in mesophilic organisms such as Paracoccus denitrificans follows a two‐step mechanism mostly governed by long‐range electrostatic interactions, the electron transfer in thermophiles is mediated mainly by apolar interactions. The terminal branch of the electron path from the bc‐complex via the soluble cytochrome c552 to the ba3 oxidase has extensively been characterized, whereas contradicting evidence has been put forward on the nature of the physiological substrate(s) of the caa3 oxidase. We have cloned and expressed a soluble fragment of the hydrophilic cytochrome c domain derived from subunit IIc of the caa3 oxidase (ccaa3) and characterized its kinetic behaviour in terms of substrate specificity and ionic strength dependency using pre‐steady state stopped‐flow techniques. The kinetics revealed fast electron transfer between the caa3 fragment and both, the cytochrome c552 and the soluble cytochrome cbc fragment of the bc‐complex, showing only a weak ionic strength dependence. These data suggest a direct intercomplex electron transfer between the bc‐complex and the caa3 oxidase without requirement for a soluble electron shuttle.
Twenty‐five years of cytochrome oxidase research in Rome with Maurizio Brunori
Authors: Antonini Giovanni , Malatesta Francesco , Sarti Paolo 
Published: August 2007

AbstractCytochrome c oxidase has been for a long time one of the central topics studied in Rome by Maurizio Brunori. The authors of this paper have had the unique opportunity of collaborating with him and his friends worldwide for many years. Among the very large number of papers on this enzyme produced by Maurizio Brunori, just a few have been selected here which are particularly representative for the three of us. Topics deal mostly with the interplay between the electrochemical potential gradient in its components and the electron transfer and the proton translocation reactions of this fascinating enzyme.
Cold‐adapted signal proteins: NMR structures of pheromones from the antarctic ciliate Euplotes nobilii
Authors: Placzek William J. , Etezady‐Esfarjani Touraj , Herrmann Torsten , Pedrini Bill , Peti Wolfgang , Alimenti Claudio , Luporini Pierangelo , Wüthrich Kurt 
Published: August 2007

AbstractCell type‐specific signal proteins, known as pheromones, are synthesized by ciliated protozoa in association with their self/nonself mating‐type systems, and are utilized to control the vegetative growth and mating stages of their life cycle. In species of the most ubiquitous ciliate, Euplotes, these pheromones form families of structurally homologous molecules, which are constitutively secreted into the extracellular environment, from where they can be isolated in sufficient amounts for chemical characterization. This paper describes the NMR structures of En‐1 and En‐2, which are members of the cold‐adapted pheromone family produced by Euplotes nobilii, a species inhabiting the freezing coastal waters of Antarctica. The structures were determined with the proteins from the natural source, using homonuclear 1H NMR techniques in combination with automated NOESY peak picking and NOE assignment. En‐1 and En‐2 have highly homologous global folds, which consist of a central three‐α‐helix bundle with an up‐down‐up topology and a 310‐helical turn near the N‐terminus. This fold is stabilized by four disulfide bonds and the helices are connected by bulging loops. Apparent structural specificity resides in the variable C‐terminal regions of the pheromones. The NMR structures of En‐1 and En‐2 provide novel insights into the cold‐adaptive modifications that distinguish the E. nobilii pheromone family from the closely related E. raikovi pheromone family isolated from temperate waters.
Evolution of allosteric models for hemoglobin
Authors: Eaton William A. , Henry Eric R. , Hofrichter James , Bettati Stefano , Viappiani Cristiano , Mozzarelli Andrea 
Published: August 2007

AbstractWe compare various allosteric models that have been proposed to explain cooperative oxygen binding to hemoglobin, including the two‐state allosteric model of Monod, Wyman, and Changeux (MWC), the Cooperon model of Brunori, the model of Szabo and Karplus (SK) based on the stereochemical mechanism of Perutz, the generalization of the SK model by Lee and Karplus (SKL), and the Tertiary Two‐State (TTS) model of Henry, Bettati, Hofrichter and Eaton. The preponderance of experimental evidence favors the TTS model which postulates an equilibrium between high (r)‐ and low (t)‐affinity tertiary conformations that are present in both the T and R quaternary structures. Cooperative oxygenation in this model arises from the shift of T to R, as in MWC, but with a significant population of both r and t conformations in the liganded T and in the unliganded R quaternary structures. The TTS model may be considered a combination of the SK and SKL models, and these models provide a framework for a structural interpretation of the TTS parameters. The most compelling evidence in favor of the TTS model is the nanosecond ‐ millisecond carbon monoxide (CO) rebinding kinetics in photodissociation experiments on hemoglobin encapsulated in silica gels. The polymeric network of the gel prevents any tertiary or quaternary conformational changes on the sub‐second time scale, thereby permitting the subunit conformations prior to CO photodissociation to be determined from their ligand rebinding kinetics. These experiments show that a large fraction of liganded subunits in the T quaternary structure have the same functional conformation as liganded subunits in the R quaternary structure, an experimental finding inconsistent with the MWC, Cooperon, SK, and SKL models, but readily explained by the TTS model as rebinding to r subunits in T. We propose an additional experiment to test another key prediction of the TTS model, namely that a fraction of subunits in the unliganded R quaternary structure has the same functional conformation (t) as unliganded subunits in the T quaternary structure.
Improved model-based, platform-independent feature extraction for mass spectrometry
Authors: Noy Karin , Fasulo Daniel 
Published: August 2007

AbstractMotivation: Mass spectrometry (MS) is increasingly being used for biomedical research. The typical analysis of MS data consists of several steps. Feature extraction is a crucial step since subsequent analyses are performed only on the detected features. Current methodologies applied to low-resolution MS, in which features are peaks or wavelet functions, are parameter-sensitive and inaccurate in the sense that peaks and wavelet functions do not directly correspond to the underlying molecules under observation. In high-resolution MS, the model-based approach is more appealing as it can provide a better representation of the MS signals by incorporating information about peak shapes and isotopic distributions. Current model-based techniques are computationally expensive; various algorithms have been proposed to improve the computational efficiency of this paradigm. However, these methods cannot deal well with overlapping features, especially when they are merged to create one broad peak. In addition, no method has been proven to perform well across different MS platforms.Results: We suggest a new model-based approach to feature extraction in which spectra are decomposed into a mixture of distributions derived from peptide models. By incorporating kernel-based smoothing and perceptual similarity for matching distributions, our statistical framework improves existing methodologies in terms of computational efficiency and the accuracy of the results. Our model is parameterized by physical properties and is therefore applicable to different MS instruments and settings. We validate our approach on simulated data, and show that the performance is higher than commonly used tools on real high- and low-resolution MS, and MS/MS data sets.Contact: daniel.fasulo@siemens.comSupplementary information: Supplementary data are available at Bioinformatics online.
pIPHULA—parallel inference of population parameters using a likelihood approach
Authors: Schmidt Heiko A. , von Haeseler Arndt , Buschbom Jutta 
Published: August 2007

AbstractSummary: pIPHULA is the parallel program to estimate the parameters of a realistic model of population growth.Availability: pIPHULA (http://www.cibiv.at/software/piphula) is written in ISO C, parallel and sequential executables run on UNIX/Linux, Windows and MacOS systems. For (free) MPI libraries see http://en.wikipedia.org/wiki/Message_Passing_Interface.Contact: heiko.schmidt@univie.ac.at or ha.schmidt@web.deSupplementary information: Supplementary data are available at Bioinformatics online.
PhylArray: phylogenetic probe design algorithm for microarray
Authors: Militon Cécile , Rimour Sébastien , Missaoui Mohieddine , Biderre Corinne , Barra Vincent , Hill David , Moné Anne , Gagne Geneviève , Meier Harald , Peyretaillade Eric , Peyret Pierre 
Published: August 2007

AbstractMotivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial ‘black-box’, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality.Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called ‘PhylArray’, designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.Availability: http://fc.isima.fr/~rimour/phylarray/Contact: pierre.peyret@univ-bpclermont.frSupplementary information: Supplementary data are available at Bioinformatics online.
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment
Authors: Tang Thomas , François Nicolas , Glatigny Annie , Agier Nicolas , Mucchielli Marie-Hélène , Aggerbeck Lawrence , Delacroix Hervé 
Published: August 2007

AbstractMotivation: Two-colour microarrays are widely used to perform transcriptome analysis. In most cases, it appears that the ‘red’ and ‘green’ images resulting from the scan of a microarray slide are slightly shifted one with respect to the other. To increase the robustness of the measurement of the fluorescent emission intensities, multiple acquisitions with the same or different PMT gains can be used. In these cases, a systematic correction of image shift is required.Results: To accurately detect this shift, we first developed an approach using cross-correlation. Second, we evaluated the most appropriate interpolation method to be used to derive the registered image. Then, we quantified the effects of image shifts on spot quality, using two different quality estimators. Finally, we measured the benefits associated with a systematic image registration. In this study, we demonstrate that registering the two images prior to data extraction provides a more reliable estimate of the two colours’ ratio and thus increases the accuracy of measurements of variations in gene expression.Availability: http://bioinfome.cgm.cnrs-gif.fr/Contact: tang@cgm.cnrs-gif.fr
Compared to What? A Comment on “A Robust Transformation Procedure for Interpreting Political Text” by Martin and Vanberg
Authors: Benoit Kenneth , Laver Michael 
Published: August 2007

In “A Robust Transformation Procedure,” Martin and Vanberg (2007, hereafter MV) propose a new method for rescaling the raw virgin text scores produced by the “Wordscores” procedure of Laver, Benoit, and Garry (2003, hereafter LBG). Their alternative method addresses two deficiencies they argue exist with the transformation of virgin text scores proposed by LBG: First, that the LBG transformation is sensitive to the selection of virgin texts, and second, that it distorts the reference metric by failing to recover the original reference scores when reference texts are scored and transformed as if they were virgin texts. Their proposed alternative is “robust” in the sense that it avoids both shortcomings. Not only is MV's transformation a welcome contribution to the Wordscores project but also the critical analysis on which it is based brings to light a number of assumptions and choices that face the analyst seeking to estimate actors' policy positions using statistical analyses of the texts they generate. When first describing the possibility of rescaling the raw virgin text estimates, we emphasized that ourparticular approach to rescaling is not fundamental to our word-scoring technique but, rather, is a matter of substantive research design unrelated to the validity of the raw virgin text scores… Other transformations are of course possible. (LBG, 316)To explore more fully into the assumptions and choices behind alternative transformations and the research designs which motivate them, we offer the following comments.