bluuebunny/crossref_metadata_2025_split huggingface dataset:
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter
Authors: Cserzo Miklos , Eisenhaber Frank , Eisenhaber Birgit , Simon Istvan 
Published: December 2003

Abstract
Summary: Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is designed to make distinction between protein sequences with and without transmembrane (TM) helices at a reasonably low rate of false positive prediction (∼1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of ∼95% among documented proteins with helical TM regions).
Availability: The server operates at three mirror sites: http://mendel.imp.univie.ac.at/sat/DAS/DAS.html, http://wooster.bip.bham.ac.uk/DAS.html and http://www.enzim.hu/DAS/DAS.html. The program is available on request.
Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles
Authors: Baerga‐Ortiz Abel , Bergqvist Simon , Mandell Jeffrey G. , Komives Elizabeth A. 
Published: December 2003

AbstractThrombin binds thrombomodulin (TM) at anion binding exosite 1, an allosteric site far from the thrombin active site. A monoclonal antibody (mAb) has been isolated that competes with TM for binding to thrombin. Complete binding kinetic and thermodynamic profiles for these two protein–protein interactions have been generated. Binding kinetics were measured by Biacore. Although both interactions have similar KDs, TM binding is rapid and reversible while binding of the mAb is slow and nearly irreversible. The enthalpic contribution to the ΔGbind was measured by isothermal titration calorimetry and van't Hoff analysis. The contribution to the ΔGbind from electrostatic steering was assessed from the dependence of the ka on ionic strength. Release of solvent H2O molecules from the interface was assessed by monitoring the decrease in amide solvent accessibility at the interface upon protein–protein binding. The mAb binding is enthalpy driven and has a slow kd. TM binding appears to be entropy driven and has a fast ka. The favorable entropy of the thrombin–TM interaction seems to be derived from electrostatic steering and a contribution from solvent release. The two interactions have remarkably different thermodynamic driving forces for competing reactions. The possibility that optimization of binding kinetics for a particular function may be reflected in different thermodynamic driving forces is discussed.
Variability‐based sequence alignment identifies residues responsible for functional differences in α and β tubulin
Authors: Fygenson D. Kuchnir , Needleman Daniel J. , Sneppen Kim 
Published: December 2003

Abstractα and β Tubulin are well‐characterized paralogs with similar structures and functions. We quantify the variability of every amino acid position in both tubulins from the aligned sequences of their numerous known orthologs. By aligning the variability profiles, we identify residues that differ significantly in variability between α and β tubulin. Most of these residues are part of well‐defined secondary structures and are clustered around the nucleotide binding pocket, the site of greatest functional difference between the two paralogs. The remaining residues of large difference in variability are located in the N‐terminal loop between H1 and S2. We therefore predict that certain residues in this unstructured region also contribute to a functional difference between α and β tubulin. Furthermore, we find the most restrictive variability‐based alignment is nearly identical to the true structure‐based alignment. Thus, by using a stringent variability‐based alignment to approximate the true alignment, the method introduced here may predict sites of functional distinction between paralogous proteins even in the absence of structural information.
FoldMiner: Structural motif discovery using an improved superposition algorithm
Authors: Shapiro Jessica , Brutlag Douglas 
Published: December 2003

AbstractWe report an unsupervised structural motif discovery algorithm, FoldMiner, which is able to detect global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classification of proteins into families. Motifs, which are discovered from pairwise superpositions of a query structure to a database of targets, are described probabilistically in terms of the conservation of each secondary structure element's position and are used to improve detection of distant structural relationships. During each iteration of the algorithm, the motif is defined from the current set of homologs and is used both to recruit additional homologous structures and to discard false positives. FoldMiner thus achieves high specificity and sensitivity by distinguishing between homologous and nonhomologous structures by the regions of the query to which they align. We find that when two proteins of the same fold are aligned, highly conserved secondary structure elements in one protein tend to align to highly conserved elements in the second protein, suggesting that FoldMiner consistently identifies the same motif in members of a fold. Structural alignments are performed by an improved superposition algorithm, LOCK 2, which detects distant structural relationships by placing increased emphasis on the alignment of secondary structure elements. LOCK 2 obeys several properties essential in automated analysis of protein structure: It is symmetric, its alignments of secondary structure elements are transitive, its alignments of residues display a high degree of transitivity, and its scoring system is empirically found to behave as a metric.
Tubulin equilibrium unfolding followed by time‐resolved fluorescence and fluorescence correlation spectroscopy
Authors: Sánchez Susana A. , Brunet Juan E. , Jameson David M. , Lagos Rosalba , Monasterio Octavio 
Published: December 2003

AbstractThe pathway for the in vitro equilibrium unfolding of the tubulin heterodimer by guanidinium chloride (GdmCl) has been studied using several spectroscopic techniques, specifically circular dichroism (CD), two‐photon Fluorescence Correlation Spectroscopy (FCS), and time‐resolved fluorescence, including lifetime and dynamic polarization. The results show that tubulin unfolding is characterized by distinct processes that occur in different GdmCl concentration ranges. From 0 to 0.5 M GdmCl, a slight alteration of the tubulin heterodimer occurs, as evidenced by a small, but reproducible increase in the rotational correlation time of the protein and a sharp decrease in the secondary structure monitored by CD. In the range 0.5–1.5 M GdmCl, significant decreases in the steady‐state anisotropy and average lifetime of the intrinsic tryptophan fluorescence occur, as well as a decrease in the rotational correlation time, from 48 to 26 nsec. In the same GdmCl range, the number of protein molecules (labeled with Alexa 488), as determined by two‐photon FCS measurements, increases by a factor of two, indicating dissociation of the tubulin dimer into monomers. From 1.5 to 4 M GdmCl, these monomers unfold, as evidenced by the continual decrease in the tryptophan steady‐state anisotropy, average lifetime, and rotational correlation time, concomitant with secondary structural changes. These results help to elucidate the unfolding pathway of the tubulin heterodimer and demonstrate the value of FCS measurements in studies on oligomeric protein systems.
Prediction of the odorant binding site of olfactory receptor proteins by human–mouse comparisons
Authors: Man Orna , Gilad Yoav , Lancet Doron 
Published: December 2003

AbstractOlfactory receptors (ORs) are a large family of proteins involved in the recognition and discrimination of numerous odorants. These receptors belong to the G‐protein coupled receptor (GPCR) hyperfamily, for which little structural data are available. In this study we predict the binding site residues of OR proteins by analyzing a set of 1441 OR protein sequences from mouse and human. The central insight utilized is that functional contact residues would be conserved among pairs of orthologous receptors, but considerably less conserved among paralogous pairs. Using judiciously selected subsets of 218 ortholog pairs and 518 paralog pairs, we have identified 22 sequence positions that are both highly conserved among the putative orthologs and variable among paralogs. These residues are disposed on transmembrane helices 2 to 7, and on the second extracellular loop of the receptor. Strikingly, although the prediction makes no assumption about the location of the binding site, these amino acid positions are clustered around a pocket in a structural homology model of ORs, mostly facing the inner lumen. We propose that the identified positions constitute the odorant binding site. This conclusion is supported by the observation that all but one of the predicted binding site residues correspond to ligand‐contact positions in other rhodopsin‐like GPCRs.
Effect of multiple symmetries on the association of R67 DHFR subunits bearing interfacial complementing mutations
Authors: Dam Julie , Blondel Arnaud 
Published: December 2003

AbstractIt was shown previously that complementation could be a powerful mean to probe protein–protein interactions in the normally tetrameric R67 DHFR. Indeed, mixing complementing inactive dimeric mutants produced active heterotetramers. This approach turned a homo‐oligomer into a hetero‐oligomer and thus allowed the use of combinatorial assays, a subtle analysis of the association forces, and a precise determination of the equilibrium dissociation constants (KD) by titrimetry. However, for some of the complementing pairs, the experimental data implied multiple equilibria involving heterodimers, although no monomers could be detected. Thus, the reactions involved had to be identified to elaborate a suitable model to determine the KD of those pairs correctly. That model suggested that homodimers associated rapidly before the protomers could be redistributed in a multiple equilibrium system. Kinetic data confirmed that view. The association data at equilibrium were analyzed by multiple curve fitting with all plausible combinations of parameters. This gave a confidence interval for KD that is safer than the usual 67% or 90% confidence interval. Finally, the KD of one specific reaction, the dissociation of a heterotetramer with the relevant symmetry into two homodimers could be determined with the relevant model for each complementing pair, although multiple equilibria were present. These KD can thus be used as a set of references data to test and improve theoretical methods such as association free energy calculations.
Are protein–protein interfaces more conserved in sequence than the rest of the protein surface?
Authors: Caffrey Daniel R. , Somaroo Shyamal , Hughes Jason D. , Mintseris Julian , Huang Enoch S. 
Published: December 2003

AbstractProtein interfaces are thought to be distinguishable from the rest of the protein surface by their greater degree of residue conservation. We test the validity of this approach on an expanded set of 64 protein–protein interfaces using conservation scores derived from two multiple sequence alignment types, one of close homologs/orthologs and one of diverse homologs/paralogs. Overall, we find that the interface is slightly more conserved than the rest of the protein surface when using either alignment type, with alignments of diverse homologs showing marginally better discrimination. However, using a novel surface‐patch definition, we find that the interface is rarely significantly more conserved than other surface patches when using either alignment type. When an interface is among the most conserved surface patches, it tends to be part of an enzyme active site. The most conserved surface patch overlaps with 39% (± 28%) and 36% (± 28%) of the actual interface for diverse and close homologs, respectively. Contrary to results obtained from smaller data sets, this work indicates that residue conservation is rarely sufficient for complete and accurate prediction of protein interfaces. Finally, we find that obligate interfaces differ from transient interfaces in that the former have significantly fewer alignment gaps at the interface than the rest of the protein surface, as well as having buried interface residues that are more conserved than partially buried interface residues.
The N‐terminal domain (IF2N) of bacterial translation initiation factor IF2 is connected to the conserved C‐terminal domains by a flexible linker
Authors: Laursen Brian Søgaard , Kjærgaard Anne Cecillie , Mortensen Kim Kusk , Hoffman David W. , Sperling‐Petersen Hans Uffe 
Published: December 2003

AbstractBacterial translation initiation factor IF2 is a multidomain protein that is an essential component of a system for ensuring that protein synthesis begins at the correct codon within a messenger RNA. Full‐length IF2 from Escherichia coli and seven fragments of the protein were expressed, purified, and characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) methods. Interestingly, resonances of the 6 kD IF2N domain located at the extreme N terminus of IF2 can be clearly identified within the NMR spectra of the full‐length 97‐kD protein. 15N NMR relaxation rate data indicate that (1) the IF2N domain is internally well ordered and tumbles in solution in a manner that is independent of the other domains of the IF2 protein, and (2) the IF2N domain is connected to the C‐terminal regions of IF2 by a flexible linker. Chemical shifts of resonances within the isolated IF2N domain do not significantly differ from those of the corresponding residues within the context of the full‐length 97‐kD protein, indicating that IF2N is a structurally independent unit that does not strongly interact with other regions of IF2. CD and NMR data together provide evidence that Domains I–III of IF2 have unstructured and flexible regions as well as substantial helical content; CD data indicate that the helical content of these regions decreases significantly at temperatures above 35°C. The features of structurally well‐ordered N‐ and C‐terminal domains connected by a flexible linker with significant helical content are reminiscent of another translation initiation factor, IF3.
Effect of the N3 residue on the stability of the α‐helix
Authors: Iqbalsyah Teuku M. , Doig Andrew J. 
Published: December 2003

AbstractN3 is the third position from the N terminus in the α‐helix with helical backbone dihedral angles. All 20 amino acids have been placed in the N3 position of a synthetic helical peptide (CH3CO‐[AAX AAAAKAAAAKAGY]‐NH2) and the helix content measured by circular dichroism spectroscopy at 273 K. The dependence of peptide helicity on N3 residue identity has been used to determine a free energy scale by analysis with a modified Lifson‐Roig helix coil theory that includes a parameter for the N3 energy (n3). The most stabilizing residues at N3 in rank order are Ala, Glu, Met/Ile, Leu, Lys, Ser, Gln, Thr, Tyr, Phe, Asp, His, and Trp. Free energies for the most destabilizing residues (Cys, Gly, Asn, Arg, and Pro) could not be fitted. The results correlate with N1, N2, and helix interior energies and not at all with N‐cap preferences. This completes our work on studying the structural and energetic preferences of the amino acids for the N‐terminal positions of the α‐helix. These results can be used to rationally modify protein stability, help design helices, and improve prediction of helix location and stability.
Migrant Travellers and Tourist Idylls: The Paintings of Jack B. Yeats and Post‐colonial Identities
Authors: Cusack Tricia 
Published: December 2003

Travellers of various kinds have long been a salient feature of Irish society. Whether tinkers, tramps, seasonal workers or emigrants, they occupied positions outside an increasingly settled and bourgeois population. Their histories are contested and inevitably bound up with colonialism. This article considers how the figures of travellers in landscape depicted in Jack B. Yeats’s paintings of the 1930s–50s might be related to the constitution of national and cultural identities in Ireland in the post‐colonial period. Particular attention is given to Yeats’s own marginal position as Anglo‐Irish.As the representation of landscape, imagined with its `natural’ inhabitants, contributes to the construction of national and cultural identities, colonialism produces contesting, and sometimes ambivalent, representations of the land and its occupants. In a period of social change and ‘re‐positioning’ for both the Irish and Anglo‐Irish, Yeats’s travellers are found to be located within the rural idyll of ‘Gaelic Ireland ’ rather than the rural idyll of anglicized Ireland/England. However, I propose that they do not quite form part of this idyll. Furthermore, the depiction of both travellers and landscape is seen to be ambivalent, questioning the security of Yeats’s relation to the ‘Irishness ’ represented.I suggest that the figure of the traveller cannot be isolated from anti‐modern discourses of poetic wandering originating outside Ireland. Yeats’s landscape represents a touristic idyll marked as ‘Irish ’ but also as Utopian and timeless. The viewer’s imagined occupancy of the role of tourist–traveller in this idyll is disturbed however by Yeats’s depiction of the traveller as unromanticized, poor and migrant. In post‐colonial Irish culture, the figure of the traveller accumulated diverse connotations associated with the needs for identity and identification generated by cultural shifts towards national definition and exclusions, as well as by the ongoing changes of modernity.
On the Margins of Discourse? Visions of New Soviet Woman in Socialist Realistic Painting 1949–50
Authors: Simpson Pat 
Published: December 2003

This paper questions the marginalization of representations of women implied by the emphasis on New Man as signifier of Soviet identity in critical revisions of the Socialist Realist canon 1949–50. The approach, partly informed by feminist critical theory and pluralist, rather than totalitarian, models of Stalinist power, also engages critically with marginalizing tendencies in some recent histories. It suggests the existence of a significant discursive practice regarding the imaging of women, based on a concept of beauty defined by the patriotism and ‘partiinost ’ of the image when viewed in relation to currently dominant constructs of gender role and nationality.Discussion focuses on two pairs of paintings by Sergei Gerasimov and the Ukrainian Tatiana Yablonskaya – one pair delegitimated, the other pair legitimated during the period. The argument examines the differences between the visions of New Soviet Woman offered by the delegitimated and legitimated paintings, offering a speculative reading of the constitution and implications of the legitimated images of peasant women. These are suggested to embody active participation in reinforcing complex patriarchal mythologies – of ‘Mother Russia ’; Soviet woman as mother; the peasant as female and Ukrainians as peasants.
Men Before the Mirror: Duchamp, Man Ray and Masculinity
Authors: Hopkins David 
Published: December 2003

This article examines the extent to which two of Duchamp’s readymades, Fountain (1917) and the textual readymade ‘Men Before the Mirror’ (1934), deal with questions of male psychology and subjectivity.The bulk of the essay is taken up with an analysis of the complexities of ‘Men Before the Mirror’, a text which, in the past, was thought ot have been appropriated by Duchamp from a female friend of Man Ray, and then signed by him using the name of his female alter ego, Rrose Sélavy.It is argued that the authorial ‘voice’ in this text is, in fact, remarkably close to that of Duchamp himself, given the wider range of his thematic preoccupations.Simultaneously arguing against the view that the gender switches of Duchamp/Rrose Sélavy can be read as deconstructive of socially inscribed gender positions, the article seeks to establish that the relationship of Duchamp’s/Rrose’s text to the photographs by Man Ray that accompany it in its original published context, reveal fundamentally masculine or ‘homosocial’ concerns. These in turn help to clarify the underlying dynamics of Duchamp’s and Man Ray’s relationship.
Ford Madox Brown, Carlyle, Macaulay and Bakhtin: The Pratfalls and Penultimates of History
Authors: Codell Julie F. 
Published: December 2003

Ford Madox Brown’s Manchester Town Hall mural series was the site of late Victorian contentions about both history and history painting. A long‐standing discourse of history, represented in Manchester’s many local histories and guidebooks, debated the ‘facts’ and significance of Manchester’s history and contributions to British history. Brown’s murals participated in this debate at the very moment of the city’s new emergence as an independent municipality with its own self‐government and new rebuilding projects.Brown’s murals commented on this discourse through imagery and the accompanying narratives he wrote. Unlike his earlier narratives for paintings, these narratives were not about Brown’s ideas and intentions. Instead, they incorporated the new historical language of satire, displacement and factual ambiguity. Brown was an avid reader of Carlyle and Macaulay who, despite their differences, shared innovative methods; a criticism of cause and effect; and a focus on quotidian, collective, and anonymous actors and motives. Brown employed their methods, including passages from Carlyle’s French Revolution, to satirize official history. His selection of ‘minor’ details and figures foregrounded the selection process itself and problematized historical content, as did Carlyle’s and Macaulay’s methods.Brown’s relationship to history painting, however, was not satirical. He admired Dyce, Maclise and the German Nazarenes without imitating their idealism. Brown eschewed high seriousness, diluted important events with banal incidents, put crucial events in the street rather than the court, and juxtaposed ‘heroes’ with anonymous passers‐by to interrogate notions of idealism and heroism. Respectfully quoting Maclise’s works through visual reversals, Brown conveyed his own `reversal’ away from idealism toward the revisionism of Carlyle and Macaulay.The murals authored and authorized Manchester history. Bakhtin’s themes of the carnival, novelization, surprise and the ‘word with a loophole’ illuminate how the murals forged a new civic history built on collectivity, working‐class contributions, and corporate capital. Radical in his support for the working class, Brown was also nationalistic in his expression of Manchester’s English pedigree and mercantile hegemony. His murals express innovations and contradictions in their melding of Manchester history into broader Victorian discourses of history, history painting, British hegemony and the Empire, while offering criticism of cherished Victorian ideals and revealing the depths of Brown’s own intellectual comprehension of changing Victorian notions of history.
Negotiating Models of Feminist Research
Authors: Deepwell Katy 
Published: December 2003

R. Betterton (ed.), An Intimate Distance: Women Artists and the BodyJ. A. Isaak (ed.), Feminism and Contemporary Art: The Revolutionary Power of Women’s LaughterGriselda Pollock (ed.), Generations and Geographies in the Visual Arts: Feminist ReadingsDinah Dysart and Hannah Fink (eds.), Asian Women ArtistsGayatri Sinha (ed.), Expressions & Evocations: Contemporary Women Artists of IndiaAnna Voigt (ed.), New Visions, New Perspectives: Voice of Contemporary Australian Women Artists