bluuebunny/crossref_metadata_2025_split huggingface dataset:
The challenge of protein structure determination—lessons from structural genomics
Authors: Slabinski Lukasz , Jaroszewski Lukasz , Rodrigues Ana P.C. , Rychlewski Leszek , Wilson Ian A. , Lesley Scott A. , Godzik Adam 
Published: October 2007

AbstractThe process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high‐throughput structure determination in structural genomics centers, we can now learn to recognize protein features correlated with failures; thus, we can recognize proteins more likely to succeed and eventually learn how to modify those that are less likely to succeed. Here, we identify several protein features that correlate strongly with successful protein production and crystallization and combine them into a single score that assesses “crystallization feasibility.” The formula derived here was tested with a jackknife procedure and validated on independent benchmark sets. The “crystallization feasibility” score described here is being applied to target selection in the Joint Center for Structural Genomics, and is now contributing to increasing the success rate, lowering the costs, and shortening the time for protein structure determination. Analyses of PDB depositions suggest that very similar features also play a role in non‐high‐throughput structure determination, suggesting that this crystallization feasibility score would also be of significant interest to structural biology, as well as to molecular and biochemistry laboratories.
Mutagenesis of the phosphate‐binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates
Authors: Cheriyan Manoj , Toone Eric J. , Fierke Carol A. 
Published: October 2007

AbstractNarrow substrate specificities often limit the use of enzymes in biocatalysis. To further the development of Escherichia coli 2‐keto‐3‐deoxy‐6‐phosphogluconate (KDPG) aldolase as a biocatalyst, the molecular determinants of substrate specificity were probed by mutagenesis. Our data demonstrate that S184 is located in the substrate‐binding pocket and interacts with the phosphate moiety of KDPG, providing biochemical support for the binding model proposed on the basis of crystallographic data. An analysis of the substrate selectivity of the mutant enzymes indicates that alterations to the phosphate‐binding site of KDPG aldolase changes the substrate selectivity. We report mutations that enhance catalysis of aldol cleavage of substrates lacking a phosphate moiety and demonstrate that electrophile reactivity correlates with the hydrophobicity of the substituted side chain. These mutations improve the selectivity for unnatural substrates as compared to KDPG by up to 2000‐fold. Furthermore, the S184L KDPG aldolase mutant improves the catalytic efficiency for the synthesis of a precursor for nikkomycin by 40‐fold, making it a useful biocatalyst for the preparation of fine chemicals.
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3
Authors: Runyon Steven T. , Zhang Yingnan , Appleton Brent A. , Sazinsky Stephen L. , Wu Ping , Pan Borlan , Wiesmann Christian , Skelton Nicholas J. , Sidhu Sachdev S. 
Published: October 2007

AbstractHigh‐temperature requirement A (HtrA) and its homologs contain a serine protease domain followed by one or two PDZ domains. Bacterial HtrA proteins and the mitochondrial protein HtrA2/Omi maintain cell function by acting as both molecular chaperones and proteases to manage misfolded proteins. The biological roles of the mammalian family members HtrA1 and HtrA3 are less clear. We report a detailed structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3 using peptide libraries and affinity assays to define specificity, structural studies to view the molecular details of ligand recognition, and alanine scanning mutagenesis to investigate the energetic contributions of individual residues to ligand binding. In common with HtrA2/Omi, we show that the PDZ domains of HtrA1 and HtrA3 recognize hydrophobic polypeptides, and while C‐terminal sequences are preferred, internal sequences are also recognized. However, the details of the interactions differ, as different domains rely on interactions with different residues within the ligand to achieve high affinity binding. The results suggest that mammalian HtrA PDZ domains interact with a broad range of hydrophobic binding partners. This promiscuous specificity resembles that of bacterial HtrA family members and suggests a similar function for recognizing misfolded polypeptides with exposed hydrophobic sequences. Our results support a common activation mechanism for the HtrA family, whereby hydrophobic peptides bind to the PDZ domain and induce conformational changes that activate the protease. Such a mechanism is well suited to proteases evolved for the recognition and degradation of misfolded proteins.
Polymer‐driven crystallization
Authors: Nauli Sehat , Farr Saman , Lee Yueh‐Jung , Kim Hye‐Yeon , Faham Salem , Bowie James U. 
Published: October 2007

AbstractObtaining well‐diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.
Short‐lived protease–serpin complexes: Partial disruption of the rat trypsin active site
Authors: Liu Lu , Mushero Nicole , Hedstrom Lizbeth , Gershenson Anne 
Published: October 2007

AbstractSerpins inhibit serine proteases by mechanically disrupting the protease active site. The protease first reacts with the serpin's reactive center loop (RCL) to form an acylenzyme. Then the RCL inserts into a β‐sheet in the body of the serpin, translocating the attached protease ∼70 Å and deforming the protease active site, thereby trapping the acylenzyme. Loop insertion (∼1 s−1) is an order of magnitude slower than hydrolysis of a typical substrate acylenzyme (∼50 s−1), indicating that the protease is inhibited during translocation. We have previously trapped a partially translocated covalent complex of rat trypsin and α1‐proteinase inhibitor (EpartI*) resulting from attractive interactions between cationic dyes and anionic rat trypsin. Here, using single pair Förster resonance energy transfer, we demonstrate that EpartI* is a metastable complex that can dissociate to free protease and cleaved serpin (I*) as well as convert to the canonical fully translocated complex EfullI*. The partitioning between these two pathways is pH dependent, with conversion favored at low pH and dissociation favored at high pH. The short lifetime of EpartI* (∼3 h at pH 7.4) and the pH dependence of EpartI* dissociation suggest that, unlike in EfullI*, the catalytic triad is intact in EpartI*. These results also demonstrate that interactions between target proteases and the body of the serpin can hinder protease translocation leading to short‐lived covalent complexes.
On the role of structural class of a protein with two‐state folding kinetics in determining correlations between its size, topology, and folding rate
Authors: Istomin Andrei Y. , Jacobs Donald J. , Livesay Dennis R. 
Published: October 2007

AbstractThe time it takes for proteins to fold into their native states varies over several orders of magnitude depending on their native‐state topology, size, and amino acid composition. In a number of previous studies, it was found that there is strong correlation between logarithmic folding rates and contact order for proteins that fold with two‐state kinetics, while such correlation is absent for three‐state proteins. Conversely, strong correlations between folding rates and chain length occur within three‐state proteins, but not in two‐state proteins. Here, we demonstrate that chain lengths and folding rates of two‐state proteins are not correlated with each other only when all‐α, all‐β, and mixed‐class proteins are considered together, which is typically the case. However, when considering all‐α and all‐β two‐state proteins separately, there is significant linear correlation between folding rate and size. Moreover, the sets of data points for the all‐α and all‐β classes define asymptotes of lower and upper limits on folding rates of mixed‐class proteins. By analyzing correlation of other topological parameters with folding rates of two‐state proteins, we find that only the long‐range order exhibits correlation with folding rates that is uniform over all three classes. It is also the only descriptor to provide statistically significant correlations for each of the three structural classes. We give an interpretation of this observation in terms of Makarov and Plaxco's diffusion‐based topomer‐search model.
Protein aggregation processes: In search of the mechanism
Authors: Frieden Carl 
Published: October 2007

AbstractAmyloid formation typically follows a time course in which there is a long lag period followed by a rapid formation of fibrils. In this review, I show that the standard mechanisms of polymerization need to be expanded to consider that the monomeric proteins/peptides involved in amyloid formation are intrinsically disordered and exist as an ensemble of disordered‐collapsed states. The review focuses primarily on events which occur in the long lag period defining these as protein folding issues, coupled with formation of oligomers. Experimental methods to explore folding and oligomerization issues over a wide range of protein concentrations using primarily fluorescence and 19F‐NMR methods are discussed.
The imprint of Quaternary glaciers on the present‐day distribution of the obligate groundwater amphipodNiphargus virei(Niphargidae)
Authors: Foulquier Arnaud , Malard Florian , Lefébure Tristan , Douady Christophe J. , Gibert Janine 
Published: October 2007

AbstractAim A plausible yet untested biogeographical scenario suggests that Quaternary glaciers shaped the present‐day distribution of the groundwater amphipodNiphargus virei. This study was designed to test two hypotheses pertaining to this scenario: (1) the probability of occurrence ofN. vireiin ice‐free areas decreases in the vicinity of the Würm glacier; and (2) dispersal is sufficiently low for the historical record of glacial effects to persist over time.Location The study area was located in the southern Jura Mountains, France.Methods A total of 497 sites were sampled to ascertain the distribution ofN. vireiin the southern Jura. Amplified fragment length polymorphism was analysed from a subset of 24 sites. The relationships between the probability of occurrence ofN. vireiand distance to the Würm glacier or elevation were investigated using a logistic regression. Spatial autocorrelation analyses were performed on both the residuals of the logistic regression and genetic distance to test the significance of dispersal and barriers to post‐glacial recolonization. The influence of catchment boundaries as barriers to dispersal was examined using different neighbouring relationships between sites. We tested the statistical significance of the reduction in deviance and gain in precision of an autologistic regression that took into consideration the influence of dispersal constraints on the distribution ofN. virei.Results Niphargus vireirarely occurred in formerly glaciated areas, and its probability of occurrence in ice‐free areas decreased in the vicinity of the Würm glacier. Combined autocorrelation analyses of spatial distribution and spatial genetic structure showed that: (1) the distance at which spatial autocorrelation was no longer significantly positive did not exceed 16 km; (2) genetic differentiation fitted a model of isolation by distance; and (3) catchment boundaries acted as barriers to dispersal. The autologistic regression with dispersal constraints significantly increased our capacity to predict the distribution ofN. virei. Maps of probabilities of occurrence suggested that post‐glacial recolonization was impeded by the extension of glacial outwash.Main conclusions The present distribution ofN. vireiin southern Jura is probably the result of a historical range reduction driven by glaciation coupled with restricted dispersal and isolation by distance.
The barriers to oceanic island radiation in bryophytes: insights from the phylogeography of the moss Grimmia montana
Authors: Vanderpoorten Alain , Devos Nicolas , Goffinet Bernard , Hardy Olivier J. , Shaw A. Jonathan 
Published: October 2007

AbstractAim  In contrast to angiosperms, bryophytes do not appear to have radiated in Macaronesia and the western Mediterranean. We evaluate if: (1) the apparent lack of radiation in bryophytes reflects our failure to recognize cryptic endemic species; (2) bryophytes are characterized by extremely low evolutionary rates; or (3) bryophytes have a high dispersal ability, which prevents genetic isolation.Location  Worldwide, with a special emphasis on Macaronesia and the western Mediterranean.Methods  Three chloroplast regions were sequenced from samples of the moss Grimmia montana from its entire distribution range. Network analyses, Fst and Nst statistics were used to describe and interpret the phylogeographical signal in the data.Results  Despite significant phylogeographical signal in the chloroplast genome, which demonstrates limits to gene flow at the continental scale, repeated sister group relationships observed among accessions from different geographical areas suggest recurrent colonization patterns. These observations are consistent with mounting evidence that intercontinental distributions exhibited by many bryophyte species result from long‐distance dispersal rather than continental drift. Madeiran and western Mediterranean island haplotypes are either shared by, or closely related to, European and North American ones. Fst values between Madeira, western Mediterranean islands, North America and Europe are not significantly different from zero, and suggest that Madeira and the south‐western Mediterranean are subject to strong transatlantic gene flow. By contrast, haplotypes found in the Canary Islands are shared or closely related to those of populations from south‐western Europe or southern Africa.Main conclusions  Multiple origins and colonization events are not consistent with the hypothesis of a relictual origin of the Macaronesian moss flora. One possible reason for the failure of taxa that experienced multiple colonization events to radiate is niche pre‐emption. We suggest that strong gene flow, coupled with the occupancy of all suitable niches, either by earlier conspecific colonizers or by other species, could be the mechanism preventing island radiation in G. montana and other cryptogams with high long‐distance dispersal abilities.
Growth‐ring variations of dwarf shrubs reflect regional climate signals in alpine environments rather than topoclimatic differences
Authors: Bär Annette , Pape Roland , Bräuning Achim , Löffler Jörg 
Published: October 2007

AbstractAim  Our main aim is to determine if ring‐width variations in Empetrum hermaphroditum reflect regional or local topoclimate signals in an alpine environment. In the case that topoclimate provides the dominant signal, a secondary aim is to link these to spatial distribution patterns of different vegetation types.Location  The study area is situated in the middle alpine belt in the Vågåmo region, Central Norwegian Scandes. Sampling sites cover different topoclimates: ridges, north‐facing slopes and south‐facing slopes.Methods  We constructed ring‐width chronologies of E. hermaphroditum for each type of microsite for the common period 1951–2004. Climate data were prepared on an hourly, daily and growing‐season time scale. Climate–growth relationships were evaluated using bivariate correlations and regression tree methods for continuous time‐series analyses. In addition, extreme growth anomalies (pointer years) were compared with the climate conditions in those years. The impact of water supply on wood anatomy was determined by correlating the conductive area (percentage of vessel per growth ring) with a running mean (sum) of 10‐day intervals for temperature and precipitation.Results  This study indicates that mean summer (June–August) temperatures determine the width of the growth rings of E. hermaphroditum irrespective of topoclimate. The length of the growing season, which is the most differentiating climatic factor between microsites, does not substantially alter the anatomical ring structure. Microsite differences in mean growth rates are attributed to the higher frequency of warm days. Extremely warm days limit ring‐width development at south‐facing slopes, while plants at ridges and north‐facing slopes still benefit from higher temperatures. As a consequence, pointer years are not developed synchronously at all microsites. Vessel formation is affected by available moisture, especially in the later part of the growing season.Main conclusions  Topoclimate induces slight modifications of annual growth‐ring increments of E. hermaphroditum at different microsites. In contrast to the distribution patterns of vegetation types that are determined by snow cover, growth‐ring variations are related to summer temperature conditions, and the prominent regional climate signal is still reflected at all microsites. This offers the opportunity to reconstruct climatic change in alpine regions from dwarf shrub ring‐width chronologies.
On the Magnet Effect of Price Limits
Authors: Abad David , Pascual Roberto 
Published: October 2007

Abstract The ‘magnet’ or ‘gravitational’ effect hypothesis asserts that, when trading halts are rule‐based, investors concerned with a likely impediment to trade advance trades in time. This behaviour actually pushes prices further towards the limit. Empirical studies about the magnet effect are scarce, most likely because of the unavailability of data on rule‐based halts. In this paper, we use a large database from the Spanish Stock Exchange (SSE), which combines intraday stock specific price limits and short‐lived rule‐based call auctions to stabilise prices, to test this hypothesis. The SSE is particularly well suited to test the magnet effect hypothesis since trading halts are price‐triggered and, therefore, predictable to some extent. Still, the SSE microstructure presents two particularities: (i) a limit‐hit triggers an automatic switch to an alternative trading mechanism, a call auction, rather than a pure halt; (ii) the trading halt only lasts 5 minutes. We find that, even when prices are within a very short distance to the price limits, the probability of observing a limit‐hit is unexpectedly low. Additionally, prices either initiate reversion (non limit‐hit days) or slow down gradually (limit‐hit days) as they come near the intraday limits. Finally, the most aggressive traders progressively become more patient as prices approach the limits. Therefore, both the price patterns and the trading behaviour reported near the limits do not agree with the price limits acting as magnetic fields. Consequently, we conclude that the switching mechanism implemented in the SSE does not induce traders to advance their trading programs in time.
A randomized, double‐blind, four‐arm parallel‐group, placebo‐controlled Phase II/III study to investigate the clinical efficacy of two galenic formulations of Polyphenon® E in the treatment of external genital warts
Authors: Gross G , Meyer K‐G , Pres H , Thielert C , Tawfik H , Mescheder A 
Published: October 2007

AbstractObjective  Clinical efficacy and safety of Polyphenon® E, a defined green tea extract, in external genital warts.Design  Randomized, double‐blind, placebo‐controlled study for up to 12 weeks with a 12‐week treatment‐free follow‐up.Setting  Twenty‐eight hospitals and practices in Germany and Russia.Patients  Two hundred forty‐two outpatients (125 men, 117 women) with 2 to 30 warts (total wart area, 12–600 mm2).Intervention(s)  Topical application of Polyphenon® E 10% Cream, Polyphenon® E 15% Ointment or placebo to all external genital warts three times a day.Main outcome measure(s)  Measurement of total wart area and local reactions/adverse events.Results  For 15% ointment, statistically significant differences to placebo were achieved regarding complete clearance of all baseline external genital warts (61.0% vs. 40.5% in males, 56.8% vs. 34.1% in females; combined gender: P = 0.0066) and 75% to 100% clearance (80.8% vs. 51.8%; P = 0.0001) in both the intent‐to‐treat and per‐protocol populations. For 10% cream, 53.8% males and 39.5% females achieved complete clearance. Recurrence rates 12 weeks after end of treatment were 10.6%, 11.8% and 10.3% for 15% ointment, 10% cream and placebo, respectively.Adverse events were observed in only 7.9% of patients, with no serious adverse events or deaths reported. Local skin reactions were generally mild to moderate and resolved with continued treatment without sequelae.Conclusions  Polyphenon® E 15% ointment, composed of a defined green tea extract, proved to be efficacious and safe for both gender in the treatment of external genital warts.
Mitral annular excursion during exercise in endurance athletes
Authors: Sundstedt Milena , Hedberg Pär , Henriksen Egil 
Published: October 2007

SummaryThe aim of the present study was to quantify the left ventricular (LV) longitudinal motion during exercise at rest and during upright exercise in 24 healthy male endurance athletes. By using M‐mode and two‐dimensional echocardiography, the relative mitral annular motion and the absolute LV longitudinal axis was measured at end‐diastole and end‐systole at rest and during exercise. From rest to peak exercise at a heart rate of 160 beats per minute (bpm) the mitral annular motion increased in the septal and lateral annular borders by 68% and 49% respectively. At rest, mitral annular excursion was significantly (13%) higher in the lateral than in the septal wall but at peak exercise at a heart rate of 160 bpm there was no difference between the septal and lateral annular motion. The total end‐diastolic LV axial length did not increase from rest to peak exercise. In conclusion, during upright exercise, mitral annular motion increased significantly with no difference between the septal and lateral annular excursion at peak exercise. The absolute increase in mitral annular motion during exercise was explained by a decrease in axial end‐systolic length.