bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced protein fold recognition using secondary structure information from nmr
Authors: Ayers Daniel J. , Gooley Paul R. , Widmer‐Cooper Asaph , Torda Andrew E. 
Published: February 2009

AbstractNMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determination. In the absence of an X‐ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial secondary structure data and threading a sequence through a library of candidate folds. Using a literature test set, the threading method alone has only a one‐third chance of producing a correct answer among the top ten guesses. With realistic secondary structure information, one can expect a 60–80% chance of finding a homologous structure. The method has then been applied to examples with published estimates of secondary structure. This implementation is completely independent of sequence homology, and sequences are optimally aligned to candidate structures with gaps and insertions allowed. Unlike work using predicted secondary structure, we test the effect of differing amounts of relatively reliable data.
The crystal structure of a bacterial, bifunctional 5, 10 methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase
Authors: Shen Betty W. , Dyer David H. , Huang Jie‐Yu , D'Ari Linda , Rabinowitz Jesse , Stoddard Barry L. 
Published: February 2009

AbstractThe structure of a bifunctional 5, 10‐methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase from Escherichia coli has been determined at 2.5 Å resolution in the absence of bound substrates and compared to the NADP‐bound structure of the homologous enzyme domains from a trifunctional human synthetase enzyme. Superposition of these structures allows the identification of a highly conserved cluster of basic residues that are appropriately positioned to serve as a binding site for the poly‐γ‐glutamyl tail of the tetrahydrofolate substrate. Modeling studies and molecular dynamic simulations of bound methylene‐tetrahydrofolate and NADP shows that this binding site would allow interaction of the nicotinamide and pterin rings in the dehydrogenase active site. Comparison of these enzymes also indicates differences between their active sites that might allow the development of inhibitors specific to the bacterial target.
Folding propensities of synthetic peptide fragments covering the entire sequence of phage 434 Cro protein
Authors: Padmanabhan S. , Jiménez M. Angeles , Rico Manuel 
Published: February 2009

AbstractThe phage 434 Cro protein, the N‐terminal domain of its repressor (R1–69) and that of phage λ (λ6–85) constitute a group of small, monomeric, single‐domain folding units consisting of five helices with striking structural similarity. The intrinsic helix stabilities in λ6–85 have been correlated to its rapid folding behavior, and a residual hydrophobic cluster found in R1–69 in 7 M urea has been proposed as a folding initiation site. To understand the early events in the folding of 434 Cro, and for comparison with R1–69 and λ6–85, we examined the conformational behavior of five peptides covering the entire 434 Cro sequence in water, 40% (by volume) TFE/water, and 7 M urea solutions using CD and NMR. Each peptide corresponds to a helix and adjacent residues as identified in the native 434 Cro NMR and crystal structures. All are soluble and monomeric in the solution conditions examined except for the peptide corresponding to the 434 Cro helix 4, which has low water solubility. Helix formation is observed for the 434 Cro helix 1 and helix 2 peptides in water, for all the peptides in 40% TFE and for none in 7 M urea. NMR data indicate that the helix limits in the peptides are similar to those in the native protein helices. The number of side‐chain NOEs in water and TFE correlates with the helix content, and essentially none are observed in 7 M urea for any peptide, except that for helix 5, where a hydrophobic cluster may be present. The low intrinsic folding propensities of the five helices could account for the observed stability and folding behavior of 434 Cro and is, at least qualitatively, in accord with the results of the recently described diffusion‐collision model incorporating intrinsic helix propensities.
Functional analyses of AmpC β‐lactamase through differential stability
Authors: Beadle Beth M. , Mcgovern Susan L. , Patera Alexandra , Shoichet Brian K. 
Published: February 2009

AbstractDespite decades of intense study, the complementarity of β‐lactams for β‐lactamases and penicillin binding proteins is poorly understood. For most of these enzymes, β‐lactam binding involves rapid formation of a covalent intermediate. This makes measuring the equilibrium between bound and free β‐lactam difficult, effectively precluding measurement of the interaction energy between the ligand and the enzyme. Here, we explore the energetic complementarity of β‐lactams for the β‐lactamase AmpC through reversible denaturation of adducts of the enzyme with β‐lactams. AmpC from Escherichia coli was reversibly denatured by temperature in a two‐state manner with a temperature of melting (Tm) of 54.6 °C and a van't Hoff enthalpy of unfolding (ΔHVH) of 182 kcal/mol. Solvent denaturation gave a Gibbs free energy of unfolding in the absence of denaturant (ΔGu ) of 14.0 kcal/mol. Ligand binding perturbed the stability of the enzyme. The penicillin cloxacillin stabilized AmpC by 3.2 kcal/mol (ΔTm = + 5.8 °C); the monobactam aztreonam stabilized the enzyme by 2.7 kcal/mol (ΔTm = +4.9 °C). Both acylating inhibitors complement the active site. Surprisingly, the oxacephem moxalactam and the carbapenem imipenem both destabilized AmpC, by 1.8 kcal/mol (ΔTm = –3.2 °C) and 0.7 kcal/mol (ΔTm = –1.2 °C), respectively. These β‐lactams, which share nonhydrogen substituents in the 6(7)α position of the β‐lactam ring, make unfavorable noncovalent interactions with the enzyme. Complexes of AmpC with transition state analog inhibitors were also reversibly denatured; both benzo(b)thiophene‐2‐boronic acid (BZBTH2B) and p‐nitrophenyl phenylphosphonate (PNPP) stabilized AmpC. Finally, a catalytically inactive mutant of AmpC, Y150F, was reversibly denatured. It was 0.7 kcal/mol (ΔTm = –1.3 °C) less stable than wild‐type (WT) by thermal denaturation. Both the cloxacillin and the moxalactam adducts with Y150F were significantly destabilized relative to their WT counterparts, suggesting that this residue plays a role in recognizing the acylated intermediate of the β‐lactamase reaction. Reversible denaturation allows for energetic analyses of the complementarity of AmpC for β‐lactams, through ligand binding, and for itself, through residue substitution. Reversible denaturation may be a useful way to study ligand complementarity to other β‐lactam binding proteins as well.
Synthesis and NMR solution structure of an α‐helical hairpin stapled with two disulfide bridges
Authors: Barthe Philippe , Roumestand Christian , Rochette Sandrine , Vita Claudio 
Published: February 2009

AbstractHelical coiled‐coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of α‐helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38‐amino acid peptide, α2p8, encompassing the α‐helical hairpin present in the structure of p8MTCP1, as an α‐helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three‐dimensional structure of this peptide has been solved using homonuclear two‐dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of α2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65 ± 0.25 and 1.51 ± 0.21 Å, respectively. Excised from its protein context, the α‐hairpin keeps its native structure: an α‐helical coiled‐coil, similar to that found in superhelical structures, with two helices spanning residues 4‐16 and 25–36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent‐exposed surface available for mutation. This α‐helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries.
Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase
Authors: Buchko Garry W. , Cushley Robert J. , Rozek Annett , Kennedy Michael A. , Kanda Patrick 
Published: February 2009

AbstractA 38‐residue protein associated with cholesteryl ester transfer inhibition has been identified in baboons (Papio sp.). The cholesteryl ester transfer inhibitor protein (CETIP) corresponds to the N‐terminus of baboon apoC‐I. Relative to CETIP, baboon apoC‐I is a weak inhibitor of baboon cholesteryl ester transferase (CET). To study the structural features responsible for CET inhibition, CETIP was synthesized by solid‐phase methods. Using sodium dodecyl sulfate (SDS) to model the lipoprotein environment, the solution structure of CETIP was probed by optical and 1HNMR spectroscopy. Circular dichroism data show that the protein lacks a well‐defined structure in water but, upon the addition of SDS, becomes helical (56%). A small blue shift of 8 nm was observed in the intrinsic tryptophan fluorescence of CETIP in the presence of saturating amounts of SDS, suggesting that tryptophan‐23 is not buried deeply in the lipid environment. The helical nature of CETIP in the presence of SDS was confirmed by upfield 1Hα secondary shifts and an average solution structure determined by distance geometry/simulated annealing calculations using 476 NOE‐based distance restraints. The backbone (N — Cα — Cα = O ) root‐mean‐square deviation of an ensemble of 17 out of 25 calculated structures superimposed on the average structure was 1.06 ± 0.30 Å using residues V4‐P35 and 0.51 ± 0.17 Å using residues A7‐S32. Although the side‐chain orientations fit the basic description of a class A amphipathic helix, both intramolecular salt bridge formation and “snorkeling” of basic side chains toward the polar face play minor, if any, roles in stabilizing the lipid‐bound amphipathic structure. Conformational features of the calculated structures for CETIP are discussed relative to models of CETIP inhibition of cholesteryl ester transferase.
Blood kinetics of four intraperitoneally administered therapeutic candidate bacteriophages in healthy and neutropenic mice
Authors: Uchiyama Jumpei , Maeda Yoshihiro , Takemura Iyo , Chess‐Williams Russ , Wakiguchi Hiroshi , Matsuzaki Shigenobu 
Published: February 2009

ABSTRACTDue to multiple‐drug resistant bacteria, phage therapy is being revisited. Although most animal experiments focus on therapeutic efficacy, the blood clearance kinetics of phages have not been well described. For further development of an efficient therapeutic strategy, information on phage blood kinetics is important. In this study, time‐course concentration changes in peripheral blood of healthy and neutropenic mice were measured using four therapeutic phages (φMR11, KPP10, φEF24C, and KEP10). The results showed a two‐ to three‐day rapid phage clearance, which fits a two‐compartment model.
Use of serum biomarkers in a diagnostic test for irritable bowel syndrome
Authors: LEMBO A. J. , NERI B. , TOLLEY J. , BARKEN D. , CARROLL S. , PAN H. 
Published: February 2009

SummaryBackground Currently, no single serum biomarker can reliably differentiate irritable bowel syndrome (IBS) from other functional gastrointestinal disorders or organic diseases of the gastrointestinal tract.Aim To develop and validate a diagnostic test using serum biomarkers to detect IBS.Methods Ten serum biomarkers were selected from a potential panel of 140 for their ability to differentiate IBS from non‐IBS disease in blood samples from patients with IBS, other gastrointestinal disorders and healthy volunteers. A predictive modelling tool was developed to assess patterns and relationships among the 10 serum biomarkers that best differentiated IBS patients from healthy controls and patients with non‐IBS gastrointestinal disease. This model was tested in a different cohort of patients and healthy controls (n = 516) to determine the predictive accuracy of differentiating IBS from non‐IBS.Results The sensitivity and specificity of the 10‐biomarker algorithm for differentiating IBS from non‐IBS was 50% and 88% respectively. The positive predictive value was 81%, and the negative predictive value was 64% at 50% IBS prevalence in the validation cohort. Overall accuracy was 70%.Conclusions Assessing serum biomarker patterns can differentiate IBS from non‐IBS with reasonable sensitivity and specificity. Assessing serum biomarkers in an overall diagnostic strategy may allow earlier diagnosis and treatment for patients with IBS.
Review article: strategies to determine whether hypergastrinaemia is due to Zollinger–Ellison syndrome rather than a more common benign cause
Authors: MURUGESAN S. V. M. , VARRO A. , PRITCHARD D. M. 
Published: February 2009

SummaryBackground  As there is considerable overlap between the fasting serum gastrin concentrations found in Zollinger–Ellison syndrome and various common conditions such as Helicobacter pylori infection and acid suppressing medication use, establishing the cause of hypergastrinaemia in individual cases can sometimes be difficult.Aim  To review the causes of hypergastrinaemia and the role of additional non‐invasive investigations in hypergastrinaemic patients.Methods  Review of articles following a Pubmed search.Results  As gastrinomas may cause serious complications and be potentially life threatening, investigation of hypergastrinaemic patients should particularly focus on confirming or refuting the diagnosis of Zollinger–Ellison syndrome. Establishing the cause of hypergastrinaemia may be difficult when there is only a mild‐to‐moderate elevation of fasting serum gastrin concentration and concurrent treatment with proton pump inhibitor drugs and the presence of H. pylori infection can both confuse the clinical picture. A variety of provocative tests are therefore useful for establishing whether a hypergastrinaemic patient has a gastrinoma and current evidence suggests that the secretin test should be used first line.Conclusions  We suggest an algorithm for the investigation of patients found to have an elevated fasting serum gastrin concentration and address the roles of gastrin stimulation tests in current clinical practice.
Chemokine CC‐ligand 5 production and eosinophil activation into the upper airways of aspirin‐sensitive patients
Authors: Fuentes‐Beltrán A. , Montes‐Vizuet R. , Valencia‐Maqueda E. , Negrete‐García M. C. , García‐Cruz M. de L. , Teran L. M. 
Published: February 2009

SummaryBackground
Airway eosinophilia is a hallmark of aspirin‐sensitive asthma/rhinitis.Objective
We have investigated chemokine CC‐ligand 5 (CCL5) production and its association with eosinophil activation in the upper airways of aspirin‐sensitive patients both in vivo and in vitro.Methods
Twenty aspirin‐sensitive asthma/rhinosinusitis patients, 18 atopic‐tolerant asthma/rhinosinusitis patients and 15 healthy control subjects took part in the study. All subjects were challenged with saline and lysine‐acetylsalicylic acid (L‐asa) on separate occasions. Nasal lavages were obtained at baseline and 120 min after challenge and analysed for mediators' release.Results
When compared with control subjects, the baseline levels of CCL5 were significantly increased in both sensitive and tolerant patients (there was no significant difference in CCL5 concentrations between these two groups, P>0.05). However, L‐asa nasal challenge induced significantly increased levels of CCL5 in the sensitive patients but not in the tolerant subjects (median: 380 vs. 140 pg/mL, P<0.0001). Similarly, the concentrations of both eosinophil cationic protein (ECP) and cysteinil leukotriene (cys‐LTs) were increased significantly in the aspirin‐sensitive but not in the tolerant patients. There was a trend towards a significant correlation between CCL5 and ECP concentrations in the sensitive patients following L‐ASA challenge. On incubation with aspirin, nasal tissue derived from aspirin‐sensitive but not that derived from tolerant subjects released increased CCL5 levels in culture. As determined by immunohistochemistry, CCL5 was predominantly localized to the nasal airway epithelium.Conclusion
Altogether, these findings suggest that CCL5 is released in aspirin‐sensitive asthma/rhinosinusitis.
Quality‐of‐life assessment in Chinese families with food‐allergic children
Authors: Leung T. F. , Yung E. , Wong Y. S. , Li C. Y. , Wong G. W. K. 
Published: February 2009

SummaryBackground
Caucasian families with food‐allergic children have a compromised quality of life (QoL) for fear of life‐threatening food reactions. Such data are limited in Asian children. Based on our recent questionnaire‐based survey, 8.1% of young children recruited from local nurseries and kindergartens had parent‐reported adverse food reactions (AFRs).Objective
This study tested the robustness of the Chinese Food Allergy Quality of Life‐Parental Burden questionnaire (FAQL‐PB) and assessed QoL in families with childhood AFR. The correlations among FAQL‐PB items were evaluated by factor analysis.Methods
Two hundred and ninety‐eight of 3677 children aged 2–7 years had parent‐reported AFR, and 197 (66.1%) of them completed the 17 items of our self‐administered FAQL‐PB. Six hundred and thirty‐nine (18.9%) children without AFR returned this questionnaire. Factor analysis was used to delineate the inter‐relationship among the FAQL‐PB items.Results
Cronbach α for our Chinese FAQL‐PB was 0.976, and the median (interquartile range) FAQL‐PB scores of children with and without parent‐reported AFR were 0.10 (0.02–0.32) and 0 (0–0.18), respectively (P<0.001). Factor analysis confirmed excellent correlations between FAQL‐PB items. The 17 items were clustered into two factors, which explained 79.7% of the total variance. Among children with AFR, FAQL‐PB scores increased with increasing numbers of foods that caused AFRs (P<0.001 for trend). Thirty (15.2%) children had impaired QoL, defined as average item FAQL‐PB score 0.5. Impaired QoL was associated with AFR that was caused by >3 foods (P=0.001), current food avoidance (P=0.005) and AFR caused by peanut (P=0.003), egg (P=0.011) and cow's milk (P=0.028), and current flexural dermatitis (P=0.011).Conclusions
FAQL‐PB is a robust measure of AFR‐specific parental QoL, which is impaired in Chinese children with parent‐reported AFR. Flexural dermatitis, current food voidance and AFR caused by multiple foods are independent risk factors for lower parental QoL.
Disturbed cognitive functions after nasal provocation in patients with seasonal allergic rhinitis
Authors: Hartgerink‐Lutgens I. , Vermeeren A. , Vuurman E. , Kremer B. 
Published: February 2009

SummaryBackground
Allergic rhinitis (AR) reduces quality of life as a result of impaired psychological well‐being and perceived impaired cognitive functioning. Few studies have measured cognitive functions objectively and it remains uncertain whether AR leads to an objective reduction in cognitive functions.Objective
The present study investigated whether AR is associated with a decrement in several aspects of cognitive functioning. Furthermore, the study investigated whether AR patients invest more ‘mental effort’ in order to achieve the same cognitive performances as healthy controls.Methods
Twenty five patients with seasonal allergic rhinitis (SAR) and 26 healthy controls, matched for age, education and sex, were tested on a battery of time‐demanding and strenuous objective cognitive tests and subjective questionnaires, both before and after nasal provocation (NP). The cognitive functions assessed were sustained attention, short‐ and long‐term memory and speed of information processing. Mental effort was assessed using visual rating scales.Results
Sustained but not short cognitive performance was impaired in patients after NP. Patients showed an increased effort on short cognitive tests.Conclusion
SAR patients suffer from cognitive performance decrements that can be compensated by additional mental effort for short tasks only.
Serum bactericidal activity against Helicobacter pylori in patients with hypogammaglobulinaemia
Authors: Desar I M E , Van Deuren M , Sprong T , Jansen J B M J , Namavar F , Vandenbroucke-Grauls C M , van Der Meer J W M 
Published: February 2009

Summary
The two major primary antibody deficiency disorders are X-linked hypogammaglobulinaemia (XLA) and common variable immunodeficiency (CVID). CVID patients have an elevated risk for gastric cancer and extra-nodal marginal zone lymphoma. Both diseases are associated with Helicobacter pylori infection. We investigated whether antibody deficiency leads to defective serum bactericidal activity against H. pylori. We also investigated the correlation with immunoglobulin (Ig)M levels and observed the terminal complement complex (TCC) activity. Sera of 13 CVID patients (four H. pylori positive), one patient with hyper-IgM syndrome, one patient with Good syndrome (both H. pylori positive), five XLA patients, four H. pylori seropositive controls, four H. pylori seronegative controls and a sample of pooled human serum (PHS) were incubated in vitro with bacterial suspensions of H. pylori for 30 min. After 72 h of culture, colony-forming units were counted. TCC formation was measured by enzyme-linked immunosorbent assay. We found that normal human serum is bactericidal for H. pylori, whereas heat-inactivated serum shows hardly any killing of H. pylori. Serum (1%) of hypogammaglobulinaemia patients has a decreased bactericidal activity against H. pylori. Helicobacter pylori-positive (HP+) normal individuals show more than 90% killing of H. pylori, whereas CVID patients show 35% killing (P = 0·007) and XLA patients only 19% (P = 0·003). Serum (1%) of HP+ volunteers showed significantly better killing compared with serum of H. pylori-negative (HP–) volunteers (P = 0·034). No correlation between (substituted) IgG levels and serum bactericidal activity was found, but a weak correlation between total serum IgM and serum bactericidal activity was found. In conclusion, serum bactericidal activity against H. pylori is decreased in patients with hypogammaglobulinaemia. Heat treatment of the serum abolished the bactericidal capacity, indicating that complement activity is essential for the bactericidal effect.