bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictors of smoking cessation in patients admitted for acute coronary heart disease
Authors: Quist-Paulsen Petter , Bakke Per S. , Gallefoss Frode 
Published: October 2005

Background Smoking cessation is probably the most important single action after a coronary event. In order to increase the effectiveness of smoking cessation programs, it is important to have knowledge of the predictors of smoking cessation. Further, it is unknown whether smoking cessation programs have impact on these predictors. Methods Data were obtained from a randomized controlled trial of smoking cessation intervention in 240 smokers aged less than 76 years admitted for myocardial infarction, unstable angina, or cardiac bypass surgery. Baseline characteristics were prospectively recorded. Smoking cessation was determined by self report and biochemical verification at 12 months follow-up. Results In multivariate logistic regression analysis, a high level of nicotine addiction, low level of self-confidence in quitting and having previous coronary heart disease were significant negative predictors of smoking cessation at 12 months follow-up. Having previous coronary heart disease and a diagnosis other than acute myocardial infarction as a reason for admission were important negative predictors of abstinence in the usual care group, in contrast to the intervention group, although this did not reach a level of significance in the subgroup interaction analyses. A high level of nicotine addiction was a strong negative predictor in both groups. Conclusion A high level of nicotine addiction is an important negative predictor of smoking cessation, even within an individualized smoking cessation program. Smoking cessation intervention seems to be especially effective in patients with previous coronary heart disease and in patients with unstable angina or coronary artery bypass surgery, compared to usual care.
Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody–hapten complex
Authors: Curcio Raffaele , Caflisch Amedeo , Paci Emanuele 
Published: September 2005

AbstractWe study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single‐chain variable‐fragment (scFv) anti‐fluorescein antibody FITC‐E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with metastable intermediates. For the wild type, the rate‐limiting step in the unbinding process corresponds to the breaking of the non‐native interactions characteristic of a specific intermediate. The H(H58)A mutation disfavors the occurrence of this intermediate. Two events where the hapten partially unbinds in the absence of pulling force are observed in extensive equilibrium simulations of the wild type, and their analysis indicates that forced unbinding and spontaneous unbinding proceed along similar pathways. The different unbinding mechanisms observed in the simulations suggest a possible reason for the difference in the experimental off‐rate between the two antibodies. We predict mutations that are expected to modulate the occurrence of the unbinding intermediate. For two such new mutants [H(H58)A and S(H52)A], our predictions are validated in silico by additional simulations. The accompanying paper in this issue by Honegger et al. reports the X‐ray structure of FITC‐E2 with a derivative of fluorescein, which was used as the starting conformation for the work presented here.
Evidence from 13C solid‐state NMR spectroscopy for a lamella structure in an alanine–glycine copolypeptide: A model for the crystalline domain of Bombyx mori silk fiber
Authors: Asakura Tetsuo , Nakazawa Yasumoto , Ohnishi Erika , Moro Fumika 
Published: September 2005

Abstract13C high‐resolution solid‐state NMR coupled with selective 13C isotope‐labeling of different Ala one methyl carbons was used to clarify the structure of (AG)15 peptide in the silk II structure as a model for the crystalline domain of Bombyx mori silk fiber. At the inner part of the peptide, the fraction of the peak at 16.6 ppm of the Ala Cβ resonance assigned to β‐turn structure increased at 11th and 19th positions. These data indicate the appearance of the most probable lamellar structure having a turn structure at these two positions, although the position of turn was distributed along the chain.
Expression of human peripheral cannabinoid receptor for structural studies
Authors: Yeliseev Alexei A. , Wong Karen K. , Soubias Olivier , Gawrisch Klaus 
Published: September 2005

AbstractHuman peripheral‐type cannabinoid receptor (CB2) was expressed inEscherichia colias a fusion with the maltose‐binding protein, thioredoxin, and a deca‐histidine tag. Functional activity and structural integrity of the receptor in bacterial protoplast membranes was confirmed by extensive binding studies with a variety of natural and synthetic cannabinoid ligands.E. colimembranes expressing CB2 also activated cognate G‐proteins in an in vitro coupled assay. Detergent‐solubilized receptor was purified to 80%–90% homogeneity by affinity chromatography followed by ion‐exchange chromatography. By high‐resolution NMR on the receptor in DPC micelles, it was determined that purified CB2 forms 1:1 complexes with the ligands CP‐55,940 and anandamide. The receptor was successfully reconstituted into phosphatidylcholine bilayers and the membranes were deposited into a porous substrate as tubular lipid bilayers for structural studies by NMR and scattering techniques.
Parallel interrogation of covalent intermediates in the biosynthesis of gramicidin S using high‐resolution mass spectrometry
Authors: Miller Leah M. , Mazur Matthew T. , McLoughlin Shaun M. , Kelleher Neil L. 
Published: September 2005

AbstractFor determination of multiple covalent intermediates bound to the ultra‐large enzymes responsible for biosynthesis via nonribosomal peptide synthesis, mass spectrometry (MS) is a promising method to provide new mechanistic insight. Application of a quadrupole‐Fourier‐transform instrument (Q‐FTMS) for direct analysis of aminoacyl intermediates is demonstrated for the first two modules (127 and 120 kDa) involved in the nonribosomal synthesis of gramicidin S. Cyanogen bromide digestions of recombinant proteins afforded detection of two active site peptides (both ∼13 kDa) that provided direct evidence for modules copurifying with their preferred amino acid substrates. Given the ability to detect multiple covalent intermediates in tandem, a competition experiment among several nonnatural substrates in parallel was performed using the first module. This defined mixture of acyl‐enzyme intermediates was used to probe the selectivity of the condensation step producing a diversity of noncognate dipeptides on the second module.
Topology characterization of a benzodiazepine‐binding β‐rich domain of the GABAA receptor α1 subunit
Authors: Xu Zhiwen , Fang Shisong , Shi Haifeng , Li Hoiming , Deng Yiqun , Liao Yinglei , Wu Jiun‐Ming , Zheng Hui , Zhu Huaimin , Chen Hueih‐Min , Tsang Shui Ying , Xue Hong 
Published: September 2005

AbstractStructural investigation of GABAA receptors has been limited by difficulties imposed by its trans‐membrane‐complex nature. In the present study, the topology of a membrane‐proximal β‐rich (MPB) domain in the C139–L269 segment of the receptor α1 subunit was probed by mapping the benzodiazepine (BZ)‐binding and epitopic sites, as well as fluorescence resonance energy transfer (FRET) analysis. Ala‐scanning and semiconservative substitutions within this segment revealed the contribution of the phenyl rings of Y160 and Y210, the hydroxy group of S186 and the positive charge on R187 to BZ‐binding. FRET with the bound BZ ligand indicated the proximity of Y160, S186, R187, and S206 to the BZ‐binding site. On the other hand, epitope‐mapping using the monoclonal antibodies (mAbs) against the MPB domain established a clustering of T172, R173, E174, Q196, and T197. Based on the lack of FRET between Trp substitutionally placed at R173 or V198 and bound BZ, this epitope‐mapped cluster is located on a separate end of the folded protein from the BZ‐binding site. Mutations of the five conserved Cys and Trp residues in the MPB domain gave rise to synergistic and rescuing effects on protein secondary structures and unfolding stability that point to a CCWCW‐pentad, reminiscent to the CWC‐triad “pin” of immunoglobulin (Ig)‐like domains, important for the structural maintenance. These findings, together with secondary structure and fold predictions suggest an anti‐parallel β‐strand topology with resemblance to Ig‐like fold, having the BZ‐binding and the epitopic residues being clustered at two different ends of the fold.
Ionic liquids as refolding additives: N′‐alkyl and N′‐(ω‐hydroxyalkyl) N‐methylimidazolium chlorides
Authors: Lange Christian , Patil Ganesh , Rudolph Rainer 
Published: September 2005

AbstractThe purpose of this work was to investigate the influence of a series of N′‐alkyl and N′‐(ω‐hydroxy‐alkyl)‐N‐methylimidazolium chlorides on the renaturation of two model proteins, namely hen egg white lysozyme and the single‐chain antibody fragment ScFvOx. All tested ionic liquids acted as refolding enhancers, with varying efficacies and efficiencies. The results of the refolding screening could be interpreted by taking into account the effect of the studied ionic liquids on protein aggregation, together with the systematic variations of their influence on the stability of native proteins in solution. More hydrophobic imidazolium cations carrying longer alkyl chains were increasingly destabilizing, while terminal hydroxylation of the alkyl chain made the salts more compatible with protein stability. The studied ionic liquids can be classified as preferentially bound, slightly to moderately chaotropic cosolvents for proteins.
Solution structure of the low‐molecular‐weight protein tyrosine phosphatase from Tritrichomonas foetus reveals a flexible phosphate binding loop
Authors: Gustafson Christin L.T. , Stauffacher Cynthia V. , Hallenga Klaas , Van Etten Robert L. 
Published: September 2005

AbstractEukaryotic low‐molecular‐weight protein tyrosine phosphatases (LMW PTPs) contain a conserved serine, a histidine with an elevated pKa, and an active site asparagine that together form a highly conserved hydrogen bonding network. This network stabilizes the active site phosphate binding loop for optimal substrate binding and catalysis. In the phosphatase from the bovine parasite Tritrichomonas foetus (TPTP), both the conserved serine (S37) and asparagine (N14) are present, but the conserved histidine has been replaced by a glutamine residue (Q67). Site‐directed mutagenesis, kinetic, and spectroscopic experiments suggest that Q67 is located near the active site and is important for optimal catalytic activity. Kinetic experiments also suggest that S37 participates in the active site/hydrogen bonding network. Nuclear magnetic resonance spectroscopy was used to determine the three‐dimensional structure of the TPTP enzyme and to further examine the roles of S37 and Q67. The backbone conformation of the TPTP phosphate binding loop is nearly superimposable with that of other tyrosine phosphatases, with N14 existing in a strained, left‐handed conformation that is a hallmark of the active site hydrogen bonding network in the LMW PTPs. As expected, both S37 and Q67 are located at the active site, but in the consensus structure they are not within hydrogen bonding distance of N14. The hydrogen bond interactions that are observed in X‐ray structures of LMW PTPs may in fact be transient in solution. Protein dynamics within the active site hydrogen bonding network appear to be affected by the presence of substrate or bound inhibitors such as inorganic phosphate.
Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum
Authors: Pédelacq Jean‐Denis , Waldo Geoffrey S. , Cabantous Stéphanie , Liong Elaine C. , Terwilliger Thomas C. 
Published: September 2005

AbstractNucleoside diphosphate (NDP) kinases are ubiquitous enzymes that transfer γ‐phosphates from nucleoside triphosphates to nucleoside diphosphates via a ping‐pong mechanism. The important role of this large family of enzymes in controlling cellular functions and developmental processes along with their crystallizability has made them good candidates for structural studies. We recently determined the structure of an evolved version of an NDP kinase from Pyrobaculum aerophilum, an extreme thermophile. This NDP kinase has similarity to the 42 other NDP kinases deposited in the Protein Data Bank (PDB) but differs significantly in sequence, structure, and biophysical properties. The P. aerophilum NDP kinase sequence contains two unique segments not present in other NDP kinases, comprising residues 66–100 and 156–165. We show that deletion mutants of the P. aerophilum NDP kinase lacking either or both of these inserts have an altered substrate specificity, allowing dGTP as the phosphate donor. A structural analysis of the evolved NDP kinase in conjunction with mutagenesis experiments suggests that the substrate specificity of the P. aerophilum NDP kinase is related to the presence of these two inserts.
Design of HIV‐1‐PR inhibitors that do not create resistance: Blocking the folding of single monomers
Authors: Broglia Ricardo A. , Tiana Guido , Sutto Ludovico , Provasi Davide , Simona Fabio 
Published: September 2005

AbstractThe main problems found in designing drugs are those of optimizing the drug–target interaction and of avoiding the insurgence of resistance. We suggest a scheme for the design of inhibitors that can be used as leads for the development of a drug and that do not face either of these problems, and then apply it to the case of HIV‐1‐PR. It is based on the knowledge that the folding of single‐domain proteins, such as each of the monomers forming the HIV‐1‐PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting, and highly conserved amino acids that play a central role in the folding process. Because LES have evolved over many generations to recognize and strongly interact with each other so as to make the protein fold fast and avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding‐inhibitor molecules suggest themselves: short peptides (or eventually their mimetic molecules) displaying the same amino acid sequence of that of LES (p‐LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV‐1‐PR that successfully avoid the action of p‐LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations, we first identify the LES of the HIV‐1‐PR and then show that the corresponding p‐LES peptides act as effective inhibitors of the folding of the protease.
Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family
Authors: Leulliot Nicolas , Quevillon‐Cheruel Sophie , Graille Marc , Schiltz Marc , Blondeau Karine , Janin Joël , Van Tilbeurgh Herman 
Published: September 2005

AbstractWe present here the structure of Yer010c protein of unknown function, solved by Multiple Anomalous Diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity A (RraA) family. In Escherichia coli, RraA has been shown to regulate the activity of ribonuclease E by direct interaction. The absence of ribonuclease E in yeast suggests a different function for this family member in this organism. Yer010cp has a few supplementary secondary structure elements and a deep pseudo‐knot at the heart of the protein core. A tunnel at the interface between two monomers, lined with conserved charged residues, has unassigned residual electron density and may constitute an active site for a yet unknown activity.
Crystal structure of the Yersinia type III secretion protein YscE
Authors: Phan Jason , Austin Brian P. , Waugh David S. 
Published: September 2005

AbstractThe plague‐causing bacterium Yersinia pestis utilizes a contact‐dependent (type III) secretion system (T3SS) to transport virulence factors from the bacterial cytosol directly into the interior of mammalian cells where they interfere with signal transduction pathways that mediate phagocytosis and the inflammatory response. The type III secretion apparatus is composed of 20–25 different Yersinia secretion (Ysc) proteins. We report here the structure of YscE, the smallest Ysc protein, which is a dimer in solution. The probable mode of oligomerization is discussed.
Protecting against anthracycline‐induced myocardial damage: a review of the most promising strategies
Authors: Wouters Karlijn A. , Kremer Leontien C. M. , Miller Tracie L. , Herman Eugene H. , Lipshultz Steven E. 
Published: September 2005

SummaryOver the last 40 years, great progress has been made in treating childhood and adult cancers. However, this progress has come at an unforeseen cost, in the form of emerging long‐term effects of anthracycline treatment. A major complication of anthracycline therapy is its adverse cardiovascular effects. If these cardiac complications could be reduced or prevented, higher doses of anthracyclines could potentially be used, thereby further increasing cancer cure rates. Moreover, as the incidence of cardiac toxicity resulting in congestive heart failure or even heart transplantation dropped, the quality and extent of life for cancer survivors would improve. We review the proposed mechanisms of action of anthracyclines and the consequences associated with anthracycline treatment in children and adults. We summarise the most promising current strategies to limit or prevent anthracycline‐induced cardiotoxicity, as well as possible strategies to prevent existing cardiomyopathy from worsening.
Immunological control of methicillin-resistantStaphylococcus aureus(MRSA) infection in an immunodeficient murine model of thermal injuries
Authors: Katakura T , Yoshida T , Kobayashi M , Herndon D N , Suzuki F 
Published: September 2005

SummaryStaphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), is a major cause of sepsis in patients who are immunosuppressed by their burns. In this study, an immunological regulation of MRSA infection was attempted in a mouse model of thermal injury. SCIDbg mice were resistant to MRSA infection, while SCIDbgMN mice (SCIDbg mice depleted of neutrophils and macrophages (Mφ)) were susceptible to the same infection. Also, thermally injured SCIDbg mice were shown to be susceptible to MRSA infection. On the other hand, the resistance of SCIDbgMN mice to the infection was completely recovered after an inoculation with Mφ from normal mice. However, anti-MRSA resistance was not shown in SCIDbgMN mice inoculated with Mφ from thermally injured mice. Mφ from MRSA-infected thermally injured mice were identified as alternatively activated Mφ, and Mφ from MRSA-infected unburned mice were characterized as classically activated Mφ. Mφ from thermally injured SCIDbg mice previously treated with 2-carboxyethylgermanium sesquioxide (Ge-132) protected SCIDbgMN mice against MRSA infection. Ge-132 has been described as an inhibitor of alternatively activated Mφ generation. These results suggest that MRSA infection in thermally injured patients is controlled immunologically through the induction of anti-MRSA effector cells and elimination of burn-associated alternatively activated Mφ, which are cells that inhibit the generation of classically activated Mφ.
Vitamin D status, seasonal variations, parathyroid adenoma weight and bone mineral density in primary hyperparathyroidism
Authors: Moosgaard B. , Vestergaard P. , Heickendorff L. , Melsen F. , Christiansen P. , Mosekilde L. 
Published: September 2005

SummaryBackground  Primary hyperparathyroidism (PHPT) and vitamin D insufficiency are common conditions that can occur in combination. However, low plasma 25‐hydroxyvitamin D (25OHD) may also enhance the risk of PHPT or modify disease severity.Aim  To compare the risk of vitamin D insufficiency and deficiency stratified by age, sex and season between PHPT patients and controls and to assess associations between plasma 25OHD and adenoma weight, biochemical variables, bone mineral density (BMD) and clinical complications.Design  Cross‐sectional study.Material  A total of 289 consecutive Caucasian patients with PHPT aged 65·9 (24–92) years, 289 sex‐, age‐ and season‐matched normocalcaemic controls and 187 healthy adult blood donors. PHPT diagnosis was confirmed in 214 by neck exploration.Results  Vitamin D insufficiency (plasma 25OHD < 50 nmol/l) was observed in 81% of PHPT patients compared with 60% of sex‐ and age‐matched controls (P < 0·001) and 35% of blood donors (P < 0·001). During summer, 77%vs. 53% (P < 0·001) and 4% (P < 0·001), respectively, had vitamin D insufficiency. Average plasma 25OHD was 41 (range 9–87) nmol/l among 27 PHPT patients compared with 87 (21–173) nmol/l (P < 0·001) among aged‐matched blood donors. During winter, 86%vs. 66% (P < 0·001) and 71% (P < 0·05), respectively, had vitamin D insufficiency. Vitamin D deficiency (plasma 25OHD < 25 nmol/l) was observed in 33% of PHPT patients compared with 20% of age‐ and sex‐matched controls (P < 0·001) and 13% of blood donors (P < 0·001). Both PHPT patients and controls showed seasonal variations in 25OHD related to the average number of sun hours, but values were lower in PHPT patients at all calendar months. In PHPT patients low plasma 25OHD was associated with higher plasma levels of calcium, PTH and alkaline phosphatase and with lower renal calcium excretion, femoral neck and forearm BMD. No association was found between plasma 25OHD and adenoma weight (total or divided into tertiles). There was a trend towards increased risk of osteoporotic fractures (P < 0·08) with low plasma 25OHD.Conclusion  Vitamin D insufficiency and deficiency are common findings in PHPT and occur more often than in a sex‐ and age‐matched control group referred from general practice and in normal blood donors irrespective of season. Low plasma 25OHD levels are associated with an aggravated clinical presentation of PHPT but do not affect adenoma size.