bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long Term Nutritional Rehabilitation by Gastrostomy in Israeli Patients with Cystic Fibrosis: Clinical Outcome in Advanced Pulmonary Disease
Authors: Efrati Ori , Mei‐Zahav Meir , Rivlin Joseph , Kerem Eitan , Blau Hannah , Barak Asher , Bujanover Yoram , Augarten Arie , Cochavi Brijit , Yahav Yaacov , Modan‐Moses Dalit 
Published: February 2006

ABSTRACTObjectives:Several studies have shown a linear correlation between nutritional status and pulmonary function in patients with cystic fibrosis. Our study aims were: 1) To evaluate the effect of nutritional supplementation via gastrostomy on nutritional, clinical, and pulmonary parameters, and 2) To identify predicting factors for success of long‐term nutritional rehabilitation.Methods:Twenty‐one Israeli patients, aged 8 months to 20 years, underwent gastrostomy insertion from 1992 to 2001. All patients were pancreatic insufficient, and all carried severe mutations (W1282X in 62% of the patients). Anthropometric and clinical data were obtained for each patient: 0−12 months before and 6−12 months and 18−24 months after gastrostomy placement. Standard deviation scores (SDS) for height, weight, and body mass index as well as percent of height‐appropriate body weight were calculated.Results:The mean percent‐of‐predicted forced expiratory volume in 1 second (FEV1) decreased significantly during the first year of gastrostomy feeding (n = 16), from 44.2% ± 13.9 to 41% ± 13.3 (P = 0.05). However, during the second year of therapy (n = 10), a trend toward improvement was observed (from 39.4 ± 12.1 to 41.4 ± 16.1). Weight, and BMI z‐scores as well as weight percent‐of ideal body weight increased significantly. Height z‐score for age decreased during the first year (from −1.9 ± 1.3 to −2.1 ± 1.4), However, a trend toward improvement was observed during the second year. A significant correlation was found between the change in weight z‐score and height z‐score during the first (r = 0.488, P = 0.016) and the second (r = 0.825, P < 0.001) years. There was no difference between compliers and noncompliers regarding height, weight, and BMI either before or after gastrostomy placement. A significant correlation between age at insertion of gastrostomy and improvement in height z‐score (r = 0.52, P = 0.016) was observed. Cystic fibrosis related diabetes (n = 8) did not affect the response to supplemental feeding.Conclusions:We observed a trend toward improvement of pulmonary disease during the second year, and a significant improvement in weight, height, and BMI z‐scores. Compliance, diabetes, and young age prior to tube insertion did not predict success of nutritional rehabilitation.
Endoscopic Outcome Beyond Esophageal Variceal Eradication in Children with Extrahepatic Portal Venous Obstruction
Authors: Itha Srivenu , Yachha Surender Kumar 
Published: February 2006

ABSTRACTObjectives:To find out the recurrence of esophageal varices, evolution of gastric varices, portal hypertensive gastropathy (PHG) and risk of rebleeding following esophageal variceal eradication.Methods:Between 1992 and 2002, children with extrahepatic portal venous obstruction (EHPVO) and bleeding from esophageal varices received endoscopic injection sclerotherapy until eradication. Surveillance endoscopy was performed initially at 3 months and subsequently at intervals of 6 months to one year to detect esophageal and gastric varices, and PHG. Gastric varices were classified as gastroesophageal (GOV) or isolated gastric varices (IGV). Gastroesophageal varices included types GOV1 and GOV2 that extend along lesser and greater curvatures respectively. Patients who had recurrence of bleeding were evaluated by emergency upper gastrointestinal endoscopy.Results:163 of 183 children who achieved esophageal variceal eradication were evaluated. Esophageal varices recurred in 40% cases. Primary gastric varices (before sclerotherapy) were seen in 61% cases [GOV 98% (83% GOV1, 15% GOV2) and IGV 2%] and secondary (after sclerotherapy) in 28% [GOV 71% (47% GOV1, 24% GOV2) and IGV 29%]. Secondary gastric varices were distributed as 20% GOV1, 42% GOV2 and 87% IGV. Frequency of gastric varices before sclerotherapy and at the last follow up showed decrease in GOV1 from 82 to 56 (P = 0.02), increase in GOV2 from 15 to 23 and increase in IGV from 2 to 15 (P < 0.001). PHG increased in frequency from 12% to 41% (P < 0.001) and severity from one patient to 12 (P < 0.001). Eleven cases had rebleeding from gastric varices (5 GOV1, 4 GOV2 and 2 IGV).Conclusions:Following esophageal variceal eradication in children with EHPVO a significant decrease in GOV1, increase in IGV and increased frequency and severity of PHG takes place. Small rebleeding risk persists from gastric varices irrespective of the type.
Nocturnal Acid Breakthrough in Children with Reflux Esophagitis Taking Proton Pump Inhibitors
Authors: Pfefferkorn Marian D , Croffie Joseph M , Gupta Sandeep K , Molleston Jean P , Eckert George J , Corkins Mark R , Fitzgerald Joseph F 
Published: February 2006

ABSTRACTObjectives:We aimed to determine if nocturnal acid breakthrough occurs in children receiving proton pump inhibitors for reflux esophagitis, and to compare the healing of esophagitis in children with nocturnal acid breakthrough receiving proton pump inhibitors ± ranitidine.Methods:This is a prospective, double‐blind study. Endoscopic and histologic esophagitis were scored 0‐4 and 0‐3, respectively. Patients were treated with a proton pump inhibitor twice daily and esophagogastric pH monitoring was performed at week 3. Patients with nocturnal acid breakthrough were randomized. One group received ranitidine and the other received placebo at bedtime in addition to proton pump inhibitor therapy. Endoscopy was performed on all patients (with pH monitoring on patients with nocturnal acid breakthrough) during the 17th week of therapy.Results:We enrolled 18 patients, ages 1 to 13 years (mean = 10.3 years). Mean baseline endoscopic and histologic scores were 3.1 +/− 1.4 and 1.8 +/− 0.7, respectively. Mean dose of proton pump inhibitor was 1.3 mg/kg +/− 0.6. Nocturnal acid breakthrough was documented in 16/18 (89%) patients. Seven patients received ranitidine and 9 received placebo. The reflux index improved: mean of 14.3 at baseline, 2.0 at week 3 (P= 0.0001), and 5.1 at week 17 (P= 0.09). Nocturnal acid breakthrough persisted in 9/12 (75%) patients, 3 of whom received ranitidine at bedtime. Esophagitis improved inallpatients following therapy: mean endoscopy and histology scores were 1.6 +/− 1.8 (P= 0.0020) and 0.8 +/− 0.9 (P= 0.0013), respectively. Symptoms significantly improved from a mean score of 2.0 at baseline to 0.4 at week 17 (P= 0.0001).Conclusions:Nocturnal acid breakthrough is common in pediatric patients treated with proton pump inhibitors. Reflux index remains normal in spite of nocturnal acid breakthrough. Symptoms and esophagitis continued to improve during therapy in spite of nocturnal acid breakthrough. There appears to be no additional benefit to supplementation with ranitidine at bedtime.
Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures
Authors: Fan Hao , Mark Alan E. 
Published: February 2006

AbstractBacterial chaperonin, GroEL, together with its co‐chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse‐grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results support the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.
A general model of G protein‐coupled receptor sequences and its application to detect remote homologs
Authors: Wistrand Markus , Käll Lukas , Sonnhammer Erik L.L. 
Published: February 2006

AbstractG protein‐coupled receptors (GPCRs) constitute a large superfamily involved in various types of signal transduction pathways triggered by hormones, odorants, peptides, proteins, and other types of ligands. The superfamily is so diverse that many members lack sequence similarity, although they all span the cell membrane seven times with an extracellular N and a cytosolic C terminus. We analyzed a divergent set of GPCRs and found distinct loop length patterns and differences in amino acid composition between cytosolic loops, extracellular loops, and membrane regions. We configured GPCRHMM, a hidden Markov model, to fit those features and trained it on a large dataset representing the entire superfamily. GPCRHMM was benchmarked to profile HMMs and generic transmembrane detectors on sets of known GPCRs and non‐GPCRs. In a cross‐validation procedure, profile HMMs produced an error rate nearly twice as high as GPCRHMM. In a sensitivity‐selectivity test, GPCRHMM's sensitivity was about 15% higher than that of the best transmembrane predictors, at comparable false positive rates. We used GPCRHMM to search for novel members of the GPCR superfamily in five proteomes. All in all we detected 120 sequences that lacked annotation and are potentially novel GPCRs. Out of those 102 were found in Caenorhabditis elegans, four in human, and seven in mouse. Many predictions (65) belonged to Pfam domains of unknown function. GPCRHMM strongly rejected a family of arthropod‐specific odorant receptors believed to be GPCRs. A detailed analysis showed that these sequences are indeed very different from other GPCRs. GPCRHMM is available at http://gpcrhmm.cgb.ki.se.
The solution structure of the methylated form of the N‐terminal 16‐kDa domain of Escherichia coli Ada protein
Authors: Takinowaki Hiroto , Matsuda Yasuhiro , Yoshida Takuya , Kobayashi Yuji , Ohkubo Tadayasu 
Published: February 2006

AbstractThe N‐terminal 16‐kDa domain of Escherichia coli Ada protein (N‐Ada16k) repairs DNA methyl phosphotriester lesions by an irreversible methyl transfer to its cysteine residue. Upon the methylation, the sequence‐specific DNA binding affinity for the promoter region of the alkylation resistance genes is enhanced by 103‐fold. Then, it acts as a transcriptional regulator for the methylation damage. In this paper, we identified the methyl acceptor residue of N‐Ada16k and determined the solution structure of the methylated form of N‐Ada16k by using NMR and mass spectrometry. The results of a 13C‐filtered 1H‐13C HMBC experiment and MALDI‐TOF MS and MS/MS experiments clearly showed that the methyl acceptor residue is Cys38. The solution structure revealed that it has two distinct subdomains connected by a flexible linker loop: the methyltransferase (MTase) subdomain with the zinc–thiolate center, and the helical subdomain with a helix‐turn‐helix motif. Interestingly, there is no potential hydrogen bond donor around Cys38, whereas the other three cysteine residues coordinated to a zinc ion have potential donors. Hence, Cys38 could retain its inherent nucleophilicity and react with a methyl phosphotriester. Furthermore, the structure comparison shows that there is no indication of a remarkable conformational change occurring upon the methylation. This implies that the electrostatic repulsion between the negatively charged DNA and the zinc–thiolate center may avoid the contact between the MTase subdomain and the DNA in the nonmethylated form. Thus, after the Cys38 methylation, the MTase subdomain can bind the cognate DNA because the negative charge of the zinc–thiolate center is reduced.
Domain:domain interactions within Hop, the Hsp70/Hsp90 organizing protein, are required for protein stability and structure
Authors: Carrigan Patricia E. , Sikkink Laura A. , Smith David F. , Ramirez‐Alvarado Marina 
Published: February 2006

AbstractThe major heat shock protein (Hsp) chaperones Hsp70 and Hsp90 both bind the co‐chaperone Hop (Hsp70/Hsp90 organizing protein), which coordinates Hsp actions in folding protein substrates. Hop contains three tetratricopeptide repeat (TPR) domains that have binding sites for the conserved EEVD C termini of Hsp70 and Hsp90. Crystallographic studies have shown that EEVD interacts with positively charged amino acids in Hop TPR‐binding pockets (called carboxylate clamps), and point mutations of these carboxylate clamp positions can disrupt Hsp binding. In this report, we use circular dichroism to assess the effects of point mutations and Hsp70/Hsp90 peptide binding on Hop conformation. Our results show that Hop global conformation is destabilized by single point mutations in carboxylate clamp positions at pH 5, while the structure of individual TPR domains is unaffected. Binding of peptides corresponding to the C termini of Hsp70 and Hsp90 alters the global conformation of wild‐type Hop, whereas peptide binding does not alter conformation of individual TPR domains. These results provide biophysical evidence that Hop‐binding pockets are directly involved with domain:domain interactions, both influencing Hop global conformation and Hsp binding, and contributing to proper coordination of Hsp70 and Hsp90 interactions with protein substrates.
Octapeptide repeat insertions increase the rate of protease‐resistant prion protein formation
Authors: Moore Roger A. , Herzog Christian , Errett John , Kocisko David A. , Arnold Kevin M. , Hayes Stanley F. , Priola Suzette A. 
Published: February 2006

AbstractA central feature of transmissible spongiform encephalopathies (TSE or prion diseases) involves the conversion of a normal, protease‐sensitive glycoprotein termed prion protein (PrP‐sen) into a pro‐tease‐resistant form, termed PrP‐res. The N terminus of PrP‐sen has five copies of a repeating eight amino acid sequence (octapeptide repeat). The presence of one to nine extra copies of this motif is associated with a heritable form of Creutzfeld‐Jakob disease (CJD) in humans. An increasing number of octapeptide repeats correlates with earlier CJD onset, suggesting that the rate at which PrP‐sen misfolds into PrP‐res may be influenced by these mutations. In order to determine if octapeptide repeat insertions influence the rate at which PrP‐res is formed, we used a hamster PrP amyloid‐forming peptide (residues 23–144) into which two to 10 extra octapeptide repeats were inserted. The spontaneous formation of protease‐resistant PrP amyloid from these peptides was more rapid in response to an increased number of octapeptide repeats. Furthermore, experiments using full‐length glycosylated hamster PrP‐sen demonstrated that PrP‐res formation also occurred more rapidly from PrP‐sen molecules expressing 10 extra copies of the octapeptide repeat. The rate increase for PrP‐res formation did not appear to be due to any influence of the octapeptide repeat region on PrP structure, but rather to more rapid binding between PrP molecules. Our data from both models support the hypothesis that extra octapeptide repeats in PrP increase the rate at which protease resistant PrP is formed which in turn may affect the rate of disease onset in familial forms of CJD.
Site‐specific labeling of proteins for single‐molecule FRET by combining chemical and enzymatic modification
Authors: Jäger Marcus , Nir Eyal , Weiss Shimon 
Published: February 2006

AbstractAn often limiting factor for studying protein folding by single‐molecule fluorescence resonance energy transfer (FRET) is the ability to site‐specifically introduce a photostable organic FRET donor (D) and a complementary acceptor (A) into a polypeptide chain. Using alternating‐laser excitation and chymotrypsin inhibitor 2 as a model, we show that chemical labeling of a unique cysteine, followed by enzymatic modification of a reactive glutamine in an N‐terminally appended substrate sequence recognition tag for transglutaminase (TGase) affords stoichiometrically D‐/A‐labeled protein suitable for single‐molecule FRET experiments. Thermodynamic data indicate that neither the presence of the TGase tag nor D/A labeling perturbs protein stability. As the N terminus in proteins is typically solvent accessible, a TGase tag can (in principle) be appended to any protein of interest by genetic engineering. Two‐step chemical/enzymatic labeling may thus represent a simple, low‐cost, and widely available strategy for D/A labeling of proteins for FRET‐based single‐molecule protein folding studies, even for non‐protein‐experts laboratories.
Methionine oxidation of monomeric λ repressor: The denatured state ensemble under nondenaturing conditions
Authors: Chugha Preeti , Sage Harvey J. , Oas Terrence G. 
Published: February 2006

AbstractAlthough poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. The most relevant conformations to cellular protein folding are the ones populated under physiological conditions. To avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric λ repressor and predominantly populate the denatured state under nondenaturing buffer conditions. The denatured ensemble populated under these conditions comprises conformations that are compact. Analytical ultracentrifugation sedimentation velocity experiments indicate a small increase in Stokes radius over that of the native state. A significant degree of α‐helical structure in these conformations is detected by far‐UV circular dichroism, and some tertiary interactions are suggested by near‐UV circular dichroism. The characteristics of the denatured state populated by methionine oxidation in nondenaturing buffer are very different from those found in chemical denaturant.
Solution structure of PcFK1, a spider peptide active against Plasmodium falciparum
Authors: Pimentel Cyril , Choi Soo‐Jin , Chagot Benjamin , Guette Catherine , Camadro Jean‐Michel , Darbon Hervé 
Published: February 2006

AbstractPsalmopeotoxin I (PcFK1) is a 33‐amino‐acid residue peptide isolated from the venom of the tarantula Psalmopoeus cambridgei. It has been recently shown to possess strong antiplasmodial activity against the intra‐erythrocyte stage of Plasmodium falciparum in vitro. Although the molecular target for PcFK1 is not yet determined, this peptide does not lyse erythrocytes, is not cytotoxic to nucleated mammalian cells, and does not inhibit neuromuscular function. We investigated the structural properties of PcFK1 to help understand the unique mechanism of action of this peptide and to enhance its utility as a lead compound for rational development of new antimalarial drugs. In this paper, we have determined the three‐dimensional solution structure by 1H two‐dimensional NMR means of recombinant PcFK1, which is shown to belong to the ICK structural superfamily with structural determinants common to several neurotoxins acting as ion channels effectors.
Fluorescence resonance energy transfer and molecular modeling studies on 4′,6‐diamidino‐2‐phenylindole (DAPI) complexes with tubulin
Authors: Arbildua José J. , Brunet Juan E. , Jameson David M. , López Maribel , Nova Esteban , Lagos Rosalba , Monasterio Octavio 
Published: February 2006

AbstractThe goal of this work was to determine the binding properties and location of 4′,6‐diamidino‐2‐phenylindole (DAPI) complexed with tubulin. Using fluorescence anisotropy, a dissociation constant of 5.2 ± 0.4 μM for the DAPI–tubulin complex was determined, slightly lower than that for the tubulin S complex. The influence of the C‐terminal region on the binding of DAPI to tubulin was also characterized. Using FRET experiments, and assuming a κ2 value of 2/3, distances between Co2+ bound to its high‐affinity binding site and the DAPI‐binding site and 2′,3′‐O‐(trinitrophenyl)guanosine 5′‐triphosphate bound to the exchangeable nucleotide and the DAPI‐binding site were found to be 20 ± 2 Å and 43 ± 2 Å, respectively. To locate potential DAPI‐binding sites on tubulin, a molecular modeling study was carried out using the tubulin crystal structure and energy minimization calculations. The results from the FRET measurements were used to limit the possible location of DAPI in the tubulin structure. Several candidate binding sites were found and these are discussed in the context of the various properties of bound DAPI.
Temperature‐induced reversible conformational change in the first 100 residues of α‐synuclein
Authors: McNulty Brian C. , Tripathy Ashutosh , Young Gregory B. , Charlton Lisa M. , Orans Jillian , Pielak Gary J. 
Published: February 2006

AbstractNatively disordered proteins are a growing class of anomalies to the structure–function paradigm. The natively disordered protein α‐synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson's disease. We noticed a dramatic difference in dilute solution 1H‐15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild‐type α‐synuclein and two disease‐related mutants (A30P and A53T), with spectra collected at 35°C showing fewer cross‐peaks than spectra acquired at 10°C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing α‐synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H‐15N HSQC spectra obtained at 35°C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of α‐synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions.