bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to Prepare Membrane Proteins for Solid‐State NMR: A Case Study on the α‐Helical Integral Membrane Protein Diacylglycerol Kinase from E. coli
Authors: Lorch Mark , Faham Salem , Kaiser Christoph , Weber Ingrid , Mason A. James , Bowie James U. , Glaubitz Clemens 
Published: September 2005

AbstractSeveral studies have demonstrated that it is viable to use microcrystalline preparations of water‐soluble proteins as samples in solid‐state NMR experiments.1–5 Here, we investigate whether this approach holds any potential for studying water‐insoluble systems, namely membrane proteins. For this case study, we have prepared proteoliposomes and small crystals of the α‐helical membrane‐protein diacylglycerol kinase (DGK). Preparations were characterised by 13C‐ and 15N‐cross‐polarization magic‐angle spinning (CPMAS) NMR. It was found that crystalline samples produce better‐resolved spectra than proteoliposomes. This makes them more suitable for structural NMR experiments. However, reconstitution is the method of choice for biophysical studies by solid‐state NMR. In addition, we discuss the identification of lipids bound to membrane‐protein crystals by 31P‐MAS NMR.
Diffusion NMR Spectroscopy: Folding and Aggregation of Domains in p53
Authors: Dehner Alexander , Kessler Horst 
Published: September 2005

AbstractProtein interactions and aggregation phenomena are probably amongst the most ubiquitous types of interactions in biological systems; they play a key role in many cellular processes. The ability to identify weak intermolecular interactions is a unique feature of NMR spectroscopy. In recent years, pulsed‐field gradient NMR spectroscopy has become a convenient method to study molecular diffusion in solution. Since the diffusion coefficient of a certain molecule under given conditions correlates with its effective molecular weight, size, and shape, it is evident that diffusion can be used to map intermolecular interactions or aggregation events. Complex models can be derived from comparison of experimental diffusion data with those predicted by hydrodynamic simulations. In this review, we will give an introduction to pulsed‐field gradient NMR spectroscopy and the hydrodynamic properties of proteins and peptides. Furthermore, we show examples for applying these techniques to a helical peptide and its hydrophobic oligomerization, as well as to the dimerization behavior and folding of p53.
NMR Methods for Studying the Structure and Dynamics of RNA
Authors: Latham Michael P. , Brown Darin J. , McCallum Scott A. , Pardi Arthur 
Published: September 2005

AbstractProper functioning of RNAs requires the formation of complex three‐dimensional structures combined with the ability to rapidly interconvert between multiple functional states. This review covers recent advances in isotope‐labeling strategies and NMR experimental approaches that have promise for facilitating solution structure determinations and dynamics studies of biologically active RNAs. Improved methods for the production of isotopically labeled RNAs combined with new multidimensional heteronuclear NMR experiments make it possible to dramatically reduce spectral crowding and simplify resonance assignments for RNAs. Several novel applications of experiments that directly detect hydrogen‐bonding interactions are discussed. These studies demonstrate how NMR spectroscopy can be used to distinguish between possible secondary structures and identify mechanisms of ligand binding in RNAs. A variety of recently developed methods for measuring base and sugar residual dipolar couplings are described. NMR residual dipolar coupling techniques provide valuable data for determining the long‐range structure and orientation of helical regions in RNAs. A number of studies are also presented where residual dipolar coupling constraints are used to determine the global structure and dynamics of RNAs. NMR relaxation data can be used to probe the dynamics of macromolecules in solution. The power dependence of transverse rotating‐frame relaxation rates was used here to study dynamics in the minimal hammerhead ribozyme. Improved methods for isotopically labeling RNAs combined with new types of structural data obtained from a growing repertoire of NMR experiments are facilitating structural and dynamic studies of larger RNAs.
Solid‐State Magic‐Angle Spinning NMR of Outer‐Membrane Protein G from Escherichia coli
Authors: Hiller Matthias , Krabben Ludwig , Vinothkumar Kutti R. , Castellani Federica , van Rossum Barth‐Jan , Kühlbrandt Werner , Oschkinat Hartmut 
Published: September 2005

AbstractUniformly 13C‐,15N‐labelled outer‐membrane protein G (OmpG) from Escherichia coli was expressed for structural studies by solid‐state magic‐angle spinning (MAS) NMR. Inclusion bodies of the recombinant, labelled protein were purified under denaturing conditions and refolded in detergent. OmpG was reconstituted into lipid bilayers and several milligrams of two‐dimensional crystals were obtained. Solid‐state MAS NMR spectra showed signals with an apparent line width of 80–120 Hz (including homonuclear scalar couplings). Signal patterns for several amino acids, including threonines, prolines and serines were resolved and identified in 2D proton‐driven spin‐diffusion (PDSD) spectra.
Structure Refinement of Cyclosporin A in Chloroform by Using RDCs Measured in a Stretched PDMS‐Gel
Authors: Klages Jochen , Neubauer Cajetan , Coles Murray , Kessler Horst , Luy Burkhard 
Published: September 2005

AbstractNew developments concerning alignment media for apolar solvents like chloroform make it possible to measure anisotropic parameters such as residual dipolar couplings (RDCs) at relatively low concentrations and natural isotopic abundance. As RDCs provide structural restraints with respect to an external coordinate system, long‐range structural arrangements of the time‐averaged structure can be determined with high precision. The method is demonstrated on the well‐studied cyclo‐undecapeptide Cyclosporin A (CsA), for which crystal and conventionally derived NMR structures are available. Neither crystal nor NMR structure are consistent with heteronuclear DCH RDCs measured in a stretched poly(dimethylsiloxane) gel, and refinement by using the anisotropic parameter results in a highly defined structure with a slightly changed backbone conformation. The applied methods and interpretation of the structural model are discussed.
Characterisation of Disulfide‐Bond Dynamics in Non‐Native States of Lysozyme and Its Disulfide Deletion Mutants by NMR
Authors: Collins Emily S. , Wirmer Julia , Hirai Kenichi , Tachibana Hideki , Segawa Shin‐ichi , Dobson Christopher M. , Schwalbe Harald 
Published: September 2005

AbstractThis report describes NMR‐spectroscopic investigations of the conformational dynamics of disulfide bonds in hen‐egg‐white lysozyme substitution mutants. The following four systems have been investigated: 2SSα, a lysozyme variant that contains C64A, C76A, C80A and C94A substitutions, was studied in water at pH 2 and 3.8 and in urea (8 M, pH 2); 2SSβ lysozyme, which has C6S, C30A, C115A and C127A substitutions, was studied in water (pH 2) and urea (8 M, pH 2). The NMR analysis of heteronuclear 15N‐relaxation rates shows that the barrier to disulfide‐bond isomerisation can vary substantially in different lysozyme mutants and depends on the residual structure present in these states. The investigations reveal cooperativity in the modulation of micro‐ to millisecond dynamics that is due to the presence of multiple disulfide bridges in lysozyme. Mutation of cysteines in one of the two structural domains substantially diminishes the barrier to rotational isomerisation in the other domain. However, the interactions between hydrophobic clusters within and across the domains remains intact.
Oligonuclear 3d–4f Complexes as Tectons in Designing Supramolecular Solid‐State Architectures: Impact of the Nature of Linkers on the Structural Diversity
Authors: Gheorghe Ruxandra , Cucos Paula , Andruh Marius , Costes Jean‐Pierre , Donnadieu Bruno , Shova Sergiu 
Published: September 2005

AbstractHeteronuclear cationic complexes, [LCuLn]3+ and [(LCu)2Ln]3+, were employed as nodes in designing high‐nuclearity complexes and coordination polymers with a rich variety of network topologies (L is the dianion of the Schiff base resulting from the 2:1 condensation of 3‐methoxysalycilaldehyde with 1,3‐propanediamine). Two families of linkers have been chosen: the first consists of exo‐dentate ligands bearing nitrogen‐donor atoms (bipyridine (bipy), dicyanamido (dca)), whereas the second consists of exo‐dentate ligands with oxygen‐donor atoms (anions derived from the acetylenedicarboxylic (H2acdca), fumaric (H2fum), trimesic (H3trim), and oxalic (H2ox) acids). The ligands belonging to the first family prefer copper(II) ions, whereas the ligands from the second family interact preferentially with oxophilic rare‐earth cations. The following complexes have been obtained and crystallographically characterized: [LCuII(OH2)GdIII(NO3)3] (1), [{LCuIIGdIII(NO3)3}2(μ‐4,4′‐bipy)] (2), ${{{1\hfill \atop \infty \hfill}}}$[LCuIIGdIII(acdca)1.5(H2O)2]⋅13 H2O (3), ${{{2\hfill \atop \infty \hfill}}}$[LCuIIGdIII(fum)1.5(H2O)2]⋅4 H2O⋅ C2H5OH (4), ${{{1\hfill \atop \infty \hfill}}}$[LCuIISmIII(H2O)(Hfum)(fum)] (5), ${{{1\hfill \atop \infty \hfill}}}$[LCuIIErIII(H2O)2(fum)]NO3⋅3 H2O (6), ${{{2\hfill \atop \infty \hfill}}}$[LCuIISmIII(fum)1.5(H2O)2]⋅4 H2O⋅C2H5OH (7), [{(LCuII)2SmIII}2fum2](OH)2 (8), ${{{1\hfill \atop \infty \hfill}}}$[LCuIIGdIII(trim)(H2O)2]⋅H2O (9), ${{{2\hfill \atop \infty \hfill}}}$[{(LCuII)2PrIII}(C2O4)0.5(dca)]dca⋅2 H2O (10), [LCuIIGdIII(ox)(H2O)3][CrIII(2,2′‐bipy)(ox)2]⋅9 H2O (11), and [LCuGd(H2O)4{Cr(CN)6}]⋅3 H2O (12). Compound 1 is representative of the whole family of binuclear CuII–LnIII complexes which have been used as precursors in constructing heteropolymetallic complexes. The rich variety of the resulting structures is due to several factors: 1) the nature of the donor atoms of the linkers, 2) the preference of the copper(II) ion for nitrogen atoms, 3) the oxophilicity of the lanthanides, 4) the degree of deprotonation of the polycarboxylic acids, 5) the various connectivity modes exhibited by the carboxylato groups, and 6) the stoichiometry of the final products, that is, the CuII/LnIII/linker molar ratio. A unique cluster formed by 24 water molecules was found in crystal 11. In compounds 2, 3, 4, 9, and 11 the CuII–GdIII exchange interaction was found to be ferromagnetic, with J values in the range of 3.53–8.96 cm−1. Compound 12 represents a new example of a polynuclear complex containing three different paramagnetic ions. The intranode CuII–GdIII ferromagnetic interaction is overwhelmed by the antiferromagnetic interactions occurring between the cyanobridged GdIII and CrIII ions.
In situ male breast carcinoma in the Surveillance, Epidemiology, and End Results database of the National Cancer Institute
Authors: Anderson William F. , Devesa Susan S. 
Published: September 2005

AbstractBACKGROUNDIn situ breast carcinoma is not so well characterized for men as for women.METHODSTherefore, the authors of the current study compared male and female in situ and invasive breast carcinomas in the Surveillance, Epidemiology, and End Results (SEER) database of the National Cancer Institute to document these patterns.RESULTSIn situ breast carcinomas composed 9.4% of all male (n = 280 of 2984) and 11.9% of all female breast carcinomas (n = 53,928 of 454,405) during the years 1973–2001. In situ rates rose 123% for men and 555% for women over this time period; whereas distant disease rates fell for both genders. Median ages at diagnosis were 62 years for in situ and 68 years for invasive breast carcinoma among men, compared with 58 years for in situ and 62 years for invasive breast carcinoma among women. Papillary in situ and invasive architectural types were more common among men than women. In contrast, lobular tumors were more common among women than men. Breast cancer‐specific survival was similar among men and women, whereas overall survival was worse for men than women.CONCLUSIONIn situ male breast carcinoma is a rare disease, occurring at older ages and with different architectural types than its more common female counterpart. Gender‐specific histopathologic differences probably reflect anatomic differences among the normal female and vestigial male breast. Rising in situ male breast carcinoma incidence rates over the past three decades suggest earlier detection over time, irrespective of mammography, because men do not participate in routine screening mammography. Worse overall survival for men than women possibly results from age‐dependent comorbid illnesses. Cancer 2005. Published 2005 American Cancer Society.
Merkel cell carcinoma
Authors: McAfee William J. , Morris Christopher G. , Mendenhall Charles M. , Werning John W. , Mendenhall Nancy Price , Mendenhall William M. 
Published: September 2005

AbstractBACKGROUNDThe purpose of the current study was to determine the outcomes of patients with previously untreated Merkel cell carcinoma of the skin who were treated with curative intent.METHODSBetween October 1984 and January 2002, 34 patients were treated with radiotherapy alone (2 patients) or combined with surgery (32 patients). Nine patients received adjuvant chemotherapy. Patients had follow‐up for a median of 3.0 years (range, 0.3 to 18.5 yrs). Follow‐up on living patients ranged from 2.2 to 18.5 years (median, 7.1 yrs).RESULTSThe 5‐year outcomes were as follows: local control, 94%, locoregional control, 80%; freedom from distant metastases, 60%; cause‐specific survival, 52%; and survival, 37%. No patient experienced a severe complication.CONCLUSIONSPatients treated aggressively with surgery and locoregional radiotherapy have about a 50% chance of cure. Limited data suggest that definitive radiotherapy alone or after incomplete macroscopic resection may control locoregional disease in a significant subset of patients. The dominant site of failure was distant. Cancer 2005. © 2005 American Cancer Society.
Phase II trial of carboplatin and paclitaxel in cisplatin‐pretreated advanced transitional cell carcinoma
Authors: Vaishampayan Ulka N. , Faulkner James R. , Small Eric J. , Redman Bruce G. , Keiser Wayne L. , Petrylak Daniel P. , Crawford E. David 
Published: September 2005

AbstractBACKGROUNDThe purpose of the study was to assess the efficacy and toxicity of carboplatin and paclitaxel administered every 3 weeks in patients with advanced urothelial carcinoma, previously treated with cisplatin‐based therapy.METHODSEligibility included metastatic or locally advanced unresectable transitional cell carcinoma of the urothelial tract. Prior chemotherapy, except taxanes, was permitted within 12 months. Adequate hematologic, hepatic, and renal function and a performance status of 0–2 were required. Treatment consisted of paclitaxel 200 mg/m2 intravenously for 3 hours followed by carboplatin, target area under the curve = 5 repeated every 3 weeks.RESULTSForty‐four patients were enrolled. Thirty‐four (77%) patients had a performance status of 0 or 1. Twenty‐five (57%) of the patients had received prior neoadjuvant or adjuvant chemotherapy, and 19 (43%) had received it for metastatic disease. In all, 181 cycles were administered (median, 3.5 cycles; range, 1–11 cycles). The predominant NCI CTC (version 2.0) Grades 3 and 4 toxicities consisted of myelosuppression in 28 patients and neuropathy in 11 patients. There were no treatment‐related deaths. Of the 44 patients, 1 (2%) had a complete response, 2 (5%) had a partial response, and 4 (9%) had an unconfirmed partial response, for an overall response rate of 16% (95% confidence interval [CI] 7–30%). The median progression‐free survival was 4 months (95% CI 3–5 months) and the median survival was 6 months (95% CI 5–8 months).CONCLUSIONSCarboplatin and paclitaxel combination is well tolerated and has modest activity in platinum refractory advanced urothelial carcinoma. Effective regimens need to be developed in cisplatin‐pretreated urothelial carcinoma. Cancer 2005. © 2005 American Cancer Society.
Prevalence of hereditary breast/ovarian carcinoma risk in patients with a personal history of breast or ovarian carcinoma in a mammography population
Authors: Dominguez Francisco J. , Jones Julie L. , Zabicki Katherina , Smith Barbara L. , Gadd Michele A. , Specht Michele , Kopans Daniel B. , Moore Richard H. , Michaelson James S. , Hughes Kevin S. 
Published: September 2005

AbstractBACKGROUNDIdentifying BRCA1 and BRCA2 mutation carriers is increasingly important as new management options show promise in decreasing morbidity and mortality in these women. The authors sought to determine the prevalence of family histories suggestive of a hereditary breast carcinoma syndrome in a cohort of patients with a personal history of breast and/or ovarian carcinoma presenting for mammography.METHODSThe authors reviewed the family histories of all women with a history of breast or ovarian carcinoma presenting for mammography over a 37‐week period. Using the Myriad model, the authors evaluated the prevalence of family histories with a ≥ 10% risk of a BRCA1 or BRCA2 mutation.RESULTSDuring the period of the current study, 14,597 women completed a family history questionnaire. Of these women, 1764 had a personal history of breast or ovarian carcinoma, 86.6% had unilateral breast carcinoma, 4.6% had bilateral breast carcinoma, 8.2% had ovarian carcinoma, and 0.5% had both breast and ovarian carcinoma. Overall, 20.6% met the criteria for a ≥ 10% risk of mutation according to the Myriad model. This incidence was higher among Ashkenazi women (47.3%) and among patients with a personal history of ovarian carcinoma (35.9%).CONCLUSIONSApplication of the Myriad model to women with a personal history of breast and ovarian carcinoma suggested that approximately 1 in 5 of these women (20.6%) will have family histories suspicious for a genetic mutation. This risk was higher for Ashkenazi women and for those with a personal history of ovarian carcinoma. This prevalence was considerably higher than the rate reported among women with no personal history of cancer, and has significant implications for their management, as well as for the capacity for risk assessment and testing. Cancer 2005. © 2005 American Cancer Society.
Mature T‐cell leukemias
Authors: Ravandi Farhad , Kantarjian Hagop , Jones Dan , Dearden Claire , Keating Michael , O'Brien Susan 
Published: September 2005

AbstractMature T‐cell and NK‐cell leukemias are a group of relatively uncommon neoplasms derived from mature or postthymic T‐cells accounting for a relatively small percentage of lymphoid malignancies. The recent availability of modern immunophenotypic and molecular tools has allowed a better distinction of these disorders from their B‐cell counterparts. Similarly, identification of recurrent cytogenetic abnormalities, as well as plausible mechanisms through which these molecular events influence cellular signaling pathways, have created further insight into the pathogenesis of these disorders. Furthermore, the availability of new agents such as alemtuzumab has generated significant interest in devising specific therapeutic strategies for these malignancies. Herein, we review the clinical and pathological features of mature T‐cell leukemias. Cancer 2005. © 2005 American Cancer Society.
The frequency of ipsilateral second tumors after breast‐conserving surgery for DCIS
Authors: Warren Joan L. , Weaver Donald L. , Bocklage Therese , Key Charles R. , Platz Charles E. , Cronin Kathleen A. , Ballard‐Barbash Rachel , Willey Shawna C. , Harlan Linda C. 
Published: September 2005

AbstractBACKGROUNDThe diagnosis of ductal carcinoma in situ (DCIS) is increasing, although to the authors' knowledge there is no consensus regarding optimal treatment. This analysis of women treated with breast‐conserving surgery (BCS) evaluated the impact of radiation therapy (RT) in patient outcomes.METHODSThe current study included a population‐based sample of 1103 women residing in selected Surveillance, Epidemiology, and End Results (SEER) registries who were diagnosed with DCIS between 1991–1992. Data were obtained from the registry, physician follow‐up, and pathology reports. Physicians were contacted in 1999 to determine whether the patient had developed a second event in the ipsilateral breast. For second events, pathology reports were reviewed to determine the presence of in situ or invasive disease. Registry data through 2001 were used to assess death rates and cause of death. Cox proportional hazards and logistic regression models were used to evaluate the rates of second events and breast carcinoma deaths between women treated with and without RT.RESULTSOver an average of 91 months, 13.2% of women developed a second event. Rates of second events were 11% for women treated with BCS and RT compared with 15% for women treated with BCS only (adjusted hazards ratio, 0.64; 95% confidence interval, 0.44–0.92). Women receiving RT were significantly less likely to develop invasive breast carcinoma in the ipsilateral breast (adjusted odds ratio, 0.40). By 2001, the rate of death from breast carcinoma was 2.7%; in the group of women treated with BCS only compared with 0.8% in the group of women treated with BCS with RT.CONCLUSIONSAmong a population‐based cohort, RT was found to significantly reduce the risk of second events in the ipsilateral breast, particularly invasive tumors, although not to the extent reported in clinical trials. Cancer 2005. © 2005 American Cancer Society.
Hydromagnetic flow and heat transfer of a conducting Casson fluid in a rectangular channel
Authors: Attia Hazem Ali , Sayed‐Ahmed Mohamed Eissa 
Published: September 2005

AbstractThe transient hydromagnetic flow of an electrically conducting viscous incompressible non‐Newtonian Casson fluid bounded by two parallel non‐conducting plates is studied with heat transfer considering the Hall effect. An external uniform magnetic field is applied perpendicular to the plates and the fluid motion is subjected to a pressure gradient in the axial direction. The lower plate is stationary and the upper plate is suddenly set into motion and simultaneously suddenly isothermally heated to a temperature other than the lower plate temperature. Numerical solutions are obtained for the governing momentum and energy equations taking the Joule and viscous dissipations into consideration. The effect of the Hall term and the parameter describing the non‐Newtonian behaviour on both the velocity and temperature distributions are studied. Copyright © 2005 John Wiley & Sons, Ltd.
Mild Synthesis of β‐Amino‐α,α‐difluoro Ketones from Acylsilanes and Trifluoromethyltrimethylsilane in a One‐Pot Imino Aldol Reaction
Authors: Jonet Sylvain , Cherouvrier Franck , Brigaud Thierry , Portella Charles 
Published: September 2005

Abstractβ‐Amino‐α,α‐difluoro ketones have been very conveniently prepared in a one‐pot procedure from acylsilanes, trifluoromethyltrimethylsilane and imines. The key intermediate in this reaction is a difluoroenoxysilane. The Lewis acid promoted imino aldol reaction was performed with BF3·OEt2 or under very mild conditions using a catalytic amount of Yb(OTf)3. The reaction with chiral benzylimines occurred in good yield with 52–78 % de. Palladium‐catalyzed hydrogenolysis furnished an unprotected β‐amino‐α,α‐difluoro ketone or a β‐amino‐α,α‐difluoro alcohol. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)