bluuebunny/crossref_metadata_2025_split huggingface dataset:
The methanol‐induced transition and the expanded helical conformation in hen lysozyme
Authors: Kamatari Yuji O. , Akasaka Kazuyuki , Konno Takashi , Kataoka Mikio 
Published: July 2010

AbstractMethanol‐induced conformational transitions of hen egg white lysozyme were investigated with a combined use of far and near‐UV CD and NMR spectroscopies, ANS binding and small‐angle X‐ray scattering. Addition of methanol induced no global change in the native conformation itself, but induced a transition from the native state to the denatured state which was highly cooperative, as shown by the coincidence of transition curves monitored by the far‐and near‐UV CD spectroscopy, by isodichroic points in the far‐ and near‐UV CD spectra and by the concomitant disappearance of individual 1H NMR signals of the native state. The ANS binding experiments could detect no intermediate conformer similar to the molten globule state in the process of the methanol denaturation. However, at high concentration of methanol, e.g., 60% (v/v) methanol/water, a highly helical state (H) was realized. The H state had a helical content much higher than the native state, monitored by far‐UV CD spectroscopy, and had no specific tertiary structure, monitored both by near‐UV CD and NMR spectroscopy. The radius of gyration in the H state, 24.9 Å, was significantly larger than that in the native state (15.7 Å). The Kratky plot for the H state did not show a clear peak and was quite similar to that for the urea‐denatured state, indicating a complete lack of globularity. Thus we conclude that the H state has a considerably expanded, flexible broken rod‐like conformation which is clearly distinguishable from the “molten globule” state. The stability of both N and H states depends on pH and methanol concentration. Thus a phase diagram involving N and H was constructed.
Serial increase in the thermal stability of 3‐isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution
Authors: Akanuma Satoshi , Yamagishi Akihiko , Oshima Tairo , Tanaka Nobuo 
Published: July 2010

AbstractWe improved the thermal stability of 3‐isopropylmalate dehydrogenase from Bacillus subtilis by an in vivo evolutionary technique using an extreme thermophile, Thermus thermophilus, as a host cell. The leuB gene encoding B. subtilis 3‐isopropylmalate dehydrogenase was integrated into the chromosome of a leuB‐deficient strain of T. thermophilus. The resulting transformant showed a leucine‐autotrophy at 56°C but not at 61°C and above. Phenotypically thermostabilized strains that can grow at 61°C without leucine were isolated from spontaneous mutants. Screening temperature was stepwise increased from 61 to 66 and then to 70°C and mutants that showed a leucine autotrophic growth at 70°C were obtained. DNA sequence analyses of the leuB genes from the mutant strains revealed three stepwise amino acid replacements, threonine‐308 to isoleucine, isoleucine‐95 to leucine, and methionine‐292 to isoleucine. The mutant enzymes with these amino acidreplacements were more stable against heat treatment than the wild‐type enzyme. Furthermore, the triple‐mutant enzyme showed significantly higher specific activity than that of the wild‐type enzyme.
Motional dynamics of residues in a β‐hairpin peptide measured by 13C‐NMR relaxation
Authors: Ramirez‐Alvarado Marnia , Dargan Vladimir A. , Mayo Kevin H. , Serrano Luis 
Published: July 2010

AbstractStructurally characterizing partially folded peptides is problematic given the nature of their transient conformational states. 13C‐NMR relaxation data can provide information on the geometry of bond rotations, motional restrictions, and correlated bond rotations of the backbone and side chains and, therefore, is one approach that is useful to assess the presence of folded structure within a conformational ensemble. A peptide 12mer, R1GITVNG7KTYGR12, has been shown to partially fold in a relatively stable β‐hairpin conformation centered at NG. Here, five residues, G2, V5, G7, Y10, G1l, were selectively 13C‐enriched, and13C‐NMR relaxation experiments were performed to obtain auto‐ and cross‐correlation motional order parameters, correlation times, bond rotation angular variances, and bond rotational correlation coefficients. Our results indicate that, of the three glycines, G7 within the hairpin β‐turn displays the most correlated ϕ(t),Ψ(t) rotations with its axis of rotation bisecting the angle defined by the H‐C‐H bonds. These positively correlated bond rotations give rise to “twisting” type motions of the HCH group. V5 and Y10 ϕ,Ψ bond rotations are also positively correlated, with their C#bTCαH groups undergoing similar “twisting” type motions. Motions of near‐terminal residues G2 and G1l are less restricted and less correlated and are best described as wobbling‐in‐a‐cone. V5 and Y10 side‐chain motions, aside from being highly restricted, were found to be correlated with ϕ,Ψ bond rotations. At 303 K, where the hairpin is considered “unfolded,” the peptide exists in a transient, collapsed state because backbone and side‐chain motions of V5, G7, and Y10 remain relatively restricted, unlike their counterparts in GXG‐based tripeptides. These results provide unique information toward understanding conformational variability in the unfolded state of proteins, which is necessary to solve the protein folding problem.
Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum
Authors: Xuan Jiancheng , Tarentino Anthony L. , Grimwood Brian G. , Plummer Thomas H. , Roey Patrick Van , Cui Tao , Guan Chudi 
Published: July 2010

AbstractThe crystal structure of recombinant glycosylasparaginase from Flavobacterium meningosepticum has been determined at 2.32 Å resolution. This enzyme is a glycoamidase that cleaves the link between the asparagine and the N‐acetylglucosamine of N‐linked oligosaccharides and plays a major role in the degradation of glycoproteins. The three‐dimensional structure of the bacterial enzyme is very similar to that of the human enzyme, although it lacks the four disulfide bridges found in the human enzyme. The main difference is the absence of a small random coil domain at the end of the α‐chain that forms part of the substrate binding cleft and that has a role in the stabilization of the tetramer of the human enzyme. The bacterial glycosylasparaginase is observed as an (αβ)2‐tetramer in the crystal, despite being a dimer in solution. The study of the structure of the bacterial enzyme allows further evaluation of the effects of disease‐causing mutations in the human enzyme and confirms the suitability of the bacterial enzyme as a model for functional analysis.
Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes
Authors: Khan Amir R. , James Micael N. G. 
Published: July 2010

AbstractProteolytic enzymes are synthesized as inactive precursors, or “zymogens,” to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an “activation segment.” The sizes of activation segments range from dipeptide units to independently folding domains comprising more than 100 residues. A common form of the activation segment is an N‐terminal extension of the mature enzyme, or “prosegment,” that sterically blocks the active site, and thereby prevents binding of substrates. In addition to their inhibitory role, prosegments are frequently important for the folding, stability, and/or intracellular sorting of the zymogen. The mechanisms of conversion to active enzymes are diverse in nature, ranging from enzymatic or nonenzymatic cofactors that trigger activation, to a simple change in pH that results in conversion by an autocatalytic mechanism. Recent X‐ray crystallographic studies of zymogens and comparisons with their active counterparts have identified the structural changes that accompany conversion. This review will focus upon the structural basis for inhibition by activation segments, as well as the molecular events that lead to the conversion of zymogens to active enzymes.
Molecular dynamics simulations of hydrophobic collapse of ubiquitin
Authors: Alonso Darwin.V. , Daggett Valerie 
Published: July 2010

AbstractNine nonnative conformations of ubiquitin, generated during two different thermal denaturation trajectories, were simulated under nearly native conditions (62 °C). The simulations included all protein and solvent atoms explicitly, and simulation times ranged from 1‐2.4 ns. The starting structures had α‐carbon root‐mean‐square deviations (RMSDs) from the crystal structure of 4‐12 Å and radii of gyration as high as 1.3 times that of the native state. In all but one case, the protein collapsed when the temperature was lowered and sampled conformations as compact as those reached in a control simulation beginning from the crystal structure. In contrast, the protein did not collapse when simulated in a 60% methanol: water mixture. The behavior of the protein depended on the starting structure: during simulation of the most native‐like starting structures (≤5 Å RMSD to the crystal structure) the RMSD decreased, the number of native hydrogen bonds increased, and the secondary and tertiary structure increased. Intermediate starting structures (5‐10 Å RMSD) collapsed to the radius of gyration of the control simulation, hydrophobic residues were preferentially buried, and the protein acquired some native contacts. However, the protein did not refold. The least native starting structures (10‐12 Å RMSD) did not collapse as completely as the more native‐like structures; instead, they experienced large fluctuations in radius of gyration and went through cycles of expansion and collapse, with improved burial of hydrophobic residues in successive collapsed states.
Solution structure and dynamics of a designed monomeric variant of the lambda Cro repressor
Authors: Mossing Michael C. 
Published: July 2010

AbstractThe solution structure of a monomeric variant of the lambda Cro repressor has been determined by multidimensional NMR. Cro K56[DGEVK] differs from wild‐type Cro by the insertion of five amino acids at the center of the dimer interface. 1H and 15N resonances for 70 of the 71 residues have been assigned. Thirty‐two structures were calculated by hybrid distance geometry/simulated annealing methods using 463 NOE‐distance restraints, 26 hydrogen‐bond, and 39 dihedral‐angle restraints. The root‐mean‐square deviation (RMSD) from the average structure for atoms in residues 3‐60 is 1.03 ± 0.44 Å for the peptide backbone and 1.6 ± 0.73 Å for all nonhydrogen atoms. The overall structure conforms very well to the original design. Although the five inserted residues form a beta hairpin as expected, this engineered turn as well as other turns in the structure are not well defined by the NMR data. Dynamics studies of backbone amides reveal T1/T2 ratios of residues in the α2‐α3, β2‐β3, and engineered turn that are reflective of chemical exchange or internal motion. The solution structure and dynamics are discussed in light of the conformational variation that has been observed in other Cro structures, and the importance of flexibility in DNA recognition.
Trapping of intermediates during the refolding of recombinant human epidermal growth factor (hEGF) by cyanylation, and subsequent structural elucidation by mass spectrometry
Authors: Wu Jiang , YingYang  , Throck Watson J. 
Published: July 2010

AbstractHuman epidermal growth factor (hEGF) contains 53 amino acids and three disulfide bonds. The unfolded, reduced hEGF is allowed to refold under mildly alkaline conditions. The folding is quenched at different time points by adjusting the pH to 3.0 with an acetic acid solution of l‐cyano‐4‐dimethylamino‐pyridinium (CDAP) which traps folding intermediates via cyanylation of free sulfhydryl groups. The mixture of cyanylated intermediates is separated by reversed‐phase HPLC; the fractions collected are identified by mass spectrometry. The disulfide structures of the intermediates are then determined by specific chemical cleavage and mass‐mapping by MALDI‐MS, a novel approach developed in our laboratory. The procedure of quenching and trapping of disulfide intermediates in acidic solution minimizes sulfhydryl‐disulfide exchange, and therefore provides a good measure of folding kinetics and preservation of intermediate species. Our cyanylation methodology for disulfide mapping is simpler, faster, and more sensitive than the more conventional approach.Among 18 folding intermediates isolated and identified at different time points, disulfide structures of seven well‐populated intermediates, including two non‐native isomers with scrambled disulfide structures, one 2‐disulfide intermediate, and four 1‐disulfide intermediates, have been characterized; most of them possess non‐native disulfide structures.
Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
Authors: Wallin Erik , Heijne Gunnar Von 
Published: July 2010

AbstractWe have carried out detailed statistical analyses of integral membrane proteins of the helix‐bundle class from eubacterial, archaean, and eukaryotic organisms for which genome‐wide sequence data are available. Twenty to 30% of all ORFs are predicted to encode membrane proteins, with the larger genomes containing a higher fraction than the smaller ones. Although there is a general tendency that proteins with a smaller number of transmembrane segments are more prevalent than those with many, uni‐cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegansandHomo sapienshave a slight preference for proteins with seven transmembrane segments. In all organisms, there is a tendency that membrane proteins either have manytransmembrane segments with short connecting loops or few transmembrane segments with large extra‐membraneous domains. Membrane proteins from all organisms studied, except possibly the archaeon Methanococcus jannaschii, follow the so‐called “positive‐inside” rule; i.e., they tend to have a higher frequency of positively charged residues in cytoplasmic than in extra‐cytoplasmic segments.
Synthesis and evaluation of immobilized androgens for affinity chromatography in the purification of nuclear androgen receptor
Authors: De Larminat Marie‐Anne , Bruchovsky Nicholas , Rennie Paul S. , Lee Sing Ping , Tertzakian Gerald 
Published: July 2010

AbstractSeven biospecific adsorbents containing immobilized androgens were synthesized: dihydro‐testosterone‐17β‐succinyl agarose, and both the unsubstituted and the 17β‐acetyl derivatives of dihydrotestosterone‐7α‐undecanoyl agarose, testosterone‐7α‐undecanoyl agarose, and 19‐nortestosterone‐7α‐undecanoyl agarose. The retention capacities for nuclear androgen receptor were generally between 40‐80% with little variation in reproducibility; the amount of binding was greatest with dihydrotestosterone‐17β‐succinyl agarose and dihydrotestoster‐one‐17β‐acetoxy‐7α‐undecanoyl agarose. Rapid flow rates were obtained with all gels, and no tendency for decomposition was observed over a period of 1 year. Factors that affected retention included the concentration of immobilized androgen, length of the linker arm, occupation of receptor sites, interval of contact with the gel, and temperature of incubation. Chemical dissociation of androgens from androgen receptor complexes with 0.2 mM mersalyl increased the retention of receptor by dihydrotestosterone‐17β‐succinyl agarose. Two elutants showed promise for the dissociation of gel‐bound receptor: 1) 0.2 mM mersalyl in the presence of 1.5 mg/ml of ovalbumin; 2) 10% (v/v) dimethylformamide:water containing 30 μM [1,2‐3H] dihydrotestosterone and 0.5 M sodium thiocyanate.
The accuracy of transrectal aspiration biopsy of the prostate: An analysis of 452 cases
Authors: Maier U. , Czerwenka K. , Neuhold N. 
Published: July 2010

AbstractThis study compares cytological findings obtained by transrectal aspiration biopsy of the prostate with histological findings obtained by simultaneously performed transperineal punch biopsy. All interventions were performed on outpatients. Complications such as hematuria, urinary infection, or epididymitis occured in 4.4% of the cases, the majority of them being attributed to punch biopsies. Exact correspondence was found in 78.8% of 433 usable specimens, the accuracy for carcinoma amounting to 71.1 %. Specimens cytologically judged either false “negative” or “suspicious” were histologically mostly well‐differentiated (G and G2) carcinomas (96.1%). The value of fine needle biopsy of the prostate as nonstaining diagnostic procedure will be discussed.
Zinc content in the epididymis, vas deferens, prostate, and seminal vesicles of juvenile rhesus monkey (Macaca mulatta): Effect of androgen and Estrogen
Authors: Srivastava Archana , Chowdhury A. R. , Setty B. S. 
Published: July 2010

AbstractThe zinc content in the three segments of the epididymis (caput, corpus, and cauda), vas deferens, seminal vesicles, and prostate of juvenile monkeys was determined by atomic absorption spectrophotometry. Zinc content (μg/gm wet weight) was found to be maximum (328) in the vas deferens; in the other organs it measured in the following order: caput 191, corpus 238, cauda 193, prostate 133 and seminal vesicles 85. In order to investigate the endocrine control of the zinc in these organs, two groups of animals were treated with testosterone propionate (2 mg) or estradiol dipropionate (10μg) once daily for 30 days. In response to androgen, a rise in both concentration and content of zinc was evident only in the prostate. The results further suggested that the prostatic zinc may be under dual hormonal control, but in the epididymis and vas deferens it may be under the influence of estrogen. It is concluded that the hormonal effects on zinc content and growth stimulation in accessory sex organs are quite separate and may be under different hormonal control.
Selectivity and destinations of ethnic minorities leaving the main gateway cities of Estonia
Authors: Tammaru Tiit , Kontuly Thomas 
Published: July 2010

AbstractChanges in the spatial distribution of minority populations and factors responsible for such changes form an important research topic in the study of the contemporary immigrant societies of Europe and North America. This paper clarifies both the trends and determinants of the spatial redistribution of mainly Russian‐speaking ethnic minorities in Estonia by focusing on out‐migration from the gateway cities or the main minority concentration areas. We use individual data from the 2000 census. The main results show that the dominant flow of migration among members of ethnic minorities is out of the main gateway cities in Estonia, and this trend is very different from the situation during the Soviet period. All of the personal characteristics that measure intentional ties with the majority population and the host country, such as proficiency in Estonian, having an Estonian partner, and Estonian citizenship, exert a positive influence on both leaving these areas and settling in non‐ethnic destinations, while the mere passage of time (generation replacement) has no straightforward influence on minority spatial redistribution. Copyright © 2010 John Wiley & Sons, Ltd.
Synthesis of CdS/TiO2 nanocomposites by using cadmium thiolate derivatives as unimolecular precursors
Authors: Resta Vincenzo , Laera Anna M. , Piscopiello Emanuela , Capodieci Laura , Ferrara Maria C. , Tapfer Leander 
Published: July 2010

AbstractHighly porous nanocrystalline films of TiO2 sensitized with semiconductor nanocrystals (NCs) are very promising for photovoltaic applications, NCs being more versatile and efficient than organic dyes as sensitizer. In this framework, the visible light absorption of TiO2 can be improved by the superposition of CdS NC absorption band, that is tunable between 2.5 and 5.2 eV. Here, we report on a novel in situ approach for the synthesis of CdS NCs in mesoporous sol–gel TiO2 anatase films by using as starting reagent for CdS, [Cd(SBz)2]MI, where MI represents 1‐methylimidazole. The precursor has been adsorbed into the TiO2 pores and then decomposed at 480 °C, the procedure being studied for TiO2 films with different porosity. The matrices have been investigated by atomic force microscopy. X‐ray diffraction measurements on TiO2 matrix and on the corresponding CdS/TiO2 nanocomposite material revealed a variation of the NCs size of both TiO2 and CdS as a function of the matrix porosity. The optical properties of the TiO2 and CdS/TiO2 have been studied by UV–Vis transmission spectroscopy. CdS/TiO2 nanocomposites, having higher absorption efficiency with respect to TiO2, are suitable as building blocks for 3rd generation solar cell design.
Theoretical study of the CO catalytic oxidation on Au/SAPO‐11 zeolite
Authors: Griffe Beulah , Sierraalta Anibal , Brito Joaquín L. 
Published: July 2010

AbstractQuantum chemistry calculations were carried out, using ONIOM2 methodology, to investigate the CO adsorption and oxidation on gold supported on Silicoaluminophospates (SAPO) molecular sieves Au/SAPO‐11 catalysts. Two models were studied, one containing one Au atom per site (AuSAPO‐11), and the other with two Au atoms per site (Au2SAPO‐11). The results reveal that the CO adsorption and oxidation are exothermic on Au/SAPO11 with an ΔE of −41.0 kcal/mol and ΔE = −52.0 kcal/mol, for the adsorption and oxidation, respectively. On the Au2SAPO‐11 model, the CO adsorption and oxidation reaction occur, with a ΔE of −29.7 kcal/mol and −52 kcal/mol, respectively. According to our results, the oxidation reaction exhibits an Eley‐Rideal type mechanism with adsorbed CO. The theoretical calculations reveal that this type of material could be interesting to disperse Au and consequently to strengthen its catalytic use for different reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2573–2582, 2010
Electronic excitation and ionization of hydrogen peroxide–water clusters: Comparison with water clusters
Authors: Ferreira Cristiane , Martiniano Hugo F. M. C. , Cabral Benedito J. Costa , Aquilanti Vincenzo 
Published: July 2010

AbstractElectronic properties of H2O2(H2O)1–6 and (H2O)1–7 clusters are reported. Emphasis was placed on the changes induced by the presence of hydrogen peroxide on the electronic properties of water aggregates. Theoretical results for excitation energies as well as vertical and adiabatic ionization energies are reported. Excitation energies were calculated with time‐dependent density functional theory and equation‐of‐motion coupled cluster with single and double excitations (EOM‐CCSD). A many‐body energy decomposition scheme recently proposed was coupled to the EOM‐CCSD method making possible an accurate prediction of the first vertical excitation energy of peroxide–water clusters. In comparison with water clusters, our results show that the presence of hydrogen peroxide in water clusters is characterized by a [1.5–1.8] eV red‐shift of the first excitation energy. The first excitation is localized on the HOOH moiety, and no significant dependence of the first excitation energy on the cluster size is observed. The differences between vertical and adiabatic ionization energies for both water and hydrogen peroxide–water clusters reflect the feature that ionization leads to proton transfer and to a significant structural and electronic density reorganization. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010