bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrogen bonding motifs of protein side chains: Descriptions of binding of arginine and amide groups
Authors: Shimoni Liat , Glusker Jenny P. 
Published: July 2010

AbstractThe modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small‐molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein‐nucleic acid and protein‐protein complexes. Analysis of the hydrogen bonding patterns of each by graph‐set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R2 2(8), R2 2(9), and R1 2(6). These three patterns are found for arginine‐like groups and for urea, whereas only the first two patterns Rl(8) and R2(9) are found for asparagine‐ and glutamine‐like groups. In each case, the entire system is planar within 0.7 Å or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein‐nucleic acid complexes between the nucleic acid base and the protein are all R2 2(9), whereas hydrogen bonding between Watson‐Crick‐like pairs of nucleic acid bases is R2 2(8). These two hydrogen bonding arrangements [R2 2(9) and R2 2(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R1 2(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins.
Crystals of the neurotrophins
Authors: Robinson Robert C. , Stuart David I. , Yvonne Jones E. , Radziejewski Czeslaw 
Published: July 2010

AbstractThe neurotrophins show a high degree of amino acid sequence homology, share similar solution properties, and display distinct but parallel functionalities. Here we report the crystallization and preliminary X‐ray characterization of three neurotrophins: brain‐derived neurotrophin, neurotrophin 3, and the heterodimer between brain‐derived neurotrophin and neurotrophin 4. These findings are related to other published crystal parameters for neurotrophins, leading to the observation that, although crystal packing is highly variant, neurotrophins share common solubilities with respect to crystal growth.
N‐terminally tagged prion protein supports prion propagation in transgenic mice
Authors: Telling Glenn C. , Tremblay Patrick , Torchia Marilyn , Dearmond Stephen J. , Cohen Fred E. , Prusiner Stanley B. 
Published: July 2010

AbstractThe eight amino acid sequence, Asp‐Tyr‐Lys‐Asp‐Asp‐Asp‐Asp‐Lys, representing the FLAG peptide, was inserted after codons 22 or 88 of the mouse (Mo) prion protein (PrP) gene. Inclusion of the FLAG sequence at these locations interfered neither with the cellular processing of PrPc nor its conversion into PrPSc. Inclusion of the FLAG epitope at residue 22 but not at residue 88 facilitated immunodetection of tagged PrP by anti‐FLAG monoclonal antibodies (mAbs). Inoculation of transgenic (Tg) mice expressing N‐terminally tagged MoPrP with Mo prions resulted in abbreviated incubation times, indicating that the FLAG sequence was not deleterious to prion propagation. Immunopurification of FLAG‐tagged MoPrPc in the brains of Tg mice was achieved using the calcium‐dependent anti‐FLAG M1 mAb and non‐denaturing procedures. Although the function of PrPc remains unknown, our studies demonstrate that some modifications of PrPc do not inhibit the one biological activity that can be measured, i.e., conversion into PrPSc. Tagged PrP molecules may prove useful in the development of improved assays for prions as well as structural studies of the PrP isoforms.
Mutational analysis of human DNase I at the DNA binding interface: Implications for DNA recognition, catalysis, and metal ion dependence
Authors: Pan Clark Q. , Uumer Jana S. , Herzka Andrea , Lazarus Robert A. 
Published: July 2010

AbstractHuman deoxyribonuclease I (DNase I), an enzyme used to treat cystic fibrosis patients, has been systematically analyzed by site‐directed mutagenesis of residues at the DNA binding interface. Crystal structures of bovine DNase I complexed with two different oligonucleotides have implicated the participation of over 20 amino acids in catalysis or DNA recognition. These residues have been classified into four groups based on the characterization of over 80 human DNase I variants. Mutations at any of the four catalytic amino acids His 134, His 252, Glu 78, and Asp 212 drastically reduced the hydrolytic activity of DNase I. Replacing the three putative divalent metal ion‐coordinating residues Glu 39, Asp 168, or Asp 251 led to inactive variants. Amino acids Gin 9, Arg 41, Tyr 76, Arg 111, Asn 170, Tyr 175, and Tyr 211 were also critical for activity, presumably because of their close proximity to the active site, while more peripheral DNA interactions stemming from 13 other positions were of minimal significance. The relative importance of these 27 positions is consistent with evolutionary relationships among DNase I across different species, DNase I‐like proteins, and bacterial sphingomyelinases, suggesting a fingerprint for a family of DNase I‐like proteins. Furthermore, we found no evidence for a second active site that had been previously implicated in Mn2+‐dependent DNA degradation. Finally, we correlated our mutational analysis of human DNase I to that of bovine DNase I with respect to their specific activity and dependence on divalent metal ions.
Tetramer‐dimer equilibrium of oxyhemoglobin mutants determined from auto‐oxidation rates
Authors: Griffon Nathalie , Baudbin Véronique , Dieryck Wilfrid , Dumoulin Antoine , Pagnier Josée , Poyart Claude , Marden Michael C. 
Published: July 2010

AbstractOne of the main difficulties with blood substitutes based on hemoglobin (Hb) solutions is the auto‐oxidation of the hemes, a problem aggravated by the dimerization of Hb tetramers. We have employed a method to study the oxyHb tetramer‐dimer equilibrium based on the rate of auto‐oxidation as a function of protein concentration. The 16‐fold difference in dimer and tetramer auto‐oxidation rates (in 20 mM phosphate buffer at pH 7.0, 37°C) was exploited to determine the fraction dimer. The results show a transition of the auto‐oxidation rate from low to high protein concentrations, allowing the determination of the tetramer‐dimer dissociation coefficient K4,2 = [Dimer]2/[Tetramer]. A 14‐fold increase in K4,2 was observed for addition of 10 mM of the allosteric effector inositol hexaphosphate (IHP). Recombinant hemoglobins (rHb) were genetically engineered to obtain Hb with a lower oxygen affinity than native Hb (Hb A). The rHb α2β2 [(C7) F41Y/(G4) N102Y] shows a fivefold increase in K4,2 at pH 7.0, 37°C. An atmosphere of pure oxygen is necessary in this case to insure fully oxygenated Hb. When this condition is satisfied, this method provides an efficient technique to characterize both the tetramer‐dimer equilibrium and the auto‐oxidation rates of various oxyHb. For low oxygen affinity Hb equilibrated under air, the presence of deoxy subunits accelerates the auto‐oxidation. Although a full analysis is complicated, the auto‐oxidation studies for air equilibrated samples are more relevant to the development of a blood substitute based on Hb solutions. The double mutants, rHb α2β2 [(C7) F41Y/(G4) N102A] and rHb α2β2 [(C7) F41Y/(E10) K66T], show a lower oxygen affinity and a higher rate of oxidation than Hb A. Simulations of the auto‐oxidation rate versus Hb concentration indicate that very high protein concentrations are required to observe the tetramer auto‐oxidation rate. Because the dimers oxidize much more rapidly, even a small fraction dimer will influence the observed oxidation rate.
High throughput protein characterization by automated reverse‐phase chromatography/electrospray tandem mass spectrometry
Authors: Ducret Axel , Oostveen Inge Van , Eng Jimmy K. , Yates John R. , Aebersold Ruedi 
Published: July 2010

AbstractWe describe an integrated workstation for the automated, high‐throughput, and conclusive identification of proteins by reverse‐phase chromatography electrospray ionization tandem mass spectrometry. The instrumentation consists of a refrigerated autosampler, a submicrobore reverse‐phase liquid chromatograph, and an electrospray triple quadrupole mass spectrometer. For protein identification, enzymatic digests of either homogeneous polypeptides or simple protein mixtures were generated and loaded into the autosampler. Samples were sequentially injected every 32 min. Ions of eluting peptides were automatically selected by the mass spectrometer and subjected to collision‐induced dissociation. Following each run, the resulting tandem mass spectra were automatically analyzed by SEQUEST, a program that correlates uninterpreted peptide fragmentation patterns with amino acid sequences contained in databases. Protein identification was established by SEQUEST_SUMMARY a program that combines the SEQUEST scores of peptides originating from the same protein and ranks the cumulative results in a short summary.The workstation's performance was demonstrated by the unattended identification of 90 proteins from the yeast Saccharomyces cerevisiae, which were separated by high‐resolution two‐dimensional PAGE. The system was found to be very robust and identification was reliably and conclusively established for proteins if quantities exceeding 1‐5 pmol were applied to the gel. The level of automation, the throughput, and the reliability of the results suggest that this system will be useful for the many projects that require the characterization of large numbers of proteins.
Context‐dependent protein stabilization by methionine‐to‐leucine substitution shown in T4 lysozyme
Authors: Lipscomb Leigh Ann , Gassner Nadine C. , Snow Sheila D. , Eldridge Aimee M. , Baase Walter A. , Drew Devin L. , Matthews Brain W. 
Published: July 2010

AbstractThe substitution of methionines with leucines within the interior of a protein is expected to increase stability both because of a more favorable solvent transfer term as well as the reduced entropic cost of holding a leucine side chain in a defined position. Together, these two terms are expected to contribute about 1.4 kcal/mol to protein stability for each Met → Leu substitution when fully buried. At the same time, this expected beneficial effect may be offset by steric factors due to differences in the shape of leucine and methionine. To investigate the interplay between these factors, all methionines in T4 lysozyme except at the amino‐terminus were individually replaced with leucine. Of these mutants, M106L and M120L have stabilities 0.5 kcal/mol higher than wild‐type T4 lysozyme, while M6L is significantly destabilized (‐2.8 kcal/mol). M102L, described previously, is also destabilized (‐0.9 kcal/mol). Based on this limited sample it appears that methionine‐to‐leucine substitutions can increase protein stability but only in a situation where the methionine side chain is fully or partially buried, yet allows the introduction of the leucine without concomitant steric interference. The variants, together with methionine‐to‐lysine substitutions at the same sites, follow the general pattern that substitutions at rigid, internal sites tend to be most destabilizing, whereas replacements at more solvent‐exposed sites are better tolerated.
Bipolar androgen therapy: The rationale for rapid cycling of supraphysiologic androgen/ablation in men with castration resistant prostate cancer
Authors: Denmeade Samuel R. , Isaacs John T. 
Published: July 2010

AbstractAndrogen ablation is highly effective palliative therapy for metastatic prostate cancer but eventually all men relapse. New findings demonstrating that androgen receptor (AR) expression continues in androgen ablated patients has resulted in the classification “Castration Resistant Prostate Cancer” (CRPC) and has led to the development of new second‐line “anti‐ligand” hormonal agents. In this background is the paradoxical observation that the growth of some AR‐expressing “androgen sensitive” human prostate cancer cells can be inhibited by supraphysiologic levels of androgens. This response may be due to effects of high‐dose androgen on inhibiting re‐licensing of DNA in cells expressing high levels of AR. It may also be due to recently described effects of androgen in inducing double strand DNA breaks. Based on available preclinical data described in this review demonstrating the effects of supraphysiologic levels of testosterone on inhibition of growth of CRPC xenografts, we initiated a clinical trial in men with CRPC testing the effect of monthly treatments with an intramuscular (IM) depot injection of testosterone. This IM formulation achieves supraphysiologic levels of testosterone that cannot be achieved with standard testosterone gel‐based applications. The supraphysiologic testosterone level is followed by a rapid drop to castrate levels of testosterone with each cycle of therapy. This “bipolar androgen therapy” will not allow time for prostate cancer cells to adapt their AR expression in response to environmental conditions. The goal is to determine if a clinical response can be achieved through this non‐adaptive rapid cycling approach in men with CRPC. Prostate 70: 1600–1607, 2010. © 2010 Wiley‐Liss, Inc.
Livin‐α promotes cell proliferation by regulating G1‐S cell cycle transition in prostate cancer
Authors: Ye Lin , Song Xishuang , Li Sheng , Yang Deyong , Zhang Jianing , Che Xiangyu , Chen Xiaochi , Wang Jianbo , Zhang Zhiwei 
Published: July 2010

AbstractBACKGROUNDProstate cancer is the third most common cancer and the second leading cause of cancer death for males in US. Livin has recently been described as a cancer‐associated member of inhibitor of apoptosis proteins family, highly expressed in prostate cancer. Livin gene encodes two splicing variants, termed Livin‐α and Livin‐β. We hypothesized that deregulation of proliferation could be due in part to Livin expression.METHODSPathological analysis of Livin was performed in 20 prostate cancer tissues and 5 benign prostatic hyperplasia tissues. The expression of Livin isoforms was also investigated by Western blot in prostate cancer cell lines LNCaP and PC3. The role of Livin‐α in vitro was further studied. Using Livin‐α knockdown and overexpression models, cell cycle analysis, Ki‐67 immunocytostaining, and MTT assay were performed respectively.RESULTSLivin expression positive ratio was shown to be 5.4%, 23.6%, 52.4%, 73.4% in benign prostatic hyperplasia, low, medium, and high grade of prostate cancer respectively, and Livin was positively correlated with clinical pathological grades of prostate cancer. Livin‐α was expressed in both LNCaP and PC3; meanwhile; Livin‐β was only detected in the PC3. Livin‐α siRNA not only resulted in G1‐S cell cycle arrest, but also strongly correlated with the descended proliferation index and survival rate in LNCaP. In comparison, overexpression of Livin‐α resulted in an accelerated S phase entry combined with elevated proliferation index and survival in LNCaP.CONCLUSIONSLivin‐α may promote cell proliferation by regulating G1‐S cell cycle transition and possibly play an important part in initiation of prostate cancer. Prostate 71: 42–51, 2011. © 2010 Wiley‐Liss, Inc.
Liposomal imatinib–mitoxantrone combination: Formulation development and therapeutic evaluation in an animal model of prostate cancer
Authors: Pinto Ana Catarina , Moreira João Nuno , Simões Sérgio 
Published: July 2010

AbstractBACKGROUNDMitoxantrone plus prednisone is a palliative treatment for hormone‐refractory prostate cancer (HRPC) but without survival benefit. Imatinib has shown activity against HRPC but only in the preclinical setting. Our previous in vitro cytotoxicity screening study established that their free combination act additively to inhibit proliferation of PC‐3 cells. We aim to develop a liposomal imatinib–mitoxantrone (LIM) formulation with improved in vivo therapeutic activity.METHODSImatinib and mitoxantrone were simultaneously co‐loaded into DSPC/Chol liposomes by means of a (NH4)2SO4‐generated proton gradient method. The optimized formulation was characterized in terms of mean size diameter, loading parameters and drug retention in human serum. In vivo antitumor activity of developed LIM formulation was evaluated in a nude mice bearing subcutaneous PC‐3 xenograft model.RESULTSLIM formulation exhibited maximal encapsulation efficiency (>95%) and enhanced drug retention for both drugs. Additionally, this LIM formulation, administered at a low mitoxantrone dose (0.5 mg/kg), showed a tumor inhibition activity (TGI = 66.7% and 4.0‐fold tumor volume increase) slightly superior to that of liposomal mitoxantrone (LM) at 2 mg/kg (TGI = 53.0% and 4.2‐fold volume increase). Therefore, therapeutic activity of mitoxantrone was significantly improved by co‐loading with imatinib since a four times lower dose was needed to achieve an equivalent growth inhibition effect.CONCLUSIONSThe loading parameters and drug retention properties of our LIM formulation, combined with its in vivo antitumor activity, make this formulation an excellent strategy to improve the therapeutic index of mitoxantrone and a promising candidate for clinical development in prostate cancer therapy. Prostate 71: 81–90, 2011. © 2010 Wiley‐Liss, Inc.
Systematic investigation on the effect of contact resistance on the performance of a‐IGZO thin‐film transistors with various geometries of electrodes
Authors: Lee Jae Sang , Chang Seongpil , Bouzid Houcine , Koo Sang‐Mo , Lee Sang Yeol 
Published: July 2010

AbstractWe demonstrate the influence of the contact resistance on the electrical properties of a‐IGZO thin‐film transistors (TFTs) with ZrO2 gate insulator grown by rf‐magnetron sputtering at room temperature by adopting various channel widths and lengths. These TFTs have all been processed at room temperature with the same channel W/L ratio (W/L = 5) but different channel widths (50, 150, 250, and 350 µm). As the channel width increases from 50 to 350 µm, the on‐current and field effect mobility increase from 0.7 to 1 mA and 19 to 31 cm2/V s, respectively. However, the subthreshold swing decreases from 0.37 to 0.19 V/decade. These results show that the contact resistance strongly affects the device performances and should be considered in these applications.
Isotope correction of mass spectrometry profiles
Authors: Eibl Günther , Bernardo Katussevani , Koal Therese , Ramsay Steven L. , Weinberger Klaus M. , Graber Armin 
Published: July 2010

AbstractIsotope correction of a profile is an important step in the analysis of mass spectrometry derived data. The problem is mathematically formulated as a system of linear equations which is general enough to include previous correction methods. For the solution of these equations when applied to the whole profile an efficient algorithm is developed. In experimental tests the resulting algorithm corrected the profile fast and successfully. Copyright © 2008 John Wiley & Sons, Ltd.
Bacterial stimulus perception and signal transduction: Response to osmotic stress
Authors: Krämer Reinhard 
Published: July 2010

AbstractWhen exposed to osmotic stress from the environment, bacteria act to maintain cell turgor and hydration by responding both on the level of gene transcription and protein activity. Upon a sudden decrease in external osmolality, internal solutes are released by the action of membrane embedded mechanosensitive channels. In response to an osmotic upshift, the concentration of osmolytes in the cytoplasm is increased both by de novo synthesis and by active uptake. In order to coordinate these processes of osmoregulation, cells are equipped with systems and mechanisms of sensing physical stimuli correlated to changes in the external osmolality (osmosensing), with pathways to transduce these stimuli into useful signals which can be processed in the cell (signal transduction), and mechanisms of regulating proper responses in the cell to recover from the environmental stress and to maintain all necessary physiological functions (osmoregulation). These processes will be described by a number of representative examples, mainly of osmoreactive transport systems with a focus on available data of their molecular mechanism. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 217–229; 2010: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.201000005
Comments and criticism. Point: Belief, understanding, and the teaching of evolution
Authors: Cobern William W. 
Published: July 2010

AbstractEducators typically think that one teaches evolution to develop students' conceptual understanding of evolution. It is assumed that if students understand evolution they will believe it. From a constructivist perspective it can be argued that understanding and belief, though related, are distinct concepts and that each is a potential goal for instruction. Though there are good reasons why belief should not be an instructional goal, achieving conceptual understanding requires that issues of belief be addressed. The point is that students are not likely to gain much understanding of something that they dismiss outright as unbelievable. What counts as believable for an individual rests on that person's worldview. This article argues that instruction on evolution can profitably begin with a dialogue on what counts as believable based on a study of the cultural history of Darwinism. The purpose of this strategy is to create in the classroom a shared meaning that certain fundamental questions are worth discussing and that the biological principles of evolution can contribute to that discussion.
Chronic toxicity of chlordane to Daphnia magna and Ceriodaphnia dubia: A comparative study
Authors: Manar Rachid , Vasseur Paule , Bessi Hlima 
Published: July 2010

AbstractChronic toxicity of chlordane, an organochlorine insecticide, was assessed on Ceriodaphnia dubia under standardized conditions of testing. Results were compared to Daphnia magna to determine the sensitivity of the two freshwater cladoceran species to this persistent organic pollutant (POP) and to explore the possibility of using the 7‐day C. dubia test as an alternative to the 21‐day D. magna test in chronic toxicity assessment of POPs. The NOEC‐7d value of chlordane on reproduction of C. dubia (2.9 μg/L) was much higher than the NOEC‐21d value of D. magna (0.18 μg/L), attesting that the 7‐day test on C. dubia was less sensitive than the 21‐day reproduction test on D. magna to chlordane. However, extending the period of exposure of C. dubia to chlordane from 7 to 14 days led to a NOEC‐14d value similar to the NOEC‐21d value in D. magna (0.18 μg/L). This study highlights the usefulness of prolonging the exposure time of the reproduction test in C. dubia from 7 to 14 days to increase the performances of the reproduction test on C. dubia for assessing chronic toxicity of POPs. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.