bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPINE: A method for the rapid detection and analysis of protein–protein interactions in vivo
Authors: Herzberg Christina , Weidinger Lope Andrés Flórez , Dörrbecker Bastian , Hübner Sebastian , Stülke Jörg , Commichau Fabian M. 
Published: November 2007

AbstractThe detection and analysis of protein–protein interactions is one of the central tasks of proteomics in the postgenomic era. For this purpose, we present a procedure, the Strep–protein interaction experiment (SPINE) that combines the advantages of the Strep‐tag protein purification system with those of reversible in vivo protein crosslinking by formaldehyde. Using two Bacillus subtilis regulator proteins, we demonstrate that this method is well suited to isolate protein complexes with high purity and virtually no background. Plasmids allowing the high‐level expression of proteins carrying an N‐ or C‐terminal Strep‐tag in B. subtilis were constructed.
Membrane proteomic analysis of human mesenchymal stromal cells during adipogenesis
Authors: Jeong Ju Ah , Ko Kyung‐Min , Park Hyung Soon , Lee Jinsook , Jang Cholsoon , Jeon Choon‐Ju , Koh Gou Young , Kim Hoeon 
Published: November 2007

AbstractMesenchymal stromal cells (MSCs) have proven useful for cell and immune therapy, but the molecular constituents responsible for their functionalities, in particular, those on the plasma membrane, remain largely unknown. Here we employed both gel and nongel based MS to analyze human MSCs' membrane proteome before and after adipogenesis. 2‐DE of cells that were pretreated with membrane impermeable fluorescent dyes revealed that both the whole cell proteome and the cell surface subproteome were independent of donors. LC coupled with tandem MS analysis of the plasma membrane‐containing fraction allowed us to identify 707 proteins, approximately half of which could be annotated as membrane‐related proteins. Of particular interest was a subset of ectodomain‐containing membrane‐bound proteins that encompass most known surface markers for MSCs, but also contain a multitude of solute carriers and ATPases. Upon adipogenic differentiation, this proteomic profile was amended to include several proteins involved in lipid metabolism and trafficking, at the expense of, most noticeably, ectoenzymes. Our results here provide not only a basis for future studies of MSC‐specific molecular mechanisms, but also a molecular inventory for the development of antibody‐based cell isolation and identification procedures.
Carbohydrate restriction, prostate cancer growth, and the insulin‐like growth factor axis
Authors: Freedland Stephen J. , Mavropoulos John , Wang Amy , Darshan Medha , Demark‐Wahnefried Wendy , Aronson William J. , Cohen Pinchas , Hwang David , Peterson Bercedis , Fields Timothy , Pizzo Salvatore V. , Isaacs William B. 
Published: November 2007

AbstractBACKGROUNDRecent evidence suggests carbohydrate intake may influence prostate cancer biology. We tested whether a no‐carbohydrate ketogenic diet (NCKD) would delay prostate cancer growth relative to Western and low‐fat diets in a xenograft model.METHODSSeventy‐five male SCID mice were fed a NCKD (84% fat–0% carbohydrate–16% protein kcal), low‐fat (12% fat–72% carbohydrate–16% protein kcal), or Western diet (40% fat–44% carbohydrate–16% protein kcal). Low‐fat mice were fed ad libitum and the other arms fed via a modified‐paired feeding protocol. After 24 days, all mice were injected with LAPC‐4 cells and sacrificed when tumors approached 1,000 mm3.RESULTSDespite consuming equal calories, NCKD‐fed mice lost weight (up to 15% body weight) relative to low‐fat and Western diet‐fed mice and required additional kcal to equalize body weight. Fifty‐one days after injection, NCKD mice tumor volumes were 33% smaller than Western mice (rank‐sum, P = 0.009). There were no differences in tumor volume between low‐fat and NCKD mice. Dietary treatment was significantly associated with survival (log‐rank, P = 0.006), with the longest survival among the NCKD mice, followed by the low‐fat mice. Serum IGFBP‐3 was highest and IGF‐1:IGFBP‐3 ratio was lowest among NCKD mice while serum insulin and IGF‐1 levels were highest in Western mice. NCKD mice had significantly decreased hepatic fatty infiltration relative to the other arms.CONCLUSIONSIn this xenograft model, despite consuming more calories, NCKD‐fed mice had significantly reduced tumor growth and prolonged survival relative to Western mice and was associated with favorable changes in serum insulin and IGF axis hormones relative to low‐fat or Western diet. Prostate 68: 11–19, 2008. © 2007 Wiley‐Liss, Inc.
The conformation of fusogenic B18 peptide in surfactant solutions
Authors: Rocha Sandra , Lúcio Marlene , Pereira M. Carmo , Reis Salette , Brezesinski Gerald 
Published: November 2007

AbstractThe interaction of B18 peptide with surfactants has been studied by circular dichroism spectroscopy and fluorescence measurements. B18 is the fusogenic motif of the fertilization sea urchin protein. The peptide forms an α‐helix structure when interacting with positively or negatively charged surfactants below and above the critical micellar concentration (CMC). The α‐helix formation is due to binding of surfactant monomers rather than the formation of surfactant micelles on the peptide. Fluorescence measurements show that the CMC of the negatively charged surfactant increases in the presence of B18, supporting the fact that there is a strong interaction between the peptide and monomers. Nonionic surfactant monomers have no effect on the peptide structure, whereas the micelles induce an α‐helical conformation. In this case the helix stabilization results from the formation of surfactant micelles on the peptide. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Combination of ellipsometry, laser scanning microscopy and Z‐scan fluorescence correlation spectroscopy elucidating interaction of cryptdin‐4 with supported phospholipid bilayers
Authors: Miszta Adam , Macháň Radek , Benda Aleš , Ouellette Andre J. , Hermens Wim Th. , Hof Martin 
Published: November 2007

AbstractThe present study has two main objectives. The first is to characterize antimicrobial peptide (AMP) cryptdin‐4 (Crp‐4) interactions with biological membranes and to compare those interactions with those of magainin 2. The second is to combine the complementary experimental approaches of laser scanning microscopy (LSM), ellipsometry, and Z‐scan fluorescence correlation spectroscopy (FCS) to acquire comprehensive information on mechanisms of AMP interactions with supported phospholipid bilayers (SPBs)—a popular model of biological membranes. LSM shows appearance of inhomogeneities in spatial distribution of lipids in the bilayer after treatment with Crp‐4. Ellipsometric measurements show that binding of Crp‐4 does not significantly change the lipid structure of the bilayer (increase in adsorbed mass without a change in thickness of adsorbed layer). Furthermore, Crp‐4 slows the lateral diffusion of lipids within the membrane as shown by Z‐scan FCS. All changes of the bilayer induced by Crp‐4 can be partially reversed by flushing the sample with excess of buffer. Bilayer interactions of magainin 2 are significantly different, causing large loss of lipids and extensive damage to the bilayer. It seems likely that differences in peptide mode of action, readily distinguished using these combined experimental methods, are related to the distinctive β‐sheet and α‐helical structures of the respective peptides. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Molecular interaction studies of peptides using steady‐state fluorescence intensity. Static (de)quenching revisited
Authors: Ribeiro Marta M. B. , Franquelim Henri G. , Castanho Miguel A. R. B. , Veiga Ana Salomé 
Published: November 2007

AbstractProtein–protein interactions, as well as peptide–peptide and peptide–protein interactions are fields of study of growing importance as molecular‐level detail is avidly pursued in drug design, metabolic regulation and molecular dynamics, among other classes of studies. In membranes, this issue is particularly relevant because lipid bilayers potentiate molecular interactions due to the high local concentration of peptides and other solutes.However, experimental techniques and methodologies to detect and quantify such interactions are not abundant. A reliable, fast and inexpensive alternative methodology is revisited in this work.Considering the interaction of two molecules, at least one of them being fluorescent, either intrinsically (e.g. Trp residues) or by grafting a specific probe, changes in their aggregation state may be reported, as long as the fluorophore is sensitive to local changes in polarity, conformation and/or exposure to the solvent. The interaction will probably lead to modifications in fluorescence intensity resulting in a decrease (‘quenching’) or enhancement (‘dequenching’). Although the presented methodology is based on static quenching methodologies, the concept is extended from quenching to any kind of interference with the fluorophore.Equations for data analysis are shown and their applications are illustrated by calculating the binding constant for several data‐sets. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Preparation and characterization of a novel exendin‐4 human serum albumin fusion protein expressed in Pichia pastoris
Authors: Huang Yan‐Shan , Chen Zhi , Chen Yi‐Qiong , MA Guo‐Chang , Shan Jian‐Feng , Liu Wei , Zhou Lin‐Fu 
Published: November 2007

AbstractA novel recombinant exendin‐4 human serum albumin fusion protein (rEx‐4/HSA) expressed in Pichia pastoris was prepared and characterized. Ex‐4 is a 39‐amino acid peptide isolated from the salivary gland of the lizard Heloderma suspectum and is thought to be a novel therapeutic agent for type 2 diabetes. But to gain a continued effect, the peptide has to be injected twice a day owing to its short plasma half‐life (t1/2 = 2.4 h). To extend the half‐life of Ex‐4 molecule in vivo, we designed a genetically engineered Ex‐4/HSA fusion protein. Between Ex‐4 and HSA, a peptide linker GGGGS was inserted and the fusion protein was expressed in methylotrophic yeast P. pastoris with native HSA secretion signal sequence. The recombinant protein was secreted correctly and was obtained with high purity (typically > 98%) by a three‐step purification procedure. cAMP assay demonstrated that the fusion protein had a bioactivity similar to Ex‐4 for interaction with GLP‐1 receptors in vitro. Results from oral glucose tolerance test indicated that rEx‐4/HSA could effectively improve glucose tolerance in diabetic db/db mice. Pharmacokinetics studies in cynomologus monkeys also showed that rEx‐4/HSA had a much longer plasma half‐life. Therefore, rEx‐4/HSA fusion protein could potentially be used as a new recombinant biodrug for type 2 diabetes therapy. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Concurrent purification of two defense proteins from French bean seeds: a defensin‐like antifungal peptide and a hemagglutinin
Authors: Leung Edwin H. W. , Wong Jack H. , Ng T. B. 
Published: November 2007

AbstractA purification protocol is described herein for concurrent isolation of two defense proteins including a 6‐kDa defensin‐like antifungal peptide and a 60‐kDa dimeric hemagglutinin from seeds of the French bean (Phaseolus vulgaris). It involved ion‐exchange chromatography on SP‐Sepharose, affinity chromatography on Affi‐gel blue gel, ion‐exchange chromatography on Q‐Sepharose, and gel filtration on Superdex Peptide (for defensin‐like antifungal peptide) or Superdex 200 (for hemagglutinin). Both antifungal and hemagglutinating activities were adsorbed on SP‐Sepharose and then on Affi‐gel blue gel. Hemagglutinin was subsequently unadsorbed and defensin‐like antifungal peptide adsorbed on Q‐Sepharose. The antifungal activity of the antifungal peptide was stable in the temperature range of 0–90 °C for 20 min, in the pH range of 4–10, and after exposure to trypsin (1 mg/ml) at 37 °C for 1 h. The hemagglutinin was stable from 10 to 80 °C, from pH 1 to 12, and after treatment with trypsin at 37 °C for 2 h. It inhibited [methyl‐3H]thymidine incorporation into breast cancer (MCF‐7), leukemia (L1210), hepatoma (HepG2) and human embryonic liver (WRL68) cells with an IC50 of 6.6, 7, 13 and 15 µM, respectively, and elicited maximal mitogenic response from mouse splenocytes at 1 µM concentration. It curtailed HIV‐1 reverse transcriptase activity with an IC50 of 1.9 µM, but was devoid of antifungal activity. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
The minimal fusion peptide of simian immunodeficiency virus corresponds to the 11 first residues of gp32
Authors: Lorin Aurélien , Lins Laurence , Stroobant Vincent , Brasseur Robert , Charloteaux Benoit 
Published: November 2007

AbstractWe had previously predicted successfully the minimal fusion peptides (FPs) of the human immunodeficiency virus 1 (HIV‐1) gp41 and the bovine leukemia virus (BLV) gp30 using an original approach based on the obliquity/fusogenicity relationship of tilted peptides. In this paper, we have used the same method to predict the shortest FP capable of inducing optimal fusion in vitro of the simian immunodeficiency virus (SIV) mac isolate and of other SIVs and human immunodeficiency virus (HIV‐2) isolates. In each case, the 11‐residue‐long peptide was predicted as the minimal FP. For the SIV mac isolate, liposome lipid‐mixing and leakage assays confirmed that this peptide is the shortest peptide inducing optimal fusion in vitro, being therefore the minimal FP. These results are another piece of evidence that the tilted properties of FPs are important for the fusion process and that our method can be used to predict the minimal FPs of other viruses. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Interfacial properties and structural analysis of the antimicrobial peptide NK‐2
Authors: Olak Claudia , Muenter Annabel , Andrä Jörg , Brezesinski Gerald 
Published: November 2007

AbstractThe structure of the antimicrobial peptide NK‐2 has been studied at the air–water interface and in different solutions using spectroscopic methods such as circular dichroism (CD) and infrared reflection absorption spectroscopy (IRRAS) as well as specular X‐ray reflectivity (XR). NK‐2 adopts an unordered structure in water, buffer, and in the presence of monomeric cationic and noncharged amphiphiles. However, it forms a stable α‐helix in 2,2,2‐trifluoroethanol (TFE) and in micellar solutions of anionic, cationic as well as nonionic amphiphiles, whereas only in sodium dodecyl sulfonate solutions the α‐helical structure can also be found below the critical micellar concentration (cmc). The amphiphilic molecule NK‐2 is surface active and forms a Gibbs monolayer at the air–buffer interface. In contrast, no adsorption was observed if NK‐2 is dissolved in water. During the adsorption process in buffer solutions, NK‐2 undergoes a conformational transition from random coil in bulk to α‐helix at the interface. This change of the peptide's secondary structure is known to be associated with its antimicrobial activity. A comparison of the experimental IRRA spectra with the simulated spectra indicates that the adsorbed NK‐2 α‐helix lies flat at the interface. This is confirmed by XR measurements which show that the thickness of the NK‐2 layer is ∼17 Å, which is the average diameter of a α‐helix, indicating that only a monomolecular adsorption layer is formed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
A novel bradykinin‐like peptide from skin secretions of the frog, Rana nigrovittata
Authors: Liu Xiuhong , You Dewen , Chen Lihua , Wang Xu , Zhang Keyun , Lai Ren 
Published: November 2007

AbstractA bradykinin‐like peptide has been isolated from the skin secretions of the frog Rana nigrovittata. This peptide was named ranakinin‐N. Its primary structure, RAEAVPPGFTPFR, was determined by Edman degradation and mass spectrometry. It is structurally related to bradykinin‐like peptides identified from skin secretions of other amphibians. Ranakinin‐N is composed of 13 amino acid residues and is related to the bradykinin identified from the skin secretions of Odorrana schmackeri, which is composed of 9 amino acid residues. Ranakinin‐N was found to exert concentration‐dependent contractile effects on isolated guinea pig ileum. cDNA sequence encoding the precursor of ranakinin‐N was isolated from a skin cDNA library of R. nigrovittata. The amino acid sequences deduced from the cDNA sequences match well with the results from Edman degradation. Analysis of different amphibian bradykinin cDNA structures revealed that the deficiency of a 15‐nucleotide fragment (agaatgatcagacgc in the cDNA encoding bradykinin from O. schmackeri) in the peptide‐coding region resulted in the absence of a dibasic site for trypsin‐like proteinases and an unusual ‐AEVA‐ insertion in the N‐terminal part of ranakinin‐N. The ‐AEAV‐ insertion resulted in neutral net charge at the N‐terminus of ranakinin‐N. Ranakinin‐N is the first reported bradykinin‐like peptide with a neutral net charge at the N‐terminus. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Activity‐dependent neurotrophic factor, ADNF, determines the structure characteristics of Colivelin, a fusion protein of ADNF9 and Humanin analog
Authors: Arakawa Tsutomu , Niikura Takako , Arisaka Fumio , Kita Yoshiko 
Published: November 2007

AbstractA 24‐amino acid long peptide, Humanin, protects neurons from Alzheimer's disease (AD)‐related cell toxicities at sub‐nM‐uM concentrations. Activity‐dependent neurotrophic factor (ADNF) is a glia‐derived neurotrophic peptide, which protects neurons from tetrodoxin treatment and AD‐related and amyotrophic lateral sclerosis‐related insults at fM concentrations. An attempt was made to further improve the activity of Humanin by fusing this peptide to ADNF9, a 9‐amino acid long core peptide of the ADNF. This fusion resulted in a novel molecule, termed Colivelin, with the neuroprotective activity at fM range, which is ∼103–107 fold higher than the activity of Humanin and Humanin analogs and follows the activity profile of fM‐active ADNF9. We have characterized the structural properties of Colivelin and compared with those of ADNF9 and Humanin in water and phosphate‐buffered saline (PBS). The secondary structure of Colivelin was similar to that of ADNF9, but not that of Humanin, and hence was not the average of the contributions of the two peptides fused. Colivelin was stable and monomeric in PBS, consistent with the monomeric property of ADNF9, while Humanin showed strong tendency to self‐associate. Thus, it is evident that the structural properties of Colivelin resemble those of ADNF9, rather than those of Humanin. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel‐like activity, and the role of the amidated C‐terminus
Authors: Dos Santos Cabrera Marcia Perez , Arcisio‐Miranda Manoel , Broggio Costa Sabrina Thais , Konno Katsuhiro , Ruggiero José Roberto , Procopio Joaquim , Ruggiero Neto João 
Published: November 2007

AbstractAnoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C‐terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C‐terminus introduced a negative charge at an all‐positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide's primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel‐like activity on anionic bilayers with a well‐defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans‐negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Stability in a high humidity environment of TCO thin films deposited at low temperatures
Authors: Minami Tadatsugu , Kuboi Takeshi , Miyata Toshihiro , Ohtani Yuusuke 
Published: November 2007

AbstractThe stability of transparent conducting Al‐ and Ga‐doped ZnO (AZO and GZO) thin films in a high humidity environment has been investigated for the purpose of finding substitutes for the indium‐tin‐oxide (ITO) thin films used in transparent electrode applications. It was found that the resistivity of polycrystalline AZO and GZO thin films prepared with a thickness in the range from 50 nm to 300 nm at a substrate temperature below 200 °C always increased when long‐term tests were conducted in air at a temperature of 60 °C and a relative humidity of 90%, whereas ITO thin films remained relatively stable in the same environment; however, AZO and GZO thin films with a thickness above approximately 200 nm were sufficiently moisture‐resistant. The resistivity stability of AZO and GZO thin films was considerably related to crystallinity factors such as crystallite size. In addition, the resistivity increase is attributed to carrier transport dominated by grain boundary scattering resulting from the trapping of free electrons due to oxygen adsorption on the grain boundary surface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Up‐conversion in nanostructured Yb3+–Tm3+ co‐doped sol–gel derived SiO2–LaF3 transparent glass‐ceramics
Authors: Méndez‐Ramos J. , Velázquez J. J. , Yanes A. C. , del‐Castillo J. , Rodríguez V. D. 
Published: November 2007

AbstractNanostructured transparent glass‐ceramics with composition of 95SiO2–5LaF3 doped with 0.1 mol% of Tm3+ or co‐doped with 0.1 mol% of Tm3+ and 0.3 mol% of Yb3+ were synthesized by thermal treatment of precursor sol–gel derived glasses. A comparative luminescence analysis in terms of different temperatures of thermal treatments has been carried out. Segregation of LaF3 nanocrystals in the matrix was con‐ firmed by X‐ray diffraction. Blue and red efficient up‐conversion emissions were observed under 980 nm excitation at room temperature. These results indicate partition of a significant fraction of co‐dopants into the precipitated LaF3 nanocrystals. The mechanisms involved in the up‐conversion emissions have been analyzed and can be ascribed to processes with two, three and four photons. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resistive memory effect in self‐assembled 3‐aminopropyltrimethoxysilane molecular multilayers
Authors: Chauhan A. K. , Aswal D. K. , Koiry S. P. , Padma N. , Saxena V. , Gupta S. K. , Yakhmi J. V. 
Published: November 2007

AbstractWe have observed a pronounced resistive memory effect with an on/off ratio of ∼2 in 3‐aminopropyltrimethoxysilane (APTMS) molecular multilayers trapped with NH+3 ions. The APTMS multilayers were deposited on SiO2/Si(p++) substrates using a self‐assembly process and characterized using various techniques, such as water contact angle, elliposmetery, X‐ray photoelectron microscopy, X‐ray diffraction and atomic force microscopy. The current–voltage characteristics of Hg/APTMS multilayer/Si(p++) devices, in the negative bias region, exhibited a reproducible hysteresis effect along with a negative differential resistance. A plausible explanation of the observed hysteresis in terms of filling and de‐filling of the positive ion traps is proposed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)