bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Deinococcus radiodurans Snf2 intein caught in the act: Detection of the Class 3 intein signature Block F branched intermediate
Authors: Brace Lear E. , Southworth Maurice W. , Tori Kazuo , Cushing Michelle L. , Perler Francine 
Published: June 2010

AbstractInteins are the protein equivalent of introns. They are remarkable and robust single turnover enzymes that splice out of precursor proteins during post‐translational maturation of the host protein (extein). The Deinococcus radiodurans Snf2 intein is the second member of the recently discovered Class 3 subfamily of inteins to be characterized. Class 3 inteins have a unique sequence signature: (a) they start with residues other than the standard Class 1 Cys, Ser or Thr, (b) have a noncontiguous, centrally located Trp/Cys/Thr triplet, and (c) all but one have Ser or Thr at the start of the C‐extein instead of the more common Cys. We previously proposed that Class 3 inteins splice by a variation in the standard intein‐mediated protein splicing mechanism that includes a novel initiating step leading to the formation of a previously unrecognized branched intermediate. In this mechanism defined with the Class 3 prototypic Mycobacteriophage Bethlehem DnaB intein, the triplet Cys attacks the peptide bond at the N‐terminal splice junction to form the class specific branched intermediate after which the N‐extein is transferred to the side chain of the Ser, Thr, or Cys at the C‐terminal splice junction to form the standard intein branched intermediate. Analysis of the Deinococcus radiodurans Snf2 intein confirms this splicing mechanism. Moreover, the Class 3 specific Block F branched intermediate was isolated, providing the first direct proof of its existence.
Isgur‐Wise functions and the Lorentz group
Authors: Le Yaouanc A. , Oliver L. , Raynal J.‐C. 
Published: June 2010

AbstractBjorken‐like sum rules have proven to be very powerful in constraining the derivatives of the Isgur‐Wise (IW) function. We expose here, adapted to the simpler case of the baryon transition Λb → Λc ℓ ν (j = 0 for the light could), that the reason behind these strong constraints is the general idea that the IW function is expressed in terms of scalar products of states of the light cloud in a Hilbert space, related by Lorentz transformations. This fact leads to strong constraints on their possible shape. Both Lorentz group and the sum rule approaches are equivalent.
Expression and function of ATIP/MTUS1 in human prostate cancer cell lines
Authors: Louis Simon N.S. , Chow Laurie , Rezmann Linda , Krezel Michael A. , Catt Kevin J. , Tikellis Chris , Frauman Albert G. , Louis William J. 
Published: June 2010

AbstractBACKGROUNDWe have previously demonstrated Ang II type 2 (AT2‐) receptor‐mediated inhibition of EGF‐induced prostate cancer cell growth in androgen‐dependent (LNCaP) and independent (PC3) prostate cancer cell lines.METHODSTo explore the signaling pathways involved in this inhibitory effect, we examined the interaction of the AT2‐receptor with its novel regulatory partner ATIP using real time PCR, over‐expression, siRNA and [3H]thymidine incorporation assays.RESULTSThe results in human prostate cancer cell lines demonstrate the presence of ATIP in both cell lines examined, and suggest that (i) the AT2‐receptor through an interaction with ATIP mediates an anti‐growth factor effect in both androgen‐dependent and androgen‐independent cell lines; (ii) ATIP expression decreases as the rate of cell growth and androgen‐independence increase; and (iii) EGF may act on cell growth in part by reducing the content of ATIP present in the cells.CONCLUSIONSThe results support our earlier proposal in normal cell lines that ATIP is an important component of the cellular response to AT2‐receptor activation. The results further suggest that a critical level of ATIP is required to mediate the effect of AT2‐receptor activation to inhibit EGF mediated increases in cell growth. They also suggest that EGF may in part induce cell growth by suppressing the level of ATIP expression. Prostate 70: 1563–1574, 2010. © 2010 Wiley‐Liss, Inc.
Exploring the role of the phospholipid ligand in endothelial protein C receptor: A molecular dynamics study
Authors: Chiappori Federica , Merelli Ivan , Milanesi Luciano , Rovida Ermanna 
Published: June 2010

AbstractEndothelial protein C receptor (EPCR) is a CD1‐like transmembrane glycoprotein with important regulatory roles in protein C (PC) pathway, enhancing PC's anticoagulant, anti‐inflammatory, and antiapoptotic activities. Similarly to homologous CD1d, EPCR binds a phospholipid [phosphatidylethanolamine (PTY)] in a groove corresponding to the antigen‐presenting site, although it is not clear if lipid exchange can occur in EPCR as in CD1d. The presence of PTY seems essential for PC γ‐carboxyglutamic acid (Gla) domain binding. However, the lipid‐free form of the EPCR has not been characterized. We have investigated the structural role of PTY on EPCR, by multiple molecular dynamics (MD) simulations of ligand bound and unbound forms of the protein. Structural changes, subsequent to ligand removal, led to identification of two stable and folded ligand‐free conformations. Compared with the bound form, unbound structures showed a narrowing of the A′ pocket and a high flexibility of the helices around it, in agreement with CD1d simulation. Thus, a lipid exchange with a mechanism similar to CD1d is proposed. In addition, unbound conformations presented a reduced interaction surface for Gla domain, confirming the role of PTY in establishing the proper EPCR conformation for the interaction with its partner protein. Single MD simulations were also obtained for 29 mutant models with predicted structural stability and impaired binding ability. Ligand affinity calculations, based on linear interaction energy method, showed that substitution‐induced conformational changes affecting helices around the A′ pocket were associated to a reduced binding affinity. Mutants responsible for this effect may represent useful reagents for experimental tests. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Can self‐inhibitory peptides be derived from the interfaces of globular protein–protein interactions?
Authors: London Nir , Raveh Barak , Movshovitz‐Attias Dana , Schueler‐Furman Ora 
Published: June 2010

AbstractIn this study, we assess on a large scale the possibility of deriving self‐inhibitory peptides from protein domains with globular architectures. Such inhibitory peptides would inhibit interactions of their origin domain by mimicking its mode of binding to cognate partners, and could serve as promising leads for rational design of inhibitory drugs. For our large‐scale analysis, we analyzed short linear segments that were cut out of protein interfaces in silico in complex structures of protein–protein docking Benchmark 3.0 and CAPRI targets from rounds 1–19. Our results suggest that more than 50% of these globular interactions are dominated by one short linear segment at the domain interface, which provides more than half of the original interaction energy. Importantly, in many cases the derived peptides show strong energetic preference for their original binding mode independently of the context of their original domain, as we demonstrate by extensive computational peptide docking experiments. As an in depth case study, we computationally design a candidate peptide to inhibit the EphB4–EphrinB2 interaction based on a short peptide derived from the G‐H loop in EphrinB2. Altogether, we provide an elaborate framework for the in silico selection of candidate inhibitory molecules for protein–protein interactions. Such candidate molecules can be readily subjected to wet‐laboratory experiments and provide highly promising starting points for subsequent drug design. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Temperature‐induced transition between polyproline I and II helices: quantitative fitting of hysteresis effects
Authors: Kuemin Michael , Engel Jürgen , Wennemers Helma 
Published: June 2010

AbstractThe conformational properties of the polyproline I (PPI) helix of oligoprolines toward heating were examined. Oligoproline H‐Pro12‐NH2 served as a model which adopts in n‐PrOH a pronounced PPI conformation with all cis amide bonds, whereas a polyproline II (PPII) conformation with all trans amide bonds is predominant in pure aqueous buffer. CD spectroscopic studies revealed that a conformational change from the PPI to the PPII helix takes place upon heating and back to the PPI helix upon cooling. This conformational transition cycle is characterized by a strong hysteresis. With a quantitative fitting of the experimentally observed hysteresis loops by a newly developed iterative integration with different starting conditions, kinetic and thermodynamic parameters for the transition from the PPI to the PPII helical conformation were determined. The transition is as expected for cis–trans isomerizations of amide bonds comparatively slow (k = 0.003 s−1 at 80 °C) and characterized by an activation energy Ea of 81.1 ± 3.6 kJ mol−1. Thermodynamically, the transition from the PPI to the PPII helix is characterized by a positive standard enthalpy (ΔH0 = 33.5 ± 2.1 kJ min−1) and a positive standard entropy (ΔS0 = 102 ± 6.6 J mol−1 K−1). Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Inhibitory effect of Thuja orientalis on TNF‐α‐induced vascular inflammation
Authors: Lee Yun Jung , Hwang Sun Mi , Yoon Jung Joo , Lee So Min , Kyung Eun Ho , Kim Jin Sook , Kang Dae Gill , Lee Ho Sub 
Published: June 2010

AbstractVascular inflammation is involved in the initiation and progression of vascular diseases including atherosclerosis. While conducting in vitro screening of 600 medicinal plant extracts, an aqueous extract of Thuja orientalis (ATO) was found to exhibit antiinflammatory activity in human umbilical vein endothelial cells (HUVEC). In the current study, the antiinflammatory activity of ATO and possible mechanisms for this were investigated in HUVEC. Preincubation with ATO (20 μg/mL) suppressed tumor necrosis factor‐α (TNF‐α)‐induced expression of adhesion molecules including intercellular adhesion molecule‐1 (ICAM‐1), vascular cell adhesion molecule‐1 (VCAM‐1) and E‐selectin at both the protein and mRNA levels. ATO also inhibited U937 monocyte adhesion to HUVEC stimulated by TNF‐α. In addition, ATO attenuated TNF‐α‐induced p65 NF‐κB translocation into the nucleus and phosphorylation of IκB‐α. Furthermore, ATO significantly inhibited TNF‐α‐induced intracellular reactive oxygen species (ROS) production. Overall, the present data suggest that ATO can suppress TNF‐α‐induced vascular inflammatory processes, possibly via inhibition of ROS and NF‐κB activation, in HUVEC. Copyright © 2010 John Wiley & Sons, Ltd.
Neuroprotective effect of honokiol and magnolol, compounds from Magnolia officinalis, on beta‐amyloid‐induced toxicity in PC12 cells
Authors: Hoi Chu Peng , Ho Yee Ping , Baum Larry , Chow Albert H. L. 
Published: June 2010

AbstractAmyloid β peptide (Aβ) induced toxicity is a well‐established pathway of neuronal cell death which might play a role in Alzheimer's disease. In this regard, the toxic effect of Aβ on a cultured Aβ‐sensitive neuronal cell line was used as a primary screening tool for potential anti‐Alzheimer's therapeutic agents. The effects of nine pure compounds (vitamin E, α‐asarone, salidroside, baicolin, magnolol, gastrodin, bilobalide, honokiol and β‐asarone) from selected Chinese herbs on neuronal cell death induced by Aβ in NGF‐differentiated PC12 cells were examined. Only two of the studied compounds, honokiol and magnolol, significantly decreased Aβ‐induced cell death. Further experiments indicated that their neuroprotective effects are possibly mediated through reduced ROS production as well as suppression of intracellular calcium elevation and inhibition of caspase‐3 activity. The results provide for the first time a scientific rationale for the clinical use of honokiol and magnolol in the treatment of Alzheimer's disease. Copyright © 2010 John Wiley & Sons, Ltd.
Dimensional compactification and two‐particle binding
Authors: Delfino A. , Timóteo V. S. , Frederico T. , Tomio Lauro , Cordeiro C. E. 
Published: June 2010

AbstractThe renormalization group equations (RGE) are applied to the study of two‐body singular interactions at the surface of an infinite long cylinder with a radius R. A single scale, independent of R, emerges from the renormalization procedure of removing the ultraviolet momentum divergence of the original interacting Green's function. This single scale implies in a R‐dependent binding energy, which is obtained from the pole of the Green's function. The binding is infinitely large in the limit R = 0, while as R goes to infinity it converges to the well‐ known two‐dimensional (2D) result in flat space. The physical scale is controlled by the energy binding value on the 2D flat surface. By exploring the effect of space dimensions D, from D = 1 to D = 3, in the physics and scales, it is also shown that by decreasing the dimensionality one favors the two‐body binding. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Ab initio multireference singles and doubles configuration interaction study of the low‐energy states of iron mononitride
Authors: de Oliveira Marcos Herrerias , Martins Filho Harley Paiva , Da Motta Neto Joaquim Delphino 
Published: June 2010

AbstractLow‐lying states of iron mononitride are studied using ab initio multireference singles and doubles configuration interaction (MR‐SDCI) calculations. For each one of the 2Δ, 4Π, 6Σ+, 2Π, 4Δ, 6Π, and 6Δ states the reference wavefunction has been obtained at the complete active space self consistent field (CASSCF) level and relativistic corrections were included. Potential energy curves are presented for all states. Spectroscopic constants have been determined for the 2Δ, 4Π, and 6Σ+ states assuming a Morse‐type potential function using a code written by one of us. For the 2Δ state, the calculated spectroscopic constants are Re = 1.567 Å, ωe = 827 cm−1, and μ = 1.68 D. Rotovibrational analysis suggests that the third vibrational level of the 2Δ state already surpasses the first vibrational levels of the 4Π and 6Σ+ states, what reassures the difficulty in correctly attributing the lines of the experimental spectrum. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Are the anions MeO(CO) (n = 1 and 2) methoxide anion donors in the gas phase? A theoretical investigation
Authors: Wang Tianfang , Eichinger Peter C. H. , Dua Suresh , Bowie John H. 
Published: June 2010

Abstract

The anions CH3O‐–CO and CH3OCO‐–CO are both methoxide anion donors. The processes CH3O‐–CO → CH3O– + CO and CH3OCO—CO → CH3O– + 2CO have ΔG values of +8 and −68 kJ mol−1, respectively, at the CCSD(T)/6‐311++G(2d, 2p)//B3LYP/6‐311++G(2d,2p) level of theory.
The reactions CH3OCOCO → CH3OCO + CO (ΔG = −22 kJ mol−1) and CH3COCH(O–)CO2CH3 → CH3COCH(O–)OCH3 + CO (ΔG = +19 kJ mol−1) proceed directly from the precursor anions via the transition states (CH3OCO…CO2)– and (CH3COCHO…CH3OCO)–, respectively.
Anion CH3COCH(O–)CO2CH3 undergoes methoxide anion transfer and loss of two molecules of CO in the reaction sequence CH3COCH(O–)CO2CH3 → CH3CH(O–)COCO2CH3 → [CH3CHO (CH3OCO‐–CO)] → CH3CH(O–)OCH3 + 2CO (ΔG = +9 kJ mol−1). The hydride ion transfer in the first step is a key feature of the reaction sequence.
Copyright © 2010 John Wiley & Sons, Ltd.
Use of high‐resolution mass spectrometry to investigate a metabolite interference during liquid chromatography/tandem mass spectrometric quantification of a small molecule in toxicokinetic study samples
Authors: Furlong Michael , Bessire Andrew , Song Wei , Huntington Christopher , Groeber Elizabeth 
Published: June 2010

AbstractDuring routine liquid chromatography/tandem mass spectrometric (LC/MS/MS) bioanalysis of a small molecule analyte in rat serum samples from a toxicokinetic study, an unexpected interfering peak was observed in the extracted ion chromatogram of the internal standard. No interfering peaks were observed in the extracted ion chromatogram of the analyte. The dose‐dependent peak area response and peak area response versus time profiles of the interfering peak suggested that it might have been related to a metabolite of the dosed compound. Further investigation using high‐resolution mass spectrometry led to unequivocal identification of the interfering peak as anN‐desmethyl metabolite of the parent analyte. High‐resolution mass spectrometry (HRMS) was also used to demonstrate that the interfering response of the metabolite in the multiple reaction monitoring (MRM) channel of the internal standard was due to an isobaric relationship between the13C‐isotope of the metabolite and the internal standard (i.e., common precursor ion mass), coupled with a metabolite product ion with identical mass to the product ion used in the MRM transition of the internal standard. These results emphasize (1) the need to carefully evaluate internal standard candidates with regard to potential interferences from metabolites during LC/MS/MS method development, validation and bioanalysis of small molecule analytes in biological matrices; (2) the value of HRMS as a tool to investigate unexpected interferences encountered during LC/MS/MS analysis of small molecules in biological matrices; and (3) the potential for interference regardless of choice of IS and therefore the importance of conducting assay robustness on incurredin vitroorin vivostudy samples. Copyright © 2010 John Wiley & Sons, Ltd.
Theoretical and experimental study of the achievable separation power in resistive‐glass atmospheric pressure ion mobility spectrometry
Authors: Kwasnik Mark , Fernández Facundo M. 
Published: June 2010

AbstractWe present a detailed investigation of the performance of our previously reported nanoelectrospray high‐resolution resistive‐glass atmospheric pressure drift tube ion mobility spectrometer constructed with monolithic resistive‐glass desolvation and drift regions. Using experimental spectral data and theoretical pulse width and diffusion variables, we compare theoretical and experimental resolving powers achievable under a variety of field strengths and ion gate pulse widths. The effects of instrumental and operational parameters on the resolution achievable in chromatographic terms are also discussed. Following characterization of the separation power of the instrument, experimental spectral peak width data is fitted by a least‐squares procedure to a pre‐existing semi‐empirical model developed to study contributions to peak width other than initial pulse width and diffusional broadening. The model suggests possible contributions to the final measured peak width from electric field inhomogeneity and minor contributions from instrumental parameters such as anode size, anode‐to‐anode grid distance and drift gas flow rate. The model also reveals an unexpected ion gate width dependence on the final measured peak width that we attribute to non‐ideal performance of the Bradbury‐Nielsen ion gate and limitations in the design of our pulsing‐electronics. Copyright © 2010 John Wiley & Sons, Ltd.
Aerial photographic analysis of channel narrowing and vegetation expansion in Canyon De Chelly National Monument, Arizona, USA, 1935–2004
Authors: Cadol D. , Rathburn S. L. , Cooper D. J. 
Published: June 2010

AbstractAerial photographs from the past 70 years show narrowing of channels in Canyon de Chelly National Monument, which coincided with the establishment and expansion of woody riparian vegetation, primarily non‐native tamarisk (Tamarix ssp.) and Russian olive (Elaeagnus angustifolia) and native cottonwood (Populus spp.). Rectified air photo sets were used to map the extent of woody riparian vegetation cover in the canyon bottom as well as the channel planform geometry for 6 years: 1935, 1964, 1975, 1981, 1989 and 2004. In 1935, vegetation covered less than 1 per cent of the canyon bottom and the channel was braided and 91 m wide on average. By 2004, the channel in the upper 75% of the canyon had narrowed to a single thread an average of 6.5 m wide and was lined by riparian vegetation, with vegetation covering up to 45% of the canyon bottom in some reaches. A relative timing index was developed that incorporates information from both channel and vegetation area expansion or contraction into a single variable. Vegetation establishment lagged channel narrowing in the upper reaches of the canyons, but narrowing and vegetation establishment occurred simultaneously in the middle and lower reaches. Narrowing progressed downstream through time, and the lowermost reaches remained braided and unincised in 2006. We interpret these patterns to suggest that riparian vegetation is responding to and interacting with changes in the channel morphology of Canyon de Chelly rather than driving channel change. Copyright © 2010 John Wiley & Sons, Ltd.
Establishing spatial trends in water chemistry and stable isotopes (δ15N and δ13C) in the Elwha River prior to dam removal and salmon recolonization
Authors: Duda J. J. , Coe H. J. , Morley S. A. , Kloehn K. K. 
Published: June 2010

AbstractTwo high‐head dams on the Elwha River in Washington State (USA) have changed the migratory patterns of resident and anadromous fish, limiting Pacific salmon to the lower 7.9 km of a river that historically supported large Pacific salmon runs. To document the effects of the dams prior to their removal, we measured carbon and nitrogen stable isotope ratios of primary producers, benthic macroinvertebrates, and fish, and water chemistry above, between and below the dams. We found that δ15N was significantly higher in fish, stoneflies, black flies, periphyton and macroalgae where salmon still have access. Fish and chloroperlid stoneflies were enriched in δ13C, but the values were more variable than in δ15N. For some taxa, there were also differences between the two river sections that lack salmon, suggesting that factors other than marine‐derived nutrients are structuring longitudinal isotopic profiles. Consistent with trophic theory, macroalgae had the lowest δ15N, followed by periphyton, macroinvertebrates and fish, with a range of 6.9, 6.2 and 7.7‰ below, between, and above the dams, respectively. Water chemistry analyses confirmed earlier reports that the river is oligotrophic. Phosphorous levels in the Elwha were lower than those found in other regional rivers, with significant differences among regulated, unregulated and reference sections. The removal of these dams, among the largest of such projects ever attempted, is expected to facilitate the return of salmon and their marine‐derived nutrients (MDN) throughout the watershed, possibly altering the food web structure, nutrient levels and stable isotope values that we documented. Published in 2010 by John Wiley & Sons, Ltd.
Temperature effects in the sputtering of a molecular solid by energetic atomic and cluster projectiles
Authors: Brenes D. A. , Willingham D. , Winograd N. , Postawa Z. 
Published: June 2010

AbstractTemperature effects in the sputtering of an organic molecule were investigated by subjecting a well defined film of coronene to Au1 and C60 primary ions at 100 and 300 K. Strong field photoionization of the sputtered neutral flux was employed to monitor the change in flight time and kinetic energy distributions of intact and fragmented species. Copyright © 2010 John Wiley & Sons, Ltd.
Retrospective sputter depth profiling using 3D mass spectral imaging
Authors: Zheng Leiliang , Wucher Andreas , Winograd Nicholas 
Published: June 2010

AbstractA molecular multilayer stack composed of alternating Langmuir‐Blodgett films was analyzed by ToF‐SIMS imaging in combination with intermediate sputter erosion using a focused C60+ cluster ion beam. From the resulting dataset, depth profiles of any desired lateral portion of the analyzed field‐of‐view can be extracted in retrospect, allowing the influence of the gating area on the apparent depth resolution to be assessed. In a similar way, the observed degradation of depth resolution with increasing depth of the analyzed interface can be analyzed in order to determine the ‘intrinsic’ depth resolution of the method. Copyright © 2010 John Wiley & Sons, Ltd.