bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pictorial representation of zero‐point energy and tunnelling contributions to primary hydrogen isotope effects
Authors: O'Ferrall R. A. More 
Published: June 2010

AbstractThe interpretation of primary hydrogen isotope effects in terms of isotopic sensitivities of zero‐point energies in the reactants and transition state is reviewed. The reader is reminded that the transition state for a hydrogen transfer reaction corresponds to the position of maximum energy on the minimum energy path defined by the motion of the heavy atoms between which hydrogen is transferred. Tunnelling occurs through the potential energy barrier separating the reactant and product channels of the potential energy surface for this reaction. It is a consequence of rapid vibrational motion of the hydrogen within a collision complex and the overlap of vibrational wave functions between reactant and product sides of the barrier. Comparing zero‐point energies of a tunnelling complex and a hydrogen bond confirms results of calculations indicating that the zero‐point energy of the complex is likely to be less than that of the reactants. It follows that there should be a compensation between contributions from zero‐point energy changes and tunnelling which may explain why tunnelling rarely leads to very large isotope effects at ambient temperatures. The isotopic sensitivity of the zero‐point energy of the transition state is discussed in terms of variations in force constants of reacting bonds within a three‐centre model. A shift in isotopic sensitivity from the reaction coordinate mode to real stretching vibration as the structure of the transition state becomes more reactant‐ or product‐like, which provides a basis for the Westheimer effect, contrasts with the behaviour of hydrogen bonds, for which there is no change in isotopic sensitivity of the two stretching modes. Copyright © 2010 John Wiley & Sons, Ltd.
The structure and evolution of the murine inhibitor of carbonic anhydrase: A member of the transferrin superfamily
Authors: Eckenroth Brian E. , Mason Anne B. , McDevitt Meghan E. , Lambert Lisa A. , Everse Stephen J. 
Published: June 2010

AbstractThe original signature of the transferrin (TF) family of proteins was the ability to bind ferric iron with high affinity in the cleft of each of two homologous lobes. However, in recent years, new family members that do not bind iron have been discovered. One new member is the inhibitor of carbonic anhydrase (ICA), which as its name indicates, binds to and strongly inhibits certain isoforms of carbonic anhydrase. Recently, mouse ICA has been expressed as a recombinant protein in a mammalian cell system. Here, we describe the 2.4 Å structure of mouse ICA from a pseudomerohedral twinned crystal. As predicted, the structure is bilobal, comprised of two α‐β domains per lobe typical of the other family members. As with all but insect TFs, the structure includes the unusual reverse γ‐turn in each lobe. The structure is consistent with the fact that introduction of two mutations in the N‐lobe of murine ICA (mICA) (W124R and S188Y) allowed it to bind iron with high affinity. Unexpectedly, both lobes of the mICA were found in the closed conformation usually associated with presence of iron in the cleft, and making the structure most similar to diferric pig TF. Two new ICA family members (guinea pig and horse) were identified from genomic sequences and used in evolutionary comparisons. Additionally, a comparison of selection pressure (dN/dS) on functional residues reveals some interesting insights into the evolution of the TF family including that the N‐lobe of lactoferrin may be in the process of eliminating its iron binding function.
Probing local structural fluctuations in myoglobin by size‐dependent thiol‐disulfide exchange
Authors: Stratton Margaret M. , Cutler Thomas A. , Ha Jeung‐Hoi , Loh Stewart N. 
Published: June 2010

AbstractAll proteins undergo local structural fluctuations (LSFs) or breathing motions. These motions are likely to be important for function but are poorly understood. LSFs were initially defined by amide hydrogen exchange (HX) experiments as opening events, which expose a small number of backbone amides to 1H/2H exchange, but whose exchange rates are independent of denaturant concentration. Here, we use size‐dependent thiol‐disulfide exchange (SX) to characterize LSFs in single cysteine‐containing variants of myoglobin (Mb). SX complements HX by providing information on motions that disrupt side chain packing interactions. Most importantly, probe reagents of different sizes and chemical properties can be used to characterize the size of structural opening events and the properties of the open state. We use thiosulfonate reagents (126–274 Da) to survey access to Cys residues, which are buried at specific helical packing interfaces in Mb. In each case, the free energy of opening increases linearly with the radius of gyration of the probe reagent. The slope and the intercept are interpreted to yield information on the size of the opening events that expose the buried thiol groups. The slope parameter varies by over 10‐fold among Cys positions tested, suggesting that the sizes of breathing motions vary substantially throughout the protein. Our results provide insight to the longstanding question: how rigid or flexible are proteins in their native states?
Developmental expression of human hemoglobins mediated by maturation of their subunit interfaces
Authors: Manning Lois R. , Popowicz Anthony M. , Padovan Julio , Chait Brian T. , Russell J. Eric , Manning James M. 
Published: June 2010

AbstractDifferent types of human hemoglobins (Hbs) consisting of various combinations of the embryonic, fetal, and adult Hb subunits are present at certain times during development representing a major paradigm of developmental biology that is still not understood and one which we address here. We show that the subunit interfaces of these Hbs have increasing bonding strengths as demonstrated by their distinct distribution of tetramers, dimers, and monomers during gel filtration at very low‐Hb concentration. This maturation is mediated by competition between subunits for more favorable partners with stronger subunit interactions. Thus, the protein products of gene expression can themselves have a role in the developmental process due to their intrinsic properties.
Topology of the disulfide bonds in the antiviral lectin scytovirin
Authors: Moulaei Tinoush , Stuchlik Olga , Reed Matthew , Yuan Weirong , Pohl Jan , Lu Wuyuan , Haugh‐Krumpe Lauren , O'Keefe Barry R. , Wlodawer Alexander 
Published: June 2010

AbstractThe antiviral lectin scytovirin (SVN) contains a total of five disulfide bonds in two structurally similar domains. Previous reports provided contradictory results on the disulfide pairing in each individual domain, and we have now re‐examined the disulfide topology. N‐terminal sequencing and mass spectrometry were used to analyze proteolytic fragments of native SVN obtained at acidic pH, yielding the assignment as Cys7–Cys55, Cys20–Cys32, Cys26–Cys38, Cys68–Cys80, and Cys74–Cys86. We also analyzed the N‐terminal domain of SVN (SD1, residues 1–48) prepared by expression/oxidative folding of the recombinant protein and by chemical synthesis. The disulfide pairing in the chemically synthesized SD1 was forced into predetermined topologies: SD1A (Cys20–Cys26, Cys32–Cys38) or SD1B (Cys20–Cys32, Cys26–Cys38). The topology of native SVN was found to be in agreement with the SD1B and the one determined for the recombinant SD1 domain. Although the two synthetic forms of SD1 were distinct when subjected to chromatography, their antiviral properties were indistinguishable, having low nM activity against HIV. Tryptic fragments, the “cystine clusters” [Cys20–Cys32/Cys26–Cys38; SD1] and [Cys68–Cys80/Cys74–C‐86; SD2], were found to undergo rapid disulfide interchange at pH 8. This interchange resulted in accumulation of artifactual fragments in alkaline pH digests that are structurally unrelated to the original topology, providing a rational explanation for the differences between the topology reported herein and the one reported earlier (Bokesh et al., Biochemistry 2003;42:2578–2584). Our observations emphasize the fact that proteins such as SVN, with disulfide bonds in close proximity, require considerable precautions when being fragmented for the purpose of disulfide assignment.
Ghrelin improves disturbed myocardial energy metabolism in rats with heart failure induced by isoproterenol
Authors: Xu Jian‐Ping , Wang Hong‐Xia , Wang Wen , Zhang Li‐Ke , Tang Chao‐Shu 
Published: June 2010

AbstractTo explore the effects of ghrelin on disturbed myocardial energy metabolism during chronic heart failure (CHF). Rats were subcutaneously injected with isoproterenol (ISO) for 10 days with or without ghrelin for another 10 days. Enzyme immunoassay was to measure ghrelin concentrations. Compared with the control group, ISO‐treated rats showed suppressed cardiac function with high ghrelin/GHS‐R expressions. These rats also showed the decreases in food consumption and weight. The decreased levels of plasma glucose and myocardial glucogen, but the high lactate in blood and myocardium showed myocardial metabolic disturbance. Compared with the group given ISO alone, the rats with ghrelin (20 and 100 µg/kg/day) improved cardiac dysfunction and increased food intake by 13.5 and 14.2% (both P < 0.01), and rate of weight gain by 95% (P < 0.05) and 1.71‐fold (P < 0.01), respectively. The plasma glucose were increased by 49.7 and 50.8% (both P < 0.01), and myocardial glucogen, by 40.5 and 51.7% (both P < 0.01), but blood lactate decreased by 1.56‐ and 1.96‐fold (both P < 0.01), and myocardial lactate by 32.1 and 48.7% (both P < 0.05), respectively. Their MCT1 mRNA and protein expressions increased. The myocardial ghrelin/GHS‐R pathway can be upregulated during CHF. The ghrelin can attenuate cardiac dysfunction and energy metabolic disturbance in CHF rats. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
NMR‐based detection of acetylation sites in peptides
Authors: Smet‐Nocca Caroline , Wieruszeski Jean‐Michel , Melnyk Oleg , Benecke Arndt 
Published: June 2010

AbstractAcetylation of histone tails as well as non‐histone proteins was found to be a major component of the ‘chromatin code’ that regulates transcription through the recruitment of transcription factors, co‐regulators and DNA‐binding proteins. Acetylation can have several effects modifying protein–protein interactions, protein activity, localization and stability. Using NMR spectroscopy, we provide a simple way to detect acetyl moieties at the ε‐amino function of lysine residues based on peptides derived from Histone H4 and TDG amino‐terminal domains. Significant changes of acetyl‐lysine resonances as compared to non‐acetylated residues allow a direct identification of specific acetylated lysine. We also show that, in unfolded peptides, acetylation of lysine side chains leads to characteristic NMR signals that vary only weakly depending on the primary sequence or the total number of acetylated sites, indicating that the acetamide group does not establish any interactions with other residues. Furthermore, resonance changes upon acetylation are restricted to residues nearby the acetylation site, indicating that acetylation does not modify the overall peptide conformation. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Preferred conformation of peptides rich in Ac8c, a medium‐ring alicyclic Cα,α‐disubstituted glycine
Authors: Moretto Vittorio , Formaggio Fernando , Crisma Marco , Bonora Gian Maria , Toniolo Claudio , Benedetti Ettore , Santini Antonello , Saviano Michele , Di Blasio Benedetto , Pedone Carlo 
Published: June 2010

AbstractA complete series of terminally blocked, monodispersed homo‐oligopeptides (to the pentamer level) from the sterically demanding, medium‐ring alicyclic Cα,α‐disubstituted glycine 1‐aminocyclooctane‐1‐carb oxylic acid (Ac8c), and two Ala/Ac8c tripeptides, were synthesized by solution methods and fully characterized. The preferred conformation of all the oligopeptides was determined in deuterochloroform solution by IR absorption and 1H‐NMR. The molecular structures of the amino acid derivative Z‐Ac8c‐OH, the dipeptide pBrBz‐ (Ac8c)2‐OH and the tripeptide pBrBz‐(Ac8c)3‐OtBu were assessed in the crystal state by X‐ray diffraction. Conformational energy computations were performed on the monopeptide Ac‐Ac8c‐NHMe. Taken together, the results obtained strongly support the view that the Ac8c residue is an effective β‐turn and helix former. A comparison is also made with the conformational preferences of α‐aminoisobutyric acid, the prototype of Cα, α‐disubstituted glycines, and of the other members of the family of 1‐aminocycloalkane‐1‐carboxylic acids (Acnc, with n=3, 5–7) investigated so far. The implications for the use of the Ac8c residue in peptide conformational design are considered.
Elucidation of the structure of constrained bicyclopeptides in solution by two‐dimensional cross‐relaxation spectroscopy: Amatoxin analogues
Authors: Isernia Carla , Falcigno Lucia , Macura Slobodan , Paolillo Livio , Pastore Anna Lisa , Zanotti Giancarlo 
Published: June 2010

AbstractThe evaluation of peptide structures in solution is made feasible by the combined use of two‐dimensional NMR in the laboratory (NOESY) and rotating frames (ROESY), and by the use of molecular dynamics calculations. The present paper describes how both the NMR method and molecular dynamics calculations were applied to very rigid synthetic bicyclic peptides that are analogues of natural amatoxins. The NMR theory, which allows the estimate of interatomic distances between interacting nuclei, is briefly discussed. The experimental data were compared with those of known solid‐state structures. Three amatoxin analogues have been examined. Of these, one is biologically active (S‐deoxo γ[R] OH‐Ile3‐amaninamide) and its structure in the solid state has recently been worked out. The second and third analogues (S‐deoxo‐Ile3 ‐Ala5‐amaninamide and S‐deoxo‐D‐Ile3 ‐amaninamide, respectively) are inactive and their solid‐state structures are unknown. The data presented confirm the authors' previous hypothesis that lack of biological activity of S‐deoxo‐Ile3‐Ala5‐ amaninamide is due to the masking of the tryptophan ring by the methyl group of L‐Ala and not to massive conformational changes of the analogue.
Solution synthesis of human midkine, a novel heparin‐binding neurotrophic factor consisting of 121 amino acid residues with five disulphide bonds
Authors: Inui Tatsuya , Bódi József , Kubo Shigeru , Nishio Hideki , Kimura Terutoshi , Kojima Soichi , Maruta Hiroshi , Muramatsu Takashi , Sakakibara Shumpei 
Published: June 2010

AbstractHuman midkine (hMK), a novel heparin‐binding neurotrophic factor consisting of 121 amino acid residues with five intramolecular disulphide bonds, was synthesized by solution procedure in order to demonstrate the usefulness of our newly developed solvent system, a mixture of dichloromethane or chloroform and trifluoroethanol. The final protected 121‐residue peptide was assembled from two large fully protected intermediates, Boc‐(1–5 9)‐OH and H‐(60–121)‐OBzl, in CHL/TFE (3:1, v/v) using water‐soluble carbodiimide in the presence of HOOBt as coupling reagents. After removal of the protecting groups by HF followed by treatment with Hg(OAc)2 in 50% acetic acid, the fully deprotected peptide was subjected to the oxidative folding reaction. The final product was confirmed to have the correct disulphide structure from its tryptic peptide mapping and to possess the same biological activities as those of the natural product. In order to clarify the active region of the hMK molecule, the N‐terminal and C‐terminal half domains [(1–59) and (60–121)] were also synthesized by the same procedure used for the hMK synthesis. The C‐half domain was confirmed to show the full pattern of bioactivities except for the neuronal cell survival activity, while the N‐half one showed much less activity in general.
Segregation, quantum confinement effect and band offset for [110] SiGe NWs
Authors: Amato Michele , Palummo Maurizia , Ossicini Stefano 
Published: June 2010

AbstractResults of first‐principles DFT simulations provide strong evidence that, at zero temperature, for [110] oriented SiGe nanowires (NWs), the segregated structure is favoured with respect to the mixed ones; for this observation two different schemes of calculations are presented and discussed. Moreover the segregation strongly influences the NWs electronic properties, inducing a reduced quantum confined effect (RQCE). We show here that it depends on the effect of strain in the plane normal to the direction of growth and not on the choice of lattice parameter in the direction of growth. A qualitative evaluation of the band offset between Si and Ge for SiGe NWs is also presented.
AFM and SNOM characterization of ordinary chondrites: A contribution to solving the problem of asteroid reddening
Authors: Pompeo Giuliano , Longo Giovanni , Girasole Marco , Moretti Pierfrancesco , Palomba Ernesto , Maras Adriana , Somma Fabrizia , Cricenti Antonio 
Published: June 2010

AbstractSpace weathering (SW) is an ensemble of processes that act on a body exposed to the space environment. Typically, the exposure to SW results in the accumulation, at the surface, of nanoparticles, that are thought to be produced through a vaporization and subsequent cooling of the metallo‐silicaceous components exposed to the space environment. The presence of such nanoparticles is responsible for the so‐called reddening of the asteroids' reflectance spectra (i.e., the increase in Vis–NIR reflectance with increase in wavelength) observed by remote‐sensing measurements. To investigate the mechanism of formation of these nanoparticles, we have employed atomic force microscopy (AFM) and scanning near‐field optical microscopy (SNOM) to morphologically and optically characterize ordinary chondrites (OC), the most abundant class of meteorites collected on Earth and whose parent bodies are the S‐type asteroids. The AFM study reveals the occurrence of a diffuse nanophase (martensite) in the meteorite's metal inclusions. Since the same areas show a reddening of the reflectivity spectra, this suggests that such spectral modification is based on a shock‐induced phase transformation of the metal components of the extraterrestrial body. To gain more insight into this nanophase and on its role in the SW of the asteroids, an optical characterization by SNOM has been performed on OCs. In this work we exploited the peculiarity of this technique to search for a correlation between the topography on the nanoscale and the spectral characteristics, at different wavelengths in the red‐NIR range, of the observed nanophase. Indeed, a high‐resolution mapping of the optical properties of the meteorite provides an interesting method to discriminate between martensite‐based and Fe‐silicaceous nanoparticles.
Spectroscopic ellipsometry of SrTiO3 crystals applied to antiferrodistortive surface phase transition
Authors: Dejneka Alexandr , Trepakov Vladimir , Jastrabik Lubomir 
Published: June 2010

AbstractThis work is devoted to the ellipsometric study of antiferrodistortive (AFD) $O_{h}^{1} $ → $D_{4h}^{18} $ cubic‐to‐tetragonal phase transition (PT) of SrTiO3 surface. Strong influence of surface defect structure on magnitude and temperature evolutions of surface refractive index related to PT was found and investigated. It is shown that even small surface imperfections result in enhancement and strong changes of the surface refractive index when approaching the temperature of PT. This effect is caused by emergence and evolutions in the surface of the structural changes corresponding to order parameter at the temperatures sufficiently higher than transition temperature in the bulk. In the case of structurally perfect crystal surface, the features of the temperature dependence of surface refractive index appeared to be very small and visible at the temperatures a little smaller than transition temperature for bulk that agrees well with predictions of Kaganov–Omel'yanchuk theory.
Excitonic effects in the nonlinear optical response of a Si(111) surface
Authors: Stamova Maria , Rebentrost Frank 
Published: June 2010

AbstractWe discuss methods to calculate the linear and nonlinear optical spectra for cyclic cluster models of an ideal Si(111) surface. The cluster approach offers the possibility to implement the excitonic effects due to the Coulomb interaction between electron and hole in a relatively straight‐forward way. In order to appproximate a situation resembling a surface we use clusters with several hundreds of Si atoms. The electronic structure is obtained from a tight‐binding parametrization of the hamiltonian. A time‐dependent density operator formalism is used to calculate the response functions $S(\tau )$ and $S(\tau _{1} ,\tau _{2} )$ for the optical polarization, which also directly describe the response to ultrashort pulses. Their Fourier transforms are the frequency‐dependent optical susceptibilities $\chi {}^{(1)} ( - \omega ;\omega )$ and $\chi {}^{(2)} ( - \omega _{1} - \omega _{2} ;\omega _{1} ,\omega _{2} )$ for second‐harmonic ($\omega _{1} = \omega _{2} $) or sum‐frequency generation from surfaces. The excitonic Coulomb interaction is treated in the time‐dependent Hartree–Fock approximation, leading to large sets of differential equations that are integrated explicitly. The results on the linear susceptibility are in accord with earlier findings on the excitonic origin of the relative intensities of the E1 and E2 peaks near 3.4 and 4.3 eV. We present new results on excitonic effects in the nonlinear spectra and investigate in particular the surface‐related peaks near 2$\hbar \omega $ = 1.3–1.5 and 2.4 eV that govern the strong enhancement observed in SHG of clean silicon surfaces.
Metal–insulator transition in Si(111)‐(4 × 1)/(8 × 2)‐In studied by optical spectroscopy
Authors: Speiser E. , Chandola S. , Hinrichs K. , Gensch M. , Cobet C. , Wippermann S. , Schmidt W.G. , Bechstedt F. , Richter W. , Fleischer K. , McGilp J. F. , Esser N. 
Published: June 2010

AbstractMeasurements of the surface vibrational modes and optical response of Si(111)‐(4 × 1)/(8 × 2)‐In are compiled and a comparison to ab initio calculations performed within DFT‐LDA formalism is given. Surface resonant Raman spectroscopy allows identifying a number of surface phonons with high spectral precision. The phase transition of the (4 × 1)–(8 × 2) surface structure is found to be accompanied by characteristic changes of the surface phonons, which are discussed with respect to various structural models suggested. The optical anisotropy of the (8 × 2) phase shows that the anisotropic Drude tail of the (4 × 1) phase is replaced by two peaks at 0.50 and 0.72 eV. The spectroscopic signatures of the (4 × 1) and (8 × 2) phases agree with a metal–insulator transition. The mid‐IR‐anisotropic optical response of the insulating (8 × 2) phase is interpreted in terms of electronic single particle excitations between surface electronic bands related to the In‐nanowire surface. Comparison of the measured optical transitions with DFT ab initio calculations for the hexagon model and the trimer model of the (8 × 2) structure shows evidence for the existence of the hexagon structure.