bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circularly permuted monomeric red fluorescent proteins with new termini in the β‐sheet
Authors: Carlson Haley J. , Cotton Darrel W. , Campbell Robert E. 
Published: June 2010

AbstractCircularly permuted fluorescent proteins (FPs) have a growing number of uses in live cell fluorescence biosensing applications. Most notably, they enable the construction of single fluorescent protein‐based biosensors for Ca2+ and other analytes of interest. Circularly permuted FPs are also of great utility in the optimization of fluorescence resonance energy transfer (FRET)‐based biosensors by providing a means for varying the critical dipole–dipole orientation. We have previously reported on our efforts to create circularly permuted variants of a monomeric red FP (RFP) known as mCherry. In our previous work, we had identified six distinct locations within mCherry that tolerated the insertion of a short peptide sequence. Creation of circularly permuted variants with new termini at the locations corresponding to the sites of insertion led to the discovery of three permuted variants that retained no more than 18% of the brightness of mCherry. We now report the extensive directed evolution of the variant with new termini at position 193 of the protein sequence for improved fluorescent brightness. The resulting variant, known as cp193g7, has 61% of the intrinsic brightness of mCherry and was found to be highly tolerant of circular permutation at other locations within the sequence. We have exploited this property to engineer an expanded series of circularly permuted variants with new termini located along the length of the 10th β‐strand of mCherry. These new variants may ultimately prove useful for the creation of single FP‐based Ca2+ biosensors.
Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein
Authors: Shetty Nishant D. , Reddy Manchi C. M. , Palaninathan Satheesh K. , Owen Joshua L. , Sacchettini James C. 
Published: June 2010

AbstractPII constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. Mycobacterium tuberculosis (Mtb) has a single homologue of PII whose precise role has as yet not been explored. We have solved the crystal structures of the Mtb PII protein in its apo and ATP bound forms to 1.4 and 2.4 Å resolutions, respectively. The protein forms a trimeric assembly in the crystal lattice and folds similarly to the other PII family proteins. The Mtb PII:ATP binary complex structure reveals three ATP molecules per trimer, each bound between the base of the T‐loop of one subunit and the C‐loop of the neighboring subunit. In contrast to the apo structure, at least one subunit of the binary complex structure contains a completely ordered T‐loop indicating that ATP binding plays a role in orienting this loop region towards target proteins like the ammonium transporter, AmtB. Arg38 of the T‐loop makes direct contact with the γ‐phosphate of the ATP molecule replacing the Mg2+ position seen in the Methanococcus jannaschii GlnK1 structure. The C‐loop of a neighboring subunit encloses the other side of the ATP molecule, placing the GlnK specific C‐terminal 310 helix in the vicinity. Homology modeling studies with the E. coli GlnK:AmtB complex reveal that Mtb PII could form a complex similar to the complex in E. coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway.
Tissue expression of IL16 in prostate cancer and its association with recurrence after radical prostatectomy
Authors: Compérat Eva , Rouprêt Morgan , Drouin Sarah J. , Camparo Philippe , Bitker Marc‐Olivier , Houlgatte Alain , Cancel‐Tassin Géraldine , Cussenot Olivier 
Published: June 2010

AbstractBACKGROUNDGenetic polymorphism located within the IL16 gene has been reported to be associated with aggressive prostate cancer (PCa). Our aim was to establish whether the tissue expression of IL16 is a prognostic factor of survival in PCa.METHODSThe files of patients who underwent radical prostatectomy (RP) between 1995 and 2001 were reviewed. The cases were selected and classified according to the D'Amico classification for risk of recurrence (intermediate or high). The value of IL16 and its receptor CCR5 (chemokine (C‐C motif) receptor 5) expression levels were determined as witness of aggressiveness patterns and markers of biological relapse in patients with PCa treated by RP. A tissue microarray of 304 cases was constructed. IL16 and CCR5 expression levels were characterized by immunohistochemistry.RESULTSIL16 expression was correlated with high Gleason score (i.e., >7) (P < 0.01). It was not significant for CCR5. IL16 and CCR5 were not associated with prostate‐specific antigen (PSA) or capsular extension of the disease. The accurate prediction of disease outcome, using stratification of cases, according to negative margins and D'Amico classification was significantly enhanced by status of IL16 expression (P ≤ 0.01). In univariate analyses, Gleason score, PSA level, stage and loss of IL16 expression were related to better biological‐free survival (P < 0.05) but not CCR5. In a multivariate analysis, IL16 expression, Gleason score, and tumor stage were independent factors for biochemical‐free survival (P = 0.001).CONCLUSIONSIL16 appears to be a useful prognostic factor in PCa. Its expression in PCa tissue was correlated to tumor aggressiveness and biochemical relapse of the disease. Prostate 70: 1622–1627, 2010. © 2010 Wiley‐Liss, Inc.
Similarity of cytochrome c oxidases in different organisms
Authors: Popovic D. M. , Leontyev I. V. , Beech D. G. , Stuchebrukhov A. A. 
Published: June 2010

AbstractMost of biological oxygen reduction is catalyzed by the heme‐copper oxygen reductases. These enzymes are redox‐driven proton pumps that take part in generating the proton gradient in both prokaryotes and mitochondria that drives synthesis of ATP. The enzymes have been divided into three evolutionarily‐related groups: the A‐, B‐, and C‐families. Recent comparative studies suggest that all oxygen reductases perform the same chemistry for oxygen reduction and comprise the same essential elements of the proton pumping mechanism, such as the proton loading and kinetic gating sites, which, however, appear to be different in different families. All species of the A‐family, however, demonstrate remarkable similarity of the central processing unit of the enzyme, as revealed by their recent crystal structures. Here we demonstrate that cytochrome c oxidases (CcO) of such diverse organisms as a mammal (bovine heart mitochondrial CcO), photosynthetic bacteria (Rhodobacter sphaeroides CcO), and soil bacteria (Paracoccus denitrificans CcO) are not only structurally similar, but almost identical in microscopic electrostatics and thermodynamics properties of their key amino‐acids. By using pKa calculations of some of the key residues of the catalytic site, D‐ and K‐ proton input, and putative proton output channels of these three different enzymes, we demonstrate that the microscopic properties of key residues are almost identical, which strongly suggests the same mechanism in these species. The quantitative precision with which the microscopic physical properties of these enzymes have remained constant despite different evolutionary routes undertaken is striking. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Rosetta in CAPRI rounds 13–19
Authors: Fleishman Sarel J. , Corn Jacob E. , Strauch Eva M. , Whitehead Tim A. , Andre Ingemar , Thompson James , Havranek James J. , Das Rhiju , Bradley Philip , Baker David 
Published: June 2010

AbstractModeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13–19 we tested the ability of various backbone remodeling strategies to capture the main‐chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large‐scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement. Proteins 2010. © Wiley‐Liss, Inc.
On the pH‐optimum of activity and stability of proteins
Authors: Talley Kemper , Alexov Emil 
Published: June 2010

AbstractBiological macromolecules evolved to perform their function in specific cellular environment (subcellular compartments or tissues); therefore, they should be adapted to the biophysical characteristics of the corresponding environment, one of them being the characteristic pH. Many macromolecular properties are pH dependent, such as activity and stability. However, only activity is biologically important, while stability may not be crucial for the corresponding reaction. Here, we show that the pH‐optimum of activity (the pH of maximal activity) is correlated with the pH‐optimum of stability (the pH of maximal stability) on a set of 310 proteins with available experimental data. We speculate that such a correlation is needed to allow the corresponding macromolecules to tolerate small pH fluctuations that are inevitable with cellular function. Our findings rationalize the efforts of correlating the pH of maximal stability and the characteristic pH of subcellular compartments, as only pH of activity is subject of evolutionary pressure. In addition, our analysis confirmed the previous observation that pH‐optimum of activity and stability are not correlated with the isoelectric point, pI, or with the optimal temperature. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Zero‐width resonances and exceptional points in molecular photodissociation
Authors: Lefebvre Roland , Atabek Osman 
Published: June 2010

AbstractIn the Hamiltonian describing the interaction of a molecule with a continuous laser field, the wavelength and the intensity of the field are two external parameters which can be varied at will, within realistic limits. Floquet formalism provides complex eigenenergies with an imaginary part giving the photodissociation rate. Two interesting features emerge from this treatment. For some specific laser intensities, the imaginary part can vanish. This means that Zero‐Width Resonances can be produced. It is also possible to choose the laser parameters to provoke the coalescence of two resonances (complex eigenenergies and wavefunctions) of the wave equation. Such points in the parameter plane are called exceptional and have been studied in many areas of physics. The existence of Zero‐Width Resonances and of Exceptional Points has important consequences which are described in the article. Advantage can be taken of them in laser control strategies dealing with vibrational purification or transfer, with the ultimate goal of molecular cooling. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The electronic terms of the finite‐length nanotubes, generated by edge states: A CASSCF study
Authors: Pavlov Mikhail , Ermilov Alexander 
Published: June 2010

AbstractLow‐lying electronic terms of the hydrocarbons [C7]q (q = 1,3…9) were calculated within CASSCF approach. The [C7]q are H‐terminated finite fragment of zigzag carbon nanotube (7,0) containing q cyclacene units. Each [C7]q with odd q has D7h point symmetry. All systems [Cn]q with arbitrary n and q have a specific set of the one‐electron states characterized by the exponential decay along the cylinder axis that has been estimated within the Huckel model. These MOs are localized near bases of the cylinder and they are frontier in all systems [Cn]q. By hypothesis, the low‐lying electronic terms of the hydrocarbons [C7]q (q = 1,3…9) are defined by four quasi‐degenerate MOs e3′, e3″, which were included in the active space CASSCF. Low‐lying electronic terms possess tier structure and systems with various q have the same order of states. The distance between tiers tends to asymptotic limit with increasing q. In this case, states in each tier become quasi‐degenerate. The lowest tier consists of close set of states 1A, 3A, 5A, and each is characterized by single occupation of the localized MOs. Ground state of [C7]q is singlet; values of splitting are well described by Heisenberg hamiltonaian. The calculation results can be interpreted as reducing interaction of states localized on opposite cylinder bases with increasing fragment length. According to CASSCF, this interaction reduces exponentially in exact accordance with the similar characteristics of the localized MOs. There is a reason to believe that the value of splitting decreases less rapidly with increasing q if level of calculation is improved. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A 2D spinless version of Dirac's equation written in a noninertial frame of reference
Authors: Nascimento D. L. , Fonseca A. L. A. 
Published: June 2010

AbstractIn this article, we present a quantized classical‐like wave equation. It is obtained by considering the equivalence between the Hamilton‐Jacobi eq. (which belongs to the usual manifold \input amssym ${\Bbb R^{3}} \otimes {\Bbb R} $ of General Relativity), with our two spinor versions of the Dirac eq. (which belongs to the associated complex manifold \input amssym ${\Bbb C}\otimes {\Bbb C} $). In which the electron is considered as a particle‐like entity, instead of the usual wave‐like interpretation of standard Quantum Mechanics. We also consider the transformation properties between the two manifolds through the corresponding groups O(3,1) and SU(2), but we assume a flat Minkowsky space as the background space. We made an illustrative application to the rather standard problem of the hydrogen and helium atoms. We propose a variational extension of the approach, through a Hylleraas‐like computational method, to take into account a many electron problem too futurely. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Stagnation graphs and topological models of magnetic‐field induced electron current density for some small molecules in connection with their magnetic symmetry
Authors: Pelloni Stefano , Lazzeretti Paolo 
Published: June 2010

AbstractSpatial models of magnetic‐field induced electronic currents have been constructed for a series of small molecules of different point group symmetry via stagnation graphs and current density maps. These tools provide fundamental help for rationalization of magnetic response properties, such as magnetizability and nuclear magnetic shielding. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Crystal and electronic structure of the room temperature organometallic ferrimagnet V(TCNE)2. Analysis of numerical DoS and magnetic properties as related to orbital and spin‐Hamiltonian models
Authors: Tchougréeff Andrei L. , Dronskowski Richard 
Published: June 2010

AbstractWe present a detailed analysis of the results of our numerical study of the crystal and electronic structure of the room temperature organometallic ferrimagnet of general composition V(TCNE)x with x ≈ 2. The results of the LSDA +U study show that the experimentally determined structure complies with the magnetic measurements and thus can serve as a prototype structure for the entire family of the M(TCNE)2 organometallic magnets. The results of the numerical study and of the magnetic experiments are interpreted using a spin‐wave treatment of the model Hamiltonians proposed here. This allowed us to obtain estimates of the critical temperature in three‐ and two‐dimensional regimes and to give an explanation of the differences in behavior of probably isostructural V(TCNE)2 and Fe(TCNE)2 species. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Computational insights into the photochemical step of the reaction catalyzed by protochlorophylide oxidoreductase
Authors: Silva Pedro J. , Ramos Maria João 
Published: June 2010

AbstractThe light‐dependent enzyme protochlorophyllide oxidoreductase (EC:1.3.1.33) catalyzes the conversion of protochlorophyllide (PChlide) into chlorophyllide during chlorophyll synthesis. The reaction has been proposed to proceed through light‐induced weakening of the C17–C18 double bond in PChlide, which then facilitates hydride transfer from a NADPH cosubstrate molecule. We have performed DFT and TDDFT computations on the reaction mechanism of this interesting enzyme. The results show that whereas in the ground state the reaction is strongly endergonic and has a very high activation free energy (38 kcal/mol), the first four excited states (corresponding to excitations within the conjugated porphyrin π‐system) afford much lower activation free energies (<25 kcal/mol) and spontaneous (or only slightly endergonic) reaction paths. The sharp shape of the potential energy surface along the reaction coordinate in these excited states allows hydrogen tunneling to occur efficiently on the first few excited state surface, lowering the barrier to values closer to experiment, in agreement with recent suggestions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Interaction of the Mn2+, Co2+, Ni2+, and Zn2+ with prion protein HGGGW pentapeptide model
Authors: Marino Tiziana , Russo Nino , Toscano Marirosa 
Published: June 2010

AbstractThe interaction between the HGGGW model pentapeptide of octapeptide domain of the prion protein and the metal ions Mn2+, Co2+, Ni2+, and Zn2+ was studied at DFT level. For every metal ion considered four complexes with different metal coordination modes were analyzed. The geometry optimizations were performed at PW91PW91 level. Other five exchange‐correlation (XC) potentials were used to verify if the energetic parameters can be affected by the choice of the XC functional. Results showed that the metal ion affinity for the considered metal ions follows the trend: Ni2+ > Cu2+ > Co2+ > Zn2+ > Mn2+, irrespective to the used XC functional. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Magnetic interactions in Ca3Fe2Ge3O12 and Ca3Cr2Ge3O12 garnets. An ab initio all‐electron quantum mechanical simulation
Authors: Meyer A. , Perger W. F. , Demichelis R. , Civalleri B. , Dovesi R. 
Published: June 2010

AbstractThe ground state electronic structure in various magnetic phases of two Ge garnets (80 atoms in the primitive cell; cubic symmetry), Ca3Fe2Ge3O12 and Ca3Cr2Ge3O12, has been investigated with the periodic ab initio CRYSTAL code by adopting an all‐electron Gaussian‐type basis set and two hybrid functionals, namely B3LYP and PBE0, which contain a fraction of exact Hartree–Fock exchange. The evaluation of the exchange coupling constants among first (J1a, and J1b: there are two different kinds of neighbors at the same distance), second (J2), and third (J3) neighbors, separated by about 5.3, 6.1, and 8.7 Å, respectively, requires calculations involving the 160 atoms conventional cell. The Ji values turn out to be in qualitative agreement with experimental data. As a consequence of the different J1a to J1b ratios, and of the opposite sign of J2, two different magnetic ground states are found for the Cr and Fe compounds, in agreement with experimental observations. The mechanism for the stabilization of the magnetic states is discussed in the context of the Anderson theory of superexchange by evaluating the kinetic energy gain in the magnetic states and examining spin density maps and profiles. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Characterization of phenolic compounds in Helichrysum melaleucum by high‐performance liquid chromatography with on‐line ultraviolet and mass spectrometry detection
Authors: Gouveia Sandra C. , Castilho Paula C. 
Published: June 2010

AbstractHelicrysum melaleucum is a medicinal plant traditionally used in the islands of the Macaronesia region for the treatment of respiratory diseases. In this work, the phenolic compounds of Helicrysum melaleucum plants collected in different geographical locations of Madeira Island and their morphological parts (total aerial parts, leaves, flowers and stems) were extracted and analyzed separately by high‐performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC‐DAD/ESI‐MSn). A total of 68 compounds were characterized based mainly on their UV and mass spectra. These included derivatives of O‐glycosylated flavonoids (flavonol and flavones type), quinic acid, caffeic acid, lignans and polyphenols. The flowers were found to be the morphological part with higher variety of phenolic compounds. The large differences in the phenolic composition of plants collected from different geographical locations allowed the identification of a few components, such as pinoresinol and methoxylated flavone derivatives, likely to be useful as geographical markers. Also, these results promote further comparison of the bioactivities of the different samples analyzed. This paper marks the first report on the chemical analysis of Helichrysum melaleucum species. Copyright © 2010 John Wiley & Sons, Ltd.
Investigation of surface topography differences in native and exotic invertebrates in the St. Lawrence River
Authors: Brown D. R. S. , Brown C. A. 
Published: June 2010

AbstractThe texture, or topography, interior of shells from native and exotic mollusks are measured and compared to determine if they can be discriminated. Area‐scale fractal analysis is used to calculate relative areas as a function of scale, and the relative areas are used to evaluate the measurements. Measurements from a scanning laser profiler and from confocal and interferometric microscopes are compared, as are measurements of an original and a replica. The relative areas indicate clear differences between the measurement instruments. The largest relative areas are calculated from the confocal measurements. The trueness of the measurements has not been determined. However, the relative areas calculated from the confocal measurements are capable of discriminating the native clam from the exotic mussels with a confidence of greater than 99% at scales below 10 µm2. SCANNING 32: 250–255, 2010. © 2010 Wiley Periodicals, Inc.
Fabrication and Mechanical Properties of Large‐Scale Freestanding Nanoparticle Membranes
Authors: He Jinbo , Kanjanaboos Pongsakorn , Frazer N. Laszlo , Weis Adam , Lin Xiao‐Min , Jaeger Heinrich M. 
Published: June 2010

AbstractThin‐film membranes consisting of nanoparticles are of interest in applications ranging from nanosieves to electric, magnetic, or photonic devices and sensors. However, the fabrication of large‐scale membranes in a simple but controlled way has remained a challenge, due to the limited understanding of their mechanical properties. Systematic experiments on ultrathin, freestanding nanoparticle membranes of different core materials, core sizes, and capping ligands are reported. The results demonstrate that a drying‐mediated self‐assembly process can be used to create close‐packed monolayer membranes that span holes tens of micrometers in diameter. Containing up to ≈107 particles, these freely suspended layers exhibit remarkable mechanical properties with Young's moduli of the order of several GPa, independent of membrane size. Comparison of three different core–ligand combinations suggests that the membrane's elastic response is set by how tightly the ligands are bound to the particle cores and by the ligand–ligand interactions.