bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels
Authors: Meissner Gerhard , Pasek Daniel A. , Yamaguchi Naohiro , Ramachandran Srinivas , Dokholyan Nikolay V. , Tripathy Ashutosh 
Published: July 2008

AbstractThe skeletal muscle (RyR1) and cardiac muscle (RyR2) ryanodine receptor calcium release channels contain a single, conserved calmodulin (CaM) binding domain, yet are differentially regulated by CaM. Here, we report that high‐affinity [35S]CaM binding to RyR1 is driven by favorable enthalpic and entropic contributions at Ca2+ concentrations from <0.01 to 100 μM. At 0.15 μM Ca2+, [35S]CaM bound to RyR2 with decreased affinity and binding enthalpy compared with RyR1. The rates of [35S]CaM dissociation from RyR1 increased as the temperature was raised, whereas at 0.15 μM Ca2+ the rate from RyR2 was little affected. The results suggest major differences in the energetics of CaM binding to and dissociation from RyR1 and RyR2. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna
Authors: Bismuto Ettore , Di Maggio Emiddio , Pleus Stefan , Sikor Martin , Röcker Carlheinz , Nienhaus G. Ulrich , Lamb Don C. 
Published: July 2008

AbstractA molecular model of the acidic compact state of apomyoglobin (A‐state) from yellowfin tuna was obtained using molecular dynamics simulations (MD) by calculating multiple trajectories. To cause partial unfolding within a reasonable amount of CPU time, both an acidic environment (pH 3 and 0.15M NaCl) and a temperature jump to 500 K were needed. Twenty‐five acidic structures of apomyoglobin were generated by MD, 10 of them can be clustered by RMSD in an average structure having a common hydrophobic core as was reported for acidic sperm whale apomyoglobin, with shortened helices A,G,E, and H (the helix A appears to be translated along the sequence). Prolonging the MD runs at 500 K did not cause further substantial unfolding, suggesting that the ensemble of generated structures is indicative of a region of the conformational space accessible to the apoprotein at acidic pH corresponding to a local energy minimum. The comparison of experimentally determined values of specific spectroscopic properties of the apomyoglobin in acidic salt conditions with the expected ones on the basis of the MD generated structures shows a reasonable agreement considering the characteristic uncertainties of both experimental and simulation techniques. We used frequency domain fluorometry, acrylamide fluorescence quenching, and fluorescence correlation spectroscopy together with far UV circular dichroism to estimate the helical content, the Stern–Volmer quenching constant and the radius of gyration of the protein. Tuna apomyoglobin is a single tryptophan protein and thus, interpretation of its intrinsic fluorescence is simpler than for other proteins. The high sensitivity of the applied fluorescence techniques enabled experiments to be performed under very dilute conditions, that is, at concentrations of subnanomolar for the FCS measurements and 6 μM for the other fluorescence measurements. As high concentrations of proteins can strongly affect the association equilibrium among partially unfolded states, fluorescence techniques can provide complementary information with respect to other techniques requiring higher sample concentrations, such as NMR. The analysis of exposed hydrophobic regions in each of the MD‐generated acidic structures reveals potential candidates involved in the aggregation processes of apomyoglobin in the acidic compact state. Our investigation represents an effective model system for studying amyloid fibril formation found in important diseases that are believed to proceed via aggregation of protein in the molten globule state. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The structure of the PP2A regulatory subunit B56γ: The remaining piece of the PP2A jigsaw puzzle
Authors: Magnusdottir Audur , Stenmark Pål , Flodin Susanne , Nyman Tomas , Kotenyova Tetyana , Gräslund Susanne , Ogg Derek , Nordlund Pär 
Published: July 2008

AbstractThe PP2A serine/threonine phosphatase regulates a plethora of cellular processes. In the cell the predominant form of the enzyme is a heterotrimer, formed by a core dimer composed of a catalytic and a scaffolding subunit, which assemble together with one of a range of different regulatory B subunits. Here, we present the first structure of a free non‐complexed B subunit, B56γ. Comparison with the recent structures of a heterotrimeric complex and the core dimer reveals several significant conformational changes in the interface region between the B56γ and the core dimer. These allow for an assembly scheme of the PP2A holoenzyme to be put forth where B56γ first complexes with the scaffolding subunit and subsequently binds to the catalytic subunit and this induces the formation of a binding site for the invariant C‐terminus of the catalytic subunit that locks in the complex as a last step of assembly. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Energetics of the loop‐to‐helix transition leading to the coiled‐coil structure of influenza virus hemagglutinin HA2 subunits
Authors: Huang Qiang , Korte Thomas , Rachakonda P. Sivaramakrishna , Knapp Ernst‐Walter , Herrmann Andreas 
Published: July 2008

AbstractFusion of influenza virus with the endosomal membrane of the host cell is mediated by the homotrimer‐organized glycoprotein hemagglutinin (HA). Its fusion activity is triggered by a low pH‐mediated conformational change affecting the structure of the HA1 and HA2 subunits. The HA2 subunits undergo a loop‐to‐helix transition leading to a coiled‐coil structure, a highly conserved motif for many fusion mediating viral proteins. However, experimental studies showed that the HA2 coiled‐coil structure is stable at neutral and low pH, implying that there is no direct relationship between low pH and the HA2 loop‐to‐helix transition. To interpret this observation, we used a computational approach based on the dielectric continuum solvent model to explore the influence of water and pH on the free energy change of the transition. The computations showed that the electrostatic interaction between HA2 fragments and water is the major driving force of the HA2 loop‐to‐helix transition leading to the coiled‐coil structure, as long as the HA1 globular domain covering the HA2 subunits in the nonfusion competent conformation is reorganized and thereby allows water molecules to interact with the whole loop segments of the HA2 subunits. Moreover, we show that the energy released by the loop‐to‐helix transition may account for those energies required for driving the subsequent steps of membrane fusion. Such a water‐driven process may resemble a general mechanism for the formation of the highly conserved coiled‐coil motif of enveloped viruses. Proteins 2009. © 2008 Wiley‐Liss, Inc.
An engineered folded PLP‐bound monomer of Treponema denticola cystalysin reveals the effect of the dimeric structure on the catalytic properties of the enzyme
Authors: Montioli Riccardo , Cellini Barbara , Bertoldi Mariarita , Paiardini Alessandro , Voltattorni Carla Borri 
Published: July 2008

AbstractCystalysin, a dimeric pyridoxal 5′‐phosphate (PLP)‐dependent lyase, is a virulence factor of the human oral pathogen Treponema denticola. Guided by bioinformatic analysis, two interfacial residues (Leu57 and Leu62) and an active site residue (Tyr64*), hydrogen‐bonded with the PLP phosphate group of the neighboring subunit, have been mutated. The wild‐type and the L57A, L62A, Y64*A, L57A/L62A, L57A/Y64*A, L57A/L62A/Y64*A mutants, all having a C‐terminal histidine tag, have been constructed, expressed, and purified. The impact of these mutations on the dimeric state of cystalysin in the apo‐ and holo‐form has been analyzed by size‐exclusion chromatography. The results demonstrate that (i) Leu57 is more critical than Leu62 for apodimer formation, (ii) Tyr64*, more than Leu62, interferes with dimerization of holocystalysin without affecting that of apoenzyme, (iii) while each single mutation is inadequate in significantly altering the extent of monomerization of both apo‐ and holo‐cystalysin, their combination leads to species which remain in a folded monomeric state at a reasonably high concentration in both the apo‐ and holo‐forms. Although L57A/L62A or L57A/Y64*A, even to a different extent, are stimulated to dimer formation in the presence of either unproductive or productive ligands, L57A/L62A/Y64*A remains prevalently monomer at a concentration up to 50 μM. Kinetic analyses show that in this monomeric species the α,β‐eliminase, alanine racemase, and D‐alanine half‐transaminase activities are almost abolished, while the L‐alanine half‐transaminase activity is slightly enhanced when compared with that of wild‐type. The structural basis of the stereospecific transaminase activity displayed by the engineered folded PLP‐bound monomer has been analyzed and discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The first high pH structure of Escherichia coli aspartate transcarbamoylase
Authors: Stieglitz Kimberly A. , Xia Jiarong , Kantrowitz Evan R. 
Published: July 2008

AbstractThe activity and cooperativity of Escherichia coli aspartate transcarbamoylase (ATCase) vary as a function of pH, with a maximum of both parameters at approximately pH 8.3. Here we report the first X‐ray structure of unliganded ATCase at pH 8.5, to establish a structural basis for the observed Bohr effect. The overall conformation of the active site at pH 8.5 more closely resembles the active site of the enzyme in the R‐state structure than other T‐state structures. In the structure of the enzyme at pH 8.5 the 80's loop is closer to its position in R‐state structures. A unique electropositive channel, comprised of residues from the 50's region, is observed in this structure, with Arg54 positioned in the center of the channel. The planar angle between the carbamoyl phosphate and aspartate domains of the catalytic chain is more open at pH 8.5 than in ATCase structures determined at lower pH values. The structure of the enzyme at pH 8.5 also exhibits lengthening of a number of interactions in the interface between the catalytic and regulatory chains, whereas a number of interactions between the two catalytic trimers are shortened. These alterations in the interface between the upper and lower trimers may directly shift the allosteric equilibrium and thus the cooperativity of the enzyme. Alterations in the electropositive environment of the active site and alterations in the position of the catalytic chain domains may be responsible for the enhanced activity of the enzyme at pH 8.5. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Prediction of turn types in protein structure by machine‐learning classifiers
Authors: Meissner Michael , Koch Oliver , Klebe Gerhard , Schneider Gisbert 
Published: July 2008

AbstractWe present machine learning approaches for turn prediction from the amino acid sequence. Different turn classes and types were considered based on a novel turn classification scheme. We trained an unsupervised (self‐organizing map) and two kernel‐based classifiers, namely the support vector machine and a probabilistic neural network. Turn versus non‐turn classification was carried out for turn families containing intramolecular hydrogen bonds and three to six residues. Support vector machine classifiers yielded a Matthews correlation coefficient (mcc) of ∼0.6 and a prediction accuracy of 80%. Probabilistic neural networks were developed for β‐turn type prediction. The method was able to distinguish between five types of β‐turns yielding mcc > 0.5 and at least 80% overall accuracy. We conclude that the proposed new turn classification is distinct and well‐defined, and machine learning classifiers are suited for sequence‐based turn prediction. Their potential for sequence‐based prediction of turn structures is discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Floral attractants for the female soybean looper, Thysanoplusia orichalcea (Lepidoptera: Noctuidae)
Authors: Stringer Lloyd D , El‐Sayed Ashraf M , Cole Lyn M , Manning Lee‐Anne M , Suckling David M 
Published: July 2008

AbstractBACKGROUND: The soybean looper, Thysanoplusia orichalcea (F.), is a polyphagous insect pest of vegetable crops. Indonesian in origin, it has spread to Europe, India, Africa, Australia and New Zealand. The identification of an attractant for female T. orichalcea could enable the development of alternative pest management strategies to those provided by insecticides or sex pheromones, which are often only attractive to males.RESULTS: Traps baited with synthetic lures derived from Canada thistle, Cirsium arvense (L.) Scop., floral volatiles attracted female T. orichalcea. Phenylacetaldehyde, a floral compound attractive to many Lepidoptera and present in C. arvense, was tested alone as an attractant for the soybean looper and caught significantly more female than male T. orichalcea. Trap catch was greatest when phenylacetaldehyde was combined with five prevalent volatiles present in C. arvense headspace collections: 2‐phenylethyl alcohol, methyl salicylate, dimethyl salicylate, benzaldehyde and benzyl alcohol. Twice as many female moths as males were collected.CONCLUSION: Successful trapping of female T. orichalcea in either a lure‐and‐kill or a mass trapping system may offer an effective way to manage its population size. Copyright © 2008 Society of Chemical Industry
Synthesis of 2‐oxoamides based on sulfonamide analogs of γ‐amino acids and their activity on phospholipase A2
Authors: Antonopoulou Georgia , Magrioti Victoria , Stephens Daren , Constantinou‐Kokotou Violetta , Dennis Edward A. , Kokotos George 
Published: July 2008

AbstractA variety of lipophilic 2‐oxoamides containing sulfonamide analogs of γ‐amino acids as well as acyl sulfonamides of γ‐aminobutyric acid were synthesized. Their ability to inhibit intracellular GIVA cPLA2 and GVIA iPLA2 as well as secreted GV sPLA2 was evaluated. The sulfonamide group seems a bioisosteric group suitable to replace the carboxyl group in 2‐oxoamide inhibitors of GVIA cPLA2. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Binding of synthetic fragments of β‐endorphin to nonopioid β‐endorphin receptor
Authors: Navolotskaya Elena V. , Kovalitskaya Yulia A. , Zolotarev Yury A. , Sadovnikov Vladimir B. 
Published: July 2008

AbstractSelective agonist of nonopioid β‐endorphin receptor decapeptide immunorphin (SLTCLVKGFY) was labeled with tritium (the specific activity of 24 Ci/mmol). [3H]Immunorphin was found to bind to nonopioid β‐endorphin receptor of mouse peritoneal macrophages (Kd = 2.0 ± 0.1 nM). The [3H]immunorphin specific binding with macrophages was inhibited by unlabeled β‐endorphin (Ki = 2.9 ± 0.2 nM) and was not inhibited by unlabeled naloxone, α‐endorphin, γ‐endorphin and [Met5]enkephalin (Ki > 10 µM). Thirty fragments of β‐endorphin have been synthesized and their ability to inhibit the [3H]immunorphin specific binding to macrophages was studied. Unlabeled fragment 12–19 (TPLVTLFK, the author's name of the peptide octarphin) was found to be the shortest peptide possessing practically the same inhibitory activity as β‐endorphin (Ki = 3.1 ± 0.3 nM). The peptide octarphin was labeled with tritium (the specific activity of 28 Ci/mmol). [3H]Octarphin was found to bind to macrophages with high affinity (Kd = 2.3 ± 0.2 nM). The specific binding of [3H]octarphin was inhibited by unlabeled immunorphin and β‐endorphin (Ki = 2.4 ± 0.2 and 2.7 ± 0.2 nM, respectively). Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
The structure of S100A11 fragment explains a local structural change induced by phosphorylation
Authors: Kouno Takahide , Mizuguchi Mineyuki , Sakaguchi Masakiyo , Makino Eiichi , Mori Yoshihiro , Shinoda Hiroyuki , Aizawa Tomoyasu , Demura Makoto , Huh Nam‐Ho , Kawano Keiichi 
Published: July 2008

AbstractS100A11 protein is a member of the S100 family containing two EF‐hand motifs. It undergoes phophorylation on residue T10 after cell stimulation such as an increase in Ca2+ concentration. Phosphorylated S100A11 can be recognized by its target protein, nucleolin. Although S100A11 is initially expressed in the cytoplasm, it is transported to the nucleus by the action of nucleolin. In the nucleus, S100A11 suppresses the growth of keratinocytes through p21CIP1/WAF1 activation and induces cell differentiation. Interestingly, the N‐terminal fragment of S100A11 has the same activity as the full‐length protein; i.e. it is phosphorylated in vivo and binds to nucleolin. In addition, this fragment leads to the arrest of cultured keratinocyte growth. We examined the solution structure of this fragment peptide and explored its structural properties before and after phosphorylation. In a trifluoroethanol solution, the peptide adopts the α‐helical structure just as the corresponding region of the full‐length S100A11. Phosphorylation induces a disruption of the N‐capping conformation of the α‐helix, and has a tendency to perturb its surrounding structure. Therefore, the phosphorylated threonine lies in the N‐terminal edge of the α‐helix. This local structural change can reasonably explain why the phosphorylation of a residue that is initially buried in the interior of protein allows it to be recognized by the binding partner. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Interface electronic structures of zinc oxide and metals: First‐principle study
Authors: Kamiya T. , Tajima K. , Nomura K. , Yanagi Hiroshi , Hosono H. 
Published: July 2008

AbstractElectronic structures and carrier transport properties were studied based on ab‐initio calculations for Au/ZnO/Au and Mg/ZnO/Mg two‐probe models. Quantum‐mechanically stable structures were obtained by density functional calculations. Electron transmission spectra and current–voltage characteristics were calculated based on a non‐equilibrium Green function method with the relaxed structures. It was found that the electronic structures of the idealized models were a Schottky contact for the Au/ZnO/Au interface and an ohmic contact for the Mg/ZnO/Mg interface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic structure of oxygen deficient amorphous oxide semiconductor a‐InGaZnO4–x: Optical analyses and first‐principle calculations
Authors: Kamiya Toshio , Nomura Kenji , Hirano Masahiro , Hosono Hideo 
Published: July 2008

AbstractThe cover picture of this issue of physica status solidi (c) has been taken from the article [1]. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interface formation in CdTe solar cells: Nucleation of CdTe on CdS(0001) and (10$ \bar 1 $0)
Authors: Siepchen Bastian , Klein Andreas , Jaegermann Wolfram 
Published: July 2008

AbstractThe growth of CdTe on (0001) and (10$ \bar 1 $0) surfaces of CdS was studied using low energy electron diffraction and photoelectron spectroscopy. The results indicate oriented growth of the CdTe films with a faster nucleation of CdTe on CdS(0001), explaining the preferred (111) orientation of CdTe films on polycrystalline substrates. The faster nucleation on the (0001) surface is attributed to the formation of a stable CdS(0001):Te surface termination, which is identified from surface sensitive Te 4d spectra and a 2√3 × 2√3 surface reconstruction. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using factorial design and multivariate analysis when experimenting in a continuous process
Authors: Vanhatalo Erik , Vännman Kerstin 
Published: July 2008

AbstractThis article discusses the design and analysis of an experiment performed in a continuous process (CP). Three types of iron ore pellets are tested on two levels of a process variable in an experimental blast furnace process, using a full factorial design with replicates. A multivariate approach to the analysis of the experiment in the form of principal component analysis combined with analysis of variance is proposed. The analysis method also considers the split‐plot‐like structure of the experiment. The article exemplifies how a factorial design combined with multivariate analysis can be used to perform product development experiments in a CP. CPs also demand special considerations when planning, performing and analyzing experiments. The article highlights and discusses such issues and considerations, for example, the dynamic characteristic of CPs, a strategy to handle disturbances during experimentation and the need for process control during experimentation. Copyright © 2008 John Wiley & Sons, Ltd.
Evaluating quality measured on a ternary ordinal scale
Authors: Bashkansky Emil , Gadrich Tamar 
Published: July 2008

AbstractThis paper deals with the evaluation of process/product quality measured via a ternary ordinal scale. Recently, a new approach for dealing with ordinal quality variables, based on constructing a quality ladder using rank and dispersion criterion, was proposed. In this method the quality of a given sample is characterized by its relative position on the constructed quality ladder. The present paper proposes a new mechanism for constructing such a quality ladder. This method is called proportion ratio and dispersion (PR&D). The underlying logic, advantage and applications of the proposed method are discussed and demonstrated using software developed by the authors. Copyright © 2008 John Wiley & Sons, Ltd.
Atomic basis sets optimization using the generalized simulated annealing approach: New basis sets for the first row elements
Authors: De Andrade M. D. , Nascimento M. A. C. , Mundim K. C. , Sobrinho A. M. C. , Malbouisson L. A. C. 
Published: July 2008

AbstractAtomic basis sets equivalent to the standard STO‐3G and STO‐6G ones were optimized for the elements of the first row using the generalized simulated annealing (GSA) approach. The atomic energies obtained with the new basis sets are substantially better than the ones obtained with the standard ones. The new basis sets were tested for several diatomic and triatomic molecules, at different levels of calculation. For the molecules at their geometries of equilibrium, the energies obtained with the GSA optimized basis are in general much better than the respective ones obtained with the standard basis. However, for molecules containing hydrogen atoms, the best results, either at the HF or CI level of calculation, are obtained with a combination of the new and the standard bases, which depend on the nature of the other atoms of the molecule. The analysis of the potential energy surfaces for the LiH, BH, and FH molecules showed that the new basis provide a better description of these molecules in all regions of the respective surfaces, although the equilibrium bond distances. The results are quite encouraging and clearly indicate that basis set of DZ and TZ quality better than the standard ones can probably be generated by the GSA approach. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations
Authors: Pickholz Mónica , Fernandes Fraceto Leonardo , de Paula Eneida 
Published: July 2008

AbstractIn this work, we report a 20‐ns constant pressure molecular dynamics simulation of prilocaine (PLC), an amine–amide local anesthetic, in a hydrated liquid crystal bilayer of 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at ∼12 Å from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, |SCD|, compared to neat bilayers, is found, in good agreement with experimental2H‐NMR studies. The decrease in |SCD| induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008