bluuebunny/crossref_metadata_2025_split huggingface dataset:
Normal‐mode‐based modeling of allosteric couplings that underlie cyclic conformational transition in F1 ATPase
Authors: Zheng Wenjun 
Published: February 2009

AbstractF1 ATPase, a rotary motor comprised of a central stalk (γ subunit) enclosed by three α and β subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse‐grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F1 ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of γ subunit via various domain motions in α3β3 hexamer (including intrasubunit hinge‐bending motions in β subunits and intersubunit rigid‐body rotations between adjacent α and β subunits). To this end, we have used a normal‐mode‐based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of γ subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and γ‐truncated F1 ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra‐ and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: Importance of the interactions between the D residue and integrin
Authors: Chen Chiu‐Yueh , Shiu Jia‐Hau , Hsieh Yao‐Husn , Liu Yu‐Chen , Chen Yen‐Chin , Chen Yi‐Chun , Jeng Wen‐Yih , Tang Ming‐Jer , Lo Szecheng J. , Chuang Woei‐Jer 
Published: February 2009

AbstractRhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin‐binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a KI of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a KI of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three two‐stranded antiparallel β‐sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four‐residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R2 value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 Å was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutant‐integrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD‐containing ligands and integrin are important for their binding. Proteins 2009. © 2009 Wiley‐Liss, Inc.
A coarse‐grained potential for fold recognition and molecular dynamics simulations of proteins
Authors: Májek Peter , Elber Ron 
Published: February 2009

AbstractA coarse‐grained potential for protein simulations and fold ranking is presented. The potential is based on a two‐point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and resampling are in the spirit of the generalized ensemble approach. No native structure information (e.g., secondary structure) is used in the calculation of the potential or in the simulation of a particular protein. The potential is subject to two tests as follows: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set) and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than 20 nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Multiscale characterization of protein conformational ensembles
Authors: Shehu Amarda , Kavraki Lydia E. , Clementi Cecilia 
Published: February 2009

AbstractWe propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse‐grained level of detail, then narrowing a refined exploration to selected low‐energy regions. The coarse‐grained exploration periodically adds all‐atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all‐atom detail. The second stage reconstructs selected low‐energy coarse‐grained conformations in all‐atom detail. A low‐dimensional energy landscape associated with all‐atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all‐atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Membrane insertion of the FYVE domain is modulated by pH
Authors: He Ju , Vora Mohsin , Haney Rachel M. , Filonov Grigory S. , Musselman Catherine A. , Burd Christopher G. , Kutateladze Andrei G. , Verkhusha Vladislav V. , Stahelin Robert V. , Kutateladze Tatiana G. 
Published: February 2009

AbstractThe FYVE domain associates with phosphatidylinositol 3‐phosphate [PtdIns(3)P] in membranes of early endosomes and penetrates bilayers. Here, we detail principles of membrane anchoring and show that the FYVE domain insertion into PtdIns(3)P‐enriched membranes and membrane‐mimetics is substantially increased in acidic conditions. The EEA1 FYVE domain binds to POPC/POPE/PtdIns(3)P vesicles with a Kd of 49 nM at pH 6.0, however associates ∼24 fold weaker at pH 8.0. The decrease in the affinity is primarily due to much faster dissociation of the protein from the bilayers in basic media. Lowering the pH enhances the interaction of the Hrs, RUFY1, Vps27p and WDFY1 FYVE domains with PtdIns(3)P‐containing membranes in vitro and in vivo, indicating that pH‐dependency is a general function of the FYVE finger family. The PtdIns(3)P binding and membrane insertion of the FYVE domain is modulated by the two adjacent His residues of the R(R/K)HHCRXCG signature motif. Mutation of either His residue abolishes the pH‐sensitivity. Both protonation of the His residues and nonspecific electrostatic contacts stabilize the FYVE domain in the lipid‐bound form, promoting its penetration and increasing the membrane residence time. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Multiple solvent crystal structures of ribonuclease A: An assessment of the method
Authors: Dechene Michelle , Wink Glenna , Smith Mychal , Swartz Paul , Mattos Carla 
Published: February 2009

AbstractThe multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6‐hexanediol, 70% isopropanol, 50% R,S,R‐bisfuran alcohol, 70% t‐butanol, 50% trifluoroethanol, or 1.0M trimethylamine‐N‐oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Graphical models of protein–protein interaction specificity from correlated mutations and interaction data
Authors: Thomas John , Ramakrishnan Naren , Bailey‐Kellogg Chris 
Published: February 2009

AbstractProtein–protein interactions are mediated by complementary amino acids defining complementary surfaces. Typically not all members of a family of related proteins interact equally well with all members of a partner family; thus analysis of the sequence record can reveal the complementary amino acid partners that confer interaction specificity. This article develops methods for learning and using probabilistic graphical models of such residue “cross‐coupling” constraints between interacting protein families, based on multiple sequence alignments and information about which pairs of proteins are known to interact. Our models generalize traditional consensus sequence binding motifs, and provide a probabilistic semantics enabling sound evaluation of the plausibility of new possible interactions. Furthermore, predictions made by the models can be explained in terms of the underlying residue interactions. Our approach supports different levels of prior knowledge regarding interactions, including both one‐to‐one (e.g., pairs of proteins from the same organism) and many‐to‐many (e.g., experimentally identified interactions), and we present a technique to account for possible bias in the represented interactions. We apply our approach in studies of PDZ domains and their ligands, fundamental building blocks in a number of protein assemblies. Our algorithms are able to identify biologically interesting cross‐coupling constraints, to successfully identify known interactions, and to make explainable predictions about novel interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Inverse‐electron‐demand Diels‐Alder reaction as a highly efficient chemoselective ligation procedure: Synthesis and function of a BioShuttle for temozolomide transport into prostate cancer cells
Authors: Pipkorn Rüdiger , Waldeck Waldemar , Didinger Bernd , Koch Mario , Mueller Gabriele , Wiessler Manfred , Braun Klaus 
Published: February 2009

AbstractHormone‐refractory prostate cancer (HRPC), insensitive to most cytostatic interventions, features low response rates and bad prognosis. Studies with HRPC treated with temozolomide (TMZ) showed a poor response and the results were discouraging. Therefore, TMZ has been considered to be ineffective for the treatment of patients with symptomatic and progressive HRPC. A solution to this problem is demonstrated in this study by combining proper solid‐phase peptide synthesis and a chemoselective new ‘click’ chemistry based on the Diels–Alder reaction with ‘inverse‐electron‐demand’ (DARinv) for the construction of a highly efficient TMZ‐BioShuttle in which TMZ is ligated to transporter and subcellular address molecules. The transport to the targeted nuclei resulted in much higher efficiency and better pharmacological effects. The reformulation of TMZ to TMZ‐BioShuttle achieved higher in vitro killing of prostate cancer cells. Accordingly, the potential of TMZ for the treatment of prostate tumors was dramatically enhanced even in a tenfold lower concentration than applied normally. This TMZ‐BioShuttle may be well suited for combining chemotherapy with other cytostatic agents or radiation therapy. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Investigation of the synthetic route to pepstatin analogues by SPPS using O‐protected and O‐unprotected statine as building blocks
Authors: Cadicamo Cosimo D. , Asante Vivian , Abu Ammar Morhaf , Borelli Claudia , Korting Hans C. , Koksch Beate 
Published: February 2009

AbstractThe synthetic route to pepstatin derivatives by a solid phase peptide synthesis using either O‐protected or O‐unprotected statine as a building block has been investigated. Statine was prepared according to a modified literature procedure, whereas protection of its 3‐hydroxyl moiety using tert‐butyldimethylsilylchloride (TBSCl) provided the novel O‐TBS‐protected statine building block. The O‐tert‐butyldimethylsilyl (TBS)‐protected statine approach provides an improved synthetic strategy for the preparation of statine‐containing peptides as demonstrated by the synthesis of the pepstatin analogue iva‐Val‐Leu‐Sta‐Ala‐Sta. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Production and isotope labeling of antimicrobial peptides in Escherichia coli by means of a novel fusion partner that enables high‐yield insoluble expression and fast purification
Authors: Vidovic Verica , Prongidi‐Fix Lydia , Bechinger Burkhard , Werten Sebastiaan 
Published: February 2009

AbstractA method is presented that allows efficient production of antimicrobial peptides in bacteria by means of fusion to the histone fold domain of the human transcription factor TAF12. This small fusion partner drives high‐level expression of peptides and leads to their accumulation in an entirely insoluble form, thereby eliminating toxicity to the host. Using the antimicrobial peptide LAH4 as an example, we demonstrate that neither affinity purification of the TAF12 fusion protein nor initial solubilization of inclusion bodies in denaturing buffers is required. Instead, crude insoluble material from bacteria is directly dissolved in formic acid for immediate release of the peptide through chemical cleavage at a unique Asp‐Pro site. This is followed by purification to homogeneity in a single chromatographic step. Because of the elevated expression levels of the histone fold domain and its small size (8 kDa), this straightforward purification scheme produces yields in excess of 10 mg active peptide per liter of culture. We demonstrate that TAF12 fusion allows expression of a wide range of antimicrobial peptides as well as efficient isotope labeling for NMR studies. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Synthesis of hepcidin derivatives in order to develop standards for immune adsorption method
Authors: Balogh Ádám , Horváti Kata , Mező Gábor , Derzbach László , Szebeni Beáta , Nagy Lajos , Prechl József , Vásárhelyi Barna , Hudecz Ferenc , Bősze Szilvia 
Published: February 2009

AbstractMeCN, acetonitrile; ECL, enhanced chemiluminescence; EDT, 1,2‐ethanedithiole; HEPC12‐A, rabbit anti‐human hepcidin IgG, affinity purified; HEPC13‐A, rabbit anti‐mouse/human hepcidin IgG, affinity purified; HEPC61‐P, human hepcidin‐25 control/blocking synthetic peptide; HRP, horseradish peroxidase; IL‐6, interleukin‐6; KLH, keyhole limpet hemocyanin; LEAP, liver‐expressed antimicrobial peptide; NEM, N‐ethylmaleimide; NMP, N‐methyl‐pirrolidone; PBS, phosphate buffered saline; PVDF, polyvinylidene difluoride; SELDI‐TOF‐MS, surface‐enhanced laser desorption ionization–time‐of‐flight mass spectrometry; TMB, tetramethylbenzidin; TNF‐α, tumor necrosis factor‐α Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Stratified structure of anodically formed mesoporous silica
Authors: Chazalviel Jean‐Noël , Cortès Robert , Maroun Fouad , Ozanam François 
Published: February 2009

AbstractFilms of mesoporous silica are formed on silicon single crystal by high‐potential anodisation in neutral fluoride electrolyte. The films formed at 7–15 V potential exhibit a bright coloured aspect, characteristic of thin films of submicrometer thickness with flat parallel surfaces. SEM examination of cleaved profiles and X‐ray reflectivity curves point to a stratified structure of these films on the nanometric scale. The stacking period, on the order of 10 nm, is an increasing function of the preparation potential. This structure is clearly related to the well‐known oscillatory electrochemical behaviour observed above 3 V potential in the silicon/acidic‐fluoride‐electrolyte system. These observations confirm the idea that this oscillatory behaviour is accompanied by significant changes in the oxide morphology, namely a modulation of the porosity. The surviving of this oscillatory behaviour even though the interface is buried below a stack of several tens of oxide layers is a challenging observation for the theoretical modelling of the oscillation mechanism. We propose that periodic cracking of the inner oxide film may originate from a tensile stress due to electrochemically‐induced desiccation near the silicon/oxide interface. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photo‐electrochemical etching of macro‐pores in silicon with grooves as etch seeds
Authors: Astrova E. V. , Nechitailov A. A. , Tolmachev V. A. , Melnikov V. A. , Perova T. S. 
Published: February 2009

AbstractRole of linear nucleation centres (surface grooves) in formation of macro‐pores has been studied for n‐type Si. It has been found that linear nucleation centres, contrary to the case of point nucleation pits, initiate formation of semi‐regular pore pattern: along the grooves the pores are arranged randomly as a result of self organization process, across the grooves they follow the prescribed period a. The average distance between the pores along a groove line depends on a, and decreases as a increases. At the optimal value of etching current density and seed period a, the distinct pores can merge, thus forming a periodic structure of one‐dimensional photonic crystal. Optical properties of grooved structures with merged pores have been investigated by means of Fourier infrared reflection micro‐spectroscopy in the spectral range from 1.45 μm to 16.5 μm. Reflectance spectra reveal presence of photonic band gaps which positions in the middle IR range are in a good agreement with calculations by transfer matrix method. The fabrication approach developed is promising for application in silicon‐based photonics. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analysis of energy levels of InAs/GaAs self‐assembled quantum dots by using C –V and deep level transient spectroscopy
Authors: Kim Jin Soak , Kim Eun Kyu , Kim Jun Oh , Lee Sang Jun , Noh Sam Kyu 
Published: February 2009

AbstractEnergy levels of InAs/GaAs self‐assembled quantum dot (QD) system were analyzed by capacitance–voltage (C –V) and deep level transient spectroscopy (DLTS) methods. The QD signals were partially separated by DLTS measurement with small bias changing. The activation energies of QD signals were varied from 66 meV to 610 meV by changing of 0.6 V applied bias, which energies are related to the confined energy levels of InAs QDs. Then, the ground states of InAs QDs were considered to be located at 0.61 eV below the conduction band edge of GaAs barrier. In addition, it showed that DLTS signal of QDs are largely affected by their density of energy state. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Two‐colour photocurrent detection technique for coherent control of a single InGaAs/GaAs quantum dot
Authors: Boyle Stephen J. , Ramsay Andrew J. , Kolodka Roman S. , Oliviera Jose B. B. , Liu Hui Yun , Hopkinson Mark , Fox A. Mark , Skolnick Maurice S. 
Published: February 2009

AbstractWe present a two‐colour photocurrent detection method for coherent control of a single InGaAs/GaAs self‐assembled quantum dot. A pulse shaping technique provides a high degree of control over picosecond optical pulses. Rabi rotations on the exciton to biexciton transition are presented, and fine structure beating is detected via time‐resolved measurements. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical probing of spin fluctuations of a single magnetic atom
Authors: Besombes Lucien , Léger Yoan , Bernos Julien , Le‐gall Claire , Boukari Herve , Poizat Jean Philippe , Mariette Henri 
Published: February 2009

AbstractWe analyzed the photoluminescence intermittency generated by a single paramagnetic spin localized in an individual semiconductor quantum dot (QD). The statistics of the photons emitted by the QD reflect the quantum fluctuations of the localized spin. We report photon correlation measurements that reveal unique signatures of these fluctuations. A phenomenological model is proposed to quantitatively describe these observations, allowing a measurement of the spin dynamics of an individual magnetic atom at zero magnetic field. The data demonstrate the existence of a spin relaxation channel arising from a spin‐exchange with individual free carriers surrounding the QD. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth and properties of defect‐free ZnSe nanowires and nanoneedles
Authors: Aichele Thomas , Tribu Adrien , Bougerol Catherine , Kheng Kuntheak , Donatini Fabrice , Dang Le Si , André Régis , Tatarenko Serge 
Published: February 2009

AbstractZnSe nanowires heterostructures were grown by molecular beam epitaxy in the vapour–liquid–solid growth mode assisted by gold catalysts. Size, shape and crystal structure are found to strongly depend on the growth conditions. Both, zinc‐blende and wurtzite crystal structures are observed using transmission electron microscopy. At low growth temperature nanoneedles are formed. For higher growth temperature, the nanowires have a high aspect ratio with sizes of 1–2 μm in length and 20–50 nm in width as observed by scanning electron microscopy. Growing a nanowire on top of the base of a nanoneedle allows us to obtain very narrow structures with a diameter less than 10 nm and a low density of stacking fault defects. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical injection of spin‐polarized electrons into single quantum dots
Authors: Kümmell T. , Arians R. , Huang J. , Wenisch J. , Brunner K. , Bacher G. 
Published: February 2009

AbstractWe demonstrate electrical spin‐injection into a single InAs quantum dot embedded in a GaAs‐based p–i–n diode structure using a diluted magnetic semiconductor (ZnMnSe) as a spin‐source. The spin‐information can be extracted directly by evaluating the polarisation degree of the single quantum dot electroluminescence signal. We obtain a spin‐polarisation up to 100% at T = 5 K that is decreasing with higher temperature. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)