bluuebunny/crossref_metadata_2025_split huggingface dataset:
A covalent S‐F heterodimer of leucotoxin reveals molecular plasticity of β‐barrel pore‐forming toxins
Authors: Roblin Pierre , Guillet Valérie , Joubert Olivier , Keller Daniel , Erard Monique , Maveyraud Laurent , Prévost Gilles , Mourey Lionel 
Published: January 2008

AbstractStaphylococcal leucotoxins, leucocidins, and γ‐hemolysins are bicomponent β‐barrel pore‐forming toxins (β‐PFTs). Their production is associated with several clinical diseases. They have cytotoxic activity due to the synergistic action of a class S component and a class F component, which are secreted as water‐soluble monomers and form hetero‐oligomeric transmembrane pores, causing the lysis of susceptible cells. Structural information is currently available for the monomeric S and F proteins and the homoheptamer formed by the related α‐hemolysin. These structures illustrate the start and end points in the mechanistic framework of β‐PFT assembly. Only limited structural data exist for the intermediate stages, including hetero‐oligomeric complexes of leucotoxins. We investigated the protein–protein interactions responsible for maintaining the final bipartite molecular architecture and describe here the high‐resolution crystal structure and low‐resolution solution structure of a site‐specific cross‐linked heterodimer of γ‐hemolysin (HlgA T28C–HlgB N156C), which were solved by X‐ray crystallography and small angle X‐ray scattering, respectively. These structures reveal a molecular plasticity of β‐PFTs, which may facilitate the transition from membrane‐bound monomers to heterodimers. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Folding and dimerization of the ionic peptide EAK 16‐IV
Authors: Yan Zhiqiang , Wang Jun , Wang Wei 
Published: January 2008

AbstractFolding and dimerization of an ionic polyalanine‐based peptide chain (EAK16‐IV) are simulated with nonspecific interactions. It is found that there is a competition between two kinds of structural motifs under different strengths of electrostatic interactions. The dominance of hairpin‐like structures would be realized with a strong electrostatic interaction both thermodynamically and kinetically, showing the importance of the electrostatic interaction on the formation of hairpin‐like structures. Simulations on the dimerization with strong electrostatic interaction are also carried out. It is found that the concentration contributes essentially to the shape of the dimers. These studies demonstrate that the strong interactions and kinetic factors might be important for the ordered amyloid aggregates. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Protein structure modeling indicates hexahistidine‐tag interference with enzyme activity
Authors: Freydank Anna‐Carolin , Brandt Wolfgang , Dräger Birgit 
Published: January 2008

AbstractUnusual kinetic characteristics of tropinone reductase, an enzyme in the family of short chain dehydrogenases, prompted to investigate a possible impact of the hexahistidine affinity tag on catalytic properties. Comparison of enzymes from Solanum dulcamara, Solanaceae, tagged at the N‐terminus or at the C‐terminus revealed that the C‐terminally tagged form was functionally impaired. Protein modeling indicated that the hexahistidine tag attached at the C‐terminus but not at the N‐terminus of the polypeptide can interfere with the active site by steric or electrostatic interactions. In consequence, protein modeling is suggested before enzyme expression with affinity tags to estimate possible interactions of affinity tags with the active center. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structure‐based classification of 45 FK506‐binding proteins
Authors: Somarelli J. A. , Lee S. Y. , Skolnick J. , Herrera R. J. 
Published: January 2008

AbstractThe FK506‐binding proteins (FKBPs) are a unique group of chaperones found in a wide variety of organisms. They perform a number of cellular functions including protein folding, regulation of cytokines, transport of steroid receptor complexes, nucleic acid binding, histone assembly, and modulation of apoptosis. These functions are mediated by specific domains that adopt distinct tertiary conformations. Using the Threading/ASSEmbly/Refinement (TASSER) approach, tertiary structures were predicted for a total of 45 FKBPs in 23 species. These models were compared with previously characterized FKBP solution structures and the predicted structures were employed to identify groups of homologous proteins. The resulting classification may be utilized to infer functional roles of newly discovered FKBPs. The three‐dimensional conformations revealed that this family may have undergone several modifications throughout evolution, including loss of N‐ and C‐terminal regions, duplication of FKBP domains as well as insertions of entire functional motifs. Docking simulations suggest that additional sequence segments outside FKBP domains may modulate the binding affinity of FKBPs to immunosuppressive drugs. The docking models also indicate the presence of a helix‐loop‐helix (HLH) region within a subset of FKBPs, which may be responsible for the interaction between this group of proteins and nucleic acids. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Evolutionary conserved N‐terminal region of human muscle fructose 1,6‐bisphosphatase regulates its activity and the interaction with aldolase
Authors: Gizak Agnieszka , Maciaszczyk Ewa , Dzugaj Andrzej , Eschrich Klaus , Rakus Darek 
Published: January 2008

AbstractN‐terminal residues of muscle fructose 1,6‐bisphosphatase (FBPase) are highly conserved among vertebrates. In this article, we present evidence that the conservation is responsible for the unique properties of the muscle FBPase isozyme: high sensitivity to AMP and Ca2+ inhibition and the high affinity to muscle aldolase, which is a factor desensitizing muscle FBPase toward AMP and Ca2+. The first N‐terminal residue affecting the affinity of muscle FBPase to aldolase is arginine 3. On the other hand, the first residue significantly influencing the kinetics of muscle FBPase is proline 5. Truncation from 5–7 N‐terminal residues of the enzyme not only decreases its affinity to aldolase but also reduces its k‐cat and activation by Mg2+, and desensitizes FBPase to inhibition by AMP and calcium ions. Deletion of the first 10 amino acids of muscle FBPase abolishes cooperativity of Mg2+ activation and results in biphasic inhibition of the enzyme by AMP. Moreover, this truncation lowers affinity of muscle FBPase to aldolase about 14 times, making it resemble the liver isozyme. We suggest that the existence of highly AMP‐sensitive muscle‐like FBPase, activity of which is regulated by metabolite‐dependent interaction with aldolase enables the precise regulation of muscle energy expenditures and might contributed to the evolutionary success of vertebrates. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions
Authors: Nonaka Yasuhiro , Aizawa Tomoyasu , Akieda Daisuke , Yasui Masanori , Watanabe Masahiro , Watanabe Nobuhisa , Tanaka Isao , Kamiya Masakatsu , Mizuguchi Mineyuki , Demura Makoto , Kawano Keiichi 
Published: January 2008

AbstractAsparaginyl deamidation is a common form of nonenzymatic degradation of proteins and peptides. As it introduces a negative charge spontaneously and irreversibly, charge heterogeneity can be accumulated in protein solution during purification, preservation, and experiments. In this study, canine milk lysozyme (CML), a useful model for the study of the molten globule state, exhibited charge heterogeneity after sample purification. Four Asn residues in CML deamidated rapidly under mild conditions: pH 8.0 and 30°C. Other than these residues, one Asn residue, which was stable in the native state, was labile to deamidation in the unfolded state. This suggests that the structural formation around Asn can suppress deamidation. Substitutions of these labile Asn residues to Gln residues prevented deamidation effectively. Because the substitutions did not disrupt the structural formation of the native and molten globule states, they will enable more precise analyses for physical and structural studies. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Probing electric fields in proteins in solution by NMR spectroscopy
Authors: Hass Mathias A. S. , Ringkjøbing Jensen Malene , Led Jens J. 
Published: January 2008

AbstractElectric fields generated in native proteins affect almost every aspect of protein function. We present a method that probes changes in the electric field at specific locations within a protein. The method utilizes the dependence of the amide 1H and 15N NMR chemical shifts on electric charges in proteins. Charges were introduced at different positions in the blue copper protein plastocyanin, by protonation of side chains or by substitution of the metal ion. It is found that the associated chemical shift perturbations (CSPs) stem mainly from long‐range electric field effects caused by the change in the electric charge. It is demonstrated that the CSPs can be used to estimate the dielectric constant at different locations in the protein, estimate the nuclear shielding polarizability, or position charges in proteins. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The size of the intermolecular energy funnel in protein–protein interactions
Authors: Hunjan Jagtar , Tovchigrechko Andrey , Gao Ying , Vakser Ilya A. 
Published: January 2008

AbstractRevealing the fundamental principles of protein interactions is essential for the basic knowledge of molecular processes and designing better predictive tools. Protein docking procedures allow systematic sampling of intermolecular energy landscapes, revealing the distribution of energy basins and their characteristics. A systematic search docking procedure GRAMM‐X was applied to a comprehensive nonredundant database of nonobligate protein–protein complexes to determine the size of the intermolecular energy funnel. The unbound structures were simulated using rotamer library. The procedure generated grid‐based matches, based on a smoothed Lennard‐Jones potential, and minimized them off the grid with the same potential. The minimization generated a distribution of distances, based on a variety of metrics, between the grid‐based and the minimized matches. The metric selected for the analysis, ligand interface RMSD, provided three independent estimates of the funnel size: based on the distribution amplitude for the near‐native matches, deviation from random, and correlation with the energy values. The three methods converge to similar estimates of ∼6–8 Å ligand interface RMSD. The results indicated dependence of the funnel size on the type of the complex (smaller for antigen–antibody, medium for enzyme–inhibitor, and larger for the rest of the complexes) and the funnel size correlation with the size of the interface. Guidelines for the optimal sampling of docking coordinates, based on the funnel size estimates, were explored. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Solution structure of At3g28950 from Arabidopsis thaliana
Authors: de la Cruz Norberto B. , Peterson Francis C. , Volkman Brian F. 
Published: January 2008

AbstractWe determined the solution structure of At3g28950 from A. thaliana, a homolog of At5g39720, whose structure we solved earlier. The secondary structure of the 165‐aa protein consists of a 5‐strand antiparallel β‐barrel domain flanked by two α‐helices and a 2‐strand β‐sheet; an additional free C‐terminal α‐helix extends into solution. Bioinformatic searches and analyses suggest that members of this growing set of structurally related proteins have been recruited to serve a wide variety of functions ranging from γ‐glutamyl cyclotransferase activity to participation in plant responses to chemical and biotic stimuli. Expression of a human homolog is elevated in bladder cancer tissues. Expression patterns for At3g28950 and its Arabidopsis paralogs suggest that each one evolved a different physiological role. The At3g28950 structure was solved as part of a structural genomics effort, and the results demonstrate how such a project can further understanding of genome evolution in addition to sequence–structure and structure–function relationships. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Protein domain annotation with integration of heterogeneous information sources
Authors: Zhao Xing‐Ming , Wang Yong , Chen Luonan , Aihara Kazuyuki 
Published: January 2008

AbstractDomains are structural and functional units of proteins and play an important role in functional genomics. Theoretically, the functions of a protein can be directly inferred if the biological functions of its component domains are determined. Despite the important role that domains play, only a small number of domains have been annotated so far, and few works have been performed to predict the functions of domains. Hence, it is necessary to develop automatic methods for predicting domain functions based on various available data.In this article, two new methods, that is, the threshold‐based classification method and the support vector machines method, are proposed for protein domain function prediction by integrating heterogeneous information sources, including protein–domain mapping features, domain–domain interactions, and domain coexisting features. We show that the integration of heterogeneous information sources improves not only prediction accuracy but also annotation reliability when compared with the methods using only individual information sources. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Phosphorescence of orthopaedic– grade ultra high molecular weight polyethylene
Authors: Chithambo M. L. 
Published: February 2008

AbstractIsothermal luminescence decay curves have been measured from orthopaedic–standard ultra high molecular weight polyethylene between 35 and 70 °C on the rising edge of the main glow peak at 70 °C. Preparatory peak‐shape analysis of the temperature‐resolved glow peak at 70 °C measured at 1 °C s−1 gave a geometrical factor close to 0.5 suggestive of second order kinetics for both the isothermal and thermally stimulated luminescence. The results of analysis of the phosphorescence of transformed monotonic‐to‐peak isothermal decay curves are also second order, as is the conclusion from thermoluminescence glow‐curve de‐convolution. All methods of analysis give an activation energy of about 0.7 eV. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Metal insulator transition in n‐BGaInAs
Authors: Teubert J. , Klar P. J. , Heimbrodt W. 
Published: February 2008

AbstractIsovalent boron is expected to form highly localized states within the conduction band of the GaInAs host which according to most present experimental findings only weakly influences the structure of the extended host states. Here we present magnetotransport (MR) measurements on three n‐type BGaInAs samples doped with silicon which vary in free carrier concentration n from 4.0 × 1016 cm−3 to 7.2 × 1017 cm−3. The three samples differ strongly in their resistivity behaviour. Whereas the sample with the highest n shows metallic behaviour, the transport behaviour of the sample with the lowest n is dominated by hopping transport. The latter is manifested by an exponential increase of the resistivity in the magnetic field. The experimental results are interpreted as a metal insulator transition (MIT). The MIT is found at unexpectedly high carrier concentration compared to GaAs which is attributed to increased alloy disorder in the quarternary alloy mainly due to the localized boron states. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preface: phys. stat. sol. (c) 5/2
Authors: Leitch Andrew 
Published: January 2008

AbstractThe Conference on Photonic Materials held at Kariega Game Reserve from 2–6 May 2007, has been a successor to the successful Conference on Photo‐responsive Materials held at the same venue in 2004. Located in pristine surroundings, the tranquillity and splendour of the reserve, a Big 5 game lodge, in the Eastern Cape Province of South Africa, is beyond doubt awesome, making it a unique venue for this conference. The conference has since grown from 60 delegates representing 12 countries to more than 80 delegates from just over 20 countries, exceeding all expectations both from a representation and an academic standard point of view.The purpose of this meeting was to bring together scientists working on various aspects of photonic materials, to share their latest research results and ideas and to foster links, consequently stimulating this all important field of solid state physics in South Africa and indeed the rest of the world.The academic programme allowed sufficient time for interaction and exchanging of views and covered a wide range of important current topics in the field. The growth and characterization of narrow gap semiconductors for light emitting applications received considerable attention, as did ZnO and GaN and a range of nano materials. An interesting contribution in the photovoltaic section suggested that printed nano particle Si composites may have a role to play in the silicon photovoltaic market. On the social front, delegates were entertained by game drives and boat cruises up the Kariega river to view the majestic fish eagle. Dinner was served around a barn fire in an African Boma, with traditional African dancers entertaining delegates while they enjoyed traditional meals.The academic programme committee members were: Reinhardt Botha and Andrew Leitch (Nelson Mandela Metropolitan University), Margit Härting (University of Cape Town), Jackie Nel (University of Pretoria) and Hendrik Swart (University of the Free State).All papers appearing in these proceedings underwent a strict reviewing process separate from the conference. We express our appreciation to the referees for there diligence in this important task.The conference was organized by the Department of Physics of the Nelson Mandela Metropolitan University (formerly known as the University of Port Elizabeth) under the auspices of the Condensed Matter Physics and Material Science (CMPMS) subgroup of the South African Institute of Physics. It was sponsored by EMF Limited (UK), the African Laser Centre (ALC), DETEK, the Council for Scientific and Industrial Research (CSIR), John Wiley & Sons, Inc. and Cambridge Chemical.
From atomic and molecular orbitals to chemical orbitals
Authors: Clementi Enrico , Corongiu Giorgina 
Published: February 2008

AbstractIn this work, we analyze the molecular orbitals (MO) one‐electron functions of the Hartree‐Fock (HF) model and the atomic orbitals (AO) of the Heitler‐London (HL) and valence bond (VB) models. The complementarity of MO with AO orbitals has been evidenced with the recent Hartree‐Fock‐Heitler‐London model. We propose a new and general one‐electron function, the chemical orbital (CO) and the corresponding determinantal wave function, the chemical orbital wave function, ΨCO. We show that the ΨCO can be decomposed into a specific HF‐HL function with ionic components, designated “adjoined HF‐HL function” and that the HF‐HL, HF, and VB wave functions can be derived from the ΨCO wave function. A single “adjoined HF‐HL function” can realistically represent molecular systems from the united atom, to equilibrium distances, to dissociation; short linear expansions of “adjoined HF‐HL functions” yield accurate nonrelativistic energies. Preliminary test computations with “adjoined HF‐HL functions” are presented for the ground state of the H2 and LiH molecules © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Cooperative use of unmanned sea surface and micro aerial vehicles at Hurricane Wilma
Authors: Murphy Robin R. , Steimle Eric , Griffin Chandler , Cullins Charlie , Hall Mike , Pratt Kevin 
Published: February 2008

AbstractOn Oct. 24, 2005, Hurricane Wilma, a category 5 storm, made landfall at Cape Romano, Florida. Three days later, the Center for Robot‐Assisted Search and Rescue at the University of South Florida deployed an iSENYS helicopter and a prototype unmanned water surface vehicle, AEOS‐1, to survey damage in parts of Marco Island, 14 km from landfall. The effort was the first known use of unmanned sea surface vehicles (USVs) for emergency response and established their suitability for the recovery phase of disaster management by detecting damage to seawalls and piers, locating submerged debris (moorings and handrails), and determining safe lanes for sea navigation. It provides a preliminary domain theory of postdisaster port and littoral inspection with unmanned vehicles for use by the human–robot interaction community. It was also the first known demonstration of the strongly heterogeneous USV–micro aerial vehicle (MAV) team for any domain. The effort identified cooperative UAV–USV strategies and open issues for autonomous operations near structures. The effort showed that the MAV provided a much‐needed external view for situation awareness and provided spotting for areas to be inspected. Concepts of operations for USV damage inspection and USV–MAV cooperation emerged, including a formula for computing the human–robot ratio: Nh = (2 × Nv) + 1, where Nh is the number of humans and Nv is the number of vehicles. The outstanding research issues span three areas: challenges for USVs operating near littoral structures, general issues for USV–MAV cooperation, and new applications. It is expected that the lessons learned will be transferrable to defense and homeland safety and security applications, such as port security, and other phases of emergency response, including rescue. © 2008 Wiley Periodicals, Inc.
Glutathione adsorption from UHV to the liquid phase at various pH on gold and subsequent modification of protein interaction
Authors: Vallée Anne , Humblot Vincent , Méthivier Christophe , Pradier Claire‐Marie 
Published: January 2008

AbstractThis study is part of a project aiming at a better understanding of polypeptide and protein interactions with a metal surface. A tripeptide (the glutathione, or GSH) was deposited, under ultra high vacuum, on Au (111). From reflection–absorption infrared spectra (RAIRS), GSH was adsorbed in its zwiterrionic form which corresponds to the solid state one. GSH was also adsorbed on Au (111) surfaces from solutions at different pH values. These GSH so‐formed monolayers were then tested to anchor a well‐known protein, the bovine serum albumin (BSA); an effect of the structure and charge of the GSH layers on the protein adsorptions was made clear.The combination of XPS and polarisation‐modulation (PM)‐RAIRS results showed that the adsorbed GSH is in an identical form as that in solution (ionic state and conformation). When BSA is adsorbed from PBS solutions on the various layers of GSH the anionic or cationic nature of the GSH layer does not influence the adsorption of protein. On the other hand, adsorption of BSA in pure water is strongly favoured on cationic layers. Copyright © 2008 John Wiley & Sons, Ltd.