bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poly(arylate‐phosphonate) copolymers with deoxybenzoin in the backbone: Synthesis, characterization, and thermal properties
Authors: Ranganathan T. , Ku Bon‐Cheol , Zilberman Joseph , Beaulieu Michael , Farris Richard J. , Coughlin E. Bryan , Emrick Todd 
Published: August 2007

AbstractDeoxybenzoin‐based copolymers containing various relative ratios of arylate and phosphonate units in the backbone were synthesized by solution polycondensation. These copolymers were characterized by gel permeation chromatography, Fourier Transform infrared spectrometry, and proton, carbon, and phosphorous nuclear magnetic resonance spectroscopy (1H, 13C, and 31P NMR). Pyrolysis combustion flow calorimetry (PCFC) performed on these copolymers revealed their very low heat release capacity, making them attractive for applications in which halogen‐free, low flammability materials are desired. Integration of phosphonate units into the polymer backbone is advantageous for achieving high molecular weight polymers with solution processbility while retaining the low flammability inherent to deoxybenzoin‐based polymers. Char yields greater than 50% and heat release capacities of 40–60 J/g K, were observed for these copolymers by PCFC. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4573–4580, 2007
Crystal structure of the flavin reductase component (HpaC) of 4‐hydroxyphenylacetate 3‐monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity
Authors: Kim Seong‐Hoon , Hisano Tamao , Iwasaki Wakana , Ebihara Akio , Miki Kunio 
Published: August 2007

AbstractThe two‐component enzyme, 4‐hydroxyphenylacetate 3‐monooxygenase, catalyzes the conversion of 4‐hydroxyphenylacetate to 3,4‐dihydroxyphenylacetate. In the overall reaction, the oxygenase component (HpaB) introduces a hydroxyl group into the benzene ring of 4‐hydroxyphenylacetate using molecular oxygen and reduced flavin, while the reductase component (HpaC) provides free reduced flavins for HpaB. The crystal structures of HpaC from Thermus thermophilus HB8 in the ligand‐free form, the FAD‐containing form, and the ternary complex with FAD and NAD+ were determined. In the ligand‐free form, two large grooves are present at the dimer interface, and are occupied by water molecules. A structural analysis of HpaC containing FAD revealed that FAD has a low occupancy, indicating that it is not tightly bound to HpaC. This was further confirmed in flavin dissociation experiments, showing that FAD can be released from HpaC. The structure of the ternary complex revealed that FAD and NAD+ are bound in the groove in the extended and folded conformation, respectively. The nicotinamide ring of NAD+ is sandwiched between the adenine ring of NAD+ and the isoalloxazine ring of FAD. The distance between N5 of the isoalloxazine ring and C4 of the nicotinamide ring is about 3.3 Å, sufficient to permit hydride transfer. The structures of these three states are essentially identical, however, the side chains of several residues show small conformational changes, indicating an induced fit upon binding of NADH. Inactivity with respect to NADPH can be explained as instability of the binding of NADPH with the negatively charged 2′‐phosphate group buried inside the complex, as well as a possible repulsive effect by the dipole of helix α1. A comparison of the binding mode of FAD with that in PheA2 from Bacillus thermoglucosidasius A7, which contains FAD as a prosthetic group, reveals remarkable conformational differences in a less conserved loop region (Gly83–Gly94) involved in the binding of the AMP moiety of FAD. These data suggest that variations in the affinities for FAD in the reductases of the two‐component flavin‐diffusible monooxygenase family may be attributed to difference in the interaction between the AMP moiety of FAD and the less conserved loop region which possibly shows structural divergence. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Molecular dynamics simulations of HIV‐1 protease monomer: Assembly of N‐terminus and C‐terminus into β‐sheet in water solution
Authors: Yan Mao‐Cai , Sha Yu , Wang Jian , Xiong Xu‐Qiong , Ren Jin‐Hong , Cheng Mao‐Sheng 
Published: August 2007

AbstractHIV‐1 protease (HIV‐PR) consists of two identical subunits that are united together through a four‐stranded antiparallel β‐sheet formed of the peptide termini of each monomer. Since the active site exists only in the dimer, a strategy that is attracting more and more attention in inhibitor design and which may overcome the serious drug resistance caused by competitive inhibitors is to block the peptide termini of the monomer, thereby interfering with formation of the active dimer. In the present work, we performed several extensive molecular dynamics (MD) simulations of the HIV‐PR monomer in water to illustrate its solvated conformation and dynamics behavior. We found that the peptide termini usually assembled into β‐sheet after several nanoseconds' simulation, and became much less flexible. This β‐sheet is stabilized by intramolecular interactions and is not easily disaggregated under the present MD simulation conditions. This transformation may be an important transition during the relaxing and equilibrating of the HIV‐PR monomer in aqueous solution, and the terminal β‐sheet may be one of the major conformations of the solvated HIV‐PR monomer termini in water. This work may provide new insights into the dynamics behavior and dimerization mechanism of HIV‐PR, and more significantly, offer a more rational receptor model for the design and discovery of novel dimerization inhibitors than crystalline structures. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A complete library of amino acid alterations at R306 in Streptomyces clavuligerus deacetoxycephalosporin C synthase demonstrates its structural role in the ring‐expansion activity
Authors: Sim Goo Kian , Song Chua Chun , Sim Tiow‐Suan 
Published: August 2007

AbstractIn a previous study, the conserved arginine residue at position 306 of Streptomyces clavuligerus deacetoxycephalsoporin C synthase (scDAOCS), when mutated to leucine, resulted in 191% increase in converting ampicillin to its expanded cephalosporin moiety compared with that of the wild‐type enzyme. However, the role of this residue in eliciting the improved enzymatic activity is not well understood. In this study, probing the molecular basis of amino acid substitutions at position 306 has underscored its importance for engineering various improvements in the ring expansion activity. Structural modeling using SwissPdbViewer revealed that R306 is surrounded by a hydrophobic cleft formed by residues Y184, L186, W297, I298, and V303. Hence, the improved activity achieved by the R306L mutation was probably because of better hydrophobic packing in this region. To evaluate the role of amino acids at position 306 of scDAOCS and its influence on the molecular status of the enzyme at this locality, alteration to 18 other amino acids was done by site‐directed mutagenesis. The effects of each substitution on the enzyme activity were determined by bioassay using penicillin substrates: ampicillin, penicillin G, phenethicillin, and carbenicillin. Results obtained showed a drastic reduction in enzyme activity when R306 was replaced with charged or polar residues, thus emphasizing the importance of hydrophobic packing around this site. The bioassay results also illustrated that apart from leucine, substitutions to nonpolar residues, isoleucine and methionine, were able to improve the ampicillin conversion activity of scDAOCS by 168 and 113% of the wild‐type enzyme activity, respectively. Similar trend of effects from each mutation was also observed for penicillin G, phenethicillin, and carbenicillin conversions. The enhanced enzyme activities were supported by spectrophotometric assay indicating that all these mutants have lower Km values (R306L: 1.09 mM; R306I: 2.64 mM; R306M: 5.68 mM) than the wild‐type enzyme (8.33 mM), resulting in improvement in the enzyme's substrate binding affinity. Hence, this mutational study of amino acids situated at 306 of scDAOCS has provided a better understanding of the significance of specific amino acid residues at this position which can improve its ring‐expansion activity when given a plethora of β‐lactam substrates to generate corresponding, possibly new, cephalosporins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Membrane‐bound structure and energetics of α‐synuclein
Authors: Mihajlovic Maja , Lazaridis Themis 
Published: August 2007

AbstractAggregation and fibrillation of α‐synuclein bound to membranes are believed to be involved in Parkinson's and other neurodegenerative diseases. On SDS micelles, the N‐terminus of α‐synuclein forms two curved helices linked by a short loop. However, its structure on lipid bilayers has not been experimentally resolved. Using MD simulations with an implicit membrane model we show here that, on a planar mixed membrane, the truncated α‐synuclein (residues 1–95) forms a bent helix. Bending of the helix is not due to the protein sequence or membrane binding, but to collective motions of the long helix. The backbone of the helix is ∼2.5 Å above the membrane surface, with some residues partially inserted in the membrane core. The helix periodicity is 11/3 (11 residues complete three full turns) as opposed to 18/5 periodicity of an ideal α‐helix, with hydrophobic residues towards the membrane, negatively charged residues towards the solvent and lysines on the polar/nonpolar interface. A series of threonines, which are characteristic for α‐synuclein and perhaps a phosphorylation site, is also located at the hydrophobic/hydrophilic interface with their side chain often hydrogen bonded to the main‐chain atom. The calculations show that the energy penalty for change in periodicity from the 18/5 to 11/3 on the anionic membrane is overcome by favorable solvation energy. The binding of truncated α‐synuclein to membranes is weak. It prefers anionic membranes but it also binds marginally to a neutral membrane, via its C‐terminus. Dimerization of helical monomers on the mixed membrane is energetically favorable. However, it slightly interferes with membrane binding. This might promote lateral diffusion of the protein on the membrane surface and facilitate assembly of oligomers that precede fibrillation. Proteins 2008. © 2007 Wiley‐Liss, Inc.
The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge
Authors: Petraglio Gabriele , Bartolini Manuela , Branduardi Davide , Andrisano Vincenza , Recanatini Maurizio , Gervasio Francesco Luigi , Cavalli Andrea , Parrinello Michele 
Published: August 2007

AbstractAlkali cations can affect the catalytic efficiency of enzymes. This is particularly true when dealing with enzymes whose substrate bears a formal positive charge. Computational and biochemical approaches have been combined to shed light on the atomic aspects of the role of Li+, Na+, and K+ on human acetylcholinesterase (hAChE) ligand binding. In this respect, molecular dynamics simulations and our recently developed metadynamics method were applied to study the entrance of the three cations in the gorge of hAChE, and their effect on the dynamical motion of a ligand (tetramethylammonium) from the bulk of the solvent into the deep narrow enzyme gorge. Furthermore, in order to support the theoretical results, KM and kcat for the acetylcholine hydrolysis in the presence of the three cations were evaluated by using an approach based on the Ellman's method. The combination of computational and biochemical experiments clearly showed that Li+, Na+, and K+ may influence the ligand binding at the hAChE gorge. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Surface recognition elements of membrane protein oligomerization
Authors: Rath Arianna , Deber Charles M. 
Published: August 2007

AbstractAlthough certain membrane proteins are functional as monomeric polypeptides, others must assemble into oligomers to carry out their biological roles. High‐resolution membrane protein structures provide a valuable resource for examining the sequence features that facilitate—or preclude—assembly of membrane protein monomers into multimeric structures. Here we have utilized a data set of 28 high‐resolution α‐helical membrane protein structures comprising 32 nonredundant polypeptides to address this issue. The lipid‐exposed surfaces of membrane proteins that have reached their fully assembled and functional biological units have been compared with those of the individual subunits that build quaternary structures. Though the overall amino acid composition of each set of surfaces is similar, a key distinction—the distribution of small‐xxx‐small motifs—delineates subunits from membrane proteins that have reached a functioning oligomeric state. Quaternary structure formation may therefore be dictated by small‐xxx‐small motifs that are not satisfied by intrachain contacts. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp‐56: A computational study
Authors: Bjelić Saša , Wieninger Silke , Jelesarov Ilian , Karshikoff Andrey 
Published: August 2007

AbstractThe protein moiety of the Braun's E. coli outer membrane lipoprotein (Lpp‐56) is an attractive object of biophysical investigation in several aspects. It is a homotrimeric, parallel coiled coil, a class of coiled coils whose stability and folding have been studied only occasionally. Lpp‐56 possesses unique structural properties and exhibits extremely low rates of folding and unfolding. It is natural to ask how the specificity of the structure determines the extraordinary physical chemical properties of this protein. Recently, a seemingly controversial data on the stability and unfolding rate of Lpp‐56 have been published (Dragan et al., Biochemistry 2004;43: 14891–14900; Bjelic et al., Biochemistry 2006;45:8931–8939). The unfolding rate constant measured using GdmCl as the denaturing agent, though extremely low, was substantially higher than that obtained on the basis of thermal unfolding. If this large difference arises from the effect of screening of electrostatic interactions induced by GdmCl, electrostatic interactions would appear to be an important factor determining the unusual properties of Lpp‐56. We present here a computational analysis of the electrostatic properties of Lpp‐56 combining molecular dynamics simulations and continuum pK calculations. The pH‐dependence of the unfolding free energy is predicted in good agreement with the experimental data: the change in ΔG between pH 3 and pH 7 is ∼60 kJ mol−1. The results suggest that the difference in the stability of the protein observed using different experimental methods is mainly because of the effect of the reduction of electrostatic interactions when the salt (GdmCl) concentration increases. We also find that the occupancy of the interhelical salt bridges is unusually high. We hypothesize that electrostatic interactions, and the interhelical salt bridges in particular, are an important factor determining the low unfolding rate of Lpp‐56. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data
Authors: Zhu Fujiang , Kapitan Josef , Tranter George E. , Pudney Paul D. A. , Isaacs Neil W. , Hecht Lutz , Barron Laurence D. 
Published: August 2007

AbstractVibrational Raman optical activity (ROA), measured as a small difference in the intensity of Raman scattering from chiral molecules in right‐ and left‐circularly polarized incident light, or as the intensity of a small circularly polarized component in the scattered light, is a powerful probe of the aqueous solution structure of proteins. The large number of structure‐sensitive bands in protein ROA spectra makes multivariate analysis techniques such as nonlinear mapping (NLM) especially favorable for determining structural relationships between different proteins. We have previously used NLM to map a large dataset of peptide, protein, and virus ROA spectra into a readily visualizable two‐dimensional space in which points close to or distant from each other, respectively, represent similar or dissimilar structures. As well as folded proteins, our dataset contains ROA spectra from many natively unfolded proteins, proteins containing both folded and unfolded domains, denatured partially structured molten globule and reduced protein states, together with folded proteins containing little or no α‐helix or β‐sheet. In this article, the relative positions of these systems in the NLM plot are used to obtain information about any residual structure that they may contain. The striking differences between the structural propensities of proteins that are unfolded in their native states and those that are unfolded due to denaturation may be responsible for their often very different behavior, especially with regard to aggregation. An ab initio simulation of the Raman and ROA spectra of an alanine oligopeptide in the poly(L‐proline) II‐helical conformation confirms previous suggestions that this conformation is a significant structural element in disordered peptides and natively unfolded proteins. The use of ROA to identify and characterize proteins containing significant amounts of unfolded structure will, inter alia, be valuable in structural genomics/proteomics since unfolded sequences often inhibit crystallization. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Ecological network analysis: an application to the evaluation of effects of pesticide use in an agricultural environment
Authors: Andras Peter , Gwyther Robert , Madalinski Agnes A , Lynden Steven J , Andras Alina , Young Malcolm P 
Published: August 2007

AbstractEcological network analysis is used to evaluate the impact of pesticide use on ecological systems in the context of agricultural farmland environments. The aim is to provide support for the design of effective and minimally damaging pest control strategies. The ecological network analysis can identify species that are important to the integrity of the ecological network. The methodology can be used to monitor the impact of shifts in terms of types of pesticide used on the ecological system. The authors' intention is to use this methodology to provide supporting evidence for the UK Voluntary Initiative programme aimed at convincing farmers voluntarily to make improved choices in the use of a wide range of pesticides. Copyright © 2007 Society of Chemical Industry
Effect of Ca substitution on transport and magnetic properties of double‐layered manganite La1.2Sr1.8Mn2O7
Authors: Reddy Y. S. , Prashanth Kumar V. , Rawat R. , Banerjee A. , Kistaiah P. , Vishnuvardhan Reddy C. 
Published: August 2007

AbstractThe resistivity, magnetoresistance (MR) and magnetization of double‐layered manganite La1.2Sr1.8–x Cax Mn2O7 (0.0 ≤ x ≤ 0.4) are studied to investigate the effect of substitution of Ca2+ for Sr2+ on the transport and magnetic properties. The resistivity data suggest that Ca doping results in the decrease of insulator‐to‐metal transition temperature, TIM. The conduction mechanism above TIM is found to be of Mott variable range hopping type. The highest MR ratios (Δρ /ρ0) of 73% (H = 1.5 T) and 93% (H = 4 T) are observed for x = 0.3 sample at ∼25 K. The variation of MR with temperature and applied magnetic field is discussed. A secondary transition at T * is observed in all the samples, which may be due to the two‐dimensional short‐range ferromagnetic ordering. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic interaction effects in rare‐earth alloys from 2D‐ACAR experiments
Authors: Biasini M. , Rusz J. 
Published: August 2007

AbstractMeasurement of the two dimensional angular correlation of the electron‐positron annihilation radiation (2D‐ACAR) complemented with ab‐initio calculations can provide decisive information about the character of the f‐electrons in rare earth compounds and are the prerequisite to the study of electron correlations. We provide examples of systems where good approximations of the archetype f‐electron localized and f‐electron itinerant behaviours, apply. i) In the case of the antiferromagnetic heavy fermion and superconductor CeIn3 the multisheet Fermi Surface (FS), reconstructed from our measurements in the paramagnetic phase, agrees closely with the predictions of band structure calculations regarding the Ce 4f electrons as fully localized. ii) On the other hand, our studies of the antiferromagnet actinide based UGa3 in the paramagnetic phase, compared with calculations which include the effects due to the non uniform positron density and the electron‐positron correlations, produce a substantial evidence that an unconstrained 5f‐electron itinerant description applies. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparative study of antioxidant properties of wild growing and cultivated Allium species
Authors: Štajner D. , Igić R. , Popović B. M. , Malenčić Dj. 
Published: August 2007

AbstractAllium species are cultivated for the edible bulb, which is used mainly as flavoring in foods. Besides that, they could prevent tumor promotion and some processes that are associated with free radicals, such as cardiovascular diseases and aging. Therefore, different Allium species, both cultivated (Allium nutans L., A. fistulosum L., A. vineale L., A. pskemense B. Fedtsch, A. schoenoprasum L., A. cepa L. and A. sativum L.) and wild (A. flavum L., A. sphaerocephalum L., A. atroviolaceum Boiss, A. vineale L., A. ursinum L., A. scorodoprasum L., A. roseum L. and A. subhirsutum L.), were investigated in order to evaluate the antioxidant properties of their bulbs. This study reports on the results obtained for the bulb antioxidant enzyme activities (superoxide dismutase, catalase, guaiacol peroxidase, glutathione peroxidase), the quantities of non‐enzymatic plant antioxidants (reduced glutathione and total flavonoids), the contents of soluble proteins, vitamin C, carotenoids, chlorophylls a and b, as well as for the quantities of malonyldialdehyde and •OH and O2•− radicals. Copyright © 2007 John Wiley & Sons, Ltd.
Determination of genotoxic, antigenotoxic and cytotoxic potential of the extract from lichen Cetraria aculeata (Schreb.) Fr. in vitro
Authors: Zeytinoglu H. , Incesu Z. , Tuylu B. Ayaz , Turk A. O. , Barutca B. 
Published: August 2007

AbstractNaturally occurring compounds can have protective effects towards mutagens and carcinogens as shown by numerous studies. In the present study, the genotoxic/antigenotoxic activities of the extract from lichen Cetraria aculeata (Schreb.) Fr., which has been identified as an antibacterial agent in former studies, were investigated against known mutagens such as 4‐nitro‐o‐phenylenediamine (4‐NPD) and 2‐aminofluorene (2‐AF) in TA98 and TA100 strains of Salmonella typhimurium in the presence or absence of metabolic activity. Further genotoxicity/antigenotoxicity of the extract against mitomycin C for micronucleus formation was also evaluated in human lymphocytes. The cytotoxic effects of the extract on mammalian cells were investigated in three different cell line types by MTT assay. The results obtained show that the extract of C. aculeata has a significant antigenotoxic activity in bacterial systems, but not in mammalian cells and cytotoxic activity in some mammalian cancer cells. However, it was not mutagenic in all systems. The findings suggest that the lichen extract may have a possible therapeutic potential and therefore this must be further investigated by other multiple in vitro bioassays for the development of therapeutic agents. Copyright © 2007 John Wiley & Sons, Ltd.