bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining time‐resolved fluorescence with synchronous fluorescence spectroscopy to study bovine serum albumin‐curcumin complex during unfolding and refolding processes
Authors: Barakat Christelle , Patra Digambara 
Published: February 2012

ABSTRACTWe investigated the complex interaction between bovine serum albumin (BSA) and curcumin by combining time‐resolved fluorescence and synchronous fluorescence spectroscopy. The interaction was significant and sensitive to fluorescence lifetime and synchronous fluorescence characteristics. Binding of curcumin significantly shortened the fluorescence lifetime of BSA with a bi‐molecular quenching rate constant of kq = 3.17 × 1012 M‐1s‐1. Denaturation by urea unfolded the protein molecule by quenching the fluorescence lifetime of BSA. The tyrosine synchronous fluorescence spectra were blue shifted whereas the position of tryptophan synchronous fluorescence spectra was red shifted during the unfolding process. However, denaturation of urea had little effect on the synchronous fluorescence peak of tyrosine in curcumin‐BSA complex except in the low concentration range; however, it shifted the peak to the red, indicating that curcumin shifted tryptophan moiety to a more polar environment in the unfolded state. Decreases in the time‐resolved fluorescence lifetime and curcumin‐BSA complex during unfolding were recovered during refolding of BSA by a dilution process, suggesting partial reversibility of the unfolding process for both BSA and curcumin‐BSA complex. Copyright © 2012 John Wiley & Sons, Ltd.
Ab initio protein modeling into CryoEM density maps using EM‐Fold
Authors: Lindert Steffen , Hofmann Tommy , Wötzel Nils , Karakaş Mert , Stewart Phoebe L. , Meiler Jens 
Published: February 2012

AbstractEM‐Fold was used to build models for nine proteins in the maps of GroEL (7.7 Å resolution) and ribosome (6.4 Å resolution) in the ab initio modeling category of the 2010 cryo‐electron microscopy modeling challenge. EM‐Fold assembles predicted secondary structure elements (SSEs) into regions of the density map that were identified to correspond to either α‐helices or β‐strands. The assembly uses a Monte Carlo algorithm where loop closure, density‐SSE length agreement, and strength of connecting density between SSEs are evaluated. Top‐scoring models are refined by translating, rotating, and bending SSEs to yield better agreement with the density map. EM‐Fold produces models that contain backbone atoms within SSEs only. The RMSD values of the models with respect to native range from 2.4 to 3.5 Å for six of the nine proteins. EM‐Fold failed to predict the correct topology in three cases. Subsequently, Rosetta was used to build loops and side chains for the very best scoring models after EM‐Fold refinement. The refinement within Rosetta's force field is driven by a density agreement score that calculates a cross‐correlation between a density map simulated from the model and the experimental density map. All‐atom RMSDs as low as 3.4 Å are achieved in favorable cases. Values above 10.0 Å are observed for two proteins with low overall content of secondary structure and hence particularly complex loop modeling problems. RMSDs over residues in secondary structure elements range from 2.5 to 4.8 Å. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 669–677, 2012.
N‐glycosylation of enhanced aromatic sequons to increase glycoprotein stability
Authors: Price Joshua L. , Culyba Elizabeth K. , Chen Wentao , Murray Amber N. , Hanson Sarah R. , Wong Chi‐Huey , Powers Evan T. , Kelly Jeffery W. 
Published: February 2012

AbstractN‐glycosylation can increase the rate of protein folding, enhance thermodynamic stability, and slow protein unfolding; however, the molecular basis for these effects is incompletely understood. Without clear engineering guidelines, attempts to use N‐glycosylation as an approach for stabilizing proteins have resulted in unpredictable energetic consequences. Here, we review the recent development of three “enhanced aromatic sequons,” which appear to facilitate stabilizing native‐state interactions between Phe, Asn‐GlcNAc and Thr when placed in an appropriate reverse turn context. It has proven to be straightforward to engineer a stabilizing enhanced aromatic sequon into glycosylation‐naïve proteins that have not evolved to optimize specific protein–carbohydrate interactions. Incorporating these enhanced aromatic sequons into appropriate reverse turn types within proteins should enhance the well‐known pharmacokinetic benefits of N‐glycosylation‐based stabilization by lowering the population of protease‐susceptible unfolded and aggregation‐prone misfolded states, thereby making such proteins more useful in research and pharmaceutical applications. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 195–211, 2012.
Effects of Lys2 to Ala2 substitutions on the structure and potency of ω‐conotoxins MVIIA and CVID
Authors: Schroeder Christina I. , Nielsen Katherine J. , Adams Denise A. , Loughnan Marion , Thomas Linda , Alewood Paul F. , Lewis Richard J. , Craik David J. 
Published: February 2012

AbstractLys2 has previously been implicated as a residue important in binding interactions between ω‐conotoxins and the N‐type calcium channel. To further assess the importance of this residue, Lys2 to Ala2 derivatives of ω‐conotoxins MVIIA and CVID were synthesized and their structures and binding potencies determined. A comparison of the 3D structures of the Ala2 mutants with the parent peptides suggest there are significant structural differences brought about by this substitution. In particular, stabilizing interactions between Lys2 and loop 2 of the ω‐conotoxins are removed, leading to greater flexibility in loop 2, which contains Tyr13, a crucial residue for ω‐conotoxin binding to the N‐ and P/Q‐type voltage‐gated calcium channel (VGCC). The significant drop in binding potencies resulting from replacement of Lys2 thus appears to relate more to entropic factors than to any direct interaction of Lys2 with the VGCC. This has significant implications for the development of a pharmacophore binding model for ω‐conotoxins, as removal of Lys2 from consideration suggests that the ω‐conotoxins residues that interact with the N‐type VGCC reside in loop 2 and 4, and thus cover a significantly smaller and more defined area of the surface of ω‐conotoxin than previously thought. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 345–356, 2012.
Efficient Synthesis of C2v‐Symmetrical Pentakisadducts of C60 as Versatile Building Blocks for Fullerene Architectures that Involve a Mixed Octahedral Addition Pattern
Authors: Hörmann Frank , Donaubauer Wolfgang , Hampel Frank , Hirsch Andreas 
Published: February 2012

AbstractWe report here on the selective synthesis of fullerene pentakisadducts 3 with an incomplete octahedral addition pattern by means of mixed [5:1]hexakisadducts 1 that involve an isoxazoline moiety as a protection group. The isoxazoline addend can be cleanly cleaved by irradiation with light. By using this protection–deprotection strategy, a variety of fullerene pentakisadducts 3 were synthesized in 29–44 % overall yield without the need of HPLC purification. This novel photolytic deprotection of 1 can be explained by an initial electron transfer that leads to a biradical, which can easily eliminate the isoxazoline added. The very efficient and straightforward syntheses of the bisfullerene 4 and the globular hexakisadduct 7, each of which involves mixed octahedral addition patterns, clearly demonstrate the advantage of fullerene pentakisadducts 3 as suitable precursors for the construction of highly functional and complex [5:1]hexakisadduct architectures. Complete structural characterization of all new compounds was carried out by MALDI mass spectrometry, UV/Vis, FTIR, 1H NMR and 13C NMR spectroscopy, as well as X‐ray diffraction.
Total Synthesis of Laulimalide: Synthesis of the Northern and Southern Fragments
Authors: Trost Barry M. , Seganish W. Michael , Chung Cheol K. , Amans Dominique 
Published: February 2012

AbstractThe first stage in the development of a synthetic route for the total synthesis of laulimalide (1) is described. Our retrosynthetic analysis envisioned a novel macrocyclization route to the natural product by using a Ru‐catalyzed alkene–alkyne coupling. This would be preceded by an esterification of the C19 hydroxyl group, joining together two equally sized synthons, the northern fragment 7 and the southern fragment 8. Our first generation approach to the northern fragment entailed a key sequential Ru/Pd coupling sequence to assemble the dihydropyran. The key reactions proceeded smoothly, but the inability to achieve a key olefin migration led to the development of an alternative route based on an asymmetric dinuclear Zn‐catalyzed aldol reaction of a hydroxyl acylpyrrole. This key reaction led to the desired diol adduct 66 with excellent syn/anti selectivity (10:1), and allowed for the successful completion of the northern fragment 7. The key step for the synthesis of the southern fragment was a chemoselective Rh‐catalyzed cycloisomerization reaction to form the dihydropyran ring from a diyne precursor. This reaction proved to be selective for the formation of a six‐membered ring, over a seven. The use of an electron‐deficient bidentate phosphine allowed for the reaction to proceed with a reduced catalyst loading.
A Concise Total Synthesis of Deoxyschizandrin and Exploration of Its Antiproliferative Effects and those of Structurally Related Derivatives
Authors: Zheng Shaojun , Aves Sarah J. , Laraia Luca , Galloway Warren R. J. D. , Pike Kurt G. , Wu Wenjun , Spring David R. 
Published: February 2012

AbstractThe natural product deoxyschizandrin has been shown to have a wide range of biological activities. In recent years the therapeutic potential of this compound against cancers has attracted significant interest. Herein we describe a concise de novo total synthesis of deoxyschizandrin based around a double organocuprate oxidation strategy. In addition, we present the results of biological studies exploring the ability of deoxyschizandrin and synthetic precursors lacking the medium ring biaryl unit to inhibit the proliferation of a human cancer cell line. These studies led to the identification of a structurally novel agent with in vitro anticancer activity.
Deconstructing signal transduction pathways that regulate the actin cytoskeleton in dendritic spines
Authors: Penzes Peter , Cahill Michael E. 
Published: February 2012

AbstractDendritic spines are the sites of most excitatory synapses in the central nervous system. Recent studies have shown that spines function independently of each other, and they are currently the smallest known processing units in the brain. Spines exist in an array of morphologies, and spine structure helps dictate synaptic function. Dendritic spines are rich in actin, and actin rearrangements are critical regulators of spine morphology and density. In this review, we discuss the importance of actin in regulating dendritic spine morphogenesis, and discuss the upstream signal transduction pathways that either foster or inhibit actin polymerization. The understanding of actin regulatory pathways is best conceptualized as a hierarchical network in which molecules function in discrete levels defined by their molecular distance to actin. To this end, we focus on several classes of molecules, including guanine nucleotide exchange factors, small GTPases, small GTPase effectors, and actin binding proteins. We discuss how individual proteins in these molecular classes impact spine morphogenesis, and reveal the biochemical interactions in these networks that are responsible for shaping actin polymerization. Finally, we discuss the importance of these actin regulatory pathways in neuropsychiatric disorders. © 2012 Wiley Periodicals, Inc.
Generalized Transition Waves and Their Properties
Authors: Berestycki Henri , Hamel François 
Published: February 2012

AbstractIn this paper, we generalize the usual notions of waves, fronts, and propagation speeds in a very general setting. These new notions, which cover all usual situations, involve uniform limits, with respect to the geodesic distance, to a family of hypersurfaces that are parametrized by time. We prove the existence of new such waves for some time‐dependent reaction‐diffusion equations, as well as general intrinsic properties, some monotonicity properties, and some uniqueness results for almost‐planar fronts. The classification results, which are obtained under some appropriate assumptions, show the robustness of our general definitions. © 2012 Wiley Periodicals, Inc.
Parallel solution of the subset‐sum problem: an empirical study
Authors: Bokhari Saniyah S. 
Published: February 2012

SUMMARYThe subset‐sum problem is a well‐known NP‐complete combinatorial problem that is solvable in pseudo‐polynomial time, that is, time proportional to the number of input objects multiplied by the sum of their sizes. This product defines the size of the dynamic programming table used to solve the problem. We show how this problem can be parallelized on three contemporary architectures, that is, a 128‐processor Cray Extreme Multithreading (XMT) massively multithreaded machine, a 16‐processor IBM x3755 shared memory machine, and a 240‐core NVIDIA FX 5800 graphics processing unit (GPU). We show that it is straightforward to parallelize this algorithm on the Cray XMT primarily because of the word‐level locking that is available on this architecture. For the other two machines, we present an alternating word algorithm that can implement an efficient solution. Our results show that the GPU performs well for problems whose tables fit within the device memory. Because GPUs typically have memories in the order of 10GB, such architectures are best for small problem sizes that have tables of size approximately 1010. The IBM x3755 performs very well on medium‐sized problems that fit within its 64‐GB memory but has poor scalability as the number of processors increases and is unable to sustain performance as the problem size increases. This machine tends to saturate for problem sizes of 1011 bits. The Cray XMT shows very good scaling for large problems and demonstrates sustained performance as the problem size increases. However, this machine has poor scaling for small problem sizes; it performs best for problem sizes of 1012 bits or more. The results in this paper illustrate that the subset‐sum problem can be parallelized well on all three architectures, albeit for different ranges of problem sizes. The performance of these three machines under varying problem sizes show the strengths and weaknesses of the three architectures. Copyright © 2012 John Wiley & Sons, Ltd.
On frequency response and stability of an optical front–end with variable‐gain current amplifier using a bipolar junction transistor translinear loop
Authors: Tadić Nikša , Zogović Milena , Gaberl Wolfgang , Zimmermann Horst 
Published: February 2012

ABSTRACTA comparative analysis of implementations of an optical front–end with variable transimpedance intended for optical storage systems in two different BiCMOS technologies is given in this article. The variable‐gain current amplifier within the optical front–end is designed by using a modified balanced type of the bipolar junction transistors translinear loop. The predictions of the optical front–end mathematical models are confirmed by the measured results. They show that a 0.6‐µm BiCMOS silicon technology implementation with worse bipolar junction transistor parameters (unity‐gain frequency, current gain β, and the Early voltage) gives much better stability than a 0.35‐µm BiCMOS silicon‐germanium technology implementation. As a consequence, the useful measured transimpedance dynamic range of the proposed optical front–end is 17.5 times larger in the 0.6‐µm BiCMOS silicon technology than that in the 0.35‐µm BiCMOS silicon‐germanium technology. Copyright © 2012 John Wiley & Sons, Ltd.
Negative density‐dependent dispersal in the American black bear (Ursus americanus) revealed by noninvasive sampling and genotyping
Authors: Roy Justin , Yannic Glenn , Côté Steeve D. , Bernatchez Louis 
Published: February 2012

AbstractAlthough the dispersal of animals is influenced by a variety of factors, few studies have used a condition‐dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex‐specific dispersal behavior in the American black bear,Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine‐scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male‐biased dispersal pattern in low‐density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine‐scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults.
Identity and relationships of the Arboreal Caatinga among other floristic units of seasonally dry tropical forests (SDTFs) of north‐eastern and Central Brazil
Authors: Santos Rubens M. , Oliveira‐Filho Ary T. , Eisenlohr Pedro V. , Queiroz Luciano P. , Cardoso Domingos B. O. S. , Rodal Maria J. N. 
Published: February 2012

AbstractThe tree species composition of seasonally dry tropical forests (SDTF) in north‐eastern and central Brazil is analyzed to address the following hypotheses: (1) variations in species composition are related to both environment (climate and substrate) and spatial proximity; (2) SDTF floristic units may be recognized based on peculiar composition and environment; and (3) the Arboreal Caatinga, a deciduous forest occurring along the hinterland borders of the Caatinga Domain, is one of these units and its flora is more strongly related to the caatinga vegetation than to outlying forests. The study region is framed by the Brazilian coastline, 50th meridian west and 21st parallel south, including the Caatinga Domain and extensions into the Atlantic Forest and Cerrado Domains. Multivariate and geostatistic analyses were performed on a database containing 16,226 occurrence records of 1332 tree species in 187 georeferenced SDTF areas and respective environmental variables. Tree species composition varied significantly with both environmental variables and spatial proximity. Eight SDTF floristic units were recognized in the region, including the Arboreal Caatinga. In terms of species composition, its tree flora showed a stronger link with that of the Cerrado Dry Forest Enclaves. On the other hand, in terms of species frequency across sample areas, the links were stronger with two other units: Rock Outcrops Caatinga and Agreste and Brejo Dry Forests. There is a role for niche‐based control of tree species composition across the SDTFs of the region determined primarily by the availability of ground water across time and secondarily by the amount of soil mineral nutrients. Spatial proximity also contributes significantly to the floristic cohesion of SDTF units suggesting a highly dispersal‐limited tree flora. These units should be given the status of eco‐regions to help driving the conservation policy regarding the protection of their biodiversity.
Two Environmentally Friendly Energetic Compounds, [Mn(AZT)4(H2O)2](PA)2·4H2O and [Co(AZT)2(H2O)4](PA)2, Based on 3‐Azido‐1,2,4‐triazole (AZT) and Picrate (PA)
Authors: Wu Bi‐Dong , Zhang Jian‐Guo , Zhang Tong‐Lai , Yang Li , Zhou Zun‐Ning 
Published: February 2012

AbstractTwo multiligand coordination compounds, [Mn(AZT)4(H2O)2](PA)2·4H2O (1) and [Co(AZT)2(H2O)4](PA)2 (2), were synthesized with 3‐azido‐1,2,4‐triazole (AZT) as a ligand and picrate (PA) as a counteranion and characterized by elemental analysis and FTIR spectroscopy. The crystal structures were determined by single‐crystal X‐ray diffraction. The results show that the crystals of 1 and 2 have a triclinic space group (P$\bar {1}$) and orthorhombic space group (Pbca), respectively. Moreover, 1 and 2 have distorted octahedral structures. Their thermal decomposition mechanisms were investigated by differential scanning calorimetry and thermogravimetric analysis. The experimental data showed that the energies of combustion were approximately equal to the energies of combustion of 1,3,5‐trinitro‐1,3,5‐triazacyclohexane (RDX) and 1,3,5,7‐tetranitro‐1,3,5,7‐tetraazocane (HMX). The nonisothermal kinetic parameters were studied by applying the methods of Kissinger and Ozawa. The sensitivity properties showed that 1 and 2 had a higher flame sensitivity than 2,4,6‐trinitrotoluene, RDX, and HMX.
A Facile Approach for Transferring PbS Colloidal Photonic Structures into Alkanol Solutions and Composite Solid Films
Authors: Li Chunguang , Bai Tianyu , Li Tao , Li Feifei , Dong Wenjun , Shi Zhan , Feng Shouhua 
Published: February 2012

AbstractVisible‐light‐responsive photonic structures have been prepared in alcohol solvents by using silica‐modified PbS colloidal nanocrystal clusters (CNCs) as building blocks. Further modification of the PbS CNCs with a coating of silica allowed the dispersion of the particles into nonaqueous solutions. Repulsive electrostatic and solvation forces contribute to the self‐assembly of the PbS@SiO2 spheres. The core–shell particles have optical properties similar to those of CNCs, and they can also be assembled into close‐packing films through simple drop‐casting on silicon substrates. Embedding droplets of such a PbS@SiO2 colloidal solution in a polymer matrix produced solid composite materials with visible‐light‐responsive optical properties with potential applications as sensors and optical switches.
Complex‐Induced Proximity Effect in the Regioselective Lithiation of Pyridine Derivatives
Authors: Dhau Jaspreet S. , Singh Amritpal , Kasetti Yoganjaneyulu , Bharatam P. V. 
Published: February 2012

AbstractThe regioselective ring lithiation of BF3‐complexed 3‐picoline (1a), 3,4‐lutidine (1b), and 3,5‐lutidine (1c) was studied. The dilithiation of 1a, 1b, and 1c was also investigated to experimentally explore the relative preference of the sites on the substituted pyridine ring for lithiation. The role of the complex‐induced proximity effect (CIPE) for inducing lithiation in these moieties was investigated using both experimental and computational studies.
Regioselective Photochemical C–OMe Bond Formation Initiated by One‐Electron Transfer and N–OMe Bond Fragmentation in Electron Donor–Acceptor Systems
Authors: Collado Daniel , Perez‐Inestrosa Ezequiel 
Published: February 2012

AbstractCompounds that integrate electron donor–acceptor subunits with N‐methoxyisoquinolinium as acceptors and substituted (methoxy)benzenes as donors were synthesized and their luminescent and photochemical properties studied. Photolysis yielded the corresponding photomethoxylation products in a two‐step process that involves N–OMe bond scission followed by C–OMe bond formation. Homolysis of the N–OMe bond restores the aromatic isoquinoline nucleus and produces a methoxy radical that can couple to the required ring carbon atom in the benzene cation radical to give the products in a regioselective process controlled by the spin density of the cation radical. This photoprocess involves two different pathways: methoxylation of the acceptor (intracomponent methoxylation) or the donor (intercomponent metoxylation). Both methoxy‐transfer pathways are controlled by the donoating ability (redox potential) of the donor subunit, consistent with the emission observed upon excitation of the charge‐transfer state in systems that undergo intermethoxylation.