bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface‐enhanced Raman difference between bombesin and its modified analogues on the colloidal and electrochemically roughen silver surfaces
Authors: Podstawka Edyta , Ozaki Yukihiro 
Published: May 2008

AbstractIn this article, surface‐enhanced Raman scattering (SERS) spectra of bombesin (BN) and its six modified analogues ([D‐Phe12]BN, [Tyr4]BN, [Tyr4,D‐Phe12]BN, [D‐Phe12,Leu14]BN, [Leu13‐®‐Leu14]BN, and [Lys3]BN) on a colloidal silver surface are reported and compared with SERS spectra of these species immobilized onto an ellectrochemically roughen silver electrode. Changes in enhancement and wavenumber of proper bands upon adsorption on different silver surfaces are consistent with BN and its analogues adsorption primarily through Trp8. Slightly different adsorption states of these molecules are observed depending upon natural amino acids substitution. For example, the indole ring in all the peptides interacts with silver nanoparticles in a edge‐on orientation. It is additionally coordinated to the silver through the N1H bond for all the peptides, except [Phe12]BN. This is in contrary to the results obtained for the silver roughen electrode that show direct but not strong N1H/Ag interaction for all peptides except [D‐Phe12,Leu14]BN and [Leu13‐®‐Leu14]BN. For BN only CO is not involved in the chemical coordination with the colloidal surface. [Lys3]BN and BN also adsorb with the CN bond of NH2 group normal and horizontal, respectively, to the colloidal surface, whereas CNH2 in other peptides is tilted to this surface. Also, the Trp8 CH2 moiety of only [Tyr4]BN, [Lys3]BN, and [Tyr4,D‐Phe12]BN coordinates to Ag, whereas the Phe12 ring of [Phe12]BN, [Tyr4,D‐Phe12]BN, and [D‐Phe12,Leu14]BN assists in the peptides binding only on the colloidal silver. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 807–819, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
NMR structure of biosynthetic engineered human insulin monomer B31Lys‐B32Arg in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer
Authors: Bocian Wojciech , Borowicz Piotr , Mikołajczyk Jerzy , Sitkowski Jerzy , Tarnowska Anna , Bednarek Elżbieta , Głąbski Tadeusz , Tejchman‐Małecka Bożena , Bogiel Monika , Kozerski Lech 
Published: May 2008

AbstractA solution NMR‐derived structure of a new long ‐acting, B31Lys‐B32Arg (LysArg), engineered human insulin monomer, in H2O/CD3CN, 65/35 vol %, pH 3.6, is presented and compared with the available X‐ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55–64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1–3 mM. The presence of long‐range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55–64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 820–830, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Complexation of β‐lactam antibiotic drug carbenicillin to bovine serum albumin: Energetics and conformational studies
Authors: Thoppil Anu A. , Sharma Ruchika , Kishore Nand 
Published: May 2008

AbstractBinding of the antibiotic drug carbenicillin to bovine serum albumin (BSA) has been studied using isothermal titration calorimetry (ITC) in combination with fluorescence and circular dichroism (CD) spectroscopies. The thermodynamic parameters of binding have been evaluated as a function of temperature, ionic strength, and in the presence of anionic, cationic and nonionic surfactants, tetrabutylammonium bromide, and sucrose. The values of van't Hoff enthalpy do not agree with the calorimetric enthalpy indicating conformational changes in the protein upon drug binding. These observations are supported by the intrinsic fluorescence and CD spectroscopic measurements. A reduction in the binding affinity of carbenicillin to BSA is observed with increase in ionic strength of the solution, thereby suggesting, prevailing of electrostatic interactions in the binding process. The involvement of hydrophobic interactions in the binding of the drug to the protein is also indicated by a slight reduction in binding constant in the presence of tetrabutylammonium bromide. The experiments in the presence of sucrose suggest that hydrogen bonding is perhaps not dominant in the binding. The anionic surfactant sodium dodecyl sulphate (SDS) is observed to completely interfere in the ionic interactions in addition to its partial denaturing capacity. However, the presence of cationic surfactant hexadecyl trimethylammonium bromide (HTAB) and nonionic surfactant Triton‐X 100 induce a slight reduction in the values of binding affinity. These calorimetric and spectroscopic results, provide quantitative information on the binding of carbenicillin to BSA and suggests that the binding is dominated by electrostatic interactions with contribution from hydrophobic interactions. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 831–840, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Determination of the secondary structure of proteins in different environments by FTIR‐ATR spectroscopy and PLS regression
Authors: Wang Yeqiu , Boysen Reinhard I. , Wood Bayden R. , Kansiz Mustafa , McNaughton Don , Hearn Milton T. W. 
Published: May 2008

AbstractThe secondary structures of proteins (α‐helical, β‐sheet, β‐turn, and random coil) in the solid state and when bound to polymer beads, containing immobilized phenyl and butyl ligands such as those as commonly employed in hydrophobic interaction chromatography, have been investigated using FTIR‐ATR spectroscopy and partial least squares (PLS) methods. Proteins with known structural features were used as models, including 12 proteins in the solid state and 7 proteins adsorbed onto the hydrophobic surfaces. A strong PLS correlation was achieved between predictions derived from the experimental data for 4 proteins adsorbed onto the phenyl‐modified beads and reference data obtained from the X‐ray crystallographic structures with r2 values of 0.9974, 0.9864, 0.9924, and 0.9743 for α‐helical, β‐sheet, β‐turn, and random coiled structures, respectively. On the other hand, proteins adsorbed onto the butyl sorbent underwent greater secondary structural changes compared to the phenyl sorbent as evidenced from the poorer PLS r2 values (r2 are 0.9658, 0.9106, 0.9571, and 0.9340). The results thus indicate that the secondary structures for these proteins were more affected by the butyl sorbent, whereas the secondary structure remains relatively unchanged for the proteins adsorbed onto the phenyl sorbent. This study has important ramifications for understanding the nature of protein secondary structural changes following adsorption onto hydrophobic sorbent surfaces. This knowledge could also enable the development of useful protocols for enhancing the chromatographic purification of proteins in their native bioactive states. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 895–905, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Differences in residual lignin properties between Betula verrucosa and Eucalyptus urograndis kraft pulps
Authors: Hänninen Tuomas A. , Kontturi Eero , Isogai Akira , Vuorinen Tapani 
Published: May 2008

AbstractBy comparing the ultrastructural features of two oxygen delignified hardwood kraft pulps (Eucalyptus urograndis and Betula verrucosa), we have demonstrated a marked difference in their residual lignin properties. In this study, properties such as crystallinity and crystal size of cellulose, molecular weights, carboxyl group contents, and carbohydrate compositions of the two kraft pulps were compared. The examined pulps were in our observations relatively similar. A significant difference, however, was observed in the size exclusion chromatography measurements, which indirectly suggested that a significant portion of residual lignin in eucalyptus pulp was associated with cellulose. Birch pulp, in contrast, exhibited a more conventional tendency for hardwood pulps: lignin mainly associated with hemicelluloses. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 889–893, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Extracellular Synthesis of Crystalline Silver Nanoparticles and Molecular Evidence of Silver Resistance from Morganella sp.: Towards Understanding Biochemical Synthesis Mechanism
Authors: Parikh Rasesh Y. , Singh Sanjay , Prasad B. L. V. , Patole Milind S. , Sastry Murali , Shouche Yogesh S. 
Published: May 2008

AbstractThere has been significant progress in the biological synthesis of nanomaterials. However, the molecular mechanism of synthesis of such bio‐nanomaterials remains largely unknown. Here, we report the extracellular synthesis of crystalline silver nanoparticles (AgNPs) by using Morganella sp., and show molecular evidence of silver resistance by elucidating the synthesis mechanism. The AgNPs were 20±5 nm in diameter and were highly stable at room temperature. The kinetics of AgNPs formation was investigated. Detectable particles were formed after an hour of reaction, and their production remained exponential up to 18 h, and saturated at 24 h. Morganella sp. was found to be highly resistant to silver cations and was able to grow in the presence of more than 0.5 mM AgNO3. Three gene homologues viz. silE, silP and silS were identified in silver‐resistant Morganella sp. The homologue of silE from Morganella sp. showed 99 % nucleotide sequence similarity with the previously reported gene, silE, which encodes a periplasmic silver‐binding protein. The homologues of silP and silS were also highly similar to previously reported sequences. Similar activity was totally absent in closely related Escherichia coli; this suggests that a unique mechanism of extracellular AgNPs synthesis is associated with silver‐resistant Morganella sp. The molecular mechanism of silver resistance and its gene products might have a key role to play in the overall synthesis process of AgNPs by Morganella sp. An understanding of such biochemical mechanisms at the molecular level might help in developing an ecologically friendly and cost‐effective protocol for microbial AgNPs synthesis.
Real‐Time Amperometric Analysis of Reactive Oxygen and Nitrogen Species Released by Single Immunostimulated Macrophages
Authors: Amatore Christian , Arbault Stéphane , Bouton Cécile , Drapier Jean‐Claude , Ghandour Hala , Koh Alaric C. W. 
Published: May 2008

AbstractMacrophages are key cells of the immune system. Immunologically activated macrophages are known to release a cocktail of reactive oxygen and nitrogen species. In this work, RAW 264.7 macrophages were activated by interferon‐γ and lipopolysaccharide, and the reactive mixture released by single cells was analyzed, in real time, by amperometry at platinized carbon microelectrodes. In comparison with untreated macrophages, significant increases in amperometric responses were observed for activated macrophages. Nitric oxide (NO.), nitrite (NO2−), and peroxynitrite (ONOO−) were the main reactive species detected. The amounts of these reactive species were quantified, and their average fluxes released by a single, activated macrophage were evaluated. The detection of ONOO− is of particular interest, as its role and implications in various physiological conditions have been widely debated. Herein, direct evidence for the formation of ONOO− in stimulated macrophages is presented. Finally, the presence of 1400W, a selective inducible nitric oxide synthase (iNOS) inhibitor, led to an almost complete attenuation of the amperometric response of activated RAW 264.7 cells. The majority of the reactive species released by a macrophage are thus likely to be derived from NO. and superoxide (O2.−) co‐produced by iNOS.
A β‐1,4‐Galactosyltransferase from Helicobacter pylori is an Efficient and Versatile Biocatalyst Displaying a Novel Activity for Thioglycoside Synthesis
Authors: Namdjou Darius‐Jean , Chen Hong‐Ming , Vinogradov Evguenii , Brochu Denis , Withers Stephen G. , Wakarchuk Warren W. 
Published: May 2008

AbstractHelicobacter pylori is a highly persistent and common pathogen in humans. It is the causative agent of chronic gastritis and its further stages. HP0826 is the β‐1,4‐galactosyltransferase involved in the biosynthesis of the LPS O‐chain backbone of H. pylori. Though it was first cloned nearly a decade ago, there are surprisingly limited data about the characteristics of HP0826, especially given its prominent role in H. pylori pathogenicity. We here demonstrate that HP0826 is a highly efficient and promiscuous biocatalyst. We have exploited two novel enzymatic activities for the quantitative synthesis of the thiodisaccharide Gal‐β‐S‐1,4‐GlcNAc‐pNP as well as Gal‐β‐1,4‐Man‐pNP. We further show that Neisseria meningitidis β‐1,4‐galactosyltransferases LgtB can be used as an equally efficient catalyst in the latter reaction. Thiodisaccharides have been extensively used in structural biology but can also have therapeutic uses. The Gal‐β‐1,4‐Man linkage is found in the Leishmania species LPG backbone disaccharide repeats and cap, which have been associated with vector binding in Leishmaniasis.
Synthesis and Characterization of a Grapevine Nanostructure Consisting of Single‐Walled Carbon Nanotubes with Covalently Attached [60]Fullerene Balls
Authors: Wu Wei , Zhu Huarui , Fan Louzhen , Yang Shihe 
Published: May 2008

AbstractA grapevine nanostructure based on single‐walled carbon nanotubes (SWNTs) covalently functionalized with [60]fullerene (C60) has been synthesized and characterized in detail. Investigations into the ball‐on‐tube carbon nanostructure by ESR spectroscopy indicate a tendency for ground‐state electron transfer from the SWNT to the C60 moieties. The cyclic‐voltammetric response of the nanostructure film exhibits reversible multiple‐step electrochemical reactions of the dispersed C60, which are strikingly similar to those of the C60 derivatives in solution, but with consistent negative shifts in the redox potential. This results from the covalent linkage of C60 to the surfaces of the SWNTs in the form of monomers and manifests the electronic interaction between the C60 and SWNT moieties.
Coupling Sol–Gel Synthesis and Microwave‐Assisted Techniques: A New Route from Amorphous to Crystalline High‐Surface‐Area Aluminium Fluoride
Authors: Dambournet Damien , Eltanamy Gehan , Vimont Alexandre , Lavalley Jean‐Claude , Goupil Jean‐Michel , Demourgues Alain , Durand Etienne , Majimel Jérôme , Rudiger Stephan , Kemnitz Erhard , Winfield John M. , Tressaud Alain 
Published: May 2008

AbstractA non‐aqueous sol–gel Al‐based fluoride has been subjected to the microwave solvothermal process. The final material depends on the temperature heat treatment used. Three types of material have been prepared: 1) for low temperature heat treatment (90 °C) X‐ray amorphous alkoxy fluoride was obtained; 2) for the highest temperature used (200 °C) the metastable form β‐AlF3 was obtained with a very large surface area of 125 m2 g−1. The mechanism of the amorphous⇄crystalline transformation has been rationalised by the occurrence of a decomposition reaction of the gel fluoride induced by the microwave irradiation. 3) Finally, at intermediate temperature (180 °C) a multi‐component material mixture exhibiting a huge surface area of 525 m2 g−1 has been obtained and further investigated after mild post‐treatment fluorination using F2 gas. The resulting aluminium‐based fluoride still possesses a high‐surface‐area of 330 m2 g−1. HRTEM revealed that the solid is built from large particles (50 nm) identified as α‐AlF3, and small ones (10 nm), relative to an unidentified phase. This new high‐surface‐area material exhibits strong Lewis acidity as revealed by pyridine adsorption and catalytic tests. By comparison with other materials, it has been shown that whatever the composition/structure of the Al‐based fluoride materials, the number of strong Lewis acid sites is related to the surface area, highlighting the role of surface reconstruction occurring on a nanoscopic scale on the formation of the strongest Lewis acid sites.
Understanding Chemical Reactivity: The Case for Atom, Proton and Methyl Transfers
Authors: Arnaut Luis G. , Formosinho Sebastião J. 
Published: May 2008

AbstractThe concept of “chemical reactivity” assumes that atoms and molecules contain the necessary information to describe their evolution over time as they transform from reactants to products. This concept was useful in the past to rationalize reactivity trends and predict the behavior of new systems. Free‐energy relationships have played a central role in this field. However, electronic effects often counter the energetic effects and give rise to “anomalies” or separate correlations. We discuss a quantification of the concept of “chemical reactivity”, emphasizing the role of molecular and electronic factors in Chemistry.
The Importance of the Long Type 1 Copper‐Binding Loop of Nitrite Reductase for Structure and Function
Authors: Sato Katsuko , Firbank Susan J. , Li Chan , Banfield Mark J. , Dennison Christopher 
Published: May 2008

AbstractThe long 15‐residue type 1 copper‐binding loop of nitrite reductase has been replaced with that from the cupredoxin amicyanin (7 residues). This sizable loop contraction does not have a significant effect on the spectroscopy, and therefore, the structures of both the type 1 and type 2 CuII sites. The crystal structure of this variant with ZnII at both the type 1 and type 2 sites has been determined. The coordination geometry of the type 2 site is almost identical to that found in the wild‐type protein. However, the structure of the type 1 centre changes significantly upon metal substitution, which is an unusual feature for this class of site. The positions of most of the coordinating residues are altered of which the largest difference was observed for the coordinating His residue in the centre of the mutated loop. This ligand moves away from the active site, which results in a more open metal centre with a coordinating water molecule. Flexibility has been introduced into this region of the protein. The 200 mV increase in the reduction potential of the type 1 copper site indicates that structural changes upon reduction must stabilise the cuprous form. The resulting unfavourable driving force for electron transfer between the two copper sites, and an increased reorganisation energy for the type 1 centre, contribute to the loop variant having very little nitrite reductase activity. The extended type 1 copper‐binding loop of this enzyme makes a number of interactions that are important for maintaining quaternary structure.
Designed Peptides with Homochiral and Heterochiral Diproline Templates as Conformational Constraints
Authors: Chatterjee Bhaswati , Saha Indranil , Raghothama Srinivasarao , Aravinda Subrayashastry , Rai Rajkishor , Shamala Narayanaswamy , Balaram Padmanabhan 
Published: May 2008

AbstractDiproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L‐Pro‐L‐Pro and D‐Pro‐L‐Pro units. Four distinct classes of model peptides have been investigated: a) isolated D‐Pro‐L‐Pro segments which form type II′ β‐turn; b) D‐Pro‐L‐Pro‐L‐Xxx sequences which form type II′‐I (βII′‐I, consecutive β‐turns) turns; c) D‐Pro‐L‐Pro‐D‐Xxx sequences; d) L‐Pro‐L‐Pro‐L‐Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv‐D‐Pro‐L‐Pro‐L‐Xxx‐NHMe are conformationally homogeneous, adopting consecutive β‐turn conformations. Peptides in the series Piv‐D‐Pro‐L‐Pro‐D‐Xxx‐NHMe and Piv‐L‐Pro‐L‐Pro‐L‐Xxx‐NHMe, display a heterogeneity of structures in crystals. A type VIa β‐turn conformation is characterized in Piv‐L‐Pro‐L‐Pro‐L‐Phe‐OMe (18), while an example of a 5→1 hydrogen bonded α‐turn is observed in crystals of Piv‐D‐Pro‐L‐Pro‐D‐Ala‐NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C‐terminal Xxx residues on the structures of diproline segments. In L‐Pro‐L‐Pro‐L‐Xxx sequences, the Xxx residues strongly determine the population of Pro‐Pro cis conformers, with an overwhelming population of the trans form in L‐Xxx = L‐Ala (19).