bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of degradation pathways of Amadori compounds obtained by glycation of opioid pentapeptide and related smaller fragments: Stability, reactions, and spectroscopic properties
Authors: Jakas Andreja , Horvat Štefica 
Published: July 2003

AbstractReactions between biological amines and reducing sugars (the Maillard reaction) are among the most important of the chemical and oxidative changes occurring in biological systems that contribute to the formation of a complex family of rearranged and dehydrated covalent adducts that have been implicated in the pathogenesis of human diseases. In this study, chemistry of the Maillard reactions was studied in four model systems containing fructosamines (Amadori compounds) obtained from the endogenous opioid pentapeptide leucine‐enkephalin (Tyr–Gly–Gly–Phe–Leu), leucine‐enkephalin methyl ester, structurally related tripeptide (Tyr–Gly–Gly), or from amino acid (Tyr). The degradation of model compounds as well as their ability to develop Maillard fluorescence was investigated under oxidative conditions in methanol and phosphate buffer pH 7.4 at two different temperatures (37 and 70°C). At 37°C, glycated leucine‐enkephalin degraded slowly in methanol (t1/2 ∼13 days) and phosphate buffer (t1/2 ∼ 9 days), producing a parent peptide compound as a major product throughout a three‐week incubation period. Whereas fluorescence slowly increased over time at 37°C, incubations off all studied Amadori compounds at 70°C resulted in a rapid appearance of a brown color and sharp increase in AGE (advanced glycation end products)‐associated fluorescence (excitation 320 nm/emmision 420 nm) as well as in distinctly higher amounts of fragmentation products. The obtained data indicated that the shorter the peptide chain the more degradation products were formed. These studies have also helped to identify a new chemical transformation of the peptide backbone in the Maillard reaction that lead to β‐scission of N‐terminal tyrosine side chain and p‐hydroxybenzaldehyde formation under both aqueous and nonaqueous conditions. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 421–431, 2003
Small angle x‐ray scattering of the hemoglobin from Biomphalaria glabrata
Authors: Arndt Márcio H. L. , Oliveira Cristiano L. P. de , Régis Wiliam C. B. , Torriani Iris L. , Santoro Marcelo M. 
Published: July 2003

AbstractThe hemoglobin from Biomphalaria glabrata is an extracellular respiratory protein of high molecular mass composed by subunits of 360 kDa, each one containing two 180 kDa chains linked by disulfide bridges. In this work, small angle x‐ray scattering (SAXS) measurements were performed with the hemoglobin at pH 5.0 and 7.5. Radii of gyration of 98.6 ± 0.5 and 101.8 ± 0.2 Å and maximum diameters of 300 ± 10 and 305 ± 10 Å, respectively, were obtained from Guinier plot extrapolation and analytical curve fitting. The pair distance distribution functions p(r) corresponded to globular particles with a somewhat anisotropic shape for both preparations. Computer analysis of the low angle part of the scattering curve led to the determination of the low resolution envelope of the protein, revealing a P222 symmetry. Shape reconstruction from ab initio calculations using the complete scattering curve furnished a compact prolate three‐dimensional (3D) bead model for the protein. Hydrodynamic parameters were obtained from experiments and theoretical calculations using the 3D model. The results of the structural and biochemical studies reported herein indicate that the multisubunit structure of this hemoglobin is compatible with a tetrameric arrangement. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 470–479, 2003
Viscoelastic and light scattering studies on thermally induced sol to gel phase transition in fish myosin solutions
Authors: Kouchi Sawa , Kondo Shingo , Ooi Kazuko , Ichikawa Hisashi , Dobashi Toshiaki 
Published: July 2003

AbstractViscoelastic (VE) and dynamic light scattering (DLS) analyses of fish (white croaker) myosin solutions were performed at myosin concentrations of 30mg/mL for VE and 0.1 mg/mL for DLS at 0.6M KCl and pH 7.0 to clarify thermally induced gelation. The hydrodynamic radius Rh considerably decreased around 30–35°C. The shear modulus G was constant below 25°C and increased by incubating the sample at 30°C. G further increased as the temperature of the incubated sample decreased. The curves of G vs T for different time courses showed a sharp peak around 35°C and a moderate peak around 60°C in the heating process, while a stepwise increase in G was observed around 30°C in the cooling process when the temperature was elevated to not more than 60°C. No distinct stepwise change was observed once the temperature of the sample exceeded 60°C. The absolute value of G strongly depended on the maximum elevated temperature and the incubation time at that temperature. The corresponding behavior of the viscosity η was observed for each time course. Based on these results, the mechanism of thermally induced gelation of myosin solutions is discussed in view of SS bridge formation in the head and tail portions and unwinding/rewinding of coiled‐coil α‐helices in the tail portion. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 498–507, 2003
Nonsequence‐specific arginine interactions in the nucleosome core particle
Authors: García‐Pérez Maria , Pinto Marta , Subirana Juan A. 
Published: July 2003

AbstractWe have analyzed the relative orientation of basic amino acid side chains towards DNA in the nucleosome core particle. The electric field created by DNA phosphates has no apparent preferential orientation: no favored orientation of the arginine guanidinium group is found. Arginine may be either directly hydrogen bonded to a phosphate oxygen or stabilized in the minor groove by van der Waals contacts and the local negative electric field. On the other hand, the phosphate oxygen atoms hydrogen bonded to arginines are always found close to the plane defined by the guanidinium group. Thus it can be concluded that the interactions of arginine are strongly directional, those of phosphate are not. We also find that a highly charged fragment of histone H2B, which is placed between two DNA turns, has a very variable conformation. An increase in protein positive charge density apparently allows multiple nonspecific protein conformations when interacting with DNA. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 432–439, 2003
Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthase
Authors: Severcan Feride , Haris Parvez I. 
Published: July 2003

AbstractPig citrate synthase (PCS) can be used as a model enzyme to gain some insight into the structural basis of protein thermostability. The thermal unfolding characteristics of the specific secondary structure elements within PCS were monitored in detail by following changes in its amide I band components. The result of our study indicates that PCS undergoes irreversible thermal denaturation. Detailed analysis reveals that the different secondary structures display a multistep transition with a major and a minor transition at different temperatures and a very small initial transition at the same temperature (30°C). A plot of temperature‐induced changes in 1H–2H exchange, the decrease in the absorbance of the α‐helical structures, and the increase in the absorbance of aggregated structures all have in common a multistep transition, the minor one centered at 45°C and the major one around 59°C. In contrast, a band that is tentatively assigned to loop structures displays these same minor and major transitions but at lower temperatures (39 and 52°C, respectively). The transition, which occurs at 39–45°C, is not associated with the appearance of aggregated structures. This transition may reflect a change in the tertiary structure of the protein. However, the final transition, which occurs at a higher temperature (52–59°C), reflects unfolding and aggregation of the polypeptide chains. The Fourier transform infrared (FTIR) analysis suggests that PCS has a thermolabile region that unfolds first, some 7°C below the main unfolding of the protein. We propose that this reflects the unfolding of the highly flexible loop segments, which in turn triggers the unfolding of the predominantly helical core structure of PCS. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 440–447, 2003
Translational diffusion coefficient of cycloamylose in aqueous sodium hydroxide
Authors: Nakata Yasushi , Amitani Keiji , Norisuye Takashi , Kitamura Shinichi 
Published: July 2003

AbstractSeven cyclic (1 → 4)‐α‐D‐glucan (cycloamylose) samples ranging in weight‐average molecular weight from 5 × 103 to 1.8 × 104 and γ‐cyclodextrin have been studied by sedimentation equilibrium in dimethylsulfoxide (at 25°C) and by dynamic light scattering in 0.5 N aqueous sodium hydroxide (at 25°C), a good solvent for linear amylose. The measured translational diffusion coefficients D in the aqueous NaOH agree fairly closely with previous Monte Carlo results for cyclic (1 → 4)‐α‐D‐glucan chains with excluded volume, when correction is made for the effects of bead diameter and fluctuating hydrodynamic interaction (HI) on the Kirkwood theory on which the computation of D was based. These D data are also explained almost quantitatively by Yamakawa and Fujii's expression for the associated KP ring (based on the Kratky–Porod wormlike chain) with the molecular parameters for linear amylose if the fluctuating HI and excluded‐volume effects are taken into account. It is concluded that the translational diffusion behavior of cycloamylose in the aqueous NaOH is consistent with the conformational characteristics derived from the conformational energy of maltose and dilute‐solution data for linear amylose. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 508–516, 2003
DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation
Authors: Andrushchenko Valery , van de Sande Hans , Wieser Hal 
Published: July 2003

AbstractInteraction of natural calf thymus DNA with Mn2+ ions was studied at room temperature and at elevated temperatures in the range from 23°C to 94°C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn2+ concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B‐form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn2+ ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55°C. DNA aggregation was observed in the presence of Mn2+ ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 529–545, 2003
Application of the Suzuki‐Miyaura cross‐coupling reaction for the modification of phenylalanine peptides
Authors: Kotha Sambasivarao , Lahiri Kakali 
Published: July 2003

AbstractWe have demonstrated an exceptionally simple and a useful methodology for modification of unusual phenylalanine peptides by adapting the building block approach using the Suzuki‐Miyaura cross‐coupling reaction as a key step. This strategy gave a good overall yield of various modified tri‐ and pentapeptides that may be useful to prepare various biologically active peptides in a short period of time. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 517–528, 2003
Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides
Authors: Dixon Ann M. , Venable Richard , Widmalm Göran , Bull T.E. , Pastor Richard W. 
Published: July 2003

AbstractThe preferred conformations and conformational flexibilities of the trisaccharides α‐D‐Glcp‐(1→2)‐β‐D‐Glcp‐(1→3)‐α‐D‐Glcp‐OMe (I) and α‐D‐Glcp‐(1→3)[β‐D‐Glcp‐(1→4)]‐α‐D‐Glcp‐OMe (II) in aqueous solution were determined using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) and Langevin dynamics (LD) simulations, and hydrodynamics calculations. Both trisaccharides have a vicinal substitution pattern in which long range (nonsequential) interactions may play an important role. LD simulation at 600 K indicated that the all‐syn conformation predominated, though other conformations were apparent. NOE data and MD and LD simulations at 298 K all indicated that trisaccharide I is a single all‐syn conformer in solution. Given that previous studies showed evidence of anti‐conformers in β‐D‐Glcp‐(1→2)‐β‐D‐Glcp‐(1→3)‐α‐D‐Glcp‐OMe, this result provides an example of how changing the anomeric configuration of one residue from β to α can make an oligosaccharide more rigid. Discrepancies in inter‐ring distances obtained by experiment and by simulation of the all‐syn conformer suggest the presence of an anti‐ψ conformation at the β‐(1→4)‐linkage for II. A combined analysis of measured and calculated translational diffusion constants and 13C T1 relaxation times yield order parameters of 0.9 for each trisaccharide. This implies that any interconversion among conformations is significantly slower than tumbling. Anisotropies of approximately 1.6 and 1.3 calculated for I and II, respectively, are consistent with the observed relatively flat T1 profiles because the tumbling is not in the motional narrowing regime. Published 2003 Wiley Periodicals, Inc. Biopolymers 69: 448–460, 2003
Molecular mechanisms of Fe2+‐induced β‐lactoglobulin cold gelation
Authors: Remondetto Gabriel E. , Subirade Muriel 
Published: July 2003

AbstractTo get more insight into the mechanisms of cold gelation of β‐lactoglobulin (β‐lg), macroscopic and molecular structural changes during Fe2+‐induced gelation of β‐lg were investigated using Fourier transform‐infrared (FTIR) spectroscopy and rheological methods. The FTIR spectroscopy results show that, upon the preheating treatment (first step of gel process), native globular proteins are denatured and aggregated molecules are found in solution. The spectra are similar to those of gels obtained in the second step of the process upon incorporation of Fe, which suggests that aggregated molecules formed during the preheating treatment constitute the structural basis of the aggregation. However, the rheological data show that the aggregation is achieved via two molecular mechanisms, both of which are modulated by the iron concentration. At 30 mM of iron, gel formation is essentially controlled by van der Waals interactions, while at 10 mM of iron, hydrophobic interactions predominate. At the two concentrations, disulfide bonds contribute to gel consolidation, the effect being more pronounced at 10 mM of iron. These mechanisms lead to the formation of gels of different microstructures. At the highest iron concentration, a strong and rapid decrease in the repulsion forces is produced, resulting in random aggregation. At the lowest iron concentration, the iron diminishes the superficial charge of both molecules and aggregated molecules, facilitating the interaction among hydrophobic regions and leading to the growth of the aggregation in the preferential direction and to filamentous gel formation. This study provides a comprehensive view of the different modes of gelation. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 461–469, 2003
Conformational analysis of the exopolysaccharide from Burkholderia caribensis strain MWAP71: Impact on the interaction with soils
Authors: Vanhaverbeke Cécile , Heyraud Alain , Mazeau Karim 
Published: July 2003

AbstractThe strain MWAP71 of Burkholderia caribensis produces a branched charged exopolysaccharide (EPS) that is responsible for soil aggregation. Understanding the conformational properties of the isolated polysaccharide is a prerequisite for proper investigation of the interactions between the polysaccharide and the soil at the atomic level. The aim of this study is first to have an overall view of the flexibility of the backbone and then to ascertain the role played by side groups in the conformational properties of the main chain. Conformational analysis of each oligomeric segment of the polysaccharide has been performed by means of adiabatic mapping of the backbone glycosidic torsion angles using the MM3(92) force field. Substitution by an acetyl group or by a Kdo unit has only a slight effect on the potential energy surfaces of the fragment model compounds. Calculated partition functions, however, indicate that the overall flexibility is slightly larger for the substituted oligomers than for the unsubstituted ones. Prediction of selected average interproton distances from the AB and BC potential energy surfaces allows comparison between modeling results and NMR measurements performed on the ABC fragment. Agreement between the experimental and the predicted data suggests that the established surfaces correctly reflect the observed conformational behavior of such fragments and validate the modeling protocol. The above results have been extended to regular and disordered long polymer chains, differing in Kdo content. It is found that Kdo affects the helical conformations of the polysaccharide. The number of stable helices is considerably larger with Kdo than without Kdo. On the contrary, Kdo has only a moderate effect on unperturbed disordered conformations of the polysaccharide. Predicted persistence length of 70 Å suggests that the polymer is semirigid with moderate extension. A further validation of the modeling results is obtained by the good concordance between this predicted value and the experimental one of 95 Å, measured from light scattering and viscosity experiments. The results lead to an understanding of the interactions of this polysaccharide with soils. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 480–497, 2003
Preliminary study on application of impregnated synthetic peptide TLC stationary phases for the pre‐screening of 5‐HT1A ligands
Authors: Zajdel PaweŁ , Bojarski Andrzej J. , Byrtus Hanna , ChŁoń‐Rzepa Grażyna , Obniska Jolanta , Chevallet Pierre , Martinez Jean , PawŁowski Maciej 
Published: July 2003

AbstractChromatographic parameters (ΔRf), defined as a difference in the migration of tested compound on the control and peptide impregnated silica gel TLC plates, were determined for 42 arylpiperazine derivatives. An amino acid sequence of the peptide used for impregnation was derived from the III transmembrane segment of the 5‐HT1A receptor in the close vicinity of aspartic acid (Asp 166) residue. It was found that the ΔRf values obtained in a model employing tetrapeptide P4LA (ADVL), as well as the calculated logP correlate with 5‐HT1A receptor affinity of the studied compounds. Copyright © 2003 John Wiley & Sons, Ltd.
Liquid chromatographic separation of the enantiomers of β‐amino acids on a ligand exchange chiral stationary phase
Authors: Hyun Myung Ho , Han Sang Cheol , Whangbo Sung Hee 
Published: July 2003

AbstractA liquid chromatographic ligand exchange chiral stationary phase (CSP) derived from (S)‐leucinol was applied in the separation of the enantiomers of 12 β‐amino acids. The resolution was quite successful especially for the enantiomers of β‐amino acids containing aromatic functional group in the side chain. The chromatographic resolution behaviors were dependent on the organic modifier and Cu(II) concentration in aqueous mobile phase and the column temperature. Copyright © 2003 John Wiley & Sons, Ltd.
The benefit of the retrofitting of a conventional LC system to micro LC: a practical evaluation in the field of bioanalysis with fluorimetric detection
Authors: Roy S. , Rieutord A. , Zhou J.Y. , Baillet A. , Prognon P. , Chaminade P. 
Published: July 2003

AbstractThe interests in liquid micro‐chromatography (higher column efficiencies, increase in sensitivity) are now well established. The enhancement of fluorimetric response induced by the reduction of the inner diameter of columns (4.6, 3.0, 1.0 and 0.3 mm respectively) coupled with adapted detection cells to control the loss of efficiency (8 µL for the two first columns and 100 nL for the two smaller ones) has been studied in the bioanalytical field, using the plasma determination of native fluorescent antibacterial agents: fluoroquinolones. Ten‐fold enhancement of the signal can easily be obtained when substituting a 0.3 mm i.d. column and 100 nL detection cell for a 4.6 mm i.d. column, and 8 µL detection cell. In addition to inner diameter reduction, the detection cell geometry appears to be an essential parameter to obtain the best enhancement of the recorded signal. Hence, the enhancement of signal with micro‐chromatography with fluorimetric detection appears to be a compromise between column inner diameter and flow cell volume reduction. Copyright © 2003 John Wiley & Sons, Ltd.
Thin layer chromatographic resolution of some 2‐arylpropionic acid enantiomers using L‐(−)‐serine, L‐(−)‐threonine and a mixture of L‐(−)‐serine and L‐(−)‐threonine‐impregnated silica gel as stationary phases
Authors: Aboul‐Enein Hassan Y. , El‐Awady Mahmoud I. , Heard Charles M. 
Published: July 2003

AbstractImpregnated silica TLC plates with L‐(−)‐serine and L‐(−)‐threonine and a mixture of L‐(−)‐serine and L‐(−)‐threonine (1:1) as chiral selectors were prepared to use as chiral stationary phases (CSPs) in thin layer chromatography. The resolution of the enantiomers of 2‐arylpropionic drugs, including ibuprofen, ibuproxam, ketoprofen, pranoprofen, benoxaprofen, flurbiprofen and tiaprofenic acid was investigated on these CSPs. A mobile phase system of acetonitrile–methanol–water (16:4:0.5, v/v/v) was used. The spots were detected with iodine vapours and the detection limits were found to range between 0.25 and 0.5 µg/mL for all racemic compounds investigated. The effect of temperature, pH and concentration of the impregnating chiral selectors on resolution has been studied. Copyright © 2003 John Wiley & Sons, Ltd.
Estimation of the lipophilicity of antiarrhythmic and antihypertensive active 1‐substituted pyrrolidin‐2‐one and pyrrolidine derivatives
Authors: Kulig Katarzyna , Malawska Barbara 
Published: July 2003

AbstractThe lipophilicity of some antiarrhythmic and antihypertensive active 1‐[2‐hydroxy‐ or 1‐[2‐acetoxy‐3‐(4‐aryl‐1‐piperazinyl)propyl]pyrrolidin‐2‐one derivatives (1–12) has been investigated. Their lipophilicity (RMO and log k′) was determined by reversed‐phase thin‐layer chromatography and reversed‐phase high‐performance liquid chromatography with mixtures of acetonitrile and Tris buffer as mobile phases. The partition coefficients of compounds 1–12 (log PScilogP) were also calculated with the ScilogP program. Comparison of RMO, log k′ and calculated log D7.0 ScilogP values enabled calculation of clog D7.0 TLC and clog D7.0 HPLC values. Preliminary quantitative structure–activity relationship studies indicated that for active compounds there is a dependence between affinity for α2‐adrenoceptors and their clog D7.0 HPLC values. Copyright © 2003 John Wiley & Sons, Ltd.