bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding of basic pancreatic trypsin inhibitor and related isoinhibitors to leukocytic elastase. Determination of thermodynamic parameters
Authors: Fioretti Evandro , Angeletti Mauro , Cottini Maria Teresa , Ascoli Franca 
Published: May 2005

AbstractThe effect of temperature, ionic strength and solvation power of mono‐ and divalent cations on the interaction of BPTI‐like inhibitors with human leukocytic elastase has been determined. The binding process is characterized by a non‐linear dependence of the equilibrium association constant on 1/T indicating a thermal transition at temperature values ranging between 20°C and 35°C depending on the solvent. The marked dependence of the thermodynamic parameters (ΔH°, ΔS°, ΔG°) and of the transition temperature on the concentration and nature of the cations present in solution seems to indicate that the transition, probably of conformational nature, is related to removal of water molecules upon enzyme/inhibitor complex formation.
Chemical and photochemical probing of DNA complexes
Authors: Nielsen Peter E. 
Published: May 2005

AbstractAn overview of the chemical and photochemical probes which over the past ten years have been used in studies of DNA/ligand complexes and of non‐B‐form DNA conformation is presented with emphasis on the chemical reactions of the probes with DNA and on their present ‘use‐profile’. The chemical probes include: dimethyl sulfate, ethyl nitroso urea, diethyl pyrocarbonate, osmium tetroxide, permanganate, aldehydes, methidiumpropyl‐EDTA‐Fell (MPE), phenanthroline metal complexes and EDTA/FeII. The photochemical probes that have been used include: psoralens, UVB, acridines and uranyl salts. The biological systems analysed by use of these probes are reviewed by tabulation.
Prediction of the secondary structure and functional sites of major histocompatibility complex molecules
Authors: Fraga S. , San‐Fabian E. , Thornton S. , Singh Bhagirath 
Published: May 2005

AbstractA method for the theoretical prediction of the antigenic determinants and the antigen‐interactive receptor sites of immunological proteins from their primary structure would constitute a useful tool for their study. Such a method developed in this laboratory uses hydrophilicity, accessibility, flexibility, and recognition profiles, together with the predicted secondary structure (α‐helices, β‐sheets, and turns). The secondary structure is determined by a modification of the method of Lim (1974), as described below. A study of human and mouse class I and class II major histocompatibility complex (MHC) antigens, central to the regulation of immune responses and to the phenomenon of graft rejection, was carried out using the above method. Comparison of the predictions with some of the available experimental and theoretical information supports the validity and usefulness of the approach.
Recognition of the acetylcholine receptor binding site of a long‐chain neurotoxin by toxin‐specific monoclonal antibodies
Authors: Charpentier Isabelle , Pillet Laurence , Karlsson Evert , Couderc Jacques , Ménez André 
Published: May 2005

AbstractThe present paper reports the preparation and characterization of two neutralizing monoclonal antibodies (Mabs), called MST1 and MST2, which bind at the central loop of a long‐chain neurotoxin from cobra venom. The central loop is a critical region for the binding of the toxin to the nicotinic acetylcholine receptor. Some of the residues incorporated in the epitopes recognized by MST1 and MST2 have been identified on the basis of competition experiments using a set of ‘chemical mutants’ of the toxin. We show that MST1 and MST2 bind at the base and at the tip of the central loop of the toxin, respectively, however, only MST2 actually overlaps the acetylcholine receptor binding site. Accordingly, only MST2 is capable of recognizing all homologous toxins so far examined. MST2, therefore, mimicks, at least partially, the site by which the nicotinic acetylcholine receptor recognizes a long‐chain neurotoxin.
Rabies virus binding to an acetylcholine receptor α‐subunit peptide
Authors: Lentz Thomas L. 
Published: May 2005

AbstractThe binding of 125I‐labeled rabies virus to a synthetic peptide comprising residues 173–204 of the α1‐subunit of the nicotinic acetylcholine receptor was investigated. Binding of rabies virus to the receptor peptide was dependent on pH, could be competed with by unlabeled homologous virus particles, and was saturable. Synthetic peptides of snake venom, curaremimetic neurotoxins and of the structurally similar segment of the rabies virus glycoprotein, were effective in competing with labeled virus binding to the receptor peptide at micromolar concentrations. Similarly, synthetic peptides of the binding domain on the acetylcholine receptor competed for binding. These findings suggest that both rabies virus and neurotoxins bind to residues 173–204 of the α1‐subunit of the acetylcholine receptor. Competition studies with shorter α‐subunit peptides within this region indicate that the highest affinity virus binding determinants are located within residues 179–192. A rat nerve α3‐subunit peptide, that does not bind α‐bungarotoxin, inhibited binding of virus to the α1 peptide, suggesting that rabies binds to neuronal nicotinic acetylcholine receptors. These studies indicate that synthetic peptides of the glycoprotein binding domain and of the receptor binding domain may represent useful antiviral agents by targeting the recognition event between the viral attachment protein and the host cell receptor, and inhibiting attachment of virus to the receptor.
Amino acid side chain interaction with chelate‐liganded crosslinked dextran, agarose and TSK gel. A mini review of recent work
Authors: Porath Jerker 
Published: May 2005

AbstractProtein adsorption and retention data collected from recent chromatographic studies on hydrophilic gels substituted with chelate‐bonded metal ions are discussed. Attempts are made to interpret the adsorption behavior in terms of molecular events caused by the affinity for the immobilized metal ions.
Aspecific and specific intermolecular interactions in aqueous media
Authors: van Oss C. J. 
Published: May 2005

AbstractAspecific as well as specific interactions involve the same noncovalent forces, consisting of Lifshitz‐van der Waals, Lewis acid/base, electrostatic, and thermal or Brownian movement interactions. In vivo, aspecific interactions between, e.g., cells and/or biopolymers usually are repulsive, while specific interactions are always attractive. The differences between the two classes of interactions can be shown to lie in the fact that aspecifically interacting bodies are large, while specifically interacting sites are small, or have a small radius of curvature, and in the fact that aspecifically interacting surfaces are homogeneous, whereas specific sites have a heterogeneous composition.
Investigation of dye/protein interaction and its application to enzyme purification
Authors: Glemža Antanas A. 
Published: May 2005

AbstractIn this review the results of the interaction of the active dyes used in the USSR textile industry with microbial enzymes and blood serum proteins are discussed. The complexity of dye/protein interaction and the dependence of this interaction on different factors is demonstrated. Some practical aspects of the use of dye containing sorbents are presented and discussed. Their suitability for RNA ligase and DNA ligase, acetate kinase, alcohol dehydrogenase, lactate dehydrogenase and glucose‐6‐phosphate dehydrogenase purification and blood serum protein fractionation is demonstrated.
Cleavage of double helical DNA by Cu2+ ion in the presence of bisintercalator containing penta(ethylene glycol) connector chain
Authors: Takenaka Shigeori , Ihara Toshihiro , Takagi Makoto 
Published: May 2005

AbstractIn designing new DNA recognizing and cleaving reagents, we introduce herein a bisacridine derivative (referred to as bisacridine) in which two acridine heterocycles are connected by a penta(ethylene glycol) bridging chain. This compound offers two possible functions: 1, stabilization of DNA bisacridine intercalator complex by metal ion. The penta(ethylene glycol) chain stabilizes metal ions binding to the phosphate site of DNA, where the penta(ethylene glycol) chain constitutes a part of a pseudomacrocyclic ligand for metal binding; and 2, enhancement of metal‐assisted hydrolytic cleavage of DNA by means of a metal concentration effect by the pseudomacrocyclic ethereal chain. The binding isotherms of bisacridine with DNA in the presence of metal ions showed that the binding was mainly governed by the cation exchange reaction on the anionic DNA polymer chain, i.e., the exchange between metal ions and the cationic bisacridine. The bisacridine showed an increased DNA binding ability compared to quinacrine, the monoacridine counterpart, and caused an enhancement of DNA cleavage in the presence of Cu2+ ions. Additional experiments which included DNase I footprinting in the presence of bisacridine and the DNA cleavage by Cu2+/bisacridine using a 32P end‐labelled DNA fragment, suggested that the Cu2+‐assisted DNA cleavage sites in the presence of bisacridine were in reasonable overlap with the DNA binding sites of bisacridine.
Haplotype specific homology scanning algorithim to predict T‐cell epitopes from protein sequences
Authors: Guillet J.‐G. , Hoebeke J. , Lengagne R. , Tate K. , Borras‐Herrera F. , Strosberg A. D. , Borras‐Cuesta F. 
Published: May 2005

AbstractWe present a homology scanning microcomputer program to predict functional T‐cell epitopes within proteins. By taking into account particular human or mouse restriction elements the predictions are made haplotype‐sepecific. The generality of this approach is confirmed by (i) identification of well‐characterized immunogenic T‐cell determinants in lysozyme (ii) search for potential T epitopes on unanalysed proteins like the human β2‐adrenoreceptor (iii) modification of non‐immunogenic peptide sequences in order to generate T‐cell determinants.
Ferredoxin electron transfer site on cytochrome c3. Structural hypothesis of an intramolecular electron transfer pathway within a tetra‐heme cytochrome
Authors: Dolla A. , Guerlesquin F. , Bruschi M. , Haser R. 
Published: May 2005

AbstractTo specify electron exchanges involving Desulfovibrio desulfuricans Norway tetra‐heme cytochrome c3, the chemical modification of arginine 73 residue performed. Biochemical and biophysical studies have shown that modified cytochrome retains its ability to both interact and act as an electron carrier with its redox partners, ferredoxin and hydrogenase. Moreover, the chemical modification effects on the cytochrome c3 1H NMR spectrum were similar to that induced by the presence of ferredoxin. This suggests that arginine 73 is localized on the cytochrome c3 ferredoxin interacting site. The identification of heme 4, the closest heme to arginine 73, as the ferredoxin interacting heme helps us to hypothesize about the role of three other hemes in the molecule. A structural hypothesis for an intramolecular electron transfer pathway, involving hemes 4, 3, and 1, is proposed on th basis of the crystal structures of D. vulgaris Miyazaki and D. desulfuricans Norway cytochromes c3. The unique of role of some structural features (α helix, aromatic residues) intervening between the heme groups, is proposed.
Immunological mapping of fine molecular surface structures of citrate synthase enzymes from different cell types
Authors: Nemeth P. , Small W. C. , Evans C. T. , Zhi W. , Persson L. O. , Srere P. A. 
Published: May 2005

AbstractCitrate synthase (EC 4.1.3.7), which is present in all living organisms as a key enzyme in aerobic energy metabolism, is one of the most highly phylogenetically conserved enzymes known in terms of its primary and active site structure. However, in terms of other parameters such as in vitro stability, tolerance to changes in pH, degree of self‐polymerization, etc., citrate syntheses different sources are markedly different. These divergences can be observed even between isoforms of the enzyme within the same species. Data documenting these diversities suggest that a high degree of difference in tertiary structures may occur. Therefore, the surface profiles of citrate synthase enzymes from yeast, pig, rat, tomato and Escherichia coli were investigated with immunological methods using monoclonal antibody families generated against either pig citrate synthase (α‐PCS) or yeast citrate synthase‐2 (α‐YCS‐2). A high degree of homology of enzyme epitopes was detected on the mitochondrial citrate synthases originating from yeast, tomato, pig and rat cells. Major differences were found between the hexameric citrate synthase originating from E. coli compared with those dimeric forms prepared from eukaryotic cells. Only modest similarities were detected between the highly homologous peroxisomal and mitochondrial yeast citrate syntheses. Furthermore, a point mutation of one of the catalytic residues (H274R on recombinant pig and H313R on yeast enzyme) of mitochondrial citrate synthase (CS‐1) resulted in a significant increase in immunological similarity with the peroxisomal isoenzyme (CS‐2). These findings are discussed in terms of the possible mechanism of evolution of CS‐2 in yeast.
Studies of the binding activity of phage G13 to synthetic trisaccharides analogous to binding structures in Salmonella typhimurium and Escherichia coli C core saccharide. Correlation between conformation and binding activity
Authors: Bruse Gert W. , Wollin Ralfh , Oscarson Stefan , Jansson Per‐Erik , Lindberg Alf A. 
Published: May 2005

AbstractPhage G13 binds to the carbohydrate part of lipopolysaccharides from rough mutants of Salmonella and Escherichia coli as the first event of infection. Equilibrium dialysis inhibition studies with native and synthetic trisaccharides as inhibitors suggested that phage G13 recognizes branched oligosaccharides having 6‐O‐α‐ or 7‐O‐α‐glycosyl groups with α‐Man(1→3) [α‐Man(1→6)]Man (Man[Man]Man) and α‐Glc(1→3)‐[α‐Hep(1→7)α‐Hep(1→3)α‐Hep(1→5) Kdo as the smallsest saccharides with inhibitory activity (Wollin et. al., 1989). Of four synthetic analogues to Man[Man]Man only Man(1→3)[α‐Gal(1→6)]α‐Man‐Ome (Man[Gal]‐Man) and α‐Glc(1→3)]α‐Hep(1→7)α‐Hep‐Ome (Glc[Hep]Hep) inhibited the binding of labelled E. coli. C core nonasaccharide ligand to G13 with activities which were 10‐ and 15‐fold lower than Man[Man]Man. The trisaccharides α‐Man(2→3)[α‐Glc(1→6)]α‐Man‐OMe (Man[Glc]Man) and α‐Man(1→3)[α‐Tal(1→6)]α‐Man‐OMe (Man[Tal]Man) showed no inhibition at concentrations 75‐fold higher than Man[Man]Man. Minimum energy conformation calculations of the saccharides using the GESA method showed that the 6‐O‐α‐Man group in Man[Man]Man and the 7‐O‐α‐Hep group in SL805 pentasaccharide expose their OH‐2 and OH‐3 groups in a similar way and these are postulated to be key structural features for binding activity. The importance of hydroxy groups at certain positions is implied from the fact that both manno‐ and galacto‐isomers are active. We also conclude that the O6‐C6‐C5‐O5‐C1 region of the 3‐O‐α‐glycosyl group in the Man[Man]Man trisaccharide, or part of it, is important for the G13 binding activity.
Making sense from antisense: A review of experimental data and developing ideas on sense–antisense peptide recognition
Authors: Tropsha Alexander , Kizer John S. , Chaiken Irwin M. 
Published: May 2005

AbstractPeptides encoded in the antisense strand of DNA have been predicted and found experimentally to bind to sense peptides and proteins with significant selectivity and affinity. Such sense–antisense peptide recognition has been observed in many systems, most often by detecting binding between immobilized and soluble interaction partners. Data obtained so far on sequence and solvent dependence of interaction support a hydrophobic‐hydrophilic (amphipathic) model of peptide recognition. Nonetheless, the mechanistic understanding of this type of molecular recognition remains incomplete. Improving this understanding likely will require expanding the types of characteristics measured for sense–antisense peptide complexes and hence the types of analytical methods applied to such interactions. Understanding the mechanism of sense–antisense peptide recognition also may provide insights into mechanisms of native (sense) peptide and protein interactions and protein folding. Such insight may be helpful to learn how to design macromolecular recognition agents in technology for separation, diagnostics and therapeutics.
Quantitative structure–activity relationship studies on benzodiazepine receptor binding: Recognition of active sites in receptor and modelling of interaction
Authors: Gupta Satya P. , Saha Ranendra N. , Mulchandani Veena 
Published: May 2005

AbstractA quantitative structure‐activity relationship study was carried out for the binding of a series of ‘classical’ benzodiazepines (BZs) and some β‐carbolines with BZ receptors to investigate the active sites in the latter and the nature of the binding of compounds with them. Using the Hansch approach, an attempt was made to correlate binding affinities of compounds with various physico‐chemical and electronic properties of substituents. The correlations obtained showed the main roles were played by the hydrophobic constant π and the Hammett constant σ (an electronic parameter) of various substituents. This led to the suggestion that BZ receptors have many additional hydrophobic, hydrogen bonding and polor sites other than those suggested by Hollinshead et al. (1990). From the present study, the Hollinshead model of interaction was found to be inadequate to account fully for the binding of all types of compounds.
Epitope analysis using kinetic measurements of antibody binding to synthetic peptides presenting single amino acid substitutions
Authors: Zeder‐Lutz Gabrielle , Altschuh Danièle , Denery‐Papini Sandra , Briand Jean Paul , Van Regenmortel Marc H. V. , Tribbick Gordon 
Published: May 2005

AbstractThe fine modulation of peptide–antibody interactions was investigated with anti‐peptide monoclonal antibodies recognizing peptide 125–136 of the coat protein of tobacco mosaic virus. Nine synthetic peptides presenting single amino acid substitutions were selected for detailed analysis on the basis of their reactivity in ELISA. Kinetic measurements of the binding of four antibodies to these peptides performed with a biosensor instrument (BIAcoreTM, Pharmacia) were used to quantify the contribution of individual residues to antibody binding. The results showed that even conservative exchanges of some residues in the epitope results in a small but significant decrease of the equilibrium affinity constant due mostly to a higher dissociation rate constant of the monoclonal antibodies. Two amino acid residues directly adjacent to the epitope, which appeared to play no role when tested by ELISA, were shown to influence the kinetics of binding. These data should be useful for computer modelling of the peptide–antibody interactions.
Effect of high of pressure of EcoRI reactions
Authors: Kabata Hiroyuki , Nomura Akihiko , Shimamoto Nobuo , Kunugi Shigeru 
Published: May 2005

AbstractThe effect of pressure on reactions of restriction endonucleases was investigated. No obvious irreversible (after) effect was observed for EcoRI, while a considerable irreversible inactivation was found for BamHI. Thus the EcoRI reactions against λ DNA, pBR322 and pBluescript were studied under high pressure and little effect was observed on the overall reaction. The Dna concentration dependence of the kinetic data apparently fits the Michaelis‐Menten type equation and the evaluated rate parameters were: Vmax = 6.2±0.24 and 7.0±0.22 (×10−2 nM/min) at 0.1 and 200 MPa, respectively; Km = 19±1.8 and 28±1.7 nM at 0.1 and 200 MPa, respectively. The apparent activation volume corresponding to kcat/Km was ca + 1 mL/mol. a characteristics effect of pressure on the sequence specificity of these enzymes was seen in their star activity. Relaxed specificity was tightened by increasing pressure (200 MPa) with respect to that induced by low salt concentration or by the presence of organic solvent.
Selective oxidation of methionyl residues in the human recombinant secretory leukocyte proteinase inhibitor. Effect on the inhibitor binding properties
Authors: Tomova Svetlana , Cutruzzolà Francesca , Barra Donatella , Amiconi Gino , Ascenzi Paolo , Carugo Kristina Djinović , Menegatti Enea , Sarti Paolo , Schnebli Hans Peter , Bolognesi Martino 
Published: May 2005

AbstractBinding of the human recombinant secretory leukocyte proteinase inhibitor (SLPI) [native and with the methionyl residues at positions 73, 82, 94 and 96 of domain 2 oxidized to the sulfoxide derivative (Met(O) SLPI)] to bovine α‐chymotrypsin (α‐chymotrypsin) [native and with the Met192 residue converted to the sufoxide derivative (Met(O) α‐chymotrypsin)] as well as to native bovine β‐trypsin (β‐trypsin), which does not contain methionyl residues, has been investigated between pH 4.0 and 8.0, and between 10.0°C ad 30.0°C, from thermodynamic and/or kinetic viewpoints. By increasing the number of oxidized methytonyl residues present at the proteinase: inhibitor contact interface (from 0 to 3), the adducts investigated are increasingly destabilized and the relaxation time of the complexes into conformers less stable is enhanced. On the other hand, the selective oxidation methionyl residues of SLPI and α‐chymotrypsin, by the reaction with chloramines T, does not affect the proteinase inhibition recognition mechanism. Therefore, even though conformational changes may occur in the conversion native SLPI and native α‐chymotrypsin to their Met(O) derivatives, a localized steric hindrance can be considered as the main structural determinant accounting for the reported results.
Interaction of mithramycin with isolated GC and CG sites
Authors: Carpenter Mark L. , Cassidy Sarah A. , Fox Keith R. 
Published: May 2005

AbstractWe have studied the interaction of the GC‐specific, minor groove‐binding ligand, mithramycin, with cloned DNA inserts containing isolated GC and CG sites flanked by regions of (AT)n and An · Tn using DNase I and hydroxyl radical footprinting. We find that mithramycin binds to GC better than CG and that AGCT is a better site than TGCA. Sites flanked by (AT)n appear to be bound better than those surrounded by An · Tn. Although no footprints are produced at T9GCA9 and T15CGA15, DNase I cleavage is enhanced with the GC sites suggesting that there is some interaction with the ligand. Mithramycin also alters the DNase I cleavage of (GA)n · (CT)n.
Identification and analysis of a template‐primer (ds‐DNA) binding cleft in E. coli DNA polymerase I: An electrostatic potential contour pattern of the modeled structure
Authors: Yadav Prem N. S. , Modek Mukund J. , Yadav Janardan S. 
Published: May 2005

AbstractIn the modeled structure of the Klenow fragment of E. coli DNA polymerase I, we have identified a distinct region that exhibits a strong electropositive potential contour. The examination of the distribution of the electropositive and negative potential across the two‐dimensional slices of the modeled structure revealed that the positive potential was concentrated around the cleft. The approximate size and shape of the region appears well suited to accommodate eight base pairs of duplex DNA and is consistent with the position of the dsDNA binding cleft reported in the crystal structure [Beese et al., Science (1993) 260, 352–355].
In search of the ‘bio‐active conformation’—Is it induced by the target cell membrane?
Authors: Schwyzer Robert 
Published: May 2005

AbstractConformations of regulatory peptides interacting lipid membranes were compared with those of chemically constrained molecules that react‐selectively with different receptor classes. Striking similarities in the topochemistry of molecules with similar activity were observed, The membrane‐induced topomers were almost congruent with the topomers that are selectively recognized by the same receptors. Finally, the ideas developed in the membrane compartments theory allow a quantitative prediction of receptor preference are compatible with our present knowledge of receptor structure.