bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive features of continuous antigenic determinants
Authors: Geysen H. Mario , Mason Tom J. , Rodda Stuart J. 
Published: May 2005

AbstractWe sought to identify the features controlling the specificity of antibody recognition and thus gain insights into molecular recognition between proteins in general. A total of 103 epitopes with in 63 well‐defined antigenic peptides homologous with the relevant antigen sequence were identified. The contribution of each amino acid residue to the antibody binding activity of each apitope was investigated by ELISA testing of complete sets of peptide analogs containing single amino acid replacements. The data are summarized in a replaceability matrix. Some of the high frequency replaceabilities were expected, such as aspartate for glutamate, serine for threonine, etc., but unexpected relationships were also found, such as a high degree of acceptability of methionine as a replacement. Replaceability with a residue of opposite charge was rare. Glycine and tyrosine were frequently of low acceptability, except for glycine as a replacement for alanine. It was found that on average only about four to five amino acid residues in epitopes were required to determine specificity and provide binding energy. Specificity and binding energy were attributed to amino acid side chains rather than main chain atoms. Propensity factors for occurrence of amino acids in antigenic determinants were calculated. The prominence of certain hydrophobic residues as residues critical to recognition by antibody suggests that the molecular surface of an antigen in its combined from with antibody is altered from that occurring in the absence of antibody. Thus, antigenicity is not a static surface phenomenon but depends on the ability of the antigen to undergo rearrangement, supporting the induced fit concept.
T4 Phage deoxyribonucleoside triphosphate synthetase: Purification of an enzyme complex and identification of gene products required for integrity
Authors: Moen Laura K. , Howell Meredith L. , Lasser Gerald W. , Mathews Christopher K. 
Published: May 2005

AbstractWe have isolated a highly enriched preparation of the multienzyme complex which synthesize Deocyribonuleoside triphosphates (dNTPs) from bacteriophage T4‐infected bacteria. By a combination of SDS polyacrylamide gel electrophoresis and assays for specific enzyme activities, we have been able to identify in our final preparation ten different gene products which were previously identified as constituents of this complex, based upon studies with crude preparation. The complex dissociates at high concentrations of NaCl and MgCl2 but is stable under ionic conditions thought to exits in vivo. The purified complex catalyzes the efficient five‐step conversion of dCTP to dTTP. Experiments with several T4 mutants have demonstrated that gene product encoded by cd, regA, nrdA, and nrdB are necessary to retain physical integrity of the complex throughout the preparative procedure, while gp44, gp55, and gppseT are not required. We conclude from this evidence that the T4 early gene products which function in dNTP biosynthesis are, in fact, physically linked as a multienzyme complex, and that regA contributes to the integrity of this complex. However, the dNTP‐synthesizing complex as we isolate it contains no detectable DNA polymerase, nor have other known replication proteins been detected.
Glycolipid‐directed FH6 monoclonal antibody recognizes high molecular weight glycprotein antigen carrying sialyl LeX‐i determinant in the culture supernatant of PC‐9 cells
Authors: Yamagata Yoko , Shigeta Katsuyoshi , Murachi Takashi , Kannagi Reiji , Masuda Tohru , Imura Hiroo , Shin Sadahito , Tachikawa Tetsuya , Noda Atsunari , Ohe Yasuo 
Published: May 2005

AbstractThe properties of the antigen recognized by monoclonal antibody FH6 have been analyzed. FH6 was originally generated against a glycolipid, i.e. a difucoganglioside isolated from human colonic adenocarcinoma, and specifically reacts with sialyl Lex‐i detreminant. Several culture supernatants of human carcinoma cell line cells were found to have high levels of FH6‐reactive antigen, and PC‐9, a human lung carcinoma cell line was used for the analysis. A solid‐phase sandwich radioimmunoassay was performed to detect the antigen. The antigenic activity was extractable in 0.6 M PCA or 7% TCA, and was sensitive to mild alkaline treatment and to Pronase digestion. Most of the antigen was eluted in the void volume of a Sepharose CL‐2B column, which indicates that its molecular weights is greater than several million. It was eluted from a DEAE‐cellulose column at a NaCl concentration in the range of 0.2–0.25 M. The immunoaffinity‐purified antigen has a high carbohydrate content of more than 80%. These data indicate that the antigen recognized by FH6 in the culture supernatant of PC‐9 is not a glycolipid, but a high molecular weight glycoprotein which could be referred to as a mucin, or a proteoglycan, which contains keratan‐sulfate like glycosaminoglycan chains, as judged from the results of the glycosidase treatments.
Fluorescence spectroscopic studies on tryptophan at the saccharide‐binding site of castor bean hemagglutinin
Authors: Yamasaki Nobuyuki , Absar Nural , Funatsu Gunki 
Published: May 2005

AbstractThe environment of tryptophan in castor bean hemagglutinin (CBH) was analyzed fluorescence spectroscopy with regard to saccharide binding. Upon binding of specfic saccharides, the fluorescence maximum of 333 nm of CBH shifted to a wavelenght 2 nm shorter, owing to the change in the environment of tryptophan at the saccharide‐binding site. By analyzing the change in the fluorescence intensity at 320nm as a function of concentration of saccharides, the association constants for binding of saccharides to CBH were determined. The results suggest that the saccharide‐binding site on each B‐chain is actually composed of a subsite with which the saccharide residue linked to galactopyranoside at the non‐reducing end can interact, and another site which recognizes the galactopyranoside moiety. Quenching data indicated that five out of 22 tryptophans in CBH are surface‐localized and are available for quenching with both KI and acrylamide, and three other tryptophans are buried and are available only to acrylamide. Binding of raffinose to CBH decreased by 2 the number of tryptophan residues accesible to quenchers in the CBH molecule. We speculate that raffinose binds to CBH in such a manner as to shield the tryptophan located at the subsite from quenching by KI and acrylamide. The results also suggest that the tryptophan located at the subsite from quenching by KI and acrylamide. The results also suggest that the tryptophan residue atresidu at the saccharide‐binding site on each B‐chain is localized near the surface, and present in the positively charged environment.
Sequence simplification and the intra‐ and intermolecular self‐recognition properties of vasopressin/neurophysin biosynthetic precursor
Authors: Fassina Giorgio , Chaiken Irwin M. 
Published: May 2005

AbstractThe self‐assembly properties of the arginine 8‐vasopression/bovine neurophysin II (AVP/BNPII) biosynthetic precursor were studied using glycopeptide‐deleted and sequence‐redesigned semisynthetic derivaties. Semisythetic precursors were prepared by chemically coupling synthetic vasopressinyl sequence domains and native protein‐derived neurophysin II domain. Measurement of precursor‐protein association by extent of affinity chromatographic retardation on agarose‐immobilizes BNPII verified that the semisynthetic precursor with native AVP sequence has an enhanced self‐association propensity similar to that predicted for native precursor. Here, the stabilizing contacts between hormone and neurophysin domains, mainly the positively charged protonated α‐amino group and tyrosyl 2 side chain of the hormone, are retained. Semisynthetic precusor variants in which the hormone domain is sequence‐simplified by introducing alanyl residues in position not considered important for neurophysin recognition show non‐reduced association to BNPII. In contrast, removal of one of the main contact element between hormone and neurophysin by acetylation of the hormone α‐amino group abolishes potentiation of precursor self‐association. The results show that the presence of the C‐termial glycopeptide sequence domain of native vaspressin precursor is not required to promote self‐assemblly of the precursor. The data verify the view proposed for the oxytocinyl precursor that intramolecular domain interaction is the triggering event which promotes the increase in affinity of precursor self‐association (intermolecular self‐recognition). The data also define some of the intramolecular self‐recognition element in the folded precursor required for the high affinity intermolecular self‐recognition.
Production of anti‐idiotypic antibodies by immunization with a pair of complementary peptides
Authors: Bost Kenneth L. , Blalock J. Edwin 
Published: May 2005

AbstractPrevious investigations have suggested that pairs of peptides specified by complementary RNA sequences (termed complementary peptides) can interact with one another. In the light of this finding, we hypothesized that an antibody directed against a peptide might interact with an antibody against its complementary peptide at the antigen combining site. To address this possibility, polyclonal antibodies against a peptide, Leu‐Glu‐Arg‐Ile‐Leu‐Leu (LERILL), and its complementary peptide, Glu‐Leu‐Cys‐Asp‐Asp‐Asp (ELCDDD), were made monospecific by affinity chromatography. Using radioimmunsassays, anti‐ELCDDD antibodies were shown to interact with 125I‐anti‐LERILL antibodies but not with 125I‐control antibodies. More importantly, the interaction of the two antibodies could be blocked using either peptide antigen, but not with control peptides. Furthermore, 125I‐anti‐LERILL binding to LERILL could be blocked with anti‐ELCDDD antibody and vice versa. We concluded therefore that antibody/antibody binding occurred at or near the antigen combining site, demonstrating that this interaction was an idiotypic/anti‐idiotypic one.
Molecular recognition in synthetic polymers. Enantiomeric resolution of amide derivatives of amino acids on molecularly imprinted polymers
Authors: O'Shannessy Daniel J. , Andersson Lars I. , Mosbach Klaus 
Published: May 2005

AbstractMolecular imprints were prepared using L‐phenylalanine anilide as the print molecule and methacrylic acid as the functional monomer. Methacrylic acid interacts ionically with the primary amine of the print molecule and via hydrogen bonding with the amide function. In the HPLC mode such polymers were shown to exhibit efficient enantiomeric resolution of a racemic mixture of the original print molecule. Enantiomeric resolution was shown to be dependent on the ratio of methacrylic acid to print molecule in the pre‐polymerization mixture and specific for the presence of both print molecule and functional monomer. Further analysis showed the importance of both the primary amino and amide functions in the correct stereochemistry for recognition and enantiomeric resolution of compounds on such polymers. Other amide derivatives of amino acids including p‐nitoranilides, β‐naphthylamides and amides were recognized by such polymers, and enantiomeric resolution was obtained for amide derivatives of amino acid ranging from alanine to tryptophan on a single polymer. The implications of these findings with respect to the mechanism of recognition and the ability to predict enantiomeric resolution of molecules on molecularly imprinted polymers will be discussed.
Interaction between phage G13 and its oligosaccharide receptor studied by equilibrium dialysis
Authors: Bruse Gert W. , Wollin Ralfh , Lindberg Alf A. 
Published: May 2005

AbstractThe reversible binding of phage G13, a ϕX174‐like single‐strand DNA phage, to a 3H‐labeled nonasaccharide from the lipopolysaccharide of its natural host Esacherichia coli C was studied with equilibrium dialysis. The binding constant (Ka) was determined to 1.3 × 107 M−1 in Scatchard and Lineweaver–Burk plots. Approximately one saccharide bound per G13 phage particle which suggests that only one of the 12 spikes in each G13 virion was engaged in the phage/receptor saccharide interaction. Equilibrium dialysis inhibition experiments with saccharides from lipopolysaccharides of an isogenic series of Salmonella typhimurium mutants showed that hepta‐ and pentasaccharides from two G13‐sensitive bacteria, i.e., with efficiencies of plating of 0.1–1.0 compared to E. coli C, were efficient inhibitors with Ka‐values ≥ 1.2 × 107 M−1. The octa‐ and hexasaccharides from two G13 resistant strains, with efficiency of plating ⩽ × 10−4, were either > 1000‐fold of > 15‐fold less efficient as inhibitors with Ka‐values ⩽8.8 − 105 M−1. The results show that phage G13 binds in a specific and reversible way to penta‐, hepta‐, and nonasaccharides from G13 sensitive bacteria with the specificity residing in the hexose and heptose region of the core lipopolysaccharide.
Molecular recognition between oligopeptides and nucleic acids. Specificity of binding of a monocationic bis‐furan lexitropsin to DNA deduced from footprinting and 1H NMR studies
Authors: Lee Moses , Krowicki Krzysztof , Shea Regan G. , Lown J. William , Pon Richard T. 
Published: May 2005

AbstractMPE‐Fe(EDTA) footprinting of a novel monocationic bis‐furan lexitropsin 6 on a HindIII/EcoRI restriction fragment of pBR322 DNA revealed a series of four‐base binding sites (all 5′ → 3′) of (primary) TGTA, TGAA, AAAT, ACAA, TTAT, and (secondary) CTAA, TCGT, TGTA, GTCA, and GGTT. Thus 6 can accept a GC pair at positions 1, 2 or 3 of the binding site with a strict 3′ (4 position) AT requirement. Marked enhancement of cleavage, particularly at GC rich sequences, is observed at regions flanking or even up to 18 base pairs remote from a given binding site. The non‐exchangeable and imino 1H NMR resonances of the 1:1 complex and d‐[CATGGCCATG]2 were assigned using a combination of NOE differences, NOESY and COSY techniques. 1H NMR studies (ligand induced chemical shifts and NOE differences) of Lexitropsin 6 with d‐[CATGGCCATG]2 show unambiguously the location and orientation of the N to C termini of 6 on the sequence 5′‐G5C6C7A8‐3′, with the C terminus oriented to A8. This orientation of 6 in the minor groove of 5′‐GCCA is confirmed by an NOE observed between H1 2a of 6 and AH8(8). This preference for binding of 6 to the sequence 5′‐GCCA when challenged with d‐[CATGGCCATG]2 is in accord with the conclusions of the footprinting experiments wherein GC base pairs can be accepted in the first three positions and with a strict 3′ terminus AT reading requirement. Collectively the data support the inference of a GC recognizing capacity for a 2,5‐substituted furan moiety within a lexitropsin. The 1H NMR data indicate that the decadeoxyribonucleotide duplex exists in the B conformation in both the 1:1 complex and the free from. The apparent binding constant of 6 to calf thymus DNA is 1.68 × 105 M−1 whereas netropsin under similar conditions gives a value of 1.85 × 107 M−1. This suggests that if advantage is to be taken of the GC recognizing property of a 2,5‐substituted furan in longer lexitropsins it should be flanked by more strongly bound moieties.
Conformational analysis of blood group A‐active glycosphingolipids using HSEA‐calculations. The possible significance of the core oligosaccharide chain for the presentation and recognition of the A‐determinant
Authors: Nyholm Per‐Georg , Samuelsson Bo E. , Breimer Michaelle , Pascher Irmin 
Published: May 2005

AbstractConformational analysis of four different A‐active glycosphingolipids, A types 1–4, was carried out using HSEA‐calculations with the GESA‐program. In their minimum energy conformations the oligosaccharide chains are more or less curved; in particular the type 3 and 4 have a strongly bent shape. When the carbohydrate structures are linked to ceramide, using the conformational features predominantly observed in crystal structures of membrane lipids, rather drastic differences in the orientation of the oligosaccharide chains are obtained. For the type 1 glycosphingolipid the model study indicates that the A‐determinant extends almost perpendicularly to the membrane plane whereas for type 2, 3 and 4 the terminal part of the oligosaccharide chains is more parallel to the membrane. The fucose branch on type 3 and type 4 thereby appears directed towards the environment whereas for type 2 it would face the membrane. Due to restrictions imposed by the membrane layer this core specific orientation is largely preserved even if the flexibility of the saccharide‐ceramide linkage is taken into account. Hydrophilic and hydrophobic sites on the surface of the different oligosaccharide chains in their minimum energy conformation were located using the GRID‐program. It is suggested that the core‐dependent presentation of the A‐determinant might explain the chain type specificity observed for different monoclonal anti‐A antibodies. The results further suggest that assay systems ensuring a membrane‐like presentation of the glycolipid antigen should be used in studies of glycolipid/protein interactions.
Model‐Building of Fnr and FixK DNA‐binding domains suggests a basis for specific DNA recognition
Authors: Cherfils Jacqueline , Gibrat Jean‐François , Levin Jonathan , Batut Jacques , Kahn Daniel 
Published: May 2005

AbstractThe DNA‐binding C‐terminal domains of the regulatory proteins Fnr from Escherichia coli and FixK from Rhizobium meliloti have been modelled on the basis of their homologies to the CAP protein from E. coli. Residues Glu181, Thr182 and Arg185 of CAP, which are exposed residues of the DNA‐recognition helix αF, are conserved in Fnr and FixK. However, Arg180 and Gly184 are substituted by Val and Ser respectively in Fnr. We propose that this valine makes a Van der Waals' contact with the first thymine in the Fnr consensus TTGA‐N6‐TCAA, and that the serine contributes to the binding by displacing a thymine‐bound water molecule. The corresponding residues in FixK, Ile and Ser allow the same interactions with a thymine. Therefore we predict that FixK may recognize the same sites as Fnr. This is supported experimentally by showing that Fnr can substitute for FixK in activating the fixN gene in E. coli.
Binding characteristics of a series of dimeric tripeptide enkephalins for δ opiate receptors in rat brain and NG108–15 cells
Authors: Shimohigashi Yasuyuki , Kodama Hiroaki , Costa Tommaso , Lutz Rudolf A. , Chen Hao‐Chia , Rodbard David 
Published: May 2005

AbstractThe N‐terminal tripeptide enkephalin analogue, Tyr‐D‐Ala‐Gly, was dimerized at the C‐terminus systematically with a series of α,ω‐diaminoalkanes, NH2(CH2)nNH2 (n = 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, and 22). The binding affinities of dimers for δ opiate receptors in rat brain were evaluated and compared with those for δ receptors in NG108–15 cells. Although the monomeric tripeptide amide was almost inactive, dimers showed a dramatic increase in binding affinity (8–900 times). The enhancement of affinity was apparently related to the number of methylene chains in the crosslinking spacer moiety, and it was maximal at n = 14–18 in the rat brain. In NG cells the activity increased progressively from n = 2 to n = 22 without reaching any apparent peak. These results suggest that δ receptors in rat brain and NG cells may have slight structural differences.
Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity
Authors: Rizzo Vincenzo , Battistini Carlo , Vigevani Aristide , Sacchi Nereo , Razzano Giuseppe , Arcamone Federico , Garbesi Anna , Colonna Francesco Paolo , Capobianco Massimo , Tondelli Luisa 
Published: May 2005

AbstractThe equilibrium and kinetic aspects of the interaction between four anthracyclines and two synthetic self‐complementary hexanucleotides was investigated by fluorescence detection. Two of the studied anthracyclines are widely used antitumor drugs: doxorubicin (1, formerly adriamycin) and daunorubicin (2, formerly daunomycin). The other two 9‐deoxydoxorubicin (3) and 3′‐deamino‐3′‐hydroxy‐4′‐epidoxorubicin (4), are doxorubicin analogues with modifications of the chemical groups that have been proposed as responsible for sequence specificity (Chen, K.‐X., Gresh, N. and Pullman, B. (1985). J. Biomol. Struct. Dyn. 3, 445–466). One of the oligonucleotides, d(CGTACG), is identical to that used in the high resolution x‐ray structure determination of the daunorubicin intercalative complex (Wang, A. H.‐J., Ughetto, G., Quigley, G. J. & Rich, A. (1987). Biochemistry 26, 1152–1163). Binding to this hexanucleotide is compared with intercalation into the d(CGCGCG) duplex, revealing sequence preferences of the four anthracyclines. Taking into account the anthracycline aggregation and the dissociation of the hexanucleotide double stranded form, results can be interpreted with a model that assumes complete fluorescence quenching at intercalative sites containing the CG base pair, and a large residual fluorescence after intercalation within the TpA fragment. All four anthracyclines show preferential intercalation at sites near the ends of both hexanucleotide duplexes, partly as a result of positive cooperativity in the formation of di‐intercalated species at these sites. Within the limits of experimental error, complete site specificity for the CpG fragment is found in the intercalation of 1 and 2 into d(CGTACG) duplex, whereas analogues 3 and 4 give increasing evidence of intercalation at other sites including the fluorescence‐preserving TpA fragment. Site specificity is less pronounced in the association with d(CGCGCG), when cooperativity is taken into account. Kinetic data corroborate the results of equilibrium studies and are interpreted with a mechanism that includes formation of an intermediate bound species followed by drug redistribution to preferential sites. Finally, from a comparison of pertinent site binding constants, approximate free energy contributions to sequence specific DNA interaction, due to C9OH on the aglycone and NH on daunosamine, are estimated not to exceed 2 kcal/mol.
Effect of intercalative binding compared to external binding on Z/B equilibrium of poly d(GMe5C) using fluorescent oxazolopyridocarbazoles as probes
Authors: Le Ber Pierre , Schwaller Marc‐Antoine , Auclair Christian 
Published: May 2005

AbstractUsing the fluorimetric determination of the binding isotherms in combination with circular dichroism, we have investigated the effect of the binding of the intercalating chromophore oxazolopyridocarbazole (OPC) to poly d(Gme5C) on B/Z equilibrium, compared to the effect of the external binder OPC derivative pentyl‐2‐OPC. The intercalating OPC appears to be very efficient in reversing left‐handed poly d(Gme5C) into the right‐handed conformation, according to a cooperative mode. For each OPC molecule intercalated into the B form, 7 base pairs were switched from the Z to B conformation. In contrast, the binding of the external binder pentyl‐OPC resulted in a limited Z to B transition, involving the switch of 1.4 base pairs from the Z to B conformation. Moreover, OPC appears much more efficient than pentyl‐OPC in inhibiting both the extent and kinetics of the salt‐induced B/Z transition. At low drug to DNA ratio (D/P = 1/50), a 7‐fold and 1.5‐fold inhibition of the B/Z transition kinetics occurs in the presence of OPC and pently‐OPC, respectively. These features are discussed in terms of the difference existing between the entropic contribution in the DNA binding of intercalating agents, compared to external binders.