Search PubMed⌕ Search

Biomedical subjects

D S Linthicum

Publications and source records attributed to D S Linthicum.

At least 37 records · Page 2Linked to original sources
PubMed1996

Hypothesis: a possible role for mast cells and their inflammatory mediators in the pathogenesis of autoimmune encephalomyelitis.

Mast cells and their potent chemical mediators are known to initiate and modulate a number of important inflammatory cascades. With respect to the central nervous system, the role of mast cells as participants in the promotion and resolution of inflammation has been widely underestimated. Mast cell-derived histamine, serotonin, kallikreins, and tumor necrosis factor-alpha (TNF-alpha) can enhance microvascular permeability, leukocyte rolling, adhesion, and extravasation of inflammatory cells into the brain and spinal cord. Mast cell mediators may play an important role in autoimmune encephalomyelitis and multiple sclerosis by promoting the entry of autoreactive T cells and the recruitment of nonspecific monocytes across the blood:brain barrier.

Animals↗
PubMed1996

Circular dichroism spectroscopy of monoclonal antibodies that bind a superpotent guanidinium sweetener ligand.

Three monoclonal antibodies (mAb) with nanomolar affinity to the superpotent trisubstituted guanidinium sweetener ligand N-(p-cyanophenyl)-N'-(diphenylmethyl)guanidineacetic acid were studied by circular dichroism (CD) spectroscopy. Two mAb, NC6.8 (IgG2b,kappa) and NC10.8 (IgG3, kappa) exhibited similar CD spectra, but mAb NC10.14 (IgG2b, lambda) had very different CD spectra in both far- and near-UV regions. Some of these differences may be due to effects of aromatic amino acid side chains, especially Trp and Tyr, located at the immunoglobulin intradomain surfaces. Heavy- and light-chain dissociation of reduced Fab fragments in 1 M acetic acid minimized these effects. Ligand binding changed the sign and amplitudes of the near-UV CD spectra of all three mAb. Calculation of the CD difference spectra (bound minus free) of stoichiometrically bound antibody-ligand complexes allowed us to visualize the net spectral changes. On the basis of the three-dimensional structures experimentally solved for NC6.8 and theoretical models of NC10.8 and NC10.14, we suggest that the p-cyanophenyl moiety on the sweetener ligand acts as a molecular pointer in the CD spectra and identifies contact aromatic residues in the different antibody binding pockets.

Acetates↗
PubMed1996

Modeling the structure of the combining site of an antisweet taste ligand monoclonal antibody NC10.14.

We report the predicted combining site structure of the monoclonal antibody fragment, NC10.14, which is specific for the superpotent sweetener, N-(p-cyanophenyl-N'-(diphenylmethyl) guanidine acetic acid, using computer-aided molecular modeling and experimental methods, such as fluorescence spectroscopy and circular dichroism. This is the first computer-aided modeling study on a lambda-chain antibody fragment. We have also identified the amino acids that are involved in ligand binding. Aromatic residues, L:91(W), L:96(W), and H:100G(Y) are predicted to make van der Waals contacts with the p-cyanophenyl moiety of the ligand. Residue H:56(K) is predicted to provide a counterion for the acetic acid moiety, and H:50(E) provides the negatively charged potential for interaction with the positive guanidinium group. We also make a comparison of the binding site architecture of NC10.14 with that of a related monoclonal antibody fragment NC6.8.

Acetates↗
PubMed1996

Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking.

A mouse monoclonal anti-TNP IgE antibody (IgE-La2) was screened by a competitive-binding ELISA with a random pool of over 2000 small molecules, mostly drugs, drug derivatives and metabolites. Thirteen of these (naproxene, beta-carboxy-chi-naphthol, oxolinic acid, hymecromone, 8-aminoquinoline, beta-naphthylamine, chi-nitrilo-cinnamic acid, 1,5-diaminonaphthaline, prolonium iodide, diaspirin, 3,4,5-trimethoxy-cinnamic acid, cycrimine, hemimellitic acid) were found to bind as strongly, or stronger, to the antibody as the immunizing hapten. We have used a Monte Carlo search technique for simulated docking of the DNP and non-DNP ligands to a model of the Fv region of IgE(La2). The validity of structural predictions made by the AutoDock program were tested on IgG(ANO2), the three-dimensional structure of which had been obtained previously by X-ray crystallography and 2D-NMR. The rms differences between the experimentally determined and auto-docked complexes in the energetically most favored binding modes were 0.31-0.44 A. Evaluation of structures of IgE(La2)-ligand complexes [including 2,4-dinitrophenol (DNP), 16 DNP amino acids, and the 13 non-DNP ligands listed above] obtained by computer-aided automated docking, suggested the existence of two subsites within an approximately 12 x 18 A2 groove extending between the H and L CDRs. Some of the ligands (DNP-Glu, 8-aminoquinoline, prolonium-I, beta-naphthylamine) were found to bind exclusively to subsite 1, others (DNP-Ala, chi-nitrilo-cinnamic acid, hemimellitic acid, beta-carboxy-chi-naphthol) to subsite 2. The majority of DNP amino acids and other ligands (oxolinic acid, 3,4,5-trimethoxy-cinnamic acid, diaspirin, [R]-cycrimine) were found to occupy an overlapping area including subsites 1 and 2, while some of the compounds (DNP-Asn, DNP-Pro, hymecromone, 1,5-naphthylenediamine) were predicted to interact with either of these subsites with comparable probabilities. When all of the docked La2-ligand complexes were taken into account, five tyrosine residues (H33, L32, L91, L92, L96) were found to provide the majority (53.4%) of all observed contact points. Thus, a multitude of interactions with aromatic residues, and a combinatorial type of interaction within the binding region, seem to be the major factors to explain the mechanism of heteroligation by IgE(La2).

Amino Acid Sequence↗
PubMed1996

Mast cell-derived histamine and tumour necrosis factor: differences between SJL/J and BALB/c inbred strains of mice.

Mast cells cultured from bone marrow of BALB/c and SJL/J inbred strains of mice using IL-3 showed distinct patterns of growth and marked differences in their content of TNF-alpha and histamine. Mast cells derived from SJL/J mice grew and matured at a faster rate than those from BALB/c bone marrow. SJL/J mast cells were found to contain more than twice the amount of histamine and TNF-alpha in their granules than BALB/c-derived cells. In addition, when triggered by anti-DNP IgE antibody and specific antigen (DNP-albumin), mast cells derived from SJL/J mice released more histamine and TNF-alpha than mast cells derived from BALB/c mice. These results confirm previous observations regarding a genetic basis for mouse strain differences in mast cell growth rates, and extend previous observations to document differences in mast cell mediator contents. These results are consistent with the concept that genetically controlled differences in the numbers of central nervous system (CNS)-associated mast cells and their vasogenic mediators may play an important role in modulating oedema and inflammation in CNS trauma and diseases in mice.

Animals↗
PubMed1996

ABGEN: a knowledge-based automated approach for antibody structure modeling.

Immunoglobulin (Ig) amino acid sequences are highly conserved and often have sequence homology ranging from 70 to 95%. Antigen binding fragments (Fab), variable region fragments (Fv), and single chain Fv (scFv) of more than 50 myeloma proteins and monoclonal antibodies (mAb) have been crystallized and display a high degree of structural similarity. Based on this observation, several homology modeling approaches have been developed for the prediction of Fab and Fv structures prior to their experimental determination. We have extracted features from existing Ig sequences, 44 known Fab and Fv structures to create an automated AntiBody structure GENeration (ABGEN) algorithm for obtaining structural models of antibody fragments. ABGEN utilizes a homology based scaffolding technique, and includes the use of invariant and strictly conserved residues, structural motifs of known Fab, canonical features of hypervariable loops, torsional constraints for residue replacements and key inter-residue interactions. The validity of the ABGEN algorithm has been tested using a five-fold cross validation with the existing Fab structures. Molecular mechanics and dynamics methods have been implemented with ABGEN models to accurately predict two Fab structures of anti-sweetener antibodies prior to crystallographic determinations.

Algorithms↗
PubMed1996

Microvascular leakage in mouse pial venules induced by bradykinin.

The actions of bradykinin on pial venule leaky site formation were measured intra-vitally in two inbred strains of mice (BALB/c and SJL/J). Pial venules were visualized using an open cranial window microscopy technique and the microvascular leaky site formation was assessed visually using a fluorescein-dextran (70 kDa) INDICATOR. The SJL/J strain was found to be very sensitive to bradykinin-induced microvascular leakage. Pial venule leaky site formation was observed after exposure to 10 pM of bradykinin. In contrast, the BALB/c strain was found to be refractory to bradykinin-induced leakage. Pial arterioles were dilated in response to bradykinin in both strains of mice. These results support the concept that genetically controlled differences in vascular sensitivity and localization of inflammatory peptides play important roles in the generation of vasogenic oedema and inflammation in CNS trauma and disease.

Animals↗
PubMed1996

Molecular probes for sweeteners: immunorecognition of superpotent guanidinium compounds.

Monoclonal antibodies (MAb) were made to two different superpotent guanidino sweet tasting ligands, N-(p-cyanophenyl)-N'-(diphenylmethyl)-guanidineacetic acid and N-(p-cyanophenyl)-N'-(cyclooctyl)-guanidineacetic acid. In the present study we examined the binding specificity of three MAb clones (denoted as NC10.7, NC10.13, and NC37.3). The isotypes of these MAb were determined to be IgG1 kappa for NC10.7 and NC37.3, while NC10.13 was IgG2b, kappa. The dissociation constants for the MAb were 19 nM (NC10.7), 28 nM (NC10.13), and 16 nM (NC37.3). The binding specificity of each MAb was characterized by a competitive inhibition radioimmunoassay using related sweetener analogues. Antibodies to this family of sweet tasting compounds may be useful probes for the study of sweet taste chemistry and identification of novel sweet taste ligands.

Acetates↗
PubMed1995

Expression of mRNA for 55-kDa and 75-kDa tumor necrosis factor (TNF) receptors in mouse cerebrovascular endothelium: effects of interleukin-1 beta, interferon-gamma and TNF-alpha on cultured cells.

The interactions between tumor necrosis factor-alpha (TNF-alpha) and its receptors have been implicated to play an important role in the pathogenesis of experimental autoimmune encephalomyelitis (EAE). The effects of cytokines on the steady state levels of TNF receptor (TNFr) mRNA in cerebrovascular endothelial cells (CVE) cultured from EAE-susceptible (SJL/J) and EAE-resistant (BALB/c) mice were examined. Interferon-gamma and interleukin-1 beta up-regulated the levels of both the 55-kDa and 75-kDa TNFr mRNA, while TNF-alpha had no effect. No differences were observed in cytokine-induced TNFr mRNA levels between BALB/c and SJL/J CVE that might explain differences in EAE susceptibility.

Animals↗
PubMed1995

Absorption spectroscopy of the complexation between superpotent guanidinium sweeteners and specific monoclonal antibodies.

Spectroscopic studies of antibody-antigen interactions can provide useful information about the interactive motifs and energetics involved in the intermolecular association process. In this study we used absorption spectroscopy to examine the interactions between five different monoclonal antibodies (mAb) and four superpotent ligand sweeteners. Quantitative changes in the absorption spectra in the wavelength range of 230-800 nm were utilized for the determination of intrinsic association constants and thermodynamic parameters of the mAb-ligand complexes. The intrinsic association constants for the mAb-ligand complexes were found to be in the range of 10(7)-10(5) lM-1 and were in agreement with previous radioimmunoassay determinations. For two mAb, qualitative changes in the spectra in the 340 nm range could be identified and were related to the presence of charge-transfer interaction between the guanidinium ligand and aromatic residues in the binding site of the mAb. A charge transfer spectra was observed in mAb NC10.8 with two different sweetener ligands. The thermodynamic parameters of the ligand-mAb interactions were analyzed by van't Hoff plots and in almost all cases the reactions were found to be enthalpically driven. The determinations of intrinsic affinity and thermodynamic parameters may be useful in computer-aided molecular modelling studies of the antibody binding pocket and predicted ligand docking orientations. Antibody NC6.8 was found to react with this set of sweetener ligands in a rank order that is related to their sweetness potencies and the spectroscopic findings for NC6.8 are in agreement with the X-ray diffraction data of the Fab-ligand crystal structures.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetates↗
PubMed1995

Structural predictions of the binding site architecture for monoclonal antibody NC6.8 using computer-aided molecular modeling, ligand binding, and spectroscopy.

Monoclonal antibody NC6.8 binds the superpotent sweetener ligand N-(p-cyanophenyl)-N'-(diphenylmethyl) guanidineacetic acid with high affinity (Kd = 53 nM). Using computer-aided molecular modeling and several experimental techniques, such as competitive ligand binding, absorbance spectroscopy, and fluorescence spectroscopy, we have predicted the structure of the variable domain fragment (Fv) and identified the key residues in the combining site of the antibody. We have identified nine specific amino acids as being involved in ligand recognition and complexation. Most notable are H:33W, which is responsible for ligand-induced tryptophan fluorescence quenching, H:56R, which forms a salt bridge with the carboxylate moiety of the ligand, and L:34H, which, deep in the binding site, interacts with the cyanophenyl portion of the ligand. Two residues located deep in the putative binding pocket, H:35E and H:50E, provide the negatively charged potential for interaction with the protonated aryl nitrogen and the positive guanidinium group. These modeling predictions were made before the solution of high-resolution structures of the native Fab (2.6 A) and the Fab-ligand complex (2.2 A). Comparisons between the theoretical model and experimental native and liganded Fab structures are made.

Acetates↗
PubMed1995

Intramolecular signaling upon complexation.

Crystal habits can be used as indicators of conformational changes in their constituent proteins. As in the conversion of unliganded hemoglobin to the oxygenated form, the addition of a small hapten to a suspension of platy crystals of an unliganded Fab (NC6.8) results in the immediate disintegration of the plates and their replacement with prisms of the ligand-protein complex. Examination of the native and liganded forms by X-ray crystallography reveals that the space groups and protein structures are different. During complexation there are ligand-induced conformational changes both in the antigen combining site (local alterations) and in more distal portions of the molecule (allosteric changes). There is an extension of the light chain (10 A increase in length), a commensurate shortening of the heavy chain (by flexing), and a decrease in the "elbow bend" angle of 31 degrees (184 degrees to 153 degrees). Relative to the variable domains, the constant domain pair moves mainly as a unit in such a way that the carboxyl end of the heavy chain is displaced by 19 A. In an intact antibody this displacement may be relayed as a tug (by tensile forces) on the segment connecting the Fab to the Fc region, perhaps altering the orientations of the constituents responsible for such effector functions as complement activation.

Animals↗
PubMed1994

Identification of residues in monoclonal antibody NC10.8 that bind to the sweetener N-(p-cyanophenyl)-N'-(diphenylmethyl)guanidinoacetic acid by using radioligand binding, absorption and fluorescence spectroscopy, computer-aided molecular modeling, and site-directed mutagenesis.

The interactive residues for mouse mAb NC10.8, which binds a superpotent guanidinium sweetener N-(p-cyanophenyl)-N'-(diphenylmethyl)guanidinoacetic acid with high affinity (Kd = 5 nM), were examined by using radioligand competitive binding, photoaffinity labeling, absorption and fluorescence spectroscopy, computer-aided molecular modeling, and site-directed mutagenesis. Competitive ligand analogue binding data revealed important structural features and a pH sensitivity for ligand binding. Spectroscopy of the sweetener-mAb complex revealed ligand-induced fluorescence quenching and the presence of a charge-transfer band. Site-directed mutagenesis of L:96W abolished the ligand-induced fluorescence quenching and reduced Ab affinity. The apparent Kd increased from 5 nM to more than 200 nM after such modification. A theoretical model of the Fv region was generated with use of a knowledge-based algorithm, and this model was used to identify the locations of key residues in the complementarity determining regions. These experimental and theoretical studies support the prediction that the sweetener ligand coordinates with the following residues: L:34H contacts the cyanophenyl ring, L:27DR forms a salt bridge with the acetic acid moiety, L:96W forms a pi-pi interaction with the cyanophenyl ring, and H:95E contacts the positively charged aryl nitrogen. These studies are important to our understanding of Ab-ligand specificity and may also shed light on the important chemical motifs responsible for elevated levels of sweetness potency in organic compounds.

Acetates↗
PubMed1994

Local and transmitted conformational changes on complexation of an anti-sweetener Fab.

Crystal structures of an Fab (NC6.8) from a murine IgG2b(kappa) antibody and its complex with a sweet-tasting, N-,N'-,N"-trisubstituted guanidine compound (NC174) have been determined by X-ray analysis. Both crystal forms are produced by a microseeding technique in polyethylene glycol (PEG) 8000 but the habits and space groups are very different. The native protein crystallizes as plates in the monoclinic space group C2 and the complex crystallizes as prisms in the orthorhombic space group P2(1)2(1)2. The structures were solved by molecular replacement methods, with the Fab fragments from the 4-4-20, HyHel-5 and BV04-01 antibodies as starting models. On binding of the ligand, N-(p-cyanophenyl)-N'-(diphenylmethyl)-N"-(carboxymethyl)g uan idine, the protein exhibits significant local conformational changes in the active site, particularly in the third complementarity-determining region (CDR3) of the heavy chain. The ligand enters the small crevice by end-on insertion with the cyanophenyl group in the lead and the diphenyl rings partially protruding from the entrance. No strict pi-pi stacking interactions are observed. However, tyrosine L32 (CDR1), tyrosine L96 (CDR3) and tryptophan H33 (CDR1) help immobilize the cyanophenyl ring and guanido group, and tyrosine H96 moves about 4.5 A to lie between the rings of the diphenyl group. The positive charge on the guanido group is compensated by glutamic acid H50 (CDR2) while the negative charge on acetic acid is neutralized by arginine H56 (CDR2) and by hydrogen bonding with asparagine H58 (CDR2). Water molecules participate in the binding process by hydrogen bonding with the cyano and guanido groups. The mechanism of binding is a clear example of induced fit. Like hemoglobin, the NC6.8 Fab can be classified as an allosteric protein, since its overall structure is altered by the binding of a small ligand. In crystals of the native Fab the elbow bend angle is 184 degrees while in crystals of the complex the elbow angle is 153 degrees. There is also a reciprocal push-pull type of change where the heavy chain is flexed and the light chain is extended. The tail of the heavy chain, which would be connected to the Fc in an intact antibody, is displaced 19 A relative to its position in the unliganded Fab. Within the limited series of sweetener-Fab complexes we have thus far examined, only the NC174 hapten has produced such results.(ABSTRACT TRUNCATED AT 400 WORDS)

Acetates↗
PubMed1994

Spectroscopic evidence for charge-transfer complexation in monoclonal antibodies that bind opiates.

Molecular complexes of four monoclonal anti-morphine antibodies (mAb) with the opiate ligands morphine, oxymorphone, and naloxone were studied using UV-VIS absorption spectroscopy. Although strong overlaps in the absorption spectra of the antibodies, ligands, and complexes were observed, a curve-fitting method was developed to correlate the absorbance with the concentration of the ligand-antibody complex. Using this technique, we determined the intrinsic association constants for the mAb with morphine to be in the nanomolar range, while association constants for oxymorphone and naloxone were in the micromolar range. These values were found to be in agreement with previous radioimmunoassay determinations. We also observed different changes in the absorbancy of the mAb upon complexation with different ligands and such changes were found to be different for all four mAb examined. Upon complexation with the ligand morphine, two of the mAb (clone numbers MOR368-21 and MOR10.5) displayed distinct charge-transfer spectral bands in the 320-nm region. These observations suggest that mAb binding site tryptophans may participate in the formation of the antibody-ligand complex and such complexation involves a charge-transfer interaction.

Antibodies, Monoclonal↗
PubMed1994

Mechanism of allergenic cross-reactions--IV. Evidence for participation of aromatic residues in the ligand binding site of two multi-specific IgE monoclonal antibodies.

The binding sites of two IgE monoclonal antibodies (mAbs), LA2 and LB4, were examined by absorption, fluorescence spectroscopy and computer-aided molecular modeling (CAMM). Absorption spectra revealed the formation of 1:1 molecular complexes for both LA2 and LB4 with a variety of structurally different ligands. For mAb LA2, the binding constants for ligands consisting of different amino acid derivatives coupled to DNP could be divided into two groups, suggesting that certain amino acid side chains (e.g. hydrophobic) of the derivatives were a contributing feature in ligand recognition. The presence of a charge-transfer band (320-340 nm) was also observed for complexation with several different ligands, indicative of aromatic ligand interactions with mAb binding site tryptophans. CAMM studies of the Fv region for both mAb support of the empirical observations and inspection of the Fv models reveal numerous binding site aromatic residues that are likely candidates for ligand recognition and complexation. The multi-specificity of these mAbs for different ligands may be due to a multitude of interactions with aromatic residues in the binding sites.

Amino Acid Sequence↗
PubMed1994

Computer-aided molecular modeling of the binding site architecture for eight monoclonal antibodies that bind a high potency guanidinium sweetener.

Computer-aided molecular modeling of the antibody binding site of eight different monoclonal antibodies (mAb) that bind the intense sweetener ligand (N-(p-cyanophenyl)-N'-diphenylmethyl) guanidine acetic acid was completed using canonical loop structures and framework regions from known immunoglobulins as "parent structures" for the molecular scaffoldings. The models of the fragment variable (Fv) region of the mAb were analyzed for the presence and location of residues predicted to be involved in ligand binding. Several binding site tryptophan residues in these models were located in positions that support previous flurospectroscopic observations of the mAb-ligand complexation. Computer-aided renderings of the electrostatic potential at the van der Waals surface of the Fv region were compared and found to be consistent with the ligand binding specificity profiles for the different mAb. The Fv model of mAb NC6.8 was consistent with the binding site features determined in the Fab structure recently solved by X-ray diffraction techniques. These Fv models should provide an adequate basis for site-directed mutagenesis experiments in order to characterize interactive motifs in the mAb binding site.

Acetates↗