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Biomedical subjects

S Subramaniam

Publications and source records attributed to S Subramaniam.

At least 109 records · Page 6Linked to original sources
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

Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane.

In this paper we report on the molecular dynamics simulation of a fluid phase hydrated dimyristoylphosphatidylcholine bilayer. The initial configuration of the lipid was the x-ray crystal structure. A distinctive feature of this simulation is that, upon heating the system, the fluid phase emerged from parameters, initial conditions, and boundary conditions determined independently of the collective properties of the fluid phase. The initial conditions did not include chain disorder characteristic of the fluid phase. The partial charges on the lipids were determined by ab initio self-consistent field calculations and required no adjustment to produce a fluid phase. The boundary conditions were constant pressure and temperature. Thus the membrane was not explicitly required to assume an area/phospholipid molecule thought to be characteristic of the fluid phase, as is the case in constant volume simulations. Normal to the membrane plane, the pressure was 1 atmosphere, corresponding to the normal laboratory situation. Parallel to the membrane plane a negative pressure of -100 atmospheres was applied, derived from the measured surface tension of a monolayer at an air-water interface. The measured features of the computed membrane are generally in close agreement with experiment. Our results confirm the concept that, for appropriately matched temperature and surface pressure, a monolayer is a close approximation to one-half of a bilayer. Our results suggest that the surface area per phospholipid molecule for fluid phosphatidylcholine bilayer membranes is smaller than has generally been assumed in computational studies at constant volume. Our results confirm that the basis of the measured dipole potential is primarily water orientations and also suggest the presence of potential barriers for the movement of positive charges across the water-headgroup interfacial region of the phospholipid.

Crystallography, X-Ray↗
PubMed1995

Computer modeling of electrostatic steering and orientational effects in antibody-antigen association.

Brownian dynamics simulations are performed to investigate the role of long-range electrostatic forces in the association of the monoclonal antibody HyHEL-5 with hen egg lysozyme. The electrostatic field of the antibody is obtained from a solution of the nonlinear Poisson-Boltzmann using the x-ray crystal coordinates of this protein. The lysozyme is represented as an asymmetric dumbell consisting of two spheres of unequal size, an arrangement that allows for the modeling of the orientational requirements for docking. Calculations are done with the wild-type antibody and several point mutants at different ionic strengths. Changes in the charge distribution of the lysozyme are also considered. Results are compared with experiment and a simpler model in which the lysozyme is approximately by a single charged sphere.

Animals↗
PubMed1995

Anticonvulsant efficacy of ADCI (5-aminocarbonyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imine) after acute and chronic dosing in mice.

ADCI (5-aminocarbonyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5, 10-imine), a low-affinity uncompetitive N-methyl-D-aspartate (NMDA) antagonist, is a broad-spectrum anticonvulsant with a favorable side-effect profile. In the present study, we sought to determine if tolerance develops to the anticonvulsant activity of ADCI, using the maximal electroshock (MES) test to assess seizure protection. Mice were treated with three daily injections of a 2 x ED50 dose for MES protection (18 mg/kg, intraperitoneally, i.p.) or vehicle for 7 or 14 days. On the day after the chronic treatment protocol, all animals received a challenge dose of ADCI (18 mg/kg) and 15 min later were evaluated in the MES test. In control animals, 83-94% of animals were protected and the ADCI plasma levels immediately after the MES test were 5.5-9.7 micrograms/ml. In treated animals, 29 and 0% of animals were protected at 7 and 14 days, respectively, and the ADCI plasma levels were 77 and 52% of the control values. [3H]Dizocilpine binding to brain NMDA receptors was unaltered by the chronic drug treatment. In subsequent experiments, we determined that 14-day chronically treated animals could be completely protected by increased doses of ADCI (ED50 28.9 mg/kg). In both naive and chronically treated animals receiving a challenge dose of ADCI, plasma drug levels decreased in two phases, the first with a time constant of approximately 55 min and the second with a much slower rate. The estimated plasma concentrations of ADCI reflecting threshold (3-5 micrograms/ml) and 50% protection (5-7.5 micrograms/mg) were similar in naive and chronic animals.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Felbamate block of the N-methyl-D-aspartate receptor.

The anticonvulsant felbamate may act as an N-methyl-D-aspartate (NMDA) receptor antagonist, but the mechanism of block has not been fully characterized. We sought to identify the sites at which felbamate exerts its NMDA receptor blocking action using radioligand binding to rat forebrain membranes and whole-cell voltage clamp and single-channel recordings from cultured rat hippocampal neurons. Equilibrium binding isotherms for [3H]dizocilpine, a channel blocking ligand, were obtained in the presence of saturating glutamate and glycine. At a concentration of 1 mM, felbamate competitively inhibited specific [3H]dizocilpine binding, indicating that felbamate interacts with the channel blocking site. At a higher concentration (3 mM), felbamate also reduced the maximal saturation binding, demonstrating an additional allosteric action. The dissociation constant (Kb), estimated from fits to the binding isotherms, was 0.7-1.1 mM. It has been proposed that felbamate block of NMDA receptors occurs via competitive glycine site antagonism. However, the slowing of [3H]dizocilpine dissociation by felbamate, unlike the slowing produced by 7-chlorokynurenic acid, was not reversed by increasing the glycine concentration. In addition, felbamate did not reduce specific binding of [3H]5,7-dichlorokynurenic acid, a glycine site ligand. In whole-cell voltage clamp recordings of NMDA receptor currents, its blocking time constant (69 +/- 0.4 msec) was substantially faster than the dissociation time constant of glycine (390 +/- 23 msec), whereas the time constant for 5,7-dichlorokynurenic acid (390 +/- 20 msec) was similar. These observations indicate that felbamate block of NMDA receptors does not occur by an action at the glycine site.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Vitamin E protects intestinal basolateral membrane from CMF-induced damages in rat.

CMF is a combination of anticancer chemotherapeutic agents Cyclophosphamide, Methotrexate and 5-Fluorouracil. Vitamin E protects the basolateral membrane (BSM) from CMF induced lipid peroxidative damages. Rats were treated intravenously with cyclophosphamide-10 mg, methotrexate-1.0 mg and 5-fluorouracil-10 mg per kg body weight for six cycles. Vitamin E (600 mg/kg body weight) was administered orally, daily. Intestinal basolateral membrane bound ATPases (3.6.1.3), Alkalinephosphatase (3.1.1) and 5'-Nucleotidase (3.1.3.5) were protected by co-administration of vitamin E with CMF. In CMF treated rats the lipid peroxidation levels were found to be elevated with a significant depletion in membrane sulfhydryl groups. In vitamin E co-administered animals, the enzyme activities were found to be restored with concomitant reduction in malondialdehyde levels and an increase in the sulfhydryl groups. The membrane cholesterol and phospholipid levels which were altered in CMF treated rats were bought back to the normal in co-administration of vitamin E.

Animals↗
PubMed1994

Activation and regeneration of rhodopsin in the insect visual cycle.

Light absorption by rhodopsin generates metarhodopsin, which activates heterotrimeric guanine nucleotide-binding proteins (G proteins) in photoreceptor cells of vertebrates and invertebrates. In contrast to vertebrate metarhodopsins, most invertebrate metarhodopsins are thermally stable and regenerate rhodopsin by absorption of a second photon. In experiments with Rh1 Drosophila rhodopsin, the thermal stability of metarhodopsin was found not to be an intrinsic property of the visual pigment but a consequence of its interaction with arrestin (49 kilodaltons). The stabilization of metarhodopsin resulted in a large decrease in the efficiency of G protein activation. Light absorption by thermally stable metarhodopsin initially regenerated an inactive rhodopsin-like intermediate, which was subsequently converted in the dark to active rhodopsin. The accumulation of inactive rhodopsin at higher light levels may represent a mechanism for gain regulation in the insect visual cycle.

Animals↗
PubMed1994

Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation.

The nonlinear Poisson-Boltzmann equation (NPBE) provides a continuum description of the electrostatic field in an ionic medium around a macromolecule. Here, a novel approach to the solution of the full NPBE is developed. This robust and efficient algorithm combines multilevel techniques with a damped inexact Newton's method. The CPU time required for solution of the full NPBE, which is less than that for standard single-grid approaches in solving the corresponding linearized equation, is proportional to the number of unknowns enabling applications to very large macromolecular systems. Convergence of the method is demonstrated for a variety of protein systems. Comparison of the solutions to the linearized Poisson-Boltzmann equation shows that the damping of the electrostatic field around the charge is increased and that the potential scales logarithmically with charge. The inclusion of the full nonlinearity thus reduces the impact of highly charged residues on protein surfaces and provides a more realistic representation of electrostatic effects. This is demonstrated through calculation of potential around the active site regions of the 1,266-residue tryptophan synthase dimer and in the computation of rate constants from Brownian dynamics calculations in the superoxide dismutase-superoxide and antibody-antigen systems.

Algorithms↗
PubMed1994

RTI-4793-14, a new ligand with high affinity and selectivity for the (+)-MK801-insensitive [3H]1-]1-(2-thienyl)cyclohexyl]piperidine binding site (PCP site 2) of guinea pig brain.

[3H]TCP, an analog of the dissociative anesthetic phencyclidine (PCP), binds with high affinity to two sites in guinea pig brain membranes, one that is MK-801 sensitive and one that is not. The MK-801-sensitive site (PCP site 1) is associated with NMDA receptors, whereas the MK-801-insensitive site (PCP site 2) may be associated with biogenic amine transporters (BAT). Although several "BAT ligands" are known that bind selectively to PCP site 2 and not to PCP site 1 (such as indatraline), these compounds have low affinity for site 2 (Ki values > 1 microM). Here we demonstrate that the novel pyrrole RTI-4793-14 is a selective, high affinity ligand for PCP site 2. We determined the IC50 values of RTI-4793-14 and several reference compounds [PCP, (+)-MK801 and indatraline] for PCP site 1 (assayed with [3H](+)-MK801), PCP site 2 (assayed with [3H]TCP in the presence of 500 nM (+)-MK801) and a variety of BAT-related measures ([3H]CFT binding to the DA transporter, [3H]nisoxetine binding to the norepinephrine transporter, [3H]dopamine uptake, [3H]serotonin uptake). In addition, we determined the ability of RTI-4793-14 to block NMDA responses in cultured hippocampal neurons under voltage clamp. (+)-MK801 had high affinity for PCP site 1 (4.6 nM) and potently inhibited NMDA-induced responses, but was much less potent in the BAT-related measures (IC50 s > 10 microM). PCP had high affinity at PCP site 1 (IC50 = 92 nM) and PCP site 2 (IC50 = 117 nM), and was moderately potent in all BAT-related measures except [3H]nisoxetine binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1994

Polyamine effects on the NMDA receptor in human brain.

Polyamines are thought to modulate the activation of NMDA receptors through a unique allosteric regulatory site. The effects of polyamines on the binding of [3H]MK-801 were measured in cortical and hippocampal tissue surgically removed from patients with temporal lobe epilepsy (TLE). The polyamine agonist spermidine increased the binding of [3H]MK-801 in the cortex in a dose-dependent manner and this effect could be blocked by the weak partial agonist diethylenetriamine (DET). Spermidine decreased the Kd of [3H]MK-801 for the NMDA receptor but did not alter the density of receptors. Spermidine had essentially the same effect on Kd and Bmax measured in the dentate gyrus of TLE subjects and the cortex and dentate gyrus of postmortem controls. Moreover, there was no difference in the density of binding sites between postmortem and TLE subjects in either region. The binding of [3H]MK-801 in human cortex was decreased by 30% by incubation with DET or by prewashing the tissue sections. In contrast, DET did not alter the binding of [3H]MK-801 in rat cortex and prewashing sections produced an increase rather than a decrease in binding. These results suggest that there are different endogenous modulators for the polyamine site in rat and human tissue. The inverse agonist 1,10-diaminodecane decreased the binding of [3H]MK-801 in a dose-dependent manner. These results suggest that the fundamental modulatory properties of polyamines in rat and human tissues are essentially the same and that endogenous polyamines may regulate human NMDA receptors.

Adult↗
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↗
PubMed1994

Inhibition of NO synthase increases the severity of kainic acid-induced seizures in rodents.

The nitric oxide (NO) synthase inhibitor N omega-nitro-L-arginine (NNA) and the putative brain-selective NO synthase inhibitor 7-nitroindazole (7-NI) were used to determine the role of endogenous NO on seizures induced by kainic acid (KA) in rats and KA, pilocarpine, bicuculline, picrotoxin and pentylenetetrazole (PTZ) in mice. Rats given a subconvulsant dose of KA (6 mg/kg, i.p.) had seizures after they had been pretreated with NNA (50 mg/kg, i.p.). With a higher dose of KA (12 mg/kg, i.p.), NNA caused an increase in wild running seizures and mortality. Unlike NNA, 7-NI had no effect on KA-induced seizures. Similarly, NNA but not 7-NI caused a worsening of seizures in mice measured as a shortening of seizure latency and an increase in wild running and mortality. The effect of NNA on seizure latency was completely reversed by the competitive substrate for NO synthase, L-arginine. NNA had no effect on seizure latency following any of the other convulsants and increased mortality following pilocarpine and picrotoxin alone. Our results indicate that NNA may enhance the severity of KA-induced seizures through suppression of NO synthase activity in the vascular endothelium. The resulting impairment of cerebrovascular autoregulation may cause a mismatch between metabolic demand and blood flow during seizures leading to facilitation of spread. The absence of a comparable effect of NNA on other seizure models may indicate differences in the degree to which seizure activity in different models is influenced by the metabolic impairment secondary to decreased blood flow.

Amino Acid Oxidoreductases↗
PubMed1994

Regional profile of developmental changes in the sensitivity of the N-methyl-D-aspartate receptor to polyamines.

The NMDA receptor exhibits increased sensitivity to stimulation during early development compared with the adult. In this study, we examined modulation of the NMDA receptor by polyamines during development to see if it correlates with differences in the functional responsiveness of the NMDA receptor. [3H]MK-801 binding was measured in discrete brain regions in the presence and absence of polyamines in 3-, 7-, 15-, 25-, and 60-day-old Sprague-Dawley rats. [3H]MK-801 binding increased between postnatal days 3 and 15, with adult levels of binding being reached between days 15 and 25. Spermidine (75 microM) caused maximal stimulation of [3H]MK-801 binding during early development, ranging from 250% in the thalamus to 450% in the caudate putamen at postnatal day 3. This effect gradually declined to levels seen in the adult by postnatal days 15-25. During all developmental stages, the stimulation seen was greater in the caudate putamen compared with the hippocampus. Diethylenetriamine (1 mM) exhibited similar developmental and regional heterogeneity in its effects on [3H]MK-801 binding, producing substantial stimulation of binding in the neonate, but not in the adult. The EC50 and Emax values for the stimulatory effect of spermidine were significantly higher at day 7 compared with the adult. Unlike spermidine and diethylenetriamine, there was no regional variation in the effects of the putative "polyamine site" inverse agonist 1,10-diaminodecane at any age and only a slightly attenuated inhibition at postnatal day 3 compared with the adult.(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗
PubMed1994

Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation.

A new method for solving the full nonlinear Poisson-Boltzmann equation is outlined. This method is robust and efficient, and uses a combination of the multigrid and inexact Newton algorithms. The novelty of this approach lies in the appropriate combination of the two methods, neither of which by themselves are capable of solving the nonlinear problem accurately. Features of the Poisson-Boltzmann equation are fully exploited by each component of the hybrid algorithm to provide robustness and speed. The advantages inherent in this method increase with the size of the problem. The efficacy of the method is illustrated by calculations of the electrostatic potential around the enzyme Superoxide Dismutase. The CPU time required to solve the full nonlinear equation is less than half that needed for a conjugate gradient solution of the corresponding linearized Poisson-Boltzmann equation. The solutions reveal that the field around the active sites is significantly reduced as compared to that obtained by solving the corresponding linearized Poisson-Boltzmann equation. This new method for the nonlinear Poisson-Boltzmann equation will enable fast and accurate solutions of large protein electrostatics problems.

Algorithms↗
PubMed1994

Role of electrostatics in antibody-antigen association: anti-hen egg lysozyme/lysozyme complex (HyHEL-5/HEL).

A recently developed multigrid-based Newton method for solving the nonlinear Poisson-Boltzmann equation is applied in an investigation of molecular recognition in the system consisting of the monoclonal antibody HyHEL-5 and hen egg lysozyme. The electrostatic free energy of binding is calculated for the wild-type complex and various mutants in which electrostatic interactions between the two proteins are altered. Mutations which neutralize or reverse the charge of any of the residues involved in salt-links in the native system always yield decreased binding affinities. The stability of the complex can be enhanced through the formation of a new salt-bridge obtained by mutating an asparagine residue of the lysozyme to the negatively-charged aspartate. Ionic strength effects are also examined and found to be significant in some cases.

Amino Acid Sequence↗
PubMed1994

Alterations in erythrocyte membrane structure of breast cancer patients treated with CMF--a lipid profile.

Most of the breast cancer patients are treated with CMF which is a combination of three anticancer agents namely cyclophosphamide, methotrexate and 5-fluorouracil. The metabolites of CMF induce the level of lipid peroxides in the system, which are circulated in the blood. The present study reports the effect of CMF on the levels of cholesterol and phospholipids in erythrocytes of breast cancer patients showing a significant increase in the level of phospholipids. As the cholesterol/phospholipid ratio increases, the fluidity of the membrane decreases, thereby altering the architecture of the erythrocyte membrane in the breast cancer patients treated with CMF.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1994

Erythrocyte antioxidant enzyme activity in CMF treated breast cancer patients.

Most of breast cancer patients are treated with CMF, which is a combination of three anticancer agents, cyclophosphamide, methotrexate and 5-fluorouracil. Metabolites of CMF induce lipid peroxidation by inactivating the antioxidant enzymes, thereby rendering the system inefficient in management of the free radical attack. Acrolein and phosphoramide mustard are the metabolites of cyclophosphamide which are among the causative agents which reduce the activity of superoxide dismultase, catalase, glutathione peroxidase, glutathione reductase, glutathione-S-transferase and glucose-6-phosphate dehydrogenase in erythrocytes of CMF treated breast cancer patients.

Antineoplastic Combined Chemotherapy Protocols↗