Search PubMed⌕ Search

Biomedical subjects

S Subramaniam

Publications and source records attributed to S Subramaniam.

At least 127 records · Page 7Linked to original sources
PubMed1994

Heriditary pattern of cancer.

Three thousand nine hundred and twelve patients with cancer in various sites reporting to the out patient department were questioned for history of cancer among blood relatives. A positive history of cancer was obtained in 154 of whom 89 were male and 65 female. Thirty nine patients gave history of cancer among siblings and five gave history of cancer among spouses related by consanguneous marriage. The other 110 gave history of cancer among second and third generation relatives. Sixty one percent maternal relatives of the female patients had cancer as compared to only 33 percent of paternal relatives. This difference was not seen among male patients where there were about 45 percent of maternal and 47 paternal relatives giving history of cancer. Further it was found that 6 of 20 patients with cancer of the breast, 7 of 22 with stomach cancer and 4 of 12 with cervix cancer had blood relatives with the same type of cancer.

Adolescent↗
PubMed1994

Hydrophobic interactions of n-alkyl diamines with the N-methyl-D-aspartate receptor: voltage-dependent and -independent blocking sites.

We examined the block of N-methyl-D-aspartate (NMDA) receptors by n-alkyl (straight chain) diamines and related monoamines and triamines using whole-cell voltage clamp recording of NMDA receptor currents in cultured rat hippocampal neurons and [3H] dizocilpine binding to rat forebrain homogenates. At -60 mV, the diamines (carbon chain lengths 3-12) produced a concentration-dependent inhibition of NMDA receptor current (IC50 values, 6128-7.3 microM). For diamines of carbon chain lengths greater than 6, the inhibition was partially, but not completely, relieved by depolarization, indicating that the block occurs at distinct voltage-dependent and voltage-independent sites. The block produced by short-chain diamines (carbon chain lengths 3-6) was completely relieved by depolarization, indicating little or no interaction with the voltage-independent site. In comparison with the corresponding diamines, homologous monoamines exhibited very low potency, whereas homologous triamines were of equal or lower potency. For long-chain diamines, inhibitory potency at both the voltage-dependent and voltage-independent sites was correlated with carbon chain length (binding energy increasing 600-700 cal/mol-CH2), suggesting that binding to each of the sites is stabilized by a hydrophobic interaction. Affinities for the voltage-dependent blocking site (transformed to 0 mV) and for the voltage-independent blocking site were similar. These values were also similar to the inhibitory potencies of the diamines in the [3H]dizocilpine binding assay. Analysis of the voltage-dependence of block at the voltage-dependent site yielded z delta values for diamines of intermediate length (carbon chain lengths 7-9) that decreased with increasing length from 0.91 to 0.63 [approaching the z delta values of monovalent blockers (approximately 0.54) and one-half of the z delta values of shorter diamines (approximately 1.1)], suggesting that the intermediate length diamines block in a linear, extended chain conformation with one of the charges having incomplete access to a deep binding site. Longer chain diamines (carbon chain lengths 10 and 12) exhibited larger z delta values (0.78 and 0.98, respectively), presumably because enhanced conformational flexibility permitted a folded-over conformation. From the interchange distances of the intermediate length diamines in their lowest energy conformation, we estimated that the total voltage drop within the NMDA receptor channel occurs over a distance of approximately 20 A. The putative polyamine facilitatory site antagonist diethylenetriamine inhibited NMDA-induced currents at the voltage-dependent site (IC50, 654 microM; -60 mV).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1993

Hydrophobic amino acids in the retinal-binding pocket of bacteriorhodopsin.

The hydrophobic amino acids Met-20, Val-49, Ala-53, Met-118, Gly-122, and Met-145 are believed to be among the amino acids that form the retinal-binding pocket in bacteriorhodopsin. We have now replaced the above amino acids, one at a time, and report on the effects of these replacements (M20A/E, V49A/L, A53G, M118A/E, G122C, and M145A/E) on the properties of bacteriorhodopsin. With the exception of Met-20, replacements at all of the other positions resulted in (i) altered rates of in vitro chromophore formation that ranged from 20-fold faster to 45-fold slower than wild-type bacteriorhodopsin, (ii) blue shifts in the visible spectra of up to 80 nm, and (iii) caused changes in the retinal isomer compositions of the mutant chromophores. Specific effects were also observed in the photocycles of the Met-118, Met-145, and Val-49 mutants, suggesting that these 3 amino acids have important roles in light transduction by bacteriorhodopsin. These results are discussed together with previous studies on the effects of amino acid replacements in the retinal-binding pocket of bacteriorhodopsin.

Amino Acid Sequence↗
PubMed1993

Polyamines modulate the neurotoxic effects of NMDA in vivo.

The ability of polyamines to alter NMDA-induced neurotoxicity in neonatal rats was examined to determine whether polyamines modulate NMDA receptor activity in vivo. Unilateral injections of NMDA and/or polyamines were made into the striatum of 7-day-old rats. After 5 days, the brains were removed and 20 microns thick coronal sections were cut and stained with Cresyl violet. A computer-based image analysis system was used to densitometrically measure the cross-sectional area of intact tissue in the control and injected hemispheres. Administration of NMDA (5-40 nmol) produced a dose-dependent tissue damage that ranged from 7 to 52% of the area of the uninjected hemisphere. The polyamine agonist spermine (10-500 nmol) dose-dependently exacerbated the toxicity of a 15 nmol dose of NMDA, increasing the size of the lesion by up to 50%. Administration of spermine alone produced dose-dependent tissue damage that ranged from 9 to 52%. The damage produced by both NMDA and spermine could be completely inhibited by co-administration of the NMDA antagonist MK-801. The polyamine inverse agonist 1,10-diaminodecane (DA-10, 50-400 nmol) inhibited the damage produced by NMDA in a dose-dependent manner, with a maximal inhibition of 50%. Administration of DA-10 alone produced limited damage at doses above 100 nmol. The weak partial agonist diethylenetriamine had no effect by itself or on NMDA-induced toxicity at the doses tested. These results indicate that polyamines can modulate the activity of NMDA receptors in vivo and suggest that polyamines or related compounds may have important therapeutic potential as neuroprotective agents.

Animals↗
PubMed1993

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

Structural changes are central to the mechanism of light-driven proton transport by bacteriorhodopsin, a seven-helix membrane protein. The main intermediate formed upon light absorption is M, which occurs between the proton release and uptake steps of the photocycle. To investigate the structure of the M intermediate, we have carried out electron diffraction studies with two-dimensional crystals of wild-type bacteriorhodopsin and the Asp96-->Gly mutant. The M intermediate was trapped by rapidly freezing the crystals in liquid ethane following illumination with a xenon flash lamp at 5 and 25 degrees C. Here, we present 3.5 A resolution Fourier projection maps of the differences between the M intermediate and the ground state of bacteriorhodopsin. The most prominent structural changes are observed in the vicinity of helices F and G and are localized to the cytoplasmic half of the membrane.

Amino Acid Sequence↗
PubMed1993

Brownian dynamics simulations of molecular recognition in an antibody-antigen system.

The crystal structure for an antibody-antigen system, that of the anti-hen egg lysozyme monoclonal antibody HyHEL-5 complexed to lysozyme, is used as the starting point for computer simulations of diffusional encounters between the two proteins. The investigation consists of two parts: first, the linearized Poisson-Boltzmann equation is solved to determine the long-range electrostatic forces between antibody and antigen, and then, the relative motion as influenced by these forces is modeled within Brownian motion theory. The effects of various point mutations on the calculated reaction rate are considered. It is found that charged residues close to the binding site exert the greatest influence in steering the proteins into a configuration favorable for their binding, while more distant mutations are qualitatively described by the Smoluchowski model for the mutual diffusion of two uniformly charged spheres. The antibody residues involved in forming salt links with the lysozyme, Glu-H35 and Glu-H50, appear to be particularly important in electrostatic steering, as neutralization of both of them yields reaction rates that are two to three orders of magnitude below those of wild-type rates. The relative rates obtained from the simulations can be tested through kinetic measurements on mutant protein complexes. Kinetically efficient partners can also be designed and constructed through directed mutagenesis.

Amino Acid Sequence↗
PubMed1993

Regional heterogeneity of polyamine effects on the N-methyl-D-aspartate receptor in rat brain.

Polyamines have pronounced effects on N-methyl-D-aspartate (NMDA) receptors in vitro and may be important modulators of NMDA receptor activity in vivo. There is considerable regional heterogeneity in the effects of polyamines on [3H]MK-801 binding in rat brain sections. For example, spermidine enhances the binding of [3H]MK-801 to a much greater extent in the striatum than in the cortex. To further explore the basis for this regional heterogeneity, the effects of polyamines on [3H]MK-801 binding were measured in well-washed membranes prepared from frontal cortex and striatum. There was no difference in the concentration-response relationship for spermidine or the KD for [3H]MK-801 in the presence of 75 microM spermidine, suggesting that the regional difference seen in tissue sections is due to an endogenous factor that is either removed or inactivated during the preparation of membranes. Comparison of spermidine concentration-response curves in washed and unwashed tissue sections revealed that washing selectively enhanced the Emax value in the ventromedial caudate putamen without changing the EC50. This is consistent with the possibility that a noncompetitive polyamine antagonist is being removed from this region during washing. There was no regional variability in the effects of the putative inverse agonist 1,10-diaminodecane, consistent with recent suggestions that this polyamine inhibits the NMDA receptor at a site distinct from the one at which polyamines act to enhance NMDA receptor function. Agents that modulate the redox state of the NMDA receptor did not eliminate the regional heterogeneity of polyamine effects. Furthermore, the stimulatory effect of glycine in these regions did not correlate with that of spermidine. These results suggest the existence of one or more endogenous factors that noncompetitively influence the effects of polyamines in a region-specific manner.

Analysis of Variance↗
PubMed1993

Constructive induction and protein tertiary structure prediction.

To date, the only methods that have been used successfully to predict protein structures have been based on identifying homologous proteins whose structures are known. However, such methods are limited by the fact that some proteins have similar structure but no significant sequence homology. We consider two ways of applying machine learning to facilitate protein structure prediction. We argue that a straightforward approach will not be able to improve the accuracy of classification achieved by clustering by alignment scores alone. In contrast, we present a novel constructive induction approach that learns better representations of amino acid sequences in terms of physical and chemical properties. Our learning method combines knowledge and search to shift the representation of sequences so that semantic similarity is more easily recognized by syntactic matching. Our approach promises not only to find new structural relationships among protein sequences, but also expands our understanding of the roles knowledge can play in learning via experience in this challenging domain.

Artificial Intelligence↗
PubMed1993

Comparison of HIV antibody profiles in intravenous drug users and individuals infected by the sexual route.

HIV-1 antibody patterns in two groups, those infected by the intravenous route (IV drug users) and those infected by the sexual route (prostitutes, male homosexuals and sexually transmitted disease patients) were compared using the Western blot technique. A total of 160 cases were studied. The intravenous drug user (IVDU) group appeared to respond to fewer antibody markers than the sexually infected group, the difference being significant for markers p31, p51, p55, p66, gp41 and gp120. Furthermore, a higher proportion (63%) of the sexually infected group carried antibodies to all Western blot markers as compared to the IVDU group (49%).

Acquired Immunodeficiency Syndrome↗
PubMed1992

Effect of introducing different carboxylate-containing side chains at position 85 on chromophore formation and proton transport in bacteriorhodopsin.

During the initial stages of the bacteriorhodopsin photocycle, a proton is transferred from the Schiff base to the deprotonated carboxylate of Asp85. Earlier studies have shown that replacement of Asp85 by Asn completely abolishes proton transport activity, whereas extension of the side chain by an additional carbon-carbon bond (Asp85-->Glu) results in a functional proton pump. Here we show that extension of the Asp85 side chain by two additional bond lengths also results in a functional proton pump as long as the terminal group is a carboxylate moiety. These side chains were created by modification of the cysteine residue in the Asp85-->Cys mutant with either iodoacetic acid or iodoacetamide. In vitro chromophore formation studies show that the rate of Schiff base protonation in mutants that contain a carboxylate at residue 85 is invariably faster than in mutants that contain neutral substitutions at this position. We conclude that in bacteriorhodopsin, there is considerable tolerance in the volume of the side chain that can be accommodated at position 85 and that the presence of a carboxylate at residue 85 is important both for proton pumping and for stabilizing the protonated Schiff base.

Amino Acid Sequence↗
PubMed1992

Aspartic acid 85 in bacteriorhodopsin functions both as proton acceptor and negative counterion to the Schiff base.

In bacteriorhodopsin Asp85 has been proposed to function both as a negative counterion to the Schiff base and as proton acceptor in the early stages of the photocycle. To test this proposal further, we have replaced Asp85 by His. The rationale for this replacement is that although His can function as a proton acceptor, it cannot provide a negative charge at residue 85 to serve as a counterion to the protonated Schiff base. We show here that the absorption spectrum of the D85H mutant is highly sensitive to the pH of the external medium. From spectroscopic titrations, we have determined the apparent pK for deprotonation of the Schiff base to be 8.8 +/- 0.1 and the apparent pK for protonation of the His85 side chain to be approximately 3.5. Between pH 3.5 and 8.8, where the Schiff base is protonated, and the His side chain is deprotonated, the D85H mutant is completely inactive in proton transport. Time-resolved studies show that there is no detectable formation of an M-like intermediate in the photocycle of the D85H mutant. These experiments show that the presence of a neutral proton-accepting moiety at residue 85 is not sufficient for carrying out light-driven proton transport. The requirements at residue 85 are therefore for a group that serves both as a negatively charged counterion and as a proton acceptor.

Amino Acid Sequence↗
PubMed1992

1,10-Diaminodecane and 1,12-diaminododecane block NMDA receptor currents by an open channel mechanism.

In whole-cell recordings from cultured rat hippocampal neurons (VH = -60 mV), 1,10-diaminodecane (DA10) and 1,12-diaminododecane (DA12) produced a concentration-dependent block of NMDA-induced current (IC50 = 30 and 7 microM, resp.). In contrast, the diamines failed to affect AMPA and kainate currents. The inhibition of NMDA currents was highly voltage-dependent and was substantially relieved at positive holding potentials. In outside-out patches, DA10 and DA12 produced a voltage-dependent flickery block of NMDA-activated single-channel currents. These results indicate that DA10 and DA12 antagonize NMDA responses via an open channel mechanism. DA10 and DA12 have been proposed to be inverse agonists at the spermine facilitatory site on the NMDA receptor. However, the channel blocking effects of the diamines complicate the interpretation of their actions at this site.

Animals↗
PubMed1992

Effects of chronic treatment with selective agonists on the subtypes of dopamine receptors.

The effects of chronic administration of selective dopaminergic agonists on D1 and D2 receptor density, affinity and function were measured in Sprague-Dawley rats. Animals received daily injections (i.p.) of the D1-selective agonist SKF-38393 (10 mg/kg), the D2-selective agonist quinpirole (1 mg/kg), SKF-38393 plus quinpirole, or saline for 14 days. Quantitative autoradiographic analysis revealed that the density of D2 receptors was decreased following chronic treatment with quinpirole alone or in combination with SKF-38393 whereas SKF-38393 by itself had no effect on this receptor. In contrast, the density of D1 receptors was increased following treatment with SKF-38393. Although quinpirole by itself had no effect on D1 receptors, co-administration with SKF-38393 attenuated the up-regulation of D1 receptors produced by SKF-38393 in the caudate-putamen and nucleus accumbens but not in the substantia nigra. The up-regulation of D1 receptors in response to chronic SKF-38393 may be attributed to the partial agonist properties of SKF-38393 which may not provide sufficient D1 receptor stimulation to down-regulate the receptor. Quinpirole-induced hypothermia and SKF-38393-induced hyperthermia were measured before and after chronic agonist treatments to examine the effects of these treatments on thermoregulatory functions mediated by each receptor subtype. Treatment with quinpirole or quinpirole plus SKF-38393 resulted in desensitization of quinpirole-induced hypothermia, whereas treatment with SKF-38393 alone had no effect. All of the chronic treatments produced sensitization of SKF-38393-induced hyperthermia. Since not all treatments result in an increase in the density of D1 receptors, up-regulation of D1 receptors is not the sole mechanism for this sensitization.

2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-ben↗
PubMed1992

Anti-insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody.

A knowledge-based three-dimensional model of an anti-insulin antibody, 125, was constructed using the structures of conserved residues found in other known crystallographic immunoglobulins. Molecular modeling and mechanics were done with the 125 amino acid sequences using QUANTA and CHARMm on a Silicon Graphics 4D70GT workstation. A minimal model was made by scaffolding using crystallography coordinates of the antibody HyHEL-5, because it had the highest amino acid sequence homology with 125 (84% light chain, 65% heavy chain). The three hypervariable loop turns that are longer in 125 than in HyHEL-5 (L1, L3, and H3) were modeled separately and incorporated into the HyHEL-5 structure; then other amino acid substitutions were made and torsions optimized. The 125 model maintains all the structural attributes of an antibody and the structures conserved in known antibodies. Although there are many polar amino acids (especially serines) in this site, the overall van der Waals surface shape is determined by positions of aromatic side chains. Based on this model, it is suggested that hydrogen bonding may be key in the interaction between the human insulin A chain loop antigenic epitope and 125.

Amino Acid Sequence↗
PubMed1992

Modeling the antigen combining site of an anti-dinitrophenyl antibody, ANO2.

A model structure has been constructed for a monoclonal anti-dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., & McConnell, H.M., 1984, Biochemistry 23, 1138-1142). Its amino acid sequence shows striking homology with the anti-lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2. The CONGEN conformational sampling algorithm (Bruccoleri, R.E. & Karplus, M., 1987, Biopolymers 26, 127-196) was used to model the six hypervariable loops that contain the antigen-combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent-accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the beta-barrel, namely, L2-H1-L3-H2-H3-L1. The model structures thus obtained were compared to the high resolution X-ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., & Fox, R.O., 1991, J. Mol. Biol. 221, 239-256).

Algorithms↗
PubMed1992

Sudden death in a young adult due to coronary artery aneurysm secondary to suspected Kawasaki disease.

A healthy 17-year-old Chinese male suddenly collapsed and died during a game of badminton. The autopsy examination revealed a solitary calcified aneurysm of the left common coronary artery with marked stenosis of the orifices of the anterior descending and circumflex branches. Histology of the aneurysm was non-specific with hyalinised scar tissue and foci of calcification. The only illness of significance in the past was an episode of 'pyrexia of unknown origin' at the age of 8 months. A review of the notes of that hospital admission revealed that the illness was most probably Kawasaki disease.

Adolescent↗