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Biomedical subjects

N Srinivasan

Publications and source records attributed to N Srinivasan.

At least 109 records · Page 6Linked to original sources
PubMed1994

Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).

Plasminogen-related growth factors, a new family of polypeptide growth factors with the basic domain organization and mechanism of activation of the blood proteinase plasminogen, include hepatocyte growth factor/scatter factor (HGF/SF), a potent effector of the growth, movement, and differentiation of epithelia and endothelia, and hepatocyte growth factor-like/macrophage stimulating protein (HGF1/MSP), an effector of macrophage chemotaxis and phagocytosis. Phylogeny of the serine proteinase domains and analysis of intron-exon boundaries and kringle sequences indicate that HGF/SF, HGF1/MSP, plasminogen, and apolipoprotein (a) have evolved from a common ancestral gene that consisted of an N-terminal domain corresponding to plasminogen activation peptide (PAP), 3 copies of the kringle domain, and a serine proteinase domain. Models of the N domains of HGF/SF, HGF1/MSP, and plasminogen, characterized by the presence of 4 conserved Cys residues forming a loop in a loop, have been modeled based on disulfide-bond constraints. There is a distinct pattern of charged and hydrophobic residues in the helix-strand-helix motif proposed for the PAP domain of HGF/SF; these may be important for receptor interaction. Three-dimensional structures of the 4 kringle and the serine proteinase domains of HGF/SF were constructed by comparative modeling using the suite of programs COMPOSER and were energy minimized. Docking of a lysine analogue indicates a putative lysine-binding pocket within kringle 2 (and possibly another in kringle 4). The models suggest a mechanism for the formation of a noncovalent HGF/SF homodimer that may be responsible for the activation of the Met receptor. These data provide evidence for the divergent evolution and structural similarity of plasminogen, HGF/SF, and HGF1/MSP, and highlight a new strategy for growth factor evolution, namely the adaptation of a proteolytic enzyme to a role in receptor activation.

Amino Acid Sequence↗
PubMed1994

Comparative modelling of major house dust mite allergen Der p I: structure validation using an extended environmental amino acid propensity table.

A model of the 3-D structure of a major house dust mite allergen Der p I associated with hypersensitivity reactions in humans was built from its amino acid sequence and its homology to three known structures, papain, actinidin and papaya proteinase omega of the cysteine proteinase family. Comparative modelling using COMPOSER was used to arrive at an initial model. This was refined using interactive graphics and energy minimization with the AMBER force field incorporated in SYBYL (Tripos Associates). Compatibility of the Der p I amino acid sequence with the cysteine proteinase fold was checked using an environment-dependent amino acid propensity table incorporated into a new program HARMONY with a variable length windowing facility. A five-residue window was used to probe local conformational integrity. Propensities were derived from a structural alignment database of homologous proteins using a robust entropy-driven smoothing procedure. Der p I shares essential structural and mechanistic features with other papain-like cysteine proteinases, including cathepsin B. The active-site thiolate-imidazolium ion pair comprises the side chains of Cys34 and His170. A cystine disulfide not present in other known structures bridges residue 4 of an N-terminal extension and the core residue 117. Two conserved disulfide bridges are formed by residues 31 and 71 and residues 65 and 103. Model building of peptide substrate analogue complexes suggests a preference for phenylalanyl or basic residues at the P2 position, whilst selectivity may be of minor importance at the S1 subsite. The electrostatic influences on the Der p I active-site ion pair and extended peptide binding region are markedly different from those in known structures. A highly immunogenic surface exposed region (residues 107-131), comprising several overlapping T cell epitope sites, has no shared sequence identity with human liver cathepsin B and contains three insertion-deletion sites. The structure provides a basis for testing the substrate specificity of Der p I and the potential role of proteinase activity in hypersensitivity reactions. These studies may offer a new treatment strategy by hyposensitization with inactive mutants or mutants with significantly altered proteinase activity, either alone or complexed with antibody.

Algorithms↗
PubMed1994

Conformational characteristics of asparaginyl residues in proteins.

Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed alpha-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi, psi) regions of left-handed alpha-helix right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha L, which seems to be characteristic of non-glycyl residues at that position. In the liners connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha L or alpha R conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein.

Asparagine↗
PubMed1994

Knowledge-based protein modeling.

Knowledge, both from the three-dimensional structures of homologous proteins and from the general analysis of protein structure, is of value in modeling a protein of known sequence but unknown structure. While many models are still constructed at least in part by manual methods on graphics devices, automated procedures have come into greater use. These procedures include those that assemble fragments of structure from other known structures and those that derive coordinates for the model from the satisfaction of restraints placed on atomic positions.

Amino Acid Sequence↗
PubMed1993

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure.

A 3-D model of a protein can be constructed from its amino acid sequence and the 3-D structures of one or more homologues by annealing three sets of fragments: the structurally conserved regions, structurally variable regions and the side chains. The method encoded in the computer program COMPOSER was assessed by generating 3-D models of eight proteins whose crystal structures are already known and for which 3-D structures of homologues are available. In the structurally conserved regions, differences between modelled and X-ray structures are smaller than the differences between the X-ray structures of the modelled protein and the homologues used to build the model. When several homologues are used, the contributions of the known structures are weighted, preferably by the square of sequence similarity; this is especially important when the similarities of the homologues to the modelled structure differ greatly. The 'collar' extension approach, in which a similar region of different length in a homologue is used to extend the framework, can result in a more accurate model. If known homologues comprise more than one related group of proteins and they are both distantly related to the unknown, then alignment of the sequence to be modelled with each group of homologues facilitates identification of structurally conserved regions of the unknown and leads to an improved model. Models have root mean square differences (r.m.s.d.s) with the structures defined by X-ray analysis of between 0.73 and 1.56 A for all C alpha atoms, for seven the eight models. For the model of mucor pepsin, where the closest homologue has 33% sequence identity and 20% of the residues are in structurally variable regions, the r.m.s.d. for the framework region is 1.71 A and the r.m.s.d. for all C alpha atoms is 3.47 A.

Amino Acid Sequence↗
PubMed1993

Effects of prolactin and androgens on enzymes of carbohydrate metabolism in seminal vesicles of castrated mature bonnet monkeys, Macaca radiata.

Effects of prolactin(Prl), bromocriptine(Br), testosterone propionate (TP), dihydrotestosterone (DHT) and combinations of these androgens with Prl/Br on the maximum catalytic capacities of seminal vesicular enzymes involved in the glycolytic and pentose phosphate pathways in castrated mature monkeys were studied. Castration decreased the activities of all of the enzymes studied such as hexokinase(HK), 6-phosphofructokinase(PFK), glyceraldehyde-3-phosphate dehydrogenase(G3PD), pyruvate kinase(PK), glucose 6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase(6PGD) in the seminal vesicles. Prl restored the activities of all of the enzymes to their normal values except G3PD. TP/DHT maintained all the enzyme activities at the normal tissue intact level. Prl given along with androgens further enhanced the androgen action with regard to all the enzymes activities except G3PD. Br decreased all of the enzymes but Br with androgens maintained all the enzyme activities at the normal level. Castration decreased significantly serum T/DHT titres but Prl did not alter Prl levels. Prl+TP/DHT elevated Prl levels. Br alone decreased serum Prl, T and DHT titres, but Br+TP/DHT decreased only Prl, elevated T and maintained DHT levels. These results suggest that Prl has a direct as well as a synergistic action with androgens on the activities of the enzymes of glycolysis and pentose phosphate pathways in the seminal vesicles of castrated monkeys.

Androgens↗
PubMed1992

Orthogonal beta beta motifs in proteins.

A super-secondary structural motif comprising two orthogonally oriented beta-strands connected by short linking segments of less than or equal to 5 residues has been identified from a data set of 65 independent protein crystal structures. Of the 42 examples from 14 proteins, a vast majority have only a single residue as the linking element. Analysis of the conformational angles at the junction reveals that the recently described type VIII beta-turn occurs frequently at the connecting hinge, while the type II beta-turn is also fairly common.

Animals↗
PubMed1992

Influence of corticosterone acetate on the spleen in intact and ovariectomized rats.

Increasing evidence of the interaction of glucocorticoids and ovarian steroids prompted the current study. Effects of exogenously administered corticosterone acetate (3.5 mg/100 g b.w/day for one week) were examined on splenic nucleic acids, protein, lactate, and on lactate dehydrogenase (LDH) specific activity and its isozymes in ovariectomized and ovary-intact Wistar rats (65-75 days old). Ovariectomy resulted in no significant change in the parameters studied except DNA which increased significantly. The administration of corticosterone to these rats did not produce any remarkable change in the ovariectomy caused increase in splenic DNA content. Nevertheless, it decreased the ratio of heart type subunits (H)/muscle type subunits (M) [H/M] of LDH isozymes. In the case of ovary-intact rats, corticosterone produced an increase in the concentration of splenic lactate but a decrease in the H/M ratio. Exogenously administered corticosterone exerts selective synergistic interaction with ovarian hormones on splenic lactate. The specific activity of LDH and the concentrations of RNA and protein remained unchanged during the interaction between ovarian hormones and corticosterone.

Analysis of Variance↗
PubMed1992

Effects of prolactin and androgens on enzymes of carbohydrate metabolism in prostate of castrated bonnet monkeys Macaca radiata (Geoffroy).

Effects of prolactin (PRL), bromocriptine (Br), testosterone propionate (TP), dihydrotestosterone (DHT) and the combinations of these androgens with PRL/Br on the specific activities of caudal and cranial prostatic cellular enzymes involved in carbohydrate metabolism in castrated mature bonnet monkeys have been studied. Castration decreased all the enzymes studied such as hexokinase (HK), 6-phosphofructokinase (6-PFK), glyceraldehyde-3-phosphate dehydrogenase (G-3-PD), pyruvate kinase (PK), glucose-6-phosphate dehydrogenase (G-6-PD) and 6-phosphogluconate dehydrogenase (6-PGD) in the cranial and caudal prostates. PRL elevated the activities of all the enzymes above normal except G-3-PD of cranial lobe. In the caudal lobe, PRL brought back the activities of HK, PFK, PK, G-6-PD to normal and 6-PGD above normal except G-3-PD. TP/DHT treatment increased all the enzymes in both the lobes. PRL given along with TP/DHT further enhanced the androgen action with regard to HK, PK, G-6-PD and 6-PGD of cranial and PFK, G-3-PD, PK, G-6-PD and 6-PGD of caudal lobe. Br treatment did not produce any alteration of these enzymes in both the lobes. In the cranial lobe, during Br+TP/DHT treatment, the stimulating effects of androgen were unaffected on all the enzymes except PK. On the other hand in the caudal, the stimulatory effects of androgens were affected and the activities of HK, PFK, PK and 6-PGD were significantly decreased. The present results suggest that PRL has a direct as well as a synergistic action with androgens on enzymes of EMP and HMP shunt in the prostates of monkeys.

Androgens↗
PubMed1992

Interaction of androgens and prolactin on prostatic enzymes of the pyruvate-malate cycle involved in lipogenesis in castrated mature monkey, Macaca radiata.

Effects of androgens, prolactin (Prl) and bromocriptine (Br) on the specific activities of prostatic (caudal and cranial) enzymes of the pyruvate-malate cycle were studied in castrated mature bonnet monkeys. Castration decreased the activity of NADP+ isocitrate dehydrogenase (ICDH), ATP citrate lyase, malate dehydrogenase (MDH), malic enzyme and fatty acid synthase (FAS). Administration of testosterone propionate (TP)/dihydrotestosterone (DHT) increased the activities of all these enzymes in both lobes. Malate dehydrogenase maintained normal activity. Prl also had a stimulatory effect on the enzymes and was further enhanced when Prl was given in combination with TP/DHT. Unlike Prl, bromocriptine treatment inhibited all the enzymes in both lobes. Thus, prolactin was found to have a direct as well as a synergistic effect with androgens on enzymes of the pyruvate-malate cycle in the prostate of castrated mature monkeys.

ATP Citrate (pro-S)-Lyase↗
PubMed1991

Increased degradation of dermal collagen in diabetic rats.

The effect of alloxan induced diabetes on the dermal collagen content of albino rats was studied in relation to few lysosomal enzymes. Diabetes decreased the dermal collagen content. The specific activities of the lysosomal enzymes studied in the diabetic rat skin were elevated. It has been established that lysosomal enzymes degrade the connective tissue components. Thus, it may be suggested that the increase in the lysosomal enzymes studied should have facilitated the decrease in dermal collagen content of diabetic rats by increasing the degradation of dermal collagen.

Animals↗
PubMed1990

Conformations of disulfide bridges in proteins.

The conformational characteristics of disulfide bridges in proteins have been analyzed using a dataset of 22 protein structures, available at a resolution of less than or equal to 2.0 A, containing a total of 72 disulfide crosslinks. The parameters used in the analysis include (phi, psi) values at Cys residues, bridge dihedral angles chi ss, chi i1, chi j1, chi i2, and chi j2, the distances C alpha i-C alpha j and C beta i-C beta j between the C alpha and C beta atoms of Cys(i) and Cys(j). Eight families of bridge conformations with three or more occurrences have been identified on the basis of these stereochemical parameters. The most populated family corresponds to the "left handed spiral" identified earlier by Richardson [1981) Adv. Protein Chem. 34, 167-330). Disulfide bridging across antiparallel extended strands is observed in alpha-lytic protease, crambin, and beta-trypsin and this structure is shown to be very similar to those obtained in small cystine peptides. Solvent accessible surface area calculations show that the overwhelming majority of disulfide bridges are inaccessible to solvent.

Cystine↗
PubMed1990

Influence of prolactin, androgens and bromocriptine on seminal vesicular and prostatic adenosine triphosphatases in castrated adult monkeys Macaca radiata.

E ects of prolactin (PRL), bromocriptine (Br), testosterone propionate (TP), dihydrotestosterone (DHT) and the combinations of these androgens with PRL/Br on specific activities of adenosine triphosphatases (ATPases) of seminal vesicles and cranial and caudal prostates were studied in castrated adult bonnet monkeys. Castration decreased all ATPases (sodium/potassium, magnesium and calcium dependent) of seminal vesicles and both the lobes of prostate. PRL restored the normal activities of all ATPases in both the organs. Br given alone decreased all ATPases of prostate but caused no significant alteration, particularly calcium dependent ATPases of seminal vesicles and caudal prostate. TP/DHT replacement restored all ATPases of both the organs to the normal levels. PRL + TP/DHT further enhanced all the ATPases activities of all the regions studied. Br + TP/DHT decreased all ATPases but it did not produce any alteration in the calcium ATPases of seminal vesicles. The results suggest that prolactin facilitates membrane transport enzymes in the cranial and caudal prostate and seminal vesicles of adult castrated bonnet monkeys.

Adenosine Triphosphatases↗
PubMed1989

Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.

A computer modeling procedure for assessing the stereochemical suitability of pairs of residues in proteins as potential sites for introduction of cystine disulfide crosslinks has been developed. Residue pairs with C alpha-C alpha distances of less than or equal to 6.5 A and C beta-C beta distances of less than or equal to 4.5 A are chosen for geometrical fixation of S atoms using the program MODIP. The stereochemistry of the modeled disulfides is evaluated using limits for the structural parameters of the various torsion angles and S-S bond length in the disulfide bridge. The ability of the procedure to correctly model disulfides has been checked with examples of cystine peptides of known crystal structures and 103 disulfide bridges from 25 available protein crystal structures determined at less than or equal to 2 A resolution. An analysis of results on three proteins with engineered disulfides, T4 lysozyme, dihydrofolate reductase and subtilisin, is presented. Two positions for the introduction of 'stereochemically optimal' disulfides are identified in subtilisin.

Disulfides↗
PubMed1989

Effect of corticosterone on epididymal lipids in pubertal rat.

Serum corticosterone excess was induced by the administration of corticosterone acetate to adrenal intact rats. Different lipid classes were studied in unwashed and washed (epididymal sperm and fluid free) caput and cauda epididymides. The unwashed caput epididymidis registered a significant decrease in total lipid, cholesterol and phospholipid while total glyceride glycerol and its fractions were not altered after corticosterone treatment. Among phospholipid fractions phosphatidyl inositol, choline and ethanolamine showed a significant decrease. Unlike the unwashed caput epididymidis, the washed caput region recorded a marked increase in total lipid, glyceride glycerol and its fractions. However, total lipid in the washed cauda region significantly increased and the increase was mainly due to triacyl glycerol. Though the phospholipid fractions phosphatidyl choline and ethanolamine showed an increase, the total phospholipid was not altered significantly. Serum testosterone and prolactin registered a significant decrease while gonadotropins were unaltered. On the withdrawal of corticosterone treatment, all the lipid classes turned to normalcy along with serum testosterone and prolactin. It is concluded that corticosterone excess favours lipid accumulation in the sperm free epididymal tissue and its influence on epididymis is region specific and reversible.

Animals↗
PubMed1989

Utilization behaviour patterns of Siddha clinics in Salem, Tamil Nadu.

In Tamil Nadu, indigenous Siddha medicine (SM) is officially recognized and extensively used. Yet very little research information or published material is available on the extent of utilization behaviour of Siddha medicine in urban settings. This study examines the current patterns of utilization and consumer behavioural characteristics of SM through a field-based questionnaire survey of a sample of 300 patients attending 15 Siddha clinics in Salem, Tamil Nadu. Four areas were investigated: Socio-economic characteristics of the users; utilization behaviour pattern of patients; reasons for choice of Siddha therapy; opinions, attitudes, perception and satisfaction of users regarding Siddha therapy. The survey points out there is an inverse relationship between the number of patients using SM and income, education and distance travelled. Various factors were cited in choosing SM-such as, effectiveness of treatment, social influences of a relative or friend. Survey indicates that both modern medicine and SM seem to act as supporting rather than as competitive systems in a setting like Salem. People tend to seek both the system in search of a permanent cure.

Adolescent↗
PubMed1989

Effects of prolactin and androgens on seminal vesicular lipids of castrated mature bonnet monkeys Macaca radiata.

Effects of prolactin (PRL), bromocriptine (Br), testosterone propionate (TP), dihydrotestosterone (DHT) and the combination of these androgens with PRL/Br on the total lipid, total cholesterol, total glyceride glycerols, total phospholipid and their fractions in seminal vesicles of castrated mature monkeys were studied. Glyceride glycerols formed the major portion (50%) of total lipids in normal monkeys. Cholesterol and phospholipids were of equal share (25%). Esterified cholesterol formed major share (75%) of total cholesterol. Diacyl glycerol was the major (60%) glyceride glycerol and phosphatidyl choline and ethanolamine were the major phospholipid classes. Except triacyl glycerol castration markedly decreased all the lipid classes. PRL restored normal free and esterified cholesterol and phosphatidyl inositol but Br invariably decreased all the lipid classes. TP/DHT treatment stimulated the free and esterified cholesterol more than the control; it restored the normal glyceride glycerols. Phosphatidyl inositol, choline and ethanolamine were stimulated by androgens and other phospholipid classes were brought to normal. Addition of PRL + TP/DHT markedly increased esterified cholesterol, phosphatidyl inositol, choline, ethanolamine and phosphatidic acid. In all these aspects, Br counteracted the effects of androgens and PRL.

Animals↗