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N Srinivasan

Publications and source records attributed to N Srinivasan.

At least 73 records · Page 4Linked to original sources
PubMed2001

PALI-a database of Phylogeny and ALIgnment of homologous protein structures.

PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super-position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 'orphans' (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pauling.mbu.iisc.ernet. in/ approximately pali.

Databases, Factual↗
PubMed2001

PALI: a database of alignments and phylogeny of homologous protein structures.

PALI is a database of structure-based sequence alignments and phylogenetic relationships derived on the basis of three-dimensional structures of homologous proteins. This database enables grouping of pairs of homologous protein structures on the basis of their sequence identity calculated from the structure-based alignment and PALI also enables association of a new sequence to a family and automatic generation of a dendrogram combining the query sequence and homologous protein structures.

Databases, Factual↗
PubMed2001

Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins.

The database PALI (Phylogeny and ALIgnment of homologous protein structures) consists of families of protein domains of known three-dimensional (3D) structure. In a PALI family, every member has been structurally aligned with every other member (pairwise) and also simultaneous superposition (multiple) of all the members has been performed. The database also contains 3D structure-based and structure-dependent sequence similarity-based phylogenetic dendrograms for all the families. The PALI release used in the present analysis comprises 225 families derived largely from the HOMSTRAD and SCOP databases. The quality of the multiple rigid-body structural alignments in PALI was compared with that obtained from COMPARER, which encodes a procedure based on properties and relationships. The alignments from the two procedures agreed very well and variations are seen only in the low sequence similarity cases often in the loop regions. A validation of Direct Pairwise Alignment (DPA) between two proteins is provided by comparing it with Pairwise alignment extracted from Multiple Alignment of all the members in the family (PMA). In general, DPA and PMA are found to vary rarely. The ready availability of pairwise alignments allows the analysis of variations in structural distances as a function of sequence similarities and number of topologically equivalent Calpha atoms. The structural distance metric used in the analysis combines root mean square deviation (r.m.s.d.) and number of equivalences, and is shown to vary similarly to r.m.s.d. The correlation between sequence similarity and structural similarity is poor in pairs with low sequence similarities. A comparison of sequence and 3D structure-based phylogenies for all the families suggests that only a few families have a radical difference in the two kinds of dendrograms. The difference could occur when the sequence similarity among the homologues is low or when the structures are subjected to evolutionary pressure for the retention of function. The PALI database is expected to be useful in furthering our understanding of the relationship between sequences and structures of homologous proteins and their evolution.

Algorithms↗
PubMed2001

F X Nottingham and F X Taunton. Two novel mutations in factor X resulting in loss of functional activity and an interpretation using molecular modelling.

We report two novel mutations in the Factor X gene which result in a bleeding tendency in two unrelated Caucasian families. Although the mutations occur at adjacent codons in exon 8 and result in reduced functional activity with normal antigen levels, the patterns of inheritance appear to be quite distinct. Factor X Nottingham (alanine 404 threonine) appears to be associated with an autosomal recessive pattern of inheritance. In contrast, Factor X Taunton (arginine 405 glycine) results in a mode of inheritance consistent with an autosomal dominant pattern, all five of the heterozygotes in this family being clinically affected. Molecular modelling studies suggest that, in the case of Factor X Nottingham, a drastic conformational change causes major unfolding of the protein. For Factor X Taunton, less extreme conformational changes occur causing loss of functional activity such that substrate binding sites might be maintained. It is proposed that competition with wild type for substrate binding could occur leading to a dominant negative effect.

Adolescent↗
PubMed2000

Biochemical characterization of the intracellular domain of the human guanylyl cyclase C receptor provides evidence for a catalytically active homotrimer.

Guanylyl cyclase C (GCC) is the receptor for the family of guanylin peptides and bacterial heat-stable enterotoxins (ST). The receptor is composed of an extracellular, ligand-binding domain and an intracellular domain with a region of homology to protein kinases and a guanylyl cyclase catalytic domain. We have expressed the entire intracellular domain of GCC in insect cells and purified the recombinant protein, GCC-IDbac, to study its catalytic activity and regulation. Kinetic properties of the purified protein were similar to that of full-length GCC, and high activity was observed when MnGTP was used as the substrate. Nonionic detergents, which stimulate the guanylyl cyclase activity of membrane-associated GCC, did not appreciably increase the activity of GCC-IDbac, indicating that activation of the receptor by Lubrol involved conformational changes that required the transmembrane and/or the extracellular domain. The guanylyl cyclase activity of GCC-IDbac was inhibited by Zn(2+), at concentrations shown to inhibit adenylyl cyclase, suggesting a structural homology between the two enzymes. Covalent cross-linking of GCC-IDbac indicated that the protein could associate as a dimer, but a large fraction was present as a trimer. Gel filtration analysis also showed that the major fraction of the protein eluted at a molecular size of a trimer, suggesting that the dimer detected by cross-linking represented subtle differences in the juxtaposition of the individual polypeptide chains. We therefore provide evidence that the trimeric state of GCC is catalytically active, and sequences required to generate the trimer are present in the intracellular domain of GCC.

Amino Acid Sequence↗
PubMed2000

Altered corticosterone status impairs steroidogenesis in the granulosa and thecal cells of Wistar rats.

Hypo- and hyper-corticosteronisms have adverse effects on ovarian endocrine and exocrine functions. In the present study, the mechanism by which corticosterone in excess or insufficiency impairs steroidogenesis in granulosa and thecal cells was investigated in adult albino Wistar rats. In this regard, rats were administered with corticosterone-21-acetate (2 mg/100 g b.wt., s.c., twice daily) or metyrapone (11beta-hydroxylase blocker) (10 mg/100 g b.wt., s.c., twice daily) for 15 days and a group of corticosterone/metyrapone treated rats was withdrawn of treatment and maintained for another 15 days and killed during their diestrus phase. Administration of corticosterone-21-acetate while elevated the serum corticosterone levels, metyrapone diminished the same. Administration of metyrapone reduced the serum levels of LH and estradiol; corticosterone reduced the levels of FSH in addition to LH and estradiol. In vitro production of progesterone and estradiol by the granulosa and thecal cells was decreased due to altered corticosterone status. Whereas administration of corticosterone significantly reduced the activity of 3beta-hydroxysteroid dehydrogenases (3beta-HSD) in granulosa and thecal cells, it reduced the activity of 17beta-HSD only in granulosa cells. While metyrapone treatment reduced the activity of 17beta-HSD in granulosa as well as thecal cells, it reduced the activity of 3beta-HSD only in thecal cells. The findings of the present investigation clearly demonstrate that excess or insufficiency in corticosterone affects steroidogenic process in the ovary. This is achieved by decreasing the levels of gonadotropins probably by their diminished synthesis and secretion and by interfering at the signal transduction process of these gonadotropins.

17-Hydroxysteroid Dehydrogenases↗
PubMed2000

The carboxy terminal WD domain of the pre-mRNA splicing factor Prp17p is critical for function.

In Saccharomyces cerevisiae, Prp17p is required for the efficient completion of the second step of pre-mRNA splicing. The function and interacting factors for this protein have not been elucidated. We have performed a mutational analysis of yPrp17p to identify protein domains critical for function. A series of deletions were made throughout the region spanning the N-terminal 158 amino acids of the protein, which do not contain any identified structural motifs. The C-terminal portion (amino acids 160-455) contains a WD domain containing seven WD repeats. We determined that a minimal functional Prp17p consists of the WD domain and 40 amino acids N-terminal to it. We generated a three-dimensional model of the WD repeats in Prp17p based on the crystal structure of the beta-transducin WD domain. This model was used to identify potentially important amino acids for in vivo functional characterization. Through analysis of mutations in four different loops of Prp17p that lie between beta strands in the WD repeats, we have identified four amino acids, 235TETG238, that are critical for function. These amino acids are predicted to be surface exposed and may be involved in interactions that are important for splicing. Temperature-sensitive prp17 alleles with mutations of these four amino acids are defective for the second step of splicing and are synthetically lethal with a U5 snRNA loop I mutation, which is also required for the second step of splicing. These data reinforce the functional significance of this region within the WD domain of Prp17p in the second step of splicing.

Amino Acid Sequence↗
PubMed2000

Impact of oestradiol and progesterone on the glycosaminoglycans and their depolymerizing enzymes of the rat mammary gland.

The influence of oestradiol and progesterone either singly or in combination with each other on the levels of hyaluronic acid, heparan sulphate, chondroitin sulphate, and on the activity of hyaluronidase and chondroitinase were investigated in the mammary gland of ovary-intact and in ovariectomized rats, administered oestradiol and/or progesterone. Administration of oestradiol to ovary-intact rats elevated the levels of hyaluronic acid and decreased the levels of heparan sulphate while progesterone, when administered alone, could elevate only chondroitin sulphate when compared with controls. The steroids when administered in combination, however, increased the levels of all glycosaminoglycans studied. Ovariectomized animals showed a decrease in heparan sulphate alone as compared with controls while administration of oestradiol to these rats elevated the levels of both heparan sulphate and chondroitin sulphate as compared with ovariectomized rats. Also the administration of progesterone either singly or in combination increased the levels of heparan sulphate and also decreased the levels of hyaluronic acid with no impact on the levels of chondoritin sulphate. In ovary-intact animals administration of oestradiol alone had no effect on hyaluronidase activity. Progesterone either singly or in combination with oestradiol reduced the activity of hyaluronidase, whereas it had no influence on the activity of chondroitinase. The activities of both the enzymes were decreased in ovariectomized animals and administration of oestradiol and/or progesterone to the above groups resulted in an increase. This study demonstrates that oestradiol anzd progesterone play an important role in modulating glycosaminoglycans and their depolymerizing enzymes, thereby influencing the activities of the mammary epithelium.

Animals↗
PubMed2000

Diffuse and localized nerve fiber layer loss measured with a scanning laser polarimeter: sensitivity and specificity of detecting glaucoma.

PURPOSE: To differentiate normal from diseased retinal nerve fiber layers (NFL) using a new method of analyzing polarimetry data that specifically targets patterns of diffuse and localized NFL loss. METHODS: The NFL from a sample of 34 patients with primary open-angle glaucoma (POAG), 34 patients with ocular hypertension, and 34 normal subjects were imaged using a scanning laser polarimeter (GDx; Laser Diagnostic Technologies, Inc., San Diego, CA). Diffuse loss was defined as a reduction in the peak-to-trough amplitude of the double-hump NFL pattern, and localized loss was defined as a lowering of the correlation of thickness values between local regions shown previously to correspond in normal subjects. RESULTS: Significant differences were found between the groups of normal subjects, patients with hypertension, and patients for both the amplitude and the correlational measures. The sensitivity and specificity calculated using optimal criterion values were 94% and 91%, respectively. CONCLUSIONS: These results suggest that NFL analysis targeting specific patterns of loss may be beneficial for differentiating normal NFL patterns from diseased NFL patterns, as well as for identifying patients at high risk.

Adult↗
PubMed2000

Fourier analysis of nerve fiber layer measurements from scanning laser polarimetry in glaucoma: emphasizing shape characteristics of the 'double-hump' pattern.

PURPOSE: The pattern of the distribution of nerve fiber layer (NFL) thickness values across the retina may provide an early anatomic indication of glaucomatous disruption. We developed a method of analyzing polarimetry measurements that emphasizes the shape of the pattern of NFL thickness values. Sensitivity and specificity for detecting glaucoma was obtained for these measures and compared with those for conventional measures. METHODS: Nerve fiber thickness was inferred from retardation shift measured by a scanning laser polarimeter (Laser Diagnostic Technologies, Inc., San Diego, CA) in 34 healthy subjects (68 eyes) and 34 patients with glaucoma (68 eyes). Fourier analysis was performed on the polarimetry data to emphasize the shape in the evaluation of the distribution of thickness values around the optic disc (along a 1.7-disc diameter ring). This was computed separately on superior and inferior hemiretinas. RESULTS: Significant differences were found in the Fourier shape measures between healthy subjects and patients with glaucoma. The sensitivity and specificity using Fourier coefficients with this particular sample was 96% and 90%, respectively. CONCLUSION: The evaluation of NFL measurements with Fourier analysis to emphasize the holistic shape of the "double-hump" pattern was found to be a useful tool as an analysis strategy.

Adult↗
PubMed1999

Non-iron metalloporphyrins: potent antibacterial compounds that exploit haem/Hb uptake systems of pathogenic bacteria.

A new group of potent antibacterial compounds, non-iron metalloporphyrins (MPs), is described. MPs possess a strong antibacterial activity against Gram-positive bacteria, Gram-negative bacteria and mycobacteria. Anaerobically grown bacteria and microorganisms that do not respire and/or express haem uptake systems were resistant to MPs. Antibacterial activity of MPs was not affected by known antibiotic resistance mechanisms operating in bacteria. The most potent MP against Y. enterocolitica, methicillin-resistant S. aureus and M. smegmatis was gallium protoporphyrin IX (Ga-PPIX). When tested alone, Ga ions and metal-free porphyrins had approximately 100-fold higher minimum inhibitory concentration (MIC) values for these organisms. Ga-PPIX was not degraded by MP-sensitive bacteria, indicating that the whole molecule is responsible for antibacterial activity. MPs are antibacterial 'Trojan horses', as they exploit haem transport systems of Gram-negative bacteria as portals of entry into the cell. Bacterial mutants in superoxide dismutases, catalases and stationary-phase sigma factors were hypersensitive to Ga-PPIX. The extreme sensitivity of sod mutants to MPs and the requirement for active respiration for MP activity suggests that these compounds stimulate the production of reactive oxygen radicals in bacteria. Ga-PPIX was not toxic to primary human fibroblasts, several established cell lines and experimental animals at concentrations > 100-fold higher than the MIC for sensitive bacteria.

Anaerobiosis↗
PubMed1999

The effect of hypo- and hyperthyroidism on uterine and cervical collagens and glycosidases in albino rats.

The effect of hypo- and hyperthyroidism on uterine and cervical collagen and glycosidases were studied in mature albino rats. Hypothyroidism significantly increased the salt-soluble, acid-soluble, insoluble and total collagen in the uterus and cervix. However, all of these collagens were significantly decreased in the hyperthyroid condition. The activities of alpha- and beta-galactosidases and glucosidases were significantly decreased in the uterus and cervix of hypothyroid rats, whereas, in hyperthyroid rats, all of these enzymes were significantly increased in the uterus and cervix. The data obtained in the present study suggested that the increase in lysosomal enzymes increased the degradation of uterine and cervical collagen. In contrast, the decrease in lysosomal enzymes in hypothyroid condition increased uterine and cervical collagen by decreasing degradation.

Animals↗
PubMed1999

Effects of ethanol ingestion on sperm monosaccharides and fertility.

Chronic alcohol abuse is often associated with reproductive disorders. Sperm monosaccharides play an indispensable role in sperm-egg interactions and fertilization. Ethanol (3 g/kg body weight as 25%, v/v) was given by gastric intubation twice daily for 30 days while in another group, rats which had been treated with ethanol were withdrawn from treatment for a further period of 30 days, in order to assess the reversibility of the ethanol-induced effects. Epididymal ethanol content, sperm monosaccharides and the fertility of ethanol treated and ethanol withdrawn rats were assessed. Ethanol ingestion caused a significant decrease in sperm monosaccharides suggesting defective glycosylation of sperm surface proteins. Sperm monosaccharides and fertility were returned to normal following the withdrawal of ethanol. Ethanol-induced changes in sperm monosaccharides may be one of the reasons for the reduced fertility of ethanol treated rats.

Animals↗
PubMed1999

Structural interpretation of site-directed mutagenesis and specificity of the catalytic subunit of protein kinase CK2 using comparative modelling.

The catalytic subunit of protein kinase casein kinase 2 (CK2alpha), which has specificity for both ATP and GTP, shows significant amino acid sequence similarity to the cyclin-dependent kinase 2 (CDK2). We constructed site-directed mutants of CK2alpha and used a three-dimensional model to investigate the basis for the dual specificity. Introduction of Phe and Gly at positions 50 and 51, in order to restore the pattern of the glycine-rich motif, did not seriously affect the specificity for ATP or GTP. We show that the dual specificity probably originates from the loop situated around the position His115 to Asp120 (HVNNTD). The insertion of a residue in this loop in CK2 alpha subunits, compared with CDK2 and other kinases, might orient the backbone to interact with the base A and G; this insertion is conserved in all known CK2alpha. The mutant deltaN118, the design of which was based on the modelling, showed reduced affinity for GTP as predicted from the model. Other mutants were intended to probe the integrity of the catalytic loop, alter the polarity of a buried residue and explore the importance of the carboxy terminus. Introduction of Arg to replace Asn189, which is mapped on the activation loop, results in a mutant with decreased k(cat), possibly as a result of disruption of the interaction between this residue and basic residues in the vicinity. Truncation at position 331 eliminates the last 60 residues of the alpha subunit and this mutant has a reduced catalytic efficiency compared with the wild-type. Catalytic efficiency is restored in the truncation mutant by the replacement of a potentially buried Glu at position 252 by Lys, probably owing to a higher stability resulting from the formation of a salt bridge between Lys252 and Asp208.

Amino Acid Sequence↗
PubMed1999

The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein.

The TRANSPARENT TESTA GLABRA1 (TTG1) locus regulates several developmental and biochemical pathways in Arabidopsis, including the formation of hairs on leaves, stems, and roots, and the production of seed mucilage and anthocyanin pigments. The TTG1 locus has been isolated by positional cloning, and its identity was confirmed by complementation of a ttg1 mutant. The locus encodes a protein of 341 amino acid residues with four WD40 repeats. The protein is similar to AN11, a regulator of anthocyanin biosynthesis in petunia, and more distantly related to those of the beta subunits of heterotrimeric G proteins, which suggests a role for TTG1 in signal transduction to downstream transcription factors. The 1.5-kb TTG1 transcript is present in all major organs of Arabidopsis. Sequence analysis of six mutant alleles has identified base changes producing truncations or single amino acid changes in the TTG1 protein.

Alleles↗
PubMed1999

Interactions of protein kinase CK2 subunits.

Several approaches have been used to study the interactions of the subunits of protein kinase CK2. The inactive mutant of CK2alpha that has Asp 156 mutated to Ala (CK2alphaA156) is able to bind the CK2beta subunit and to compete effectively in this binding with wild-type subunits alpha and alpha'. The interaction between CK2alphaA156 and CK2beta was also demonstrated by transfection of epitope-tagged cDNA constructs into COS-7 cells. Immunoprecipitation of epitope-tagged CK2alphaA156 coprecipitated the beta subunit and vice-versa. The assay of the CK2 activity of the extracts obtained from cells transiently transfected with these different subunits yielded some surprising results: The CK2 specific phosphorylating activity of these cells transfected with the inactive CK2alphaA156 was considerably higher than the control cells transfected with vectors alone. Assays of the immunoprecipitated CK2alphaA156 expressed in these cells, however, demonstrated that the mutant was indeed inactive. It can be concluded that transfection of the inactive CK2alphaA156 affects the endogenous activity of CK2. Transfection experiments with CK2alpha and beta subunits and CK2alphaA156 were also used to confirm the interaction of CK2 with the general CDK inhibitor p21WAF1/CIP1 co-transfected into these cells. Finally a search in the SwissProt databank for proteins with properties similar to those derived from the amino acid composition of CK2beta indicated that CK2beta is related to protein phosphatase 2A and to other phosphatases as well as to a subunit of some ion-transport ATPases.

Amino Acid Sequence↗
PubMed1998

Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies.

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Amino Acid Sequence↗