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Biomedical subjects

R Prasad

Publications and source records attributed to R Prasad.

At least 109 records · Page 6Linked to original sources
PubMed1998

Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.

DNA polymerase beta (beta-pol) cleaves the sugar-phosphate bond 3' to an intact apurinic/apyrimidinic (AP) site (i.e. AP lyase activity). The same bond is cleaved even if the AP site has been previously 5'-incised by AP endonuclease, resulting in a 5' 2-deoxyribose 5-phosphate (i.e. dRP lyase activity). We characterized these lyase reactions by steady-state kinetics with the amino-terminal 8-kDa domain of beta-pol and with the entire 39-kDa polymerase. Steady-state kinetic analyses show that the Michaelis constants for both the dRP and AP lyase activities of beta-pol are similar. However, kcat is approximately 200-fold lower for the AP lyase activity on an intact AP site than for an AP endonuclease-preincised site. The 8-kDa domain was also less efficient with an intact AP site than on a preincised site. The full-length enzyme and the 8-kDa domain efficiently remove the 5' dRP from a preincised AP site in the absence of Mg2+, and the pH profiles of beta-pol and 8-kDa domain dRP lyase catalytic efficiency exhibit a broad alkaline pH optimum. An inhibitory effect of pyridoxal 5'-phosphate on the dRP lyase activity is consistent with involvement of a primary amine (Lys72) as the Schiff base nucleophile during lyase chemistry.

Carbon-Oxygen Lyases↗
PubMed1998

Functional analysis of the amino-terminal 8-kDa domain of DNA polymerase beta as revealed by site-directed mutagenesis. DNA binding and 5'-deoxyribose phosphate lyase activities.

The amino-terminal 8-kDa domain of DNA polymerase beta functions in binding single-stranded DNA (ssDNA), recognition of a 5'-phosphate in gapped DNA structures, and as a 5'-deoxyribose phosphate (dRP) lyase. NMR and x-ray crystal structures of this domain have suggested several residues that may interact with ssDNA or play a role in the dRP lyase reaction. Nine of these residues were altered by site-directed mutagenesis. Each mutant was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. CD spectra of these mutant proteins indicated that the alteration did not adversely affect the global protein structure. Single-stranded DNA binding was probed by photochemical cross-linking to oligo(dT)16. Several mutants (F25W, K35A, K60A, and K68A) were impaired in ssDNA binding activity, whereas other mutants (H34G, E71Q, K72A, E75A, and K84A) retained near wild-type binding activity. The 5'-phosphate recognition activity of these mutants was examined by UV cross-linking to a 5-nucleotide gap DNA where the 5' terminus in the gap was either phosphorylated or unphosphorylated. The results indicate that Lys35 is involved in 5'-phosphate recognition of DNA polymerase beta. Finally, the dRP lyase activity of these mutants was evaluated using a preincised apurinic/apyrimidinic DNA. Alanine mutants of Lys35 and Lys60 are significantly reduced in dRP lyase activity, consistent with the lower ssDNA binding activity. More importantly, alanine substitution for Lys72 resulted in a greater than 90% loss of dRP lyase activity, without affecting DNA binding. Alanine mutants of Lys68 and Lys84 had wild-type dRP lyase activity. The triple alanine mutant, K35A/K68A/K72A, was devoid of dRP lyase activity, suggesting that the effects of the alanine substitution at Lys72 and Lys35 were additive. The results suggest that Lys72 is directly involved in formation of a covalent imino intermediate and are consistent with Lys72 as the predominant Schiff base nucleophile in the dRP lyase beta-elimination catalytic reaction.

Catalysis↗
PubMed1998

Deletion of transmembrane domain 12 of CDR1, a multidrug transporter from Candida albicans, leads to altered drug specificity: expression of a yeast multidrug transporter in baculovirus expression system.

Cdr1p, an ATP-binding cassette transporter from the pathogenic yeast Candida albicans, confers resistance to several unrelated drugs including anti-Candida drugs (Prasad et al., 1995b). We demonstrate that the deletion of 237 bp (79 aa) from the 3' end of CDR1 (which encompasses the transmembrane domain (TM) 12 of the putative transporter) did not result in the total loss of its ability to efflux cytotoxic agents. While the expression of deltaCDR1 in yeast resulted in impaired sensitivity to drugs like cycloheximide, anisomycin, sulfomethuron methyl and antifungal nystatin, its ability to confer resistance remained unaltered to drugs such as o-phenanthroline, 4-nitroquinoline-N-oxide, cerulenin, azoles, oligomycin, erythromycin, and benomyl. Similar to human MDR1p. Cdr1p might also have localized drug binding sites in TM 12, but that might not be the case for all the drugs. The TM 12 deletion also did not lead to any significant impairment in NTPase activities. Both ATPase and UTPase activities of complete Cdr1p and deltaCdr1p were not significantly altered, as was the case with respect to their ability to efflux Rh123 and steroid hormone like [3H]-beta-estradiol. To further dissect the functionality of Cdr1p, its truncated version was overexpressed in a baculovirus-insect cell expression system. The synthesis of deltaCdr1p in Sf9 cells was temporally regulated as a function of the baculovirus polyhedrin gene promoter. The Sf9 derived deltaCdr1p was approximately 130 kDa, which was lower than the expected size, probably due to the differences in glycosylation. This, however, did not affect the functionality of deltaCdr1p. The deletion of TM 12 did not affect the targeting of the protein and deltaCdr1p was exclusively localized in plasma membrane of Sf9 cells as detected by immunofluorescence. The expression of deltaCdr1p in the baculovirus-insect expression system generated a high drug-stimulated plasma membrane-bound ATPase activity which was not demonstrable when deltaCdr1p was expressed in yeast.

ATP-Binding Cassette Transporters↗
PubMed1998

Purified arginine permease of Candida albicans is functionally active in a reconstituted system.

We have for the first time purified arginine permease from a pathogenic yeast, Candida albicans, to homogeneity by affinity chromatography using L-arginine-linked agarose matrix as affinity column. The purified protein (PP) was of 66 kDa with no subunit structure. Two kinetically distinct binding affinities of PP were evident where high affinity binding (S1) revealed a dependence on acidic pH while pH did not have dramatic effect on low affinity (S2) binding. The specificity of L-arginine binding to PP with regard to other amino acids, structural analogues and inhibitors, was essentially similar to arginine transport observed in the intact cells of C. albicans (Rao et al., 1986). The purified arginine permease was reconstituted into proteoliposomes and its functionality was tested by imposing a valinomycin-induced membrane potential. All the characteristic features of L-arginine transport displayed by the reconstituted system were similar to those observed in intact cells. Thus homogeneous purified arginine permease was also functionally active.

Amino Acid Transport Systems↗
PubMed1998

Expression of CDR1, a multidrug resistance gene of Candida albicans: transcriptional activation by heat shock, drugs and human steroid hormones.

We have examined the expression of CDR1 (Candida drug resistance gene) in different stress conditions. There was a significant but transient enhancement of CDR1 expression associated with elevated temperatures. Most noteworthy transcriptional activation was observed with miconazole and vinblastine. Interestingly, beta-estradiol and progesterone were also able to enhance CDR1 expression. Elevated levels of CDR1 and CDR2 (a homologue of CDR1) mRNA were found in some azole-resistant clinical isolates of C. albicans. CaMDR1 (benomyl-resistant) expression, however, did not differ among all the resistant isolates. Our results confirm the existence of multiple mechanisms of azole resistance in C. albicans.

Antifungal Agents↗
PubMed1998

Subunits of human replication protein A are crosslinked by photoreactive primers synthesized by DNA polymerases.

Human replication protein A (huRPA) is a multisubunit protein which is involved in DNA replication, repair and recombination processes. It exists as a stable heterotrimer consisting of p70, p32 and p14 subunits. To understand the contribution of huRPA subunits to DNA binding we applied the photoaffinity labeling technique. The photoreactive oligonucleotide was synthesized in situ by DNA polymerases. 5-[N-(2-nitro-5-azidobenzoyl)-trans -3-aminopropenyl-1]deoxyuridine-5'-triphosphate (NABdUTP) was used as substrate for elongation of a radiolabeled primer logical ortemplate either by human DNA polymerase alpha primase (polalpha), human DNA polymerase beta (polbeta) or Klenow fragment of Escherichia coli DNA polymerase I (KF). The polymerase was incubated with NABdUTP and radiolabeled primer-template in the presence or absence of huRPA. The reaction mixtures were then irradiated with monochromatic UV light (315 nm) and the crosslinked products were separated by SDS-PAGE. The results clearly demonstrate crosslinking of the huRPA p70 and p32 subunits with DNA. The p70 subunit appears to bind to the single-stranded part of the DNA duplex, the p32 subunit locates near the 3'-end of the primer, while the p14 subunit locates relatively far from the 3'-end of the primer. This approach opens new possibilities for analysis of huRPA loading on DNA in the course of DNA replication and DNA repair.

Azides↗
PubMed1998

Characterisation of human steroid hormone transport mediated by Cdr1p, a multidrug transporter of Candida albicans, belonging to the ATP binding cassette super family.

Cdr1p, a multidrug transporter from a pathogenic yeast Candida albicans, confers resistance to several unrelated drugs including anti-Candida drugs. We demonstrate that Cdr1p can specifically transport human steroid hormones namely beta-estradiol and corticosterone. Saccharomyces cerevisiae transformant S-12, harbouring the CDR1 gene, accumulated about 3-fold less [3H] beta-estradiol and about 2-fold less [3H]corticosterone than the non-transformed strain. When CDR1 was expressed in AD strain (AD-CDR1) which had seven ATP binding cassette (ABC) superfamily of putative transporter genes disrupted, the net accumulation of these hormones as compared to S-12 was significantly lower. Efflux of beta-estradiol and corticosterone was inhibited by a 100-fold higher (200 nM) concentration of beta-estradiol, corticosterone, ergosterol or dexamethasone, but progesterone which could not be transported by Cdr1p did not affect the efflux and thus accumulation. Interestingly, some of the drugs viz. cycloheximide, chloramphenicol, fluconazole and o-phenanthroline, to which CDR1 confers resistance, could also prevent efflux and enhance accumulation to some extent. In conclusion, we show that human steroid hormones could be the substrates for Cdr1p and the energy dependent transport mediated by it is specific for estradiol and corticosterone.

ATP-Binding Cassette Transporters↗
PubMed1998

Viability of fibroblast-seeded ligament analogs after autogenous implantation.

Fibroblast-seeded collagen scaffolds or ligament analogs are potentially useful for reconstruction of the anterior cruciate ligament of the knee. To provide lasting benefits, the seeded cells must survive implantation within the harsh synovial environment of the knee joint. Our objective was to determine the in vivo fate of autogenous fibroblast-seeded ligament analogs as a function of fibroblast source (anterior cruciate ligament or skin), implantation site (knee joint or subcutaneous space), and time after implantation (1, 2, 4, 6, or 8 weeks). Before implantation, fibroblasts were labeled with PKH26-GL, a fluorescent membrane dye. Immediately after retrieval of the implant, the viability of the labeled seeded cells was assessed under a fluorescent microscope. Viable seeded fibroblasts remained attached to the collagen fibers within the ligament analogs for at least 4 weeks (skin fibroblasts) or 6 weeks (anterior cruciate ligament fibroblasts) after implantation. A larger number of viable seeded cells were consistently observed in the subcutaneous space than in the knee joint. Scaffold resorption prevented observation at the 8-week time period. Fibroblast-seeded ligament analogs remained viable for prolonged periods in the knee joint and therefore have the potential to influence the formation and remodeling of neoligament tissue after reconstruction of the anterior cruciate ligament.

Animals↗
PubMed1998

A critical evaluation of copper metabolism in Indian Wilson's disease children with special reference to their phenotypes and relatives.

Wilson's disease is an autosomal recessive disorder of copper accumulation in various organs, with most common clinical manifestations such as hepatic, neurological, and renal dysfunctions. Serum copper and ceruloplasmin in Wilson's disease were significantly lower as compared to normals, controls, and relatives of Wilson's disease patients, whereas marked hypercupriuria (145+/-7 microg/24 h) was observed in Wilson's children only. A good correlation (r=0.92) was found between non-ceruloplasmin-bound copper and 24-h urinary copper excretion in Wilson's disease patients. Further, copper studies among the different phenotypes of Wilson's disease revealed substantially low serum ceruloplasmin and a marked hypercupriuria in Wilson's disease children associated with renal tubular acidosis as compared to the patients with either hepatological or neurological manifestations. Serum ceruloplasmin levels in 14 patients of Wilson's disease were between 14 and 20 mg/dL. These patients of Wilson's disease were confirmed by measuring liver biopsy copper, which was about nine times higher than normal hepatic copper content. During the family screening by copper studies, four asymptomatic siblings were diagnosed for Wilson's disease. These subjects were then started on D-penicillamine therapy because presymptomatic treatment prevents progression of the disease complications.

Adolescent↗
PubMed1998

Identification of polymorphic mutant alleles of CaMDR1, a major facilitator of Candida albicans which confers multidrug resistance, and its in vitro transcriptional activation.

CaMDR1 (Candida albicans Multi Drug Resistance) encodes a major facilitator whose expression in Saccharomyces cerevisiae confers resistance to several unrelated drugs. We describe here the identification and molecular characterization of seven mutant alleles of CaMDR1 (CaMDR1-1 to 1-7). The complete sequencing of CaMDR1 alleles revealed several in-frame point mutations leading to a change in amino-acid residues where insertion/replacement of an aspartate residue in a serine-asparagine-aspartate-rich domain was most noteworthy. Interestingly, these alleles showed a distinct drug resistance profile. The expression of CaMDR1, or of its alleles, in C. albicans cells was enhanced by benomyl, methotrexate and several other unrelated drugs, and was more pronounced in at least one of the azole-resistant clinical isolates.

Alleles↗
PubMed1998

Pituitary-gonadal hormones during prolonged residency in Antarctica.

Plasma luteinizing hormone (LH), follicle stimulating hormone (FSH), prolactin (PRL) and testosterone levels were measured in nine eugonadal men in New Delhi and during the 1st week of different months of their stay at Dakshin Gangotri in Antarctica. During their 12-month stay in Antarctica, they were exposed to a severely cold climate, long polar nights and polar days, high wind velocity, increased amounts of solar and ultraviolet radiation and geomagnetism, as well as physical and social isolation. Plasma testosterone tended to increase in March, but a significant increase (P < 0.05) was not seen until April. The mean testosterone levels in May, June, September and November were also significantly higher than the March or New Delhi values. The absolute values of LH, FSH and PRL did not show any month-to-month changes in Antarctica. However, when the hormone levels were expressed as a percentage of the individual annual Antarctic mean, significant differences as a percentage of the individual annual Antarctic mean, significant differences were observed. The testosterone peak in April, May and June was associated with an increase in LH. The nadirs of testosterone, LH, FSH and PRL were seen in either July or August. FSH showed the highest values in March, whereas the highest PRL values were seen in November. These observations suggest the presence of circannual variations in gonadotropin, PRL and LH in Antarctica which are independent of polar days and polar nights. It appears that factors other than the duration of daylight might be involved in regulating these changes. The significance of maintenance of testosterone levels in the supra-physiological range in Antarctica remains unknown but may be important in acclimatization/habituation to the extreme polar cold by increasing basal metabolic rate, protein synthesis and erythropoiesis.

Acclimatization↗
PubMed1998

Effect of growth hormone therapy in burn patients on conservative treatment.

Evaluation of growth hormone therapy in burns is limited and none is reported from developing countries where burns still carry high mortality. We analysed serial observations on the clinical and biochemical profiles in 13 patients with second and third degree burns who received recombinant human growth hormone (rhGH) (0.5 IU/kg body wt) for 2 weeks in addition to standard conservative treatment and in 9 patients who were managed with standard conservative treatment only. The two groups of patients had burns, comparable in extent and severity. Additional rhGH treatment resulted in improved wound healing (p < 0.001), delayed separation of eschars (p < 0.01), increase in haemoglobin (p < 0.05), serum albumin (p < 0.01), calcium (p < 0.05), phosphorus (p < 0.001), glomerular filtration rate (p < 0.05) and 7 fold elevation in IGF-1. Also, a reduction in weight loss (p < 0.01), nitrogen production rate (p < 0.05), catabolic index (p < 0.01), duration of sepsis (p < 0.01) and hospital stay by 40% (p < 0.01) was noted with rhGH therapy. Transient hypercalcemia (3 patients), albuminuria (2 patients) and elevated blood glucose (one patient) were noted in the rhGH treated group not necessitating any specific therapy. Mortality in rhGH treatment group was 8.3% compared to 44.5% in the "no rhGH" treatment group. These observations suggest significant benefits of short term rhGH treatment in burn patients on conservative management.

Adolescent↗
PubMed1998

Identification of a novel copper-binding protein from the liver of Indian childhood cirrhosis: purification and physicochemical characterization [corrected].

A novel copper-binding protein was identified in the liver supernatant (100,000 x g) of Indian childhood cirrhosis (ICC), purified to apparent homogeneity and characterized [corrected]. Purified major copper-binding protein (MCuBP) is solely responsible for binding about 35% of the total supernatant copper. Elution profile of ICC liver supernatant on Sephadex G-75 column chromatography showed three peaks. About 60% of the total supernatant copper was resolved in peak II, whereas zinc content was insignificant in this peak. But peak II was almost missing in a gel elution profile of control liver supernatant. The control group included cases of various liver diseases viz. neonatal hepatitis, septicemia, and mixed nodular cirrhosis. Copper-binding proteins of peak II further purified on ion-exchange chromatography and elution profile showed that peak II was a MCuBP with high copper-binding capacity (10 g atoms/mol of native protein). SDS-PAGE of this protein also revealed the existence of a single band with molecular mass of about 50 kD. UV spectra of MCuBP showed the maximal absorbance at 254 nm. Unlike the classical metallothionein, the amino acid composition of MCuBP revealed the presence of aromatic amino acids and higher content of glutamic acid and aspartic acid followed by glycine and serine. The ratio (0.3) of basic amino acids to acidic amino acids strongly indicates that it is an acidic protein. The cysteine content in this protein was insignificant, which further corroborates the possibility that the acidic amino acids might be prominent candidates for binding copper. Thus, the 50-kD MCuBP apparently makes a major contribution to the total copper-binding activity in ICC liver cytosol and may play a significant role in hepatic intracellular copper accumulation.

Amino Acids↗
PubMed1998

Plasma insulin and growth hormone during antarctic residence.

Circulatory levels of insulin and growth hormone (GH) were estimated in nine tropical euglycemic men in New Delhi and during the first week of every month of stay in Dakshin Gangotri, Antarctica. Prolonged residency in Antarctica did not alter GH levels because mean GH values during Austral summer and Austral winter were not significantly different from the New Delhi values. Compared with GH, the insulin levels during March, April, and June were found to be significantly lower than the New Delhi values. In Antarctica, the insulin levels in March, April, May, June, July, and August were also found to be significantly lower than the December values. This decline in insulin in Antarctica might be important in increasing substrate availability for heat production by facilitating lipolysis and hepatic glucose output.

Acclimatization↗
PubMed1998

Plasma zinc status in Indian childhood tuberculosis: impact of antituberculosis therapy.

SETTING: Department of Paediatrics and Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India. OBJECTIVE: To assess the plasma zinc status in children with tuberculosis and to correlate it with nutritional status, activity and severity of disease in relation to antituberculosis therapy. DESIGN: The plasma zinc status of 50 children with different forms of tuberculosis was compared with 10 healthy and 10 malnourished children without tuberculosis at 0, 1, 2, 3 and 6 months of antituberculosis therapy. RESULT: The mean plasma zinc concentration in children with pulmonary tuberculosis (n = 20) was 68.65+/-2.50 microg/dl, central nervous system (CNS) tuberculosis (n = 10) was 64.20+/-3.82 microg/dl, tuberculous lymphadenitis (n = 10) was 63.2+/-3.77 microg/dl and disseminated tuberculosis (n = 10) was 59.0+/-2.75 microg/dl at 0 months. The mean plasma zinc level of healthy children was 129.10+/-3.01 microg/dl and in malnourished non-tuberculous children it was 108.40+/-3.16 microg/dl. Thus children with tuberculosis had significantly lower plasma zinc level than those without tuberculosis, irrespective of their nutritional status (P < 0.001). There was a significant rise in zinc level at the end of 6 months of antituberculosis therapy (P < 0.001). CONCLUSION: Plasma zinc status may prove to be a good objective marker for monitoring the severity of the disease and the response to therapy.

Antitubercular Agents↗
PubMed1997

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.

Catalysis↗
PubMed1997

Structure and expression pattern of human ALR, a novel gene with strong homology to ALL-1 involved in acute leukemia and to Drosophila trithorax.

The ALL-1 gene is involved in human acute leukemia through chromosome translocations or internal rearrangements. ALL-1 is the human homologue of Drosophila trithorax. The latter is a member of the trithorax group (trx-G) genes which together with the Polycomb group (Pc-G) genes act as positive and negative regulators, respectively, to determine the body structure of Drosophila. We have cloned a novel human gene, ALR, which encodes a gigantic 5262 amino acid long protein containing a SET domain, five PHD fingers, potential zinc fingers, and a very long run of glutamines interrupted by hydrophobic residues, mostly leucine. The SET motif, PDH fingers, zinc fingers and two other regions are most similar to domains of ALL-1 and TRX. The first two motifs are also found in other trx-G and Pc-G proteins. The ALR gene was mapped to chromosome band 12q12-13, adjacent to the VDR gene. This region is involved in duplications and translocations associated with cancer. The analysis of ALR expression showed that its approximately 18 kb long mRNA is expressed, like ALL-1, in most adult tissues, including a variety of hematopoietic cells, with the exception of the liver. Whole mount in situ hybridization to early mouse embryos indicates expression in multiple tissues. Based on similarities in structure and expression pattern, ALR is likely to play a similar role to ALL-1 and trx, although its target genes have yet to be identified.

Age Factors↗