Biomedical subjects

A Dutta

Publications and source records attributed to A Dutta.

At least 73 records · Page 4Linked to original sources

PubMed1997

Identification of HsORC4, a member of the human origin of replication recognition complex.

A new member of human origin recognition complex (ORC) has been cloned and identified as the human homologue of Saccharomyces cerevisiae ORC4. HsORC4 is a 45-kDa protein encoded by a 2.2-kilobase mRNA whose amino acid sequence is 29% identical to ScORC4. HsORC4 has a putative nucleotide triphosphate binding motif that is not seen in ScORC4. HsORC4P also reveals an unsuspected homology to the ORC1-Cdc18 family of proteins. HsORC4 mRNA expression and protein levels remain constant through the cell cycle. HsORC4P is coimmunoprecipitated from cell extracts with another subunit of human ORC, HsORC2P, consistent with it being a part of the putative human origin recognition complex.

Amino Acid Sequence↗

PubMed1997

Roles of the structure and orientation of ligands and ligand mimics inside the ligand-binding pocket of the vitamin D-binding protein.

1alpha,25-Dihydroxyvitamin D3, the vitamin D hormone, manifests its diverse biological properties by specifically binding to the vitamin D sterol-binding pockets of vitamin D-binding protein (DBP) and vitamin D receptor. In the past, several affinity, photoaffinity, and chemical modification studies have been carried out to probe the vitamin D sterol-binding pocket of DBP and to evaluate the relationship between the structure of this pocket and the functions of the protein. In the present study, we examined the steric requirements inside this pocket by considering conformational structures of various bromoacetate derivatives of 25-hydroxyvitamin D3 and 1alpha,25-dihydroxyvitamin D3 and their abilities to covalently and specifically modify this pocket. We observed that, although 25-hydroxyvitamin D3 3beta-bromoacetate (25-OH-D3-3-BE), 1alpha,25-dihydroxyvitamin D3 3beta-bromoacetate [1alpha,25(OH)2D3-3-BE], 1alpha,25-dihydroxyvitamin D3 1alpha-bromoacetate [1alpha,25(OH)2D3-1-BE], and 1alpha,25-dihydroxyvitamin D3 1alpha,3beta-dibromoacetate [1alpha,25(OH)2D3-1,3-di-BE] bound DBP in a specific manner, only [3H]-25-OH-D3-3-BE and [3H]-1alpha,25(OH)2D3-3-BE affinity labeled the protein. BNPS-skatole cleavages of [3H]-25-OH-D3-3-BE- and 3H-1alpha,25(OH)2D3-3-BE-labeled DBP samples produced the same labeled peptide (N-terminal), demonstrating the specificity of labeling by these analogs. Energy-minimized conformational structures of these bromoacetate derivatives indicated significant changes in the A-ring conformations of these analogs. These structural changes were invoked to explain the inability of [3H]-1alpha,25(OH)2D3-1-BE and [3H]-1alpha,25(OH)2D3-1,3-di-BE to affinity label DBP. Overall, these studies suggested that the vitamin D sterol-binding pocket in DBP is sterically quite restrictive. This information could be potentially important in designing future vitamin D-based drugs for several diseases.

Acetates↗

PubMed1997

p21CIP1 and Cdc25A: competition between an inhibitor and an activator of cyclin-dependent kinases.

Cdc25A, a phosphatase essential for G1-S transition, associates with, dephosphorylates, and activates the cell cycle kinase cyclin E-cdk2. p21CIP1 and p27 are cyclin-dependent kinase (cdk) inhibitors induced by growth-suppressive signals such as p53 and transforming growth factor beta (TGF-beta). We have identified a cyclin binding motif near the N terminus of Cdc25A that is similar to the cyclin binding Cy (or RR LFG) motif of the p21CIP1 family of cdk inhibitors and separate from the catalytic domain. Mutations in this motif disrupt the association of Cdc25A with cyclin E- or cyclin A-cdk2 in vitro and in vivo and selectively interfere with the dephosphorylation of cyclin E-cdk2. A peptide based on the Cy motif of p21 competitively disrupts the association of Cdc25A with cyclin-cdks and inhibits the dephosphorylation of the kinase. p21 inhibits Cdc25A-cyclin-cdk2 association and the dephosphorylation of cdk2. Conversely, Cdc25A, which is itself an oncogene up-regulated by the Myc oncogene, associates with cyclin-cdk and protects it from inhibition by p21. Cdc25A also protects DNA replication in Xenopus egg extracts from inhibition by p21. These results describe a mechanism by which the Myc- or Cdc25A-induced oncogenic and p53- or TGF-beta-induced growth-suppressive pathways counterbalance each other by competing for cyclin-cdks.

Animals↗

PubMed1997

Initiation of DNA replication in eukaryotic cells.

The recent identification of proteins that recognize origins of DNA replication and control the initiation of eukaryotic DNA replication has provided critical molecular tools to dissect this process. Dynamic changes in the assembly and disassembly of protein complexes at origins are important for the initiation of DNA replication and occur throughout the cell cycle. Herein, we review the key proteins required for the initiation of DNA replication, their involvement in the protein complex assembly at replication origins, and how the cell cycle machinery regulates this process.

Animals↗

PubMed1996

p21Cip1/Waf1 disrupts the recruitment of human Fen1 by proliferating-cell nuclear antigen into the DNA replication complex.

Fen1 or maturation factor 1 is a 5'-3' exonuclease essential for the degradation of the RNA primer-DNA junctions at the 5' ends of immature Okazaki fragments prior to their ligation into a continuous DNA strand. The gene is also necessary for repair of damaged DNA in yeast. We report that human proliferating-cell nuclear antigen (PCNA) associates with human Fen1 with a Kd of 60 nM and an apparent stoichiometry of three Fen1 molecules per PCNA trimer. The Fen1-PCNA association is seen in cell extracts without overexpression of either partner and is mediated by a basic region at the C terminus of Fen1. Therefore, the polymerase delta-PCNA-Fen1 complex has all the activities associated with prokaryotic DNA polymerases involved in replication: 5'-3' polymerase, 3'-5' exonuclease, and 5'-3' exonuclease. Although p21, a regulatory protein induced by p53 in response to DNA damage, interacts with PCNA with a comparable Kd (10 nM) and a stoichiometry of three molecules of p21 per PCNA trimer, a p21-PCNA-Fen1 complex is not formed. This mutually exclusive interaction suggests that the conformation of a PCNA trimer switches such that it can either bind p21 or Fen1. Furthermore, overexpression of p21 can disrupt Fen1-PCNA interaction in vivo. Therefore, besides interfering with the processivity of polymerase delta-PCNA, p21 also uncouples Fen1 from the PCNA scaffold.

Binding Sites↗

PubMed1996

Expression of cell cycle-regulated proteins in prostate cancer.

Markers of cellular proliferation have proven to be useful prognostic markers in several tumor types. Recently, immunoreactivity for cyclins was found to provide an independent marker of tumor proliferation in breast cancer. In this study, we sought to determine the pattern of immunoreactivity for cyclins A, B, E, and Ki-67 in surgically resected prostate cancer and to determine their possible prognostic significance. Twenty-eight tumors of American Urological Association stages B and C were selected for study. Immunoreactivity for cyclins A and B was detected in most tumors and was present at significantly reduced levels as compared with breast cancer. Staining for cyclin E was present in four tumors and was present only in focal areas in two of the four. Such focal variation in expression of cell cycle regulators may reflect genetic instability in a tumor. Immunoreactivity for cyclins A and B was correlated with both Ki-67 index (the percentage of cells with Ki-67 immunoreactivity) and with each other. A Ki-67 index greater than 4.0 was associated with shorter time to prostate-specific antigen-detected relapse (P = 0.026). The fraction of cells staining for cyclins A and B divided by the fraction of cells staining for Ki-67 [(A+B)/K] was highly predictive of relapse, with values less than 0.50 associated with more rapid progression (P < 0.001). This latter result remained statistically significant after controlling for Gleason score by stratification. Our results suggest that immunoreactivity for markers of cellular proliferation may provide useful prognostic information in localized prostate cancer, and they need to be validated in a larger numbers of patients.

Adenocarcinoma↗

PubMed1996

Phosphorylation of human replication protein A by the DNA-dependent protein kinase is involved in the modulation of DNA replication.

The single-stranded DNA-binding protein, Replication Protein A (RPA), is a heterotrimeric complex with subunits of 70, 32 and 14 kDa involved in DNA metabolism. RPA may be a target for cellular regulation; the 32 kDa subunit (RPA32) is phosphorylated by several cellular kinases including the DNA-dependent protein kinase (DNA-PK). We have purified a mutant hRPA complex lacking amino acids 1-33 of RPA32 (rhRPA x 32delta1-33). This mutant bound ssDNA and supported DNA replication; however, rhRPA x 32delta1-33 was not phosphorylated under replication conditions or directly by DNA-PK. Proteolytic mapping revealed that all the sites phosphorylated by DNA-PK are contained on residues 1-33 of RPA32. When wild-type RPA was treated with DNA-PK and the mixture added to SV40 replication assays, DNA replication was supported. In contrast, when rhRPA x 32delta1-33 was treated with DNA-PK, DNA replication was strongly inhibited. Because untreated rhRPA x 32delta1-33 is fully functional, this suggests that the N-terminus of RPA is needed to overcome inhibitory effects of DNA-PK on other components of the DNA replication system. Thus, phosphorylation of RPA may modulate DNA replication indirectly, through interactions with other proteins whose activity is modulated by phosphorylation.

DNA Replication↗

PubMed1996

Dissection of functional domains of the human DNA replication protein complex replication protein A.

Replication protein A (RPA) is a mammalian single-stranded DNA binding factor essential for DNA replication, repair, and recombination. It is composed of three subunits of 70, 34, and 13 kDa (Rpa1, Rpa2, and Rpa3, respectively). Deletion mapping of the Rpa2 subunit identified the domain required for interaction with Rpa1 and Rpa3 which does not include the N-terminal domain that is phosphorylated during S phase. Deletion mapping of Rpa1 defined three domains. The C-terminal third of the Rpa1 polypeptide binds Rpa2 which itself forms a bridge between Rpa1 and Rpa3. The N-terminal third of Rpa1 bound single-stranded DNA under low stringency conditions only (0.1 M NaCl), while a central domain binds to single-stranded DNA under both low and high stringency conditions (0.5 M NaCl). Binding to p53 requires the N-terminal third of Rpa1 with some contribution from the C-terminal third. The evolutionarily conserved putative zinc finger near the C terminus of Rpa1 was not required for binding to single-stranded DNA, Rpa2, or p53. However, all three subdomains of Rpa1 and the zinc finger were essential for supporting DNA replication in vitro. These experiments are a first step toward defining peptide components responsible for the many functions of the RPA protein complex.

Animals↗

PubMed1996

Loss of transactivation and transrepression function, and not RPA binding, alters growth suppression by p53.

The tumor suppressor protein p53 activates transcription from promoters with specific p53 binding elements, represses transcription from promoters without such elements and interacts with and inhibits the single-stranded DNA binding activity of the human DNA replication factor RPA. All these activities involve the N terminal 70 amino acids of p53. Dissection of the domains of p53 which bind RPA suggest that multiple sub-domains of the protein synergize to give strong RPA binding. Point-mutations in one of these sub-domains of p53 significantly diminish its ability to interact with RPA. A multimer of a peptide from p53 which includes these residues, or of a peptide from the acidic activation domain of the prototypic trans-activator protein VP16, can itself bind to RPA. Comparison of sequences of these multimeric peptides suggests that aromatic amino acids flanked by negatively charged residues are important for binding RPA. Several alleles of p53 with point mutations in the N terminal region were analysed for their relative abilities to bind RPA, activate or repress transcription, and suppress growth of p53 null SaOs2 and H1299 cells. Both mutants of p53 with decreased RPA binding suppressed cell growth as well as wild-type p53, suggesting that p53 can suppress growth without interacting with RPA. The allele that lost most of the transcription activation function also lost most of its transcription repression activity suggesting that interaction with the same basal transcription factors are involved in both functions. This same allele bound RPA well but was defective in growth suppression. Therefore, transcription activation and/or repression appear to be more important for the growth suppression function of p53 than RPA binding.

Amino Acid Sequence↗

PubMed1996

A 39 amino acid fragment of the cell cycle regulator p21 is sufficient to bind PCNA and partially inhibit DNA replication in vivo.

The cell cycle regulator p21 interacts with and inhibits the DNA replication and repair factor proliferating cell nuclear antigen (PCNA). We have defined a 39 amino acid fragment of p21 which is sufficient to bind PCNA with high affinity (Kd 10-20 nM). This peptide can inhibit DNA replication in vitro and microinjection of a GST fusion protein containing this domain inhibited S phase in vivo. Despite its high affinity for PCNA, the free 39 amino acid peptide does not have a well-defined structure, as judged from circular dichroism and nuclear magnetic resonance measurements, suggesting an induced fit mechanism for the PCNA-p21 interaction. The association of the small peptide with PCNA was thermolabile, suggesting that portions of p21 adjoining the minimal region of contact stabilize the interaction. In addition, a domain containing 67 amino acids from the N-terminus of PCNA was defined as both necessary and sufficient for binding to p21.

Amino Acid Sequence↗

PubMed1996

Oxygen tension profiles in isolated hamster retractor muscle at different temperatures.

Oxygen tension (P0(2)) profiles within unperfused hamster retractor muscles were obtained at 25, 30, and 37 degrees by using sharpened, recessed oxygen microelectrodes. The microelectrode was driven vertically into freshly excised muscle lying on a flat, impermeable boundary inside a diffusion chamber. Intramuscular P0(2) profiles were measured as a function of electrode depth in 10-mu m steps during both inward and outward penetrations when the upper surface of the muscles was exposed to humidified gases containing 10, 21, 50, and 100% 0(2). The ratio of the 0(2) consumption (M) to the 0(2) permeability (K, Krogh diffusion coefficient = D alpha, diffusion coefficient-solubility product) was estimated by curve-fitting the experimental steady-state distribution of 0(2) through muscles to the analytic solution of the diffusion equation assuming that M obeys zero-order kinetics and K is constant, uniform, and independent of P0(2). The ratios of M/K were independent of temperature and were found to be independent of surface P0(2) and muscle thickness. The average value of M/K was 3.9 +/- 0.45 (SE; n = 30) x 10(5) mm Hg/cm(2), which is consistent with that estimated from previous measurements of M and D using different non-steady-state techniques (Bentley et aL, 1993). These results are consistent with other in vitro 0(2) consumption measurements (Sullivan and Pittman, 1984) and do not provide evidence for nonclassical respiratory activity in resting mammalian skeletal muscle.

Animals↗

PubMed1996

Evaluation of agonist-antagonist properties of nitrogen mustard and cyano derivatives of delta 8-tetrahydrocannabinol.

delta 8-Tetrahydrocannabinol (delta 8-THC) is a naturally occurring cannabinoid with a characteristic pharmacological profile of in vivo effects. Previous studies have shown that modification of the structure of delta 8-THC by inclusion of a nitrogen-containing functional group alters this profile and may alkylate the cannabinoid receptor, similar to the manner in which beta-funaltrexamine (beta-FNA) alkylates the micro-opioid receptor. Two novel analogs of delta 8-THC were synthesized: a nitrogen mustard analog with a dimethylheptyl side chain (NM-delta 8-THC) and a cyano analog with a dimethylpentyl side chain (CY-delta 8-THC). Both analogs showed high affinity for brain cannabinoid receptors and when administered acutely, produced characteristic delta 9-THC-like effects in mice, including locomotor suppression, hypothermia, antinociception and catalepsy. CY-delta 8-THC shared discriminative stimulus effects with CP 55,940; for NM-delta 8-THC, these effects also occurred, but were delayed. Although both compounds attenuated the effects of delta 9-THC in the mouse behavioral tests, evaluation of potential antagonist effects of these compounds was complicated by the fact that two injections of delta 9-THC produced similar results, suggesting that acute tolerance or desensitization might account for the observations. NM-delta 8-THC, but not CY-delta 8-THC, attenuated the discriminative stimulus effects of CP 55,940 in rats several days following injection. Hence, addition of a nitrogen-containing functional group to a traditional cannabinoid structure does not eliminate agonist effects and may produce delayed attenuation of cannabinoid-induced pharmacological effects.

Animals↗

PubMed1996

Influence of non-Newtonian behavior of blood on flow in an elastic artery model.

Two different non-Newtonian models for blood, one a simple power law model exhibiting shear thinning viscosity, and another a generalized Maxwell model displaying both shear thinning viscosity and oscillatory flow viscoelasticity, were used along with a Newtonian model to simulate sinusoidal flow of blood in rigid and elastic straight arteries. When the spring elements were removed from the viscoelastic model resulting in a purely viscous shear thinning fluid, the predictions of flow rate and WSS were virtually unaltered. Hence, elasticity of blood does not appear to influence its flow behavior under physiological conditions in large arteries, and a purely viscous shear thinning model should be quite realistic for simulating blood flow under these conditions. When a power law model with a high shear rate Newtonian cutoff was used for sinusoidal flow simulation in elastic arteries, the mean and amplitude of the flow rate were found to be lower for a power law fluid compared to a Newtonian fluid experiencing the same pressure gradient. The wall shear stress was found to be relatively insensitive to fluid rheology but strongly dependent on vessel wall motion for flows driven by the same pressure gradient. The effect of wall motion on wall shear stress could be greatly reduced by matching flow rate rather than pressure gradient. For physiological flow simulation in the aorta, an increase in mean WSS but a reduction in peak WSS were observed for the power law model compared to a Newtonian fluid model for a matched flow rate waveform.

Aorta, Thoracic↗

PubMed1996

Cyclin-binding motifs are essential for the function of p21CIP1.

The cyclin-dependent kinase (Cdk) inhibitor p21 is induced by the tumor suppressor p53 and is required for the G1-S block in cells with DNA damage. We report that there are two copies of a cyclin-binding motif in p21, Cy1 and Cy2, which interact with the cyclins independently of Cdk2. The cyclin-binding motifs of p21 are required for optimum inhibition of cyclin-Cdk kinases in vitro and for growth suppression in vivo. Peptides containing only the Cy1 or Cy2 motif partially inhibit cyclin-Cdk kinase activity in vitro and DNA replication in Xenopus egg extracts. A monoclonal antibody which recognizes the Cy1 site of p21 specifically disrupts the association of p21 with cyclin E-Cdk2 and with cyclin D1-Cdk4 in cell extracts. Taken together, these observations suggest that the cyclin-binding motif of p21 is important for kinase inhibition and for formation of p21-cyclin-Cdk complexes in the cell. Finally, we show that the cyclin-Cdk complex is partially active if associated with only the cyclin-binding motif of p21, providing an explanation for how p21 is found associated with active cyclin-Cdk complexes in vivo. The Cy sequences may be general motifs used by Cdk inhibitors or substrates to interact with the cyclin in a cyclin-Cdk complex.

Amino Acid Sequence↗

PubMed1995

A theoretical analysis of intracellular oxygen diffusion.

Oxygen diffusion rates within cells may be heterogeneous, with more rapid diffusion occurring along intracellular pathways of high oxygen solubility, such as mitochondria. Recent experimental data indicate that tissue oxygen permeability rises sharply in a temperature range associated with phase transitions in lipid membranes suggesting that membranes may function as oxygen "pathway". The experimental data have been analyzed using theoretical models of diffusion in two-phase media. By assuming muscles to be composed entirely of aqueous cytosol and lipids, cytosolic permeability was determined as a function of temperature by matching the experimental values of tissue permeability with those of model predictions using in vitro values of lipid permeability. Cytosolic permeability ranged from 50% of water permeability (low temperature) to 90% of water permeability (high temperature) and its temperature dependence was distinctly different from that of water. An upper bound for cytosolic permeability was calculated using a physiologic value for protein volume fraction, and lipid permeability was obtained using this cytosolic permeability. A model with a parallel arrangement of lipid and cytosol yielded a value of lipid permeability that was 71% higher than the in vitro value. Intracellular permeabilities calculated from tissue permeability values were found to be inconsistent with experimentally reported values for rat cardiac myocytes. Comparison of three different muscles exhibited the same trend of higher permeability with higher lipid content. It is concluded that both lipid and cytosol permeabilities and, hence, tissue permeabilities are different among different muscles and one should exercise caution when data from one muscle is used to calculate or extrapolate values in other muscles. It is conceivable that muscles with very high mitochondrial content, such as diaphragm and cardiac muscles may exhibit an oxygen permeability which is significantly higher than commonly accepted values. These results warrant additional measurements of tissue oxygen permeability at 37 degrees C, especially for oxidative muscles with high lipid content.

Animals↗

PubMed1995

Cyclins as markers of tumor proliferation: immunocytochemical studies in breast cancer.

We have developed methods to use anticyclin A, B, and E antibodies as reagents to specifically detect proliferating cells in specific phases of the cell cycle in formalin-fixed, paraffin-embedded sections of tissues and cells. Staining of 48 archival cases of breast cancer showed that these antibodies estimate the tumor proliferation fraction and therefore are potentially useful for the prediction of prognosis. A subset of cancers had a high frequency of tumor cells expressing cyclins A and E, out of proportion to other proliferation markers, suggesting that these tumors may have deregulated cyclin expression. In addition to recognizing authentic cyclin E in the nucleus of proliferating cells, anticyclin E antibody cross-reacted with a cytoplasmic protein in nonproliferating endothelial cells. This cross-reaction allows the simultaneous visualization and quantitation of microvessels in the tumors, measuring a second potential predictor of breast cancer prognosis, tumor angiogenesis.

Animals↗

PubMed1995

Separate domains of p21 involved in the inhibition of Cdk kinase and PCNA.

The protein p21 (WAF1, CIP1 or sdi1), induced by the tumour-suppressor protein p53, interacts with and inhibits two different targets essential for cell-cycle progression. One of these is the cyclin-Cdk family of kinases and the other is the essential DNA replication factor, proliferating-cell nuclear antigen (PCNA). We report here that separate domains of p21 are responsible for interacting with and inhibiting the two targets. An amino-terminal domain inhibits cyclin-Cdk kinases and a carboxy-terminal domain inhibits PCNA. Using these separated domains, we have determined that p21 inhibits different biological systems through different targets. The PCNA-binding domain is sufficient for inhibition of DNA replication based on simian virus 40, whereas the Cdk2-binding domain is sufficient for inhibition of DNA replication based on Xenopus egg extract and for growth suppression in transformed human cells.

Animals↗

PubMed1995

Cross-task cross talk in memory and perception.

The application of the additive factors method depends on finding factors that selectively influence processing stages. When all the processes for a task are in series, a factor directly influencing a process might change its output and thereby have indirect influence on succeeding processes. We investigate whether such indirect influence is possible between processes associated with different tasks being performed together. In two dual-task memory scanning and arithmetic experiments with digits as the stimuli for both tasks, information relevant for only one of the tasks nonetheless affected performance of the other. When the same digit was relevant for the two tasks, cross-task facilitation and interference were observed in some cases. Displaying the same digit for both tasks led to relatively fast response times, paralleling the effect of flankers in the response competition paradigm. But repetition of digits in memory slowed responses. It is suggested that the need for control processes to keep task information segregated is responsible for the pattern of effects.

Adult↗