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D K Chattoraj

Publications and source records attributed to D K Chattoraj.

At least 37 records · Page 2Linked to original sources
PubMed1997

Chaperone-mediated reduction of RepA dimerization is associated with RepA conformational change.

RepA, the initiator protein of plasmid P1, binds to multiple sites (iterons) in the origin. The binding normally requires participation of chaperones, DnaJ, DnaK and GrpE. When purified, RepA appears dimeric and is inactive in iteron binding. On reaction with chaperones, a species active in iteron binding is formed and found to be monomeric. To test whether the chaperones can reduce dimerization, RepA was used to replace the dimerization domain of the lambda repressor. The hybrid protein repressed the lambda operator efficiently, indicating that RepA can dimerize in vivo. A further increase in repressor activity was seen in dnaJ mutant cells. These results are consistent with a chaperone-mediated reduction of RepA dimerization. We also found that RepA mutants defective in dimerization still depend on DnaJ for iteron binding. Conversely, RepA mutants that no longer require chaperones for iteron binding remain dimerization proficient. These results indicate that the chaperone dependence of RepA activity is not solely owing to RepA dimerization. Our results are most simply explained by a chaperone-mediated conformational change in RepA protomer that activates iteron binding. This conformational change also results in reduced RepA dimerization.

Amino Acid Sequence↗
PubMed1997

Binding of water and solute to protein-mixture and protein-coated alumina.

Extent of water vapour adsorption (n1) of gelatin and bovine serum albumin and their mixtures in different proportion respectively has been measured by isopiestic vapour pressure methods at various values of water activity (a1) ranging between zero and unity. Similar measurements have also been carried out with gelatin and BSA coated alumina powder. At a given value of a1, n1 for the protein mixture is found to be significantly less than their ideal value obtained from the additivity rule. Such decrease is probably due to the protein-protein interaction as a result of which some of the water binding sites become unavailable for water vapour adsorption. On the other hand when a protein is mixed with alumina powder, the water vapour adsorption of the protein coated alumina surface at a given water activity is found to be 2 to 3 times larger than its ideal value obtained from the additivity rule. The standard free energy changes for hydration of protein mixtures and protein-coated alumina have been evaluated using Bull equation. The extent of excess hydration of these proteins and their mixtures as well as protein-coated alumina in the presence of excess neutral salts and urea respectively have been evaluated using the isopiestic method. In all cases, the moles of water and solute respectively bound in absolute amount to biopolymers, biopolymer mixtures and protein-coated alumina have been evaluated in the limited range of solute concentrations in the medium. Based on the Gibbs-Duhem equations, a rigorous expression for the standard free energy change for binding of excess solute and solvent to biopolymer have been evaluated with reference to unit solute mole fraction as standard state. Free energies of excess hydration of different biopolymer systems have been evaluated using this equation.

Aluminum Oxide↗
PubMed1996

Dissociation kinetics of RepA dimers: implications for mechanisms of activation of DNA binding by chaperones.

BACKGROUND: The replication initiator of plasmid P1, RepA, binds DNA as monomer. The binding is stimulated by the chaperones DnaJ, DnaK and GrpE of Escherichia coli. Two models of chaperone action have been proposed. (i) Chaperones dissociate RepA dimers, which are inactive in DNA binding, into active monomers. (ii) The dissociation occurs spontaneously but the monomeric products require the chaperones for refolding into the active form. The latter model was based on the observation that RepA diluted 1000-fold below the K(D) for dimer dissociation, still required the chaperones for DNA binding. RESULTS: We have confirmed that under the condition of DNA binding experiments, the RepA dimers dissociate reversibly into monomers with a K(D) value of 1.1 +/- 0.1 microM. In the vicinity of this concentration, the sedimentation coefficient of RepA was concentration dependent, allowing estimation of s(20,w) coefficients for the RepA monomer (2.95 S) and dimer (4.01 S). Dynamic light scattering experiments indicated an increase of the monomer fraction within 5 min of RepA dilution. Circular dichroism (CD) measurements were consistent with these results. CONCLUSION: RepA monomerization is efficient without the mediation of chaperones. They are required to activate RepA most likely because they are needed to re-fold RepA monomers.

Circular Dichroism↗
PubMed1996

Biopolymer-surfactant interaction: 4. Kinetics of binding of cetyltrimethyl ammonium bromide with gelatin, hemoglobin, beta-lactoglobulin and lysozyme.

The binding of CTAB with the proteins, gelatin, hemoglobin, beta-lactoglobulin and lysozyme follow first order kinetics and occurs either in two or three distinct stages. The number of stages depends on the overall configuration of the biopolymers. The denatured protein, gelatin has shown three-stage kinetics under all conditions, whereas the native proteins, hemoglobin, beta-lactoglobulin and lysozyme have exhibited two stage kinetics. Heat treated lysozyme in 8 mol dm-3 urea medium has also shown a two-stage kinetics. On the basis of non interacting binding sites on the proteins and independent sequential binding, the rates of reaction have been observed to increase with temperature and follow the trend k1 >> k2 > k3. The interaction of CTA+ with the proteins is both electrostatic and hydrophobic. Hemoglobin has shown maximum reaction rate whereas, beta-lactoglobulin has shown a minimum. The activation parameters for the kinetic process have exhibited almost non-variant delta G++ and delta H++ < T delta S++. The formation of activation complex in the Eyring model is entropy controlled so also the overall kinetics. An isokinetic entropy-enthalpy compensation phenomenon has been observed for the respective kinetic stages.

Biopolymers↗
PubMed1996

Kinetics of adsorption of denatured protein at alumina-water interface.

The kinetics of adsorption of soluble denatured protein, gelatin has been studied at the alumina-water interface as a function of protein concentration, pH, temperature and ionic strength. The rate of adsorption of gelatin has been compared with rate of adsorption of BSA denatured by 8 M urea or 0.05 M SDS. The initial stage for the adsorption process is diffusion-controlled and the surface diffusion coefficients evaluated from equations of Ward and Tordai and by Bull for globular and denatured proteins are found to be widely different from each other. The kinetic data for gelatin fit into a first order rate equation with two rate constants, k1a and k2a. Using Arrhenius equation, the activation energies delta E1* and delta E2* have been evaluated from the values of k1a and k2a respectively. The corresponding changes in values of enthalpy of activation (delta H*), entropy of activation (delta S*) and free energy of activation (delta G*) have been evaluated using Eyring's equation for absolute reaction rate. It has been found that for both gelatin and denatured BSA, in the first kinetic step delta H1* > T delta S1* and for the second step T delta S2* > delta H2.

Adsorption↗
PubMed1996

Thermodynamics of water-lipid interaction in presence and absence of salts.

Extents of hydration of different lipids such as cholesterol, lecithin, lysolecithin, gangliosides, hydroxy cerebrosides, sphingomyelin, Dalda (hydrogenated fat), coconut oil and sunflower oil in the presence and absence of some inorganic electrolytes, sucrose and urea have been studied using the isopiestic vapour pressure technique. Except triglycerides, the shape of the water vapour adsorption isotherms for other lipids are in agreement with type II or type III BET isotherms respectively. The overall shape of each curve for triglycerides does not agree with any of the shapes of five types of BET isotherms. At water activity (1) approaching unity, maximum number of moles of water bound (delta n1zero) per mole of cholesterol are 1.6 and 2.6 at 28 degrees C and 37 degrees C, respectively. Values of delta n1zero at 23 degrees C stand in the following order: Ganglioside > lysolecithin > sphingomyelin > hydroxy cerebrosides. For triglycerides n1 increases with increase of a1 and reaches maximum in between 0.95 to 0.98 beyond which it sharply decreases to zero as a1 approaches unity. Standard free energy changes (delta Gzero) and enthalpy changes (delta Hzero) for cholesterol and lysolecithin have been evaluated from the experimental data. The excess hydration of cholesterol in the presence of several inorganic salts, urea and sucrose have been estimated from isopiestic experiments and free energies of excess hydration have been evaluated.

Lipids↗
PubMed1994

Negative control of plasmid DNA replication by iterons. Correlation with initiator binding affinity.

Initiation of DNA replication and negative control of initiation frequency in many bacterial plasmids are mediated by multiple binding sites (iterons) for the replicon-encoded initiator protein. Here we show that a single iteron of plasmid P1, when cloned in a multicopy vector, pUC19, can control replication of a miniP1 plasmid effectively. Using this assay system, several iterons with single point mutations were analyzed. The degree of control was directly correlated with the binding affinity of the iterons for the initiator protein in vitro. The control was also unaffected whether or not a wild type iteron was flanked with strong transcription terminators. We conclude that initiator binding is the only activity of P1 iteron sequences relevant to replication control.

Bacterial Proteins↗
PubMed1994

Relaxation of replication control in chaperone-independent initiator mutants of plasmid P1.

Escherichia coli chaperones DnaJ, DnaK and GrpE increase P1 plasmid initiator binding to the origin by promoting initiator folding. The binding allows initiation and also promotes pairing of origins which is believed to control initiation frequency. Chaperone-independent DNA binding mutants are often defective in replication control. We show here that these mutants have increased rates of association for DNA binding and defects in origin pairing. The increases in association rates were found to be due either to increased protein folding into active forms or to increases in the association rate constant, kon. Since the dissociation rate constants for DNA release with these mutants are not changed, it is unlikely that the DNA binding domain is affected. The pairing domain may thus control replication and modulate DNA binding. The role of the pairing domain in DNA binding can be significant in vivo as the selection for chaperone-independent binding favors pairing-defective mutants.

Bacterial Proteins↗
PubMed1994

Missing-base and ethylation interference footprinting of P1 plasmid replication initiator.

RepA, the replication initiator protein of plasmid P1, binds to specific 19 bp sequences on the plasmid DNA. Earlier footprinting studies with dimethylsulfate identified the guanines that contact RepA through the major groove of DNA. In this study, base elimination was used to identify the contribution of all four bases to the binding reaction. Depurination and depyrimidation of any base in the neighborhood of the contacting guanines was found to decrease RepA binding. These results are consistent with the notion that RepA contacts bases of two consecutive major grooves on the same face of DNA. We also observed that depurination but not methylation of three guanines (G3, G8 and G9) affected binding. We identified the DNA phosphate groups (3 in the top strand, one of which mapped between G8 and G9, and 4 in the bottom strand, one of which was adjacent to C3) that strongly interfered with RepA binding upon ethylation. These results indicate that certain bases (e.g. G3, G8 and G9) may not contact RepA directly but contribute to base and backbone contacts by maintaining proper structure of the binding site.

Alkylation↗
PubMed1994

Thermodynamics of binding water and solute to powdered long-chain salts of fatty acids.

Hydration of powdered fatty acids and their salts has been studied both in presence and absence of neutral salts, sucrose and urea using the isopiestic vapour pressure technique. Moles of water vapour adsorbed per mole or kg of soaps like sodium palmitate, sodium stearate, sodium myristate and sodium laurate have been measured in presence and absence of salts and compared with that of detergents (SDS, CTAB, DTAB and MTAB). For each case of positive excess adsorption of water vapour and negative excess adsorption of inorganic salts, urea and sucrose to different soaps, the standard free energy change (delta G degrees) per kg of substrate in bringing the bulk mole fraction from zero to unity have been calculated using an appropriate thermodynamic equation and the values so obtained have been compared critically.

Fatty Acids↗
PubMed1994

Effect of denaturants and stabilisers on protein adsorption at solid-liquid interfaces.

The adsorption isotherms of different proteins from aqueous solution to the surface of different solids have been compared in the presence of additives such as urea, surfactants and high concentration of various neutral salts. The adsorption isotherms of lysozyme on alumina are not affected much in the presence of 8 M urea showing the rigid structure of lysozyme whereas isotherms of hemoglobin show surface coagulation even in presence of 2 M urea. In presence of 8 M urea, adsorption isotherms of BSA on alumina show two distinct steps. The extent of protein adsorption in the presence of surfactants depends on the nature of surfactants as well as of the underlying surface. The adsorption isotherms of BSA and lysozyme in presence of 2 M concentration of different neutral salts have also been compared with each other. In the presence of denaturants such as NaI and LiCl, the proteins are adsorbed in unfolded beta-conformation whereas in the presence of protein stabilizers such as NaCl, KCl and Na2SO4, amount of protein adsorbed at saturation is zero or extremely small showing that unfolding of proteins at the interface is necessary for initial stage of protein adsorption. The standard free energy change (delta G degrees) per square meter of the surface, signifying relative affinity of adsorption at the state of monolayer saturation, have been calculated. The magnitude of standard free energy of transfer (delta G degrees B) of one mole of protein to the surface in presence of all the additives was found close to 40 kJ/mole.

Absorption↗
PubMed1993

Information analysis of sequences that bind the replication initiator RepA.

The replication initiator protein RepA of plasmid P1 can bind to 14 sites on the plasmid. These sites are variously used to autoregulate RepA synthesis and for initiation and control of DNA replication. Analysis of information (degree of conservation) at the sites revealed three sequence patches of high conservation. By saturation mutagenesis, the conservation at the outer two patches was found to contribute to RepA binding more critically. The guanine bases that are likely to contact RepA through the major groove were identified by methylation interference and methylation protection experiments. These bases mapped to the outer two patches and were separated by one turn of the helix. Therefore, they belong to major grooves on the same face of DNA. All backbone contacts of the protein, determined by hydroxyl radical footprinting, also mapped to the same face. We conclude from this that RepA binds to its site on one face of the DNA. Information analysis of binding sites for several prokaryotic repressors and activators, where the nature of DNA-protein contacts are known, revealed a correlation between the positions of high conservation and the positions of major grooves that faced the protein. The middle patch of high conservation in the RepA binding sites is an exception since in this region a minor groove is likely to face the protein. The simplest model for minor groove contacts suggests that in B-form DNA a T.A base-pair cannot easily be distinguished from an A.T pair by inspection of the minor groove. Yet in the RepA site, a T-->A mutation in the middle patch significantly affects binding. Therefore, the simplest models for both minor and major groove contacts are unlikely. It is possible that the patch determines the proper conformation of the site and thereby contributes to recognition indirectly.

Bacterial Proteins↗
PubMed1993

Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK.

RepA protein of plasmid P1 binds to arrays of 19 bp repeat sequences (iterons) and mediates initiation of replication and its control. Escherichia coli heat shock proteins DnaJ and DnaK can stimulate iteron binding activity of RepA in an ATP-dependent fashion. It has been proposed that RepA binds to DNA as monomers and that the stimulation in binding involves monomerization of RepA dimers which are inactive in the binding reaction. RepA-iteron and RepA-RepA interactions have been measured in this study to determine the equilibrium constants of the two reactions. The apparent KD value for RepA-iteron binding decreased from 10 nM to no more than 0.2 nM at increasing concentrations of the heat shock proteins. The stimulation of binding appears to be due to an increase in active RepA fraction and not to a change in the maximum binding capacity of the active species. This view was deduced from measurements of active RepA fraction, which increased in the presence of heat shock proteins, and from measurements of dissociation rate constants, which were independent of the heat shock protein concentrations. Accounting for the active fractions, the true KD value was estimated to be 0.10(+/- 0.09) nM in 20 mM Tris.HCl (pH 8), 100 mM NaCl, 40 mM KCl, 10 mM MgCl2, 1 mM dithiothreitol, 0.1 mM EDTA, ATP (50 microM), bovine serum albumin (50 micrograms/ml), calf thymus DNA (50 micrograms/ml) and glycerol (5%). The dissociation rate constant was 1.5 x 10(-2) s-1 and the calculated association rate constant was 1.5 x 10(8) M-1 s-1. Ultracentrifugation analyses of RepA at 15,000 r.p.m. in the above buffer but without ATP, bovine serum albumin, calf thymus DNA and glycerol, revealed that the protein was in monomer-dimer equilibrium with a KD of 2.6(+/- 0.2) microM at 5 degrees C. Therefore, at protein concentrations used in the binding reactions, RepA is monomeric (> 99.5%), in confirmation of the earlier result that RepA binds as a monomer. It follows that the species that is stimulated to bind by the heat shock proteins is also a monomeric form of RepA.

Bacterial Proteins↗
PubMed1993

Conformation of the origin of P1 plasmid replication. Initiator protein induced wrapping and intrinsic unstacking.

The origin of plasmid DNA replication in bacteriophage P1 has five 19 base-pair sites that bind the plasmid-encoded initiator, RepA. Here we show, using a DNA band retardation assay, that RepA can bend DNA that carries one or more of the RepA binding sites. RepA binding to supercoiled DNA carrying the five sites, directly repeated and phased two turns of B-DNA apart, absorbs about one positive superhelical turn of DNA as determined by two-dimensional gel electrophoresis. This indicates that the DNA is wrapped around RepA as a consequence of in-phase bending at the individual binding sites. The RepA-DNA complexes did not show elevated sensitivity to KMnO4, a reagent specific for pyrimidine bases (T >> C) in unstacked DNA. The wrapping of the DNA around RepA, therefore, does not lead to significant unwinding of the double helix. Extensive unwinding, suitable for the initiation of DNA replication, most likely requires participation of factors other than RepA. We also noted that the thymine bases of the sequence 5'-ATC-3', of which there are 20 in the origin, all reacted to KMnO4 strongly whether or not RepA was present. The preferential reactivity of ATC sequences was specific to the origin region, as thymine residues including those in the ATC sequences did not display elevated sensitivity to KMnO4 in a DNA fragment from pBR322. On one of two strands of the origin the selective reactivity at the ATC sequences was supercoiling dependent. These results indicate that the origin includes unstacked DNA bases, the significance of which remains to be determined.

Bacterial Proteins↗
PubMed1993

Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication.

Replication of P1 plasmid requires both the plasmid-specific initiator, RepA, and the host initiator, DnaA. Here we show that DnaA can make the P1 origin reactive to the single-strand specific reagents KMnO4 and mung bean nuclease. Addition of RepA further increased the KMnO4 reactivity of the origin, although RepA alone did not influence the reaction. The increased reactivity implies that the two initiators interact in some way to alter the origin conformation. The KMnO4 reactivity was restricted to one strand of the origin. We suggest that the roles of DnaA in P1 plasmid and bacterial replication are similar: origin opening and loading of the DnaB helicase. The strand-bias in chemical reactivity at the P1 origin most likely indicates that only one of the strands is used for the loading of DnaB, a scenario consistent with the unidirectional replication of the plasmid.

Bacterial Proteins↗
PubMed1993

Heat shock proteins DnaJ, DnaK, and GrpE stimulate P1 plasmid replication by promoting initiator binding to the origin.

Binding of the P1-encoded protein RepA to the origin of P1 plasmid replication is essential for initiation of DNA replication and for autoregulatory repression of the repA promoter. Previous studies have shown defects in both initiation and repression in hosts lacking heat shock proteins DnaJ, DnaK, and GrpE and have suggested that these proteins play a role in the RepA-DNA binding required for initiation and repression. In this study, using in vivo dimethyl sulfate footprinting, we have confirmed the roles of the three heat shock proteins in promoting RepA binding to the origin. The defects in both activities could be suppressed by increasing the concentration of wild-type RepA over the physiological level. We also isolated RepA mutants that were effective initiators and repressors without requiring the heat shock proteins. These data suggest that the heat shock proteins facilitate both repression and initiation by promoting only the DNA-binding activity of RepA. In a similar plasmid, F, initiator mutants that confer heat shock protein independence for replication were also found, but they were defective for repression. We propose that the initiator binding involved in repression and the initiator binding involved in initiation are similar in P1 but different in F.

Bacterial Proteins↗
PubMed1992

Absolute reaction rate and kinetics of protein adsorption at solid-liquid interfaces.

Extents of adsorption of bovine serum albumin from aqueous solution to the surface of alumina, silica, carbon and chromium powder have been studied as function of time for various values of bulk protein concentration, pH, ionic strength and temperature. The rates of adsorption in all cases have been observed to fit in the first order rate equation with two different rate constants Ka1 and Ka2. Effects of addition of SDS, CTAB and neutral salts on values of Ka1 and Ka2 have also been studied. Using Arrhenius equation the activation energy values Ea1 and Ea2 have been evaluated from the values of Ka1 and Ka2 at three different temperatures, respectively. The corresponding values of enthalpy of activation (delta H*), entropy of activation (delta S*), and free energy of activation (delta G*) have been evaluated using Eyring's equation of absolute reaction rate. The mechanism of protein adsorption has been discussed in the light of basic principles of absolute reaction rate. It has been found that for Ka1 the delta H*1 greater than T delta S*1 and for Ka2 T delta S*2 greater than H*2, i.e. the anchorage and binding of protein to the surface are enthalpy controlled processes whereas the surface denaturation as well as rearrangement and folding is an entropy controlled process. The role of diffusion on rate of adsorption has also been discussed.

Adsorption↗