Biomedical subjects

G Krishnamoorthy

Publications and source records attributed to G Krishnamoorthy.

At least 37 records · Page 2Linked to original sources

PubMed2001

Structural stabilization of [2Fe-2S] ferredoxin from Halobacterium salinarum.

The ferredoxin of the extreme haloarchaeon Halobacterium salinarum requires high (>2 M) concentration of salt for its stability. We have used a variety of spectroscopic probes for identifying the structural elements which necessitate the presence of high salt for its stability. Titration of either the fluorescence intensity of the tryptophan residues or the circular dichroism (CD) at 217 nm with salt has identified a structural form at low (<0.1 M) concentration of salt. This structural form (L) exhibits increased solvent exposure of W side chain(s) and decreased level of secondary structure compared to the native (N) protein at high concentrations of salt. The L-form, however, contains significantly higher levels of both secondary and tertiary structures compared to the form (U) found in highly denaturing conditions such as 8 M urea. The structural integrity of the L-form was highly pH dependent while that of N- or U-form was not. The pH dependence of either fluorescence intensity or CD of the L-form showed the presence of two apparent pK values: approximately 5 and approximately 10. The structural integrity of the L-form at low (<5) pH was very similar to that of the N-form. However, titration with denaturants showed that the low pH L-form is significantly less stable than the N-form. The increased destabilization of the L-form with the increase in pH was interpreted to be due to mutual Coulombic repulsion of carboxylate side chains (pK approximately 6) and due to the disruption of salt bridge(s) between ionized carboxylates and protonated amino groups (pK approximately 10). Estimation of solvent accessibility of W residues by fluorescence quenching, and measurement of decay kinetics of fluorescence intensity and anisotropy strongly support the above model. Polylysine interacted stoichiometrically with the L-form of ferredoxin resulting in nativelike structure. In conclusion, our studies show that high concentration of salt stabilizes the haloarchaeal ferredoxin in two ways: (i) neutralization of Coulombic repulsion among carboxyl groups of the acidic residues, and (ii) salting out of hydrophobic residues leading to their burial and stronger interaction.

Circular Dichroism↗

PubMed2001

Spectral characteristics of 2-(4'-N,N-dimethylaminophenyl)pyrido[3,4-d]imidazole in AOT/n-heptane/water reverse micelles.

Spectral characteristics of 2-(4'-N,N-dimethylaminophenyl)pyrido[3,4-d]imidazole (DMAPPI) have been studied in AOT/n-heptane/water reverse micelles at w0 > or = 0. Absorption, fluorescence excitation and fluorescence spectra have revealed that the monocation (MC) of DMAPPI, protonated at the imidazole nitrogen (MC2) (Scheme 2) is present in the S0 state at w0 = 0, along with the MC, protonated at pyridine nitrogen (MC3) and only normal emission is observed from both MC2 and MC3. With increase in w0 (water amount), the equilibrium is shifted towards the MC, protonated at -NMe2 group (MC1) and MC3 in the S0 state. Biprotonic phototautomerism is observed in MC1 to generate MC2 in the S1 state. The twisted intramolecular charge transfer (TICT) emission replaces the normal emission in MC3. All the MCs are present near the anionic polar head group of AOT in the bound water region.

Absorption↗

PubMed2001

Structure is lost incrementally during the unfolding of barstar.

Coincidental equilibrium unfolding transitions observed by multiple structural probes are taken to justify the modeling of protein unfolding as a two-state, N <==> U, cooperative process. However, for many of the large number of proteins that undergo apparently two-state equilibrium unfolding reactions, folding intermediates are detected in kinetic experiments. The small protein barstar is one such protein. Here the two-state model for equilibrium unfolding has been critically evaluated in barstar by estimating the intramolecular distance distribution by time-resolved fluorescence resonance energy transfer (TR-FRET) methods, in which fluorescence decay kinetics are analyzed by the maximum entropy method (MEM). Using a mutant form of barstar containing only Trp 53 as the fluorescence donor and a thionitrobenzoic acid moiety attached to Cys 82 as the fluorescence acceptor, the distance between the donor and acceptor has been shown to increase incrementally with increasing denaturant concentration. Although other probes, such as circular dichroism and fluorescence intensity, suggest that the labeled protein undergoes two-state equilibrium unfolding, the TR-FRET probe clearly indicates multistate equilibrium unfolding. Native protein expands progressively through a continuum of native-like forms that achieve the dimensions of a molten globule, whose heterogeneity increases with increasing denaturant concentration and which appears to be separated from the unfolded ensemble by a free energy barrier.

Amino Acid Substitution↗

PubMed2000

The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain.

The slow folding of a single tryptophan-containing mutant of barstar has been studied in the presence of 2 M urea at 10 degrees C, using steady state and time-resolved fluorescence methods and far and near-UV CD measurements. The protein folds in two major phases: a fast phase, which is lost in the dead time of measurement during which the polypeptide collapses to a compact form, is followed by a slow observable phase. During the fast phase, the rotational correlation time of Trp53 increases from 2.2 ns to 7.2 ns, and its mean fluorescence lifetime increases from 2.3 ns to 3.4 ns. The fractional changes in steady-state fluorescence, far-UV CD, and near-UV CD signals, which are associated with the fast phase are, respectively, 36 %, 46 %, and 16 %. The product of the fast phase can bind the hydrophobic dye ANS. These observations together suggest that the folding intermediate accumulated at the end of the fast phase has: (a) about 20 % of the native-state secondary structure, (b) marginally formed or disordered tertiary structure, (c) a water-intruded and mobile protein interior; and (d) solvent-accessible patches of hydrophobic groups. Measurements of the anisotropy decay of Trp53 suggest that it undergoes two types of rotational motion in the intermediate: (i) fast (tau(r) approximately 1 ns) local motion of its indole side-chain, and (ii) a slower (tau(r) approximately 7.2 ns) motion corresponding to global tumbling of the entire protein molecule. The ability of the Trp53 side-chain to undergo fast local motion in the intermediate, but not in the fully folded protein where it is completely buried in the hydrophobic core, suggests that the core of the intermediate is still poorly packed. The global tumbling time of the fully folded protein is faster at 5.6 ns, suggesting that the volume of the intermediate is 25 % more than that of the fully folded protein. The rate of folding of this intermediate to the native state, measured by steady-state fluorescence, far-UV CD, and near-UV CD, is 0.07(+/-0.01) min(-1) This rate compares to a rate of folding of 0.03(+/-0.005) min(-1), determined by double-jump experiments which monitor directly formation of native protein; and to a rate of folding of 0.05 min(-1), when determined from time-resolved anisotropy measurements of the long rotational correlation time, which relaxes from an initial value of 7.2 ns to a final value of 5. 6 ns as the protein folds. On the other hand, the amplitude of the short correlation time decreases rapidly with a rate of 0.24(+/-0.06) min(-1). These results suggest that tight packing of residues in the hydrophobic core occurs relatively early during the observable slow folding reaction, before substantial secondary and tertiary structure formation and before final compaction of the protein.

Bacterial Proteins↗

PubMed2000

Dual Fluorescence of 2-(4'-N,N-dimethylaminophenyl)pyrido

The spectral characteristics of 2-(4'-N,N-dimethylaminophenyl)-pyrido[3,4-d]imidazole (DMAPPI) have been studied in a TritonX-100 (TX-100)/n-hexanol/water reverse micelle in cyclohexane as a function of water (w(0)), surfactant, cosurfactant, pH, and trifluoroacetic acid. Under the neutral conditions, dual fluorescence (normal and twiste intramolecular charge transfer) is observed, even at w(0)=0, suggesting that the TICT state is stabilized by the hydrogen bonding from n-hexanol. These studies indicate that DMAPPI molecules are present near the interface of the water pool and the micellar phase toward the micellar side, and the changes observed in the spectral characteristics with change of w(0) are due to the formation of the reverse micelles and the alignment of cosurfactant around DMAPPI. Variation of pH in the range 3-10 has no effect on the spectral characteristics of DMAPPI, suggesting that the protons do not penetrate the reverse micelles, whereas the trifluoroacetic acid protonates DMAPPI to form monocations (MCs). At w(0)=0, MC2 and MC3 (see Scheme 1) are the MCs present both in the S(0) and S(1) states, whereas with an increase in w(0), the MC2 shifts toward MC1. Biprotonic phototautomerism is observed in MC1, which leads to the formation of MC2 in the S(1) state. Copyright 2000 Academic Press.

Journal Article↗

PubMed1999

Twisted Intramolecular Charge Transfer Emission of 2-(4'-N,N-dimethylaminophenyl)benzimidazole in Micelles.

Spectral characteristics of 2-(4'N,N-dimethylaminophenyl)benzimidazole have been studied as a function of surfactant concentration and as a function of acid concentration in three surfactants. Dual fluorescence is observed in all the micelles. Fluorescence intensities of the local emission (B band) and twisted intramolecular charge transfer (A band, TICT) increase by an 17-30% and 38 to 64% respectively. When dissolved in micelles lifetimes of both the states also increase in the presence of micelles. The increase in the fluorescence intensities is attributed to the decrease in the non-radiative decay constant. cmc of the surfactants can be determined from the variation in the fluorescence intensity and the lifetime data. The equilibrium constants are determined for the prototropic reactions of the fluorophore in all the micelles in S0 and S1 states and the values obtained are discussed. Copyright 1999 Academic Press.

Journal Article↗

PubMed1999

Solvent-exposed tryptophans probe the dynamics at protein surfaces.

The dynamics of single tryptophan (W) side chain of protease subtilisin Carlsberg (SC) and myelin basic protein (MBP) were used for probing the surface of these proteins. The W side chains are exposed to the solvent, as shown by the extent of quenching of their fluorescence by KI. Time-resolved fluorescence anisotropy measurements showed that the rotational motion of W is completely unhindered in the case of SC and partially hindered in the case of MBP. The rotational correlation time (phi) associated with the fast local motion of W did not scale linearly with the bulk solvent viscosity (eta) in glycerol-water mixtures. In contrast, phi values of either W side chains in the denatured proteins or the free W scaled almost linearly with eta, as expected by the Stokes-Einstein relationship. These results were interpreted as indicating specific partitioning of water at the surface of the proteins in glycerol-water mixtures.

Biophysical Phenomena↗

PubMed1999

Effect of the methanolic extract of Glinus lotoides on Dalton's ascitic lymphoma.

The antitumour activity of the methanolic extract of Glinus lotoides (MGL) has been evaluated against Dalton's ascitic lymphoma (DAL) in Swiss albino mice. A significant enhancement of mean survival time of tumour bearing mice and peritoneal cell count in normal mice was observed with respect to the control group. When these MGL treated animals underwent i.p. inoculation with DAL cells, tumour cell growth was found to be inhibited. After 14 d of inoculation, MGL is able to reverse the changes in the haemotological parameters, protein and packed cellular volume consequent to tumour inoculation.

Animals↗

PubMed1999

RecA interacts with Klenow and enhances fidelity of DNA synthesis in vitro.

To understand the molecular basis of RecA-mediated DNA-repair, we tested the replicative fidelity of the large fragment of Pol I (Klenow) in RecA-DNA complexes in vitro. Klenow synthesis was error-prone in naked DNA substrates but essentially error-free in RecA coated complexes. Escherichia coli SSB, causes no such improvement in Klenow fidelity. RecA filaments promote better exonucleolytic proofreading by Klenow than on naked DNA substrates at select sites when replication is "stalled" due to a missing dNTP. Addition of RecA to pyrene sulfonylchloride-labeled Klenow resulted in a specific increase in steady-state fluorescence anisotropy and a concomitant decrease in fluorescence lifetime. These observations suggest the possibility of a direct interaction between RecA and Klenow even in the absence of DNA which may mediate the observed improvement in Klenow fidelity.

Base Sequence↗

PubMed1998

Probing the dynamics of planar supported membranes by Nile red fluorescence lifetime distribution.

The structure and dynamics of planar supported membranes were studied by using the fluorescence probe Nile red. The width of fluorescence lifetime distribution of Nile red was used to infer the heterogeneity of membranes. The width of fluorescence lifetime was larger and the lifetime was shorter in supported membranes when compared to vesicle membranes. This was interpreted as due to the presence of water-filled membrane discontinuity leading to a heterogeneous surface in supported membranes. Microdomain causing agents such as cholesterol, sphingomyelin, etc. caused a larger level of heterogeneity in supported membranes when compared to vesicle membranes.

Entropy↗

PubMed1997

Time-resolved fluorescence microscopy could correct for probe binding while estimating intracellular pH.

Estimation of intracellular pH by fluorescence ratiometry overcomes many of the limitations such as variations in the pathlength of observation and concentration of the probe, light scattering, and photobleaching. However, binding of probes to membranes and macromolecules is generally not taken into account. By using time-resolved fluorescence microscopy on a variety of cell types, we have shown that the dual-emission fluorescent pH probe carboxy SNARF-1 binds to cellular components in significant levels. The bound population could be resolved in the timescale since its fluorescence lifetime (approximately 3 ns) is significantly larger than that of the free probe. Intracellular pH was estimated from the relative amplitudes corresponding to free probes. This procedure was validated in simple model systems where carboxy SNARF-1 was present in solutions of bovine serum albumin. It was shown that the intracellular pH could be overestimated by as much as 1 pH unit in the absence of correction for probe binding.

3T3 Cells↗

PubMed1997

Cell type and spatial location dependence of cytoplasmic viscosity measured by time-resolved fluorescence microscopy.

Information on the cell type and spatial location dependence of cytoplasmic viscosity would be very useful in understanding some of the processes occurring in the cell. For this purpose, fluorescent dye kiton red (sulforhodamine B) was loaded into a variety of cells such as Swiss 3T3 fibroblasts, human mononuclear cells, Sarcoma-180 tumor cells, Chinese hamster ovary cells, plant cells from Digitalis lanata, stamen hair cells of Tradescantia, and guard mother cells of Allium cepa. Space-resolved measurements of cytoplasmic viscosity were carried out by using an experimental set-up wherein a picosecond laser system was coupled with an epifluorescence microscope. The spatial resolution of this set-up was approximately 1.0 micron, and reliable dynamic fluorescence measurements could be obtained from 10(2) to 10(3) fluorescent molecules. Fluorescence lifetime measurements showed that a large fraction (approximately 70%) of kiton red was in the free form. Fluorescence anisotropy decay of kiton red in cells was analyzed by a two population (free and bound) model. The microviscosity of cytoplasm was estimated from the anisotropy decay kinetics of the free probe. It was found that the cytoplasmic viscosity is dependent on both the cell type and spatial location within a cell. Furthermore, both the average value of viscosity and spatial variation within a cell were larger in the plant cells when compared to the animal cells. Model studies in various simpler systems have shown that the higher viscosity observed in some part of the cell could be due to either physical restriction and/or the presence of high concentrations of small solutes and macromolecules.

3T3 Cells↗

PubMed1996

Motional dynamics of a buried tryptophan reveals the presence of partially structured forms during denaturation of barstar.

A double mutant of the single-domain protein barstar having a single tryptophan (W53) was made by mutating the remaining two tryptophans (W38 and W44) into phenylalanines. W53 is buried in the core of barstar. Time-resolved fluorescence of the mutant barstar (W38FW44F) showed that W53 has a single fluorescence lifetime in the native (N) state and has three lifetimes in the molten globule-like low-pH (A) form. Quenching of fluorescence by either KI or acrylamide showed that W53 is solvent inaccessible in the N-state and fairly accessible in the A-form. The denaturation of W38FW44F by guanidine hydrochloride (GdnHCI) was monitored by several probes: near-UV and far-UV circular dichroism (CD), fluorescence intensity, and steady-state and time-resolved fluorescence anisotropy. While the unfolding transitions observed through CD and fluorescence intensity coincided with each other (midpoint approximately 1.8 M GdnHCI), the transition observed through the steady-state fluorescence anisotropy was markedly different from others. Initially, the anisotropy increased with the increase in the concentration of GdnHCI and decreased subsequently. The midpoint of this titration was 2.2 M GdnHCI. Picosecond time-resolved fluorescence anisotropy showed that W38FW44F has a single rotational correlation time of 4.1 ns in the native (N) state and 1.5 as in the unfoled (U) state (6 M GdnHCI). These could be explained as being due to the absence of motional freedom of W53 in the N-state and the presence of rotational freedom in the U-state. In the intermediate concentration region (1.8-3.0 M GdnHCI), the anisotropy decays showed at least two coorrelation times, approximately 1 and 6-12 ns. These two correlation times are ascribed to partially structured forms leading to hindered rotation of W53. Thus, the usefulness of time-resolved fluorescence anisotropy in detecting partially folded structures is demonstrated.

Bacterial Proteins↗

PubMed1994

Anomalous response of oxonol-V to membrane potential in mitochondrial proton pumps.

The response of the fluorescent membrane potential probe oxonol-V (bis[3-phenyl 5 oxoisoxazol-4-yl]pentamethine oxonol) in submitochondrial particles (SMP) was dependent upon whether the potential (inside positive) was generated by active proton pumps or by valinomycin-aided passive K+ influx. The fluorescence intensity showed a decrease in the former case and an increase in the latter situation. This anomalous behavior was not observed with other similar anionic probes. Gradual inhibition of proton pumping activity showed that the difference in the response of oxonol-V is not due to possible difference in the magnitude of membrane potential generated in these two situations. In the presence of membrane permeant anions such as TPB- (tetraphenyl boron) or chlorate, the direction of response of oxonol-V fluorescence was the same in both situations. Time-resolved fluorescence of the oxonol-V-SMP system showed three populations: one free form (fluorescence lifetime approximately 60 ps) and two SMP-bound forms (lifetimes of 0.45 ns and 1.4 ns). A fourth population was created during the action of proton pumps. The shorter lifetime (approximately 250 ps) of this new bound form suggest this population to be an aggregated form. This population was absent during the action of proton pumps in the presence of TPB- or chlorate. These results suggest the creation of a charge separated state during the action of proton pumps. The decrease in fluorescence intensity could be the result of aggregation of oxonol-V around the positive end of a proton pump existing in a dipole or charge separated state.

Animals↗

PubMed1994

Probing of coenzyme quinone binding site of mitochondrial NADH:CoQ reductase by fluorescence dynamics.

The coenzyme quinone (CoQ) binding region of mitochondrial NADH:CoQ reductase (complex-I) was investigated by the fluorescent probes erythrosine-5'-iodoacetamide (ER) and 3,3'-diethyloxadicarbocyanine iodide (DODCI). Both steady-state and time-resolved fluorescence was used in these experiments. Both probes competed for the binding site of 2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinone (DB), an analogue of CoQ. The fluorescence lifetimes of the complex-I bound probes were approximately 600 ps and approximately 1.7 ns in the cases of ER and DODCI, respectively. Binding of the probes was not affected by the binding of the inhibitor rotenone. However, rotenone binding caused some changes in the lifetime of the bound probes. Reduction of the enzyme caused an increase in the level of binding of ER and a decrease in the level of binding of DODCI. The level of binding of cationic DODCI increased with the increase in pH, and in the case of anionic of ER the trend was reverse. Binding of Ca2+ to complex-I resulted in an increase in the level of binding of ER and a decrease in the level of binding of DODCI. Reaction with N,N'-dicyclohexylcarbodiimide (DCCD) resulted in alterations in the time-resolved fluorescence profiles of dye: complex-I system. All these results were interpreted as due to the presence of carboxyl group(s) with pKa approximately 6 in the probe/CoQ binding region. The rotational correlation time (tau r) of DODCI bound at the CoQ region was 2-3 ns.(ABSTRACT TRUNCATED AT 250 WORDS)

Acids↗

PubMed1994

Similarity of fluorescence lifetime distributions for single tryptophan proteins in the random coil state.

The picosecond time-resolved fluorescence decay data of nine single-tryptophan (trp) proteins and two multi-trp proteins in their native and denatured states were analyzed by the maximum entropy method (MEM). In the denatured state (6 M guanidine hydrochloride) a majority of the single-trp proteins show bimodal (at 25 degrees C) and trimodal (at 85 degrees C) distributions with similar patterns and similar values for average lifetimes. In the native state of the proteins the lifetime distributions were bimodal or trimodal. These results (multimodal distributions) are contradictory to the unimodal Lorentzian distribution of lifetimes reported for some proteins in the native and denatured states. MEM analysis gives a unimodal distribution of lifetimes only when the signal-to-noise ratio is poor in the time-resolved fluorescence decay data. The unimodal distribution model is therefore not realistic for proteins in the native and denatured states. The fluorescence decay components of the bi- or trimodal distribution are associated with the rotamer structures of the indole moiety when the protein is in the random coil state.

Amino Acid Sequence↗

PubMed1994

Enzymes of carbohydrate metabolism in human breast carcinoma: relationship with serum hormones.

The enzymes involved in carbohydrate metabolism and their relationship with circulating estradiol (ET2) and prolactin (Prl) were studied in premenopausal and postmenopausal women with fibroadenoma and carcinoma of breast. The activities of all the glycolytic enzymes studied were increased in breast carcinoma tissues except for glyceraldehyde-3-phosphate dehydrogenase which showed decreased activity. Among the glycolytic enzymes studied, hexokinase, phosphofructokinase and glucose-6-phosphate dehydrogenase were found to be stimulated by elevated levels of serum ET2 and further stimulated by a simultaneous increase in Prl. However, the activity of lactate dehydrogenase was more specifically stimulated by Prl rather than ET2. None of the glycolytic enzymes studied was altered in fibroadenoma breast tissues.

Adolescent↗

PubMed1993

Plasma membrane enzymes in human breast carcinoma: relationship with serum hormones.

Alkaline phosphatase, 5'nucleotidase and gammaglutamyl transferase were studied in premenopausal and post-menopausal women with fibroadenoma and breast carcinoma tissues. The relationship of circulating estradiol (E2) and prolactin (Prl) with these enzymes was also investigated. All the three enzyme activities were found to be elevated in the breast carcinoma tissues of both pre- and postmenopausal groups. None of the membrane bound enzymes studied was altered in fibroadenoma breast tissues. The activities of all the three enzymes in breast carcinoma tissues were stimulated by the elevated level of serum Prl and further stimulated by a simultaneous increase in E2.

5'-Nucleotidase↗