Biomedical subjects

J K Bhattacharjee

Publications and source records attributed to J K Bhattacharjee.

At least 19 recordsLinked to original sources

PubMed2006

Nonequilibrium statistical physics with fictitious time.

Problems in nonequilibrium statistical physics are characterized by the absence of a fluctuation dissipation theorem. The usual analytic route for treating these vast class of problems is to use response fields in addition to the real fields that are pertinent to a given problem. This line of argument was introduced by Martin, Siggia, and Rose. We show that instead of using the response field, one can, following the stochastic quantization of Parisi and Wu, introduce a fictitious time. In this extra dimension a fluctuation dissipation theorem is built in and provides a different outlook to problems in nonequilibrium statistical physics.

Journal Article↗

PubMed2005

Functional analysis through site-directed mutations and phylogeny of the Candida albicans LYS1-encoded saccharopine dehydrogenase.

Candida albicans LYS1-encoded saccharopine dehydrogenase (CaLys1p, SDH) catalyzes the final biosynthetic step (saccharopine to lysine + alpha-ketoglutarate) of the novel alpha-aminoadipate pathway for lysine synthesis in fungi. The reverse reaction catalyzed by lysine-alpha-ketoglutarate reductase (LKR) is used exclusively in animals and plants for the catabolism of excess lysine. The 1,146 bp C. albicans LYS1 ORF encodes a 382 amino acid SDH. In the present investigation, we have used E. coli-expressed recombinant C. albicans Lys1p for the determination of both forward and reverse SDH activities in vitro, compared the sequence identity of C. albicans Lys1p with other known SDHs and LKRs, performed extensive site-directed mutational analyses of conserved amino acid residues and analyzed the phylogenetic relationship of C. albicans Lys1p to other known SDHs and LKRs. We have identified 14 of the 68 amino acid substitutions as essential for C. albicans Lys1p SDH activity, including two highly conserved functional motifs, H93XXF96XH98 and G138XXXG142XXG145. These results provided new insight into the functional and phylogenetic characteristics of the distinct biosynthetic SDH in fungi and catabolic LKR in higher eukaryotes.

Amino Acid Motifs↗

PubMed2004

Time-dependent perturbation theory with a classical limit.

We construct a quantum mechanical perturbation theory which uses the multiple time scale technique. Working with the time translation operator, we use a variant on the method of Bender and Bettencourt. Our perturbation theory smoothly crosses over to the classical result as Planck's -->0. It is seen that this technique has a nonperturbative element built into it.

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PubMed2004

Approach to equilibrium in adiabatically evolving potentials.

For a potential function (in one dimension) which evolves from a specified initial form V(i)(x) to a different V(f)(x) asymptotically, we study the evolution, in an overdamped dynamics, of an initial probability density to its final equilibrium. There can be unexpected effects that can arise from the time dependence. We choose a time variation of the form V(x,t) = V(f)(x) + (V(i) - V(f)) e(-lambda t). For a V(f)(x), which is double welled and a V(i)(x) which is simple harmonic, we show that, in particular, if the evolution is adiabatic, this results in a decrease in the Kramers time characteristic of V(f)(x). Thus the time dependence makes diffusion over a barrier more efficient. There can also be interesting resonance effects when V(i)(x) and V(f)(x) are two harmonic potentials displaced with respect to each other that arise from the coincidence of the intrinsic time scale characterizing the potential variation and the Kramers time. Both these features are illustrated through representative examples.

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PubMed2004

Posttranslational activation, site-directed mutation and phylogenetic analyses of the lysine biosynthesis enzymes alpha-aminoadipate reductase Lys1p (AAR) and the phosphopantetheinyl transferase Lys7p (PPTase) from Schizosaccharomyces pombe.

Alpha-aminoadipate reductase (AAR), the signature enzyme for lysine biosynthesis in fungi, catalyses the conversion of alpha-aminoadipate to alpha-aminoadipate-semiadehyde in the presence of ATP and NADPH. In Saccharomyces cerevisiae and Candida albicans, the LYS2-encoded AAR is posttranslationally activated by CoA and the LYS5-encoded PPTase. The fission yeast Schizosaccharomyces pombe is evolutionarily highly diverged from S. cerevisiae and C. albicans. We report here several unusual activation characteristics of Sz. pombe Lys1p and Lys7p, isofunctional to Lys2p (AAR) and Lys5p (PPTase), respectively. Unlike the Lys2p from S. cerevisiae and C. albicans, the Sz. pombe Lys1p was active when expressed in E. coli and exhibited significant AAR activity without the addition of CoA or the Sz. pombe Lys7p intron free PPTase. Somewhat higher AAR activity was obtained with the addition of CoA and the Sz. pombe Lys7p PPTase. Substitution of G910A, S913T or S913A in the Sz. pombe Lys1p activation domain (IGGHSI) resulted in no AAR activity. Similarly, substitutions of several amino acid residues in the Sz. pombe Lys7p PPTase domain (G79A, R80K and P81A in Core 1; F93W, D94E, F95W and N96D in Core 1a; G124A, V125I and D126E in Core 2; K172R, E173D and K177R in Core 3) also resulted in no activation of Lys1p and no AAR activity. The Sz. pombe Lys1p amino acid sequence showed a high degree of similarity to other fungal Lys2p proteins; however, the Lys7p amino acid sequence showed much less similarity to other bacterial, fungal and animal PPTases representing several phylogenetic groups.

Aldehyde Oxidoreductases↗

PubMed2003

Site-directed mutational analysis of the novel catalytic domains of alpha-aminoadipate reductase (Lys2p) from Candida albicans.

The alpha-aminoadipate reductase, a novel enzyme in the alpha-aminoadipic acid pathway for the biosynthesis of lysine in fungi, catalyzes the conversion of alpha-aminoadipic acid to alpha-aminoadipic-delta-semialdehyde in the presence of ATP, NADPH and MgCl(2). This reaction requires two distinct gene products, Lys2p and Lys5p. In the presence of CoA, Lys5p posttranslationally activates Lys2p for the alpha-aminoadipate reductase activity. Sequence alignments indicate the presence of all functional domains required for the activation, adenylation, dehydrogenation and alpha-aminoadipic acid binding in the Lys2p. In this report we present the results of site-directed mutational analysis of the conserved amino acid residues in the catalytic domains of Lys2p from the pathogenic yeast Candida albicans. Mutants were generated in the LYS2 sequence of pCaLYS2SEI by PCR mutagenesis and expressed in E. coli BL21 cells. Recombinant mutants and the wild-type Lys2p were analyzed for their alpha-aminoadipate reductase activity. Substitution of threonine 416, glycine 418, serine 419, and lysine 424 of the adenylation domain (TXGSXXXXK, residues 416-424) resulted in a significant reduction in alpha-aminoadipate reductase activity compared to the unmutagenized Lys2p control. Similarly replacement of glycine 978, threonine 980, glycine 981, phenylalanine 982, leucine 983 and glycine 984 of the NADPH binding domain (GXTGFLG, residues 978-984) caused a drastic decrease in alpha-aminoadipate reductase activity. Finally, substitution of histidine 460, aspartic acid 461, proline 462, isoleucine 463, glutamine 464, arginine 465, and aspartic acid 466 of the putative alpha-aminoadipic acid binding domain (HDPIQRD, residues 460-466) resulted in a highly reduced alpha-aminoadipate reductase activity. These results confirm the hypothesis that specific amino acid residues in highly conserved catalytic domains of Lys2p are essential for the alpha-aminoadipate reductase activity.

Adenosine Triphosphate↗

PubMed2002

Realizability of stationary spherically symmetric transonic accretion.

The spherically symmetric stationary transonic (Bondi) flow is considered a classic example of an accretion flow. This flow, however, is along a separatrix, which is usually not physically realizable. We demonstrate, using a pedagogical example, that it is the dynamics which selects the transonic flow.

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PubMed2001

Zero-frequency critical bulk viscosity: is the amplitude ratio truly universal?

It was shown by Onuki that the zero-frequency bulk viscosity is associated with a universal amplitude ratio that was calculated to be around 0.10. We show that the sound attenuation data can be used to extract a value for this universal number and we find this number to be around 0.18, reasonably close to Onuki's estimate. However, we argue that a reconsideration of this amplitude ratio shows that this ratio is not truly universal. It has a logarithmic correction instead.

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PubMed2001

Rayleigh-Marangoni convection in a critical fluid: a tale of two crossovers.

We show that if we take a thin layer of fluid where surface tension effects are supposed to dominate and gradually bring the mean temperature of the layer closer and closer to the liquid vapor critical point, then first there is a crossover from Marangoni to Rayleigh-Benard convection and thence to a convection whose onset is determined by the Schwarzchild criterion.

Journal Article↗

PubMed2001

Frequency-dependent viscosity near the critical point: the scale to two-loop order.

The recent accurate measurements of Berg, Moldover, and Zimmerli [Phys. Rev. Lett. 82, 920 (1999); Phys. Rev. E 60, 4079 (1999)] of the viscoelastic effect near the critical point of xenon has shown that the scale factor involved in the frequency scaling is about twice the scale factor obtained theoretically. We show that this discrepancy is a consequence of using first order perturbation theory. Including two-loop contribution goes a long way towards removing the discrepancy.

Journal Article↗

PubMed2001

Novel posttranslational activation of the LYS2-encoded alpha-aminoadipate reductase for biosynthesis of lysine and site-directed mutational analysis of conserved amino acid residues in the activation domain of Candida albicans.

The alpha-aminoadipate pathway for lysine biosynthesis is present only in fungi. The alpha-aminoadipate reductase (AAR) of this pathway catalyzes the conversion of alpha-aminoadipic acid to alpha-aminoadipic-delta-semialdehyde by a complex mechanism involving two gene products, Lys2p and Lys5p. The LYS2 and LYS5 genes encode, respectively, a 155-kDa inactive AAR and a 30-kDa phosphopantetheinyl transferase (PPTase) which transfers a phosphopantetheinyl group from coenzyme A (CoA) to Lys2p for the activation of Lys2p and AAR activity. In the present investigation, we have confirmed the posttranslational activation of the 150-kDa Lys2p of Candida albicans, a pathogenic yeast, in the presence of CoA and C. albicans lys2 mutant (CLD2) extract as a source of PPTase (Lys5p). The recombinant Lys2p or CLD2 mutant extract exhibited no AAR activity with or without CoA. However, the recombinant 150-kDa Lys2p, when incubated with CLD2 extract and CoA, exhibited significant AAR activity compared to that of wild-type C. albicans CAI4 extract. The PPTase in the CLD2 extract was required only for the activation of Lys2p and not for AAR reaction. Site-directed mutational analysis of G882 and S884 of the Lys2p activation domain (LGGHSI) revealed no AAR activity, indicating that these two amino acids are essential for the activation. Replacement of other amino acid residues in the domain resulted in partial or full AAR activity. These results demonstrate the posttranslational activation and the requirement of specific amino acid residues in the activation domain of the AAR of C. albicans.

Aldehyde Oxidoreductases↗

PubMed2000

Wall-bounded turbulent shear flow: Analytic result for a universal amplitude.

In the turbulent boundary layer above a flat plate, the velocity profile is known to have the form v=v(0)[(1/kappa)ln z+const]. The distance from the wall in dimensionless units is z and v(0) is a uniquely defined velocity scale. The number kappa is universal, and measurements over several decades have shown that it is nearly 0.42. We use a randomly stirred model of turbulence to derive the above law and find kappa=sqrt[108/125pi] approximately 0.52.

Journal Article↗

PubMed2000

Nonlinear model for Marangoni convection.

We have constructed a Lorenz-like model for Marangoni convection with finite wave number in large aspect ratio situations. Within the model, there is exchange of stabilities at the onset of convection and beyond the onset there is onset of oscillations due to the presence of surface fluctuations. The oscillations become chaotic as the Marangoni number is increased.

Journal Article↗

PubMed1999

Characterization of a double gene disruption in the LYS2 locus of the pathogenic yeast, Candida albicans.

The 4.2 kbp LYS2 gene of Candida albicans encodes the 150 kDa subunit of the 180 kDa heterodimeric enzyme alpha-aminoadipate reductase. To facilitate structural and functional studies of the LYS2 gene, in this investigation both alleles were sequentially disrupted in C. albicans CAI4. The disruptions were performed using a targeting vector that contained a 2.2 kbp portion of LYS2 from which a 600-bp fragment had been deleted and replaced with a hisG-URA3-hisG cassette. Disruption of both alleles of the LYS2 locus was confirmed by Southern hybridization with appropriate probes. To determine the physiological effect of the LYS2 disruption, cell extracts were assayed for the LYS2-encoded alpha-aminoadipate reductase activity. The parent, heterozygote and LYS2-disrupted strains exhibited significant, partial and no activity, respectively. Transformation of the LYS2-disrupted strain with the LYS2 gene reversed the mutant phenotype as shown by growth on selective media and restored alpha-aminoadipate reductase activity. These results demonstrated that the LYS2 gene of C. albicans is responsible for the synthesis of functional alpha-aminoadipate reductase.

Aldehyde Oxidoreductases↗

PubMed1999

Marangoni convection on an inhomogeneous substrate.

We consider an inhomogeneous substrate for Marangoni convection. The inhomogeneity shows up in a nonuniform temperature distribution which we model by a periodic variation. The response can exhibit parametric resonance. Both resonant and nonresonant responses are considered and a possible strong effect on wave number selection indicated.

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PubMed1999

Heap corrugation and hexagon formation of powder under vertical vibrations.

We report free-surface instabilities in a deep bed of fine granular material of irregular shape under vertical vibrations. At low frequency of vibration, the conical heap due to convective flow becomes unstable above a critical amplitude of vibration and acquires an azimuthal dependence which makes the heap surface corrugated. At even higher amplitude, the heap is no longer stable and splits into small heaps on a hexagonal lattice. At high frequency, we observe standing waves (stripes) at the same frequency as the driving one. The main mechanism of these instabilities can be traced back to the presence of the surrounding gas, since they vanish under vacuum conditions.

Journal Article↗

PubMed1999

Extended self-similarity and dissipation range dynamics of three-dimensional turbulence.

We carry out a self-consistent calculation of the structure functions in the dissipation range using the Navier-Stokes equation. Combining these results with the known structures in the inertial range, we actually propose crossover functions for the structure functions that take one smoothly from the inertial to the dissipation regime. These crossover functions are shown to exhibit extended self-similarity properties consistent with experimental findings.

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PubMed1998

Nucleotide sequence of the Schizosaccharomyces pombe lys1+ gene and similarities of the lys1+ protein to peptide antibiotic synthetases.

The 4.2 kbp lys1+ gene of Schizosaccharomyces pombe encoding the large subunit of alpha-aminoadipate reductase (EC1.2.1.31), an enzyme specific to lysine synthesis in higher fungi, was completely sequenced at the nucleotide level from pLYS1H. The S. pombe lys1+ gene product consists of 1415 amino acid residues and has a putative molecular weight of 155.8 kDa. The encoded protein converts alpha-aminoadipic acid to alpha-aminoadipate-delta-semialdehyde by an ATP-mediated adenylation. Analysis of the sequence showed that the putative protein encoded by lys1+ shares strong homology with the peptide antibiotic synthetases which also use in adenylation step.

Aldehyde Oxidoreductases↗