Biomedical subjects

Chaitali Mukhopadhyay

Publications and source records attributed to Chaitali Mukhopadhyay.

16 recordsLinked to original sources

PubMed2006

Binding diversity of the two binding sites of ricin B lectin.

Ricin B is a galactose-binding protein, which contains two binding sites. We have compared the binding properties of the two binding sites of ricin B chain toward different mono- and disaccharide ligands. The free energies of binding are calculated using the free energy perturbation simulation (thermodynamic integration method) and linear interaction energy approach using CHARMM force field. The second binding site of the protein was found to be weaker compared to the first. The details of the hydrogen-bonding scheme suggested the origin of the epimeric specificity of the protein. The reason for the weaker binding capacity of the second binding site has been addressed.

Binding Sites↗

PubMed2006

Specificity of Prodan for the self-associating domain of spectrin: a molecular docking study.

The hydrophobic fluorescent probe Prodan binds to the self-associating domain of spectrin with 1:1 stoichiometry. A model of the self-associating domain was generated based on its homology with other domains of spectrin. Prodan was then docked onto the model, and several sites with low interaction energy were identified. To verify whether the binding of Prodan is specific towards the self-associating domain of spectrin, it was docked on to several other domains of spectrin, having a known three-dimensional structure. Analysis of the docking results suggests that the binding of Prodan to the self-associating domain of spectrin will involve hydrophobic and hydrophilic groups of Prodan. The results clearly indicate the preference of Prodan for a particular binding site of the self-associating domain.

Amino Acid Sequence↗

PubMed2005

Unfolding dynamics of the protein ubiquitin: insight from simulation.

The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known " state" of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process.

Computer Simulation↗

PubMed2005

Stability and conformation of the complexes of riboflavin with aromatic hydroxy compounds in an aqueous medium.

Overall equilibrium constants K' for the formation of molecular complexes of riboflavin with the conjugate forms of different aromatic hydroxy compounds are greater in magnitude than those involving the protonated forms of the hydroxy compounds. There is good agreement between the K(B) values determined by using absorption and emission methods. Based on the magnitude of K(B), it is possible to differentiate between the donor capacities of the hydroxy compounds in the charge transfer complexes with riboflavin. Molecular modeling studies indicate stacking interactions for all the systems in an aqueous medium.

Hydrocarbons, Aromatic↗

PubMed2005

Interaction and structural study of kinin peptide bradykinin and ganglioside monosialylated 1 micelle.

Partitioning of small proteins and peptides from the aqueous to membrane phase is often coupled with folding. In this work we examine the binding and folding of the kinin peptide, bradykinin (BK), in the presence of the ganglioside monosialylated 1 (GM1) micelle. Using two-dimensional NMR techniques, we have shown that at low concentration, GM1 micelle is able to induce a turn conformation to BK. A pulsed-field gradient diffusion NMR study indicated that the peptide partitions into the GM1 micelle with a DeltaG(part) of -3.14 +/- 0.03 kcal/mol. A saturation transfer difference (STD) NMR study indicated that the binding is mostly through hydrophobic residues.

Amino Acid Sequence↗

PubMed2005

Studies on the riboflavin-resorcinol interaction in an aqueous medium and its pH dependence.

The equilibrium constants, K', for the formation of the molecular association complex between riboflavin and resorcinol in the pH range 6-8 were found to be in the range 5-25 mol(-1)dm(3) by difference absorption spectroscopy. The equilibrium constants from emission spectroscopy were estimated to be in the range 38-55 mol(-1)dm(3) over the same pH range. Both sets of K' show a remarkable dependence on pH. The equilibrium constants K(A) and K(B) describing the interaction of riboflavin with neutral and ionic forms of resorcinol, respectively, obtained by resolving K', shows that K(B) is much greater than K(A). Molecular modeling studies suggest a stacked conformation of the two components in the complexed form. The interaction energies obtained from modeling studies also suggest a stronger interaction between the ionic form of resorcinol and riboflavin.

Hydrogen-Ion Concentration↗

PubMed2005

Binding and folding of melittin in the presence of ganglioside GM1 micelles.

In this work we examine the binding and folding of the membrane-active peptide, melittin in the presence of ganglioside GM1 micelle. The membrane bilayer is capable of inducing folding to small proteins and peptides upon binding. Using two-dimensional NMR techniques we have shown that at low concentration, GM1 micelle is able to induce an extended helical conformation to MLT. The pulsed-field gradient diffusion NMR study indicates that the peptide partition into GM1 micelle along with about 32% binding. While looking for the binding between MLT and GM1 using saturation transfer difference NMR spectroscopy, Val5, Leu9, Thr11, Ile17, Ser18, and Trp19 have been identified as the residues that are in close proximity to GM1 micelles.

Animals↗

PubMed2005

Co-inheritance of the Hb Sun Prairie mutation with a point mutation at 5'-UTR in the eastern Indian population.

Haemoglobin (Hb) Sun Prairie (alpha2-globin cd130, GCT-->CCT, Ala-->Pro) is detected in three unrelated chromosomes, in association with a C-->T transition in the 5'-untranslated region (UTR), two bases upstream from the translation start site. Reported inversion of alpha/beta-mRNA ratio observed in Hb Sun Prairie mutants might stem from the second mutation and should be investigated. Molecular modelling studies indicate that the 130th residue of alpha-globin faces primarily the central cavity of the molecule and is not in contact with any beta-chain residue; further, no significant disruption of the Hb structure because of the Sun Prairie mutation is discernible. Depression of translation because of the second mutation of a conserved base in the 5'-UTR might explain the observed clinical severity.

5' Untranslated Regions↗

PubMed2004

Anomalous behavior of water around sodium dodecyl sulphate micelles.

The dynamics, structural properties, and energetics of hydration water around a sodium dodecyl sulphate micelle have been investigated using molecular dynamics simulation. A clear revelation of the slow dynamics of the hydration water has been made by separate measurements of the rotational and translational properties. Calculated diffusion coefficients fall within the range of experimentally observed quantities. The water-micelle head group (MHG) hydrogen bond is more stable (by an amount approximately 7.0 kcal/mol) compared to the water-water hydrogen bond. The difference in stability of the water monomers forming different numbers of hydrogen bonds (n=0,1,2) with the MHG has clearly been shown from the analyses of their rotational relaxation, residence times, as well as the energy of interaction with different components of the system. The singly hydrogen-bonded water species is the most abundant and stable. The entropy plays the key role in controlling the relative abundance of the different species.

Colloids↗

PubMed2004

Conformational alteration of bradykinin in presence of GM1 micelle.

We report here the interaction of bradykinin with ganglioside GM1 by circular dichroism, steady-state fluorescence, and one-dimensional 1H NMR spectroscopy. Circular dichroism spectroscopy is indicative of a turn formation of bradykinin backbone in the presence of GM1 micelle. The fluorescence quenching efficiencies of iodide and acrylamide are substantially reduced, indicating a shielding of phenylalanine residue of bradykinin from aqueous environment. Significant line broadening of NMR resonances of bradykinin, suggestive of motional restriction, is observed.

Animals↗

PubMed2003

Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation.

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.

Biophysical Phenomena↗

PubMed2003

Structural alterations of enkephalins in the presence of GM1 ganglioside micelles.

The enkephalins are endogenous neurotransmitters and bind with high affinity at the delta-receptor. Gangliosides, the major glycans of nerve cells, known to interact both with receptors and ligands on the cell surface, have been implicated to modulate the actions of opioid receptors by allosteric regulation (Wu, G.; Lu, Z. H.; Wei, T. J.; Howells, R. D.; Christoffers, K.; Leeden R. W. Ann NY Acad Sci 1998, 845, 126-138). We have studied the interactions between enkephalins and monosialylated ganglioside GM1 using NMR spectroscopy and fluorescence. The structural models of enkephalins in the presence of GM1 micelles were generated using two-dimensional (1)H-ROESY experiments along with restrained molecular dynamics simulations. We report a conformational alteration of enkephalins in the presence of GM1 micelles.

Animals↗

PubMed2003

Lysophosphatidylcholine regulates human microvascular endothelial cell expression of chemokines.

The role of lysophosphatidylcholine (LPC) in the induction of MCP-1, IL-8 and RANTES, which are chemotactic factors to monocytes, neutrophils and lymphocytes, respectively, by human vascular endothelial cells (EC), was examined. LPC induced the expression of MCP-1 and IL-8 in a concentration- and time-dependent manner in microvascular EC (MVEC) and in large vessel EC from aorta, pulmonary artery and umbilical vein. LPC also induced RANTES in MVEC but not in large vessel EC. Signaling pathways responsible for LPC induction of chemokines were examined in MVEC. LPC and TNFalpha, a cytokine secreted in sites of inflammation, additively stimulated RANTES expression. LPC did not augment TNFalpha induction of MCP-1 or IL-8. A platelet-activating factor receptor antagonist (BN52021) failed to block LPC induction of MVEC chemokines, but the G(i)-protein inhibitor pertussis toxin partially blocked LPC induction of RANTES and IL-8. LPC activated multiple kinases in MVEC; it increased the phosphorylation of ERK1/2, AKT and p38 MAP kinase in a time-dependent manner. An inhibitor of the MAPK/ERK pathway, PD98059, blocked the phosphorylation of ERK1/2 and RANTES induction by LPC, but augmented IL-8 induction. LY294002, a specific inhibitor of phosphoinositide 3 kinase (PI3 kinase), blunted the phosphorylation of AKT and inhibited LPC induction of RANTES more strongly than IL-8. Inhibition of p38 MAP kinase pathway by SB202190 also blocked LPC-induced expression of IL-8 and RANTES. Our results suggest that LPC induction of chemokines in MVEC is distinct from that in large vessel EC, and required the activities of MAP kinases and PI3 kinase for the induction of RANTES and IL-8. We speculate that the presence of LPC, a bioactive lipid product of phospholipase A(2) (PLA(2)) and a constituent of oxidized low-density lipoprotein, can differentially influence the chemotaxis of particular leukocyte subpopulations during inflammation.

Aorta↗

PubMed2002

Melittin-GM1 interaction: a model for a side-by-side complex.

We report here the interaction of melittin with ganglioside GM1 by steady-state fluorescence, one-dimensional (1)H NMR spectroscopy and molecular modeling. In the presence of GM1 the emission maximum of melittin is blue shifted and fluorescence quenching efficiencies of iodide and acrylamide are substantially reduced, indicating a shielding of tryptophan of melittin from aqueous environment. Significant line broadening of NMR resonances of melittin, suggestive of motional restriction, is observed. Molecular modeling indicates a melittin-GM1 complex with N-terminal hydrophobic stretch of melittin associating with the ceramide tail and C-terminal hydrophilic end of melittin having favorable electrostatic interaction with the carbohydrate head group of GM1.

Computer Simulation↗

PubMed2002

Molecular dynamics simulation of GM1 in phospholipid bilayer.

We report molecular dynamics simulation of fully hydrated lipid bilayer of dimyristoyl phosphatidyl choline (DMPC) at room temperature with ganglioside GM1 attached to it in the upper layer under periodic boundary conditions. The simulation results indicate that the presence of a single GM1 molecule has local effects on the bilayer. Three sugar residues (GalNAc-Gal-Glc) of the pentasaccharide head group of GM1 remain on the lipid surface where as the NeuNAc residue extends out in the aqueous layer. The radial distribution functions suggest ordering of water molecules near the glycerol and carboxyl group of the sialic acid in the upper layer. One of the ceramide chains of GM1, the sphingosine chain, folds up and is stacked under the sugar residues lying on the surface. The other ceramide chain is inserted into the lipid bilayer. The arrangement of the polar head group as well as the acyl chains of the lipids which are immediate neighbours of the GM1 are modified compared to the non-neighbour ones and others at the lower layer. The time average conformation of GM1-pentasaccharide is stabilized by a number of inter residue hydrogen bonds that were observed experimentally. The trajectory average conformation of GM1-pentasaccharide was docked on to the cholera toxin molecule and the minimized complex reveals alternative binding modes between the toxin and the GM1-pentasaccharide moiety. The results of these simulation studies might help to understand the structure and nature of the effects of GM1 on the membrane at atomic resolution.

Cholera Toxin↗

PubMed2002

Binding free energy calculations of galectin-3-ligand interactions.

Galectins show remarkable binding specificity towards beta-galactosides. A recently developed method for calculating binding free energies between a protein and its substrates has been used to evaluate the binding specificity of galectin-3. Five disaccharides and a tetrasaccharide were used as the substrates. The calculated binding free energies agree quite well with the experimental data and the ranking of binding affinities is well reproduced. For all the six protein-ligand complexes it was observed that electrostatic interactions oppose binding whereas the non-polar contributions drive complex formation. The observed binding specificity of galectin-3 for galactosides rather than glucosides is discussed in light of our results.

Carbohydrate Conformation↗