http://192.168.1.40:8080/xmlui/handle/123456789/1119 2026-05-31T13:44:01Z http://192.168.1.40:8080/xmlui/handle/123456789/2460 Homology modeling of allergenic cyclophilins: IgE-binding site and structural basis of cross-reactivity Roy, Debjani; Ghosh, D.; Gupta-Bhattacharya, Swati Cross-reactivity among allergens is of considerable scientific as well as clinical interest. Proteins belonging to the allergenic cyclophilin family share a high degree of sequence homology and are cross-reactive. Until date no three-dimensional structural information is available on these proteins and the shared structural features of the epitopes which are the most important determinants of cross-reactivity. Cyclophilins are also known to bind with the immuno-suppressive drug cyclosporin. Comparative molecular modeling of these allergenic cyclophilin proteins of different sources was performed in order to investigate the structural basis of their cross-reactivity. All the proteins studied revealed a similarity in the shape of the cross-reactive epitopes with varying degrees of accessibility. Cyclosporin binding and allergenic properties of these proteins were also found to be structurally related. DOI: 10.1016/S0006-291X(03)01193-8 2003-07-25T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2434 Sequence divergence of Entamoeba histolytica tubulin is responsible for its altered tertiary structure Roy, Debjani; Lohia, A. Atypical microtubular structures of the protozoan parasite Entamoeba histolytica (Eh) have been attributed to amino acid sequence divergence of Eh tubulin. To investigate if this sequence divergence leads to significant differences in the tertiary structure of the Eh alphabeta-tubulin heterodimer, we have modeled alphabeta-tubulin heterodimer of Eh based on the crystal structure of mammalian tubulin. The predicted 3D homology model exhibits an overall resemblance with the known crystal structure of mammalian tubulin except for the 16 residue long carboxy terminal region of Eh beta-tubulin. We propose that this C-terminal region may provide steric hindrance in the polymerization of Eh alphabeta-tubulin for microtubule formation. Using docking studies, we have identified the binding sites for different microtubule specific drugs on Eh beta-tubulin. Our model provides a rational framework, both for understanding the contribution of Eh beta-tubulin C-terminal region to alphabeta-tubulin polymerization and design of new anti-protozoan drugs in order to control amoebiasis. DOI: 10.1016/j.bbrc.2004.05.079 2004-07-02T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2359 Small cationic protein from a marine turtle has beta-defensin-like fold and antibacterial and antiviral activity Chattopadhyay, S.; Sinha, N. K.; Banerjee, S.; Roy, Debjani; Chattopadhyay, D.; Roy, S. Egg white of marine turtle Caretta caretta contains a small cationic protein but lacks lysozyme. The protein was sequenced by a combination of sequential Edman degradation, carboxypeptidase digestion, nuclear magnetic resonance (NMR) and electrospray ionization tandem mass spectrometry. The protein contains 36 amino acid residues of which six are half-cysteines. The three-dimensional structure of the protein was deduced from two-dimensional NMR experiments and was observed to be similar to vertebrate beta-defensins. However, disulfide connectivity is C1-C6/C2-C5/C3-C4; different from that of the vertebrate beta-defensins. The protein showed strong antibacterial activity against Escherichia coli and Salmonella typhimurium. The protein also showed significant antiviral activity against an enveloped rhabdovirus, Chandipura virus, which is an emerging human pathogen. This virus is also closely related to the vesicular stomatitis virus, whose growth was also inhibited. This small cationic protein is part of the innate immunity of this organism and replaces lysozyme in the egg. It has the potential to be developed as an antibacterial and antiviral agent. DOI: 10.1002/prot.20963 2006-08-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2357 Structural features of a cold-adapted Alaskan bacterial lipase Roy, Debjani; Sengupta, S. The three dimensional model of cold-adapted Alaskan psychrotroph Pseudomonas species (Strain B11-1) lipase has been constructed by homology modeling based on the crystal structure of acetyl esterase from Rhodococcus species and refined by molecular dynamics methods. Our model locates the substrate-binding cavity and further suggests that Ser-155, Asp-250, and His-280 are the members of the catalytic triad. Substrate specificity of the modeled lipase has been examined by docking experiments, which indicates that the ester of C(6) fatty acid has the highest affinity for the enzyme. Our model also identifies the oxyanion hole that plays an important role in the stabilization of the tetrahedral intermediate during catalysis. Comparison of this cold-adapted lipase with the crystal structure of a thermophilic Bacillus stearothermophilits P1 lipase supported the assumption that cold-adapted enzymes have a more flexible three-dimensional structure than their thermophilic counterparts. The conformational flexibility of this modeled cold-adapted lipase at low temperature probably originates from a combination of factors compared to its thermophilic counterpart, i.e., lower number of salt bridges and cation-pi interactions, increase in the non-polar surface area exposed to solvent. Our study may help in understanding the structural features of a cold-adapted lipase and can further be used in engineering lipase that can function at or near extreme temperatures with considerable biotechnological potential. DOI: 10.1080/07391102.2007.10507134 2007-04-01T00:00:00Z