Comparative modeling of retinol-binding protein-3 and retinal S-antigen in Eales’ disease and prediction of their binding sites using computational methods

Retinal S-antigen and interphotoreceptor retinoid-binding protein-3 play a significant role in the etiopathogenesis of Eales' disease. Protein 3D structures are functionally very important and play a significant role in progression of the disease, hence these 3D structures are better target for further drug designing and relative studies. We developed 3D model structure of retinol-binding protein-3 and retinal S-antigen protein of human involved in Eales' disease. Functional site prediction is a very important and related step; hence, in the current course of analysis, we predicted putative functional site residues in the target proteins. Molecular models of these proteins of Eales' disease as documented in this study may provide a valuable aid for designing an inhibitor or better ligand against Eales' disease and could play a significant role in drug design.     

Protein thermostability in Archaea and Eubacteria

In order to survive at high temperatures, thermophilic prokaryotes (Archaea and Eubacteria) adopt different strategies. Among several important contributing factors for stability of proteins are CG-rich codons, the ratio of charged amino acids compared to uncharged amino acids, ionic interactions, amino acid preferences and their distribution, post-translational modifications, and solute accumulation. However, these factors may differ from taxon to taxon, both within and between species depending upon the composition of proteins found in these organisms. This is exemplified in the case of differences in strategies adopted by soluble proteins and membrane proteins. Therefore, it appears that no single factor or combination of factors together can be universally attributed to the provision of thermal stability in proteins.     

Atypical D-FISH patterns of BCR/ABL gene rearrangements in 169 chronic myeloid leukemia patients

The Philadelphia (Ph) chromosome, a hallmark chromosomal anomaly observed in 95 percent of chronic myeloid leukemia (CML) cases, is known to involve the Abelson (ABL) proto-oncogene on chromosome 9 and the breakpoint cluster region (BCR) gene on chromosome 22, producing BCR/ABL mRNA encoding an abnormal tyrosine kinase protein. In the process of generating BCR-ABL fusion, the deletion of residual BCR or ABL occurs in 15-30 percent of CML patients. In addition, some rearrangements are complex, and do not yield the ABL/BCR fusion due to the involvement of a third chromosome in the rearrangement. The possible role of these deletions and complex rearrangements in disease outcome is an ongoing topic of research. We report our results of cytogenetic analysis with GTG banding and fluorescence in situ hybridization using dual color dual fusion probe (D-FISH) from Vysis Inc, USA in 169 (109 male and 60 female) CML patients registered at The Gujarat Cancer and Research Institute (GC and RI) from April 2004 to December 2005. GTG banding was carried out in 123 cases having analyzable metaphases. Of these 123 cases, D-FISH revealed atypical signal patterns in 57 patients (46%), and 12 cases revealed additional complex translocations indicative of disease progression. Out of 57 cases with atypical FISH patterns, 22 included metaphase FISH results, and the rest had only interphase FISH performed. In addition to the hallmark Philadelphia chromosome, other chromosomal aberrations in CML revealed heterogeneity of molecular events. Pooling of more data may lead to identification of new CML sub-groups and hence help in the analysis of clinical trials. Patients enrolled in our prospective study of prognostic significance will be followed up for disease free and overall survival in correlation with ABL-BCR deletion status.     

Formulation of medium constituents by multiresponse analysis of central composite design to enhance chitinase production in Pantoea dispersa

In the present study, a high chitinase producing strain Pantoea dispersa was isolated from the sea dumps at Bhavnagar, India. Chitin, urea, CaCl2 and MgSO4 x 7H2O were variables used in central composite design for chitinase production. Chitinase, biomass and pH were the responses used in different models to evaluate individually fit ones. Quadratic model was found to be fit for chitinase response whereas in the case of biomass and pH, linear model was found to be fit without the effect of others. Chitinase production was optimized with respect to other responses such as biomass and pH in multiresponse analysis of response surface design by using desirability approach. In multiresponse analysis, following medium formulation (g/l), chitin, 15; urea, 0.32; CaCl2, 0.10 and MgSO4 x 7H2O, 0.08 was found to predict optimum chitinase production of 482.77 units/ml with overall highest desirability of 0.854 as compared to other formulations. The selection of model was done on the basis of high Adjusted R-squared value and lowered p-value for each model in individual analysis of each response. In multiresponse experiment, it was found that for response chitinase quadratic model and for responses pH and biomass linear models were well fit. Through desirability analysis, it was found that in the chitinase production, pH was essential as compared to biomass in P. dispersa. Endochitinase and chitobiase actvities were also studied.     

The LLSGIV stretch of the N-terminal region of HIV-1 gp41 is critical for binding to a model peptide,T20

A number of peptides and peptide analogs derived from the membrane proximal region of gp41 ectodomain are found to be effective inhibitors of human immunodeficiency virus type 1 (HIV-1)-mediated fusion events. One of them, T20 (aa 638-673), was found disordered and sparingly soluble in water, but became soluble upon mixing with selected, structured peptides from the amino terminal heptad repeat (HR1) region of gp41 using a simple and sensitive method of reduction in the scattering of T20 suspension. From the results on mapping the locus of interaction with T20 by employing partially overlapping peptides derived from HR1, it was concluded that the LLSGIV segment was a critical docking site for the C-terminal peptide of gp41 in its putative inhibitory action consistent with a previous fluorescence study. It was also found that peptides capable of solubilizing T20 dispersion have a high content of helix, as well as beta-strand, conformation in aqueous solution. Specificity of T20/HR1-derived peptide binding was ascertained by using a scrambled sequence of a T20-active peptide and a plateau in scattering reduction of T20 suspension with variation in the concentration of a T20-active HR1 peptide. Implications on the mechanism of T20 inhibition and the sequence of folding of the gp41 core structure are discussed.     

The use of Irradiated Allografts in Posterior Spinal Fusion for Healed Tubercular Kyphosis in Children

Post-tubercular spinal kyphosis in children is not only cosmetically unacceptable but functionally disabling as well, as with the progression of the deformity there is a very significant risk of late onset paraplegia. We present our preliminary results in a prospective study of 12 cases of healed post-tubercular kyphosis in children treated with isolated posterior spinal fusion using irradiated allografts and autogenous cancellous grafts.The study included 12 patients of healed post-tubercular kyphosis documented by clinical, radiological and haematological criteria, with >2 spine at risk signs radiologically. The mean age was 7 years. In situ posterior spinal fusion with irradiated allografts and autogenous cancellous bone graft without any instrumentation was done for all the patients. The total follow-up is 5 years (mean 2.8 years).Eight patients (66%) showed a correction of the kyphosis, 3 patients (25%) were static and only 1 patient showed worsening of the deformity. Eleven patients had sound fusion and 1 patient had good fusion but a pseudoarthrosis at the lower vertebral level.Good posterior fusion was achieved because of the judicious use of morcellised, irradiated cancellous allografts with autogenous cancellous grafts. The proposed mechanism of correction is selective anterior column growth vis-à-vis posterior fused mass leading to gradual self-correction and remodelling.Conclusion. In situ posterior spinal fusion with irradiated allografts is a simple, safe, easily reproducible, less morbid surgical procedure with good results which may alter the long term disability of the patients.     

Bioinorganic study on [Fe(promethazine)2H2O Cl]2+ complex

The coordination chemistry of iron (III) is the environment of an antihistaminic drug, promethazine has been explained to include a low spin, six-coordinate complex [Fe(Prometha)2(H2O) Cl] Cl2. Metaldrug interaction in vitro in aqueous KCl phase was studied polarographically at physiological pH and temperature. On the basis of elemental, magnetic, conductometric, IR, UV-visible, NMR spectroscopic analysis it is concluded that in solid phase two promethazine molecules with their N,N donor sites encompass the metal. Mass spectral study on the complex confirms that one of the three chlorides is involved in the coordination. The respective changes in the antihistaminic activity of the drug as a result of complexation has been determined and a possible mechanism is suggested.     

Development of potent glucagon antagonists: structure-activity relationship study of glycine at position 4.

We examined the functional role of glycine at position 4 in the potent glucagon antagonist [desHis(1), Glu(9)]glucagon amide, by substituting the L- and D-enantiomers of alanine and leucine for Gly(4) in this antagonist. The methyl and isobutyl side-chain substituents were introduced to evaluate the preference shown by the glucagon receptor, if any, for the orientation of the N-terminal residues. The L-amino acids demonstrated only slightly better receptor recognition than the D-enantiomers. These results suggest that the Gly(4) residue in glucagon antagonists may be exposed to the outside of the receptor. The enhanced binding affinities of analogs 1 and 3 compared with the parent antagonist, [desHis(1), Glu(9)]glucagon amide, may have resulted from the strengthened hydrophobic patch in the N-terminal region and/or the increased propensity for a helical conformation due to the replacement of alanine and leucine for glycine. Thus, as a result of the increased receptor binding affinities, antagonist activities of analogs 1-4 were increased 10-fold compared with the parent antagonist, [desHis(1), Glu(9)]glucagon amide. These potent glucagon antagonists have among the highest pA(2) values of any glucagon analogs reported to date.     

A Simple Method for the Purification of Organelle DNA of Plants

We report here a simple procedure for the purification of the organelle DNA. Mitochondrial DNA from Sorghum and the chloroplast DNA from Populus and spinach were purified using this protocol. The method utilizes a quick centrifugation of the isolated organelle DNA through a two step CsCl density gradient for removal of small molecular weight nucleic acids which pose a major problem for getting clean restriction patterns. This method of purification can be adopted with any isolation procedure for organelle DNA.