On the regulation of L-hydroxyproline dissimilatory pathway inPseudomonas aeruginosa PAO

The enzymes involved in the regulation of L-hydroxyproline degradation inPseudomonas aeruginosa PAO were investigated. L-hydroxyproline when present in the growth medium induces all the four enzymes in the pathway. Growth of the cells in L-proline also weakly induced the enzymes. The organism failed to utilize D-allo-hydroxyproline due to permeability factors. Mutants blocked in the oxidative pathway of L-hydroxyproline were isolated and enzymatically characterized. In all the mutants lacking any one of enzymes of the metabolic pathway, L-hydroxyproline is still active in inducing the remaining enzymes of the pathway suggesting that L-hydroxyproline has intrinsic inducer activity.     

Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property

More than 100 years of research on Alzheimer’s disease didn’t yield a potential cure for this dreadful disease. Poor Blood Brain Barrier (BBB) permeability and P-glycoprotein binding of BACE1 inhibitors are the major causes for the failure of these molecules during clinical trials. The design of BACE1 inhibitors with a balance of sufficient affinity to the binding site and little or no interaction with P-glycoproteins is indispensable. Identification and understanding of protein–ligand interactions are essential for ligand optimization process. Structure-based drug design (SBDD) efforts led to a steady accumulation of BACE1-ligand crystal complexes in the PDB. This study focuses on analyses of 153 BACE1-ligand complexes for the direct contacts (hydrogen bonds and weak interactions) observed between protein and ligand and indirect contacts (water-mediated hydrogen bonds), observed in BACE1-ligand complex crystal structures. Intraligand hydrogen bonds were analyzed, with focus on ligand P-glycoprotein efflux. The interactions are dissected specific to subsites in the active site and discussed. The observed protein-ligand and intraligand interactions were used to develop the linear discriminant model for the identification of BACE1 inhibitors with less or no P-glycoprotein binding property. Excellent statistical results and model’s ability to correctly predict a new data-set with an accuracy of 92% is achieved. The results are retrospectively analyzed to give input for the design of potential BACE1 inhibitors.     

Cholesterol Conjugated Uniform and Gapmer Phosphorothioate Oligonucleotides Targeted Against PKC-α and C-raf Gene Expression

Abstract

In vitra and in vivo antitumor activity of phosphorothioate antisense oligonucleotides targeted against two protein kinases within the mitogen-activated protein (MAP) kinase signaling cascade has been well documented by ISIS 3521/CGP 6412XA (targeted against PKC-α protein) and ISIS 5132KGP69846A (targeted against C-rwfl kinase). For both of these compounds, cationic lipid formulations are necessary to observe any pharmacological activity in cell culture. In contrast, in vivo functional delivery of phosphorothioate oligonucleotides to cells in tissues does not appear to be a prohlem. These oligonucleotides have demonstrated reduction in either PKC-α or C-raf gene expression in tissues or human tumor xenografts following systemic administration.     

Mapping of the locus involved in the catabolic oxidation of D-amino acids in Pseudomonas aeruginosa PAO.

Summary Mutants of Pseudomonas aeruginosa PAO deficient in their utilization of DL-valine have been found to have lost their capacity to utilize DL-alanine and L-proline. Use of conjugal and transductional mediated gene transfers have established the chromosomal location of this gene and also its pleotropic function in the induction of the D-amino acid oxidase, involved in the oxidative utilization of DL-valine, DL-alanine and L-proline. These point mutations are clustered in a single locus designated as Val D and mapped around the 19th minute on the chromosome.     

ECMIS: computational approach for the identification of hotspots at protein-protein interfaces

Background

Various methods have been developed to computationally predict hotspot residues at novel protein-protein interfaces. However, there are various challenges in obtaining accurate prediction. We have developed a novel method which uses different aspects of protein structure and sequence space at residue level to highlight interface residues crucial for the protein-protein complex formation.

Results

ECMIS (Energetic Conservation Mass Index and Spatial Clustering) algorithm was able to outperform existing hotspot identification methods. It was able to achieve around 80% accuracy with incredible increase in sensitivity and outperforms other existing methods. This method is even sensitive towards the hotspot residues contributing only small-scale hydrophobic interactions.

Conclusion

Combination of diverse features of the protein viz. energy contribution, extent of conservation, location and surrounding environment, along with optimized weightage for each feature, was the key for the success of the algorithm. The academic version of the algorithm is available at http://caps.ncbs.res.in/download/ECMIS/ECMIS.zip.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-303) contains supplementary material, which is available to authorized users.     

PEG-induced fusion of phosphatidylcholine-liposomes with protoplasts and post-fusion evaluation of plating efficiency and enrichment in plasmamembrane phosphatidylcholine of protoplasts in Datura innoxia Mill

Liposomes entrapping fluorescein diacetate were fused with protoplasts of Datura innoxia Mill by employing polyethylene glycol (PEG) as the fusogen. Factors that influence liposome-protoplast fusion were optimized as a function of PEG-concentration and incubation duration, liposome composition and surface charge and liposome:protoplast ratio. Phosphatidylcholine-liposomes were found ideal for the objectives of the study. Fusion index based on per cent fluorescing protoplasts varied among the protoplast types. PEG-incubation duration in the fusion assay and growth ability of protoplasts to form microcalli subsequent to liposome-protoplast fusion was determined based on protoplast plating-efficiency. Plating efficiency of post-fusion protoplasts increased due to incorporation of liposome-phosphatidylcholine in the plasmamembrane of protoplasts. Results are discussed in relation to the application of liposome-protoplast fusion system in selective modification of plasmamembrane phospholipids of protoplasts.