Sonu Kumar

The G protein-coupled receptors in the pufferfish Takifugu rubripes

BackgroundGuanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as “molecular switches” in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and their role in several physiological functions, being active players in detecting the presence of light, a variety of smells and tastes, amino acids, nucleotides, lipids, chemicals etc. in the environment of the cell. Comparative genomic studies on model organisms provide information on target receptors in humans and their function. The Japanese teleost Fugu has been identified as one of the smallest vertebrate genomes and a compact model to study the human genome, owing to the great similarity in its gene repertoire with that of human and other vertebrates. Thus the characterization of the GPCRs of Fugu would provide insights to the evolution of the vertebrate genome.ResultsWe classified the GPCRs in the Fugu genome and our analysis of its 316 membrane-bound receptors, available on the public databases as well as from literature, detected 298 GPCRs that were grouped into five main families according to the GRAFS classification system (namely, Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin). We also identified 18 other GPCRs that could not be grouped under the GRAFS family and hence were classified as ‘Other 7TM’ receptors. On comparison of the GPCR information from the Fugu genome with those in the human and chicken genomes, we detected 96.83% (306/316) and 96.51% (305/316) orthology in GPCRs among the Fugu-human genomes and Fugu-chicken genomes, respectively.ConclusionsThis study reveals the position of pisces in vertebrate evolution from the GPCR perspective. Fugu can act as a reference model for the human genome for other protein families as well, going by the high orthology observed for GPCRs between Fugu and human. The evolutionary comparison of GPCR sequences between key vertebrate classes of mammals, birds and fish will help in identifying key functional residues and motifs so as to fill in the blanks in the evolution of GPCRs in vertebrates.

ZiF-Predict: A Web Tool for Predicting DNA-Binding Specificity in C2H2 Zinc Finger Proteins

Engineering zinc finger protein motifs for specific DNA targets in genomes is critical in the field of genome engineering. We have developed a computational method for predicting recognition helices for C2H2 zinc fingers that bind to specific target DNA sites. This prediction is based on artificial neural network using an exhaustive dataset of zinc finger proteins and their target DNA triplets. Users can select the option for two or three zinc fingers to be predicted either in a modular or synergistic fashion for the input DNA sequence. This method would be valuable for researchers interested in designing specific zinc finger transcription factors and zinc finger nucleases for several biological and biomedical applications. The web tool ZiF-Predict is available online at http://web.iitd.ac.in/~sundar/zifpredict/.

Controlling aggregation propensity in A53T mutant of alpha-synuclein causing Parkinson’s disease

Understanding alpha-synuclein in terms of fibrillization, aggregation, solubility and stability is fundamental in Parkinsons disease (PD). The three familial mutations, namely, A30P, E46K and A53T cause PD because the hydrophobic regions in alpha-synuclein acquire beta-sheet configuration, and have a propensity to fibrillize and form amyloids that cause cytotoxicity and neurodegeneration. On simulating the native form and mutants (A30P, E46K and A53T) of alpha-synuclein in water solvent, clear deviations are observed in comparison to the all-helical 1XQ8 PDB structure. We have identified two crucial residues, (40)Val and (74)Val, which play key roles in beta-sheet aggregation in the hydrophobic regions 36-41 and 68-78, respectively, leading to fibrillization and amyloidosis in familial (A53T) PD. We have also identified V40D_V74D, a double mutant of A53T (the most amyloidogenic mutant). The simultaneous introduction of these two mutations in A53T nearly ends its aggregation propensity, increases its solubility and positively enhances its thermodynamic stability.