Biomedical subjects

Sharmila Anishetty

Publications and source records attributed to Sharmila Anishetty.

8 recordsLinked to original sources

PubMed2007

Independent origin of 185delAG BRCA1 mutation in an Indian family.

BRCA1 and BRCA2 are the two major breast cancer susceptibility genes. We tested members of a family with multiple cases of breast cancer, for mutations in the BRCA1 gene. Analysis of the PCR amplicons of all the exons (22) of the BRCA1 gene using conformation sensitive gel electrophoresis (CSGE) revealed a heteroduplex band pattern in exon 2 of the proband (III-3) in this family. The amplicon was further sequenced to assess the nature of the mutation, which revealed a deletion of AG nucleotides at the 185th position (185delAG). The two base pair deletion introduces a stop codon at the 39th amino acid residue. A similar analysis was carried out on other extended family members to evaluate their allelic status. We detected the same deletion in 7 of the 19 members tested. Two of them are males. Haplotype analysis suggested an independent origin for this mutation. Our study highlights the importance of testing hereditary cases of breast/ovarian cancer for BRCA1 mutations in extended families in order to identify high-risk individuals at a pre-clinical stage and provide genetic counseling.

BRCA1 Protein↗

PubMed2006

In silico identification of putative metal binding motifs.

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. In this study, we have performed an in silico analysis of metal binding proteins and have identified putative metal binding motifs for the ions of cadmium, cobalt, zinc, arsenic, mercury, magnesium, manganese, molybdenum and nickel. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high-specificity of the motifs. Motifs were also validated against PDB structures and site directed mutagenesis studies.

Amino Acid Motifs↗

PubMed2006

Understanding mutations and protein stability through tripeptides.

A novel methodology to predict the local conformational changes in a protein as a consequence of missense mutations is proposed. A pentapeptide at the locus of mutation plays the dominant role and it is analyzed in terms of tripeptides. A measure for spatial and temporal fluctuations in a pentapeptide is devised and validated. The method does not involve any prior knowledge of structural templates from sequence homology studies. Structural deformations can be predicted with about 70-80% reliability in any protein. Disease causing mutations and benign mutations have been addressed. In particular, p53, retinoblastoma protein and lipoprotein lipase are studied in detail.

Amino Acid Motifs↗

PubMed2005

Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis.

The emergence of multidrug resistant varieties of Mycobacterium tuberculosis has led to a search for novel drug targets. We have performed an insilico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen M. tuberculosis. Enzymes from the biochemical pathways of M. tuberculosis from the KEGG metabolic pathway database were compared with proteins from the host H. sapiens, by performing a BLASTp search against the non-redundant database restricted to the H. sapiens subset. The e-value threshold cutoff was set to 0.005. Enzymes, which do not show similarity to any of the host proteins, below this threshold, were filtered out as potential drug targets. We have identified six pathways unique to the pathogen M. tuberculosis when compared to the host H. sapiens. Potential drug targets from these pathways could be useful for the discovery of broad spectrum drugs. Potential drug targets were also identified from pathways related to lipid metabolism, carbohydrate metabolism, amino acid metabolism, energy metabolism, vitamin and cofactor biosynthetic pathways and nucleotide metabolism. Of the 185 distinct targets identified from these pathways, many are in various stages of progress at the TB Structural Genomics Consortium. However, 67 of our targets are new and can be considered for rational drug design. As a case study, we have built a homology model of one of the potential drug targets MurD ligase using WHAT IF software. The model could be further explored for insilico docking studies with suitable inhibitors. The study was successful in listing out potential drug targets from the M. tuberculosis proteome involved in vital aspects of the pathogen's metabolism, persistence, virulence and cell wall biosynthesis. This systematic evaluation of metabolic pathways of host and pathogen through reliable and conventional bioinformatic methods can be extended to other pathogens of clinical interest.

Amino Acid Sequence↗

PubMed2005

Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations.

Pseudomonas aeruginosa lipase is a 29-kDa protein that, following the determination of its crystal structure, was postulated to have a lid that stretched between residues 125 and 148. In this paper, using molecular dynamics simulations, we propose that there exists, in addition to the above-mentioned lid, a novel second lid in this lipase. We further show that the second lid, covering residues 210-222, acts as a triggering lid for the movement of the first. We also investigate the role of hydrophobicity in the movement of the lids and show that two residues, Phe214 and Ala217, play important roles in lid movement. To our knowledge, this is the first time that a double-lid movement of the type described in our manuscript has been presented to the scientific community. This work also elucidates the interplay of hydrophobic interactions in the dynamics, and hence the function, of an enzyme.

Computer Simulation↗

PubMed2004

Functionally specified protein signatures distinctive for each of the different blue copper proteins.

BACKGROUND: Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance of using patterns or signatures to retrieve out related sequences. Blue copper proteins are found in the electron transport chain of prokaryotes and eukaryotes. The signatures already existing in the databases like the type 1 copper blue, multiple copper oxidase, cyt b/b6, photosystem 1 psaA&B, psaG&K, and reiske iron sulphur protein are not specified signatures for blue copper proteins as the name itself suggests. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. This work describes the signatures designed based on the copper metal binding motifs in blue copper proteins. The common feature in all blue copper proteins is a trigonal planar arrangement of two nitrogen ligands [each from histidine] and one sulphur containing thiolate ligand [from cysteine], with strong interactions between the copper center and these ligands. RESULTS: Sequences that share such conserved motifs are crucial to the structure or function of the protein and this could provide a signature of family membership. The blue copper proteins chosen for the study were plantacyanin, plastocyanin, cucumber basic protein, stellacyanin, dicyanin, umecyanin, uclacyanin, cusacyanin, rusticyanin, sulfocyanin, halocyanin, azurin, pseudoazurin, amicyanin and nitrite reductase which were identified in both eukaryotes and prokaryotes. ClustalW analysis of the protein sequences of each of the blue copper proteins was the basis for designing protein signatures or peptides. The protein signatures and peptides identified in this study were designed involving the active site region involving the amino acids bound to the copper atom. It was highly specific for each kind of blue copper protein and the false picks were minimized. The set of signatures designed specifically for the BCP's was entirely different from the existing broad spectrum signatures as mentioned in the background section. CONCLUSIONS: These signatures can be very useful for the annotation of uncharacterized proteins and highly specific to retrieve blue copper protein sequences of interest from the non redundant databases containing a large deposition of protein sequences.

Amino Acid Sequence↗

PubMed2004

Mutation analysis of congenital cataracts in Indian families: identification of SNPS and a new causative allele in CRYBB2 gene.

PURPOSE: To study some functional candidate genes in cataract families of Indian descent. METHODS: Nine Indian families, clinically documented to have congenital/childhood cataracts, were screened for mutations in candidate genes such as CRYG (A-->D), CRYBB2, and GJA8 by PCR analyses and sequencing. Genomic DNA samples of either probands or any representative affected member of each family were PCR amplified and sequenced commercially. Documentation of single nucleotide polymorphisms (SNPs) and candidate mutations was done through BLAST SEARCH (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?). RESULTS: Several single nucleotide polymorphisms in CRYG, CRYBB2, and GJA8 genes were observed. Because they do not co-segregate with the phenotype, they were excluded as candidates for the cataract formation in these patients. However, a substitution (W151C in exon 6 of CRYBB2) was identified as the most likely causative mutation underlying the phenotype of central nuclear cataract in all affected members of family C176. Protein structural interpretations demonstrated that no major structural alterations could be predicted and that even the hydrogen bonds to the neighboring Leu166 were unchanged. Surprisingly, hydropathy analysis of the mutant betaB2-crystallin featuring the amino acids at position 147 to 155, further increased the hydrophobicity, which might impair the solubility of the mutant protein. Finally, the Cys residue at position 151 might possibly be involved in intramolecular disulphide bridges with other cysteines during translation, possibly leading to dramatic structural changes. CONCLUSIONS: Exon 6 of CRYBB2 appears to be a critical region susceptible for mutations leading to lens opacity.

Adolescent↗

PubMed2002

Tripeptide analysis of protein structures.

BACKGROUND: An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (<or= 2.0 degrees A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures. RESULTS: Tripeptides have been classified into three categories: rigid, non-rigid and intermediate, based on the relative structural rigidity between Calpha and Cbeta atoms in a tripeptide. We found that 18% of the tripeptides in the dataset can be classified as rigid, 4% as non-rigid and 78% as intermediate. Many rigid tripeptides are made of hydrophobic residues, however, there are tripeptides with polar side chains forming rigid structures. The bulk of the tripeptides fall in the intermediate class while very small numbers actually fall in the non-rigid class. Structurally all rigid tripeptides essentially form two structural classes while the intermediate and non-rigid tripeptides fall into one structural class. This notion of rigidity and non-rigidity is designed to capture side chain interactions but not secondary structures. CONCLUSIONS: Rigid tripeptides have no correlation with the secondary structures in proteins and hence this work is complementary to such studies. Tripeptide data may be used to predict plausible structures for oligopeptides and for denovo protein design.

Molecular Structure↗