Biomedical subjects

Anurag Sethi

Publications and source records attributed to Anurag Sethi.

3 recordsLinked to original sources

PubMed2005

The evolutionary history of Cys-tRNACys formation.

The recent discovery of an alternate pathway for indirectly charging tRNA(Cys) has stimulated a re-examination of the evolutionary history of Cys-tRNA(Cys) formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA(Cys) with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA(Cys) aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.

Amino Acid Sequence↗

PubMed2005

Evolutionary profiles from the QR factorization of multiple sequence alignments.

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS.

Algorithms↗

PubMed2002

Purification and characterization of a short insect toxin from the venom of the scorpion Buthus tamulus.

A short chain peptide has been isolated from the venom of a red scorpion of Indian origin, Buthus tamulus. This peptide was purified using ion exchange and reverse phase chromatography and was characterized by molecular weight determination and amino acid sequence. The primary structure analysis shows that BtITx3 is a short peptide of 35 amino acid residues having a molecular weight of 3796 Da. The toxin shows toxicity towards the Lepidopteran species of insect Helicoverpa armigera causing flaccid paralysis and even death within 24 h. It shows more than 50% homology with the short insectotoxins having four disulfide bridges, which suggests that the toxin belongs to the class of short chain toxins blocking the chloride ion channels. This sequence homology study has also helped to bring out the structure-function relationship between the various short toxins. Homology modeling done by using template structure of a known toxin indicated that this toxin consists of a similar alpha/beta scaffold, as present in other scorpion toxins.

Amino Acid Sequence↗