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The database PALI (Phylogeny and ALIgnment of homologous protein structures) consists of families of protein domains of known three-dimensional (3D) structure. In a PALI family, every member has been structurally aligned with every other member (pairwise) and also simultaneous superposition (multiple) of all the members has been performed. The database also(More)
The GAFa domain of the cGMP-binding, cGMP-specific phosphodiesterase (PDE5A) was modeled on the crystal structure of PDE2A GAF domain and residues involved in cGMP binding identified. Tandem GAFa and GAFb domains of PDE5A, expressed in Escherichia coli, bound cGMP (K(d) 27 nM). Mutation of aspartate-299 in GAFa, suggested earlier to be critical for cGMP(More)
Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities(More)
Occurrence and accommodation of charged amino acid residues in proteins that are structurally equivalent to buried non-polar residues in homologues have been investigated. Using a dataset of 1,852 homologous pairs of crystal structures of proteins available at 2A or better resolution, 14,024 examples of apolar residues in the structurally conserved regions(More)
During the last three decades, a number of B-lymphocyte specific surface antigens have been defined some of which may also show activation/differentiation specific expression. Here, we review the various signaling events and the receptor-ligand interactions for B-cell development, activation and differentiation. Our discussion and presentation include(More)
Malaria is most prevalent in tropical climate and causes 1–3 million deaths annually. RIO-2 kinase, an atypical kinase regulates ribosome biogenesis and is necessary for cell cycle progression. Structural characterization of PFD0975w (PfRIO-2 kinase) indicates N-terminal DNA binding winged helix domain (1–84), a linker region (85–147), and C-terminal kinase(More)
An exceptional probe comprising indole-3-carboxaldehyde fluorescein hydrazone (FI) performs multiple tasks, namely, disaggregating amyloid β (Aβ) aggregates in different biomarker environments such as cerebrospinal fluid (CSF), Aβ1-40 fibrils, β-amyloid lysozyme aggregates (LA), and U87 MG human astrocyte cells. Additionally, the probe FI binds with Cu(2+)(More)
Toxic byproducts from infected RBC cause rheological alteration and RBC aggregation. Malaria culture supernatant has the ability to exhibit RBC aggregation. Ammonium sulfate fractionation and immunodepletion of methemoglobin from culture supernatant confirms methemoglobin as a major aggregant. In vitro treatment of RBC with methemoglobin induces(More)
BACKGROUND Primaquine (Pq) metabolic products are responsible for drug-associated hemotoxicity and limit primaquine usage. METHODS Methemoglobin (MetHb)-Pq molecular modeling was used to identify the Pq binding pocket. UPLC, mass spectrometry, and other indirect analytical methods were used to predict the metabolite. MetHb generation, development of(More)
Availability of the human genome data has enabled the exploration of a huge amount of biological information encoded in it. There are extensive ongoing experimental efforts to understand the biological functions of the gene products encoded in the human genome. However, computational analysis can aid immensely in the interpretation of biological function by(More)