Department of Biochemistry: Recent submissions
Now showing items 101-120 of 237
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Entamoeba Shows Reversible Variation in Ploidy under Different Growth Conditions and between Life Cycle Phases
(WILEY-BLACKWELL, 2010-07)We have discovered four sirtuin genes in Entamoeba histolytica, two of which are similar to eukaryotic sirtuins and two to bacterial and archaeal sirtuins. The eukaryotic sirtuin homolog, EhSir2a showed NAD+ dependent ... -
Stabilization of the primary sigma factor of Staphylococcus aureus by core RNA polymerase
(KOREAN SOCIETY BIOCHEMISTRY & MOLECULAR BIOLOGY, 2010-03-31)The primary sigma factor (sigma(A)) of Staphylococcus aureus, a potential drug target, was little investigated at the structural level. Using an N-terminal histidine-tagged sigma(A) (His-sigma(A)), here we have demonstrated ... -
Physicochemical properties and distinct DNA binding capacity of the repressor of temperate Staphylococcus aureus phage phi 11
(WILEY-BLACKWELL PUB., 2009-04)The repressor protein and cognate operator DNA of any temperate Staphylococcus aureus phage have not been investigated in depth, despite having the potential to enrich the molecular biology of the staphylococcal system. ... -
Cavities in protein–DNA and protein–RNA interfaces
(OXFORD UNIV PRESS, 2009-08)An analysis of cavities present in protein-DNA and protein-RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient ... -
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display
(BIOMED CENTRAL, 2009-04-08)Background: Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which also determine how many other residues are found around them. The close packing of residues ... -
Structural and unfolding features of HlyT, a tetrameric LysR type transcription regulator of Vibrio cholerae
(ELSEVIER SCIENCE BV, 2009-08)HlyT from Vibrio cholerae is a positive regulator of Na+/H+ antiporter, important for the survival of the organism in an aquatic environment and within the human host. Here we report cloning, over-expression and purification ... -
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes
(SPRINGER, 2009-09)We report a simple algorithm to scan interfaces in protein-protein complexes for identifying binding 'hot spots'. The change in side-chain solvent accessible area (ΔASA) of interface residues has been related to change in ... -
Structure and Activity of Lysozyme on Binding to ZnO Nanoparticles
(AMER CHEMICAL SOC, 2010-03-02)The interaction between ZnO nanoparticles (NPs) and lysozyme has been studied using calorimetric as well as spectrophotometric techniques, and interpreted in terms of the three-dimensional structure. The circular ... -
Dissection, residue conservation, and structural classification of protein-DNA interfaces
(WILEY-LISS, 2009-02-15)The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in ... -
Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins
(BIOMED CENTRAL, 2009-12-28)Background: Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerable ... -
A novel galacto-glycerolipid from Oxalis corniculata kills Entamoeba histolytica and Giardia Iambiia
(AMER SOC MICROBIOLOGY, 2010-11)Oxalis corniculata is a naturally occurring weed that has been used in traditional medicine for the cure of dysentery and diarrhea in India. One of the common causes of dysentery is due to infection by the protist pathogen ... -
Studies on Escherichia coli HflKC suggest the presence of an unidentified lambda factor that influences the lysis-lysogeny switch
(BIOMED CENTRAL, 2011-02-17)Background: The lysis-lysogeny decision in the temperate coliphage γ is influenced by a number of phage proteins (CII and CIII) as well as host factors, viz. Escherichia coli HflB, HflKC and HflD. Prominent among these are ... -
Staphylococcus aureus ClpC Divergently Regulates Capsule via sae and codY in Strain Newman but Activates Capsule via codY in Strain UAMS-1 and in Strain Newman with Repaired saeS
(AMER SOC MICROBIOLOGY, 2011-02)ClpC is an ATPase chaperone found in most Gram-positive low-GC bacteria. It has been recently reported that ClpC affected virulence gene expression in Staphylococcus aureus. Here we report that ClpC regulates transcription ... -
Detection of the cell wall-affecting antibiotics at sublethal concentrations using a reporter Staphylococcus aureus harboring drp35 promoter-lacZ transcriptional fusion
(KOREAN SOCIETY BIOCHEMISTRY & MOLECULAR BIOLOGY, 2010-07-31)Previously, various inhibitors of cell wall synthesis induced the drp35 gene of Staphylococcus aureus efficiently. To determine whether drp35 could be exploited in antistaphylococcal drug discovery, we cloned the promoter ... -
The budding yeast protein Sum1 functions independently of its binding partners Hst1 and Sir2 histone deacetylases to regulate microtubule assembly
(WILEY-BLACKWELL, 2010-09)The budding yeast protein Sum1 is a transcription factor that associates with the histone deacetylase Hst1p or, in its absence, with Sir2p to form repressed chromatin. In this study, SUM1 has been identified as an ... -
Escherichia coli HflK and HflC can individually inhibit the HflB (FtsH)-mediated proteolysis of lambda CII in vitro
(ELSEVIER SCIENCE, 2010-09-15)lambda CII is the key protein that influences the lysis/lysogeny decision of by activating several phage promoters The effect of CII is modulated by a number of phage and host proteins including Escherichia colt HflK and ... -
A lethal cardiotoxic-cytotoxic protein from the Indian monocellate cobra (Naja kaouthia) venom
(PERGAMON-ELSEVIER SCIENCE LTD, 2010-09-15)A lethal cardiotoxic-cytotoxic protein (mol wt. 6.76 kDa) has been purified from the Indian monocellate cobra (Naja kaouthia) venom by ion-exchange chromatography and HPLC. CD spectra indicated the presence of 23% alpha ... -
The effect of zinc oxide nanoparticles on the structure of the periplasmic domain of the Vibrio cholerae ToxR protein
(WILEY-BLACKWELL, 2010-10)Proteins adsorbed on nanoparticles (NPs) are being used as biosensors and in drug delivery. However, our understanding of the effect of NPs on the structure of proteins is still in a nascent state. In this work we report ... -
Regions and Residues of an Asymmetric Operator DNA Interacting with the Monomeric Repressor of Temperate Mycobacteriophage L1
(AMER CHEMICAL SOC, 2010-05-18)Previously, the repressor protein of mycobacteriophage L1 bound to two operator DNAs with dissimilar affinity. Surprisingly, the putative operator consensus sequence, 5'GGTGGa/cTGTCAAG, lacks the dyad symmetry reported for ... -
Characterization of an unusual cold shock protein from Staphylococcus aureus
(WILEY-V C H VERLAG GMBH, 2010-12)Of the three cold shock proteins expressed by Staphylococcus aureus, CspC is induced poorly by cold but strongly by various antibiotics and toxic chemicals. Using a purified CspC, here we demonstrate that it exists as a ...