Tej P Singh - Academia.edu (original) (raw)
Papers by Tej P Singh
Biochemistry and Biophysics Reports, 2015
The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to inte... more The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10 À 4 M-10 À 7 M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.
Analytica Chimica Acta, 1961
PAN(1-(2-pyridylazo)-2-naphthol) is proposed for the solvent extraction ; and spectrophotometric ... more PAN(1-(2-pyridylazo)-2-naphthol) is proposed for the solvent extraction ; and spectrophotometric determination of manganese, iron, cadmium, mercury, ; gallium, and yttrium. The reagent, which is highly specific for iron, is applied ; to the determination of iron in clay and anorthosite, the separation of yttrium ; from lanthanun, and the separation of manganese from nickel. (auth);
Zeitschrift für Kristallographie - New Crystal Structures, 2002
C42H59N5O8, monoclinic, P\2\ 1 (No. 4), a = 11.324(2) Â, b= 15.558(9)k,c= 13.010(2)Â,/?= 106.15(2... more C42H59N5O8, monoclinic, P\2\ 1 (No. 4), a = 11.324(2) Â, b= 15.558(9)k,c= 13.010(2)Â,/?= 106.15(2)°, V=2201.7 Â 3 , Ζ = 2, RgtíF) = 0.072, wRretfF 2) = 0.190, T= 293 K. Source of material The title peptide has been synthesised using the mixed anhydride coupling and the azalactone method according to [1] and [2], respectively. The peptide was crystallised from its solution in acetone-water mixture (4:1) by slow evaporation method.
Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, Jan 16, 2017
Hyperbilirubinemia and hypoalbuminemia are features of hepatic dysfunction that associate with di... more Hyperbilirubinemia and hypoalbuminemia are features of hepatic dysfunction that associate with disease severity. This is because hepatic insufficiency causes hypoalbuminemia, which indirectly increases the circulating levels of free bilirubin. Circular dichroism (CD) spectroscopy can be used to quantify the molecular ellipticity (ME) of the albumin-bilirubin complex, and might associate with the severity or outcome of severe alcoholic hepatitis (SAH). We performed a cross-sectional study of 265 patients with SAH admitted in the Department of Hepatology, Institute of Liver and Biliary Sciences in New Delhi, India from January 2014 through January 2016. Blood samples were collected and patients were followed for 12 months or death. The molar ratios of bilirubin: albumin and albumin-bilirubin complexes were determined for a discovery cohort (30 patients who survived the study period and 60 patients who did not survive) and compared with those of 60 patients with alcoholic cirrhosis and...
Indian journal of biochemistry & biophysics
For the first time, it is demonstrated that exposure of an enzyme to anhydrous organic solvents a... more For the first time, it is demonstrated that exposure of an enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes, namely, proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin were exposed to acetonitrile at 70 degrees C for three hr. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, proteinase K was analyzed in detail using X-ray diffraction method. The overall structure of the enzyme was found to be similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad remained intact after the treatment. However, the water structure in the substrate binding site underwent some rearrangement as some of the water molecules were either displaced or completely absent. The most striking observation conce...
International journal of biochemistry and molecular biology, Jan 13, 2013
Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include mye... more Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The LPO is found in exocrine secretions including milk. It is responsible for the inactivation of a wide range of micro-organisms and hence, is an important component of defense mechanism in the body. With the help of hydrogen peroxide, it catalyzes the oxidation of halides, pseudohalides and organic aromatic molecules. Historically, LPO was isolated in 1943, nearly seventy years ago but its three-dimensional crystal structure has been elucidated only recently. This review provides various details of this protein from its discovery to understanding its structure, function and applications. In order to highlight species dependent variations in the structure and function of LPO, a detailed comparison of sequence, structure and function of LPO from various species have been made. The structural basis of ligand bin...
Journal of Molecular Modeling, 2011
Articles-Sorted by Date 1. Nucl Med Commun. 2012 Jun 10. [Epub ahead of print] 18F-FDG PET-CT for... more Articles-Sorted by Date 1. Nucl Med Commun. 2012 Jun 10. [Epub ahead of print] 18F-FDG PET-CT for detecting recurrent gastric adenocarcinoma: results from a Non-Oriental Asian population.
Journal of Biological Chemistry, 2011
Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated... more Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to...
Clinica Chimica Acta, 2009
Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14 ... more Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14 th century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.
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](Acta Crystallographica Section E Structure Reports Online, 2005
The title compound, [Pb 2 O 2 (C 6 H 4 N 3) 2 ] n , exhibits anti-corrosion properties. The coord... more The title compound, [Pb 2 O 2 (C 6 H 4 N 3) 2 ] n , exhibits anti-corrosion properties. The coordination around each Pb atom is different, with coordination numbers of four and five. The compound forms a polymeric chain with pairs of oxo bridges between metal centers.
Phosphorus, Sulfur, and Silicon and the Related Elements, 1993
An increasing investigation of organotin(IV) complexes has focused on acquiring well-defined soli... more An increasing investigation of organotin(IV) complexes has focused on acquiring well-defined solid-state structures in order to learn about the nature of their versatile coordination chemistry, wide industrial applications and biological activities, 1 especially those of organotin(IV) derivatives from heterocyclic thionates containing a nitrogen atom (or more) and an adjacent, exocyclic thioketo group. 2 A characteristic feature of these complexes in the solid state is that the ligands chelate the tin atom through S and N atoms. In our previous work, we studied the coordination chemistry of four ligands of such type: 2-mercaptonicotinic acid, 1-(4-hydroxyphenyl)-1H-tetrazole-5-thiol, and 2,5-dimercapto-1,3,4-thiodiazole, which possess one or two deprotonated heterocyclic thioamide groups (N-C-S)-3. In this paper we report on the synthesis and crystal structure of a x69
Acta crystallographica, Apr 1, 2007
Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized b... more Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P4 3 2 1 2, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V M value of 2.5 Å 3 Da À1. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution.
Protein Engineering, Design and Selection, 2001
Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range o... more Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range of applications including enzyme stability and enhancement of its catalytic activity. Despite all this, the enzyme behaviour in this process still remains unknown. A serine proteinase, proteinase K, was subjected to three-phase partitioning (TPP). A 3 ml volume of proteinase K solution (3 mg/ml in 0.05 M acetate buffer, pH 6.0) was brought to 30% (w/v) ammonium sulphate saturation by addition of saturated ammonium sulphate. tert-Butanol (6 ml) was added to this solution and the mixture was incubated at 25°C for 1 h. The precipitated protein in the mid-layer was dissolved in 3 ml of 0.05 M acetate buffer, pH 6.0. The specific activity of the processed enzyme was estimated and was found to be 210% of the original enzyme activity. In order to understand the basis of this remarkable enhancement of the enzyme activity, the structure of the TPP-treated enzyme was determined by X-ray diffraction at 1.5 Å resolution. The overall structure of the TPPtreated enzyme is similar to the original structure in an aqueous environment. The hydrogen bonding system of the catalytic triad is intact. However, the water structure in the substrate binding site has undergone a rearrangement as some of the water molecules are either displaced or completely absent. Two acetate ions were identified in the structure. One is located in the active site and seems to mimic the role of water in the enzyme activity and stability. The other is located at the surface of the molecule and is involved in stabilizing the local structure of the enzyme. The most striking observation in respect of the present structure pertains to a relatively higher overall temperature factor (B ⍧ 19.7 Å 2) than the value of 9.3 Å 2 in the original enzyme. As a result of a higher B-factor, a number of residues, particularly their side chains, were found to adopt more than one conformation. It appears that the protein exists in an excited state which might be helping the enzyme to function more rapidly than the original enzyme in aqueous media. Summarily, the basis of increased enzymatic activity could be attributed to (i) the presence of an acetate ion at the active site and (ii) its excited state as reflected by an overall higher B-factor.
PLOS ONE, 2015
Cellular methylamines are osmolytes (low molecular weight organic compounds) believed to offset t... more Cellular methylamines are osmolytes (low molecular weight organic compounds) believed to offset the urea's harmful effects on the stability and function of proteins in mammalian kidney and marine invertebrates. Although urea and methylamines are found at 2:1 molar ratio in tissues, their opposing effects on protein structure and function have been questioned on several grounds including failure to counteraction or partial counteraction. Here we investigated the possible involvement of cellular salt, NaCl, in urea-methylamine counteraction on protein stability and function. We found that NaCl mediates methylamine counteracting system from no or partial counteraction to complete counteraction of urea's effect on protein stability and function. These conclusions were drawn from the systematic thermodynamic stability and functional activity measurements of lysozyme and RNase-A. Our results revealed that salts might be involved in protein interaction with charged osmolytes and hence in the urea-methylamine counteraction.
Frontiers in genetics, 2018
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune disea... more Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis u...
Indian Journal of Chemistry Sect B Organic Chemistry Including Medical Chemistry, 2004
Distal effect on mass spectral fragmentations of glycolamide esters of 6-methoxy-2-naphthylacetic... more Distal effect on mass spectral fragmentations of glycolamide esters of 6-methoxy-2-naphthylacetic acid (6-MNA) and the crystal structure of N,N /-dimethylglycolamide ester of 6-MNA
PLOS ONE, 2015
An increasing number of cancer patients worldwide, especially in third world countries, have rais... more An increasing number of cancer patients worldwide, especially in third world countries, have raised concern to explore natural drug resources, such as the less explored fresh water filamentous cyanobacteria. Six strains of cyanobacteria (Phormidium sp. CCC727, Geitlerinema sp. CCC728, Arthrospira sp. CCC729, Phormidium sp. CCC731, Phormidium sp. CCC730, and Leptolyngbya sp. CCC732) were isolated (paddy fields and ponds in the Banaras Hindu University, campus) and five strains screened for anticancer potential using human colon adenocarcinoma (HT29) and human kidney adenocarcinoma (A498) cancer cell lines. Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 were the most potent as determined by examination of morphological features and by inhibition of growth by graded concentrations of crude extracts and thin-layer chromatography (TLC) eluates. Cell cycle analysis and multiplex assays using cancer biomarkers also confirmed Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 as cancer drug resources. Apoptotic studies in the cells of A498 (cancer) and MCF-10A (normal human epithelial) exposed to crude extracts and TLC fractions revealed no significant impact on MCF-10A cells emphasizing its importance in the development of anticancer drug. Identification of biomolecules from these extracts are in progress.
Enzyme Research, 2013
Acinetobacter baumanniiis a multidrug resistant pathogenic bacteria associated with hospital acqu... more Acinetobacter baumanniiis a multidrug resistant pathogenic bacteria associated with hospital acquired infections. This bacterium possesses a variety of resistance mechanisms which makes it more difficult to control the bacterium with conventional drugs, and, so far no effective drug treatment is available against it. Nucleoside diphosphate kinase is an important enzyme, which maintains the total nucleotide triphosphate pool inside the cell by the transfer ofγ-phosphate from NTPs to NDPs. The role of nucleoside diphosphate kinase (Ndk) has also been observed in pathogenesis in other organisms. However, intensive studies are needed to decipher its other putative roles inAcinetobacter baumannii. In the present study, we have successfully cloned the gene encoding Ndk and achieved overexpression in bacterial host BL-21 (DE3). The overexpressed protein is further purified by nickel-nitrilotriacetic acid (Ni-NTA) chromatography.
Protein Science, 2005
This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A 2 (PLA 2)... more This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A 2 (PLA 2) and also to a PLA 2 with Asp 49. The fatty acid identified as n-tridecanoic acid is observed at the substrate recognition site of PLA 2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA 2 was determined using the cDNA method. Three-dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 Å. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n-tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium-binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n-tridecanoic acid was clearly fitted. The MALDI-TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA 2 by 212 Da over the native PLA 2. A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA 2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium-binding loop.
Biochemistry and Biophysics Reports, 2015
The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to inte... more The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10 À 4 M-10 À 7 M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.
Analytica Chimica Acta, 1961
PAN(1-(2-pyridylazo)-2-naphthol) is proposed for the solvent extraction ; and spectrophotometric ... more PAN(1-(2-pyridylazo)-2-naphthol) is proposed for the solvent extraction ; and spectrophotometric determination of manganese, iron, cadmium, mercury, ; gallium, and yttrium. The reagent, which is highly specific for iron, is applied ; to the determination of iron in clay and anorthosite, the separation of yttrium ; from lanthanun, and the separation of manganese from nickel. (auth);
Zeitschrift für Kristallographie - New Crystal Structures, 2002
C42H59N5O8, monoclinic, P\2\ 1 (No. 4), a = 11.324(2) Â, b= 15.558(9)k,c= 13.010(2)Â,/?= 106.15(2... more C42H59N5O8, monoclinic, P\2\ 1 (No. 4), a = 11.324(2) Â, b= 15.558(9)k,c= 13.010(2)Â,/?= 106.15(2)°, V=2201.7 Â 3 , Ζ = 2, RgtíF) = 0.072, wRretfF 2) = 0.190, T= 293 K. Source of material The title peptide has been synthesised using the mixed anhydride coupling and the azalactone method according to [1] and [2], respectively. The peptide was crystallised from its solution in acetone-water mixture (4:1) by slow evaporation method.
Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, Jan 16, 2017
Hyperbilirubinemia and hypoalbuminemia are features of hepatic dysfunction that associate with di... more Hyperbilirubinemia and hypoalbuminemia are features of hepatic dysfunction that associate with disease severity. This is because hepatic insufficiency causes hypoalbuminemia, which indirectly increases the circulating levels of free bilirubin. Circular dichroism (CD) spectroscopy can be used to quantify the molecular ellipticity (ME) of the albumin-bilirubin complex, and might associate with the severity or outcome of severe alcoholic hepatitis (SAH). We performed a cross-sectional study of 265 patients with SAH admitted in the Department of Hepatology, Institute of Liver and Biliary Sciences in New Delhi, India from January 2014 through January 2016. Blood samples were collected and patients were followed for 12 months or death. The molar ratios of bilirubin: albumin and albumin-bilirubin complexes were determined for a discovery cohort (30 patients who survived the study period and 60 patients who did not survive) and compared with those of 60 patients with alcoholic cirrhosis and...
Indian journal of biochemistry & biophysics
For the first time, it is demonstrated that exposure of an enzyme to anhydrous organic solvents a... more For the first time, it is demonstrated that exposure of an enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes, namely, proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin were exposed to acetonitrile at 70 degrees C for three hr. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, proteinase K was analyzed in detail using X-ray diffraction method. The overall structure of the enzyme was found to be similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad remained intact after the treatment. However, the water structure in the substrate binding site underwent some rearrangement as some of the water molecules were either displaced or completely absent. The most striking observation conce...
International journal of biochemistry and molecular biology, Jan 13, 2013
Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include mye... more Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The LPO is found in exocrine secretions including milk. It is responsible for the inactivation of a wide range of micro-organisms and hence, is an important component of defense mechanism in the body. With the help of hydrogen peroxide, it catalyzes the oxidation of halides, pseudohalides and organic aromatic molecules. Historically, LPO was isolated in 1943, nearly seventy years ago but its three-dimensional crystal structure has been elucidated only recently. This review provides various details of this protein from its discovery to understanding its structure, function and applications. In order to highlight species dependent variations in the structure and function of LPO, a detailed comparison of sequence, structure and function of LPO from various species have been made. The structural basis of ligand bin...
Journal of Molecular Modeling, 2011
Articles-Sorted by Date 1. Nucl Med Commun. 2012 Jun 10. [Epub ahead of print] 18F-FDG PET-CT for... more Articles-Sorted by Date 1. Nucl Med Commun. 2012 Jun 10. [Epub ahead of print] 18F-FDG PET-CT for detecting recurrent gastric adenocarcinoma: results from a Non-Oriental Asian population.
Journal of Biological Chemistry, 2011
Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated... more Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to...
Clinica Chimica Acta, 2009
Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14 ... more Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14 th century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.
Acta Crystallographica Section E Structure Reports Online, 2005
The title compound, [Pb 2 O 2 (C 6 H 4 N 3) 2 ] n , exhibits anti-corrosion properties. The coord... more The title compound, [Pb 2 O 2 (C 6 H 4 N 3) 2 ] n , exhibits anti-corrosion properties. The coordination around each Pb atom is different, with coordination numbers of four and five. The compound forms a polymeric chain with pairs of oxo bridges between metal centers.
Phosphorus, Sulfur, and Silicon and the Related Elements, 1993
An increasing investigation of organotin(IV) complexes has focused on acquiring well-defined soli... more An increasing investigation of organotin(IV) complexes has focused on acquiring well-defined solid-state structures in order to learn about the nature of their versatile coordination chemistry, wide industrial applications and biological activities, 1 especially those of organotin(IV) derivatives from heterocyclic thionates containing a nitrogen atom (or more) and an adjacent, exocyclic thioketo group. 2 A characteristic feature of these complexes in the solid state is that the ligands chelate the tin atom through S and N atoms. In our previous work, we studied the coordination chemistry of four ligands of such type: 2-mercaptonicotinic acid, 1-(4-hydroxyphenyl)-1H-tetrazole-5-thiol, and 2,5-dimercapto-1,3,4-thiodiazole, which possess one or two deprotonated heterocyclic thioamide groups (N-C-S)-3. In this paper we report on the synthesis and crystal structure of a x69
Acta crystallographica, Apr 1, 2007
Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized b... more Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P4 3 2 1 2, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V M value of 2.5 Å 3 Da À1. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution.
Protein Engineering, Design and Selection, 2001
Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range o... more Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range of applications including enzyme stability and enhancement of its catalytic activity. Despite all this, the enzyme behaviour in this process still remains unknown. A serine proteinase, proteinase K, was subjected to three-phase partitioning (TPP). A 3 ml volume of proteinase K solution (3 mg/ml in 0.05 M acetate buffer, pH 6.0) was brought to 30% (w/v) ammonium sulphate saturation by addition of saturated ammonium sulphate. tert-Butanol (6 ml) was added to this solution and the mixture was incubated at 25°C for 1 h. The precipitated protein in the mid-layer was dissolved in 3 ml of 0.05 M acetate buffer, pH 6.0. The specific activity of the processed enzyme was estimated and was found to be 210% of the original enzyme activity. In order to understand the basis of this remarkable enhancement of the enzyme activity, the structure of the TPP-treated enzyme was determined by X-ray diffraction at 1.5 Å resolution. The overall structure of the TPPtreated enzyme is similar to the original structure in an aqueous environment. The hydrogen bonding system of the catalytic triad is intact. However, the water structure in the substrate binding site has undergone a rearrangement as some of the water molecules are either displaced or completely absent. Two acetate ions were identified in the structure. One is located in the active site and seems to mimic the role of water in the enzyme activity and stability. The other is located at the surface of the molecule and is involved in stabilizing the local structure of the enzyme. The most striking observation in respect of the present structure pertains to a relatively higher overall temperature factor (B ⍧ 19.7 Å 2) than the value of 9.3 Å 2 in the original enzyme. As a result of a higher B-factor, a number of residues, particularly their side chains, were found to adopt more than one conformation. It appears that the protein exists in an excited state which might be helping the enzyme to function more rapidly than the original enzyme in aqueous media. Summarily, the basis of increased enzymatic activity could be attributed to (i) the presence of an acetate ion at the active site and (ii) its excited state as reflected by an overall higher B-factor.
PLOS ONE, 2015
Cellular methylamines are osmolytes (low molecular weight organic compounds) believed to offset t... more Cellular methylamines are osmolytes (low molecular weight organic compounds) believed to offset the urea's harmful effects on the stability and function of proteins in mammalian kidney and marine invertebrates. Although urea and methylamines are found at 2:1 molar ratio in tissues, their opposing effects on protein structure and function have been questioned on several grounds including failure to counteraction or partial counteraction. Here we investigated the possible involvement of cellular salt, NaCl, in urea-methylamine counteraction on protein stability and function. We found that NaCl mediates methylamine counteracting system from no or partial counteraction to complete counteraction of urea's effect on protein stability and function. These conclusions were drawn from the systematic thermodynamic stability and functional activity measurements of lysozyme and RNase-A. Our results revealed that salts might be involved in protein interaction with charged osmolytes and hence in the urea-methylamine counteraction.
Frontiers in genetics, 2018
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune disea... more Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis u...
Indian Journal of Chemistry Sect B Organic Chemistry Including Medical Chemistry, 2004
Distal effect on mass spectral fragmentations of glycolamide esters of 6-methoxy-2-naphthylacetic... more Distal effect on mass spectral fragmentations of glycolamide esters of 6-methoxy-2-naphthylacetic acid (6-MNA) and the crystal structure of N,N /-dimethylglycolamide ester of 6-MNA
PLOS ONE, 2015
An increasing number of cancer patients worldwide, especially in third world countries, have rais... more An increasing number of cancer patients worldwide, especially in third world countries, have raised concern to explore natural drug resources, such as the less explored fresh water filamentous cyanobacteria. Six strains of cyanobacteria (Phormidium sp. CCC727, Geitlerinema sp. CCC728, Arthrospira sp. CCC729, Phormidium sp. CCC731, Phormidium sp. CCC730, and Leptolyngbya sp. CCC732) were isolated (paddy fields and ponds in the Banaras Hindu University, campus) and five strains screened for anticancer potential using human colon adenocarcinoma (HT29) and human kidney adenocarcinoma (A498) cancer cell lines. Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 were the most potent as determined by examination of morphological features and by inhibition of growth by graded concentrations of crude extracts and thin-layer chromatography (TLC) eluates. Cell cycle analysis and multiplex assays using cancer biomarkers also confirmed Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 as cancer drug resources. Apoptotic studies in the cells of A498 (cancer) and MCF-10A (normal human epithelial) exposed to crude extracts and TLC fractions revealed no significant impact on MCF-10A cells emphasizing its importance in the development of anticancer drug. Identification of biomolecules from these extracts are in progress.
Enzyme Research, 2013
Acinetobacter baumanniiis a multidrug resistant pathogenic bacteria associated with hospital acqu... more Acinetobacter baumanniiis a multidrug resistant pathogenic bacteria associated with hospital acquired infections. This bacterium possesses a variety of resistance mechanisms which makes it more difficult to control the bacterium with conventional drugs, and, so far no effective drug treatment is available against it. Nucleoside diphosphate kinase is an important enzyme, which maintains the total nucleotide triphosphate pool inside the cell by the transfer ofγ-phosphate from NTPs to NDPs. The role of nucleoside diphosphate kinase (Ndk) has also been observed in pathogenesis in other organisms. However, intensive studies are needed to decipher its other putative roles inAcinetobacter baumannii. In the present study, we have successfully cloned the gene encoding Ndk and achieved overexpression in bacterial host BL-21 (DE3). The overexpressed protein is further purified by nickel-nitrilotriacetic acid (Ni-NTA) chromatography.
Protein Science, 2005
This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A 2 (PLA 2)... more This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A 2 (PLA 2) and also to a PLA 2 with Asp 49. The fatty acid identified as n-tridecanoic acid is observed at the substrate recognition site of PLA 2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA 2 was determined using the cDNA method. Three-dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 Å. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n-tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium-binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n-tridecanoic acid was clearly fitted. The MALDI-TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA 2 by 212 Da over the native PLA 2. A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA 2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium-binding loop.