Department of Biochemistry: Recent submissions
Now showing items 21-40 of 237
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Role of C-terminal residues in oligomerization and stability of λ CII: Implications for lysis-lysogeny decision of the phage
(ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, 2005-01-14)A crucial element in the lysis-lysogeny decision of the temperate coliphage lambda is the phage protein CII, which has several interesting properties. It promotes lysogeny through activation of three phage promoters p(E), ... -
Improved Model of a LexA Repressor Dimer Bound to recA Operator
(ADENINE PRESS, 2004-04)complete three dimensional model for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor was proposed from our laboratory when no crystal ... -
pH-dependent autocleavage of lambda repressor occurs in the operator-bound form: characterization of lambda repressor autocleavage
(PORTLAND PRESS, 2004-04-15)The first-order rate constants for the RecA-independent, spontaneous, pH-dependent autocleavage of the lambda cl repressor was measured in the present study at pH 10.6 at 27, 37 and 42 degreesC respectively. Autocleavage ... -
Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR)
(ELSEVIER SCIENCE BV, 2005-01)The protozoan parasite Entamoeba histolytica express a cytosine-5 DNA methyltransferase (Ehmeth) that belongs to the DNMT2 protein family. The biological function of members of this DNMT2 family is unknown. In the present ... -
Inhibition of gene expression with double strand RNA interference in Entamoeba histolytica
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2004-08-06)In order to inhibit gene expression in Entamoeba histolytica, we have developed a method based on expressing double strand RNA interference constructs in stable transformants. The 5' end of Eh Dia was cloned head to head ... -
The Iml3 protein of the budding yeast is required for the prevention of precocious sister chromatid separation in meiosis I and for sister chromatid disjunction in meiosis II
(SPRINGER, 2004-08)The mitotic kinetochore of the budding yeast contains a number of proteins which are required for chromosome transmission but are non-essential for vegetative growth. We show that one such protein, Iml3, is essential for ... -
Sequence divergence of Entamoeba histolytica tubulin is responsible for its altered tertiary structure
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2004-07-02)Atypical microtubular structures of the protozoan parasite Entamoeba histolytica (Eh) have been attributed to amino acid sequence divergence of Eh tubulin. To investigate if this sequence divergence leads to significant ... -
A Dissection of Specific and Non-specific Protein-Protein Interfaces
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2004-02-27)We compare the geometric and physical-chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are ... -
Disulfide bonds, their stereospecific environment and conservation in protein structures
(OXFORD UNIV PRESS, 2004-11)We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms ... -
The B-ring substituent at C-7 of colchicine and the alpha-C-terminus of tubulin communicate through the "tail-body" interaction
(WILEY-LISS, 2004-11-15)The carboxy terminals of alphabeta-tubulins are flexible regions rich in acidic amino acid residues that play an inhibitory role in the polymerization of tubulin to microtubules. We have shown that the binding of colchicine ... -
Sulfonamide drugs binding to the colchicine site of tubulin: Thermodynamic analysis of the drug-tubulin interactions by isothermal titration calorimetry
(AMER CHEMICAL SOC, 2005-01-27)The discovery of several sulfonamide drugs paved the way toward the synthesis of 6 (N-12-[(4-hydroxyphenyl)amino]-3-pyridinyl]-4-methoxybenzenesulfonamide: E7010) and 7 (N-(3fluoro-4-methoxyphenyl)pentafluorobenzenesulfonamide, ... -
-NH-dansyl isocolchicine exhibits a significantly improved tubulin-binding affinity and microtubule inhibition in comparison to isocolchicine by binding tubulin through its A and B rings
(AMER CHEMICAL SOC, 2005-03-08)Structure-activity relationship studies have established that the A and C rings of colchicine comprise the minimum structural feature necessary for high affinity drug-tubulin binding. Thus, colchicine acts as a bifunctional ... -
Purification and characterization of a deoxyriboendonuclease from Mycobacterium smegmatis
(SPRINGER SINGAPORE PTE LTD, 2006-03-31)A deoxyriboendonuclease has been purified to near homogeneity from a fast growing mycobacterium species, M. smegmatis and characterized to some extent. The size of enzyme is about 43 kDa as determined by a denaturing gel ... -
Studies on codon usage in Thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer
(WILEY-V C H VERLAG GMBH, 2005)Codon usage studies have been carried out on the coding sequences of Thermoplasma acidophilum, which is an archaeon and grows at very low pH and high temperature. Overall codon usage data analysis indicates that all the ... -
Synonymous codon usage bias in 16 Staphylococcus aureus phages: Implication in phage therapy
(ELSEVIER, 2005-11)To reveal the factors influencing architecture of protein-coding genes in staphylococcal phages, relative synonymous codon usage variation has been investigated in 920 protein-coding genes of 16 staphylococcal phages. As ... -
Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes
(ADENINE PRESS, 2005-08)To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, ... -
Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ
(BLACKWELL, 2005-09)To reveal how the AT-rich genome of bacteriophage PhiKZ has been shaped in order to carry out its growth in the GC-rich host Pseudomonas aeruginosa, synonymous codon and amino acid usage bias of PhiKZ was investigated and ... -
Cyclic AMP-dependent functional forms of cyclic AMP receptor protein from Vibrio cholerae
(ELSEVIER SCIENCE INC, 2006-03-01)The cyclic AMP receptor protein (CRP) from Escherichia coli, involved in the transcriptional regulation of a number of genes and operons, works by binding to specific sites upstream of promoters. CRP also binds cyclic AMP ... -
310-Helix adjoining α-helix and β-strand: Sequence and structural features and their conservation
(WILEY-BLACKWELL, 2005-06-15)Does the amino acid use at the terminal positions of an α-helix become altered depending on the context-more specifically, when there is an adjoining 310-helix, and can a single helical cylinder encompass the resultant ... -
Hydration of protein-protein interfaces
(WILEY-BLACKWELL, 2005-07-01)We present an analysis of the water molecules immobilized at the protein-protein interfaces of 115 homodimeric proteins and 46 protein-protein complexes, and compare them with 173 large crystal packing interfaces representing ...