Biomedical subjects

Kanagaraj Sekar

Publications and source records attributed to Kanagaraj Sekar.

3 recordsLinked to original sources

PubMed2006

Crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein C from Thermus thermophilus.

The gram-negative aerobic eubacterium Thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in Japan. The molybdenum cofactor in this organism is considered to be an essential component required by enzymes that catalyze diverse key reactions in the global metabolism of carbon, nitrogen and sulfur. The molybdenum-cofactor biosynthesis protein C derived from T. thermophilus was crystallized in two different space groups. Crystals obtained using the first crystallization condition belong to the monoclinic space group P2(1), with unit-cell parameters a = 64.81, b = 109.84, c = 115.19 A, beta = 104.9 degrees; the crystal diffracted to a resolution of 1.9 A. The other crystal form belonged to space group R32, with unit-cell parameters a = b = 106.57, c = 59.25 A, and diffracted to 1.75 A resolution. Preliminary calculations reveal that the asymmetric unit contains 12 monomers and one monomer for the crystals belonging to space group P2(1) and R32, respectively.

Coenzymes↗

PubMed2006

SMS: sequence, motif and structure--a database on the structural rigidity of peptide fragments in non-redundant proteins.

Structure prediction methods aim to identify the relationship between the amino acid sequence of an unknown protein and information comprised in databases of known protein structures. Towards this end, we created a database by combining the amino acid sequences and the corresponding three-dimensional atomic coordinates for all the 25% non-redundant protein chains available in the Protein Data Bank. It contains information about the peptide fragments that are 5 to 10 residues long. In addition, options are provided for the users to visualize the individual motifs and the superposed fragments in the client machine. Further, useful functionalities areprovided to look for similar sequence motifs in all the sequence databases like PDB, 90% non-redundant protein chains, Genome database, PIR and Swiss-Prot. The database is being updated at regular intervals and the same can be accessed over the World Wide Web interface at the following URL: http://pranag.physics.iisc.ernet.in/sms/.

Amino Acid Sequence↗

PubMed2005

PSST-2.0: Protein Data Bank Sequence Search Tool.

UNLABELLED: PSST-2.0 (Protein Data Bank [PDB] Sequence Search Tool) is an updated version of the earlier PSST (Protein Sequence Search Tool), and the philosophy behind the search engine has remained unchanged. PSST-2.0 is a Web-based, interactive search engine developed to retrieve required protein or nucleic acid sequence information and some of its related details, primarily from sequences derived from the structures deposited in the PDB (the database of 3-dimensional [3-D] protein and nucleic acid structures). Additionally, the search engine works for a selected subset of 25% or 90% non-homologous protein chains. For some of the selected options, the search engine produces a detailed output for the user-uploaded, 3-D atomic coordinates of the protein structure (PDB file format) from the client machine through the Web browser. The search engine works on a locally maintained PDB, which is updated every week from the parent server at the Research Collaboratory for Structural Bioinformatics, and hence the search results are up to date at any given time. AVAILABILITY: PSST-2.0 is freely accessible via http://pranag.physics.iisc.ernet.in/psst/ or http://144.16.71.10/psst/.

Algorithms↗