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Online Journal of Bioinformatics ©
Volume 14 (2): 226-234, 2013
Virtual analysis of catalytic site in Plasmodium yoelii yoelii
Department of Bioinformatics, Uttaranchal College of Science & Technology, Dehradun, India.
Kumar A., Virtual analysis of catalytic site in Plasmodium yoelii yoelii, Onl J Bioinform., 14 (2): 226-234, 2013. Protein sequence of Plasmodium yoelii yoelii. “prt_seq“ was extracted from GenPept database (ACCESSION EAA21357) and used to predict hydrophobicity, atomic and amino acid composition, PEST region, solvent accessibility, molecular mass, theoretical pI and its catalytic site in 3D. The PEST region suggested an intracellular half-life <2hr. The molecule was composed of 1395 carbon, 2254 hydrogen, 462 oxygen, 386 nitrogen and 7 sulfur atoms. Aspargine concentration was 13.9% and the N-terminal was Methionine. Total number of negatively charged residues was 44 and positive 42 with total atoms 4504. Secondary structure composition was determined with Hidden Markov model, and disulphide bonds, effect of point mutation prediction and catalytic site identification with HeatMap. Online active site prediction was determined by matching protein sequences with a library of catalytic sites yielding 26 regions with a maximum score of 0.015 for Orotidine “ 5'-monophosphate decarboxylase” and a minimum of 0.004 for “Endo-alpha-sialidase”. The molecular weight of the protein sequence was 32049.9 and Theoretical Pi value 6.08. Protein close to given Pi and molecular mass was matched using TagIdent yielding 126466 proteins. The Instability Index was 36.19 and stable. The aliphatic Index occupied alanine, valine, isoleucine, and leucine was 80.77. The three dimensional structure of catalytic site was visualized using Jmol software.
Keywords: Catalytic site, Heatmap representation, Propsearch, Solvent accessibility, PEST region.