©1996-2019.
All Rights Reserved. Online Journal of Bioinformatics.
You may not store these pages in any form except for your own personal use. All
other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the
before mentioned must be gained in writing from the publisher. This
article is exclusively copyrighted in its entirety to OJVR. This article may be
copied once but may not be, reproduced or re-transmitted without the express
permission of the editors. This journal satisfies the refereeing requirements
(DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or
any pages linking to this page you must link directly to this page only here
rather than put up your own page.
OJBTM
Online Journal of Bioinformatics ©
Volume 14 (2): 226-234, 2013
Virtual analysis of catalytic site in Plasmodium yoelii yoelii
Akash Kumar.
Department
of Bioinformatics, Uttaranchal College of Science & Technology,
Dehradun, India.
ABSTRACT
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.
FULL-TEXT (SUBSCRIBE OR
PURCHASE TITLE $25USD)