Affiliations: Department of Pharmacy, Faculty of Medicine,
Universiti Malaya, 50603 Kuala Lumpur, Malaysia | School of Pharmaceutical Sciences, Universiti Sains
Malaysia, 11800, USM, Penang, Malaysia | Laboratory of Biocrystallography and Bioinformatics
Structure, Universiti Sains Malaysia, 11800, USM, Penang, Malaysia | Department of Molecular Medicine, Faculty of Medicine,
Universiti Malaya, 50603 Kuala Lumpur, Malaysia | Department of Chemistry, Faculty of Science,
Universiti Malaya, 50603 Kuala Lumpur, Malaysia
Abstract: Multiple sequence alignment was performed against eight proteases
from the Flaviviridae family using ClustalW to illustrate conserved domains.
Two sets of prediction approaches were applied and the results compared.
Firstly, secondary structure prediction was performed using available structure
prediction servers. The second approach made use of the information on the
secondary structures extracted from structure prediction servers, threading
techniques and DSSP database of some of the templates used in the threading
techniques. Consensus on the one-dimensional secondary structure of Den2
protease was obtained from each approach and evaluated against data from the
recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB).
Results indicated the second approach to show higher accuracy compared to the
use of prediction servers only. Thus, it is plausible that this approach is
applicable to the initial stage of structural studies of proteins with low
amino acid sequence homology against other available proteins in the PDB.
Keywords: Dengue virus type 2, serine protease, secondary structure prediction, consensus, protein structure