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Global consensus sequence development and analysis of dengue NS3 conserved domains
Ambreen Ayub1, Usman A Ashfaq, Sobia Idrees
1Department of Bioinformatics and Biotechnology, Government College University , Faisalabad, Pakistan .
Bioresearch Open Access
|October 2, 2013
Summary
This study analyzed conserved regions in the dengue virus NS3 protein across all serotypes. Identified conserved peptides in key functional sites offer potential for developing new antiviral drugs against dengue.
Area of Science:
- Virology
- Molecular Biology
- Drug Discovery
Background:
- Dengue virus (DENV) poses a global health threat due to its high mutation rate and four serotypes.
- The DENV NS3 protein, with its protease and helicase domains, is crucial for viral replication and a potential antiviral target.
Purpose of the Study:
- To perform a conservancy analysis of the DENV NS3 protein across all four serotypes.
- To identify conserved residues and peptides within the NS3 protein that could be targeted for antiviral drug development.
Main Methods:
- Retrieved and aligned 127 DENV NS3 sequences from all four serotypes using CLC Workbench.
- Constructed a phylogenetic tree to understand evolutionary relationships.
- Performed conservancy analysis to identify conserved regions and residues.
Main Results:
- Identified highly conserved residues in critical functional sites, including catalytic pocket and divalent cation binding sites.
- Discovered 14 conserved peptides within the DENV NS3 protein, potentially useful for developing peptide inhibitors.
- The phylogenetic analysis indicated that all DENV serotypes evolved from dengue serotype 4.
Conclusions:
- Conserved regions and peptides within the DENV NS3 protein are potential targets for broad-spectrum antiviral agents.
- Understanding the evolutionary relationships and conserved residues is vital for developing effective dengue therapies.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...