The document discusses the global consensus sequence development and analysis of conserved domains in the NS3 protein of dengue virus. It describes how over 125 sequences of the NS3 protein from the four dengue virus serotypes were aligned and analyzed. Key conserved domains that encode the serine protease and helicase functions were identified. The phylogenetic tree analysis grouped the sequences by serotype. Suggestions for potential antiviral peptides targeting conserved motifs in these domains to disrupt protein functions and reduce viral replication are provided.

2. Global Consensus Sequence Development
and Analysis of Dengue NS3 Conserved
Domains

3. Introduction
Umaira Kanwal
Roll No.2021
Department Of Biotechnology and Bioinformatics
Government College University Faisalabad

4. Dengue Virus
 The dengue virus (DENV) in one of five serotypes is the
cause of dengue fever. It is a mosquito-borne single
positive-stranded RNA virus of the family Flaviviridae;
genus Flavivirus. All four serotypes can cause the full
spectrum of disease

5. Dengue infection
Major Health
Problem
More then 100
countries
In Pakistan

6. Most Prevalent
in Pakistan
Dengue Virus Serotypes
DENV
DENV4
DENV2 DENV1 DENV3

7. Dengue Proteins
Structural
Proteins
Envelop
Capsid
Non-Structural
Proteins
Membrane
Seven Proteins:
NS1, NS2A,NS2B, NS3,
NS4A, NS4B, and NS5,
NS3: Enzymetic
Reaction and Viral
Replication
Dengue Virus Structure

8. NS3 Conserved
Domain
N-Terminal C-Terminal

9.  It has also been reported that NS3 has DNA
unwinding activity. Despite the high mutation rate
of DENV, some residues that actively participate
in viral replication remain conserved. These
conserved residues can be important in
developing specific antiviral agents and inhibitors
against DENVs.

10. Methodology
Kainat Arif
Roll No. 2027
Department Of Biotechnology and Bioinformatics
Government College University Faisalabad

11. 127
sequence
OF Dengue
NS3 Protein
(NCBI)
30 seq
of
DENV1
31 seq of
DENV4
33 seq
of
DENV2
31 seq
of
DENV3

12. Peptides designing for potential peptide vaccine
127 seq’NCBI
Consensus Seq
Of Each
Serotype (CLC
work bench)
Global
consensus Seq.
Consensus of
all serotype
Short peptid Oh
highly conserved

13. Global Consensus Sequence

14. Phylogenetic tree analysis
125 sequence
first aligned in CLC
Workbench,
Evolutionary TREE
The UPGMA
method is based on
pairwise
similarity/
dissimilarity
distance matrix.1

15. NS3 Result and Discussion
Athar Hussain
Department Of Biotechnology and Bioinformatics
Government College University Faisalabad

16. NS3 Protein
• Two domains ,serine protease (protease
domain ->six β-strands(two β-barrels
formed by residues 1–180 ) and NTPase
helicase(Involve in Viral replication)
• Cofactor NS2B wraps around the NS3
protease domain and becomes part of
the active site
• Second largest protein of DENV genome.

17. Sequence Alignment for Consensus sequence
Histidine
Peptidase S7
Aspertine
Serine

18. Mutation in residues (Y163
and G164) to alanine can
completely abrogate the
enzyme activity.
Helicase Domain

19. Consensus Sequence Domain encoding
Helps in processing of the
NS3 poly-protein precursor
into mature proteins

21. Phylogenetic tree of NS3 sequences
DENV2 DENV3 DENV1 DENV4

22. Suggestions
The consensus sequence alignment shows that:
1.Residue L226 to L245 encodes the P-loop NTPase superfamily. It has two
motifs [Walker A, GK(S/T), and Walker B, Dex (D/H)], designing antipeptides
against the Walker A/Walker B region can significantly reduce RNA processing
efficiency.
2.I349 to R357 encodes helicase DEAD-box domain. Designing Antipeptides against
DEAD-Box can control Viral activites
3.The peptide string from 465 to 473 (QRR267 GR469 XGRN) is the part of the
helicase domain , mutation in R467 and R469 that will reduce the activity of
helicase
4.Mutation in residues (Y159 and G160) to alanine can completely
abrogate the enzyme activity