Global Consensus Sequence Development

and Analysis of Dengue NS3 Conserved

Domains

Introduction

Umaira Kanwal

Roll No.2021Department Of Biotechnology and Bioinformatics

Government College University Faisalabad

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

Dengue infe

cti

on

Major Health Problem

More then 100 countries

In Pakistan

Most Prevalent

in Pakistan

DENV

DENV2 DENV1 DENV3

DENV4

Dengue Virus Serotypes

Dengue Proteins

Structural Proteins

Envelop

Capsid

Non-Structural Proteins

Seven Proteins:

NS1, NS2A,NS2B, NS3, NS4A, NS4B, and NS5,

Membrane

NS3: Enzymetic

Reaction and Viral

Replication

Dengue Virus Structure

NS3 Conserved Domain

N-Terminal C-Terminal

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.

Methodology

Kainat Arif

Roll No. 2027Department Of Biotechnology and Bioinformatics

Government College University Faisalabad

127 sequence

OF Dengue NS3 Protein

(NCBI)

30 seqof

DENV1

31 seq of DENV4

33 seqof

DENV2

31 seqof

DENV3

Peptides designing for potential peptide vaccine

127 seq’NCBI

Consensus SeqOf Each

Serotype (CLC work bench)

Consensus of all serotype

Global consensus Seq.

Short peptid Oh

highly conserved

Global Consensus Sequence

Phylogenetic tree analysis

125 sequence

first aligned in CLCWorkbench,

The UPGMA method is based on

pairwise similarity/

dissimilarity distance matrix.1

Evolutionary TREE

NS3 Result and Discussion

Athar Hussain

Department Of Biotechnology and Bioinformatics

Government College University Faisalabad

NS3 Protein

• Two domains ,serine protease (protease domain ->six β-strands(two β-barrels formed by residues 1–180 ) and NTPasehelicase(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.

Sequence Alignment for Consensus sequence

HistidinePeptidase S7

Aspertine

Serine

Mutation in residues (Y163

and G164) to alanine can

completely abrogate the

enzyme activity.

Helicase Domain

Consensus Sequence Domain encoding

Helps in processing of the

NS3 poly-protein precursor

into mature proteins

DENV4DENV1DENV3DENV2

Phylogenetic tree of NS3 sequences

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 antipeptidesagainst the Walker A/Walker B region can significantly reduce RNA processing efficiency.

Suggestions

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

helicase4.Mutation in residues (Y159 and G160) to alanine can completely

abrogate the enzyme activity