Limits...
Comparison of structural architecture of HCV NS3 genotype 1 versus Pakistani genotype 3a.

Fatima K, Azhar E, Mathew S, Damanhouri G, Qadri I - Biomed Res Int (2014)

Bottom Line: We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling.Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER.This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.

View Article: PubMed Central - PubMed

Affiliation: IQ Institute of Infection and Immunity, P.O. Box 54000, Lahore, Punjab, Pakistan.

ABSTRACT
This study described the structural characterization of Pakistani HCV NS3 GT3a in parallel with genotypes 1a and 1b NS3. We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling. Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER. Sixty models were produced and clustered into groups and the best model of PK-NCVI/Pk3a NS3 was selected and studied further to check the variability with other HCV NS3 genotypes. This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.

Show MeSH
Multiple sequence alignment of different reported NS3 structures and target sequences of PK-NCVI/Pk3a NS3. Motifs I-VI are marked by boxes on the first sequence and labeled, respectively. The conserved sequences are shown as dots.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4221965&req=5

fig2: Multiple sequence alignment of different reported NS3 structures and target sequences of PK-NCVI/Pk3a NS3. Motifs I-VI are marked by boxes on the first sequence and labeled, respectively. The conserved sequences are shown as dots.

Mentions: We have done the pairwise alignment and phylogenetic analysis in order to identify percentage identity of reported NS3 GT3a (NZL1) with our target sequence PK-NCVI/Pk3a NS3 by comparative modeling. The target sequence and crystallographic analysis of PDB Id. 3O8B and 1CU1 shared the phylogenetic branch of target sequence as compared to other crystallographic studies (Figure 1(a)). Phylogenetic analysis was further confirmed by the multiple alignment percentage identity of 76.06% among their residues by using ClustalW and T-Coffee along with rapid scanning and correction of multiple sequence alignments (Figure 1(b)). The resulting multiple alignments were visualized and annotated using the sequence alignment protocol in CLC sequence viewer. It was found that most of the sequence variations were divided among all of the domains but N-terminal and middle portion of the reported NS3 protein were comparatively rich in variations (Figure 2). NS3-NS4A is composed of six subdomains (Figure 3(a)). The helicase, usually referred to as α-helical subdomain, consists of two structurally related β-α-β subdomains and a third subdomain of three short β strands and seven helices. The protease domain is folded into dual barrel fold, like other members of chymotrypsin serine protease family. The 13-residue NS4A proved to be a protease activation domain and is considered to be the sixth subdomain (Figure 3(a)). By using NMRCLUST, sixty models were produced and clustered into groups. The best structural model was selected using the results of NMRCLUST, ERRAT score, and MODELLER. Inspection of the final structural model indicates that some major mutations are present in the helicase and non-functional regions of PK-NCVI/Pk3a which presents some new non-covalent intermolecular (IM) interactions alongside of conserved sequence (Figure 3(b)). Major domains including motifs I (Walker motif: G207SGKSTK), Ia (Y223KVLVLNPSVA), II (Walker B: D290ECH), III (V319LATATPP), IV (L365IFCHSKKK), V (A410TDALMTGYTGDF), and VI (V456SRSQRRGRTGR) were conserved in the all HCV NS3 proteins of different genotypes. Structural architecture of these motives presented that those motifs make a border to ATP binding cleft and project some residues into the nucleic acid binding site. The residues of these motives transform the chemical energy derived from ATP hydrolysis into a mechanical force necessary for helicase movements for the disruption of ssRNA or RNA base pairs. Analogous IM interaction pattern of those domains was seen in all of the crystal studies and comparative model of reported NS3 except for mutations of Lys224Asn in motif Ia and Tyr418Phe in motif V (Supplementary Figure 1 available online at http://dx.doi.org/10.1155/2014/749254). Results implicated that mutation in motif 1a was strengthening its confirmation while motif V was loosely bound.


Comparison of structural architecture of HCV NS3 genotype 1 versus Pakistani genotype 3a.

Fatima K, Azhar E, Mathew S, Damanhouri G, Qadri I - Biomed Res Int (2014)

Multiple sequence alignment of different reported NS3 structures and target sequences of PK-NCVI/Pk3a NS3. Motifs I-VI are marked by boxes on the first sequence and labeled, respectively. The conserved sequences are shown as dots.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4221965&req=5

fig2: Multiple sequence alignment of different reported NS3 structures and target sequences of PK-NCVI/Pk3a NS3. Motifs I-VI are marked by boxes on the first sequence and labeled, respectively. The conserved sequences are shown as dots.
Mentions: We have done the pairwise alignment and phylogenetic analysis in order to identify percentage identity of reported NS3 GT3a (NZL1) with our target sequence PK-NCVI/Pk3a NS3 by comparative modeling. The target sequence and crystallographic analysis of PDB Id. 3O8B and 1CU1 shared the phylogenetic branch of target sequence as compared to other crystallographic studies (Figure 1(a)). Phylogenetic analysis was further confirmed by the multiple alignment percentage identity of 76.06% among their residues by using ClustalW and T-Coffee along with rapid scanning and correction of multiple sequence alignments (Figure 1(b)). The resulting multiple alignments were visualized and annotated using the sequence alignment protocol in CLC sequence viewer. It was found that most of the sequence variations were divided among all of the domains but N-terminal and middle portion of the reported NS3 protein were comparatively rich in variations (Figure 2). NS3-NS4A is composed of six subdomains (Figure 3(a)). The helicase, usually referred to as α-helical subdomain, consists of two structurally related β-α-β subdomains and a third subdomain of three short β strands and seven helices. The protease domain is folded into dual barrel fold, like other members of chymotrypsin serine protease family. The 13-residue NS4A proved to be a protease activation domain and is considered to be the sixth subdomain (Figure 3(a)). By using NMRCLUST, sixty models were produced and clustered into groups. The best structural model was selected using the results of NMRCLUST, ERRAT score, and MODELLER. Inspection of the final structural model indicates that some major mutations are present in the helicase and non-functional regions of PK-NCVI/Pk3a which presents some new non-covalent intermolecular (IM) interactions alongside of conserved sequence (Figure 3(b)). Major domains including motifs I (Walker motif: G207SGKSTK), Ia (Y223KVLVLNPSVA), II (Walker B: D290ECH), III (V319LATATPP), IV (L365IFCHSKKK), V (A410TDALMTGYTGDF), and VI (V456SRSQRRGRTGR) were conserved in the all HCV NS3 proteins of different genotypes. Structural architecture of these motives presented that those motifs make a border to ATP binding cleft and project some residues into the nucleic acid binding site. The residues of these motives transform the chemical energy derived from ATP hydrolysis into a mechanical force necessary for helicase movements for the disruption of ssRNA or RNA base pairs. Analogous IM interaction pattern of those domains was seen in all of the crystal studies and comparative model of reported NS3 except for mutations of Lys224Asn in motif Ia and Tyr418Phe in motif V (Supplementary Figure 1 available online at http://dx.doi.org/10.1155/2014/749254). Results implicated that mutation in motif 1a was strengthening its confirmation while motif V was loosely bound.

Bottom Line: We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling.Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER.This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.

View Article: PubMed Central - PubMed

Affiliation: IQ Institute of Infection and Immunity, P.O. Box 54000, Lahore, Punjab, Pakistan.

ABSTRACT
This study described the structural characterization of Pakistani HCV NS3 GT3a in parallel with genotypes 1a and 1b NS3. We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling. Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER. Sixty models were produced and clustered into groups and the best model of PK-NCVI/Pk3a NS3 was selected and studied further to check the variability with other HCV NS3 genotypes. This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.

Show MeSH