New insights regarding HCV-NS5A structure/function and indication of genotypic differences

Abstract

Background: HCV is prevalent throughout the world. It is a major cause of chronic liver disease. There is no effective vaccine and the most common therapy, based on Peginterferon, has a success rate of ~50%. The mechanisms underlying viral resistance have not been elucidated but it has been suggested that both host and virus contribute to therapy outcome. Non-structural 5A (NS5A) protein, a critical virus component, is involved in cellular and viral processes.

Methods: The present study analyzed structural and functional features of 345 sequences of HCV-NS5A genotypes 1 or 3, using in silico tools.

Results: There was residue type composition and secondary structure differences between the genotypes. In addition, second structural variance were statistical different for each response group in genotype 3. A motif search indicated conserved glycosylation, phosphorylation and myristoylation sites that could be important in structural stabilization and function. Furthermore, a highly conserved integrin ligation site was identified, and could be linked to nuclear forms of NS5A. ProtFun indicated NS5A to have diverse enzymatic and nonenzymatic activities, participating in a great range of cell functions, with statistical difference between genotypes.

Conclusion: This study presents new insights into the HCV-NS5A. It is the first study that using bioinformatics tools, suggests differences between genotypes and response to therapy that can be related to NS5A protein features. Therefore, it emphasizes the importance of using bioinformatics tools in viral studies. Data acquired herein will aid in clarifying the structure/function of this protein and in the development of antiviral agents.

Figure 1

Statistical analysis in second Structure composition (%) distribution of the NS5A sequences. Plot: Difference in helix (A), sheet (B) and coil (C) percentage in the NS5A protein between genotype 1 and 3/therapy outcome. X-axis describes the percentage of each second structure type in total protein; y-axis means density (number of sequences with correspond percentage/total number of sequences) ETR-End of therapy responder, NR-nonresponder, R-responder.

Figure 2

Statistical analysis in second structure composition (%) variance of the NS5A genotype 3 sequences. Plot: Statistical results for helix (A), sheet (B) and coil (C) variance in genotype 3. Square in the left shows the calculated values for each test. Note the variance different distribution in each response group. StDev-standard deviation.

Figure 3

Results of MEMSAT3 and Prosite. Summary for NS5A reference AF009606. TM: transmembrane region, CRS: cytoplasmic retention site, PKR-bd: PKR binding site, NLS: nuclear localization site, V3: variable region 3. Lines-purple: n-glycosylation sites, blue: phosphorylation sites, green: n-myristoylation sites, orange: RGD site.