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Open Access Highly Accessed Research article

Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR

Govindarajan Sudha1, Subburaj Yamunadevi12, Nidhi Tyagi13, Saumitra Das4 and Narayanaswamy Srinivasan1*

Author Affiliations

1 Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India

2 German cancer research center, Bioquant, Heidelberg, Germany

3 European Bioinformatics Institute, Hinxton, Cambridge, UK

4 Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India

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BMC Structural Biology 2012, 12:28  doi:10.1186/1472-6807-12-28

Published: 13 November 2012

Additional files

Additional file 1:

Multiple sequence alignment of members among casein kinase 1 family. The additional file provides multiple sequence alignment and the details of substrate interacting residues in human ck1α conserved within casein kinase 1 family. Arginine 214, lysine 260 is absolutely conserved and conservatively substituted respectively. Glycine 251 is not conserved because the main chain nitrogen is involved in its interaction with the substrate constraint residue – phosphoserine 229. These substrate interacting residues are highlighted in blue. The aspartic acid 140 of human ck1α probably avoids the proximity of substrate constraint acidic residue phosphoserine 229 of NS5A. Aspartic acid is conservatively substituted among the ck1 family and is highlighted in yellow.

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Additional file 2:

Prediction of PKR interacting residues in NS5A 1b. (1) Alignment of PKR dimerisation region with ISDR (Interferon sensitivity determining region) of NS5A. (a) Dimer interface residues are colored in magenta in PKR sequence. The residues in NS5A 1b, 3a equivalent to the dimer interface residues of PKR are colored in cyan and yellow respectively. (b) Dimer interface residues are colored in magenta in PKR sequence. The residues in NS5A 1b, 2a equivalent to the dimer interface residues of PKR are colored in cyan and green respectively. (2) Trace residues are identified when NS5A from genotype 1b which interacts and inhibits PKR is compared with NS5A 3a and NS5A 2a which are unable to bind and inhibit PKR efficiently in few representative sequences. All the trace residues highlighted are highly conserved (> 80%) in the entire dataset. (a) Trace residues picked when MSA of genotype 1b Vs 3a is compared. (b) Trace residues picked when MSA of genotype 1b Vs 2a is compared. (c) Trace residues picked when MSA of genotype 1b Vs 3a and 2a are compared.

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