1. In silico investigation on molecular mechanism of HCV infection
caused by mutations in Claudin-1 protein.
Bhavaniprasad Vipperla and Jayanthi S
Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore, India.
The double mutation conformations from all the 5 clusters showed significant changes from the original structure.
Introduction
Structural Validation Results
Claudins are transmembrane proteins involved in the formation of tight junctions.
Claudin family has a major role in the paracellular sealing of the cells.
Claudin Family comprises of 15 sub types.
Claudin-1 mutations plays a major role Hepatitis C Virus envelope glycoprotein mediated fusion into the cytosol.
The introduction of mutant I32M and E48K results in partially permissive to Hepatitis C Virus infection.
The double mutation, a combination of both mutations was highly permissive to HCV infection.
Claudin-1 modeled structure was validated using SAVS and ProSA servers.
The Ramachandran plot statistics shows 99.7% of amino acid residues in the allowed region, having 90.7% in most favored regions which show a good Stereo-chemical quality.
ProSA score of -2.8 was obtained for the structure.
Molecular Dynamics Results
The Root Mean Square Deviation (RMSD) and the Root Mean Square Fluctuations (RMSF) exhibited higher RMSD and significant loss in stability .in the mutant Forms.
The H-bonds were significantly lost in all mutant forms, but highly in case of double mutation which might be due to the changes occurring in the secondary structure.
The Solvent Accessible Surface Area was increased vastly for the double mutation form than each of the point mutations and the native forms.
Conclusion:
Methodology
ITASSER server was used for modeling
the structure of Claudin1.
SwissPDB viewer used for modeling
the mutant proteins.
Claudin-1 was inserted in a pre-equilibrated lipid bilayer consisting
of 340 molecules of 1-palmitoyl-2-oleoyl
-sn-glycero-3-phosphoethanolamine
(POPE).
Analysis of the MD trajectories in terms of protein structure stability, secondary structure fluctuations, intra-molecular hydrogen bonds indicated the instability that is caused by the Claudin-1 mutations.
From the clustering analysis it is evident that double mutation causes major structural changes in the overall structure and destabilizes the protein more than the single point mutations.
The double mutations resulted in the distortion of specific regions that increased the surface accessibility of the protein, which in turn support the HCV entry more extensively.
References
MJ. Evans, T. von Hahn, DM. Tscherne, AJ. Syder, M Panis, B Wolk et al. Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry. NATURE| Vol 446| 12 April 2007.
HJ Harris, MJ Farquhar, CJ Mee, C Davis, GM Reynolds, A Jennings et al. CD81 and Claudin 1 Coreceptor Association: Role in Hepatitis C Virus Entry. J. Virol. May 2008 vol. 82 no
Clustering technique was used to probe the most populated average conformations from the clusters obtained for every single trajectory.
An average structure is generated as a representative of each cluster based on the RMSD-matrix produced
The most populated conformations for the native have maintained the secondary structure.
GROMACS used for Molecular Dynamics (MD) simulation analysis.
All simulations were performed for 25 ns.
Clustering Analysis was performed using GROMOS algorithm.
Acknowledgements :
The authors take this opportunity to thank the management of Vellore Institute of Technology University for providing the facilities and encouragement to carry out this work.