Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

32-POS

Board 32

Structural Investigation on the Intrinsic Disordered Region of the HCV Protein NS5A and

Its Role in Viral RNA Replication

Neha S. Gandhi

, Marie Dujardin

2,3

, Vanesa Madan

, François-Xavier Cantrelle

, Robert

Schneider

, Helene Launay

, Guy Lippens

2,6

, Ralf Bartenschlager

, Xavier Hanoulle

Queensland University of Technology, Brisbane, Queensland, Australia,

CNRS UMR 8576,

Université Lille1, Villeneuve d’Ascq, Hauts de France, France,

CNRS UMR 5086, Université

Lyon 1, Lyon, Auvergne-Rhône-Alpes, France,

University of Heidelberg, Heidelberg, Baden-

Württemberg, Germany,

INSERM U 1068, CNRS UMR 7258, Aix-Marseille University,

Marseille, Provence-Alpes-Côte d'Azur, France,

University of Toulouse, Toulouse, Occitanie,

France.

The Non-structural 5A (NS5A) protein of hepatitis C virus (HCV) plays an important role in

cellular and viral processes [1]. We have performed Gaussian accelerated molecular dynamics

(MD) and nuclear magnetic resonance (NMR) to investigate the native conformational

preferences of the wild type NS5A-D2 (residues 308 to 327) peptide and its mutants (P306A,

P310A, P315A, P319A; P320A, A311G, D316E and DY316-317EN) from JFH1 strain. We used

dihedral principal component analysis (dPCA) to map a conformational ensemble of fast

interconverting conformations and further constructed dPCA-based free energy landscapes (FES)

of these peptides. The analysis of the FES and chemical shifts showed that the motif Pro314–

Trp316 does not randomly explore the conformational space in solution except for the A311G

NS5A-D2 peptide. Our simulation captured intrinsic conformational characteristics of proline-

rich NS5A-D2 that are in good agreement with the NMR data like presence of a prominent

“turn” [2]. Indeed, our results indicate that the absence of a turn in the A311G NS5A-D2 mutant

does not allow HCV RNA replication in a cell-based assay. Our current work highlights that very

small structural motifs like a turn present in intrinsically disordered proteins are essential for

performing a very specific function.

References 1). Ross-Thriepland and Harris, Gen. Virol.,727-738, 2015. 2). Dujardin, M et al., J.

Biol.Chem., 19104–19120, 2015.