The solution structures of the cucumber mosaic virus and tomato aspermy virus coat proteins explored with molecular dynamics simulations.
The three-dimensional structures of two cucumovirus coat proteins (CP), namely Cucumber mosaic virus (CMV) and Tomato aspermy virus (TAV), were explored by molecular dynamics (MD) simulations. The N-terminal domain and the C-terminal tail of the CPs proved to be intrinsically unstructured protein regions in aqueous solution. The N-terminal alpha-helix had a partially unrolled conformation. The thermal factor analysis of the CP loop regions demonstrated that the CMV CP had more flexible loop regions than the TAV CP. The principal component analysis (PCA) of the MD trajectories showed that the first three eigenvectors represented the three main conformational motions in the CPs. The first motion components with the highest variance contribution described an opening movement between the hinge and the N-terminal domain of both CPs. The second eigenvector showed a closing motion, while the third eigenvector represented crosswise conformational fluctuations. These new findings, together with previous results, suggest that the hinge region of CPs plays a central role in the recognition and binding of viral RNA.
Gellért
Akos
A
Agricultural Research Institute of the Hungarian Academy of Sciences, Department of Applied Genomics, H-2462 Martonvásár, Brunszvik u. 2. Hungary. gellerta@mail.mgki.hu
Balázs
Ervin
E
D000595:Amino Acid Sequence; D036022:Capsid Proteins / Q000737:chemistry*; D016000:Cluster Analysis; D018360:Crystallography, X-Ray; D017799:Cucumovirus / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010942:Plant Viruses / Q000737:chemistry*; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D012996:Solutions
D036022:Capsid Proteins; D012996:Solutions