in silico Binding Free Energy Characterization of Cowpea Chlorotic Mottle Virus Coat Protein Homodimer Variants

  • Armando Díaz-Valle
  • Gabriela Chávez-Calvillo
  • Mauricio Carrillo-Tripp
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 232)


The viral capsid’s main function is to transport and protect its nucleic acid. It is formed by the self-assembly of multiple copies of one, or a few, coat proteins (CP). The molecular mechanisms of how the spontaneous self-assembly process takes place still remains obscure. Cowpea Chlorotic Mottle Virus (CCMV), an icosahedral plant pathogen, was used as model for understanding the assembly of symmetrical aggregates of biomolecules. Six potential key residues in the capsid interfaces of CCMV were identfied. in silico free energy of binding was estimated for two functional CP dimers; WT and the sextuple mutant. Our results show that perturbation of these specific residues will likely destabilize the capsid structure as a whole. This provides insights into how viral coat proteins recognize each other inside the cell, and suggest ways to develop mechanisms to prevent their assembly, thereby blocking the infection.


viral self-assembly capsid coat protein plant icosahedral virus 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Damodaran, K.V., Reddy, V.S., Johnson, J.E., Brooks III, C.L.: A general method to quantify quasi-equivalence in icosahedral viruses. J. Mol. Biol. 324, 723–737 (2002)CrossRefGoogle Scholar
  2. 2.
    Reddy, V.S., Giesing, H.A., Morton, R.T., Kumar, A., Post, C.B., Brooks III, C.L., Johnson, J.E.: Energetics of quasiequivalence: Computational analysis of protein-protein interactions in icosahedral viruses. Biophys. J. 74, 546–558 (1998)CrossRefGoogle Scholar
  3. 3.
    Zhao, X., Fox, J.M., Olson, N.H., Baker, T.S., Young, M.J.: In vitro assembly of cowpea chlorotic mottle virus from coat protein expressed in Escherichia coli and in vitro-transcribed viral cDNA. Virology 207, 486–494 (1995)CrossRefGoogle Scholar
  4. 4.
    Reddy, V., Johnson, J.: Structure-derived insights into virus assembly. Advances in Virus Research 64, 45–68 (2005)CrossRefGoogle Scholar
  5. 5.
    Lemkul, J., Bevan, D.: Assessing the stability of alzheimer’s amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry B 114(4), 1652–1660 (2010)CrossRefGoogle Scholar
  6. 6.
    Carrillo-Tripp, M., Brooks, C., Reddy, V.: A novel method to map and compare protein-protein interactions in spherical viral capsids. Proteins 73(3), 644–655 (2008)CrossRefGoogle Scholar
  7. 7.
    Carrillo-Tripp, M., Shepherd, C., Borelli, I., Venkataraman, S., Lander, G., Natarajan, P., Johnson, J., Brooks, C., Reddy, V.: VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Research 37(Database issue), D436–D442 (2009)Google Scholar
  8. 8.
    Periole, X., Knepp, A., Sakmar, T., Marrink, S., Huber, T.: Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. Journal of the American Chemical Society 134(26), 10959–10965 (2012)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Armando Díaz-Valle
    • 1
  • Gabriela Chávez-Calvillo
    • 1
  • Mauricio Carrillo-Tripp
    • 1
  1. 1.Biomolecular Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)Cinvestav Sede IrapuatoMéxico CityMéxico

Personalised recommendations