Oral Presentation 2014 International Biophysics Congress

Contributions of different protein-protein interactions to the mechanical stability and assembly pathways of CCMV capsids — a multiscale simulation study (#109)

Christine Peter 1 2 , Christoph Globisch 1 2 , Venkatramanan Krishnamani 3 , Tristan Bereau 2 3 , Markus Deserno 3
  1. University of Konstanz, Germany, Konstanz, Germany
  2. Max Plank Insitute for Polymer Research, Mainz, Germany
  3. Carnegie Mellon University, Pittsburgh, PA, USA

A combined approach of classical atomistic and different coarse grained (CG) simulation levels is used to investigate the 180-protein icosahedral capsid of Cowpea Chlorotic Mottle Virus (CCMV). First, a suitable CG model is used in combination with clustering algorithms and free energy reweighting methods to explore the conformational equilibrium of unstructured regions of the CCMV capsid proteins for which experimental data is lacking or limited. In particular, we have focused on the folding process of converging strands at the protein-protein interfaces, more precisely at the 3-fold (hexameric) and 5-fold (pentameric) symmetry points of the capsid. The CG simulations reproduce the experimentally found folding behavior, and – in combination with a suitable backmapping routine and atomistic simulations – can be used to propose a multi-conformational ensemble for the experimentallyunresolved regions of the pentameric protein interface. In a second step, we use atomistic reference simulations to refine a CG protein model in such a way that it reproduces the elastic behavior of individual proteins and protein dimers in solution. The resulting bottom-up CG model correctly predicts structural and elastic properties of bigger aggregates (intermediates in the assembly process) and mechanical properties of an entire virus capsid such as the force response of the capsid under external stress – which is in excellent agreement with data from Atomic Force Microscopy – not just for the linear regime of small stresses, but all the way to structural failure. Based on a detailed analysis of the rupture process of the capsid we can propose an assembly model via well-defined oligomeric intermediates where the assembly order is regulated by the strengths of the interfacial binding, with a post-assembly reinforcement of weak spots by cooperative folding.