As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

PLoS Comput Biol. 2016 Nov 29;12(11):e1005211. doi: 10.1371/journal.pcbi.1005211. eCollection 2016 Nov.

Abstract

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered.

MeSH terms

  • Computer Simulation
  • Elastic Modulus
  • Micromanipulation / methods
  • Microscopy, Atomic Force / methods*
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Protein Unfolding*
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Stress, Mechanical

Substances

  • Proteins

Grants and funding

SSP is supported by the Alberta Prion Research Institute (APRI Research Team Program, grant #PTM13007), the Canadian Institutes of Health Research (CIHR Transitional Operating Grant #2682), and the Natural Sciences and Engineering Research Council of Canada (NSERC Discovery Grant #250041-2011). SSP also acknowledges WestGrid (www.westgrid.ca) and Compute Canada/Calcul Canada (www.computecanada.ca) for providing computing resources. JR is supported by the Natural Sciences and Engineering Research Council of Canada (NSERC Discovery Grant #327247-2011). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.