Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution

Structure determination using cryo-electron microscopy (cryo-EM) medium-resolution density maps is often facilitated by flexible fitting. Avoiding overfitting, adjusting force constants driving the structure to the density map, and emulating complex conformational transitions are major concerns in the fitting. To address them, we develop a new method based on a three-step multi-scale protocol. First, flexible fitting molecular dynamics (MD) simulations with coarse-grained structure-based force field and replica-exchange scheme between different force constants replicas are performed. Second, fitted C alpha atom positions guide the all-atom structure in targeted MD. Finally, the all-atom flexible fitting refinement in implicit solvent adjusts the positions of the side chains in the density map. Final models obtained via the multi-scale protocol are significantly better resolved and more reliable in comparison with long all-atom flexible fitting simulations. The protocol is useful for multi-domain systems with intricate structural transitions as it preserves the secondary structure of single domains.

Automated summary

A new method based on a three-step multi-scale protocol is developed for structure determination, involving flexible fitting molecular dynamics simulations and refinement in implicit solvent. Final models obtained through this protocol are significantly better resolved and more reliable compared to long all-atom flexible fitting simulations, especially suitable for multi-domain systems with complex structural transitions.