Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Accurate atomic models of macromolecular complexes are crucial for understanding biological function.
• Low-resolution cryo-electron microscopy (cryo-EM) maps present challenges for direct atomic model fitting.
• Existing methods often struggle to account for conformational flexibility during model fitting.

Purpose of the Study:

• To present and validate a new normal mode flexible fitting (NMFF) method for fitting high-resolution structures into low-resolution cryo-EM maps.
• To demonstrate the capability of NMFF in capturing large, functionally relevant conformational changes.
• To apply NMFF to experimental cryo-EM data from diverse biological systems.

Main Methods:

• Development of an iterative method using a linear combination of low-frequency normal modes to deform structures.
• Optimization of structural conformation to match low-resolution electron density maps using gradient-following techniques.
• Application of NMFF to both all-atom and C-alpha atom representations for multi-scale flexible fitting.

Main Results:

• Successful application of NMFF to simulated and experimental cryo-EM maps.
• Elucidation of large conformational changes in elongation factor G (EF-G) bound to the ribosome.
• Determination of conformational states for Escherichia coli RNA polymerase and cowpea chlorotic mottle virus.

Conclusions:

• NMFF provides an effective approach for flexible fitting of high-resolution models into low-resolution cryo-EM data.
• The method accurately captures functionally significant conformational dynamics of macromolecular machines.
• NMFF enhances the interpretability of cryo-EM maps by enabling detailed structural analysis.