Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Refining atomic structures within cryo-electron microscopy (cryo-EM) density maps is crucial for understanding protein function.
• Flexible fitting protocols are essential for accurately modeling dynamic protein structures.
• Existing methods may not fully capture the inherent flexibility of proteins.

Purpose of the Study:

• To introduce RIBFIND, a novel method for identifying rigid bodies from protein secondary structural elements (SSEs).
• To evaluate the efficacy of RIBFIND in improving flexible fitting of atomic models into cryo-EM maps.
• To compare the performance of RIBFIND-based rigid bodies against individual SSEs in refinement protocols.

Main Methods:

• Developed RIBFIND to cluster SSEs into rigid bodies, capturing protein flexibility.
• Integrated RIBFIND into the Flex-EM flexible fitting protocol.
• Benchmarked the method using 13 protein structure pairs with corresponding cryo-EM maps (5-15Å resolution).

Main Results:

• RIBFIND-based rigid body refinement significantly improved fits into cryo-EM maps compared to using individual SSEs.
• At 15Å resolution, RIBFIND improved fits by an average of 40.64%, versus 26.52% for individual SSEs.
• A two-stage refinement protocol (RIBFIND followed by SSE-based) further enhanced fits at sub-nanometer resolution.

Conclusions:

• RIBFIND effectively identifies rigid bodies for enhanced protein structure refinement in cryo-EM.
• The method offers a significant improvement over traditional SSE-based flexible fitting.
• RIBFIND serves as a versatile, stand-alone tool for guiding flexible fitting in cryo-EM data analysis.