Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Modeling protein conformational changes is crucial for understanding biological function.
• Experimental techniques like Double Electron-Electron Resonance (DEER) spectroscopy provide distance information but integrating it into modeling remains challenging.

Purpose of the Study:

• To develop and validate an approach for integrating DEER distance restraints into the Rosetta modeling suite.
• To enable accurate prediction of alternative protein conformations.

Main Methods:

• A novel multilateration algorithm was developed to fit DEER decay data and optimize rotamer ensembles simultaneously.
• The approach was applied to model the protonation-dependent transition of the multidrug transporter PfMATE.

Main Results:

• The algorithm achieved comparable distance distributions to existing packages while coupling DEER fitting and rotamer optimization.
• The modeled inward-facing conformation of PfMATE showed less than 2Å Cα RMSD deviation from the experimental structure.
• The method reduced spin label rotamer entropy, leading to more accurate and clustered Rosetta models.

Conclusions:

• This integrated approach enhances the accuracy and robustness of protein conformational change modeling.
• It provides a powerful tool for studying dynamic protein processes using experimental distance restraints.