A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta

Area of Science:

• Structural biology
• Biophysics
• Computational biology

Background:

• Oligomeric proteins are crucial targets for structural studies in solution.
• Determining protein-protein interfaces de novo is difficult with conventional NMR methods.
• The bet-V1 superfamily protein Aha1 from Colwellia psychrerythraea presents unique interface challenges.

Purpose of the Study:

• To develop and highlight a new approach for determining protein-protein interfaces in solution.
• To investigate conformational plasticity within the dimeric interface of Aha1.
• To reconcile crystallographic data with NMR and SAXS data for Aha1.

Main Methods:

• Utilizing sparse experimental data (NMR and SAXS) instead of dense restraints.
• Employing a physically realistic energy function for optimization.
• Limiting conformational search space based on sparse data.

Main Results:

• Observed that crystallographic interfaces for the bet-V1 superfamily are inconsistent with Aha1's solution data.
• Successfully applied a novel method to analyze Aha1's dimeric interface.
• Demonstrated the ability to study minor conformational changes and structural plasticity in solution.

Conclusions:

• The developed approach offers a new strategy for studying oligomeric protein interfaces in solution.
• Sparse data combined with energy optimization can overcome limitations of conventional methods.
• This work advances the understanding of structural plasticity in protein dimers.