DEERefiner-assisted structural refinement using pulsed dipolar spectroscopy: a study on multidrug transporter LmrP.

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Pulsed dipolar spectroscopy, including double electron-electron resonance (DEER), offers valuable spatial information for protein structure determination but remains underutilized.
• Accurate protein structure modeling is crucial for understanding protein function and biological processes.

Purpose of the Study:

• To develop and validate DEERefiner, a user-friendly GUI program for protein structure modeling using DEER distance restraints.
• To demonstrate the application of DEERefiner in modeling ligand-dependent conformational changes of the proton-drug antiporter LmrP.

Main Methods:

• Development of DEERefiner, a MATLAB-based GUI integrating initial structures with DEER distance restraints.
• Application of DEERefiner to model the conformational states of the proton-drug antiporter LmrP.

Main Results:

• DEERefiner successfully modeled the ligand-dependent conformational changes of LmrP to an extracellular-open-like state with 0.76 Å precision.
• A previously hypothesized extracellular-closed/partially intracellular-open conformation of LmrP was resolved with 1.16 Å precision.
• The study highlights DEER spectroscopy's capability in precise protein structure modeling.

Conclusions:

• DEERefiner provides an accessible and effective tool for precise protein structure modeling using DEER data.
• The software advances the application of DEER spectroscopy in structural biology.
• Accurate modeling of LmrP conformations offers deeper insights into its function and mechanism.