Improved technologies now routinely provide protein NMR structures useful for molecular replacement

Area of Science:

• Structural biology
• Biophysics
• X-ray crystallography

Background:

• Molecular replacement (MR) is a key technique for solving the phase problem in X-ray crystallography.
• Historically, Nuclear Magnetic Resonance (NMR) structures have shown limited success as MR search models.

Purpose of the Study:

• To comprehensively investigate the utility of protein NMR ensembles as MR search models.
• To assess the effectiveness of modern NMR structure preparation protocols for MR.

Main Methods:

• Utilized 25 pairs of X-ray and NMR structures solved with modern NMR methods.
• Employed the FindCore protocol for preparing NMR ensembles.
• Applied Rosetta refinement to NMR structures.
• Tested performance against homologous structures.

Main Results:

• Correct MR solutions were obtained for 22 out of 25 targets using NMR ensembles prepared with FindCore.
• Automatic model rebuilding was successful based on these MR solutions.
• Rosetta refinement yielded MR solutions for two additional proteins.
• Prepared NMR ensembles performed comparably to X-ray crystal structures as MR search models for homologous targets (>40% sequence identity).

Conclusions:

• Improved preparation protocols significantly enhance the utility of NMR ensembles for molecular replacement.
• NMR ensembles are a viable and effective alternative to traditional search models in X-ray crystallography.
• This approach facilitates structure determination, particularly for homologous proteins.