NMR hawk-eyed view of AlphaFold2 structures

Area of Science:

• Structural biology
• Computational biology
• Biophysics

Background:

• The advent of AlphaFold2 has revolutionized protein structure prediction, achieving atomic accuracy from amino acid sequences.
• Predicted structures for nearly the entire human proteome are now publicly accessible.

Purpose of the Study:

• To evaluate the accuracy of AlphaFold2-predicted protein structures in representing their solution conformations.
• To compare AlphaFold2 structures with high-resolution experimental structures obtained via Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Methods:

• Selected small proteins with well-resolved NMR solution structures.
• Compared AlphaFold2 predicted structures with experimental data, including distance restraints and residual dipolar couplings (RDCs).
• Assessed backbone conformation quality by fitting experimental RDCs to AlphaFold2 structures.

Main Results:

• Experimental RDCs showed excellent agreement with AlphaFold2 structures for GB3, DinI, and ubiquitin.
• For GB3, the AlphaFold2 structure's accuracy exceeded that of a high-resolution crystal structure.
• Identified representative solution conformations using AlphaFold2 structures and RDC fitting, exemplified by calmodulin.

Conclusions:

• AlphaFold2-predicted structures can highly accurately represent protein conformations in solution.
• Combining AlphaFold2 predictions with RDCs offers a potent strategy for investigating protein structural dynamics.