Protein quaternary structures in solution are a mixture of multiple forms

Area of Science:

• Biochemistry
• Structural Biology
• Proteomics

Background:

• Over 50% of E. coli cytoplasmic proteins form oligomeric structures.
• Static protein structures often fail to capture the dynamic equilibrium of quaternary states, especially for homo-oligomers.

Purpose of the Study:

• To re-evaluate the solution oligomeric states of 17 bacterial proteins.
• To compare the accuracy of traditional methods and AlphaFold Multimer in predicting protein quaternary structures.

Main Methods:

• Native mass spectrometry (MS)
• Mass photometry (MP)
• Size exclusion chromatography (SEC)
• Small-angle X-ray scattering (SAXS)

Main Results:

• Most proteins exhibited multiple oligomeric states in solution.
• Some proteins did not display mass-action driven equilibrium.
• Public databases often underestimated the complexity of protein quaternary structures.
• AlphaFold Multimer accurately predicted potential multimeric states for most proteins.

Conclusions:

• Protein oligomeric states are more complex and dynamic than often assumed.
• AlphaFold Multimer shows promise in resolving uncertainties regarding protein solution states.