Determining subunit stoichiometry — Which combination of methods lets you find both subunit molecular weight and the number of subunits in a protein's quaternary structure?

Difficulty: Medium

Correct Answer: Combine SDS–PAGE (subunit MW) with gel filtration (native MW) to infer subunit number

Explanation:


Introduction:
Determining quaternary structure often requires knowing both the mass of the intact native assembly and the masses of its individual subunits. Integrating orthogonal separation data provides a practical route to subunit stoichiometry.


Given Data / Assumptions:

  • SDS–PAGE estimates individual polypeptide molecular weights under denaturing conditions.
  • Size-exclusion (gel filtration) estimates the native molecular weight of the intact complex.
  • Subunit count ≈ native MW / dominant subunit MW (accounting for heterogeneity if present).


Concept / Approach:
Use SDS–PAGE to identify subunit sizes and relative band intensities; use gel filtration to estimate the native complex mass. The ratio provides an integer consistent with known subunit composition, validated against standards and known oligomeric forms.


Step-by-Step Solution:

1) Run SDS–PAGE → determine subunit masses (e.g., 25 kDa and 30 kDa).2) Run gel filtration → determine native complex (e.g., ~110 kDa).3) Compare: 110 kDa vs subunits implies likely stoichiometries (e.g., 2 * 25 + 2 * 30 = 110 → heterotetramer).


Verification / Alternative check:
Cross-check with native PAGE or mass spectrometry. Non-reducing SDS–PAGE can reveal disulfide-linked oligomers complementing gel filtration data.


Why Other Options Are Wrong:

a) Reveals subunit MW but not intact native mass.b) Reveals native mass but not individual subunits.d) Resolves by pI, not mass; insufficient for stoichiometry alone.e) Lacks calibration and denatured subunit information.


Common Pitfalls:
Interpreting anomalous elution due to shape or glycosylation as true mass; ignoring hetero-oligomer composition when dividing masses.


Final Answer:
Combine SDS–PAGE with gel filtration.

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