4. Deducing quaternary structure via SDS-PAGE. SDS-PAGE is a convenient method for separating polypeptides solely on the basis of size. Small polypeptides travel faster than large ones; rate of migration through the gel is inversely proportional to the logarithm of molecular weight. The subunit structure of a multimeric protein often can be deduced using this technique in conjunction with a protein cross-linking agent. Cross-linking agents react with amino acid residues of two polypeptides that are in contact, thereby linking them by covalent bonds. After limited treatment with the reagent, so that some but not all subunits become cross-linked to their neighbors, the protein is subjected to SDS-PAGE and the molecular weights of the resulting proteins (bands) are estimated. The results of such experiments on two proteins (Protein A and Protein B) are shown below. What is the most likely subunit structure of each protein? Protein A SDS-PAGE cross-linking agent MW 105,000 70,000 35,000 Protein B SDS-PAGE cross-linking agent MW 55,000 40,000 15,000

Biochemistry
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Chapter1: Biochemistry: An Evolving Science
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**Deducing Quaternary Structure via SDS-PAGE**

SDS-PAGE is a convenient method for separating polypeptides solely based on size. Smaller polypeptides travel faster through the gel than larger ones; the rate of migration through the gel is inversely proportional to the logarithm of the molecular weight.

The subunit structure of a multimeric protein can be deduced using this technique in conjunction with a protein cross-linking agent. Cross-linking agents react with amino acid residues of two polypeptides that are in contact, thereby linking them by covalent bonds. After limited treatment with the reagent, so that some but not all subunits become cross-linked to their neighbors, the protein is subjected to SDS-PAGE, and the molecular weights of the resulting proteins (bands) are estimated.

The results of such experiments on two proteins (Protein A and Protein B) are shown below. What is the most likely subunit structure of each protein?

**Graph Descriptions:**

- **Protein A**: 
  - Without cross-linking: Bands appear at 70,000 and 35,000 molecular weight (MW).
  - With cross-linking: A single band appears at 105,000 MW.
  
- **Protein B**: 
  - Without cross-linking: Bands appear at 40,000 and 15,000 MW.
  - With cross-linking: Bands appear at 55,000, 40,000, and 15,000 MW.

**Interpretation:**

For Protein A, the data suggests it likely consists of two subunits with molecular weights of 70,000 and 35,000 that, when cross-linked, form a single unit with a total molecular weight of 105,000. 

For Protein B, it appears to consist of subunits with molecular weights of 40,000 and 15,000. The partial cross-linking results in additional band formation at 55,000 MW, suggesting the formation of a dimer involving both subunits. 

This analysis helps deduce the quaternary structure of the proteins by identifying their subunit composition and the interactions between them.
Transcribed Image Text:**Deducing Quaternary Structure via SDS-PAGE** SDS-PAGE is a convenient method for separating polypeptides solely based on size. Smaller polypeptides travel faster through the gel than larger ones; the rate of migration through the gel is inversely proportional to the logarithm of the molecular weight. The subunit structure of a multimeric protein can be deduced using this technique in conjunction with a protein cross-linking agent. Cross-linking agents react with amino acid residues of two polypeptides that are in contact, thereby linking them by covalent bonds. After limited treatment with the reagent, so that some but not all subunits become cross-linked to their neighbors, the protein is subjected to SDS-PAGE, and the molecular weights of the resulting proteins (bands) are estimated. The results of such experiments on two proteins (Protein A and Protein B) are shown below. What is the most likely subunit structure of each protein? **Graph Descriptions:** - **Protein A**: - Without cross-linking: Bands appear at 70,000 and 35,000 molecular weight (MW). - With cross-linking: A single band appears at 105,000 MW. - **Protein B**: - Without cross-linking: Bands appear at 40,000 and 15,000 MW. - With cross-linking: Bands appear at 55,000, 40,000, and 15,000 MW. **Interpretation:** For Protein A, the data suggests it likely consists of two subunits with molecular weights of 70,000 and 35,000 that, when cross-linked, form a single unit with a total molecular weight of 105,000. For Protein B, it appears to consist of subunits with molecular weights of 40,000 and 15,000. The partial cross-linking results in additional band formation at 55,000 MW, suggesting the formation of a dimer involving both subunits. This analysis helps deduce the quaternary structure of the proteins by identifying their subunit composition and the interactions between them.
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