Hydropathy: The Plot Thickens. A hydropathy plot can be used to predict the structure of a membrane protein based on its amino acid sequence and the hydrophobicity values of the amino acids. Hydrophobicity is measured as the standard free energy change,
, for the transfer of a given amino acid residue from a hydrophobic solvent into water, in kilojoules/mole
The hydropathy index is calculated by averaging the hydrophobicity values for a series of short segments of the polypeptide, with each segment displaced one amino acid further from the N-terminus. The hydropathy index of each successive segment is then plotted as a function of the location of that segment in the amino acid sequence, and the plot is examined for regions of high hydropathy index. (a) Why do scientists try to predict the structure of a membrane protein by this indirect means when the technique of
-ray crystallography would reveal the structure directly? (b) Given the way it is defined, would you expect the hydrophobicity index of a hydrophobic residue such as valine or isoleucine to be positive or negative? What about a hydrophilic residue such as aspartic acid or arginine? (c) Listed below are four amino acids and four hydrophobicity values. Match the hydrophobicity values with the correct amino acids, and explain your reasoning. Amino acids: alanine; arginine; isoleucine; serine Hydrophobicity (in kJ/mol):
(d) Shown in Figure
is a hydropathy plot for a specific integral membrane protein. Draw a horizontal bar over each transmembrane segment as identified by the plot. How long is the average transmembrane segment? How well does that value compare with the number you calculated in Problem
How many transmembrane segments do you think the protein has? Can you guess which protein this might be
The Correct Answer and Explanation is:
(a) Why do scientists try to predict the structure of a membrane protein by this indirect means when X-ray crystallography would reveal the structure directly?
Scientists use hydropathy plots to predict the structure of membrane proteins because X-ray crystallography has certain limitations. Membrane proteins are often difficult to crystallize due to their amphipathic nature (having both hydrophobic and hydrophilic regions), which makes it challenging to form high-quality crystals for X-ray diffraction. Additionally, X-ray crystallography requires a stable and ordered crystalline form of the protein, something that membrane proteins, which are dynamic and flexible, often do not form under conventional conditions. In contrast, hydropathy plots can be generated using the amino acid sequence alone and can provide useful insights into the general topology of the membrane protein, such as identifying potential transmembrane regions, even before the protein’s three-dimensional structure is fully resolved.
(b) Given the way it is defined, would you expect the hydrophobicity index of a hydrophobic residue such as valine or isoleucine to be positive or negative? What about a hydrophilic residue such as aspartic acid or arginine?
Hydrophobic residues, like valine or isoleucine, have a positive hydrophobicity index. This is because these amino acids have high free energy when they are transferred from a hydrophobic environment to water, indicating they prefer to stay in a hydrophobic environment, such as within a lipid bilayer. Hydrophilic residues, such as aspartic acid or arginine, would have a negative hydrophobicity index, as these residues interact favorably with water and are more likely to be found in aqueous environments, such as on the surface of the protein, rather than within the lipid bilayer.
(c) Match the hydrophobicity values with the correct amino acids, and explain your reasoning.
- Alanine: Hydrophobicity = +1.8 kJ/mol
Alanine is a small, non-polar amino acid with a moderate hydrophobicity. This value aligns with alanine’s preference for hydrophobic environments. - Arginine: Hydrophobicity = -4.5 kJ/mol
Arginine is a charged, polar amino acid, meaning it interacts strongly with water. Its negative hydrophobicity index reflects this. - Isoleucine: Hydrophobicity = +4.5 kJ/mol
Isoleucine is a branched-chain, hydrophobic amino acid, and its positive value reflects its strong preference for hydrophobic environments. - Serine: Hydrophobicity = -0.8 kJ/mol
Serine is polar but not highly charged, with a lower hydrophobicity compared to charged amino acids. Its slightly negative value reflects its amphipathic nature.
(d) Hydropathy plot and transmembrane segments
To answer this part accurately, I’d need the specific hydropathy plot for the membrane protein in question. However, in general, transmembrane segments in membrane proteins typically range from about 20-25 amino acids in length, as this is the length required to span the lipid bilayer. To estimate the number of transmembrane segments, you would look for regions in the hydropathy plot that show high hydrophobicity, indicating regions of the protein likely embedded in the hydrophobic core of the membrane. If the protein has multiple high hydropathy regions, you can estimate how many transmembrane segments it might have. This value should be compared to the experimentally calculated number based on the protein’s overall sequence.
Can you provide the specific hydropathy plot mentioned in the question? This would help in giving more accurate predictions regarding the transmembrane segments and the protein.
