The image below shows aspects of the secondary structure of an important human protein. Several amino acids are highlighted by a ball and stick representation. A number of non-covalent interactions are also shown. (Note that atoms are coloured by element, where blue is nitrogen and red is oxygen.) Which ONE statement below is true?

Question

BlackTom AI · Accepted Answer

In this question, we are asked to evaluate which statement about the displayed protein fragment is true. The provided option is: b. The side-chain nitrogen of a lysine residue is forming a hydrogen bond with a side chain oxygen of an aspartate.

First, recall some general principles: lysine has a long, flexible side chain ending in a positively charged amino group (the terminal NZ), which, in many contexts, can participate in hydrogen bonding or ionic interactions with acceptors such as carbonyl oxygens or carboxylate oxygens. Aspartate (D) has a side chain with a protonated or deprotonated carboxyl group; its side-chain oxygens (one carbonyl O and one hydroxyl-like O in certain representations) typically act as hydrogen bond acceptors. When lysine is protonated, its amino nitrogen can donate a hydrogen bond to an electronegative acceptor like an oxygen on aspartate. In the image, the blue dashed lines (which commonly denote non-covalent interactions) appear to connect a lysine side-chain nitrogen to an aspartate side-chain oxygen, consistent with a hydrogen-bonding interaction or, more strongly, a salt-bridge scenario if the aspartate is deprotonated.

Why this could be true: 
- Lysine’s side-chain amine is a good hydrogen-bond donor and can interact with electronegative oxygens, such as the carboxylate oxygen of aspartate. 
- In a protein environment, such an interaction is common and can contribute to stabilization through hydrogen bonding or electrostatic attraction.
- The color-coded atoms (blue for nitrogen, red for oxygen) and the dashed lines in the figure support a hydrogen-bonding interaction between a lysine nitrogen and an aspartate oxygen, which aligns with the statement.

Why other potential interpretations might be incorrect (even though not listed here):
- If the interaction were between a lysine backbone nitrogen and an aspartate oxygen, it would involve a different atom alignment than the side chain. The statement specifies side-chain nitrogen, which is a more specific match to common interactions seen in helices and loops.
- If the lysine were neutral in this environment (not protonated), the interaction would be weaker or differently characterized (more of a hydrogen bond donor-acceptor mismatch rather than a salt bridge). However, in many protein structures at physiological pH, lysine remains positively charged, increasing the likelihood of a strong interaction with a negatively charged aspartate.

Given the information in the image and the typical chemistry of Lys-NH3+ and Asp-COO−, the statement describing a hydrogen bond between the lysine side-chain nitrogen and the aspartate side-chain oxygen is plausible and consistent with common non-covalent interactions observed in proteins.

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