The protein vMIP-II from Kaposi's sarcoma-associated herpesvirus (which subverts the host immune system by blocking the migration of white blood cells) consists of a 3-stranded β-sheet packed against an α-helix.

The side chain of residue Lys-61 is located on the exposed surface of the α-helix.

Examine the structure of vMIP-II (in the vicinity of Lys-61) in the PDB 3D View or by downloading the PDB file 1HFG into PyMOL.

Which of the following mutations is most likely to result in a new ionic interaction with the side chain of Lys-61, causing the folded structure of vMIP-II to be more stable at neutral pH (but not at pH 3 or pH 11)?

A research student is investigating the factors that stabilise the folded structure of a protein. They note that residues Phe-26 and Ile-75 contribute to a well-defined hydrophobic cluster in the core of the protein. To determine the contribution of these residues’ hydrophobic side chains to protein stability, they make mutants F26A and I75A. They then determine the stability of the wild type (WT) protein and each mutant.

What is the expected order of stability (from most stable to least stable), assuming that the main contribution of these residues to stability is through their side chain hydrophobic interactions?

A research student is investigating the factors that stabilise the folded structure of a protein. They note that residues Trp-38 and Leu-144 contribute to a well-defined hydrophobic cluster in the core of the protein. To determine the contribution of these residues’ hydrophobic side chains to protein stability, they make mutants W38A and L144A. They then determine the stability of the wild type (WT) protein and each mutant.

What is the expected order of stability (from most stable to least stable), assuming that the main contribution of these residues to stability is through their side chain hydrophobic interactions?

The protein CCL7 (which regulates migration of white blood cells in inflammation) consists of a 3-stranded β-sheet packed against an α-helix.

The side chain of residue X forms ionic interactions with the side chains of both Lys-58 and Lys-65 on the surface of the α-helix. This interaction stabilises the folded structure of CCL7 at neutral pH (but not at pH 3 or pH 11).

Examine the structure of CCL7 in the PDB 3D View or by downloading the PDB file 1BO0 into PyMOL.

What is the most likely identity of residue X?