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These results are consistent with available structural data which suggest that the larger residue at position 148 may partially occlude O2 binding.
It can be further observed that β-strand residues (red-color) tend to have larger residue depth values, implying that they are more deeply buried compared with other secondary structure-annotated residues.
Substitution with a larger residue, such as Trp, has no effect on the PXN IC50.
Mutation to a larger residue such as phenylalanine has been proposed to restrict movement along this pathway.
Restricted movement within a cavity or along a tunnel due to the mutation to a larger residue also changed the potential pathways.
I25W mutant: The effect of mutation Ile25 to a larger residue such as tryptophan had previously been expected to restrict ligand docking in the Xe4 cavity.
Similar(49)
In that study, docking results were skewed towards di-peptides composed of larger residues.
However, a bias toward the presence of larger residues, like Trp or Tyr, in the place of smaller residues, like Val, is observed in low-abundant proteins (Figure 3A).
Two fully conserved Ala residues, Ala398 and Ala401, are mutated in patients and the structure suggests that larger residues cannot be accommodated.
Thus, it is likely that our simple models do not properly account for all of the changes in protein conformation that are needed to accommodate the larger residues.
Mutations to larger residues (D139E and D139K) partially break the formed water structures, partially compensated by direct hydrogen bonding between the cofactor and the amino acid side chain.
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