Can the Structure of the Hydrophobic Core Determine the Complexation Site? - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 48

If, in turn, the latter assumption is true then it follows that the ligand affects the
polypeptide chain during the folding process. As the ligand tries to find an optimal
place to adhere to the emerging protein, the polypeptide chain “acknowledges” its
presence and folds in a manner consistent with the presence of the ligand. This phe-
nomenon can explain the highly selective nature of certain proteins (in terms of
binding ligands) and enables us to search for potential binding sites based on the
distribution of local maxima in the

Δ H pro fi le.
The 3DRC protein is an enzyme (dihydrofolate reductase - EC#:1.5.1.3) (3 C
Warren et al. 1991 ) which forms a complex with methotrexate. The structure of its
hydrophobic core roughly corresponds to the theoretical model, although eliminating
residues responsible for ligand complexation significantly improves this alignment.
Elimination of residues involved in ion binding (Cl − ) does not affect the remainder
of the protein as far as the structure of its hydrophobic core is concerned. Similarly,
cleaving catalytic residues has negligible impact on the core. There are, however,
molecules in which the act of eliminating residues responsible for enzymatic catalysis
(based on O/T and O/R values) greatly improves the agreement between the theoretical
and observed hydrophobicity distributions in the remainder of the protein body.
Calculation of O/T and O/R for molecules stripped of interacting residues
requires repeated normalization of O and T values (for polypeptide chains in which
the corresponding residues were eliminated). The data given in Table 3.1 presents
the protein 1BDD - the protein representing the hydrophobicity core structure
accordant with the idealized form expressed by 3-D Gauss function.
Protein 1 G85 in its complete form represents the hydrophobic core not accordant
with idealized structure. The elimination of residues (# residues engaged in ligand
complexation) engaged in ligand binding (NO LIGAND) reveals the structure of the
rest of protein molecule as representing hydrophobicity core structure accordant
with the idealized form. It means that the deformation of hydrophobic core structure
is introduced by residues engaged in ligand binding - and in consequence - presence
of ligand influences the core structure. The elimination of residues engaged in
protein-protein interaction (NO P-P) reveals the structure of the hydrophobic core
accordant with assumed model.
Protein 3DRC represents the structure of hydrophobic core as accordant with
idealized structure. Elimination of residues engaged in ligand binding (NO LIGAND)
either ion complexation (NO ION) or residues engaged in catalytic activity (NO
CATALYTIC) does not change the status of the hydrophobic core status which is
accordant with the assumed one in all these cases.
Before we analyze the role of the ligand in protein folding we should first deter-
mine to what extent the presented “idealized” hydrophobic core model is realized in
actual proteins. To achieve this goal a study has been conducted, where a variety of
small proteins (ca. 60 amino acids) was checked for structural accordance with
theoretical predictions. The analyzed proteins exhibited a broad range of properties
and biological activity profiles. They included enzymes, chaperonins, metal-
complexing proteins, scaffold proteins, protein-ligand complexes etc. (Prymula
et al. 2009, 2010 ; Prymula and Roterman 2009 ; Minervini et al. 2008 ) . Our analysis
points to two groups of proteins whose structure is highly accordant with the