Interatomic interaction analysis
Protein-protein interactions are essential for regular biological
processes and for the regulation of cellular reactions that affect the
function and expression of genes. Several studies [49] have
elucidated the role of protein-protein complex interface residues in
conferring specificity and stability. Interface residues of proteins are
known to interact with main chain and side chain atoms of their
interacting partners. However, the impact and relative contribution of
inter-protein interactions involving interface residue as compared to
intra-protein interactions in protein-protein complexes are unclear. In
order to ensure that essential interactions involved in the binding
affinity and stability of the hypothetical hs CENP-HIKM complex
are not overlooked, we report the observed changes in interatomic
interactions of the wild-type and mutant protein complex subunits (Table
7 and 8). A comparative study of the wild-type and mutant protein
complexes showed that both inter- and intra-model interactions
contributed to the stability of the complex (Supplementary Figures
S8-S10). Upon the mutation of each residue, a dramatic loss of specific
interatomic interactions (van der Waals interactions, hydrogen bond
interactions and hydrophobic interactions) were observed, which
speculatively led to the reported reduction in the experimental and
predicted binding affinity of the mutants.
Table 7. Tabular representation of the interatomic interactions
for the wild-type hypothetical hs CENP-HIKM complex. The first and
second column shows the chains and residues of interest, while the
remaining columns represent the observed interaction types (van der
Waals, hydrogen bond and hydrophobic interactions respectively).
Specific chains and residues that forms a interaction with the residues
of interest (wild-type residues) are presented in corresponding columns
for each interaction types.