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.