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Since rapidly increasing three-dimensional structure complexes in Protein Data Bank (PDB), many structure-based works have been proposed to utilize physical interacting interfaces of these complexes to study protein-protein interactions [ 7- 10], MHC-peptide interactions [ 11, 12], and structural systems biology [ 13- 15].
Then, the MCLE analysis of the wt native state reveals two interacting interfaces for PrPC ligands acting as inhibitors of the misfolding process, either through antibody binding (residues 141 147) or through chemical chaperone interference (residues 187 198).
Using computed MSEP of pMHC and TR interacting interfaces we are able to successfully explain the common docking geometry of almost all TR proteins on their respective pMHC binding interfaces.
The DNA and CBF-β interfacesg interfares are on opposite sides of the Runt domain.
The interacting interfaces are slightly different from those in BPP-1, but nonetheless, are also complementary to other another.
Analyses of various interacting interfaces between linear peptide and protein domains help us in distinguishing transient and permanent complexes [20 22].
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The influence on binding of disordered regions outside the interacting interface has been theoretically predicted [32] and experimentally observed before [33].
Approaches have included the use of complete gene sequences, conserved regions and regions at the interacting interface.
We considered two residues as interacting (interface residue) if their corresponding Cβ atoms are within a distance of 7 Å (Malhotra et al., 2014).
We consider two residues as interacting (interface residue) if their corresponding Cβ atoms were found within the distance of 7 Å (Malhotra et al., 2014 ).
We propose that Ndc80 comprises two microtubule-interacting interfaces: the N-terminal region directly binds the microtubule lattice, while the internal loop interacts with the plus end of microtubules via Dis1/TOG.
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