The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2.

The telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1 and TRF2 in the presence/absence of the TIN2 (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results suggest that TIN2 is necessary to ensure the stability of TRF1 homodimer but not the TRF2 homodimer. In TRF1-TIN2-TRF2 complex, the peptide enhances the protein-protein interactions to yield a stable heterodimer. Both monomers in TRF1 homodimer interact almost equally with the peptide, whereas in TRF2 homodimer, monomer TRF2(M1) exhibits more dominant interactions than the TRF2(M2). The common residues of TRF1/2(M1) that form interactions with TIN2 in all peptide-bound systems originate from the H3 (helix) and L3 (loop) regions. Additionally, in the homodimer systems, residues of TRF1/2(M2) also interact with the peptide. The residue pair E71-K213 is responsible for different conformations of TRF1 homodimers; specifically, this residue pair enhances the protein-peptide/protein interactions in peptide-bound/unbound systems, respectively. TRF1 and TRF2 proteins have a conserved but different interface responsible for the protein-protein/peptide interactions that exist in the corresponding dimers.