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_TRFH and TRF2_TRFH in the presence/absence of the TIN2_TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results suggest that TIN2_TBM is necessary to ensure the stability of TRF1_TRFH homodimer but not the TRF2_TRFH homodimer. In TRF1-TIN2-TRF2 complex, the peptide enhances the protein-protein interactions to yield a stable heterodimer. Both monomers in TRF1_TRFH homodimer interact almost equally with the peptide, whereas in TRF2_TRFH homodimer, monomer TRF2_TRFH(M1) exhibits more dominant interactions than the TRF2_TRFH(M2). The common residues of TRF1/2_TRFH(M1) that form interactions with TIN2_TBM in all peptide-bound systems originate from the H3 (helix) and L3 (loop) regions. Additionally, in the homodimer systems, residues of TRF1/2_TRFH(M2) also interact with the peptide. The residue pair E71-K213 is responsible for different conformations of TRF1_TRFH homodimers; specifically, this residue pair enhances the protein-peptide/protein interactions in peptide-bound/unbound systems, respectively. TRF1_TRFH and TRF2_TRFH proteins have a conserved but different interface responsible for the protein-protein/peptide interactions that exist in the corresponding dimers.