Comparative Analysis of Mitonuclear Protein Interaction Interfaces and Conformational Differences Between the T3 and I1 Mitochondrial Haplogroups in Mongolian Cattle

Abstract Background Coordination between the mitochondrial and nuclear genomes is essential for the assembly and function of oxidative phosphorylation (OXPHOS) complexes. However, whether structural differences occur at mitonuclear protein interfaces between the T3 and I1 mitochondrial haplogroups in Mongolian cattle remains unclear. We compared mitochondrially encoded protein sequences from 10 Mongolian cattle per haplogroup. We integrated bovine OXPHOS complex structures, AlphaFold 3 predictions, docking with High Ambiguity Driven protein–protein DOCKing (HADDOCK), and Protein–Ligand Interaction Profiler (PLIP) and contact-map analyses to assess associations between amino acid substitutions and local structural differences at mitonuclear interfaces. Results Nineteen amino acid substitutions consistently distinguished the haplogroups across eight mitochondrially encoded proteins. Eight occurred at mitonuclear interfaces involving nine nuclear-encoded interaction partners and 11 candidate interaction pairs. Overall backbone conformations were largely conserved between haplogroups, whereas differences were concentrated in local contact networks near substitution sites. Notable haplogroup-associated contact differences occurred at the ND4–NDUFA8 and ND5–NDUFA11 interfaces in complex I and the ATP8–ATP5PD interface in complex V. Because confidence in the ATP8 model was relatively low, the ATP8–ATP5PD results should be interpreted cautiously. Conclusions These findings identify three key candidate mitonuclear interfaces for subsequent functional validation and provide structural clues for investigating mitonuclear interaction mechanisms.