Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2–MND1

The
HOP2–MND1 heterodimer is essential for meiotic homologous
recombination in plants and other eukaryotes and promotes the repair
of DNA double-strand breaks. We investigated the conformational flexibility
of HOP2–MND1, important for understanding the mechanistic details
of the heterodimer, with chemical cross-linking in combination with
mass spectrometry (XL–MS). The final XL–MS workflow
encompassed the use of complementary cross-linkers, quenching, digestion,
size exclusion enrichment, and HCD-based LC–MS/MS detection
prior to data evaluation. We applied two different homobifunctional
amine-reactive cross-linkers (DSS and BS2G) and one zero-length
heterobifunctional cross-linker (EDC). Cross-linked peptides of four
biological replicates were analyzed prior to 3D structure prediction
by protein threading and protein–protein docking for cross-link-guided
molecular modeling. Miniaturization of the size-exclusion enrichment
step reduced the required starting material, led to a high amount
of cross-linked peptides, and allowed the analysis of replicates.
The major interaction site of HOP2–MND1 was identified in the
central coiled-coil domains, and an open colinear parallel arrangement
of HOP2 and MND1 within the complex was predicted. Moreover, flexibility
of the C-terminal capping helices of both complex partners was observed,
suggesting the coexistence of a closed complex conformation in solution.