Natural variant frequencies across domains from different sarcomere proteins cross-correlate to identify inter-protein contacts associated with cardiac muscle function and disease

Coordinated sarcomere proteins produce contraction force for muscle shortening. In human ventriculum they include the cardiac myosin motor (βmys), repetitively converting ATP free energy into work, and myosin binding protein C (MYBPC3) that in complex with βmys is regulatory. Single nucleotide variants (SNVs) causing hereditary heart diseases frequently target this protein pair. The βmys/MYBPC3 complex models a regulated motor and is used here to study how the proteins couple. SNVs in βmys or MYBPC3 survey human populations worldwide. Their protein expression modifies domain structure affecting phenotype and pathogenicity outcomes. When the SNV modified domain locates to inter-protein contacts it could affect complex coordination. Domains involved, one in βmys the other in MYBPC3, form coordinated domains (co-domains). Co-domain bilateral structure implies the possibility for a shared impact from SNV modification in either domain suggesting a correlated response to a common perturbation could identify their location. Genetic divergence over human populations is proposed to perturb SNV probability coupling that is detected by cross-correlation in 2D correlation genetics (2D-CG). SNV probability data and 2D-CG identify three critical sites, two in MYBPC3 with links to several domains across the βmys motor, and, one in βmys with links to the MYBPC3 regulatory domain. MYBPC3 sites are hinges sterically enabling regulatory interactions with βmys. The βmys site is the actin binding C-loop (residues 359-377). The C-loop is a trigger for actin-activated myosin ATPase and a contraction velocity modulator. Co-domain identification implies their spatial proximity suggesting a novel approach for in vivo protein complex structure determination. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43556-021-00056-x.