Fig. 2: Energy profiles govern co-translational interface formation.
a Interface energy contribution (ΔΔG [kcal/mol]) per residue in each subunit, as calculated by MMPBSA along the last 20 ns of the 300 ns simulations, at 25 °C. 500 evenly spaced frames were sampled. Both NatA auxiliary and NatB catalytic subunits have a cluster of residues crucial for interface formation just before co-translational interaction initiates, indicated by a dashed line. Mean ± SD, n = 3 independent production simulations. b Cumulative binding free energy, with all the contributions normalized to ΔG < 1. The cluster of residues crucial for interface formation can be seen as the steep fall in the cumulative energy, 30 residues before the co-translational interaction initiates, indicated by a dashed line. The cumulative distributions were found to be significantly different based on two-sample Kolmogorov-Smirnov test with a p value = 1.688e-09 for the catalytic subunits and p value = 2.313e-07 for the auxiliary subunits. c Interface residues according to the cryo-EM structures, as determined by Cα-atoms in a 4 Å proximity from a Cα-atom of its partner subunit, displayed as orange spheres. d Interface Cα-atoms which contribute < −2 kcal/mol ΔΔG to interface formation, displayed as red spheres. e Chaperones binding sites, as obtained by SeRP (data derived from accession code GSE93830), displayed as violet spheres. f Ribosome binding sites, as obtained from solved structures of NatA (PDB: 6HD7) and NatB (PDB: 8BIP) on the ribosome, displayed as light blue spheres. Cα-atoms within 4 Å from any heavy atoms of the ribosome are marked. g Electrostatic potentials as calculated by the Adaptive Poisson–Boltzmann Solver81,82 (APBS). The colors [red, white, blue] are mapped on a [−10, 0, 10] range in units of kJ/mol/e. NatA and NatB display diverging electrostatic potentials, contributing to the diverging interface energy profiles. NatA catalytic subunit’s unique IDRs, participating in interface formation, display strong negative potential, which is complemented by the NatA auxiliary subunits’ positive potential.
