2.11. Computation of Dipole Moments

Dipole moments were computed for TM2b of the E. coli SecY translocon. Close inspection of the only high-resolution structure PDB ID:5GAE indicated that the distance between the Cα atoms of P398 and F399 is ~8Å, which is too long for two amino acid residues that ought to be covalently bound to each other. We thus prepared a homology model of the E. coli SecY translocon using the sequence UniProt ID {"type":"entrez-protein","attrs":{"text":"P0AGA2","term_id":"84028701","term_text":"P0AGA2"}}P0AGA2 as a template, and Phyre2 [20] for homology modeling. Hydrogen atoms were constructed using Chemistry at Harvard Molecular Mechanics (CHARMM) [21]. The protein was oriented along the membrane normal using visual molecular dynamics (VMD) [22] and placed with its center of mass in the center of coordinates. The L80D and L80K mutants of E. coli SecY were prepared using CHARMM. Partial atomic charges for the translocon atoms were taken from the CHARMM 36 all-atom force field [23,24,25]. The dipole moment computations were performed using VMD [22].