. Author manuscript; available in PMC: 2023 Jul 28.

Published in final edited form as: Proteins. 2022 Dec 13;91(4):555–566. doi: 10.1002/prot.26449

TABLE 3.

Energy (kcal/mol) obtained from MMPBSA calculations.

Model No.	Organism	Mutation	$Δ Δ E_{vdw}$	$Δ Δ E_{coul}$	$Δ Δ E_{PB}$	$Δ Δ W_{np}$	$Δ Δ E_{el}$	$Δ Δ E_{np}$	$Δ Δ E_{bind}$
1, 3	Human	W50A	−0.40	−21.67	20.54	0.07	−1.13	−0.33	−1.46
2, 4	Human	W50A	−4.82	−37.19	32.33	6.93	−4.86	2.11	−2.75
1, 5	Human	Y68A	−3.95	−28.66	11.40	1.59	−17.26	−2.36	−19.62
2, 6	Human	Y68A	−2.64	−65.20	48.45	−0.09	−16.75	−2.73	−19.48
15, 17	Mouse	W50A	−2.30	−0.93	−3.65	4.80	−4.57	2.50	−2.08
16, 18	Mouse	W50A	0.72	−21.51	14.70	4.58	−6.81	5.30	−1.51
15, 19	Mouse	Y68A	1.77	−86.55	72.45	−4.38	−14.10	−2.62	−16.72
16, 20	Mouse	Y68A	−0.48	−52.27	36.56	−1.72	−15.71	−2.20	−17.91

Note: The energy is computed according to the final 25-ns simulations of human and mouse MEIG1–PACRG complexes. $Δ Δ E_{vdw}$ and $Δ Δ E_{coul}$ are the van der Waals and electrostatic interactions, respectively, between the wild type and mutants. $Δ Δ W_{PB}$ is the polar solvation free energy calculated by the Poisson–Boltzmann model. $Δ Δ W_{np}$ is the nonpolar contribution of the solvation energy. $Δ Δ E_{el}$ represents the sum of $Δ Δ E_{coul}$ and $Δ Δ W_{PB}$ . $Δ Δ E_{np}$ represents the sum of $Δ Δ E_{vdw}$ and $Δ Δ W_{np}$ . ΔΔ indicates the changes between the calculations from the mutated and wild type state. The model numbers in the first column indicate the two states used to calculate ΔΔ.

Abbreviations: MEIG1, meiosis-expressed gene 1; MMPBSA, Molecular Mechanics Poisson–Boltzmann Surface Area; PACRG, Parkin co-regulated gene.