Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics

Table 2 Binding energies (kcal/mol) between PR and its substrates calculated with MM/PBSA.

		ΔG_vdw	ΔG_ele	ΔG_sol/elec	ΔG_sol/np	ΔG_b^a_total	ΔΔG_b^b
CA-p2	consB	-75.7 ± 4	-82 ± 6	92.2 ± 12.1	-7.1 ± 0.4	-72.6 ± 2.8	-4.1
	M36I	-73.5 ± 5	-75.3 ± 5	87.6 ± 11	-7.3 ± 0.3	-68.5 ± 2.9
MA-CA	consB	-94.7 ± 4	-66.2 ± 9	141.3 ± 14	-8.5 ± 0.4	-28.1 ± 3.4	-7.2
	M36I	-84.4 ± 7	-70.4 ± 6	142.8 ± 14	-8.9 ± 0.4	-20.9 ± 3.1
p1-p6	consB	-85.7 ± 3	47 ± 7	-12.7 ± 9.9	-7.4 ± 0.4	-58.8 ± 1.5	-1.6
	M36I	-79.9 ± 5	37.2 ± 8	-7.7 ± 8	-6.8 ± 0.3	-57.2 ± 1.3
p2-NC	consB	-84.9 ± 4	-51.6 ± 5	57.7 ± 12.1	-7.5 ± 0.3	-86.3 ± 2.1	-4.8
	M36I	-79.6 ± 3	-64.3 ± 5	70.4 ± 13	-8 ± 0.3	-81.5 ± 2.3
RH-IN	consB	-74.9 ± 6	-72.4 ± 6	113.4 ± 19	-7.3 ± 0.4	-41.2 ± 2.8	4.9
	M36I	-80.5 ± 7	-77.4 ± 9	120.5 ± 17	-8.7 ± 0.3	-46.1 ± 2.6
RT-RH	consB	-77.6 ± 6	-307.1 ± 6	356.8 ± 14	-7.3 ± 0.4	-35.2 ± 1.9	0.6
	M36I	-76.5 ± 7	-298.1 ± 12	346.1 ± 12	-7.3 ± 0.3	-35.8 ± 1.5

^aThe entropic contribution " -TΔS", is not included (see methods for details)
^bDifference from the WT binding energies $(ΔΔ G_{b} = Δ {G_{b}}^{WT} - Δ {G_{b}}^{M36I})$

ISSN: 1471-2164