Table 1.

Results of molecular dynamics simulations (MD) for the kissing loop complexes of the HIV-1 wild type structures and the mutants derived from it and used in tectosquare design and modeling. The redesigned sequences are listed explicitly in Fig. 1. Mean RMSDs were calculated relative to the starting states of the production MD runs. PDB ids in the parentheses indicate the NMR (2F4X) and X-ray crystallography (1PXE and 2B8R) data used as the starting structures in MD simulations. The MD Conditions column indicates variations in the neutralizing ions and salt conditions. For example, Na⁺; NaCl indicates that sodium ions were used to neutralize phosphate group charges along the backbone and Na⁺/Cl⁻ pairs were added to the solvent. The word “Restraints” indicated parabolic restrains added to the hydrogen bonds of the Watson–Crick base pairs at the 5′ and 3′ ends of each of two chains comprising the KL complex. All MD simulations were performed for approximately 20 ns, with exception of the 25 ns run for the lowest (in the table) WT kissing loop structure, from which all four mutants were derived. Refer to the text for the details of MD protocols and the definitions of the angles listed (Section 3.2 and 4.1).

Kissing loop	MD conditions	Mean RMSD, (Angstrom)	Mean Bending angle	Mean Torsion angle	Min. torsion angle	Max torsion angle
WT HIV-1 (2F4X)	Na+; NaCl	4.8 ± 1.0	139.5 ± 10.4	−8.5 ± 18.9	−57.3	+36.8
WT HIV-1 (1XPE)	Na+ and Mg2+; MgCl2	3.9 ± 0.7	155.8 ± 7.5	20.5 ± 11.6	−15.4	+61.9
WT HIV-1 (2B8R)	Na+; NaCl; Restraints	4.1 ± 1.1	160.1 ± 9.4	14.9 ± 18.1	−40.3	+60.0
WT HIV-1 (2B8R)	Na+ only	5.1 ± 1.1	160.4 ± 9.1	−8.1 ± 14.2	−54.5	+47.9
WT HIV-1 (2B8R)	Na+; NaCl	2.6 ± 0.6	161.3 ± 8.8	−5.7 ± 11.7	−40.2	+44.1
MUT A1D2	Na+; NaCl	2.3 ± 0.6	163.3 ± 10.3	11.4 ± 15.1	−37.2	+51.5
MUT A2B1	Na+; NaCl	2.6 ± 0.5	163.6 ± 7.2	1.8 ± 13.7	−39.0	+46.6
MUT B2C1	Na+; NaCl	2.5 ± 0.6	155.7 ± 11.1	−3.6 ± 11.6	−40.0	+33.3
MUT C2D1	Na+; NaCl	2.8 ± 0.7	154.5 ± 12.7	−11.3 ± 14.7	−48.1	+32.8