MD simulation of the HIV-1 gp120 outer domain.
The V3 subset conferring the neutralization-resistant phenotype is referred to in this study as rV3: it has net positive charges of +2 to +4, an N-glycosylation site, and a capability to direct viral CCR5 tropism. The non-rV3 renders HIV-1 more susceptible to blood antibody neutralization. It has net positive charges of greater than +4 and a capability to direct viral CXCR4 tropism. (A) Examples of the MD simulation of two recombinant virus p120 outer domains with rV3 (TH09) and non-rV3 (B1). Distance between the Cα atom of P318 at the V3 tip and the Cα atom of Q433 at the β20β21 loop were monitored for 5 nanoseconds. (B) Superimposition of the gp120 monomers with the TH09 V3 (blue) or B1 V3 (red) at the simulation time of 5 nanoseconds. (C) Close-up view of the base-stem region of the TH09 V3. Orange dotted lines around the tip of the orange arrow indicate three hydrogen bonds at the V3 base. (D) Shannon entropy scores of the amino acids at the positions of 330, 332, and 424 in the public database. The positions in the gp120 of the HIV-1LAI  are used for the amino acid numbering.