The third variable (V3) element of the human immunodeficiency virus type 1 (HIV-1) envelope gp120 protein is usually composed of 35 amino acids. The element forms a protruding loop-like structure on the gp120 outer domain, is rich in basic amino acids, and has aromatic amino acids for the aromatic stacking interaction with proteins. The V3 loop participates in direct binding to the entry coreceptor and constitutes the most critical determinant for the coreceptor use of HIV-1.

In addition, the tip of V3 is highly immunogenic and contains neutralization epitopes for antibodies although the epitopes can be inaccesible in the gp120 trimer on a virion of the HIV-1 primary isolates or HIV-1 recombinants with less positively charged V3. Moreover, the V3 is reported to be the major determinant of HIV-1 sensitivity to neutralization by the soluble form of CD4, a recombinant protein that binds to the cleft of the gp120 core]. Thus, the V3 loop plays a key role in modulating biological and immunological phenotypes of HIV-1. However, the molecular mechanisms underlying these modulations remain poorly understood.

It has been reported that the net charge of the V3 loop is tightly linked to the phenotype of HIV-1. The V3 loops of CCR5 tropic HIV-1s are usually less positively charged than those of CXCR4 tropic HIV-1s. An increase in the V3 net charge can convert CCR5 tropic viruses into CXCR4 tropic viruses, and antibody resistant viruses into sensitive viruses. Thus the V3 loop may be viewed as an electrostatic modulator of the structure of the gp120 interaction surface, an assumption that is largely unexamined.

Increasing evidence has indicated that the dynamics property of molecules in solution is critical for protein function and thus for many biological processes. Molecular dynamic (MD) simulation is a powerful method that predicts the structural dynamics of biological molecules in solution, which is often difficult to analyze by experiments alone. Recent advances in biomolecular simulation have rapidly improved the precision and application performance of this technique. We have previously applied this technique to investigating the structural factors that regulate biological phenotype of viruses. In this study, by combining MD simulations with antibody neutralization experiments and diversity analysis of the viral protein sequences, we studied a structural basis for the regulation of HIV-1 phenotype by V3 loop.