Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop

Abstract

HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity.

Figure 1

Molecular graphics image of the entire simulation system corresponding to the complex with the lowest average binding free energy. The V3 loop is shown in tube and transparent surface representation in red color, and its 16–20 residue moiety is shown in thick tube representation. The CXCR4 is shown in cartoon representation, and the coloring used for different protein domains is as follows: (blue) N-terminal domain; (green) intramembrane helix 1 (IH1); (light gray) intracellular loop 1 (ICL1); (purple) IH2L; (light gray) ECL1; (yellow) IH3; (light gray) ICL 2; (medium gray) IH4; (ochre) ECL2; (pink) IH5; (light gray) ICL3; (cyan) IH6; (lime) ECL3; (orange) IH7; and (light gray) C-terminal domain. (van der Waals sphere) N-terminal Cα atom of CXCR4. (Thick transparent licorice representation) V3 loop disulfide bridge. The definition of CXCR4 and V3 loop domains is presented in the Supporting Material (colors appear in the online version only).

Figure 2

Molecular graphics images of important polar interactions corresponding to the complex with the lowest average binding free energy. Panels (A) and (B) depict the salt bridges and the most important hydrogen bonds, respectively, according to residue pair-wise interaction free energies. Panel (B) is rotated by approximately 180° with respect to (A) around the z (membrane) axis. The V3 loop is shown in tube and in red color, and its 16–20 residue moiety is shown in fat tube representation. The CXCR4 is shown in light gray transparent tube representation. The salt bridge and hydrogen bonds in panels (A) and (B) are denoted in dashed lines and the participating V3 loop and CXCR4 residue moieties are shown in licorice; V3 loop and CXCR4 residues are annotated in red and black, color respectively. Hydrogen atoms are omitted for clarity and the V3 loop disulfide bridge is shown in fat transparent licorice representation. (colors appear in the online version only).