Oligomeric modeling and electrostatic analysis of the gp120 envelope glycoprotein of human immunodeficiency virus

Abstract

The human immunodeficiency virus envelope glycoproteins, gp120 and gp41, function in cell entry by binding to CD4 and a chemokine receptor on the cell surface and orchestrating the direct fusion of the viral and target cell membranes. On the virion surface, three gp120 molecules associate noncovalently with the ectodomain of the gp41 trimer to form the envelope oligomer. Although an atomic-level structure of a monomeric gp120 core has been determined, the structure of the oligomer is unknown. Here, the orientation of gp120 in the oligomer is modeled by using quantifiable criteria of carbohydrate exposure, occlusion of conserved residues, and steric considerations with regard to the binding of the neutralizing antibody 17b. Applying similar modeling techniques to influenza virus hemagglutinin suggests a rotational accuracy for the oriented gp120 of better than 10 degrees. The model shows that CD4 binds obliquely, such that multiple CD4 molecules bound to the same oligomer have their membrane-spanning portions separated by at least 190 A. The chemokine receptor, in contrast, binds to a sterically restricted surface close to the trimer axis. Electrostatic analyses reveal a basic region which faces away from the virus, toward the target cell membrane, and is conserved on core gp120. The electrostatic potentials of this region are strongly influenced by the overall charge, but not the precise structure, of the third variable (V3) loop. This dependence on charge and not structure may make electrostatic interactions between this basic region and the cell difficult to target therapeutically and may also provide a means of viral escape from immune system surveillance.

FIG. 1

Coordinate system used to model the envelope oligomer shown in the context of the various interactions of gp120 during virus-cell attachment. CD4 (yellow) is shown reaching from the target cell membrane (gray) to bind gp120 (120; brownish red), which is arranged in a symmetrical fashion around the ectodomain of the trimeric gp41 (41; blue), shown jutting out of the viral membrane (orange). The V3 loop (green) can be seen on gp120 just above the cell membrane. The coordinate system used for modeling has the z axis coincident with the gp41 trimer axis, the x axis connecting the center of mass of a gp120 protomer with the z axis, and the y axis mutually perpendicular to the x and z axis and sharing a common origin. Thus, X and Y rotations (that is, about the x axis and y axis, respectively) specify the orientation of a gp120 protomer with respect to the membranes, and rotations about the z axis determine the orientation with respect to the envelope oligomer.

FIG. 2

Quantitative modeling of the gp120 oligomer. Quantitative modeling employed three criteria: carbohydrate exposure (open circles), occlusion of conserved residues which are solvent exposed on a gp120 protomer (filled symbols), and steric considerations of 17b binding (forbidden regions [shaded]). These criteria have been graphed with respect to their distances from the trimer axis (depicted here on the vertical axis) as the rotational parameter (horizontal axis) was varied. The coordinate system was as defined in the legend to Fig. 1. (a) Rotational orientation of the HIV gp120 core. (Left panel) The orientations of X and Y in this panel were determined by the superposition of CD4 in the gp120-CD4 complex (32) with its orientation in the four-domain CD4 structure (60). The maximum (filled squares) and minimum (filled triangles) distances of the conserved, solvent-exposed residues from the trimer axis were determined at 10° intervals in Z; minimum values correspond to regions of greater oligomer occlusion. The distance of the carbohydrate (open circles) from the trimer axis is shown at 10° intervals; peaks correspond to carbohydrate-free regions at which the overall exposure of carbohydrate is greatest. The highest peak in this panel corresponds to a large carbohydrate-free region centered about the first helix in the inner domain of core gp120 (32). The second-highest peak corresponds to the CD4 binding site, which is also free of carbohydrate. (Middle panel). Given the optimal Z orientation, rotations were made around the x axis. Here the minimum and maximum distances for the conserved, solvent-exposed residues have been averaged (filled triangles). The 0 of the X rotation corresponds to the orientation of X as determined by the initial superposition with CD4. (Right panel) Given the optimal orientation for X and Z as determined in the previous two panels, the remaining rotational axis was varied. Again, the minimum and maximum distances for the conserved, solvent-exposed residues have been averaged (filled triangles). The extended carbohydrate-free region corresponds to the overlap between the carbohydrate-free chemokine receptor region and the presumed oligomer interface. Steric constraints from binding of the 17b antibody (forbidden regions [shaded]) helped to distinguish these regions. As with the X rotation, the 0 of the Y rotation corresponds to the orientation of Y as determined by the initial superposition with CD4, independent of the modeling criteria used here. (b) Surface criterion optimization of the influenza virus hemagglutinin HA top. The origin of each panel corresponds to the orientation of the HA top superimposed on the HA1-HA2 heterotrimer (59). The symbols used for the criteria are the same as described for panel a. (c) Surface criteria depicted from the perspective of the viral membrane at the (0° 0° 30°) orientation for the gp120 core and the (0° 0° 0°) orientation for the HA top. (Left image) the gp120 core is depicted as a copper-brown Cα backbone worm. The molecular surfaces of all of the N-acetylglucosamine residues used in the modeling are colored cyan. The molecular surfaces of the side chains of the conserved exposed residues on the monomeric gp120 core are colored magenta. The gp120 protomer has been positioned such that the distance of its center of mass from the trimer axis is proportional to that observed in hemagglutinin. (Right image) The HA top is depicted as a black Cα backbone worm. The molecular surfaces of side chains that are sites of glycosylation in at least 1% of the 485 aligned hemagglutinin sequences are shown in blue. The molecular surfaces of side chains which are conserved and exposed on the HA top monomer are colored magenta. The orientation shown here corresponds to the superposition of the HA top onto the HA1-HA2 heterotrimer.

FIG. 2

Quantitative modeling of the gp120 oligomer. Quantitative modeling employed three criteria: carbohydrate exposure (open circles), occlusion of conserved residues which are solvent exposed on a gp120 protomer (filled symbols), and steric considerations of 17b binding (forbidden regions [shaded]). These criteria have been graphed with respect to their distances from the trimer axis (depicted here on the vertical axis) as the rotational parameter (horizontal axis) was varied. The coordinate system was as defined in the legend to Fig. 1. (a) Rotational orientation of the HIV gp120 core. (Left panel) The orientations of X and Y in this panel were determined by the superposition of CD4 in the gp120-CD4 complex (32) with its orientation in the four-domain CD4 structure (60). The maximum (filled squares) and minimum (filled triangles) distances of the conserved, solvent-exposed residues from the trimer axis were determined at 10° intervals in Z; minimum values correspond to regions of greater oligomer occlusion. The distance of the carbohydrate (open circles) from the trimer axis is shown at 10° intervals; peaks correspond to carbohydrate-free regions at which the overall exposure of carbohydrate is greatest. The highest peak in this panel corresponds to a large carbohydrate-free region centered about the first helix in the inner domain of core gp120 (32). The second-highest peak corresponds to the CD4 binding site, which is also free of carbohydrate. (Middle panel). Given the optimal Z orientation, rotations were made around the x axis. Here the minimum and maximum distances for the conserved, solvent-exposed residues have been averaged (filled triangles). The 0 of the X rotation corresponds to the orientation of X as determined by the initial superposition with CD4. (Right panel) Given the optimal orientation for X and Z as determined in the previous two panels, the remaining rotational axis was varied. Again, the minimum and maximum distances for the conserved, solvent-exposed residues have been averaged (filled triangles). The extended carbohydrate-free region corresponds to the overlap between the carbohydrate-free chemokine receptor region and the presumed oligomer interface. Steric constraints from binding of the 17b antibody (forbidden regions [shaded]) helped to distinguish these regions. As with the X rotation, the 0 of the Y rotation corresponds to the orientation of Y as determined by the initial superposition with CD4, independent of the modeling criteria used here. (b) Surface criterion optimization of the influenza virus hemagglutinin HA top. The origin of each panel corresponds to the orientation of the HA top superimposed on the HA1-HA2 heterotrimer (59). The symbols used for the criteria are the same as described for panel a. (c) Surface criteria depicted from the perspective of the viral membrane at the (0° 0° 30°) orientation for the gp120 core and the (0° 0° 0°) orientation for the HA top. (Left image) the gp120 core is depicted as a copper-brown Cα backbone worm. The molecular surfaces of all of the N-acetylglucosamine residues used in the modeling are colored cyan. The molecular surfaces of the side chains of the conserved exposed residues on the monomeric gp120 core are colored magenta. The gp120 protomer has been positioned such that the distance of its center of mass from the trimer axis is proportional to that observed in hemagglutinin. (Right image) The HA top is depicted as a black Cα backbone worm. The molecular surfaces of side chains that are sites of glycosylation in at least 1% of the 485 aligned hemagglutinin sequences are shown in blue. The molecular surfaces of side chains which are conserved and exposed on the HA top monomer are colored magenta. The orientation shown here corresponds to the superposition of the HA top onto the HA1-HA2 heterotrimer.

FIG. 3

Trimeric model of gp120. Three orientations of the model are shown. The images at the top depict the view from the orientation of the viral membrane. The middle images depict the view from the side, in between the viral and target cell membranes. The images at the bottom depict the view from the target cell membrane. The left-most three images are Cα worm representations of core gp120 (copper brown) and the two membrane-distal domains of CD4 (yellow). Also shown are the gp120 carbohydrate cores (blue), the (N-acetylglucosamine)₂-(mannose)₃ cores shared by both high-mannose and complex N-linked glycan moieties. The carbohydrate shown here represents approximately half the carbohydrate on gp120, with the rest extending further from the gp120 surface. The middle images show the electrostatic surface of gp120 for the core. The electrostatic potential is depicted at the solvent-accessible surface, which is colored according to the local electrostatic potential, ranging from dark blue (most positive) to red (negative). The right-most images show the gp120 core with carbohydrate, with the solvent-accessible surface colored cyan for carbohydrate, yellow for the surface of gp120 less than 3 Å from CD4, green for the surface of gp120 less than 3 Å from the 17b antibody, and copper brown for the remaining surface of core gp120. The degree to which carbohydrate covers all of the solvent-accessible trimer surface is remarkable. Other than a small region at the viral proximal portion of the oligomer (where the missing N and C termini most likely reside), the only carbohydrate-free surfaces large enough to serve as an antibody epitope correspond to regions of receptor binding.

FIG. 4

Robustness of the basic cell-facing surface of core gp120 to variations in modeling parameters. The oligomer modeling was dependent on four independent parameters, one translational (trans) and three rotational (rot). The effect of varying these parameters on the basicity of the cell-facing surface of the proposed envelope oligomer is shown here. All of the images in this figure are depicted from the view of the target cell membrane. A Cα worm diagram of core gp120 (copper brown) with carbohydrate (blue) is shown to aid in orienting each variation in modeling parameter. The surface diagrams depict the local electrostatic potential. A dark blue (basic) surface can be seen on core gp120 (HIV-1, HXBc2 isolate) in all modeling parameter variations.

FIG. 5

Conservation of basic cell-facing surface on core gp120. Homology modeling was used to construct the corresponding structures of core gp120 for HIV-1 clades C and O as well as HIV-2 and SIV, starting with the crystal structure of HIV-1 clade B core gp120 (32) modeled as the envelope oligomer. The electrostatic potentials are depicted at the solvent-accessible surface, from the perspective of the target cell membrane. A basic (dark blue) surface can be seen in all isolates, although the precise charge distribution and the degree of overall basicity show variation.

FIG. 6

Modeling and electrostatic contribution of the V3 loop. (a) Different V3 loop models were constructed: alpha (green), beta (dark green; toward the back left of gp120 in this orientation), Haiti (forest green; depicted as the front right model in this orientation), and nmr (light green) (see text for details). These are displayed as Cα worm diagrams in the context of core gp120 (copper brown) and the 17b Fab fragment (purple violet). As can be seen, steric constraints, primarily from 17b, separate the V1/V2 stem from the V3 loop on a gp120 protomer, although quite diverse V3 loop structures can be successfully grafted onto the gp120 core. The position of the trimer axis (as determined by quantitative modeling) and the N and C termini of core gp120 are labeled for reference. (b) Cα worm diagrams for the different V3 loops (green) are depicted by themselves (top) and with core gp120 (copper brown) (bottom) for the HXBc2 strain of HIV-1 gp120 as arranged in the envelope oligomer. The orientation of each image is shown from the perspective of the target cell membrane. (c) Analysis of the electrostatic potential of the cell-facing region. Models of the trimeric gp120 core have been constructed with different V3 loops (described above for panels a and b), and the charge on the V3 loop for each of these structure has been varied between 0 and 9. For each of these 15 different models, the electrostatic potential has been calculated at various positions, either along the trimer axis x = 0 or below the center of mass of a protomer x = 35. Increasing numbers in z correspond to increasing distances away from gp120 (moving away from the virus). The position in z varies from z = 0, which corresponds to 0.5 Å below the gp120 core, to z = 40, which is 40.5 Å below the core but only approximately 25 Å below the V3 loop. The difference between core and V3 loop distances occurs because the V3 loop models extend roughly 15 Å below the core (as can be seen in panel a). (Left panels) The electrostatic potential from each model, that is, the three different V3 loop models shown in panel b, is graphed as a function of structure. No simple correspondence is seen. (Center and right panels) The electrostatic potential from each model is graphed as a function of charge. A rough linear correspondence is seen. This has been least-squares fitted (solid line), and the r² fit, which shows how well the data correlate to the line, is depicted (an r² of 1.0 corresponds to a perfect fit). The correlation is poor close to the gp120 core but increases as the distance from the virus increases. The dotted line corresponds to the least-squares fit if the potential is calculated for only the V3 loop. For the top three panels on the right, in order to use a reasonable scale, two outlier points, for charges of 6 and 9, are not depicted, although they have been used in the least-squares fitting.

FIG. 6

Modeling and electrostatic contribution of the V3 loop. (a) Different V3 loop models were constructed: alpha (green), beta (dark green; toward the back left of gp120 in this orientation), Haiti (forest green; depicted as the front right model in this orientation), and nmr (light green) (see text for details). These are displayed as Cα worm diagrams in the context of core gp120 (copper brown) and the 17b Fab fragment (purple violet). As can be seen, steric constraints, primarily from 17b, separate the V1/V2 stem from the V3 loop on a gp120 protomer, although quite diverse V3 loop structures can be successfully grafted onto the gp120 core. The position of the trimer axis (as determined by quantitative modeling) and the N and C termini of core gp120 are labeled for reference. (b) Cα worm diagrams for the different V3 loops (green) are depicted by themselves (top) and with core gp120 (copper brown) (bottom) for the HXBc2 strain of HIV-1 gp120 as arranged in the envelope oligomer. The orientation of each image is shown from the perspective of the target cell membrane. (c) Analysis of the electrostatic potential of the cell-facing region. Models of the trimeric gp120 core have been constructed with different V3 loops (described above for panels a and b), and the charge on the V3 loop for each of these structure has been varied between 0 and 9. For each of these 15 different models, the electrostatic potential has been calculated at various positions, either along the trimer axis x = 0 or below the center of mass of a protomer x = 35. Increasing numbers in z correspond to increasing distances away from gp120 (moving away from the virus). The position in z varies from z = 0, which corresponds to 0.5 Å below the gp120 core, to z = 40, which is 40.5 Å below the core but only approximately 25 Å below the V3 loop. The difference between core and V3 loop distances occurs because the V3 loop models extend roughly 15 Å below the core (as can be seen in panel a). (Left panels) The electrostatic potential from each model, that is, the three different V3 loop models shown in panel b, is graphed as a function of structure. No simple correspondence is seen. (Center and right panels) The electrostatic potential from each model is graphed as a function of charge. A rough linear correspondence is seen. This has been least-squares fitted (solid line), and the r² fit, which shows how well the data correlate to the line, is depicted (an r² of 1.0 corresponds to a perfect fit). The correlation is poor close to the gp120 core but increases as the distance from the virus increases. The dotted line corresponds to the least-squares fit if the potential is calculated for only the V3 loop. For the top three panels on the right, in order to use a reasonable scale, two outlier points, for charges of 6 and 9, are not depicted, although they have been used in the least-squares fitting.

FIG. 7

Selected features of the oligomeric gp120 model. (a) The entire extracellular portion of CD4 (yellow Cα worm) is shown binding to the oriented gp120 oligomer (copper-brown Cα worm). Carbohydrate on the gp120 is colored cyan. Distances between adjacent CD4 molecules are shown for the Cα of residue 178 at the end of the second domain and the Cα of residue 363, the last ordered residues prior to the transmembrane-spanning region. The contact region highlighted in panel b has been circled. The hemagglutinin proportionate model is used here, and thus the gp120 is close to the minimum protomer packing distance. (b) An enlargement of the contact site between gp120 core protomers in the oligomer. The coloring for one protomer is the same as in panel a; the other protomers are colored black. In addition, the molecular surfaces of side chains of conserved exposed residues in this contacting region (residues 195 to 210) are colored magenta. Starting from the top of the figure, these include residues 196, 197, 198, 201, 204, 208, and 209. Residue 197 is glycosylated, and its carbohydrate has been depicted in magenta. This region is sensitive to the binding of CD4, which is seen to the right of the figure in close proximity. The orientation of both images is shown from the perspective of the target cell membrane.