Paradigm development: comparative and predictive 3D modeling of HIV-1 Virion Infectivity Factor (Vif)

Abstract

Obtaining structural information about Vif is of interest for several reasons that include the study of the interaction of Vif with APOBEC3G, a resistance factor. Vif is a potential drug target and its function is essential for the HIV-1 infectivity process. To study Vif mechanism of action, we need to decipher its structure. Pivotal in this approach is the painstaking prediction of its protein structure. The three-dimensional (3D) crystal structure for Vif has not been established. In order to understand its mechanism of action, information on the structure of Vif is very much needed. Therefore we undertook this study based on the hypothesis that information from structurally homologous proteins can be used to predict the 3D structure of Vif by computer modeling and threading. As a result the structure of HIV-1 Vif has been modeled and deposited in the theoretical models section and accepted with the PDB code 1VZF. Here, we present the results of the comparative modeling strategy we used to predict the 3D structure of Vif.

Figure 1

Sequence alignment between target (Vif) and template (PDB: 1BK0) shows 24.667% sequence identity

Figure 2

Secondary structure profile of Vif shown in A and for the template (1BK0) in B

Figure 3

Structural alignment of template [PDB ID: 1BK0] and target (HIV- 1Vif). Aligned regions are shown in blue whereas unaligned regions are shown in green color. Target is superimposed and shown in red color

Figure 4

Structure of the template [PDB ID: 1BK0].Regions of the templates used for modeling is shown in blue and those regions not used for modeling is shown in green color

Figure 5

The Ramachandran plot of the protein Vif (for details refer text)

Figure 6

(a), (b) & (c) Ramachandran plots for individual amino acids in the protein Vif (for details refer text)

Figure 7

(a) & (b) Side-chain torsion angle plots (chi1 & chi2) for the modeled protein

Figure 8

(a) Main-chain parameters for Vif; (b) Side-chain parameters for Vif (for details refer text)

Figure 9

(a) & (b): Residue properties for Vif (for details refer text)

Figure 10

(a) Main-chain bond lengths of the protein Vif (for details refer text); (b), (c): Main-chain bond angles of the protein Vif (for details refer text)

Figure 11

(a) RMS distances from planarity for different planar groups in Vif (for details refer text); (b) Distorted geometry in Vif (for details refer text)

Figure 12

VERIFY3D plot for the modeled protein Vif

Figure 13

Structure of the final model of VIF (PDB code 1VZF) showing its secondary structural elements

Figure 14

Ser146 is in the highly conserved SLQXLA motif at positions 144–149, highlighted as yellow ‘ball and stick’ representation

Figure 15

(a) Mutation of Ser146 (red) with Ala 146 (blue), represented as stick model; (b) Magnified mutated area shows the hook like Serine 146 (red) and Alanine 146 (blue) shows the loss of the hydroxyl hook

Figure 16

Helical Wheel presents the nature of the C-terminal residues from 146-195, which has the highly conserved SLQXLA motif. Hydrophilic residues are represented as circles, hydrophobic residues as diamonds, potentially negatively charged as triangles, and potentially positively charged as pentagons. Hydrophobicity is color coded as well: the most hydrophobic residue is green, and the amount of green is decreasing proportionally to the hydrophobicity, with zero hydrophobicity coded as yellow. Hydrophilic residues are coded red with pure red being the most hydrophilic (uncharged) residue, and the amount of red decreasing proportionally to the hydrophilicity. The potentially charged residues are light blue

Figure 17

Kyte and Doolittle's hydropathy plot for Vif C-terminal (for details refer text)

Figure 18

(a) & (b): Visualization of the helix-helix interaction for helices 2 and 3 (Left-hand side), as well as 2 and 5 (Right-hand side) of Vif (PDB ID: 1VZF). Part (A) shows hydrogen bonding within the two helices with geometric characteristics. Part (B) focuses specifically on the helix-helix interface; the surface depicted between the helices is formed by the shared polyhedra faces derived from the Voronoi packaging calculation

Figure 19

The electrostatic potential of the Vif structure shows the basic charge distribution on the surface of the model. Electrostatic potentials are computed using simple coulomb interaction by DeepView

Figure 20

(a) Computed molecular surface of the modeled Vif, colored by electrostatic potential; (b) The hydroxyl hook of Ser 146 partially obstructing the cleft is marked by an arrow in (a) is magnified here

Figure 21

(a) Computed solvent accessible surface of the modeled Vif, showing transparent secondary structural elements; (b) Magnified figure shows the hydroxyl hook (in front of cleft) of neutral amino acid (Ser 146) and an acidic amino acid Asp 106, which is nearer to this