STRUCTURAL DATA

Figure 1: PDB 4xfx , the hexamer structure of the native HIV-1 mature capsid protein.
(credit: Pierrick Craveur)





One Crystallographic (X-Ray) Data

When this project started, several X-ray structures of the mature capsid protein were available in the Protein Data Bank (PDB). Only one (PDB: 4xfx)[ref 1] corresponded to the full and native form, without any (engineered) mutations in the sequence of amino-acids.

The structure was solved after crystallization of the hexamer form of the capsid (see Figure 1), which is the building block of the whole capsid core of the HIV (see Figure 2 in the Home Page Overview).

The crystallographic data provides 3D coordinates of the most energetically favorable conformation of the protein needed to form a crystal. In this case, this data are a wealth of information on the topology of the structure and on the atomic interactions involve at the interface of two successive monomers.


Figure 2: The 2 models of the capsid core assembly.
(credit: Pierrick Craveur)

Two Models of the Core Assembly

After maturation of the virus, the CA protein assembles with thousands of copies to form the capsid Core. This cone shape assembly (see Figure 1 & 2 in the Home Page Overview) encloses the RNA viral genome. It will be the compartment for reverse transcription after entry of the HIV in the host cell, and his dissociation will lead to the importation of DNA viral genome in the host cell's nucleus.

When this project started, two models of the whole core were available in the PDB (3j3q & 3j3y). They are composed of ~200 hexamers, and exactly 12 pentamers are needed to close this particular shape (see Figure 2).

These models were built using crystallographic data, cryo-electron microscopy & tomographic images, and simulated molecular dynamics [ref 2].

The thousands of monomer structures used to build these models, provide a large set of different conformations which could be used to investigate the flexible behaviour of the capsid structure. Compare to the crystal conformation, the structures from these models include some slight differences at the interface of two monomers, which could be consequent to the cone's curvature.


References

  1. PDB 4xfx : Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. X-Ray Structures of Native HIV-1 Capsid Protein Reveal Conformational Variability. Science (New York, NY). 2015;349(6243):99-103.
  2. PDB 3j3q & 3j3y : Zhao G, Perilla JR, Yufenyuy EL, et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 2013;497(7451):643-646.


TARGET SELECTION

Figure 3: Distinction between backbone and side chains of the HIV-1 capsid monomer.
(credit: Pierrick Craveur)


Flow Chart

The selection of the targeted structures is a key step in a virtual screening campaign. The main idea behind this selection is to end with a set of structures which could represents as much as possible the different conformations that the ligands could face off when they will interact with the capsid proteins in the cell.
Indeed, sligth changes in the backbone conformation and/or in the side-chains orientation (see Figure 3) could lead to completely different results in docking experiments of the same drug.

Then, this is obvious that the flexibility study of the capsid is the main part of the selection process. Here the Flow Chart presents the successive steps which lead to the targets selection for this project.

First, based on the structure 4xfx and the thousands of structures from the two models 3j3q & 3j3y (see above), a study of the backbone flexibility was done. This leads to the identification of positions where the backbone is rigid in the vicinity of each of the 4 pockets of interest (see Figure 3 in the Home Page Overview).

Based on these positions the thousands of structures used to build the core models were aligned and compared. Structures which represent the most distributed conformations around each pocket were selected.

In parrallel, the flexibility of the side chains near each pockets were also investigated. The most flexible ones, for which the change in the orientation could considerably modify the binding sites of the ligands, were identified.

A total of 36 differents structures were selected, with specific combinaisons of side chains which have to be made flexible during the virtual screening. These combinaisons are function of the pocket on which the docking is focus, and of which context (Hexamer or Pentamer) the structure comes from.

See the summary of the selected targets in the table below.

SUMMARY TABLE


A total of 36 different structures of the HIV-1 capsid protein are used for the computations.


POCKETS Targets from HEXAMER Flexible Side Chains Combo PENTAMER Flexible Side Chains Combo
1 1 from crystal
5 from model
A-LYS70
F-SER41
F-ASN139
F-ARG173
F-LYS182
4 from model A-MET66
A-LYS70
F-ASN139
F-ARG173
F-LYS182
2 1 from crystal
3 from model
A-LYS170
A-ARG167
4 from model A-LYS170
A-ARG167
3 1 from crystal
3 from model
A-GLN13
F-LEU43
F-GLN13
4 from model A-GLN13
F-GLN13
4 1 from crystal
4 from model
A-ARG18
A-ASN21
A-GLU28
F-ARG18
F-LYS30
F-MET39
5 from model A-ARG18
A-ASN21
A-GLU28
F-ARG18
F-LYS30
F-MET39
19 17

Each target is used either as a full rigid structure, and with a specific combinaison of flexible side chains.