Example 9: Cleaved, Asymmetric HIV-1 AD8 Env Ectodomain Trimer

PDB ID 8fad is a structure of the cleaved, asymmetric HIV-1 AD8 Env ectodomain trimer.

The molecules with the resname 83G are bound instances of the entry inhibitor model BMS-806, which is a small molecule related to the drug Temsavir. 83G was parameterized using the CGenFF server, so it was done prior to the build.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Simple build of solvated HIV-1 Env trimer 8fad
#
# Notes:
#   - Missing protein is built-in
#   - Drug molecules (resname 83G) is included (previously parameterized using cgenff)
#   - mmCIF input file requires careful attention to chainIDs and
#     residue numbers
#   - Fine-tuning ramachandran rotations performed to avoid steric
#     clashes when building in missing residues
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: prod_8fad.tgz
#
title: HIV-1 Env Trimer 8fad
tasks:
  - fetch:
      sourceID: 8fad
      source_format: cif
  - psfgen:
      mods:
        crotations:
          - phi,F,29,43,-90.0
          - psi,F,29,43,-120.0
  - validate:
      tests:
        - residue_test:
            name: 83G ligands are present
            selection: resname 83G
            measure: residue_count
            value: 3
  - md:
      ensemble: minimize
  - ligate:
      steer:
        nsteps: 4000
  - validate:
      tests:
        - connection_test:
            name: chain F gap ligation
            selection: protein and chain F and resid 43 44
            connection_type: interresidue
            connection_count: 1
  - md:
      ensemble: minimize
  - md:
      cpu-override: True
      ensemble: NVT
  - solvate:
  - md:
      ensemble: minimize
  - md:
      ensemble: NVT
  - md:
      ensemble: NPT
      nsteps: 200
  - md:
      ensemble: NPT
      nsteps: 400
  - md:
      ensemble: NPT
      nsteps: 800
  - md:
      ensemble: NPT
      nsteps: 1600
  - md:
      ensemble: NPT
      nsteps: 13200
  - mdplot:
      timeseries:
        - density
      basename: solvated
      grid: True
  - terminate:
      basename: my_8fad
      artifacts: artifacts
      package:
        basename: prod_8fad
        namd:
          ensemble: NPT
Pipeline task summary

Step

Task

Details

1

fetch

PDB 8FAD

2

psfgen

crotations

3

validate

1 test(s)

4

md

minimize

5

ligate

ligate chain breaks (steered MD, 4,000 steps)

6

validate

1 test(s)

7

md

minimize → NVT (2,000 steps)

8

solvate

water box

9

md

minimize → NVT (2,000 steps) → NPT (16,200 steps, 5 phases)

10

mdplot

equilibration time-series plots → mdplots/

11

terminate

basename: my_8fad; package: prod_8fad
../../_images/8fad-graphic.png

The cleaved, asymmetric HIV-1 AD8 Env ectodomain trimer (PDB ID 8fad) with the entry inhibitor BMS-806 (83G) bound. Glycan rings are shown as solid shapes, and the 83G ligands are shown in VdW representation.

Parameterization of 83G

The following procedure was used to parameterize 83G.

  1. Use VMD to generate a PDB file of a single copy of the 83G ligand from the 8fad structure. The PDB file has no H atoms.

    vmd > mol new 8fad
vmd > set lig [atomselect top "chain C and resname 83G"]
vmd > $lig writepdb 83G_8fad_C.pdb

  2. Use Open Babel to add hydrogens first, and then to create the mol2 file needed for cgenff.

    $ obabel -ipdb 83G_8fad_C.pdb -h --minimize -opdb -O tmp.pdb
$ obabel -ipdb tmp.pdb -h -omol2 -O 83G-1.mol2
$ cat 83G-1.mol2 | sed s/"tmp.pdb"/"83G"/g > 83G.mol2

  3. Upload 83G.mol2 to the CGenFF server, and follow the instructions to generate a parameter file. The server will generate a 83G-cgenff.str file that contains the parameters for 83G. (A future release of Pestifer will interface with the cgenff executable, which is free for educational users.)

  4. Copy the contents of 83G-cgenff.str into a new file called 83G-cgenff.str in the pestifer/resources/charmmff/custom/ directory. This makes pestifer aware of the new residue.

  5. Ensure that 83G is listed in one of the segtypes in pestifer/core/labels. For example, it can be added to the ligand segtype:

    'ligand': {
    'macro': True,
    'resnames' : [
        'EIC', 'VCG', 'HEM', 'ADP', 'ATP', '83G']},

    It does not matter which segtype it is added, so long as it is not one associated with polymeric molecules like proteins or nucleic acids.

Reference

  • Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles. Wang, K., Zhang, S., Go, E.P., Ding, H., Wang, W.L., Nguyen, H.T., Kappes, J.C., Desaire, H., Sodroski, J., Mao, Y. Commun Biol 6: 535 DOI 10.1038/s42003-023-04916-w (2023)

Example author: Cameron F. Abrams   Contact: cfa22@drexel.edu