Example 11: Open, Symmetric D9/CD4-liganded HIV-1 SOSIP Env Ectodomain Trimer (ligands removed)¶

PDB ID 7txd is a structure of the HIV-1 Env BG505 SOSIP-664 ectodomain trimer in an open conformation, with the two-domain soluble CD4 construct (sCD4) and 17b Fab fragment bound. This structure is missing the so-called V1/2 loop between residues 100 and 162 on each gp120. Here, we substitute that span of residues with a literal triglycine (Gly-Gly-Gly) sequence–this ensures psfgen doesn’t just pop standard N- and C-terminal patches across that gap. This is an alternative to what we did in 4zmj, where we opted to build in missing residues following sequence. We also model in residues missing from gp41’s and fold them into alpha-helices. The ligands are removed from the structure, and the system is solvated in a water box.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Simple build of solvated HIV-1 Env trimer 7txd
#
# Notes:
#   - Missing protein is built-in
#   - mmCIF input file requires careful attention to chainIDs and
#     residue numbers
#   - Fab and sCD4 chains excluded
#   - zero-occupancy residues at C-terminus of each gp41 are built
#     and folded into an alpha-helix
#   - Missing V1/2 residues in each gp120 replaced with GGG
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: prod_7txd.tgz
#
title: HIV-1 Env Trimer 7txd, substitutions, no ligands
tasks:
  - fetch:
      sourceID: 7txd
      source_format: cif
  - psfgen:
      source:
        cif_residue_map_file: cif2user.csv
        biological_assembly: 1
        exclude:
          - chainID in ['G', 'H', 'I', 'J', 'K', 'L']  # mmCIF
        sequence:
          build_zero_occupancy_C_termini: [B, D, F]
      mods:
        mutations: # undo the SOSIP mutations on each protomer (cif resid)
          - A:CYS,469,ALA
          - C:CYS,469,ALA
          - E:CYS,469,ALA
          - B:PRO,48,ILE
          - D:PRO,48,ILE
          - F:PRO,48,ILE
          - B:CYS,94,THR
          - D:CYS,94,THR
          - F:CYS,94,THR
        crotations:
          - alpha,B,33,52
          - alpha,B,144,153
          - alpha,D,32,52
          - alpha,D,144,153
          - phi,D,34,52,-30
          - phi,D,33,52,15
          - psi,D,29,52,-5
          - alpha,F,33,50
          - alpha,F,144,153
          - phi,F,32,50,30
          - phi,F,31,50,45
          - psi,C,368,378,180
        substitutions:
          - A:100-162,GGG
          - C:100-162,GGG
          - E:100-162,GGG
  - validate:
      tests:
        - attribute_test:
            name: undo sos mutation on gp120
            selection: protein and chain A C E and resid 469 and name CA
            attribute: resname
            value: ALA
            value_count: 3
        - attribute_test:
            name: undo ip mutation on gp41
            selection: protein and chain B D F and resid 48 and name CA
            attribute: resname
            value: ILE
            value_count: 3
        - attribute_test:
            name: undo sos mutation on gp41
            selection: protein and chain B D F and resid 94 and name CA
            attribute: resname
            value: THR
            value_count: 3
        - connection_test:
            name: loop substitutions on gp120
            selection: protein and chain A C E and resid 99 100 102 163
            connection_type: interresidue
            connection_count: 6
        - attribute_test:
            name: loop substitutions on gp120 (placeholder)
            selection: protein and chain A C E and resid 100 101 102 and name CA
            attribute: resname
            value: GLY
            value_count: 9
  - md:
      cpu-override: True
      ensemble: minimize
  - ligate:
      steer:
        temperature: 600
        nsteps: 3000
  - validate:
      tests:

        - connection_test:
            name: gp120 gaps ligation
            selection: protein and chain A C E and resid 378 379
            connection_type: interresidue
            connection_count: 3
        - connection_test:
            name: gp41 gaps ligation
            selection: protein and chain B D F and resid 50 51
            connection_type: interresidue
            connection_count: 3
  - md:
      cpu-override: True
      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_7txd
      artifacts: artifacts
      package:
        basename: prod_7txd
        namd:
          ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 7TXD
2	`psfgen`	exclusions, mutations, loop substitutions, crotations
3	`validate`	5 test(s)
4	`md`	minimize
5	`ligate`	ligate chain breaks (steered MD, 3,000 steps)
6	`validate`	2 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_7txd`; package: `prod_7txd`