Example 18: E. coli Replicative DNA Polymerase Complex Bound to DNA

PDB ID 5fkw is a structure of E. coli polymerase bound to a 12-mer DNA duplex. This example demonstrates that pestifer can handle simple nucleic acids. It also shows how Pestifer can build in missing nucleic acid residues; in this case, there are 3 unresolved nucleotides at the 5’-end of chain T.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
#
# E. Coli replicative DNA polymerase complex 
# bound to a primer-template DNA
#
# Demonstration of nucleic acid building
# Three unresolved nucleic acid at 5' end of chain T are modeled in
#
title: E. Coli replicative DNA polymerase complex bound to a primer-template DNA
tasks:
  - fetch:
      sourceID: 5fkw
  - psfgen:
      source:
        sequence:
          build_zero_occupancy_N_termini: [T]
          loops:
            min_loop_length: 2
            declash:
              maxcycles: 40
      mods:
        crotations:
          - PHI,D,187,207,90.0
  - md:
      ensemble: minimize
  - ligate:
      steer:
        nsteps: 3600
  - md:
      ensemble: minimize
  - validate:
      tests:
        - residue_test:
            name: resids 9, 10, and 11 of chain T present
            selection: chain T and resid 9 10 11
            measure: residue_count
            value: 3
  - md:
      cpu-override: True
      ensemble: NVT
      nsteps: 2400
  - solvate:
        salt_con: 0.15
        cation: SOD
        anion: CLA
  - 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:
      basename: solvated
      timeseries:
        - density
  - terminate:
      basename: my_5fkw
      artifacts: artifacts
      package:
        basename: prod_5fkw
        namd:
          ensemble: NPT
Pipeline task summary

Step

Task

Details

1

fetch

PDB 5FKW

2

psfgen

crotations

3

md

minimize

4

ligate

ligate chain breaks (steered MD, 3,600 steps)

5

md

minimize

6

validate

1 test(s)

7

md

NVT (2,400 steps)

8

solvate

water box + 0.15 M SOD/CLA

9

md

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

10

mdplot

equilibration time-series plots → mdplots/

11

terminate

basename: my_5fkw; package: prod_5fkw
../../_images/ecoli-polymerase.png

E coli polymerase complex (PDB ID 5fkw) with DNA shown in yellow and brown cartoon. The orange chain (chainID D) has a 20-residue loop that pestifer built.

Reference