Talk from the 5th Users' Conference of IT4Innovations, Ostrava, Czech Republic

Created using Reveal.js.

Use right arrow for browsing.

Peptide deformylase as a probe of
Long-range allostery between ribosome surface and interior

Michal H. Kolář

November 10, 2021




Felipe C. Nepomuceno
Michaela Černeková
Hugo McGrath
Tereza Svatoňová
Iva Švecová

Petr Chalupský
Jan Kejla
Petr Linhart
Jan Michna
Vít Turčin



  1. Build systems with and without PDF.
  2. Using MD simulations generate conformational ensembles.
  3. Analyze structure and dynamics and search for differences caused by PDF.
  4. Perturb MD simulations and analyze systems' responses.

Technical details

  • Amber force field, explicit SPC/E water
  • 2M particles
  • Gromacs 2020, CPU-only implementation
  • 1000 ns/traj, 4 independent trajs/system, 3.3M corehours

Maximally correlated motion

Hub, de Groot, PLoS Comput. Biol. 2009.

Aim: Get a statistical model to predict F.

  1. Cartesian coordinates ⟶ principle components (PCs).
  2. Dimensionality reduction (~100 PCs).
  3. Linear combination of selected PCs to correlate with F.

F ... true function (training)
mF ... model function (prediction)

10-residue uL22 tip


  • Surface of the ribosome and tunnel interior exchange information.
  • A model predicts presence/absence of PDF.
  • uL22 response depends on PDF.

Open questions

  • The connecting path remains to be described.
  • Some technical details need to be tested.