Invited seminar at the Department of Biology and Ecology of the Faculty of Science, University of Ostrava, Czech Republic.

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Atomistic computer simulations of the ribosome

Michal H. Kolář

@MhkoScience

michal@mhko.science



19-06479Y, 23-05557S, 23-05764S


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

Josef Cikhart
Aneta Hrádková
Petr Chalupský
Jan Kejla
Aneta Leskourová
Petr Linhart
Martin Mašek
Jan Michna
Arian Adam Ott

1. Atomistic simulations

2. Ribosome essentials

3. Stalling by VemP

4. Long-range allostery

1. Atomistic simulations

2. Ribosome essentials

3. Stalling by VemP

4. Long-range allostery

„Prediction is very difficult, especially if it’s about the future.“

whiteboard section

1. Atomistic simulations

2. Ribosome essentials

3. Stalling by VemP

4. Long-range allostery

VMD section

1. Atomistic simulations

2. Ribosome essentials

3. Stalling by VemP

4. Long-range allostery



Helmut Grubmüller
Lars V. Bock
Gabor Nagy

Sara M. Vaiana
John Kunkel

Published

Bock et al. PMID: 29202442

Kolář et al. PMID: 35150281

Vibrio alginolyticus

Vibrio Export Monitoring Polypeptide (VemP)

 

photo courtesy: Dr. Gary Gaugler, Visuals Unlimited, Inc.
Ishii et al., PMID: 26392525

VemP

  • cryo-EM shows extreme compation in the exit tunnel
  • Su et al., PMID: 28556777

 

  • inner helix inactivates two nucleobases needed for peptidyl transfer

VemP Questions

  • Why does VemP fold in the tunnel?
  • How does VemP respond to external force?

Answers

  • The tunnel walls play a decisive role in folding VemP.
  • VemP unfolds sequentially from the N-terminus.

1. Atomistic simulations

2. Ribosome essentials

3. Stalling by VemP

4. Long-range allostery

 

Strategy

  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.

Published

McGrath et al., PMID: 36335428

Principal Component Regression

A story about stalking a bartender

whiteboard section

Hub, de Groot, PMID: 19714202

Aim: Get a statistical model to predict F.

Atomistic computer simulations of the ribosome

Michal H. Kolář

@MhkoScience

michal@mhko.science

Technical details

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