Simulating Protein Folding

1
Simulating Protein Folding

• - Some Ideas

Christian Hedegaard Jensen Dmitry Nerukh
2
Outline

• Introduction
• Transition Matrix
• Wang-Landau

3
Outline

• Introduction
• Transition Matrix
• Wang-Landau

4
Introduction

• We are simulation protein folding using Molecular
  Dynamics, and understanding using complexity
  analysis.
• Try to do statistics on trajectories, to see if
  there are any patterns in where they go.
  (Transition Matrix)
• Try and look at the paths that a protein can take
  when it folds. (Wang-Landau)

5
Outline

• Introduction
• Transition Matrix
• Wang-Landau

6
Transition Matrix

• Find states in trajectory
• Find transitions between states in trajectory
• Write up transition matrix for system
• Possibly include some memory into the system.

7
Transition Matrix
8
Transition Matrix
9
Transition Matrix

• We have a molecular dynamics simulation of a
  tripeptide.
• Trianaline
• 300 K, 1 atm
• 12 ps (2fs)
• OPLSAA-2001 force field
• GROMACS

10
Transition Matrix
Ramachandran Plot
11
Transition Matrix
12
Transition Matrix
13
Transition Matrix

• Gives useful information about what is going on
  in the system.
• Find out where we end and with what
  probabilities.
• Look at transitions between clusters of states.

14
Outline

• Introduction
• Transition Matrix
• Wang-Landau

15
Wang-Landau

• Wang-Landau simulations, using a combination of
  Molecular Dynamics and Monte Carlo.

16
Wang-Landau

• Wang-Landau gives the (relative) density of
  states.
• The dos of a simple protein was obtained, d(E).
• Try to calculate d(?,E) or d(?, ,E) .

17
Wang-Landau
18
Wang-Landau

• Define reaction coordinates
• Sample as function of these coordinates
• Method does not say what the system does, but is
  says what is possible.

19
Wang-Landau

• Matlab

20
Thank you!