Page AktinAnalysis

TODO
Person	Task	State
Martin	calculation of electrostatic potential map of (closed_atp_dimer, closed_atp),( closed_adp_dimer, closed_adp)	undone
Martin	testing conditional state probabilities of simulation trajectories for convergence using HMM state definition (s-closed, closed, open)	undone
Splette	MD runs of actin trimers to obtain relaxed filament part	undone
Splette	calculation of 'mean' trimer structures which will serve as a basis for binding energy calculations	undone
Martin	binding energy calculations of closed_atp/closed_adp/superclosed_atp trimer	undone

Analysis Protocol

• Analysis of state trajectories
  • equidistant discretization of state coordinate using 150 boxes
  • computation of transition matrix based on discretized trajectory
  • determining number of clusters (noc) by considering eigenvalues of transition matrix which are greater than 0.9
  • run HMMGaussian to determine noc clusters in state coordinate
  • resulting clustering is displayed in first figure of each trajectory (x axis shows time, y axis distance, coloring indicates clustering)
  • cluster indices over time can be found in clustered.tar.gz

• Analysis of depth trajectories
  • equidistant discretization of depth coordinate using 150 boxes
  • computation of transition matrix based on discretized trajectory
  • determining number of clusters (noc) by considering eigenvalues of transition matrix which are greater than 0.8
  • run HMMGaussian to determine noc clusters in depth coordinate
  • resulting clustering is displayed in second figure of each trajectory (x axis shows time, y axis inversed depth, coloring indicates clustering)
  • cluster indices over time can be found in clustered.tar.gz

• Computation of Cross-Correlation between state and depth trajectory
  • to compute cross-correlation (link) median of each trajectory was substracted first, additonally the depth coordinate was inverted
  • cross-correlation was computed for possible time shifts from 0 to 250 steps in both directions
  • the resulting correlation values are depicted in the third plot, the maximal values is given in the title of it (remark: y axis should be named cross-correlation instead of auto-correlation)

Calculation of Electrostatic Potential

• steps
  • removal of water and ions except MG-Ion (VMD selection: 'all and not water and not resname POT and not resname CLA and not resname SOD')
  • rename residue of first 6 atoms in PDB file to ACE, change ID to 0
  • do the same thing in PSF file
  • remove ATOMS 1046, 1047, 1048 from PDB and PQR
  • replace 1045 with HE2 in PDB and PSF PSF-PLOT '1045 ACTI 72 HSE HE2 H 0.000000 1.0080 0'
  • RUN pdb2pqr by: ~/progs/pdb2pqr-1.2.1/pdb2pqr.py --apbs-input --ff=charmm --ffout=charmm PDB_FILE TARGET_PQR
  • change 5785 - 5787 RESNAME to PHE in PQR-File
  • RUN replacement script: ../../scripts/assignCorrectChargesToPQR.pl actin_namd.psf actin_namd_clean.pqr actin_namd_repl.pqr

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Analysed Simulation Data

• ADP Simulations

• ATP Simulations

• closed ADP

• closed ATP (single trjs) | closed ATP (combined trj)

• open ADP (single trjs) | open ADP (combined trj)

• open ATP (single trjs) | open ATP (combined trj)

• open profilin ADP (single trjs) | open profilin ADP (combined trj)

• open profilin ATP (single trjs) | open profilin ATP (combined trj)

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