Difference between revisions of "ASPA Structure Based Mutation Analysis"

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==FoldX==
  
==FoldX==
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Running foldx on our protein returned the following results:
   
 
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==Minimise==
  
==Minimise==

Revision as of 23:03, 31 August 2011

FoldX

Running foldx on our protein returned the following results:

Mutation BackHbond SideHbond Energy_VdW Electro SolvP SolvH vdwclash torsion bb_vdwclash Entropy_sidec Entropy_mainc water bonds helix dipole loop_entropy cis_bond disulfide kn electrostatic partial covalent interactions Ionisation Entropy Complex Total
WT -351.60 -113.32 -753.77 -34.77 991.74 -1003.86 94.80 42.16 375.34 372.13 941.00 -1.73 -1.78 0.00 9.05 0.00 -0.94 -26.09 2.96 0.00 165.97
CM055097 -355.76 -113.21 -759.56 -33.94 986.09 -1010.92 170.97 80.70 377.29 374.36 942.29 0.00 -1.21 0.00 9.03 0.00 -0.63 0.00 3.65 0.00 291.86
CM063847 -355.74 -112.37 -759.94 -34.09 985.12 -1012.35 178.46 80.88 377.32 374.49 942.56 0.00 -1.44 0.00 9.03 0.00 -0.63 0.00 3.68 0.00 297.66
CM940124 -355.67 -113.51 -760.79 -33.98 989.54 -1012.11 185.56 80.68 377.55 375.73 942.35 0.00 -1.76 0.00 9.03 0.00 -0.63 0.00 3.64 0.00 308.08
CM990193 -355.77 -113.23 -760.51 -33.74 987.84 -1011.65 194.71 80.60 377.51 374.59 944.00 0.00 -1.44 0.00 9.03 0.00 -0.63 0.00 3.79 0.00 317.61
CM990195 -355.82 -113.22 -759.67 -34.61 989.16 -1009.25 179.53 80.75 377.29 374.77 942.43 0.00 -1.36 0.00 9.03 0.00 -0.63 0.00 3.64 0.00 304.76
CM994594 -355.60 -113.20 -756.93 -33.66 982.92 -1007.28 169.81 80.49 376.73 373.69 941.91 0.00 -1.44 0.00 9.03 0.00 -0.63 0.00 3.64 0.00 292.75
RS104894548 -355.81 -113.21 -760.68 -33.70 989.00 -1011.59 187.60 80.73 377.34 375.06 942.60 0.00 -1.39 0.00 9.03 0.00 -0.63 0.00 3.64 0.00 310.63
RS104894551 -355.68 -113.48 -757.12 -31.38 979.51 -1008.38 168.90 80.33 376.85 372.68 942.57 0.00 -1.45 0.00 9.03 0.00 -0.63 0.00 3.11 0.00 288.02
RS104894553 -355.73 -113.24 -759.08 -35.12 985.71 -1010.41 173.40 80.55 377.28 374.26 942.65 0.00 -1.41 0.00 9.03 0.00 -0.63 0.00 4.03 0.00 294.00
RS80099330 -355.61 -113.21 -758.06 -33.77 984.24 -1008.91 170.10 80.58 377.03 373.24 942.10 0.00 -1.44 0.00 9.03 0.00 -0.63 0.00 3.64 0.00 291.29

Minimise

Mutation WT cm055097 cm063847 cm940124 cm990193 cm990195 cm994594 rs104894548 rs104894551 rs104894553 rs80099330
Energy -14776.478983 -14054.020681 -12533.719784 -11003.916326 -12670.140717 -11757.261266 -14164.353463 -8677.102143 -14220.689449 -14035.011150 -14141.901598



Gromacs

The script fetchPDB used to download the PDB file first pulls the gzipped version of the PDB file from the PDB website, then unpacks it.

We cleaned the PDB file using repairPDB with the options -nosol and -noh to extract just the protein. Other options available include -seq, which extracts the protein sequence and return it as a string and -cleansol, which cleans up the solvent for use with Gromacs.

We afterwards extracted chain A; since both chains show little in the way of diffences, we decided to use A.

Then we generated mutated PDBs using SCWRL; we had to extract the sequence of the protein from the PDB file beforehand using repairPDB with the option -seq and edit it to be lowercase with just the mutated position in uppercase.

We measured the run time for different values for nsteps and plotted the results in a graph, with nsteps on the x axis and the time in seconds on the y axis.

ASPA Timegraph.png


Pictures

The following pictures were created using PyMOL to illustrate the effects of the mutations generated by SCWRL:

WildtypeMutation
RS104894553Wt rs104894553.pngMut rs104894553.png
CM940124Wt cm940124.pngMut cm940124.png
CM063847Wt cm063847.pngMut cm063847.png
RS80099330Wt rs80099330.pngMut rs80099330.png
CM990193Wt cm990193.pngMut cm990193.png
RS104894548Wt rs104894548.pngMut rs104894548.png
CM990195Wt cm990195.pngMut cm990195.png
CM055097Wt cm055097.pngMut cm055097.png
RS104894551Wt rs104894551.pngMut rs104894551.png
CM994594Wt cm994594.pngMut cm994594.png


Results of the Minimization

The following graphs illustrate the results of the minimization step.

cm055097

Mut 2O53 cm055097 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm055097 onlyprot A gromacs angle.png

cm055097

Mut 2O53 cm055097 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm055097 onlyprot A gromacs bond.png

cm055097

Mut 2O53 cm063847 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm055097 onlyprot A gromacs potential.png

cm063847

Mut 2O53 cm063847 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm063847 onlyprot A gromacs angle.png

cm063847

Mut 2O53 cm063847 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm063847 onlyprot A gromacs bond.png

cm063847

Mut 2O53 cm940124 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm063847 onlyprot A gromacs potential.png

cm940124

Mut 2O53 cm940124 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm940124 onlyprot A gromacs angle.png

cm940124

Mut 2O53 cm940124 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm940124 onlyprot A gromacs bond.png

cm940124

Mut 2O53 cm990193 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm940124 onlyprot A gromacs potential.png

cm990193

Mut 2O53 cm990193 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm990193 onlyprot A gromacs angle.png

cm990193

Mut 2O53 cm990193 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm990193 onlyprot A gromacs bond.png

cm990193

Mut 2O53 cm990195 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm990193 onlyprot A gromacs potential.png

cm990195

Mut 2O53 cm990195 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm990195 onlyprot A gromacs angle.png

cm990195

Mut 2O53 cm990195 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm990195 onlyprot A gromacs bond.png

cm990195

Mut 2O53 cm994594 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm990195 onlyprot A gromacs potential.png

cm994594

Mut 2O53 cm994594 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 cm994594 onlyprot A gromacs angle.png

cm994594

Mut 2O53 cm994594 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 cm994594 onlyprot A gromacs bond.png

cm994594

Mut 2O53 rs104894548 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 cm994594 onlyprot A gromacs potential.png

rs104894548

Mut 2O53 rs104894548 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 rs104894548 onlyprot A gromacs angle.png

rs104894548

Mut 2O53 rs104894548 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 rs104894548 onlyprot A gromacs bond.png

rs104894548

Mut 2O53 rs104894551 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 rs104894548 onlyprot A gromacs potential.png

rs104894551

Mut 2O53 rs104894551 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 rs104894551 onlyprot A gromacs angle.png

rs104894551

Mut 2O53 rs104894551 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 rs104894551 onlyprot A gromacs bond.png

rs104894551

Mut 2O53 rs104894553 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 rs104894551 onlyprot A gromacs potential.png

rs104894553

Mut 2O53 rs104894553 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 rs104894553 onlyprot A gromacs angle.png

rs104894553

Mut 2O53 rs104894553 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 rs104894553 onlyprot A gromacs bond.png

rs104894553

Mut 2O53 rs80099330 onlyprot A gromacs angle.png

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 rs104894553 onlyprot A gromacs potential.png

rs80099330

Mut 2O53 rs80099330 onlyprot A gromacs bond.png

AverageErr.Est.RMSDTot-Drift
angleavgerrestrmsdtotdriftMut 2O53 rs80099330 onlyprot A gromacs angle.png

rs80099330

Mut 2O53 rs80099330 onlyprot A gromacs potential.png

AverageErr.Est.RMSDTot-Drift
bondavgerrestrmsdtotdriftMut 2O53 rs80099330 onlyprot A gromacs bond.png

rs80099330

AverageErr.Est.RMSDTot-Drift
potentialavgerrestrmsdtotdriftMut 2O53 rs80099330 onlyprot A gromacs potential.png
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