I-Mutant2.0: a tool for predicting protein stability upon mutation

Predicting of stability change starting from protein sequence

For this prediction only the protein sequence is required. To activate this option click the “Protein Sequence” radio button on the I-Mutant2.0 home page and then click Enter (see fig. 1).

Predicting the value of free energy change

A test case
Suppose that the task is predicting the protein stability change when Glu (E) 200 is mutated into Lys (K) in the Prion Protein  at pH 7 and Temperature equal to 5 °C (Fig.2) and that the sequence is available. This can be done either with proteins that are already known with atomic resolution or  with any  protein sequence available.

Input 

The following operations are required:

• Fill in the Protein Sequence box with the one letter code sequence of your protein.
• In the Position box insert the number of the residue that undergoes mutation.
• In New Residue insert the required one letter code mutation (optional).
  
• The boxes pH and Temperature can be filled with the experimental conditions at which the experiment is simulated.

The following operations are required:

• Fill in the Protein Sequence box with the one letter code sequence of your protein.
• In the Position box insert the PDB number of the residue that undergoes mutation.
• The boxes pH and Temperature can be filled with the experimental conditions at which the experiment is simulated.

The selection of the radio button “Free Energy change value (DDG)” allows the prediction of the free energy change value. The output of the predictor will be send to the your e-mail to address, if required or given directly to you.

 Output

The results obtained for the given test case are listed below:

		  SEQ File: /junk/I-Mutant/Mut17864/fileseq.txt

		  Position   WT  NEW     DDG    pH    T
		       200    E    V    0.75   7.0    5
		       200    E    L    0.86   7.0    5
		       200    E    I    1.31   7.0    5
		       200    E    M    0.93   7.0    5
		       200    E    F    1.99   7.0    5
		       200    E    W    0.47   7.0    5
		       200    E    Y    1.09   7.0    5
		       200    E    G   -0.61   7.0    5
		       200    E    A   -0.30   7.0    5
		       200    E    P   -0.05   7.0    5
		       200    E    S    0.76   7.0    5
		       200    E    T    0.59   7.0    5
		       200    E    C    0.15   7.0    5
		       200    E    H   -0.06   7.0    5
		       200    E    R    1.18   7.0    5
		       200    E    K    0.10   7.0    5
		       200    E    Q    0.13   7.0    5
		       200    E    N   -0.03   7.0    5
		       200    E    D    0.19   7.0    5
	
		  WT:  Aminoacid in Wild-Type Protein
		  NEW: New Aminoacid after Mutation
		  DDG: DG(NewProtein)-DG(WildType) in Kcal/mol
		         DDG<0: Decrease Stability
		         DDG>0: Increase Stability
		  T:   Temperature in Celsius degrees
		  pH:  -log[H+]
			
              

If you do not ask for a specific mutation in the position at hand, all the possible mutations will be taken into consideration, including the one that may be of specific interest. However if you are asking only one mutation, by activating the "New Residue" option, only one prediction will be returned. The free energy change corresponding to the mutation of Glu (E) 200 to Lys (K) in Prion Protein at temperature of 5 Celsius degree and pH 7 is 0.10 Kcal/mol and is highlighted in red.