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

Predicting the stability changes upon mutation starting from protein structure

For this prediction the protein 3D structure is required [1]. The program will be interrupted if the PDB protein file contains structural interruptions or only C-alpha carbon coordinates. To activate this option, click the radio button "Protein Structure" 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 (PDB: 1HJM chain A) at pH 7 and Temperature equal to 5 °C (Fig.2).

Input 

The following operations are required:

• Fill in the PDB Code box with the PDB code of your protein.
• In Chain box, put the chain label of the protein under study, if necessary.
• In the Position box insert the PDB 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.

Output

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

		  PDB File: /junk/I-Mutant/Mut16807/pdb1hjm.ent Chain: A

		  Position   WT  NEW     DDG    pH    T   RSA
		       200    E    V    0.23   7.0    5  89.3
		       200    E    L    0.87   7.0    5  89.3
		       200    E    I    0.03   7.0    5  89.3
		       200    E    M    0.70   7.0    5  89.3
		       200    E    F    1.16   7.0    5  89.3
		       200    E    W    0.27   7.0    5  89.3
		       200    E    Y    0.49   7.0    5  89.3
		       200    E    G   -0.06   7.0    5  89.3
		       200    E    A    0.31   7.0    5  89.3
		       200    E    P   -0.92   7.0    5  89.3
		       200    E    S   -0.09   7.0    5  89.3
		       200    E    T    0.92   7.0    5  89.3
		       200    E    C   -0.14   7.0    5  89.3
		       200    E    H   -0.58   7.0    5  89.3
		       200    E    R    0.54   7.0    5  89.3
		       200    E    K   -0.27   7.0    5  89.3
		       200    E    Q   -0.23   7.0    5  89.3
		       200    E    N    0.54   7.0    5  89.3
		       200    E    D    0.33   7.0    5  89.3

		  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+]
		  RSA: Relative Solvent Accessible Area


              

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,  one prediction will be returned. The free energy change corresponding to the mutation of Glu (E) 200 to Lys (K) in 1HJM chain A at temperature of 5 Celsius degree and pH 7 is -0.27 Kcal/mol and is highlighted in red. The RSA column  lists the relative solvent accessible surface calculated with the DSSP program [2].

[1] Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.

[2] Kabsch W, Sander C (1983). Dictionary of protein secondary structure: pattern of hydrogen-bonded and geometrical features. Biopolymers. 22, 2577-2637.