SDM--a server for predicting effects of mutations on protein stability and malfunction

Abstract

The sheer volume of non-synonymous single nucleotide polymorphisms that have been generated in recent years from projects such as the Human Genome Project, the HapMap Project and Genome-Wide Association Studies means that it is not possible to characterize all mutations experimentally on the gene products, i.e. elucidate the effects of mutations on protein structure and function. However, automatic methods that can predict the effects of mutations will allow a reduced set of mutations to be studied. Site Directed Mutator (SDM) is a statistical potential energy function that uses environment-specific amino-acid substitution frequencies within homologous protein families to calculate a stability score, which is analogous to the free energy difference between the wild-type and mutant protein. Here, we present a web server for SDM (http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php), which has obtained more than 10,000 submissions since being online in April 2008. To run SDM, users must upload a wild-type structure and the position and amino acid type of the mutation. The results returned include information about the local structural environment of the wild-type and mutant residues, a stability score prediction and prediction of disease association. Additionally, the wild-type and mutant structures are displayed in a Jmol applet with the relevant residues highlighted.

Figure 1.

The thermodynamic cycle can be used to calculate protein stability changes between wild-type and mutant proteins.

Figure 2.

Screenshot of SDM analysis results for the example of mutation Y231N in Dystrophin (PDB code 1DXX, chain A). On the left hand side information about the wild-type and mutant residue is displayed such as the secondary structure, solvent accessibility and hydrogen bonds formed by the sidechain. Underneath this information is the predicted effect on protein stability. In this case, SDM predicts that the mutation is highly destabilizing and disease-associated. In fact, this mutation is associated with muscular dystrophy and has been shown to decrease protein stability (73). In the middle, the structural context of the wild-type and mutant amino acids are shown in the Jmol applet with the residues coloured according to their chemical properties (key displayed on right hand side). Using the menus on the right hand side the user can manipulate the Jmol applet and control what is shown.