A fast method for predicting amino acid mutations that lead to unfolding.
Amino acid mutation(s) that cause(s) partial or total unfolding of a protein can lead to disease states and failure to produce mutants. It is therefore very useful to be able to predict which mutations can retain the conformation of a wild-type protein and which mutations will lead to local or global unfolding of the protein. We have developed a fast and reasonably accurate method based on a backbone-dependent side-chain rotamer library to predict the (folded or unfolded) conformation of a protein upon mutation. This method has been tested on proteins whose wild-type 3D structures are known and whose mutant conformations have been experimentally characterized to be folded or unfolded. Furthermore, for the cases studied here, the predicted partially folded or denatured mutant conformation correlate with a decrease in the stability of the mutant relative to the wild-type protein. The key advantage of our method is that it is very fast and predicts locally or globally unfolded states fairly accurately. Hence, it may prove to be useful in designing site-directed mutagenesis, X-ray crystallography and drug design experiments as well as in free energy simulations by helping to ascertain whether a mutation will alter or retain the wild-type conformation.
Wright
J D
JD
Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC.
Lim
C
C
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry* / Q000235:genetics*; D024322:Amino Acids, Aromatic / Q000737:chemistry / Q000235:genetics; D001665:Binding Sites; D016384:Consensus Sequence; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D011392:Proline; D011487:Protein Conformation; D011489:Protein Denaturation; D015202:Protein Engineering; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D013816:Thermodynamics; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000235:genetics
D000596:Amino Acids; D024322:Amino Acids, Aromatic; D011994:Recombinant Proteins; D016159:Tumor Suppressor Protein p53; D011392:Proline