| Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability (2007) | |||||||||||||
Abstract | |||||||||||||
| When incorporated into a polypeptide chain, Proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The φ dihedral angle of Pro is constrained to values close to -65o and Pro lacks an amide hydrogen. Consequently, mutations which result in introduction of Pro can significantly affect protein stability. In the present work, we describe a procedure to accurately predict the effect of proline introduction on protein thermodynamic stability. 77 of the 97 non-Pro amino acid residues in the model protein, CcdB, were individually mutated to proline and the in vivo activity of each mutant was characterized. A decision tree to classify the mutation as perturbing or non-perturbing was created by correlating stereochemical properties of mutants to activity data. The stereochemical properties including main chain dihederal angle φ and main chain amide hydrogen bonds were determined from 3D models of the mutant proteins built using MODELLER. We assessed the performance of the decision tree on 75 nsSNPs and 37 other proline substitutions from the literature. The overall accuracy of this algorithm was found to be 86% in the case of CcdB, 71% in the case of nsSNPs and 86% in the case of other proline substitution data. The accuracy of Proline scanning mutagenesis for secondary structure assignment was also assessed and found to be at best 69%, lower than accuracies of current sequence based secondary structure prediction algorithms. Our prediction procedure will be useful in annotating uncharacterized nsSNPs of disease-associated proteins and for protein engineering and design. | |||||||||||||
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