In silico Mapping of Protein Unfolding Mutations for Inherited Disease

Abstract

The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference. UMS was tested with 16 crystal structures to evaluate the unfolding for 1391 mutations from the ProTherm database. Our results showed that the computational accuracy of the unfolding calculations was similar to the accuracy of previously published free energy changes but provided a better scale. Our residue identity control helps to improve protein homology models. The unfolding predictions for proteins involved in age-related macular degeneration, retinitis pigmentosa, and Leber’s congenital amaurosis matched well with data from previous studies. These results suggest that UMS could be a useful tool in the analysis of genotype-to-phenotype associations and next-generation sequencing data for inherited diseases.

Dataset of eye disease-related proteins analyzed using the unfolding mutation screen

“…The internal control program for the analysis of unfolding propensities is explained in depth in McCafferty & Sergeev 5 . In this work the internal control was adjusted from UMS to calculate the difference in the free energy of the side chain rotamers for the same amino acid.…”

“…A full description of the UMS program can be found in the methods section of McCafferty & Sergeev 5 . In summary, the program is written in Python, R, and Bash programing languages.…”

“…The final map used to convey UMS is the patterned foldability structure. The 3D structures were colored using the foldability value of the residues 5 . These foldability values can then be used to identify critical residues in the protein structure.…”

“…It may be used as a tool to analyze the complicated relationship between missense mutations, protein folding, and disease 5 . UMS reads a protein structure file (PDB file) and predicts the unfolding effect for a list of every possible missense mutation that may occur in the protein structure including an identity mutation.…”

“…This analysis includes the preparation of 13 homology models of human proteins. The UMS program has been subjected to intensive validation using the Protherm database and 3 proteins from retinal disease (rhodopsin, complement factor H, and RPE65) 5 . We present 10 new homology models for human proteins related to retinal diseases that have been verified using the internal control.…”