Large scale analysis of protein stability in OMIM disease related human protein variants

Pier Luigi Martelli, Piero Fariselli, Castrense Savojardo, Giulia Babbi, Francesco Aggazio, Rita Casadio

Modern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability. We develop INPS3D, a new predictor based on protein structure for computing the effect of single residue variations on protein stability (ΔΔG), scoring at the state-of-the-art (Pearson's correlation value of the regression is equal to 0.72 with mean standard error of 1.15 kcal/mol on a blind test set comprising 351 variations in 60 proteins). We then filter 368 OMIM disease related proteins known with atomic resolution (where the three dimensional structure covers at least 70 % of the sequence) with 4717 disease related single residue variations and 685 polymorphisms without clinical consequence. We find that the effect on protein stability of disease related variations is larger than the effect of polymorphisms: in particular, by setting to |1 kcal/mol| the threshold between perturbing and not perturbing variations of the protein stability, about 44 % of disease related variations and 20 % of polymorphisms are predicted with |ΔΔG| > 1 kcal/mol, respectively. A consistent fraction of OMIM disease related variations is however predicted to promote |ΔΔG| ≤ 1 kcal/mol and we focus here on detecting features that can be associated to the thermodynamic property of the protein variant. Our analysis reveals that some 47 % of disease related variations promoting |ΔΔG| ≤ 1 are located in solvent exposed sites of the protein structure. We also find that the increase of the fraction of variations that in proteins are predicted with |ΔΔG| ≤ 1 kcal/mol, partially relates with the increasing number of the protein interacting partners, corroborating the notion that disease related, non-perturbing variations are likely to impair protein-protein interaction (70 % of the disease causing variations, with high accessible surface are indeed predicted in interacting sites). The set of OMIM surface accessible variations with |ΔΔG| ≤ 1 kcal/mol and located in interaction sites are 23 % of the total in 161 proteins. Among these, 43 proteins with some 327 disease causing variations are involved in signalling, structural biological processes, development and differentiation. We compute the effect of disease causing variations on protein stability with INPS3D, a new state-of-the-art tool for predicting the change in ΔΔG value associated to single residue substitution in protein structures.  The analysis indicates that OMIM disease related variations in proteins promote a much larger effect on protein stability than polymorphisms non-associated to diseases. Disease related variations with a slight effect on protein stability (|ΔΔG| < 1 kcal/mol) frequently occur at the protein accessible surface suggesting that they are located in protein-protein interactions patches in putative human biological functional networks. The hypothesis is corroborated by proving that proteins with many disease related variations that slightly perturb protein stability are on average more connected in the human physical interactome (IntAct) than proteins with variations predicted with |ΔΔG| > 1 kcal/mol.