On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

Abstract

BackgroundNon-synonymous coding SNPs (nsSNPs) that are associated to disease can also be related with alterations in protein stability. Computational methods are available to predict the effect of single amino acid substitutions (SASs) on protein stability based on a single folded structure. However, the native state of a protein is not unique and it is better represented by the ensemble of its conformers in dynamic equilibrium. The maintenance of the ensemble is essential for protein function. In this work we investigated how protein conformational diversity can affect the discrimination of neutral and disease related SASs based on protein stability estimations. For this purpose, we used 119 proteins with 803 associated SASs, 60% of which are disease related. Each protein was associated with its corresponding set of available conformers as found in the Protein Conformational Database (PCDB). Our dataset contains proteins with different extensions of conformational diversity summing up a total number of 1023 conformers.ResultsThe existence of different conformers for a given protein introduces great variability in the estimation of the protein stability (ΔΔG) after a single amino acid substitution (SAS) as computed with FoldX. Indeed, in 35% of our protein set at least one SAS can be described as stabilizing, destabilizing or neutral when a cutoff value of ±2 kcal/mol is adopted for discriminating neutral from perturbing SASs. However, when the ΔΔG variability among conformers is taken into account, the correlation among the perturbation of protein stability and the corresponding disease or neutral phenotype increases as compared with the same analysis on single protein structures. At the conformer level, we also found that the different conformers correlate in a different way to the corresponding phenotype.ConclusionsOur results suggest that the consideration of conformational diversity can improve the discrimination of neutral and disease related protein SASs based on the evaluation of the corresponding Gibbs free energy change.

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“…In terms of changes in structure stability, it was previously found in FoldX calculations (Juritz et al, 2012) that the best discrimination cutoff for G values between polymorphic and disease-associated SASs was ±2 kcal/mol. Taking these values into account, we classified SASs as stabilizing for those with a G ࣙ 2 kcal/mol, destabilizing for those below (−2 kcal/mol), and neutral for those with values in between.…”

“…As a protein's native state is better represented by an ensemble of conformers, the effect of SASs should be evaluated on each of the available conformers of the protein. Following this approach, we found that the damaging effect of SASs on protein function evaluated in different conformations could help in the understanding of disease associated SASs (Juritz et al, 2012). For this reason, and to obtain a mechanistic analysis of the SAS effect, we explicitly studied the described SASs with regards to the conformational diversity of the EGFR protein.…”

Homology modeling in a dynamical world

“…). Conformational diversity is a key concept to understand many processes and mechanisms in protein function, such as enzyme catalysis, promiscuity in protein interactions, protein‐protein recognition, signal transduction, mechanisms of disease‐related mutations, immune escape, the origin of neurodegenerative diseases, protein evolutionary rates, conformer‐specific substitution patterns, the origins of new biological functions, molecular motors, and co‐evolutionary measurements between residues (for a recent review please see). Furthermore, we have recently shown that the distribution of CD in a large dataset of proteins, with experimentally determined CD (approximately 5000 proteins), results in three main groups of proteins with different structure‐function relationships .…”

Homology modeling in a dynamical world

“…First, we found that the extent of the CD could be as large as the MSD (Fig 1). Conformational diversity is a key concept to understand many processes and mechanisms in protein function, such as enzyme catalysis [49], promiscuity in protein interactions [50], protein-protein recognition [51], signal transduction [52], mechanisms of disease-related mutations [53], immune escape [54], the origin of neurodegenerative diseases [55], protein evolutionary rates [56], conformer-specific substitution patterns [57], the origins of new biological functions [58], molecular motors [59], and co-evolutionary measurements between residues [24,60] (for a recent review please see [17]).…”