Characterization of pathogenic germline mutations in human protein kinases

Abstract

Background: Protein Kinases are a superfamily of proteins involved in crucial cellular processes such as cell cycle regulation and signal transduction. Accordingly, they play an important role in cancer biology. To contribute to the study of the relation between kinases and disease we compared pathogenic mutations to neutral mutations as an extension to our previous analysis of cancer somatic mutations. First, we analyzed native and mutant proteins in terms of amino acid composition. Secondly, mutations were characterized according to their potential structural effects and finally, we assessed the location of the different classes of polymorphisms with respect to kinase-relevant positions in terms of subfamily specificity, conservation, accessibility and functional sites.

Results: Pathogenic Protein Kinase mutations perturb essential aspects of protein function, including disruption of substrate binding and/or effector recognition at family-specific positions. Interestingly these mutations in Protein Kinases display a tendency to avoid structurally relevant positions, what represents a significant difference with respect to the average distribution of pathogenic mutations in other protein families.

Conclusions: Disease-associated mutations display sound differences with respect to neutral mutations: several amino acids are specific of each mutation type, different structural properties characterize each class and the distribution of pathogenic mutations within the consensus structure of the Protein Kinase domain is substantially different to that for non-pathogenic mutations. This preferential distribution confirms previous observations about the functional and structural distribution of the controversial cancer driver and passenger somatic mutations and their use as a proxy for the study of the involvement of somatic mutations in cancer development.

Figure 1

Consensus model structure of summarizing the human Protein Kinase family The model structure of human Protein Kinase, based on MAP3K1, shows the basic two-lobe kinase fold, with the N- and C-terminal (green and orange respectively) lobes joined by a hinge region (magenta). Substrate recognition is through interaction with the activation segment (blue), a region in the C-terminal lobe. The substrate-binding groove is located between the catalytic loop, the P+1 loop (activation segment), helix D, helix F, helix G and helix H. ATP binds at a site between the two lobes (yellow) that includes five conserved residues: (i) Lysine 74 that interacts with the alpha and beta phosphates of ATP and thereby stabilizing it; (ii) a nearby glutamic acid (E96) forms a salt bridge with lysine 74 increasing the stabilization network; (iii) Aspartate 171 is the catalytic base that initiates phosphotransfer by deprotonating the acceptor serine, threonine or tyrosine; (iv) Asparagine 176 interacts with a secondary divalent cation, thereby positioning the gamma-phosphate of ATP, and finally (v) Aspartate 190 which chelates the primary divalent cation, indirectly positioning ATP at the same time.

Figure 2

Histograms of the distribution of distances between mutated resides and the analyzed features. (A) Catalytic residues according to FireDB. (B) Catalytic Residues according to Knight et al (2007). (C) Tree-Determinants (D) Buried residues.