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Unmasking determinants of specificity in the human kinome.

Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R - Cell (2015)

Bottom Line: Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues.We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions.Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark. Electronic address: creixell@mit.edu.

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Evolutionary Aspects of DoS and Their Co-existence with Kinase Spines(A) As can be observed from the different panels on this DoS-based Dendrogram, where several kinases are localized discordantly with whole-domain evolution, peptide specificity evolution cannot be directly inferred from whole-domain specificity. These differences highlight how kinases have accumulated mutations on these specific residues, i.e., DoS, in order to evolve different specificities. For further explanation and information, please refer to Experimental Procedures and Figures S5.(B) We next investigated how DoS co-evolved with residues involved in structural changes related to catalysis (kinase spines). As can be seen here, there are different possible degrees to which DoS and spines could co-exist, ranging from complete overlap (left) to complete exclusion (right). In (C), we investigate which of these models is more supported by our data.(C) By comparing the relative localization of the DoS (top-left structure) together with the residues belonging to the catalytic spine (in yellow, bottom-left structure), the regulatory spine (in red, top-right structure) or all residues together (bottom-right structure), our data suggest that the subgroups of residues that are DoS or spines are mutually exclusive or, in other words, that residues classified as DoS are not part of the catalytic or regulatory spines. Like in Figure 4A, the structure used is that of Akt/PKB in complex with GSK3 peptide (PDB ID: 1O6K; Yang et al., 2002).(D) Evolutionary conservation for the different subsets of residues (whole domain, DoS, C-spine, and R-spine) was computed as the negative of entropy, using AL2CO algorithm with its default parameters (50), and shown to be significantly lower in DoS compared to the whole domain and the spines (p = 0.014 and p = 1.4 × 10−6 using Wilcoxon test, respectively).
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fig5: Evolutionary Aspects of DoS and Their Co-existence with Kinase Spines(A) As can be observed from the different panels on this DoS-based Dendrogram, where several kinases are localized discordantly with whole-domain evolution, peptide specificity evolution cannot be directly inferred from whole-domain specificity. These differences highlight how kinases have accumulated mutations on these specific residues, i.e., DoS, in order to evolve different specificities. For further explanation and information, please refer to Experimental Procedures and Figures S5.(B) We next investigated how DoS co-evolved with residues involved in structural changes related to catalysis (kinase spines). As can be seen here, there are different possible degrees to which DoS and spines could co-exist, ranging from complete overlap (left) to complete exclusion (right). In (C), we investigate which of these models is more supported by our data.(C) By comparing the relative localization of the DoS (top-left structure) together with the residues belonging to the catalytic spine (in yellow, bottom-left structure), the regulatory spine (in red, top-right structure) or all residues together (bottom-right structure), our data suggest that the subgroups of residues that are DoS or spines are mutually exclusive or, in other words, that residues classified as DoS are not part of the catalytic or regulatory spines. Like in Figure 4A, the structure used is that of Akt/PKB in complex with GSK3 peptide (PDB ID: 1O6K; Yang et al., 2002).(D) Evolutionary conservation for the different subsets of residues (whole domain, DoS, C-spine, and R-spine) was computed as the negative of entropy, using AL2CO algorithm with its default parameters (50), and shown to be significantly lower in DoS compared to the whole domain and the spines (p = 0.014 and p = 1.4 × 10−6 using Wilcoxon test, respectively).

Mentions: We next set out to explore whether evolutionary insights could be derived from these results. It has previously been observed that the evolution of the kinase domain as a whole is not an accurate reflection of how different kinases have evolved different peptide specificities (Miller et al., 2008, Rausell et al., 2010). Thus, we speculated that a Dendrogram based solely on residues identified as DoS by KINspect could carry significant differences compared to a domain-wide phylogenetic tree. Indeed, Figure 5A (and Figure S5) illustrates how the relationships between kinases (and even between kinase families) appear to deviate when addressed from the DoS’ perspective. This DoS-based tree (Figures 5A and S5) illustrates interesting differences including: (1) the embedding of kinase families within other families, such as in the case of the PKN family, embedded within the PKC family, (2) clustering of seemingly unrelated families, such as the Yank and GRK families, or (3) the splitting of families in two sets displaying marked amino acid differences on their DoS, such as in the case of the Ste20 family.


Unmasking determinants of specificity in the human kinome.

Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R - Cell (2015)

Evolutionary Aspects of DoS and Their Co-existence with Kinase Spines(A) As can be observed from the different panels on this DoS-based Dendrogram, where several kinases are localized discordantly with whole-domain evolution, peptide specificity evolution cannot be directly inferred from whole-domain specificity. These differences highlight how kinases have accumulated mutations on these specific residues, i.e., DoS, in order to evolve different specificities. For further explanation and information, please refer to Experimental Procedures and Figures S5.(B) We next investigated how DoS co-evolved with residues involved in structural changes related to catalysis (kinase spines). As can be seen here, there are different possible degrees to which DoS and spines could co-exist, ranging from complete overlap (left) to complete exclusion (right). In (C), we investigate which of these models is more supported by our data.(C) By comparing the relative localization of the DoS (top-left structure) together with the residues belonging to the catalytic spine (in yellow, bottom-left structure), the regulatory spine (in red, top-right structure) or all residues together (bottom-right structure), our data suggest that the subgroups of residues that are DoS or spines are mutually exclusive or, in other words, that residues classified as DoS are not part of the catalytic or regulatory spines. Like in Figure 4A, the structure used is that of Akt/PKB in complex with GSK3 peptide (PDB ID: 1O6K; Yang et al., 2002).(D) Evolutionary conservation for the different subsets of residues (whole domain, DoS, C-spine, and R-spine) was computed as the negative of entropy, using AL2CO algorithm with its default parameters (50), and shown to be significantly lower in DoS compared to the whole domain and the spines (p = 0.014 and p = 1.4 × 10−6 using Wilcoxon test, respectively).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4644237&req=5

fig5: Evolutionary Aspects of DoS and Their Co-existence with Kinase Spines(A) As can be observed from the different panels on this DoS-based Dendrogram, where several kinases are localized discordantly with whole-domain evolution, peptide specificity evolution cannot be directly inferred from whole-domain specificity. These differences highlight how kinases have accumulated mutations on these specific residues, i.e., DoS, in order to evolve different specificities. For further explanation and information, please refer to Experimental Procedures and Figures S5.(B) We next investigated how DoS co-evolved with residues involved in structural changes related to catalysis (kinase spines). As can be seen here, there are different possible degrees to which DoS and spines could co-exist, ranging from complete overlap (left) to complete exclusion (right). In (C), we investigate which of these models is more supported by our data.(C) By comparing the relative localization of the DoS (top-left structure) together with the residues belonging to the catalytic spine (in yellow, bottom-left structure), the regulatory spine (in red, top-right structure) or all residues together (bottom-right structure), our data suggest that the subgroups of residues that are DoS or spines are mutually exclusive or, in other words, that residues classified as DoS are not part of the catalytic or regulatory spines. Like in Figure 4A, the structure used is that of Akt/PKB in complex with GSK3 peptide (PDB ID: 1O6K; Yang et al., 2002).(D) Evolutionary conservation for the different subsets of residues (whole domain, DoS, C-spine, and R-spine) was computed as the negative of entropy, using AL2CO algorithm with its default parameters (50), and shown to be significantly lower in DoS compared to the whole domain and the spines (p = 0.014 and p = 1.4 × 10−6 using Wilcoxon test, respectively).
Mentions: We next set out to explore whether evolutionary insights could be derived from these results. It has previously been observed that the evolution of the kinase domain as a whole is not an accurate reflection of how different kinases have evolved different peptide specificities (Miller et al., 2008, Rausell et al., 2010). Thus, we speculated that a Dendrogram based solely on residues identified as DoS by KINspect could carry significant differences compared to a domain-wide phylogenetic tree. Indeed, Figure 5A (and Figure S5) illustrates how the relationships between kinases (and even between kinase families) appear to deviate when addressed from the DoS’ perspective. This DoS-based tree (Figures 5A and S5) illustrates interesting differences including: (1) the embedding of kinase families within other families, such as in the case of the PKN family, embedded within the PKC family, (2) clustering of seemingly unrelated families, such as the Yank and GRK families, or (3) the splitting of families in two sets displaying marked amino acid differences on their DoS, such as in the case of the Ste20 family.

Bottom Line: Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues.We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions.Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark. Electronic address: creixell@mit.edu.

Show MeSH
Related in: MedlinePlus