Biology subjects

Kornev, A. P.

Publications and source records attributed to Kornev, A. P..

4 recordsLinked to original sources

bioRxiv2023

Protein Kinase Structure and Dynamics: Role of the αC-β4 Loop

Although the C-{beta}4 loop is a stable feature of all protein kinases, the importance of this motif as a conserved element of secondary structure, as well as its links to the hydrophobic architecture of the kinase core, has been underappreciated. We first review the motif and then describe how it is linked to the hydrophobic spine architecture of the kinase core, which we first discovered using a computational tool, Local Spatial Pattern (LSP) alignment. Based on NMR predictions that a mutation in this motif abolishes the synergistic high-affinity binding of ATP and a pseudo substrate inhibitor, we used LSP to interrogate the F100A mutant. This comparison highlights the importance of the C-{beta}4 loop and key residues at the interface between the N- and C-lobes. In addition, we delved more deeply into the structure of the apo C-subunit, which lacks ATP. While apo C-subunit showed no significant changes in backbone dynamics of the C-{beta}4 loop, we found significant differences in the side chain dynamics of K105. The LSP analysis suggests disruption of communication between the N- and C-lobes in the F100A mutant, which would be consistent with the structural changes predicted by the NMR spectroscopy.

molecular biology↗

bioRxiv2023

Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration

Conventional protein kinase C (PKC) isozymes tune the signaling output of cells, with loss-of-function somatic mutations associated with cancer and gain-of-function germline mutations identified in neurodegeneration. PKC with impaired autoinhibition is removed from the cell by quality-control mechanisms to prevent accumulation of aberrantly active enzyme. Here, we examine how a single residue in the C1A domain of PKC{beta}, arginine 42 (R42), permits quality-control degradation when mutated to histidine in cancer (R42H) and blocks downregulation when mutated to proline in the neurodegenerative disease spinocerebellar ataxia (R42P). Using FRET-based biosensors, we determined that mutation of R42 to any residue, including lysine, resulted in reduced autoinhibition as indicated by higher basal activity and faster agonist-induced plasma membrane translocation. R42 is predicted to form a stabilizing salt bridge with E655 in the C-tail and mutation of E655, but not neighboring E657, also reduced autoinhibition. Western blot analysis revealed that whereas R42H had reduced stability, the R42P mutant was stable and insensitive to activator-induced ubiquitination and downregulation, an effect previously observed by deletion of the entire C1A domain. Molecular dynamics (MD) simulations and analysis of stable regions of the domain using local spatial pattern (LSP) alignment suggested that P42 interacts with Q66 to impair mobility and conformation of one of the ligand-binding loops. Additional mutation of Q66 to the smaller asparagine (R42P/Q66N), to remove conformational constraints, restored degradation sensitivity to that of WT. Our results unveil how disease-associated mutations of the same residue in the C1A domain can toggle between gain- or loss-of-function of PKC.

molecular biology↗

bioRxiv2022

Calculation of centralities in protein kinase A

Topological analysis of amino acid networks is a common method that can help to understand the roles of individual residues. The most popular approach for network construction is to create a connection between residues if they interact. These interactions are usually weighted by absolute values of correlation coefficients or mutual information. Here we argue that connections in such networks have to reflect levels of cohesion within the protein instead of a simple fact of interaction between residues. If this is correct, an indiscriminate combination of correlation and anti-correlation, as well as the all-inclusive nature of the mutual information metrics, should be detrimental for the analysis. To test our hypothesis, we studied amino acid networks of the protein kinase A created by Local Spatial Pattern alignment, a method that can detect conserved patterns formed by C-C{beta} vectors. Our results showed that, in comparison with the traditional methods, this approach is more efficient in detecting functionally important residues. Out of four studied centrality metrics, Closeness centrality was the least efficient measure of residue importance. Eigenvector centrality proved to be ineffective as the spectral gap values of the networks were very low due to the bilobal structure of the kinase. We recommend using joint graphs of Betweenness centrality and Degree centrality to visualize different aspects of amino acid roles. Author Summary Protein structures can be viewed as networks of residues with some of them being a part of highly interconnected hubs and some being connectors between the hubs. Analysis of these networks can be helpful for understanding of possible roles of single amino acids. In this paper, we challenged existing methods for the creation of such networks. A traditional way is to connect residues if they can interact. We propose that residues should be connected only if they retain their mutual positions in space during molecular dynamic simulation, that is they move cohesively. We show that this approach improves the efficiency of the analysis indicating that a significant revision of the existing views on amino acid networks is necessary.

bioinformatics↗

bioRxiv2021

Protein Kinase C gamma Mutations Drive Spinocerebellar Ataxia Type 14 by Impairing Autoinhibition

Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DG)/Ca2+-regulated protein kinase C gamma (PKC{gamma}), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. The majority of the approximately 50 identified variants cluster to the DG-sensing C1 domains. Here, we use a FRET- based activity reporter to show that ataxia-associated PKC{gamma} mutations enhance basal activity by compromising autoinhibition. Although impaired autoinhibition generally leads to PKC degradation, the C1 domain mutations protect PKC{gamma} from phorbol ester-induced downregulation. Furthermore, it is the degree of disrupted autoinhibition, not changes in the amplitude of agonist- stimulated activity, that correlate with disease severity. This enhanced basal signaling rewires the brain phosphoproteome, as assessed by phosphoproteomic analysis of cerebella from mice expressing a human PKC{gamma} transgene harboring a SCA14 C1 domain mutation, H101Y. Validating that the pathology arises from disrupted autoinhibition, we show that the degree of impaired autoinhibition correlates inversely with age of disease onset in patients: mutations that cause high basal activity are associated with early onset, whereas those that only modestly increase basal activity, including a previously undescribed variant, D115Y, are associated with later onset. Molecular modeling indicates that almost all SCA14 variants that are not in the C1 domains are at interfaces with the C1B domain, and bioinformatics analysis reveals that variants in the C1B domain are under-represented in cancer. Thus, clustering of SCA14 variants to the C1B domain provides a unique mechanism to enhance PKC{gamma} basal activity while protecting the enzyme from downregulation, deregulating the cerebellar phosphoproteome. One Sentence SummarySCA14 driver mutations in PKC{gamma} impair autoinhibition, with defect correlating inversely with age of disease onset.

biochemistry↗