Protein kinases: evolution of dynamic regulatory proteins

Abstract

Eukaryotic protein kinases evolved as a family of highly dynamic molecules with strictly organized internal architecture. A single hydrophobic F-helix serves as a central scaffold for assembly of the entire molecule. Two non-consecutive hydrophobic structures termed “Spines” anchor all the elements important for catalysis to the F-helix. They make firm, but flexible, connections within the molecule providing a high level of internal dynamics of the protein kinase. During the course of evolution, protein kinases developed a universal regulatory mechanism associated with a large Activation Segment that can be dynamically folded and unfolded in the course of cell functioning. Protein kinases thus represent a unique, highly dynamic and precisely regulated set of switches that control most biological events in eukaryotic cells.

Why nature really chose phosphate

“…As a result, there is strong interest in finding effective inhibitors for these key enzymes (Blaskovich, 2009 ;Cohen, 2002). Significant effort has also been invested into structural and mechanistic studies (Adams, 2001 ;Taylor & Kornev, 2011 ;Zhang, 2003). There are more than 500 protein kinases encoded in the human genome, representing one of the largest protein families (Manning et al 2002), and, despite sequence and structural diversity, many share nearly conserved catalytic domains (Taylor & Radzio-Andzelm, 1994).…”

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

“…This conserved hydrophobic structure connects four residues from critical sites in the kinase monomer,16a, 17 including the active site. The R‐spine is anchored to the αF‐helix via a hydrogen bond between a carboxylate group at the N‐terminal end of the αF‐helix and the backbone of the HRD motif 16b.…”

Substrate Affinity Differentially Influences Protein Kinase C Regulation and Inhibitor Potency

“…Given that kinases are one of the largest gene families in eukaryotes and are involved in nearly every cellular function (3), significant work has focused on understanding the mechanisms that dictate substrate-kinase pairings (4). Although the catalytic domains of eukaryotic kinases are structurally conserved (5,6), the local environment around the substrate binding pocket of the kinase catalytic domain varies between kinases (7). This has led to the view that phosphorylation site recognition occurs through conserved residues flanking the phospho-residue on the substrate.…”

“…Crystallographic and NMR approaches have provided detailed structural information on the catalytic domains of individual kinases in complex with a variety of nucleotide analogs and inhibitors (6,12,13). However, the lack of defined secondary structure surrounding the phospho-motif and the inherent transient nature of the interaction has limited efforts to dissect the different states of the kinase-substrate interaction in the catalytic cycle.…”