Abstract
TRPM7/ChaK1 is a recently discovered atypical protein kinase that has been suggested to selectively phosphorylate the substrate residues located in α-helices. However, the actual structure of kinase-substrate complex has not been determined experimentally and the recognition mechanism remains unknown. In this work we explored possible kinase-substrate binding modes and the likelihood of an α-helix docking interaction, within a kinase active site, using molecular modeling. Specifically kinase ChaK1 and its two peptide substrates were examined; one was an 11-residue segment from the N-terminal domain of annexin-1, a putative endogenous substrate for ChaK1, and the other was an engineered 16-mer peptide substrate determined via peptide library screening. Simulated annealing (SA), replica-exchange molecular dynamics (REMD) and steered molecular dynamics (SMD) simulations were performed on the two peptide substrates and the ChaK1-substrate complex in solution. The simulations indicate that the two substrate peptides are unlikely to bind and react with the ChaK1 kinase in a stable α-helical conformation overall. The key structural elements, sequence motifs, and amino acid residues in the ChaK1 and their possible functions involved in the substrate recognition are discussed.PACS Codes: 87.15.A-
Highlights
Protein kinases are a large class of enzymes that catalyze the phosphorylation of proteins [1]
Conformational propensities From the replica-exchange molecular dynamics (REMD) simulation, we have investigated the conformational distribution of the two peptide substrates, free in water as well as bound to kinase
REMD trajectories derived from all 217 replicas were analyzed using the temperature weighted histogram analysis method (T-WHAM) [55,56] to evaluate the conformational preference of each residue at room temperature
Summary
Protein kinases are a large class of enzymes that catalyze the phosphorylation of proteins [1]. The atypical protein kinases (APKs) are a class of protein kinases that lack sequence homology to CPKs. The first two APKs in the so called “alpha-kinases” family [2,3] were myosin heavy chain kinase A (MHCK A) from Dictyostelium [4,5], and elongation factor 2 kinase (eEF-2 kinase [6]). The first two APKs in the so called “alpha-kinases” family [2,3] were myosin heavy chain kinase A (MHCK A) from Dictyostelium [4,5], and elongation factor 2 kinase (eEF-2 kinase [6]) These kinases are involved in the regulation of a wide range of different processes, including protein translation (eEF-2 kinase [7]), myosin association (MHCK [8]), ion channel regulation (TRPM6/ChaK2, TRPM7/ ChaK1 [9,10]), and cardiomyocyte differentiation (Midori [11]). Many more APKs of unknown function have been identified in the genomes of a wide variety of different eukaryotes
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