Interactions of calmodulin with death-associated protein kinase peptides: experimental and modeling studies

New insights into the characteristics of DRAK2 and its role in apoptosis: From molecular mechanisms to clinically applied potential

As a member of the death-associated protein kinase (DAPK) family, DAP kinase-associated apoptosis-inducing kinase 2 (DRAK2) performs apoptosis-related functions. Compelling evidence suggests that DRAK2 is involved in regulating the activation of T lymphocytes as well as pancreatic β-cell apoptosis in type I diabetes. In addition, DRAK2 has been shown to be involved in the development of related tumor and non-tumor diseases through a variety of mechanisms, including exacerbation of alcoholic fatty liver disease (NAFLD) through SRSF6-associated RNA selective splicing mechanism, regulation of chronic lymphocytic leukemia and acute myeloid leukemia, and progression of colorectal cancer. This review focuses on the structure, function, and upstream pathways of DRAK2 and discusses the potential and challenges associated with the clinical application of DRAK2-based small-molecule inhibitors, with the aim of advancing DRAK2 research.

Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites

The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation.

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Members of the DAPK family share a specific basic-loop-mediated dimerization motif

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DAPK2 contains a kinase-mediated and dimerization-regulated CaM-binding site

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Autoregulatory segment CaM binding depends on kinase-mediated CaM binding

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DAPK2 activity is regulated by coupled CaM binding to two different sites

Folding and binding energy of a calmodulin-binding cell antiproliferative peptide

We carry out a computational study of a calmodulin-binding peptide shown to be effective in reducing cell proliferation. We find several folded states for two short variants of different length of the peptide and determine the location of the binding site on calmodulin, the binding free energy for the different conformers and structural details that play a role in optimal binding. Binding to a hydrophobic pocket in calmodulin occurs via an anchoring phenylalanine residue of the natively disordered peptide, and is enhanced when a neighbouring hydrophobic residue acts as a co-anchor. The shorter sequence possesses better binding to calmodulin, which is encouraging in terms of the development of non-peptide analogues as therapeutic agents.

Molecular mechanisms of protein kinase regulation by calcium/calmodulin

Many human protein kinases are regulated by the calcium-sensor protein calmodulin, which binds to a short flexible segment C-terminal to the enzyme's catalytic kinase domain. Our understanding of the molecular mechanism of kinase activity regulation by calcium/calmodulin has been advanced by the structures of two protein kinases-calmodulin kinase II and death-associated protein kinase 1-bound to calcium/calmodulin. Comparison of these two structures reveals a surprising level of diversity in the overall kinase-calcium/calmodulin arrangement and functional readout of activity, as well as complementary mechanisms of kinase regulation such as phosphorylation.

Molecular modeling of peptides

This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.

The many structural faces of calmodulin: a multitasking molecular jackknife

Calmodulin (CaM) is a highly conserved protein and a crucial calcium sensor in eukaryotes. CaM is a regulator of hundreds of diverse target proteins. A wealth of studies has been carried out on the structure of CaM, both in the unliganded form and in complexes with target proteins and peptides. The outcome of these studies points toward a high propensity to attain various conformational states, depending on the binding partner. The purpose of this review is to provide examples of different conformations of CaM trapped in the crystal state. In addition, comparisons are made to corresponding studies in solution. The different CaM conformations in crystal structures are also compared based on the positions of the metal ions bound to their EF hands, in terms of distances, angles, and pseudo-torsion angles. Possible caveats and artifacts in CaM crystal structures are discussed, as well as the possibilities of trapping biologically relevant CaM conformations in the crystal state.

Modeling the interactions between MC2R and ACTH models from human

Melanocortin system is composed of four peptide hormones namely α-, β-, -γ, and adrenocorticotropic hormone (ACTH), derived from post-translational cleavage of a polypeptide precursor 'proopiomelanocortin (POMC).' Among these hormones, ACTH, a 38 amino acid residue peptide fragment is an important hormone as it is involved in steroid secretion. In addition to this, to cite a few, this hormone is also known to induce variety of other effects, such as alterations in motor/sexual behavior, improvement in memory, and anti-inflammatory effects. To date, five melanocortin receptors (MC1R-MC5R) have been characterized with tissue-specific expression patterns and different binding affinities for each of the melanocortin hormones to regulate various biological functions. In the present work, three-dimensional (3D) models of MC2R and ACTH from human have been predicted, followed by docking and molecular dynamics simulation. While the 3D model of MC2R receptor has been predicted through threading approach, structure of ACTH was built based on ab initio technique. The MC2R model was later successfully docked onto the ACTH structure. Molecular dynamics (MD) simulation for 20 ns was used to compute the binding free energy of MC2R with ACTH model under implicit solvent conditions.

Interplay of calcium and cadmium in mediating cadmium toxicity

The environmentally important toxic metal, cadmium, exists as the Cd(2+) ion in biological systems, and in this state structurally resembles Ca(2+). Thus, although cadmium exerts a broad range of adverse actions on cells by virtue of its propensity to bind to protein thiol groups, it is now well appreciated that Cd(2+) participates in a number of Ca(2+)-dependent pathways, attributable to its actions as a Ca(2+) mimetic, with a central role for calmodulin, and the Ca(2+)/calmodlin-dependent protein kinase II (CaMK-II) that mediates effects on cytoskeletal dynamics and apoptotic cell death. Cadmium interacts with receptors and ion channels on the cell surface, and with the intracellular estrogen receptor where it binds competitively to residues shared by Ca(2+). It increases cytosolic [Ca(2+)] through several mechanisms, but also decreases transcript levels of some Ca(2+)-transporter genes. It initiates mitochondrial apoptotic pathways, and activates calpains, contributing to mitochondria-independent apoptosis. However, the recent discovery of the role CaMK-II plays in Cd(2+)-induced cell death, and subsequent implication of CaMK-II in Cd(2+)-dependent alterations of cytoskeletal dynamics, has opened a new area of mechanistic cadmium toxicology that is a focus of this review. Calmodulin is necessary for induction of apoptosis by several agents, yet induction of apoptosis by Cd(2+) is prevented by CaMK-II block, and Ca(2+)-dependent phosphorylation of CaMK-II has been linked to increased Cd(2+)-dependent apoptosis. Calmodulin antagonism suppresses Cd(2+)-induced phosphorylation of Erk1/2 and the Akt survival pathway. The involvement of CaMK-II in the effects of Cd(2+) on cell morphology, and particularly the actin cytoskeleton, is profound, favouring actin depolymerization, disrupting focal adhesions, and directing phosphorylated FAK into a cellular membrane. CaMK-II is also implicated in effects of Cd(2+) on microtubules and cadherin junctions. A key question for future cadmium research is whether cytoskeletal disruption leads to apoptosis, or rather if apoptosis initiates cytoskeletal disruption in the context of Cd(2+).

Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix

Calmodulin is one of the most well characterized proteins and a widely used model system for calcium binding and large-scale protein conformational changes. Its long central helix is usually cut in half when a target peptide is bound. Here, two new crystal structures of calmodulin are presented, in which conformations possibly representing the first steps of calmodulin conformational collapse have been trapped. The central helix in the two structures is bent in the middle, causing a significant movement of the N- and C-terminal lobes with respect to one another. In both of the bent structures, a nearby polar side chain is inserted into the helical groove, disrupting backbone hydrogen bonding. The structures give an insight into the details of the factors that may be involved in the distortion of the central helix upon ligand peptide binding.

Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.

Retention of conformational entropy upon calmodulin binding to target peptides is driven by transient salt bridges

Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable binding sequences in target proteins. To identify how binding affects CaM motions, and its relationship to conformational entropy and target peptide sequence, we have employed fully atomistic, explicit solvent molecular dynamics simulations of unbound CaM and CaM bound to five different target peptides. The calculated CaM conformational binding entropies correlate with experimentally derived conformational entropies with a correlation coefficient R(2) of 0.95. Selected side-chain interactions with target peptides restrain interhelical loop motions, acting to tune the conformational entropy of the bound complex via widely distributed CaM motions. In the complex with the most conformational entropy retention (CaM in complex with the neuronal nitric oxide synthase binding sequence), Lys-148 at the C-terminus of CaM forms transient salt bridges alternating between Glu side chains in the N-domain, the central linker, and the binding target. Additional analyses of CaM structures, fluctuations, and CaM-target interactions illuminate the interplay between electrostatic, side chain, and backbone properties in the ability of CaM to recognize and discriminate against targets by tuning its conformational entropy, and suggest a need to consider conformational dynamics in optimizing binding affinities.