How phosphorylation activates the protein phosphatase-1 • inhibitor-2 complex

Protein phosphatase-1: dual activity regulation by Inhibitor-2

Inhibitor-2 (I2) ranks amongst the most ancient regulators of protein phosphatase-1 (PP1). It is a small, intrinsically disordered protein that was originally discovered as a potent inhibitor of PP1. However, later investigations also characterized I2 as an activator of PP1 as well as a chaperone for PP1 folding. Numerous studies disclosed the importance of I2 for diverse cellular processes but did not describe a unifying molecular principle of PP1 regulation. We have re-analyzed the literature on I2 in the light of current insights of PP1 structure and regulation. Extensive biochemical data, largely ignored in the recent I2 literature, provide substantial indirect evidence for a role of I2 as a loader of active-site metals. In addition, I2 appears to function as a competitive inhibitor of PP1 in higher eukaryotes. The published data also demonstrate that several segments of I2 that remain unstructured in the PP1 : I2 complex are in fact essential for PP1 regulation. Together, the available data identify I2 as a dynamic activity-modulator of PP1.

Accurate Identification of Human Phosphorylated Proteins by Ensembling Supervised Kernel Self-organizing Maps

Protein phosphorylation is a vital physiological process, which plays a critical role in controlling survival differentiation, cell growth, metabolism and apoptosis. The accurate identification of whether a protein will be phosphorylated solely from protein sequence is especially useful for both basic research and drug development. In this study, a new predictor specifically designed for the prediction of human phosphorylated proteins is proposed. The proposed method first train two supervised kernel self-organizing maps (SKSOMs): one is trained with feature from protein physiochemical composition view, while the other is trained with feature from protein evolutionary information view. Then, the two trained SKSOMs are ensembled to perform the final prediction. Rigorous computational experiments show that the proposed method achieves 78.75 % and 0.561 on ACC and MCC, which are 6.96 % and 12.5 % higher than that of the state-of-the-art predictor. Overall, the study demonstrated a new sensitive avenue to identify human phosphorylated proteins and could be readily extended to recognize phosphorylated proteins for other species.

Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays

Protein phosphatase 1 (PP1) is a critical regulator of several processes, such as muscle contraction, neuronal signaling, glycogen synthesis, and cell proliferation. Dysregulation of PP1 has recently been found to be implicated in cardiac dysfunctions, which indicates that PP1 could be an attractive therapeutic target. However, discovery of PP1 inhibitors with satisfied safety and efficiency is still a challenge. Here, in order to discover potential PP1 inhibitors, compounds extracted from traditional Chinese medicine (TCM) were screened by a novel integrated virtual screening protocol including pharmacophore modeling and docking approaches. Combined with protein phosphatase inhibition assay, ZINC43060554 showed strongly inhibitory activity with IC₅₀ values of 26.78 μM. Furthermore, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area binding free-energy analysis were performed to examine the stability of ligand binding modes. These novel scaffolds discovered in the present study can be used for rational design of PP1 inhibitors with high affinity.Communicated by Ramaswamy H. Sarma.

Novel phosphorylation-dependent regulation in an unstructured protein

This work explores how phosphorylation of an unstructured protein region in inhibitor-2 (I2) regulates protein phosphatase-1 (PP1) enzyme activity using molecular dynamics (MD). Free I2 is largely unstructured; however, when bound to PP1, three segments adopt a stable structure. In particular, an I2 helix (i-helix) blocks the PP1 active site and inhibits phosphatase activity. I2 phosphorylation in the PP1-I2 complex activates phosphatase activity without I2 dissociation. The I2 Thr74 regulatory phosphorylation site is in an unstructured domain in PP1-I2. PP1-I2 MD demonstrated that I2 phosphorylation promotes early steps of PP1-I2 activation in explicit solvent models. Moreover, phosphorylation-dependent activation occurred in PP1-I2 complexes derived from I2 orthologs with diverse sequences from human, yeast, worm, and protozoa. This system allowed exploration of features of the 73-residue unstructured human I2 domain critical for phosphorylation-dependent activation. These studies revealed that components of I2 unstructured domain are strategically positioned for phosphorylation responsiveness including a transient α-helix. There was no evidence that electrostatic interactions of I2 phosphothreonine74 influenced PP1-I2 activation. Instead, phosphorylation altered the conformation of residues around Thr74. Phosphorylation uncurled the distance between I2 residues Glu71 to Tyr76 to promote PP1-I2 activation, whereas reduced distances reduced activation. This I2 residue Glu71 to Tyr76 distance distribution, independently from Thr74 phosphorylation, controls I2 i-helix displacement from the PP1 active site leading to PP1-I2 activation.

Chronic β-adrenergic stimulation reverses depressed Ca handling in mice overexpressing inhibitor-2 of protein phosphatase 1

RATIONALE

A higher expression/activity of type 1 serine/threonine protein phosphatase 1 (PP1) may contribute to dephosphorylation of cardiac regulatory proteins triggering the development of heart failure.

OBJECTIVE

Here, we tested the putatively protective effects of PP1 inhibitor-2 (I₂) overexpression using a heart failure model induced by chronic β-adrenergic stimulation.

METHODS AND RESULTS

Transgenic (TG) and wild-type (WT) mice were subjected to isoprenaline (ISO) or isotonic NaCl solution supplied via osmotic minipumps for 7 days. I₂ overexpression was associated with a depressed PP1 activity. Basal contractility was unchanged in catheterized mice and isolated cardiomyocytes between TG^NaCl and WT^NaCl. TG^ISO mice exhibited more fibrosis and a higher expression of hypertrophy marker proteins as compared to WT^ISO. After acute administration of ISO, the contractile response was accompanied by a higher sensitivity in TG^ISO as compared to WT^ISO. In contrast to basal contractility, the peak amplitude of [Ca]_i and SR Ca load were reduced in TG^NaCl as compared to WT^NaCl. These effects were normalized to WT levels after chronic ISO stimulation. Cardiomyocyte relaxation and [Ca]_i decay kinetics were hastened in TG^ISO as compared to WT^ISO, which can be explained by a higher phospholamban phosphorylation at Ser¹⁶. Chronic catecholamine stimulation was followed by an enhanced expression of GSK3β, whereas the phosphorylation at Ser⁹ was lower in TG as compared to the corresponding WT group. This resulted in a higher I₂ phosphorylation that may reactivate PP1.

CONCLUSION

Our findings suggest that the basal desensitization of β-adrenergic signaling and the depressed Ca handling in TG by inhibition of PP1 is restored by a GSK3β-dependent phosphorylation of I₂.

Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations

Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (Egap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design.

Advances in NMR Methods To Map Allosteric Sites: From Models to Translation

The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.

Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds

A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.

Protein phosphorylation detection using dual-mode field-effect devices and nanoplasmonic sensors

Phosphorylation by kinases is an important post-translational modification of proteins. It is a critical control for the regulation of vital cellular activities, and its dysregulation is implicated in several diseases. A common drug discovery approach involves, therefore, time-consuming screenings of large libraries of candidate compounds to identify novel inhibitors of protein kinases. In this work, we propose a novel method that combines localized surface plasmon resonance (LSPR) and electrolyte insulator semiconductor (EIS)-based proton detection for the rapid identification of novel protein kinase inhibitors. In particular, the selective detection of thiophosphorylated proteins by LSPR is achieved by changing their resonance properties via a pre-binding with gold nanoparticles. In parallel, the EIS field-effect structure allows the real-time electrochemical monitoring of the protein phosphorylation by detecting the release of protons associated with the kinases activity. This innovative combination of both field-effect and nanoplasmonic sensing makes the detection of protein phosphorylation more reliable and effective. As a result, the screening of protein kinase inhibitors becomes more rapid, sensitive, robust and cost-effective.

Interactor-guided dephosphorylation by protein phosphatase-1

Protein phosphatase-1 (PP1) is an essential enzyme for every eukaryotic cell and catalyzes more than half of all protein dephosphorylations at serine and threonine residues. The free catalytic subunit of PP1 shows little substrate selectivity but is tightly regulated in vivo by a large variety of structurally unrelated PP1-interacting proteins (PIPs). PIPs form highly specific dimeric or trimeric PP1 holoenzymes by acting as substrates, inhibitors, and/or substrate-specifiers. The surface of PP1 contains many binding sites for short PP1-docking motifs that are combined by PIPs to create a PP1-binding code that is universal, specific, degenerate, nonexclusive, and dynamic. These properties of the PP1-binding code can be used for the rational design of small molecules that disrupt subsets of PP1 holoenzymes and have a therapeutic potential.