A dynamic model of membrane-bound phospholipase Cβ2 activation by Gβγ subunits

Molecular regulation of PLCβ signaling

Phospholipase C (PLC) enzymes convert the membrane phospholipid phosphatidylinositol-4,5-bisphosphate (PIP2) into inositol-1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 and DAG regulate numerous downstream pathways, eliciting diverse and profound cellular changes and physiological responses. In the six PLC subfamilies in higher eukaryotes, PLCβ is intensively studied due to its prominent role in regulating crucial cellular events underlying many processes including cardiovascular and neuronal signaling, and associated pathological conditions. In addition to GαqGTP, Gβγ generated upon G protein heterotrimer dissociation also regulates PLCβ activity. Here, we not only review how Gβγ directly activates PLCβ, and also extensively modulates Gαq-mediated PLCβ activity, but also provide a structure-function overview of PLC family members. Given that Gαq and PLCβ are oncogenes, and Gβγ shows unique cell-tissue-organ specific expression profiles, Gγ subtype-dependent signaling efficacies, and distinct subcellular activities, this review proposes that Gβγ is a major regulator of Gαq-dependent and independent PLCβ signaling.

Heterotrimeric G Protein Subunit Gαq Is a Master Switch for Gβγ-Mediated Calcium Mobilization by Gi-Coupled GPCRs

Mechanisms that control mobilization of cytosolic calcium [Ca²⁺]_i are key for regulation of numerous eukaryotic cell functions. One such paradigmatic mechanism involves activation of phospholipase Cβ (PLCβ) enzymes by G protein βγ subunits from activated Gα_i-Gβγ heterotrimers. Here, we report identification of a master switch to enable this control for PLCβ enzymes in living cells. We find that the Gα_i-Gβγ-PLCβ-Ca²⁺ signaling module is entirely dependent on the presence of active Gα_q. If Gα_q is pharmacologically inhibited or genetically ablated, Gβγ can bind to PLCβ but does not elicit Ca²⁺ signals. Removal of an auto-inhibitory linker that occludes the active site of the enzyme is required and sufficient to empower "stand-alone control" of PLCβ by Gβγ. This dependence of Gi-Gβγ-Ca²⁺ on Gα_q places an entire signaling branch of G-protein-coupled receptors (GPCRs) under hierarchical control of Gq and changes our understanding of how Gi-GPCRs trigger [Ca²⁺]_i via PLCβ enzymes.

Activation of Phospholipase C β by Gβγ and Gαq Involves C-Terminal Rearrangement to Release Autoinhibition

Phospholipase C (PLC) enzymes hydrolyze phosphoinositide lipids to inositol phosphates and diacylglycerol. Direct activation of PLCβ by Gα_q and/or Gβγ subunits mediates signaling by Gq and some Gi coupled G-protein-coupled receptors (GPCRs), respectively. PLCβ isoforms contain a unique C-terminal extension, consisting of proximal and distal C-terminal domains (CTDs) separated by a flexible linker. The structure of PLCβ3 bound to Gα_q is known, however, for both Gα_q and Gβγ; the mechanism for PLCβ activation on membranes is unknown. We examined PLCβ2 dynamics on membranes using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Gβγ caused a robust increase in dynamics of the distal C-terminal domain (CTD). Gα_q showed decreased deuterium incorporation at the Gα_q binding site on PLCβ. In vitro Gβγ-dependent activation of PLC is inhibited by the distal CTD. The results suggest that disruption of autoinhibitory interactions with the CTD leads to increased PLCβ hydrolase activity.

G-protein βγ subunits as multi-functional scaffolds and transducers in G-protein-coupled receptor signaling

G-protein βγ subunits are key participants in G-protein signaling. These subunits facilitate interactions between receptors and G proteins that are critical for the G protein activation cycle at the plasma membrane. In addition, they play roles in directly transducing signals to an ever expanding range of downstream targets, including integral membrane and cytosolic proteins. Emerging data indicate that Gβγ may play additional roles at intracellular compartments including endosomes, the Golgi apparatus, and the nucleus. Here, we discuss the molecular and structural basis for their ability to coordinate this wide range of cellular activities.

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.

Direct observation of conformational dynamics of the PH domain in phospholipases Cϵ and β may contribute to subfamily-specific roles in regulation

Phospholipase C (PLC) enzymes produce second messengers that increase the intracellular Ca2+ concentration and activate protein kinase C (PKC). These enzymes also share a highly conserved arrangement of core domains. However, the contributions of the individual domains to regulation are poorly understood, particularly in isoforms lacking high-resolution information, such as PLCϵ. Here, we used small-angle X-ray scattering (SAXS), EM, and functional assays to gain insights into the molecular architecture of PLCϵ, revealing that its PH domain is conformationally dynamic and essential for activity. We further demonstrate that the PH domain of PLCβ exhibits similar dynamics in solution that are substantially different from its conformation observed in multiple previously reported crystal structures. We propose that this conformational heterogeneity contributes to subfamily-specific differences in activity and regulation by extracellular signals.

Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes

Dok7 is a peripheral membrane protein that is associated with the MuSK receptor tyrosine kinase. Formation of the Dok7/MuSK/membrane complex is required for the activation of MuSK. This is a key step in the complex exchange of signals between neuron and muscle, which lead to neuromuscular junction formation, dysfunction of which is associated with congenital myasthenic syndromes. The Dok7 structure consists of a Pleckstrin Homology (PH) domain and a Phosphotyrosine Binding (PTB) domain. The mechanism of the Dok7 association with the membrane remains largely unknown. Using multi-scale molecular dynamics simulations we have explored the formation of the Dok7 PH/membrane complex. Our simulations indicate that the PH domain of Dok7 associates with membranes containing phosphatidylinositol phosphates (PIPs) via interactions of the β1/β2, β3/β4, and β5/β6 loops, which together form a positively charged surface on the PH domain and interact with the negatively charged headgroups of PIP molecules. The initial encounter of the Dok7 PH domain is followed by formation of additional interactions with the lipid bilayer, and especially with PIP molecules, which stabilizes the Dok7 PH/membrane complex. We have quantified the binding of the PH domain to the model bilayers by calculating a density landscape for protein/membrane interactions. Detailed analysis of the PH/PIP interactions reveal both a canonical and an atypical site to be occupied by the anionic lipid. PH domain binding leads to local clustering of PIP molecules in the bilayer. Association of the Dok7 PH domain with PIP lipids is therefore seen as a key step in localization of Dok7 to the membrane and formation of a complex with MuSK.

Neuromuscular junction formation and maintenance is an essential biological process, the disruption of which leads to congenital myasthenic syndromes and premature death. Dok7 is a key member in formation, maintenance and signaling in neuromuscular junctions. Dok7 is a peripheral membrane protein that is necessary for full activation of the receptor tyrosine kinase MuSK, a receptor tyrosine kinase residing in the postsynaptic membrane. The structure of Dok7 consists of both a PH domain and a PTB domain. The interaction of Dok7 with cell membranes is not well understood. Here, we use molecular simulations to show that the Dok7 PH domain preferentially binds to PIP lipid molecules when associating with a membrane. Dok7 interacts with the bilayer in both a canonical binding mode and an alternative binding mode. Our simulations also demonstrate the presence of both a canonical and an atypical binding site for PIPs in agreement with recent crystallographic studies of the ASAP1 PH domain. Analysis of density landscapes for the interaction of the Dok7 PH domain with PIP-containing lipid bilayers is also able to identify both canonical and alternative binding modes. Our improved understanding of how Dok7 interacts with a membrane is key to examining Dok7/MuSK signaling.

Decoding Gαq signaling

Gαq signals with phospholipase C-β (PLC-β) to modify behavior in response to an agonist-bound GPCR. While the fundamental steps which prime Gαq to interact with PLC-β have been identified, questions remain concerning signal strength with PLC-β and other effectors. Gαq is generally viewed to function as a simple ON and OFF switch for its effector, dependent on the binding of GTP or GDP. However, Gαq does not have a single effector, Gαq has many different effectors. Furthermore, select effectors also regulate Gαq activity. PLC-β is a lipase and a GTPase activating protein (GAP) selective for Gαq. The contribution of G protein regulating activity to signal amplitude remains unclear. The unique PLC-β coiled-coil domain is essential for maximum Gαq response, both lipase and GAP. Nonetheless, coiled-coil domain associations necessary to maximum response have not been revealed by the structural approach. This review discusses progress towards understanding the basis for signal strength with PLC-β and other effectors. Shared and effector-specific interactions have been identified. Finally, the evidence for allosteric regulation of lipase stimulation by protein kinase C, the membrane, phosphatidic acid, phosphatidylinositol-4, 5-bisphosphate and GPCR is explored. Endogenous allosteric regulators can suppress or enhance maximum lipase stimulation dependent on the PLC-β coiled-coil domain. A better understanding of allosteric modulation may therefore identify a wealth of new targets to regulate signal strength and behavior.

Molecular mechanisms of phospholipase C β3 autoinhibition

Phospholipase C β (PLCβ) enzymes are dramatically activated by heterotrimeric G proteins. Central to this response is the robust autoinhibition of PLCβ by the X-Y linker region within its catalytic core and by the Hα2' helix in the C-terminal extension of the enzyme. The molecular mechanism of each and their mutual dependence are poorly understood. Herein, it is shown that distinct regions within the X-Y linker have specific roles in regulating activity. Most important,an acidic stretch within the linker stabilizes a lid that occludes the active site, consistent with crystal structures of variants lacking this region. Inhibition by the Hα2' helix is independent of the X-Y linker and likely regulates activity by limiting membrane interaction of the catalytic core. Full activation of PLCβ thus requires multiple independent molecular events induced by membrane association of the catalytic core and by the binding of regulatory proteins.

Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations

Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.

Structural insights into phospholipase C-β function

Phospholipase C (PLC) enzymes convert phosphatidylinositol-4,5-bisphosphate into the second messengers diacylglycerol and inositol-1,4,5-triphosphate. The production of these molecules promotes the release of intracellular calcium and activation of protein kinase C, which results in profound cellular changes. The PLCβ subfamily is of particular interest given its prominent role in cardiovascular and neuronal signaling and its regulation by G protein-coupled receptors, as PLCβ is the canonical downstream target of the heterotrimeric G protein Gαq. However, this is not the only mechanism regulating PLCβ activity. Extensive structural and biochemical evidence has revealed regulatory roles for autoinhibitory elements within PLCβ, Gβγ, small molecular weight G proteins, and the lipid membrane itself. Such complex regulation highlights the central role that this enzyme plays in cell signaling. A better understanding of the molecular mechanisms underlying the control of its activity will greatly facilitate the search for selective small molecule modulators of PLCβ.

Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain

Phospholipase C-β (PLCβ) is directly activated by Gα_q, but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present both the crystal structure and cryo-EM 3D reconstructions of human full-length PLCβ3 in complex with murine Gα_q. The distal CTD forms an extended, monomeric helical bundle consisting of three anti-parallel segments with structural similarity to membrane-binding bin–amphiphysin–Rvs (BAR) domains. Sequence conservation of the distal CTD identifies putative membrane and protein interaction sites, the latter of which bind the N-terminal helix of Gα_q in both the crystal structure and cryo-EM reconstructions. Functional analysis suggests the distal CTD plays roles in membrane targeting and in optimizing the orientation of the catalytic core at the membrane for maximal rates of lipid hydrolysis.

Membrane sculpting by F-BAR domains studied by molecular dynamics simulations

Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy.

To generate organelles, eukaryotic cells sculpt their membranes into compartments, often employing proteins as chaperones, for example, F-BAR domains. The latter induce formation of tubular and vesicular membranes. Functional and structural studies suggest that F-BAR domains sculpt membranes through electrostatic interactions, driving the membrane to match the concave surface of the protein's banana-like shape. Cryo-electron microscopy (cryo-EM) studies provide an average static picture of how F-BAR domains form lattices on the surface of membranes to induce tube formation. Complementing the cryo-EM images, molecular dynamics simulations reported here offer a detailed, dynamic picture of membrane tubulation by a lattice of F-BAR domains and identified lattice types optimally attuned to producing high membrane curvature. The simulations reproduced also a process lasting 350 µs in which lattices of F-BAR domains form a complete tube out of an initially flat membrane. The molecular dynamics study offers, thereby, both a large-scale picture of membrane sculpting by F-BAR domain lattices as well as atomic-level dynamic information about the involvement of the individual F-BAR domain and its interactions with partner F-BAR domains and membrane in the sculpting process.

The correlation between multidomain enzymes and multiple activation mechanisms--the case of phospholipase Cβ and its membrane interactions

Phospholipase Cβ2 (PLCβ2) is a large, multidomain enzyme that catalyzes the hydrolysis of the signaling lipid phosphoinositol 4,5 bisphosphate (PIP2) to promote mitogenic and proliferative changes in the cell. PLCβ2 is activated by Gα and Gβγ subunits of heterotrimeric G proteins, as well as small G proteins and specific peptides. Activation depends on the nature of the membrane surface. Recent crystal structures suggest one model of activation involving the movement of a small autoinhibitory loop upon membrane binding of the enzyme. Additionally, solution studies indicate multiple levels of activation that involve changes in the membrane orientation as well as interdomain movement. Here, we review the wealth of biochemical studies of PLCβ2-G protein activation and propose a comprehensive model that accounts for both the crystallographic and solution results.