PIP2 Binding Research Articles

Investigating The Role Of ARAP3 In The Regulation Of Hematopoietic Stem and Progenitor Cells

ARAP3 is a member of the dual Arf-and-Rho GTPase-activating proteins (GAP) family, functioning specifically to inactivate its substrates Arf6 and RhoA GTPases. ARAP3 is translocated to the plasma membrane after PIP3 binding to the first two of its five PH domains, facilitating its GAP activity in a PI3K-mediated manner. Rho family GTPases are found to play critical roles in many aspects of hematopoietic stem and progenitor cells (HSPCs), such as engraftment and migration, while a role for Arf family GTPases in hematopoiesis is less defined.Previous studies found that either exogenous ARAP3 expression in epithelial cells or RNAi-mediated ARAP3 depletion in endothelial cells disrupts F-actin or lamellipodia formation, respectively, resulting in a cell rounding phenotype and failure to spread. This implies that ARAP3 control of Arf6 and RhoA is tightly regulated, and maintaining precise regulation of ARAP3 levels is crucial to actin organization in the cell. Although ARAP3 was first identified in porcine leukocytes, its function in the hematopoietic system is incompletely understood.Germline deletion of Arap3 results in embryonic lethality due to angiogenic defects. Since endothelial cells are important for the emergence of HSCs during embryonic development, early lethality precludes further studying the role of ARAP3 in definitive hematopoiesis. Therefore, we generated several transgenic mouse models to manipulate ARAP3 in the hematopoietic compartment: (1) Arap3fl/fl;Vav-Cretg conditional knockout mice (CKO) deletes ARAP3 specifically in hematopoietic cells, (2) Arap3fl/fl;VE-Cadherin -Cretg CKO mice selectively deletes ARAP3 in embryonic endothelial cells and thereby hematopoietic cells, and (3) Arap3R302,3A/R302,3A germline knock-in mice (KI/KI) mutates the first PH domain to ablate PI3K-mediated ARAP3 activity in all tissues.We found an almost 100% and 90% excision efficiency in the Vav-Cretg- and VEC-Cretg- mediated deletion of ARAP3 in the bone marrow (BM), respectively. However, the CKO mice appear normal in steady-state hematopoiesis, showing normal peripheral blood (PB) counts and normal distributions of all lineages in the BM. Interestingly, we observed an expansion of the Lin-Scal+cKit+ (LSK) stem and progenitor compartment in the CKO mice. This is due to an increase in the multi-potent progenitor (MPP) fraction, but not the long-term or short-term HSC (LT- or ST-HSC) fractions. Although loss of ARAP3 does not alter the frequency of phenotypically-characterized HSCs, we performed competitive BM transplantation (BMT) studies to investigate the functional impact of ARAP3 deficiency. 500 LSK cells from Arap3 CKO (Arap3fl/fl;Vav-Cretg and Arap3fl/fl;VEC-Cretg) or Arap3fl/fl control littermate donors were transplanted with competitor BM cells into irradiated recipients. We observed similar donor-derived reconstitution and lineage repopulation in the mice transplanted with Arap3fl/fl and Arap3 CKO HSCs. Moreover, Arap3 CKO HSCs show normal reconstitution in secondary transplants.Arap3KI/KI mice are also grossly normal and exhibit an expanded MPP compartment. Importantly, Arap3KI/KI LSKs show impaired reconstitution compared to controls in the competitive BMT assays. Upon secondary and tertiary transplantation, reconstitution in both PB and BM diminished in the Arap3KI/KI groups, in contrast to sustained reconstitution in the control group. Additionally, we observed a marked skewing towards the myeloid lineage in Arap3KI/KI transplanted secondary and tertiary recipients. These data suggest a defect in HSC function in Arap3KI/KI mice. Myeloid-skewed reconstitution also points to the possibility of selection for “myeloid-primed” HSCs and against “balanced” HSCs, as HSCs exhaust during aging or upon serial transplantation.Taken together, our data suggest that ARAP3 plays a non-cell-autonomous role in HSCs by regulating HSC niche cells. Alternatively, the ARAP3 PH domain mutant that is incapable of locating to the plasma membrane in response to PI3K may exert a novel dominant negative function in HSCs. We are investigating mechanistically how ARAP3 controls HSC engraftment and self-renewal to elucidate the potential cell-autonomous and non-cell-autonomous roles of ARAP3 in HSCs. In summary, our studies identify a previously unappreciated role of ARAP3 as a regulator of hematopoiesis and hematopoietic stem and progenitor cell function. Disclosures:No relevant conflicts of interest to declare.

Identification of compound heterozygous KCNJ1 mutations (encoding ROMK) in a kindred with Bartter's syndrome and a functional analysis of their pathogenicity

A multiplex family was identified with biochemical and clinical features suggestive of Bartter's syndrome (BS). The eldest sibling presented with developmental delay and rickets at 4 years of age with evidence of hypercalciuria and hypokalemia. The second sibling presented at 1 year of age with urinary tract infections, polyuria, and polydipsia. The third child was born after a premature delivery with a history of polyhydramnios and neonatal hypocalcemia. Following corrective treatment she also developed hypercalciuria and a hypokalemic metabolic alkalosis. There was evidence of secondary hyperreninemia and hyperaldosteronism in all three siblings consistent with BS. Known BS genes were screened and functional assays of ROMK (alias KCNJ1, Kir1.1) were carried out in Xenopus oocytes. We detected compound heterozygous missense changes in KCNJ1, encoding the potassium channel ROMK. The S219R/L220F mutation was segregated from father and mother, respectively. In silico modeling of the missense mutations suggested deleterious changes. Studies in Xenopus oocytes revealed that both S219R and L220F had a deleterious effect on ROMK-mediated potassium currents. Coinjection to mimic the compound heterozygosity produced a synergistic decrease in channel function and revealed a loss of PKA-dependent stabilization of PIP2 binding. In conclusion, in a multiplex family with BS, we identified compound heterozygous mutations in KCNJ1. Functional studies of ROMK confirmed the pathogenicity of these mutations and defined the mechanism of channel dysfunction.

Chimeras of sperm PLC reveal disparate protein domain functions in the generation of intracellular Ca2+ oscillations in mammalian eggs at fertilization

Phospholipase C-zeta (PLCζ) is a sperm-specific protein believed to cause Ca(2+) oscillations and egg activation during mammalian fertilization. PLCζ is very similar to the somatic PLCδ1 isoform but is far more potent in mobilizing Ca(2+) in eggs. To investigate how discrete protein domains contribute to Ca(2+) release, we assessed the function of a series of PLCζ/PLCδ1 chimeras. We examined their ability to cause Ca(2+) oscillations in mouse eggs, enzymatic properties using in vitro phosphatidylinositol 4,5-bisphosphate (PIP2) hydrolysis and their binding to PIP2 and PI(3)P with a liposome interaction assay. Most chimeras hydrolyzed PIP2 with no major differences in Ca(2+) sensitivity and enzyme kinetics. Insertion of a PH domain or replacement of the PLCζ EF hands domain had no deleterious effect on Ca(2+) oscillations. In contrast, replacement of either XY-linker or C2 domain of PLCζ completely abolished Ca(2+) releasing activity. Notably, chimeras containing the PLCζ XY-linker bound to PIP2-containing liposomes, while chimeras containing the PLCζ C2 domain exhibited PI(3)P binding. Our data suggest that the EF hands are not solely responsible for the nanomolar Ca(2+) sensitivity of PLCζ and that membrane PIP2 binding involves the C2 domain and XY-linker of PLCζ. To investigate the relationship between PLC enzymatic properties and Ca(2+) oscillations in eggs, we have developed a mathematical model that incorporates Ca(2+)-dependent InsP3 generation by the PLC chimeras and their levels of intracellular expression. These numerical simulations can for the first time predict the empirical variability in onset and frequency of Ca(2+) oscillatory activity associated with specific PLC variants.

ß1 Integrin Binding Phosphorylates Ezrin at T567 to Activate a Lipid Raft Signalsome Driving Invadopodia Activity and Invasion

Extracellular matrix (ECM) degradation is a critical process in tumor cell invasion and requires matrix degrading protrusions called invadopodia. The Na+/H+ exchanger (NHE1) has recently been shown to be fundamental in the regulation of invadopodia actin cytoskeleton dynamics and activity. However, the structural link between the invadopodia cytoskeleton and NHE1 is still unknown. A candidate could be ezrin, a linker between the NHE1 and the actin cytoskeleton known to play a pivotal role in invasion and metastasis. However, the mechanistic basis for its role remains unknown. Here, we demonstrate that ezrin phosphorylated at T567 is highly overexpressed in the membrane of human breast tumors and positively associated with invasive growth and HER2 overexpression. Further, in the metastatic cell line, MDA-MB-231, p-ezrin was almost exclusively expressed in invadopodia lipid rafts where it co-localized in a functional complex with NHE1, EGFR, ß1-integrin and phosphorylated-NHERF1. Manipulation by mutation of ezrins T567 phosphorylation state and/or PIP2 binding capacity or of NHE1s binding to ezrin or PIP2 demonstrated that p-ezrin expression and binding to PIP2 are required for invadopodia-mediated ECM degradation and invasion and identified NHE1 as the membrane protein that p-ezrin regulates to induce invadopodia formation and activity.

In Silico Modeling of Itk Activation Kinetics in Thymocytes Suggests Competing Positive and Negative IP4 Mediated Feedbacks Increase Robustness

The inositol-phosphate messenger inositol(1,3,4,5)tetrakisphosphate (IP4) is essential for thymocyte positive selection by regulating plasma-membrane association of the protein tyrosine kinase Itk downstream of the T cell receptor (TCR). IP4 can act as a soluble analog of the phosphoinositide 3-kinase (PI3K) membrane lipid product phosphatidylinositol(3,4,5)trisphosphate (PIP3). PIP3 recruits signaling proteins such as Itk to cellular membranes by binding to PH and other domains. In thymocytes, low-dose IP4 binding to the Itk PH domain surprisingly promoted and high-dose IP4 inhibited PIP3 binding of Itk PH domains. However, the mechanisms that underlie the regulation of membrane recruitment of Itk by IP4 and PIP3 remain unclear. The distinct Itk PH domain ability to oligomerize is consistent with a cooperative-allosteric mode of IP4 action. However, other possibilities cannot be ruled out due to difficulties in quantitatively measuring the interactions between Itk, IP4 and PIP3, and in generating non-oligomerizing Itk PH domain mutants. This has hindered a full mechanistic understanding of how IP4 controls Itk function. By combining experimentally measured kinetics of PLCγ1 phosphorylation by Itk with in silico modeling of multiple Itk signaling circuits and a maximum entropy (MaxEnt) based computational approach, we show that those in silico models which are most robust against variations of protein and lipid expression levels and kinetic rates at the single cell level share a cooperative-allosteric mode of Itk regulation by IP4 involving oligomeric Itk PH domains at the plasma membrane. This identifies MaxEnt as an excellent tool for quantifying robustness for complex TCR signaling circuits and provides testable predictions to further elucidate a controversial mechanism of PIP3 signaling.

Differential isolation and identification of PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana using an agarose-phosphatidylinositol-phosphate affinity chromatography

A phosphatidylinositol-phosphate affinity chromatographic approach combined with mass spectrometry was used in order to identify novel PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana suspension cell extracts. Most of the phosphatidylinositol-phosphate interacting candidates identified from this differential screening are characterized by lysine/arginine rich patches. Direct phosphoinositide binding was identified for important membrane trafficking regulators as well as protein quality control proteins such as the ATG18p orthologue involved in autophagosome formation and the lipid Sec14p like transfer protein. A pentatricopeptide repeat (PPR) containing protein was shown to directly bind to PI(3,5)P2 but not to PI(3)P. PIP chromatography performed using extracts obtained from high salt (0.4M and 1M NaCl) pretreated suspensions showed that the association of an S5-1 40S ribosomal protein with both PI(3)P and PI(3,5)P2 was abolished under salt stress whereas salinity stress induced an increase in the phosphoinositide association of the DUF538 domain containing protein SVB, associated with trichome size. Additional interacting candidates were co-purified with the phosphoinositide bound proteins. Binding of the COP9 signalosome, the heat shock proteins, and the identified 26S proteasomal subunits, is suggested as an indirect effect of their interaction with other proteins directly bound to the PI(3)P and the PI(3,5)P2 phosphoinositides. PI(3,5)P2 is of special interest because of its low abundance. Furthermore, no endogenous levels have yet been detected in A. thaliana (although there is evidence for its existence in plants). Therefore the isolation of novel interacting candidates in vitro would be of a particular importance since the future study and localization of the respective endogenous proteins may indicate possible targeted compartments or tissues where PI(3,5)P2 could be enriched and thereafter identified. In addition, PI(3,5)P2 is a phosphoinositide extensively studied in mammalian and yeast systems. However, our knowledge of its role in plants as well as a list of its effectors from plants is very limited.

IQGAP1 is a novel phosphatidylinositol 4,5 bisphosphate effector in regulation of directional cell migration

Phosphatidylinositol 4,5 bisphosphate (PIP₂) is a key lipid messenger for regulation of cell migration. PIP₂ modulates many effectors, but the specificity of PIP₂ signalling can be defined by interactions of PIP₂-generating enzymes with PIP₂ effectors. Here, we show that type Iγ phosphatidylinositol 4-phosphate 5-kinase (PIPKIγ) interacts with the cytoskeleton regulator, IQGAP1, and modulates IQGAP1 function in migration. We reveal that PIPKIγ is required for IQGAP1 recruitment to the leading edge membrane in response to integrin or growth factor receptor activation. Moreover, IQGAP1 is a PIP₂ effector that directly binds PIP₂ through a polybasic motif and PIP₂ binding activates IQGAP1, facilitating actin polymerization. IQGAP1 mutants that lack PIPKIγ or PIP₂ binding lose the ability to control directional cell migration. Collectively, these data reveal a synergy between PIPKIγ and IQGAP1 in the control of cell migration.

Of GIRK channels, vitamin E transfer, and a vertebrate fluorescent protein

Of GIRK channels, vitamin E transfer, and a vertebrate fluorescent protein

The PH Domain of Phosphoinositide-Dependent Kinase-1 Exhibits a Novel, Phospho-Regulated Monomer–Dimer Equilibrium with Important Implications for Kinase Domain Activation: Single-Molecule and Ensemble Studies

Phosphoinositide-dependent kinase-1 (PDK1) is an essential master kinase recruited to the plasma membrane by the binding of its C-terminal PH domain to the signaling lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3). Membrane binding leads to PDK1 phospho-activation, but despite the central role of PDK1 in signaling and cancer biology, this activation mechanism remains poorly understood. PDK1 has been shown to exist as a dimer in cells, and one crystal structure of its isolated PH domain exhibits a putative dimer interface. It has been proposed that phosphorylation of PH domain residue T513 (or the phospho-mimetic T513E mutation) may regulate a novel PH domain dimer-monomer equilibrium, thereby converting an inactive PDK1 dimer to an active monomer. However, the oligomeric states of the PH domain on the membrane have not yet been determined, nor whether a negative charge at position 513 is sufficient to regulate its oligomeric state. This study investigates the binding of purified wild-type (WT) and T513E PDK1 PH domains to lipid bilayers containing the PIP3 target lipid, using both single-molecule and ensemble measurements. Single-molecule analysis of the brightness of the fluorescent PH domain shows that the PIP3-bound WT PH domain on membranes is predominantly dimeric while the PIP3-bound T513E PH domain is monomeric, demonstrating that negative charge at the T513 position is sufficient to dissociate the PH domain dimer and is thus likely to play a central role in PDK1 monomerization and activation. Single-molecule analysis of two-dimensional (2D) diffusion of PH domain-PIP3 complexes reveals that the dimeric WT PH domain diffuses at the same rate as a single lipid molecule, indicating that only one of its two PIP3 binding sites is occupied and there is little penetration of the protein into the bilayer as observed for other PH domains. The 2D diffusion of T513E PH domain is slower, suggesting the negative charge disrupts local structure in a way that allows deeper insertion of the protein into the viscous bilayer, thereby increasing the diffusional friction. Ensemble measurements of PH domain affinity for PIP3 on plasma membrane-like bilayers reveal that the dimeric WT PH domain possesses a one order of magnitude higher target membrane affinity than the previously characterized monomeric PH domains, consistent with a dimerization-triggered, allosterically enhanced affinity for one PIP3 molecule (a much larger affinity enhancement would be expected for dimerization-triggered binding to two PIP3 molecules). The monomeric T513E PDK1 PH domain, like other monomeric PH domains, exhibits a PIP3 affinity and bound state lifetime that are each 1 order of magnitude lower than those of the dimeric WT PH domain, which is predicted to facilitate release of activated, monomeric PDK1 to the cytoplasm. Overall, the study yields the first molecular picture of PH domain regulation via electrostatic control of dimer-monomer conversion.

Molecular Mechanism of Membrane Binding of the GRP1 PH Domain

The pleckstrin homology (PH) domain of the general receptor of phosphoinositides 1 (GRP1) protein selectively binds to a rare signaling phospholipid, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), in the membrane. The specific PIP3 lipid docking of GRP1 PH domain is essential to protein cellular function and is believed to occur in a stepwise process, electrostatic-driven membrane association followed by the specific PIP3 binding. By a combination of all-atom molecular dynamics (MD) simulations, coarse-grained analysis, electron paramagnetic resonance (EPR) membrane docking geometry, and fluorescence resonance energy transfer (FRET) kinetic studies, we have investigated the search and bind process in the GRP1 PH domain at the molecular scale. We simulated the two membrane binding states of the GRP1 PH domain in the PIP3 search process, before and after the GRP1 PH domain docks with the PIP3 lipid. Our results suggest that the background anionic phosphatidylserine lipids, which constitute around one-fifth of the membrane by composition, play a critical role in the initial stages of recruiting protein to the membrane surface through non-specific electrostatic interactions. Our data also reveal a previously unseen transient membrane association mechanism that is proposed to enable a two-dimensional “hopping” search of the membrane surface for the rare PIP3 target lipid. We further modeled the PIP3-bound membrane–protein system using the EPR membrane docking structure for the MD simulations, quantitatively validating the EPR membrane docking structure and augmenting our understanding of the binding interface with atomic-level detail. Several observations and hypotheses reached from our MD simulations are also supported by experimental kinetic studies.

Energetics and Location of Phosphoinositide Binding in Human Kir2.1 Channels

Kir2.1 channels are uniquely activated by phosphoinositide 4,5-bisphosphate (PI(4,5)P2) and can be inhibited by other phosphoinositides (PIPs). Using biochemical and computational approaches, we assess PIP-channel interactions and distinguish residues that are energetically critical for binding from those that alter PIP sensitivity by shifting the open-closed equilibrium. Intriguingly, binding of each PIP is disrupted by a different subset of mutations. In silico ligand docking indicates that PIPs bind to two sites. The second minor site may correspond to the secondary anionic phospholipid site required for channel activation. However, 96-99% of PIP binding localizes to the first cluster, which corresponds to the general PI(4,5)P2 binding location in recent Kir crystal structures. PIPs can encompass multiple orientations; each di- and triphosphorylated species binds with comparable energies and is favored over monophosphorylated PIPs. The data suggest that selective activation by PI(4,5)P2 involves orientational specificity and that other PIPs inhibit this activation through direct competition.

Calmodulin boosts Itk activity to induce sustained calcium responses in T cells (P1117)

Abstract The Tec family tyrosine kinase Itk is an important transducer of T cell activating signals. Itk regulates the levels of two second messengers Ca2+ and diacylglycerol, which are required for initiating transcriptional programs important for T cell priming and differentiation. How T cells translate intracellular signaling cascades into distinct functional outcomes remains a fundamentally important question. We hypothesize that distinct mechanisms of Itk activation lead to Ca2+ patterns that result in divergent T cell responses. Itk activation requires recruitment via its Pleckstrin homology (PH) domain to its membrane ligand PIP3, which is generated by PI-3 kinase. Here, we report a role for Calmodulin (CaM) in sustaining Itk activity and Ca2+ responses. CaM is a downstream Ca2+ sensor that controls numerous cellular enzymes, including Calcineurin. We have identified a novel interaction between the Itk PH domain and CaM. NMR analyses revealed that CaM binds adjacent to the PIP3 binding pocket, leading us to hypothesize that CaM regulates PIP3 binding. CaM inhibition or genetic mutation of the CaM binding site resulted in decreased PIP3 association and Itk activation, resulting in less sustained Ca2+ responses. We propose a model in which initial Itk activation results in low Ca2+ increases that feedback to boost membrane recruitment of Itk via CaM. We speculate that T cell responses requiring sustained Ca2+ signals, such as T cell differentiation require this feedback loop.

The carboxyl tail of alpha-actinin-4 regulates its susceptibility to m-calpain and thus functions in cell migration and spreading

Alpha-actinin-4 links the cytoskeleton to sites of adhesion and has been shown to be modulated to enable cell migration. Such focal adhesions must be labile to accomplish migration, with this detachment occurring at least in part via m-calpain activation (Glading et al., 2001, 2002; Xie et al., 1998). In this study, we report that alpha-actinin-4 is initially cleaved by m-calpain between tyrosine 13 and glycine. Removal of the first 13 amino acids does not affect alpha-actinin-4 binding to actin filaments and its localization within fibroblasts but drives cell migration with less persistence. Binding of phosphoinositides PI(4,5)P2, PI(3,4,5)P3 and PI(3,4)P2 to alpha-actinin-4, as well as binding of alpha-actinin-4 to actin filaments all inhibit m-calpain cleavage of ACTN4 between tyrosine 13 and glycine 14. Interestingly, the carboxyl terminus of alpha-actinin-4 including its calcium binding motifs, is inhibitory for a secondary cleavage of alpha-actinin-4 between lysine 283 and valine 284. The minimal length of inhibitory domain is mapped to the last 11 amino acids of alpha-actinin-4. The C-terminal tail of alpha-actinin-4 is essential for maintaining its normal actin binding activity and localization within cytoplasm and also its colocalization with actin in the lamellipodia of locomoting fibroblasts. Live cell imaging reveals that the 1–890 fragment fails to rescue neither the basal or growth factor-stimulated migration nor the revert the spread area of fibroblasts to the level of NR6WT. These findings suggest that the C-terminal tail of alpha-actinin-4 is essential for its function in cell migration and adhesion to substratum.

Trio engagement via plasma membrane phospholipids and the myristoyl moiety governs HIV-1 matrix binding to bilayers

Localization of the HIV type-1 (HIV-1) Gag protein on the plasma membrane (PM) for virus assembly is mediated by specific interactions between the N-terminal myristoylated matrix (MA) domain and phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)]. The PM bilayer is highly asymmetric, and this asymmetry is considered crucial in cell function. In a typical mammalian cell, the inner leaflet of the PM is enriched in phosphatidylserine (PS) and phosphatidylethanolamine (PE) and contains minor populations of phosphatidylcholine (PC) and PI(4,5)P(2). There is strong evidence that efficient binding of HIV-1 Gag to membranes is sensitive not only to lipid composition and net negative charge, but also to the hydrophobic character of the acyl chains. Here, we show that PS, PE, and PC interact directly with MA via a region that is distinct from the PI(4,5)P(2) binding site. Our NMR data also show that the myristoyl group is readily exposed when MA is bound to micelles or bicelles. Strikingly, our structural data reveal a unique binding mode by which the 2'-acyl chain of PS, PE, and PC lipids is buried in a hydrophobic pocket whereas the 1'-acyl chain is exposed. Sphingomyelin, a major lipid localized exclusively on the outer layer of the PM, does not bind to MA. Our findings led us to propose a trio engagement model by which HIV-1 Gag is anchored to the PM via the 1'-acyl chains of PI(4,5)P(2) and PS/PE/PC and the myristoyl group, which collectively bracket a basic patch projecting toward the polar leaflet of the membrane.

The characterization of the nuclear dynamics of syntenin‐2, a PIP2 binding PDZ protein

Cellular signaling is largely dependent on the presence, that is, assembly/disassembly, of supramolecular complexes. Postsynaptic density protein, Discs-large, Zona occludens (PDZ) domains play important roles in the assembly of various signaling complexes. Syntenin-2 (S2) is a PDZ protein that interacts with nuclear phosphatidylinositol 4,5-bisphosphate (PIP2 ). Although nuclear lipids emerge as key players in nuclear processes, the global significance of nuclear phosphoinositide-protein interactions is still poorly understood. Those phosphoinositide-protein interactions that have been studied in detail appear to have profound physiological effects. To our knowledge none of these were investigated by dynamic studies such as Fluorescence Correlation Spectroscopy (FCS), Fluorescence Cross-Correlation Spectroscopy (FCCS), or Fluorescence Recovery After Photobleaching (FRAP). Although the exact function of S2 is unknown, siRNA experiments suggest that this PDZ protein plays a role in the organization of nuclear PIP2 , cell division, and cell survival. As a consequence of its PIP2 interaction, its reported self-association in a yeast two-hybrid study and its speculated interaction with many, yet unidentified, proteins one can hypothesize that S2 plays an important role in cell signaling. Therefore, we studied the dynamics of S2 using FCS, FCCS, and FRAP, utilizing an active truncated form deleted for the first 94 amino acids (S2-ΔN). We showed that S2-ΔN self-associates and is distributed in three groups. One immobile group, one slow diffusing group, which interacts with the nuclear environment and one fast diffusing group, which is not incorporated in high molecular weight complexes. In addition, our FCS and FRAP measurements on S2-ΔN mutants affected in their PIP2 binding showed that PIP2 plays an important role in the distribution of S2-ΔN among these groups, and favors the enrichment of S2-ΔN in the slow diffusing and immobile group. This work indicates that S2 relies on nuclear PIP2 to interact with practically immobile structures, possibly chromatin.

Apart from its basic function the plasma membrane Ca2+ATPase regulates Ca2+ signaling by controlling phosphatidylinositol-4,5-bisphosphate levels

Plasma membrane Ca(2+) ATPases (PMCAs, also known as ATP2B1-ATP2B4) are known targets of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P₂], but if and how they control the PtdIns(4,5)P₂ pool has not been considered. We demonstrate here that PMCAs protect PtdIns(4,5)P₂ in the plasma membrane from hydrolysis by phospholipase C (PLC). Comparison of active and inactive PMCAs indicates that the protection operates by two mechanisms; one requiring active PMCAs, the other not. It appears that the mechanism requiring activity is the removal of the Ca(2+) required for sustained PLC activity, whereas the mechanism not requiring activity is PtdIns(4,5)P₂ binding. We show that in PMCA overexpressing cells, PtdIns(4,5)P₂ binding can lead to less inositol 1,4,5-triphosphate (InsP₃) and diminished Ca(2+) release from intracellular Ca(2+) pools. Inspection of a homology model of PMCA suggests that PMCAs have a conserved cluster of basic residues forming a 'blue collar' at the interface between the membrane core and the cytoplasmic domains. By molecular dynamics simulation, we found that the blue collar forms four binding pockets for the phosphorylated inositol head group of PtdIns(4,5)P₂; these pockets bind PtdIns(4,5)P₂ strongly and frequently. Our studies suggest that by having the ability to bind PtdIns(4,5)P₂, PMCAs can control the accessibility of PtdIns(4,5)P₂ for PLC and other PtdIns(4,5)P₂-mediated processes.

K2P and Kir K+ Channels in Physiological Bilayers

We are interested in understanding the mechanism of modulation of inwardly-rectifying (Kir) and two-pore (K2P) potassium ion channels by physiological and modulatory lipids. The phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) is critical for Kir channel activity, and recent crystal structures of Kir2.2 (one of them in complex with PIP2) have shed light on PIP2–Kir channel interactions. However, the mechanism of PIP2 binding and gating is not fully understood. Here, we used a multi-scale approach, consisting of sequential coarse-grained and atomistic molecular dynamics simulations of Kir2.2 embedded in a phospolipid/PIP2 bilayer, to determine whether this computational approach leads to the same PIP2–binding site as observed in the PIP2–bound crystal structure. Our results correctly predict the PIP2 binding site in Kir2.2 even when slightly different structures were used as starting coordinates for these simulations. These results therefore demonstrate the predictive power of this computational approach for the study of protein interactions with PIP2 and possibly other modulatory lipids.Having validated this multi-scale approach, we applied it to study both Kir and K2P channels with PIP2 in physiological bilayers. TREK-1, the prototypical K2P channel, is modulated by PIP2, but the exact mechanism by which it interacts with PIP2 has not been fully elucidated. To explore these mechanisms, we have built structural models of TREK-1 based upon the recent crystal structures of the related K2P channels, TWIK-1 and TRAAK. These two different structural models of TREK-1 were validated by comparison to functional scanning mutagenesis data, which revealed that TRAAK provides the best structural template for modelling of TREK-1. This new structural model of TREK-1 now provides an opportunity to use multi-scale simulations to explore the interaction of TREK-1 with PIP2/modulatory lipids, and to gain a greater insight into the molecular mechanisms which underlie regulation of K2P channel gating.

PIP2 Dynamics underlying Muscarinic or Vasopressin Receptor-Activated TRPC3 C6 And C7 Currents

Subfamily of human expressed TRPC channels (TRPC3/6/7) are activated by ‘diacylglycerol' (DAG), a phospholipase C (PLC) hydrolyzed product of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Hofmann et al., 1999, Nature). In contrary, we have recently reported that the depletion of PI(4,5)P2 by-itself act as a potent negative regulator to all these channels even in the presence of DAG (Imai et al., 2012, J. of Physiol.). Stimulation upon the vasoconstrictile receptors coupled with PLC theoretically causes inseparable bimodal effect to these TRPC channels, i.e. activation and inhibition by DAG production and coincident PI(4,5)P2 reduction or depletion which is corresponding to the strength of PLC activities. Here, to elucidate such self-limiting regulatory function coupled to PI(4,5)P2-DAG signal, we simultaneously measure TRPC6/7 currents in the whole-cell configuration and PI(4,5)P2 dynamics by FRET using PI(4,5)P2 binding PH-domain sensor proteins in the various strength of muscarinic- or vasopressin-receptor stimulation. Our simultaneous detection approach reveals good kinetics correlation between TRPC activation/fast-inactivation and PI(4,5)P2 depletion. Furthermore, a simple self-limiting regulation model wherein experimentally determined PI(4,5)P2 binding constants incorporated aware an emergence of fast recovery of PI(4,5)P2 to produce slow inactivation (plateau phase) of TRPC currents. We find that such model implicated PI(4,5)P2 enhancement can be reproduced after the fast PI(4,5)P2 depletion under the robust agonist stimulation by the local FRET measurement near the channels. Hence, these data indicates that self-limiting regulation coupled to PI(4,5)P2-DAG signal is the pivotal mechanism to understand the receptor-PLC mediated TRPC3/6/7 channels activity.

Identification of the Regulatory Anionic Lipid Site in Kir Channels

Inwardly rectifying potassium channels (Kir) are regulated by multiple factors, including multiple lipids. In addition to a specific requirement for phosphatidyl-4,5-bisphosphate (PI(4,5)P2) for channel activity of Kir2.1, analysis of purified proteins reconstituted into liposomes has revealed a secondary requirement for non-specific anionic lipids, which increase PI(4,5)P2 sensitivity by ∼100 fold [Cheng et al. 2011, Biophys. J. 100, 620-628]. Recent crystal structures of eukaryotic Kir channels in complex with PI(4,5)P2 reveal a common PI(4,5)P2 binding site [Hansen et al, 2011, Nature. 477, 495-498; Whorton & MacKinnon, 2011, Cell. 147, 199-208], but they have not identified the synergistic anionic lipid site.We have performed extensive docking simulations to identify potential interaction sites of different phospholipids with Kir2.1 channels. These simulations indicate two distinct binding sites; a high affinity site that corresponds to the crystallographic PI(4,5)P2 binding pocket and a lower affinity site, involving two lysine residues further towards the periphery of the cytoplasmic domain, that may correspond to the secondary anionic lipid site. When the two lysine residues are mutated to cysteine, channel activity is essentially abolished, even in the presence of PIP2. Cysteine modification of these residues by decyl-MTS, which essentially provides a ‘lipid tether' to the residue, restores channel activity in the presence of low levels of PIP2. These results point strongly to the identified site as being the site for non-specific anionic lipid interaction, and support a model in which the anionic lipid interaction (or ‘lipid tethering') pulls the Kir domain towards the membrane, facilitating PI(4,5)P2-mediated channel opening.

PIP2-Mediated Gating of the Inward Rectifier Potassium Channel Kir2.2

Inward-rectifier K+ (Kir) channels are ion channels that transport potassium into the cell. They are essential to maintain the resting membrane potential and to regulate the action potential duration in excitable cells [1]. As a consequence, Kir mutations result in several diseases, such as periodic paralysis or cardiac arrhythmia [1, 2].The activity of Kir channels is regulated by phosphatidylinositol-(4,5)-bisphosphate (PIP2), a negatively charged phospholipid that has been recognized as one of the major regulators of membrane excitability [2]. Recently, the MacKinnon group has solved the crystal structure of Kir2.2 in the apo form [3] and in complex with a PIP2 derivative [4]. PIP2 binding is shown to induce a large conformational change of the linker connecting the transmembrane (TMD) and cytosolic (CTD) domains, as well as the opening of the inner helix bundle crossing (HBC) gate. However, the specific mechanism of Kir activation by PIP2 is not known yet.Here we have investigated the dynamics of PIP2-triggered channel gating by means of molecular dynamics (MD). Simulations have been performed on both the apo and holo states of the channel, embedded in a POPC membrane in the presence of KCl. The trajectories obtained give further insight into how the channel-PIP2 interactions drive the contraction of the linker and the translation of the CTD towards the TMD, resulting in the separation of the helices at the HBC gate. Additional free energy perturbation calculations will be needed to provide an estimate of the binding affinity of PIP2 to the channel and the extent of the cooperativity effect [5].[1] Physiol. Rev. 90:291-366 (2010).[2] Pflugers Arch. 460:321–341 (2010).[3] Science, 326:1668-1674 (2009)[4] Nature (Letter), 477:495-499 (2011)[5] (a) Channels, 2:19-33 (2008). (b) J. Physiol. 586:1833-1848 (2008)