Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection.

Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are major targets to increase the range and selectivity of new drugs, and there is a need for methods capable of identifying intra-molecular signalling pathways leading to allosteric effects. Here, we use an atomistic graph-theoretical approach that exploits Markov transients to extract such pathways and exemplify our results in an important allosteric protein, caspase-1. Firstly, we use Markov stability community detection to perform a multiscale analysis of the structure of caspase-1 which reveals that the active conformation has a weaker, less compartmentalised large-scale structure compared to the inactive conformation, resulting in greater intra-protein coherence and signal propagation. We also carry out a full computational point mutagenesis and identify that only a few residues are critical to such structural coherence. Secondly, we characterise explicitly the transients of random walks originating at the active site and predict the location of a known allosteric site in this protein quantifying the contribution of individual bonds to the communication pathway between the active and allosteric sites. Several of the bonds we identify have been shown experimentally to be functionally critical, but we also predict a number of as yet unidentified bonds which may contribute to the pathway. Our approach offers a computationally inexpensive method for the identification of allosteric sites and communication pathways in proteins using a fully atomistic description.

Compartmental signal modulation: Endosomal phosphatidylinositol 3-phosphate controls endosome morphology and selective cargo sorting.

It is increasingly recognized that the compartmental organization of signaling processes has a profound influence on cellular behavior. However, our inability to influence these compartmental events in a spatially restricted and acute manner limits our understanding of causation. To determine whether local compartmental loss of a phosphoinositide disrupts the normal traffic of specific cargoes through endosomes, we developed the use of a regulated dimerization device, here designed to compartmentally modify the phosphoinositide content of Rab5-positive endosomes. This modification is effected through the specific regulated recruitment of the 3-phosphatase myotubularin to endosomal membranes in intact cells. The selective manipulation of endosomal phosphatidylinositols (PIs) demonstrates that it is the phosphatidylinositol 3-phosphate (PtdIns3P) or its metabolite PtdIns(3,5)P2 within this compartment that determines the normal maturation of the endosomal compartment and the flux of receptors through it. On local loss of PtdIns3P/PtdIns(3,5)P2, the endosomal compartment itself fails to continue its normal maturation process, leading to the microtubule-dependent tubularization of the endosomal network. Furthermore, it is shown that endosomal PtdIns3P/PtdIns(3,5)P2 is necessary for transferrin receptor traffic through this compartment while having an effect on EGF receptor (EGFR) entry into and sorting from this endosome compartment. The ability to acutely and selectively influence compartmental behavior as exemplified here for endomsomes clearly illustrates the power of the approach used to dissect the role of localized signals and events.

Phosphatases as small-molecule targets: inhibiting the endogenous inhibitors of kinases.

Inositols and their phosphorylated derivatives, phosphoinositides, play an important role in diverse cellular functions. They have been recognized as second messengers and are accurately controlled by phosphatases and kinases, such as phosphoinositide 3-kinase and the phosphatidylinositol 3-phosphatase PTEN (phosphatase and tensin homologue deleted on chromosome 10). Specific inhibitors targeting phosphoinositide 3-kinase and protein phosphatases have been described and characterized, but no small-molecule tools for phosphoinositide phosphatases are currently available. The present mini-review gives an overview of representative phosphatase inhibitors and summarizes the work that has been done recently on molecules that inhibit PTEN.

Synthesis and function of 3-phosphorylated inositol lipids.

The 3-phosphorylated inositol lipids fulfill roles as second messengers by interacting with the lipid binding domains of a variety of cellular proteins. Such interactions can affect the subcellular localization and aggregation of target proteins, and through allosteric effects, their activity. Generation of 3-phosphoinositides has been documented to influence diverse cellular pathways and hence alter a spectrum of fundamental cellular activities. This review is focused on the 3-phosphoinositide lipids, the synthesis of which is acutely triggered by extracellular stimuli, the enzymes responsible for their synthesis and metabolism, and their cell biological roles. Much knowledge has recently been gained through structural insights into the lipid kinases, their interaction with inhibitors, and the way their 3-phosphoinositide products interact with protein targets. This field is now moving toward a genetic dissection of 3-phosphoinositide action in a variety of model organisms. Such approaches will reveal the true role of the 3-phosphoinositides at the organismal level in health and disease.

pp60c-src associates with the SH2-containing inositol-5-phosphatase SHIP1 and is involved in its tyrosine phosphorylation downstream of alphaIIbbeta3 integrin in human platelets.

SH2-containing inositol-5-phosphatase 1 (SHIP1) was originally identified as a 145 kDa protein that became tyrosine-phosphorylated in response to multiple cytokines. It is now well established that SHIP1 is specifically expressed in haemopoietic cells and is important as a negative regulator of signalling. We found recently that SHIP1 was present in human blood platelets as an Ins(1,3,4, 5)P(4)-phosphatase and a PtdIns(3,4,5)P(3)-5-phosphatase that became tyrosine-phosphorylated and was relocated to the cytoskeleton in an integrin-dependent manner. Here we report biochemical and pharmacological evidence that the tyrosine kinase pp60(c-src) is constitutively associated with SHIP1 and is involved in its tyrosine phosphorylation downstream of integrin engagement in thrombin-activated human platelets. The use of cytochalasin D allowed us to demonstrate that the actin cytoskeleton reorganization induced on thrombin stimulation was not required for its integrin-mediated phosphorylation. Moreover, the integrin-dependent relocation of SHIP1 to the cytoskeleton did not require its tyrosine phosphorylation. These results suggest that SHIP1 is first recruited to the integrin-linked signalling complexes and then becomes tyrosine-phosphorylated through a Src-kinase-dependent mechanism but independently of the actin cytoskeleton reorganization.

SAC1 encodes a regulated lipid phosphoinositide phosphatase, defects in which can be suppressed by the homologous Inp52p and Inp53p phosphatases.

The yeast protein Sac1p is involved in a range of cellular functions, including inositol metabolism, actin cytoskeletal organization, endoplasmic reticulum ATP transport, phosphatidylinositol-phosphatidylcholine transfer protein function, and multiple-drug sensitivity. The activity of Sac1p and its relationship to these phenotypes are unresolved. We show here that the regulation of lipid phosphoinositides in sac1 mutants is defective, resulting in altered levels of all lipid phos- phoinositides, particularly phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate. We have identified two proteins with homology to Sac1p that can suppress drug sensitivity and also restore the levels of the phosphoinositides in sac1 mutants. Overexpression of truncated forms of these suppressor genes confirmed that suppression was due to phosphoinositide phosphatase activity within these proteins. We have now demonstrated this activity for Sac1p and have characterized its specificity. The in vitro phosphatase activity and specificity of Sac1p were not altered by some mutations. Indeed, in vivo mutant Sac1p phosphatase activity also appeared unchanged under conditions in which cells were drug-resistant. However, under different growth conditions, both drug sensitivity and the phosphatase defect were manifest. It is concluded that SAC1 encodes a novel lipid phosphoinositide phosphatase in which specific mutations can cause the sac1 phenotypes by altering the in vivo regulation of the protein rather than by destroying phosphatase activity.

The SH2 domain containing inositol 5-phosphatase SHIP2 displays phosphatidylinositol 3,4,5-trisphosphate and inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity.

Distinct forms of inositol and phosphatidylinositol polyphosphate 5-phosphatases selectively remove the phosphate from the 5-position of the inositol ring from both soluble and lipid substrates. SHIP1 is the 145-kDa SH2 domain-containing inositol 5-phosphatase expressed in haematopoietic cells. SHIP2 is a related but distinct gene product. We report here that SHIP2 can be expressed in an active form both in Escherichia coli and in COS-7 cells. A truncated 103-kDa recombinant protein could be purified from bacteria that display both inositol 1,3,4,5-tetrakisphosphate (InsP4) and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) phosphatase activities. COS-7 cell lysates transfected with SHIP2 had increased PtdIns(3,4,5)P3 phosphatase activity as compared to the vector alone.

Identification and characterisation of a novel splice variant of synaptojanin1.

Synaptojanin1, the major constitutively active PtdInsP3 5-phosphatase activity in rat brain, is one of two closely related proteins both extensively spliced in their C-terminal proline rich domain. We describe here the discovery of a novel splice variant of synaptojanin1 which misses the major N-terminal part of the SAC1 domain. This deltaSAC-synaptojanin1 is expressed in rat brain tissue as shown by Northern and Western analysis. However, the deletion of the SAC1 domain does not alter PtdInsP3 5-phosphatase activity demonstrating that the SAC1 domain is not necessary for catalytic function.

Inositol lipid 5-phosphatases--traffic signals and signal traffic.

Several novel phosphoinositide 5-phosphatases have been identified and characterised, revealing a growing family of regulators of inositol lipid dependent processes. The features of these proteins, their likely partners and their involvement in signal transduction and membrane traffic is discussed.

Tyrosine phosphorylation and relocation of SHIP are integrin-mediated in thrombin-stimulated human blood platelets.

The SH2 domain-containing inositol 5-phosphatase, SHIP, known to dephosphorylate inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate has recently been shown to be expressed in a variety of hemopoietic cells. This 145-kDa protein is induced to associate with Shc by multiple cytokines and may play an important role in the negative regulation of immunocompetent cells mediated by FcgammaRIIB receptor. We report here that SHIP is present in human blood platelets and may be involved in platelet activation evoked by thrombin. Platelet SHIP was identified by Western blotting as a single 145-kDa protein. Both phosphatidylinositol 3,4,5-trisphosphate and inositol 1,3,4, 5-tetrakisphosphate 5-phosphatase activities could be demonstrated in anti-SHIP immunoprecipitates of platelet lysate. Thrombin stimulation induced a tyrosine phosphorylation of SHIP, this effect being prevented if platelets were not shaken or if RGD-containing peptides were present, indicating an aggregation-dependent, integrin-mediated event. Moreover, although the intrinsic phosphatase activity of SHIP did not appear to be significantly increased, tyrosine-phosphorylated SHIP was relocated to the actin cytoskeleton upon activation in an aggregation- and integrin engagement-dependent manner. Finally, the striking correlation observed between phosphatidylinositol 3,4-bisphosphate production and the tyrosine phosphorylation of SHIP, as well as its relocation to the cytoskeleton upon thrombin stimulation, suggest a role for SHIP in the aggregation-dependent and GpIIb-IIIa-mediated accumulation of this important phosphoinositide.

Synaptojanin is the major constitutively active phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase in rodent brain.

The major constitutive phosphatidylinositol-3,4,5-P3 (PtdIns) 5-phosphatase activity was purified and subjected to peptide sequence analysis providing extensive amino acid sequence which was subsequently used for cloning the cDNA. Peptide and cDNA sequences revealed that the purified PtdIns(3,4,5)P3 5-phosphatase was identical to a splice variant of a recently cloned inositol polyphosphate 5-phosphatase termed synaptojanin. Since synaptojanin is not known to possess PtdIns(3,4,5)P3 5-phosphatase activity, we verified that the purified PtdIns(3,4,5)P3 5-phosphatase activity and synaptojanin are identical by Western blot using specific antibodies raised against synaptojanin sequences. Immunoprecipitation from crude lysates of rat brain tissue showed that synaptojanin accounts for the major part of the active PtdIns(3, 4,5)P3 5-phosphatase activity. It is also shown that the protein is localized to the soluble fraction. Expression of a truncated recombinant protein demonstrates that the conserved 5-phosphatase region of the synaptojanin gene expresses PtdIns(3,4,5)P3 5-phosphatase activity. However, immunological analysis demonstrates that the PtdIns(3,4,5)P3 5-phosphatase activity expressed from the synaptojanin gene in brain is due to a particular splice variant which contains a 16-amino acid insert as shown by immunoprecipitation using a specific antibody raised against this particular splice variant.

Cloning and expression of a human placenta inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase.

Distinct inositol and phosphatidylinositol polyphosphate 5-phosphatases have recently been cloned. Primers were designated coding for highly conserved amino acid regions that are shared between sequences of 5-phosphatases. We used degenerate primers to amplify polymerase chain reaction products from rat brain cDNA. A product with a novel sequence was identified and used to clone a 4.9 kb cDNA from human placenta cDNA libraries (hp51CN). COS-7 cells transfected with a C-terminal truncated form of this cDNA showed an increase in Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3 hydrolyzing activity, but not in Ins(1,4,5)P3 5-phosphatase. Enzymatic activity was inhibited in the presence of 2,3-bisphosphoglycerate and p-hydroxymercuribenzoate. The presence of an SH2 domain and proline-rich sequence motifs within hp51CN suggests that this 5-phosphatase interacts with various proteins in signal transduction.

Purification and biochemical characterization of a mammalian phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase.

Characterization of the enzymes involved in metabolism of 3-phosphorylated inositol lipids and their subcellular localization revealed that in vitro a 5-phosphatase activity was responsible for the degradation of phosphatidylinositol 3,4,5-trisphosphate, whereas a 3-phosphatase activity hydrolyzed phosphatidylinositol 3-phosphate and/or phosphatidylinositol 3,4-bisphosphate. All these activities were localized in the cytosol. No phospholipase activities were detected. The cytosolic phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase activity was purified to near homogeneity using ion exchange, affinity, and size exclusion chromatography. Characterization of the purified phosphatase revealed that it is a magnesium-dependent 5-phosphatase that is able to hydrolyze phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate. The enzyme is only partially inhibited by neomycin and vanadate but is strongly inhibited by phosphatidylinositol 4,5-bisphosphate and to a slightly lesser extent by phosphatidylinositol 4-phosphate.

Activation of p70 S6 kinase and erk-encoded mitogen-activated protein kinases is resistant to high cyclic nucleotide levels in Swiss 3T3 fibroblasts.

Treatment of Swiss mouse 3T3 fibroblasts with certain cyclic nucleotide phosphodiesterase inhibitors (theophylline, SQ 20,006, and MY-5445) prevents the activation of the M(r) 70,000 S6 kinase (p70S6k) induced by a variety of external stimuli. Concentrations giving half-maximal inhibition were 800, 50, and 25 microM, respectively. Western blot analysis and immunocomplex kinase assays showed that these compounds inhibit the phosphorylation and activation of p70S6k without affecting the erk-encoded mitogen-activated protein (MAP) kinases or the rsk-encoded S6 kinase (p90rsk). A distinct collection of cAMP and cGMP agonists and analogues did not suppress p70S6k activation, indicating that 1) high intracellular cyclic nucleotide concentrations do not antagonize the p70S6k pathway and 2) phosphodiesterase inhibitors block p70S6k activation by a mechanism that is independent of cAMP or cGMP production. The effect of theophylline and SQ 20,006, but not MY-5445, on p70S6k signaling may be due in part to the inhibition of a phosphatidylinositol 3-kinase that acts upstream of p70S6k. Finally, in contrast to many other cell types, cAMP and cGMP were also found to have no inhibitory effect on the MAP kinase/p90rsk signaling pathway in Swiss 3T3 fibroblasts.

Modulation of the substrate specificity of the mammalian phosphatidylinositol 3-kinase by cholesterol sulfate and sulfatide.

The substrate specificity of the purified, mammalian phosphatidylinositol 3-kinase is subject to modulation by detergents, which are able to switch substrate specificity in vitro in favor of PtdInsP2. This effect of the detergents is due to an activation of the phosphatidylinositol biphosphate 3-kinase activity, while the phosphatidylinositol 3-kinase activity is inhibited. The selective inhibition of the phosphatidylinositol 3-kinase activity (p110 alpha/p85 alpha) is shown here also to be observed by employing cholesterol sulfate or sulfatide at low micromolar concentrations, whereas cholesterol and androsterone sulfate fail to inhibit. These naturally occurring sulfated lipids have at these concentrations no effect on the phosphatidylinositol bisphosphate 3-kinase activity but inhibit the manganese-dependent intrinsic protein kinase activity, thus switching substrate specificity toward the more highly phosphorylated inositol lipids. Cholesterol sulfate and sulfatide inhibit the free catalytic subunit p110 alpha but fail to inhibit the homologous phosphatidylinositol 3-kinase from Saccharomyces cerevisiae (Vps34p), suggesting that these sulfated lipids act specifically on the mammalian phosphatidylinositol 3-kinase. Consistent with this specificity, the regulatory subunit (p85), which is not conserved in the yeast enzyme, is found to play an important role for the affinity of these inhibitors. The implications for the phosphatidylinositol 3-kinase activity in vivo are discussed.

Activation of PRK1 by phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate. A comparison with protein kinase C isotypes.

As potential targets for polyphosphoinositides, activation of protein kinase C (PKC) isotypes (beta 1, epsilon, zeta, nu) and a member of the PKC-related kinase (PRK) family, PRK1, has been compared in vitro. PRK1 is shown to be activated by both phosphatidylinositol 4,5-bisphosphate (PtdIns 4,5-P2) as well as phosphatidylinositol 3,4,5-trisphosphate (PtdIns-3,4,5-P3) either as pure sonicated lipids or in detergent mixed micelles. When presented as sonicated lipids, PtdIns-4,5-P2 and PtdIns-3,4,5-P3 were equipotent in activating PRK1, and, furthermore, sonicated phosphatidylinositol (PtdIns) and phosphatidylserine (PtdSer) were equally effective. In detergent mixed micelles, PtdIns-4,5-P2 and PtdIns-3,4,5-P3 also showed a similar potency, but PtdIns and PtdSer were 10-fold less effective in this assay. Similarly, PKC-beta 1, -epsilon, and -nu were all activated by PtdIns-4,5-P2 and PtdIns-3,4,5-P3 in detergent mixed micelles. The activation constants for PtdIns-4,5-P2 and PtdIns-3,4,5-P3 were essentially the same for all the kinases tested, implying no specificity in this in vitro analysis. Consistent with this conclusion, the effects of PtdIns-4,5-P2 and PtdIns-3,4,5-P3 were found to be inhibited at 10 mM Mg2+ and mimicked by high concentrations of inositol hexaphosphate and inositol hexasulfate. The similar responses of these two classes of lipid-activated protein kinase to these phosphoinositides are discussed in light of their potential roles as second messengers.

Selective inhibition of p70 S6 kinase activation by phosphatidylinositol 3-kinase inhibitors.

Treatment of fibroblasts with wortmannin or demethoxyviridin, two potent inhibitors of phosphatidylinositol 3-kinase, prevents the activation of ribosomal protein S6 kinase, which is induced by a variety of external stimuli. Concentrations giving 50% inhibition of 45 nM (wortmannin) and 400 nM (demethoxyviridin) were obtained when epidermal growth factor was used as an S6 kinase activator; with platelet-derived growth factor, the concentrations giving 50% inhibition were about three-times higher. Western-blot analysis and immunocomplex kinase assays showed that wortmannin and demethoxyviridin specifically block the phosphorylation and activation of p70 S6 kinase without affecting the M(r) 90,000 ribosomal S6 kinase (p90rsk) or mitogen-activated protein kinases. Consistent with the irreversible nature of the inhibition of phosphatidylinositol 3-kinase by these compounds, treatment of cells with wortmannin, followed by washing out of the inhibitor, still led to inhibition of p70 S6 kinase activation. Several S6 kinase agonists not previously known to activate phosphatidylinositol 3-kinase (A23187, bombesin and phorbol 12-myristate 13-acetate) were found to increase the production of phosphatidylinositol 3,4,5-trisphosphate in a wortmannin-sensitive manner. These results support a model in which phosphatidylinositol 3-kinase acts upstream of p70 S6 kinase in a mitogenic signalling pathway; the existence of a phosphatidylinositol 3-kinase-independent pathway is also evident.

Biochemical characterization of the free catalytic p110 alpha and the complexed heterodimeric p110 alpha.p85 alpha forms of the mammalian phosphatidylinositol 3-kinase.

The regulatory (p85 alpha) and catalytic (p110 alpha) subunits of the mammalian phosphatidylinositol 3-kinase have been expressed in insect cells using the baculovirus sytem. The free catalytic subunit p110 alpha and the coexpressed heterodimeric complex of p85 alpha and p110 alpha were purified and their enzymological properties compared. While many kinetic parameters were similar, the coexpressed complex was found to have a 20-fold higher Km for ATP in comparison with the free catalytic subunit p110 alpha using phosphatidylinositol 4,5-bisphosphate as a substrate; no significant difference was detectable when phosphatidylinositol was used. Reconstitution of the p110 alpha.p85 alpha complex in vitro showed that it had the properties of the free p110 alpha and not the p110 alpha.p85 alpha in vivo complex. Therefore, a post-translational modification dependent upon the presence of the regulatory subunit p85 alpha rather than the physical subunit interaction itself is responsible for the observed properties of the lipid kinase activity of the p110 alpha.p85 alpha complex. Phosphatase treatment of the purified lipid kinase complex reduced the high Km for ATP, suggesting that a phosphorylation of the heterodimeric complex (p85 alpha.p110 alpha) caused this effect. This mode of regulation is discussed in the context of lipid kinase activation in vivo.