Tools used to study how protein complexes are assembled in signaling cascades

Most proteins do not function on their own but as part of large signaling complexes that are arranged in every living cell in response to specific environmental cues. Proteins interact with each other either constitutively or transiently and do so with different affinity. When identifying the role played by a protein inside a cell, it is essential to define its particular cohort of binding partners so that the researcher can predict what signaling pathways the protein is engaged in. Once identified and confirmed, the information might allow the interaction to be manipulated by pharmacological inhibitors to help fight disease. In this review, we discuss protein-protein interactions and how they are essential to propagate signals in signaling pathways. We examine some of the high-throughput screening methods and focus on the methods used to confirm specific protein-protein interactions including; affinity tagging, co-immunoprecipitation, peptide array technology and fluorescence microscopy.     

Influence of precipitated calcium carbonate (CaCO3) on shiitake (Lentinula edodes) yield and mushroom size

Synthetic substrate consisting of oak sawdust (50%), white millet (28%), winter rye (11%) and soft red wheat bran (11%) was non-supplemented or supplemented with 0.2%, 0.4% or 0.6% (dry weight basis) precipitated calcium carbonate (CaCO(3)). Shiitake (Lentinula edodes) was grown in two crops to determine the effect of three CaCO(3) levels on mushroom yield and size. Yields and biological efficiencies (averages for two crops) from substrates non-supplemented with CaCO(3) were lower by 14.1%, 18.4% and 24.9% compared to treatments supplemented with 0.2%, 0.4% and 0.6% CaCO(3), respectively. Mushroom size (weight) was larger with non-supplemented substrate (16.8 g) compared to substrate supplemented with 0.6% CaCO(3) (15.1 g). However, mushroom production was more consistent from crop to crop when 0.6% CaCO(3) was added to substrate.     

Regulation of CaCO(3) formation in coccolithophores

Coccolithophores impact the ocean carbon cycle principally through the generation of CO₂ during CaCO₃ production. Coccolithophore biomineralization has been examined most extensively in Pleurochrysis carterae and Emiliania huxleyi both of which produce mineralized scales—coccoliths—composed of elaborate calcite crystals attached to an underlying organic base plate. Calcification of preformed base plates is mediated by acidic polysaccharides and occurs in Golgi-derived structures known as mineralizing vesicles. In Pleurochrysis a high capacity calcium-binding polysaccharide PS2 is required for efficient nucleation of calcitic protocrystals. A galacturonomannan PS3 is required for the growth and transformation of the protocrystals into a massive double disc of calcite. The genes that regulate expression of the glycans have not yet been identified. In addition to the coccolith-bearing diploid phases, Pleurochrysis and Emiliania possess both haploid and diploid non-calcifying stages, which are self-perpetuating via binary fission. One non-calcifying Pleurochrysis phase fails to synthesis PS2 and spontaneously reverts to the mineralizing morphotype in laboratory cultures. As yet, there is little information on environmental factors that effect the expression or silencing of calcifying genes or favor the growth of calcifying over non-calcifying phases. These issues will need extensive investigation, if we are to appreciate the role of coccolithophores in the regulation of atmospheric CO₂ levels.     

Type II phosphatidylinositol 4-kinase(s) in cell signaling cascades

Phosphorylated derivatives of phosphatidylinositol (PtdIns) are key components of many signaling cascades. Many isoforms of PtdIns kinases, PtdIns phosphate kinases and phosphatases use these lipids in amazing networks of signaling cascades that are yet to be understood fully. PtdIns 4-kinase(s) phosphorylates PtdIns at the 4th -OH position of inositol head group and are classified in to type II and III PtdIns 4-kinases. While type III PtdIns 4-kinases are implicated in vesicular trafficking, type II PtdIns 4-kinases are suggested to play a role in cell signaling, cytoskeletal rearrangements, cell motility and in microbial pathogenicity. This paper reviews the role of type II PtdIns 4-kinases in cell signaling cascades in health and disease.     

Polysaccharide from coccoliths (CaCO3 biomineral). Influence on crystallization of calcium oxalate monohydrate

A polysaccharide associated with coccoliths of the marine alga Emiliania huxleyi (coccoliths are elaborately shaped calcite biominerals) was isolated and its influence on the crystallization of calcium oxalate monohydrate crystals was studied. Crystallization was monitored in a carefully controlled system by measuring the incorporation of 45Ca tracer from a supersaturated solution into seed crystals of calcium oxalate monohydrate in the absence and in the presence of polysaccharide. The method allowed differentiation between effects on solubility, growth and agglomeration of crystals. At the very low concentrations used in this study, the polysaccharide had no significant effect on the solubility product; it strongly inhibited the growth and strongly stimulated the agglomeration of the crystals. Thus, the two processes of growth and agglomeration, being both crystal-surface-related processes, may react in opposite directions upon surface adhesion of the additive. This finding opens new insights on how a mineralization process may be controlled. The inhibitory effect on growth is shown to proceed through a monolayer type of adsorption of the polysaccharide onto the crystal surface. The portion of the polysaccharide used for the stimulatory effect on agglomeration shows a different type of adsorption, whereby less crystal surface is covered per molecule of polysaccharide. This strongly suggests, that the mechanism whereby agglomeration is stimulated operates through 'viscous binding', with the polysaccharide bridging the gap between two crystal surfaces. In the discussion these findings are related to some possible biological functions of the polysaccharide.     

Inhibition by glycosaminoglycans of CaCO3 (calcite) crystallization.

Of a range of glycosaminoglycans, heparin and heparan sulphate were the most effective inhibitors in vitro of CaCO3 (calcite) crystallization as assayed by conductimetric measurements. The possible role of such glycosaminoglycans in modulating calcium-salt crystallizations in vivo is discussed.     

Role of MLK3 in the regulation of mitogen-activated protein kinase signaling cascades

Mixed-lineage protein kinase 3 (MLK3) is a member of the mitogen-activated protein (MAP) kinase kinase kinase group that has been implicated in multiple signaling cascades, including the NF-kappaB pathway and the extracellular signal-regulated kinase, c-Jun NH(2)-terminal kinase (JNK), and p38 MAP kinase pathways. Here, we examined the effect of targeted disruption of the murine Mlk3 gene. Mlk3(-/-) mice were found to be viable and healthy. Primary embryonic fibroblasts prepared from these mice exhibited no major signaling defects. However, we did find that MLK3 deficiency caused a selective reduction in tumor necrosis factor (TNF)-stimulated JNK activation. Together, these data demonstrate that MLK3 contributes to the TNF signaling pathway that activates JNK.     

Attenuation of noise in ultrasensitive signaling cascades

Ultrasensitive cascades often implement thresholding operations in cell signaling and gene regulatory networks, converting graded input signals into discrete all-or-none outputs. However, the biochemical and genetic reactions involved in such cascades are subject to random fluctuations, leading to noise in output signal levels. Here we prove that cascades operating near saturation have output signal fluctuations that are bounded in magnitude, even as the number of noisy cascade stages becomes large. We show that these fluctuation-bounded cascades can be used to attenuate the noise in an input signal, and we find the optimal cascade length required to achieve the best possible noise reduction. Cascades with ultrasensitive transfer functions naturally operate near saturation, and can be made to simultaneously implement thresholding and noise reduction. They are therefore ideally suited to mediate signal transfer in both natural and artificial biological networks.     

Amperometric biosensor for choline based on layer-by-layer assembled functionalized carbon nanotube and polyaniline multilayer film

Conducting polymer film was prepared by electrochemical polymerization of aniline. Multiwalled carbon nanotubes (MWNTs) were treated with a mixture of concentrated sulfuric and nitric acid to introduce carboxylic acid groups to the nanotubes. By using the layer-by-layer method, homogeneous and stable MWNTs and polyaniline (PANI) multilayer films were alternately assembled on glassy carbon (GC) electrodes. Conducting polymer of PANI had three main functions: (i) excellent antiinterference ability, (ii) protection ability in favor of increasing the amount of the MWNTs immobilized on GC electrodes, and (iii) superior transducing ability. The protection effect of PANI film and the electrostatic interaction between positively charged PANI and negatively charged MWNTs both attributed to immobilizing abundant MWNTs stably, thereby enhancing the catalytic activity. The layer-by-layer assembled MWNTs and PANI-modified GC electrodes offered a significant decrease in the overvoltage for the H2O2 and were shown to be excellent amperometric sensors for H2O2 from +0.2V over a wide range of concentrations. As an application example, by linking choline oxidase (CHOD), an amplified biosensor toward choline was prepared. The choline biosensor exhibited a linear response range of 1x10(-6) to 2x10(-3) M with a correlation coefficient of 0.997, and the response time and detection limit (S/N=3) were determined to be 3 s and 0.3 microM, respectively. The antiinterference biosensor displays a rapid response and an expanded linear response range as well as excellent reproducibility and stability.     

Enzymatic desorption of layer-by-layer assembled multilayer films and effects on the release of encapsulated indomethacin microcrystals

Polyelectrolyte multilayer films were prepared through layer-by-layer (LbL) self-assembly of chitosan (CHI) and pyrene labeled poly(2-acrylamido-2-methylpropanesulfonic acid) (APy). After incubation in an enzyme pepsin solution, multilayer films were partially destroyed as detected by a decrease in fluorescence intensity due to enzymatic degradation of CHI and desorption of APy. The multilayer desorption rate was the highest at pH 4.0. Increasing temperature from 20 degrees C to 60 degrees C accelerated desorption. The enzymatic desorption was also observed from microcapsule walls made of CHI/alginate (ALG) multilayer films directly deposited on indomethacin (IDM) microcrystals by LbL self-assembly. After pepsin erosion, the IDM release from the microcapsule monitored by UV absorbance was obviously accelerated due to desorption. The influence of incubation time, pH, and temperature of the pepsin solution on the IDM release was investigated. The release rate was the fastest after incubation in the pepsin solution at pH 4.0 due to the highest activity of pepsin. Increasing incubation temperature from 20 degrees C to 60 degrees C, however, slowed down the release rate, which was considered to be due to the formation of more perfect and compact multilayer films through the chain rearrangement at higher temperatures. The CHI/ALG multilayer film was found to maintain its barrier function to the IDM diffusion even after 6-h incubation in the pepsin solution.     

Ultrastructure of CaCO3 deposits of terrestrial isopods (Crustacea, Oniscidea)

 The ultrastructure of the sternal CaCO₃ deposits of 3 species of the Diplochaeta and 15 of the Crinochaeta was investigated by means of scanning electron microscopy of fractured surfaces. In the Diplochaeta Li-gia italica and L. oceanica, the deposits consist exclusively of individual spherules with diameters between 0.2 and 1.4 μm. No material was observed within the spaces between the spherules. In Ligidium hypnorum, two structurally distinct regions exist. A proximal layer resembling the deposit of Ligia italica and L. oceanica and a distal layer in which the spherules appear to be fused with each other. In the species of the Crinochaeta, the CaCO₃ deposits comprise a spherular region which resembles the deposits of Ligidium hypnorum, and a homogeneous layer located between the spherular part of the deposit and the hypodermal cell layer. In some species the diameters of the spherules may be up to 3.1 μm. In the homogeneous layer and the distal spherular layer more calcium per volume can be stored than in the proximal spherular layer in which the spaces between the spherules are devoid of CaCO₃. This suggests that the multiple layered deposits are an adaptation to terrestrial life, as a consequence of the need for increased resorption of cuticular calcium. Accepted: 7 January 1997     

Primary platelet signaling cascades and integrin-mediated signaling control ADP-ribosylation factor (Arf) 6-GTP levels during platelet activation and aggregation

Previous studies showed that ADP-ribosylation factor 6 (Arf6) is important for platelet function; however, little is known about which signaling events regulate this small GTP-binding protein. Arf6-GTP was monitored in platelets stimulated with a number of agonists (TRAP, thrombin, convulxin, collagen, PMA, thapsigargin, or A23187) and all led to a time-dependent decrease in Arf6-GTP. ADP and U46619 were without effect. Using inhibitors, it was shown that the decrease of Arf6-GTP is a direct consequence of known signaling cascades. Upon stimulation via PAR receptors, Arf6-GTP loss could be blocked by treatment with U-73122, BAPTA/AM, Ro-31-8220, or Gö6976, indicating requirements for phospholipase C, calcium, and protein kinase C (PKC) α/β, respectively. The Arf6-GTP decrease in convulxin-stimulated platelets showed similar requirements and was also sensitive to piceatannol, wortmannin, and {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002, indicating additional requirements for Syk and phosphatidylinositol 3-kinase. The convulxin-induced decrease was sensitive to both PKCα/β and δ inhibitors. Outside-in signaling, potentially via integrin engagement, caused a second wave of signaling that affected Arf6. Inclusion of RGDS peptides or EGTA, during activation, led to a biphasic response; Arf6-GTP levels partially recovered upon continued incubation. A similar response was seen in β3 integrin-null platelets. These data show that Arf6-GTP decreases in response to known signaling pathways associated with PAR and GPVI. They further reveal a second, aggregation-dependent, process that dampens Arf6-GTP recovery. This study demonstrates that the nucleotide state of Arf6 in platelets is regulated during the initial phases of activation and during the later stages of aggregation.Platelet activation is initiated through several classes of membrane receptors, which are stimulated by agonists produced at the vascular lesion (1–3). A second wave of signaling, caused by engagement of integrins, occurs as platelets bind to the lesion surface and aggregate (4). Together, these plasma membrane proteins initiate the platelet processes important for thrombosis (e.g. adhesion, spreading, secretion, and clot retraction). Small GTP-binding proteins, specifically members of the Ras superfamily, link signaling events from various platelet receptors to defined outcomes, such as shape change (5–7), aggregation (8, 9), and secretion (10–12). Rab proteins play roles in granule secretion, with Rab4 and Rab6 being involved in alpha granule release (10, 11) and Rab27a/b in dense core granule release (12, 13). RalA is activated in response to various stimuli (14–16) and may play a role in secretion by anchoring the exocyst complex to specific membrane sites (17). Rap1 plays a role in integrin α_IIbβ₃ activation (8, 9). Rho family GTPases (Rho, Rac, and Cdc42) play roles in platelet phosphoinositide signaling and in the regulation of the actin cytoskeleton (5–7). While these small GTP-binding proteins are clearly important to platelet function, it is equally clear that other small G proteins are present and functional in platelets (18).The ADP-ribosylation factor (Arf)² family are Ras-related, small GTPases that affect both vesicular transport and cytoskeletal dynamics (19, 20). Based on their primary sequences, this family is divided into three classes, with Arf6 as the only member of class III (19). Arf6-GTP is considered the “active state” and can interact with downstream effectors, such as phospholipase D (PLD) (21), phosphatidylinositol 4-phosphate 5-kinase type α (22), and arfaptin 2 (23, 24), resulting in the recruitment of these effectors to the plasma membrane. The Arf6 GTP/GDP cycle is mediated by interactions with guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). The large number of Arf-GEF and -GAP proteins have been discussed in recent reviews where it was noted that, unlike other small GTPases, Arf functions are generally not mediated solely by the GTP-bound state but through its cycling between states (19, 20, 25, 26).The effects that Arf6 has on the secretion and actin dynamics in nucleated cells make it an ideal candidate for function in platelets. Arf6 influences cortical actin and is important for spreading, ruffling, migration, and phagocytosis (reviewed in Ref. 19). Our previous work (27) showed that Arf6 is present on platelet membranes and is important for platelet function. Unlike other small G proteins, the Arf6 GTP-bound form is readily detectible in resting platelets and upon activation with collagen or convulxin there is a rapid conversion to the GDP-bound form. Acylated peptides, which mimic the myristoylated N terminus of Arfs have been used as isoform-specific inhibitors (28). In platelets, a myristoylated-Arf6 (myr-Arf6) peptide specifically blocks the activation-dependent loss of Arf6-GTP. This peptide also blocks aggregation, spreading on collagen, and activation of the Rho family of GTPases. Other GTPases, such as Ral and Rap, were unaffected. The simplest explanation for these data is that platelet activation stimulates the GTPase activity of Arf6, perhaps through activation of an Arf6-GAP. Alternatively, platelet activation could affect an Arf6-GEF thus reducing the production of Arf6-GTP. Regardless of mechanism, disruption of the activation-dependent loss of Arf6-GTP, with the myr-Arf6 peptide, profoundly affects the actin-based cytoskeletal rearrangements associated with platelet activation. While our initial report (27) established a role for Arf6 in platelet function, it was not clear what platelet signaling events were required to induce the loss of Arf6-GTP.In this article, we delineate the signaling cascades required for the activation-dependent loss of Arf6-GTP. We show that the Arf6-GTP to -GDP conversion was stimulated by primary agonists (thrombin, TRAP, collagen, or convulxin) but not by ADP or U46619. The decrease in Arf6-GTP, downstream of thrombin and convulxin, required PLC, and PKC activity. Loss of Arf6-GTP, via stimulation of GPVI with convulxin, additionally required Syk and PI3K activities. Pretreatment with passivators, nitric oxide (NO), and prostaglandin I₂ (PGI₂) blocked thrombin- and convulxin-induced loss of Arf6-GTP. Further experiments suggested a role for “outside-in” signaling, especially once platelet aggregates begin to form. Inclusion of RGDS peptide, EGTA, or the deletion of the β3 integrin had only minimal effects on the initial loss of Arf6-GTP but led to the partial recovery of Arf6-GTP levels. This biphasic change in Arf6-GTP levels was not seen when aggregation was allowed to occur normally. Taken together, these data show that the Arf6 nucleotide state is responsive to both initial agonist-mediated signaling and to a second wave of integrin-mediated signaling that occurs upon aggregation.     

Thrombin induced secretion of macrophage migration inhibitory factor (MIF) and its effect on nuclear signaling in endothelium

The procoagulant thrombin stimulates endothelial cells (EC) to undergo rapid cytoskeleton changes via signaling pathways that induce multiple phenotypic changes, including alterations in permeability, vasomotor tone, adhesion molecule synthesis, and leukocyte trafficking. We studied a novel role of thrombin's action on the endothelium that results in MIF secretion, which is linked to myosin light chain (MLC) and extracellular signal-regulated kinase (ERK(1/2))-dependent nuclear signaling. In bovine pulmonary artery EC (BPAEC), thrombin treatment induced intracellular MLC phosphorylation within 15 min, followed by a significant increase in MIF secretion within 30 min. Thrombin treatment induced biphasic ERK(1/2) phosphorylation with an early phase occurring at 15 min and a later phase at 120 min. To understand the role of MIF secretion in thrombin-induced biphasic activation of ERK(1/2), BPAE cells were treated with (i) recombinant MIF, and (ii) the medium collected from thrombin-treated BPAE cells. These studies demonstrated a sustained monophasic ERK(1/2) phosphorylation. Inhibition of MIF secretion by MIF siRNA or antisense-MIF treatment, along with a neutralizing antibody, attenuated the thrombin-induced second phase ERK phosphorylation, suggesting a direct involvement of MIF in the second phase of ERK(1/2) activation. Pretreatment of BPAE cells with an ERK kinase inhibitor and with antisense-MIF significantly inhibited thrombin-induced nuclear factor kappa (NF-kappaB) activation. These results indicate that MIF secretion and ERK phosphorylation both play a necessary role in thrombin induced NF-kappaB activation.     

In situ enzymatic silver enhancement based on functionalized graphene oxide and layer-by-layer assembled gold nanoparticles for ultrasensitive detection of thrombin

A highly specific in situ amplification strategy was designed for ultrasensitive detection of thrombin by combining the layer-by-layer (LBL) assembled amplification with alkaline phosphatase (ALP) and gold nanoparticles (Au) mediated silver deposition. High-density carboxyl functionalized graphene oxide (FGO) was introduced as a nanocarrier for LBL assembling of alkaline phosphatase decorated gold nanoparticles (ALP-Au), which was further adopted to label thrombin aptamer II. After sandwich-type reaction, numerous ALP were captured onto the aptasensor surface and catalyzed the hydrolysis of ascorbic acid 2-phosphate (AAP), which in situ generated ascorbic acid (AA), reducing Ag(+) to Ag nanoparticles (AgNPs) for electrochemical readout. Inspiringly, the in situ amplification strategy with ethanolamine as an effective blocking agent showed remarkable amplification efficiency, very little nonspecific adsorption, and low background signal, which was favorable to enhance the sensitivity of aptasensor. Our novel dramatic signal amplification strategy, with a detection limit of 2.7fM, showed about 2-3 orders of magnitude improvement in the sensitivity for thrombin detection compared to other universal enzyme-based electrochemical assay.