Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity, and pathway rewiring

Synthetic biosystems have been engineered that enable control of metazoan cell morphology, migration, and death. These systems possess signal specificity, but lack flexibility of input signal. To exploit the potential of Ca(2+) signaling, we designed RhoA chimeras for reversible, Ca(2+)-dependent control over RhoA morphology and migration. First, we inserted a calmodulin-binding peptide into a RhoA loop that activates or deactivates RhoA in response to Ca(2+) signals depending on the chosen peptide. Second, we localized the Ca(2+)-activated RhoA chimera to the plasma membrane, where it responded specifically to local Ca(2+) signals. Third, input control of RhoA morphology was rewired by coexpressing the Ca(2+)-activated RhoA chimera with Ca(2+)-transport proteins using acetylcholine, store-operated Ca(2+) entry, and blue light. Engineering synthetic biological systems with input versatility and tunable spatiotemporal responses motivates further application of Ca(2+) signaling in this field.     

Free Ca<Superscript>2+</Superscript> as an early intracellular biomarker of exposure of cyanobacteria to environmental pollution

Calcium functions as a versatile messenger in a wide variety of eukaryotic and prokaryotic cells. Cyanobacteria are photoautotrophs which have a great ecological impact as primary producers. Our research group has presented solid evidence of a role of calcium in the perception of environmental changes by cyanobacteria and their acclimation to these changes. We constructed a recombinant strain of the freshwater cyanobacterium Anabaena sp. PCC 7120 that constitutively expresses the calcium-binding photoprotein apoaequorin, enabling in-vivo monitoring of any fluctuation in the intracellular free calcium concentration of the cyanobacterium in response to any environmental stimulus. The “Ca²⁺ signature” is the combination of changes in all Ca²⁺ signal properties (magnitude, duration, frequency, source of the signal) produced by a specific stimulus. We recorded and analyzed the Ca²⁺ signatures generated by exposure of the cyanobacterium to different groups of environmental pollutants, for example cations, anions, organic solvents, naphthalene, and pharmaceuticals. We found that, in general, each group of tested chemicals triggered a specific calcium signature in a reproducible and dose-dependent manner. We hypothesize that these Ca²⁺ signals may be related to the cellular mechanisms of pollutant perception and ultimately to their toxic mode of action. We recorded Ca²⁺ signals triggered by binary mixtures of pollutants and a signal induced by a real wastewater sample which could be mimicked by mixing its main constituents. Because Ca²⁺ signatures were induced before toxicity was evident, we propose that intracellular free Ca²⁺ may serve as an early biomarker of exposure to environmental pollution.     

Boolean Logic Networks Mimicked with Chimeric Enzymes Activated/Inhibited by Several Input Signals

Reactions catalyzed by artificial allosteric enzymes, chimeric proteins with fused biorecognition and catalytic units, were used to mimic multi-input Boolean logic systems. The catalytic parts of the systems were represented by pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH). Two biorecognition units, calmodulin or artificial peptide-clamp, were integrated into PQQ-GDH and locked it in the OFF or ON state respectively. The ligand-peptide binding cooperatively with Ca²⁺ cations to a calmodulin bioreceptor resulted in the enzyme activation, while another ligand-peptide bound to a clamp-receptor inhibited the enzyme. The enzyme activation and inhibition originated from peptide-induced allosteric transitions in the receptor units that propagated to the catalytic domain. While most of enzymes used to mimic Boolean logic gates operate with two inputs (substrate and co-substrate), the used chimeric enzymes were controlled by four inputs (glucose – substrate, dichlorophenolindophenol – electron acceptor/co-substrate, Ca²⁺ cations and a peptide – activating/inhibiting signals). The biocatalytic reactions controlled by four input signals were considered as logic networks composed of several concatenated logic gates. The developed approach allows potentially programming complex logic networks operating with various biomolecular inputs representing potential utility for different biomedical applications.     

Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs

The family of calcium-binding proteins (CaBPs) consists of dozens of members and contributes to all aspects of the cell’s function, from homeostasis to learning and memory. However, the Ca²⁺-binding mechanism is still unclear for most of CaBPs. To identify the Ca²⁺-binding sites of CaBPs, this study presented a computational approach which combined the fragment homology modeling with molecular dynamics simulation. For validation, we performed a two-step strategy as follows: first, the approach is used to identify the Ca²⁺-binding sites of CaBPs, which have the EF-hand Ca²⁺-binding site and the detailed binding mechanism. To accomplish this, eighteen crystal structures of CaBPs with 49 Ca²⁺-binding sites are selected to be analyzed including calmodulin. The computational method identified 43 from 49 Ca²⁺-binding sites. Second, we performed the approach to large-conductance Ca²⁺-activated K⁺ (BK) channels which don’t have clear Ca²⁺-binding mechanism. The simulated results are consistent with the experimental data. The computational approach may shed some light on the identification of Ca²⁺-binding sites in CaBPs.     

A Modeling and Analysis Study Reveals That CaMKII in Synaptic Plasticity Is a Dominant Affecter in CaM Systems in a T286 Phosphorylation-Dependent Manner

NMDAR-dependent synaptic plasticity in the hippocampus consists of two opposing forces: long-term potentiation (LTP), which strengthens synapses and long-term depression (LTD), which weakens synapses. LTP and LTD are associated with memory formation and loss, respectively. Synaptic plasticity is controlled at a molecular level by Ca²⁺-mediated protein signaling. Here, Ca²⁺ binds the protein, calmodulin (CaM), which modulates synaptic plasticity in both directions. This is because Ca²⁺-bound CaM activates both LTD-and LTP-inducing proteins. Understanding how CaM responds to Ca²⁺ signaling and how this translates into synaptic plasticity is therefore important to understanding synaptic plasticity induction. In this paper, CaM activation by Ca²⁺ and calmodulin binding to downstream proteins was mathematically modeled using differential equations. Simulations were monitored with and without theoretical knockouts and, global sensitivity analyses were performed to determine how Ca²⁺/CaM signaling occurred at various Ca²⁺ signals when CaM levels were limiting. At elevated stimulations, the total CaM pool rapidly bound to its protein binding targets which regulate both LTP and LTD. This was followed by CaM becoming redistributed from low-affinity to high-affinity binding targets. Specifically, CaM was redistributed away from LTD-inducing proteins to bind the high-affinity LTP-inducing protein, calmodulin-dependent kinase II (CaMKII). In this way, CaMKII acted as a dominant affecter and repressed activation of opposing CaM-binding protein targets. The model thereby showed a novel form of CaM signaling by which the two opposing pathways crosstalk indirectly. The model also found that CaMKII can repress cAMP production by repressing CaM-regulated proteins, which catalyze cAMP production. The model also found that at low Ca²⁺ stimulation levels, typical of LTD induction, CaM signaling was unstable and is therefore unlikely to alone be enough to induce synaptic depression. Overall, this paper demonstrates how limiting levels of CaM may be a fundamental aspect of Ca²⁺ regulated signaling which allows crosstalk among proteins without requiring directly interaction.     

Conformational Changes in Calcium‐Sensor Proteins under Molecular Crowding Conditions

Fundamental components of signaling pathways are switch modes in key proteins that control start, duration, and ending of diverse signal transduction events. A large group of switch proteins are Ca²⁺ sensors, which undergo conformational changes in response to oscillating intracellular Ca²⁺ concentrations. Here we use dynamic light scattering and a recently developed approach based on surface plasmon resonance to compare the protein dynamics of a diverse set of prototypical Ca²⁺‐binding proteins including calmodulin, troponin C, recoverin, and guanylate cyclase‐activating protein. Surface plasmon resonance biosensor technology allows monitoring conformational changes under molecular crowding conditions, yielding for each Ca²⁺‐sensor protein a fingerprint profile that reflects different hydrodynamic properties under changing Ca²⁺ conditions and is extremely sensitive to even fine alterations induced by point mutations. We see, for example, a correlation between surface plasmon resonance, dynamic light scattering, and size‐exclusion chromatography data. Thus, changes in protein conformation correlate not only with the hydrodynamic size, but also with a rearrangement of the protein hydration shell and a change of the dielectric constant of water or of the protein–water interface. Our study provides insight into how rather small signaling proteins that have very similar three‐dimensional folding patterns differ in their Ca²⁺‐occupied functional state under crowding conditions.     

过饱和度、反应物化学计量比及离子强度对草酸钙晶体生长的影响

肾结石是一种普遍的疾病,全球的发病率约为10%,且其复发率高。2003年欧洲的一项统计表明,尿石患者第一次复发率为40%[1]。草酸钙(CaOxa)是肾结石的主要成分,其体外模拟引起了人们广泛的关注[2,3]。然而,普通溶液体系的模拟环境不能充分反映尿石的形成环境,用类似细胞膜的有序分     

Calbindin regulates Kv4.1 trafficking and excitability in dentate granule cells via CaMKII-dependent phosphorylation

Calbindin, a major Ca²⁺ buffer in dentate granule cells (GCs), plays a critical role in shaping Ca²⁺ signals, yet how it regulates neuronal function remains largely unknown. Here, we found that calbindin knockout (CBKO) mice exhibited dentate GC hyperexcitability and impaired pattern separation, which co-occurred with reduced K⁺ current due to downregulated surface expression of Kv4.1. Relatedly, manipulation of calbindin expression in HT22 cells led to changes in CaMKII activation and the level of surface localization of Kv4.1 through phosphorylation at serine 555, confirming the mechanism underlying neuronal hyperexcitability in CBKO mice. We also discovered that Ca²⁺ buffering capacity was significantly reduced in the GCs of Tg2576 mice to the level of CBKO GCs, and this reduction was restored to normal levels by antioxidants, suggesting that calbindin is a target of oxidative stress. Our data suggest that the regulation of CaMKII signaling by Ca²⁺ buffering is crucial for neuronal excitability regulation.Subject terms: Cellular neuroscience, Intrinsic excitability     

Determination of calcium binding sites in gas-phase small peptides by tandem mass spectrometry

Low-energy (LE) and high-energy (HE) collisionally activated decompositions (CAD) of calcium/peptide complexes of the form [M-H+Ca]⁺ and [M+Ca]²⁺ reflect the site of calcium binding in various gas-phase peptides that are models of the calcium binding site III of rabbit skeletal troponin C. The Ca²⁺ binding sites involve an aspartic acid, glutamic acid, and asparagine, which are in the metal-binding loops of calcium-binding proteins. Both fast atom bombardment (FAB) and electrospray ionization (ESI) were used to generate the metal/peptide complexes. When submitted to LE CAD, ESI-produced Ca²⁺/peptide complexes undergo fragmentations that are controlled by Ca²⁺ binding and provide information on the Ca²⁺ binding site. The LE CAD spectra are simple, indicating that Ca²⁺ binding involves specific oxygen ligands including acidic side chains and that only a few low-energy fragmentation channels exist. The HE CAD spectra of FAB-produced Ca²⁺/peptide complexes are more complex, owing to the introduction of high internal energy into the precursor ion. Interactions of the other alkaline-earth metal ions Mg²⁺ and Ba²⁺ with these peptides reveal that the ligand preferences of these metal ions are slightly different than those of Ca²⁺.     

The Regulation of the Calcium Signal by Membrane Pumps

Calcium may have a static, structure‐stabilizing role in biological organs like the bones and the teeth, or may fulfill a dynamic function in cells as a regulator of signal‐transduction pathways. This is made possible by the properties of the Ca²⁺ ion (e.g., high dehydration rate, great flexibility in coordinating ligands, largely irregular geometry of the coordination sphere). Since Ca²⁺ is a universal carrier of signals, the control of its homeostasis is of central importance for the organism. It involves exchanges between the skeleton (which is the major calcium reservoir) and the extracellular and intracellular fluids. It also involves the intestine and the kidney, the organs of Ca absorption and release, respectively. The highly integrated homeostasis process consists of a number of hormonally controlled feedback loops, and an elaborate system of membrane channels, exchangers, and pumps that control the Ca²⁺ flux into and out of cells.     

Cyclic Adenosine 5′‐Diphosphoribose (cADPR) Mimics Used as Molecular Probes in Cell Signaling

Cyclic adenosine 5′‐diphosphate ribose (cADPR) is a second messenger in the Ca²⁺ signaling pathway. To elucidate its molecular mechanism in calcium release, a series of cADPR analogues with modification on ribose, nucleobase, and pyrophosphate have been investigated. Among them, the analogue with the modification of the northern ribose by ether linkage substitution (cIDPRE) exhibits membrane‐permeate Ca²⁺ agonistic activity in intact HeLa cells, human T cells, mouse cardiac myocytes and neurosecretory PC12 cell lines; thus, cIDPRE and coumarin‐caged cIDPRE are valuable probes to investigate the cADPR‐mediated Ca²⁺ signal pathway.     

Calcium overload is essential for the acceleration of staurosporine-induced cell death following neuronal differentiation in PC12 cells

Differentiation of neuronal cells has been shown to accelerate stress-induced cell death, but the underlying mechanisms are not completely understood. Here, we find that early and sustained increase in cytosolic ([Ca²⁺]_c) and mitochondrial Ca²⁺ levels ([Ca²⁺]_m) is essential for the increased sensitivity to staurosporine-induced cell death following neuronal differentiation in PC12 cells. Consistently, pretreatment of differentiated PC12 cells with the intracellular Ca²⁺-chelator EGTA-AM diminished staurosporine-induced PARP cleavage and cell death. Furthermore, Ca²⁺ overload and enhanced vulnerability to staurosporine in differentiated cells were prevented by Bcl-X_L overexpression. Our data reveal a new regulatory role for differentiation-dependent alteration of Ca²⁺ signaling in cell death in response to staurosporine.     

Beta-arrestin inhibits CAMKKbeta-dependent AMPK activation downstream of protease-activated-receptor-2

Background  

Proteinase-activated-receptor-2 (PAR₂) is a seven transmembrane receptor that can activate two separate signaling arms: one through Gαq and Ca²⁺ mobilization, and a second through recruitment of β-arrestin scaffolds. In some cases downstream targets of the Gαq/Ca²⁺ signaling arm are directly inhibited by β-arrestins, while in other cases the two pathways are synergistic; thus β-arrestins act as molecular switches capable of modifying the signal generated by the receptor.     

Synthesis,Biological Evaluation,and Molecular Modeling of Aza-Crown Ethers

Synthetic and natural ionophores have been developed to catalyze ion transport and have been shown to exhibit a variety of biological effects. We synthesized 24 aza- and diaza-crown ethers containing adamantyl, adamantylalkyl, aminomethylbenzoyl, and ε-aminocaproyl substituents and analyzed their biological effects in vitro. Ten of the compounds (8, 10–17, and 21) increased intracellular calcium ([Ca²⁺]_i) in human neutrophils, with the most potent being compound 15 (N,N’-bis[2-(1-adamantyl)acetyl]-4,10-diaza-15-crown-5), suggesting that these compounds could alter normal neutrophil [Ca²⁺]_i flux. Indeed, a number of these compounds (i.e., 8, 10–17, and 21) inhibited [Ca²⁺]_i flux in human neutrophils activated by N-formyl peptide (fMLF). Some of these compounds also inhibited chemotactic peptide-induced [Ca²⁺]_i flux in HL60 cells transfected with N-formyl peptide receptor 1 or 2 (FPR1 or FPR2). In addition, several of the active compounds inhibited neutrophil reactive oxygen species production induced by phorbol 12-myristate 13-acetate (PMA) and neutrophil chemotaxis toward fMLF, as both of these processes are highly dependent on regulated [Ca²⁺]_i flux. Quantum chemical calculations were performed on five structure-related diaza-crown ethers and their complexes with Ca²⁺, Na⁺, and K⁺ to obtain a set of molecular electronic properties and to correlate these properties with biological activity. According to density-functional theory (DFT) modeling, Ca²⁺ ions were more effectively bound by these compounds versus Na⁺ and K⁺. The DFT-optimized structures of the ligand-Ca²⁺ complexes and quantitative structure-activity relationship (QSAR) analysis showed that the carbonyl oxygen atoms of the N,N’-diacylated diaza-crown ethers participated in cation binding and could play an important role in Ca²⁺ transfer. Thus, our modeling experiments provide a molecular basis to explain at least part of the ionophore mechanism of biological action of aza-crown ethers.     

Intrinsic specificity of Ca2+–protein binding sites

The gas-phase chemistry of anionic [M + Cat²⁺ – 3H]^? complexes between Ca²⁺-specific peptides and the alkaline earth metal ions Mg²⁺, Ca²⁺ and Ba²⁺ is reported. The metal ion complexes were studied using fast atom bombardment, collision-induced decomposition (CID) and molecular mechanical calculations. The CID reactions and molecular mechanical calculations revealed that the Ca²⁺–peptide complexes are bound differently to the Mg²⁺– and Ba²⁺–peptide complexes and that the intrinsic (gas-phase) chemistry is reflected by known aqueousphase chemistry.     

Characterization of hydromedusan Ca2+-regulated photoproteins as a tool for measurement of Ca2+concentration

Calcium ion is a ubiquitous intracellular messenger, performing this function in many eukaryotic cells. To understand calcium regulation mechanisms and how disturbances of these mechanisms are associated with disease states, it is necessary to measure calcium inside cells. Ca²⁺-regulated photoproteins have been successfully used for this purpose for many years. Here we report the results of comparative studies on the properties of recombinant aequorin from Aequorea victoria, recombinant obelins from Obelia geniculata and Obelia longissima, recombinant mitrocomin from Mitrocoma cellularia, and recombinant clytin from Clytia gregaria as intracellular calcium indicators in a set of identical in vitro and in vivo experiments. Although photoproteins reveal a high degree of identity of amino acid sequences and spatial structures, and, apparently, have a common mechanism for the bioluminescence reaction, they were found to differ in the Ca²⁺ concentration detection limit, the sensitivity of bioluminescence to Mg²⁺, and the rates of the rise of the luminescence signal with a sudden change of Ca²⁺ concentration. In addition, the bioluminescence activities of Chinese hamster ovary cells expressing wild-type photoproteins also differed. The light signals of cells expressing mitrocomin, for example, slightly exceeded the background, suggesting that mitrocomin may be hardly used to detect intracellular Ca²⁺ without modifications improving its properties. On the basis of experiments on the activation of endogenous P2Y₂ receptor in Chinese hamster ovary cells by ATP, we suggest that wild-type aequorin and obelin from O. longissima are more suitable for calcium detection in cytoplasm, whereas clytin and obelin from O. geniculata can be used for calcium measurement in cell compartments with high Ca²⁺ concentration. Figure

Hydromedusan photoproteins differ in Ca²⁺ concentration detection limit, sensitivity of bioluminescence to Mg²⁺, and rates of rise of luminescence signal with a sudden change of [Ca²⁺] despite a high degree of identity of their amino acid sequences and spatial structures, and, apparently, a common mechanism for the bioluminescence reaction.     

Chirality Transfer in Propeller‐Shaped Cyclen?Calcium(II) Complexes: Metal‐Coordinating and Ion‐Pairing Anion Procedures

A series of quadruple‐stranded Na⁺ and Ca²⁺ complexes with octadentate cyclen ligands was synthesized to produce complexes that contained four different side‐arm combinations (one triazole? coumarin group and three pyridine groups ( 1 ), four pyridine groups ( 2 ), one triazole? coumarin group and three quinoline groups ( 3 ), and four quinoline groups ( 4 )). X‐ray crystallographic analysis revealed that no significant changes occurred in the stereostructure of these complexes upon replacing one pyridine group with a triazole? coumarin moiety, or by replacing Na⁺ ions with Ca²⁺ ions, although the coordination number of the complexes in the solid state decreased when pyridine groups were replaced by quinoline groups. In solution, all of the side arms were arranged in a propeller‐like pattern to yield an enantiomer pair of Δ and Λ forms in each metal complex. The addition of a tert‐butoxycarbonyl (Boc)‐protected amino acid anion, that is, a coordinative chiral carboxylate anion, to the cyclen? Ca²⁺ complex induced circular dichroism (CD) signals in the aromatic region by forming a 1:1 mixture of diastereomeric ternary complexes with opposite complex chirality, whilst the corresponding Na⁺ complexes rarely showed any response. In complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺, this chirality‐transfer process was efficiently followed by considering the induction of the CD signals at two different wavelengths, that is, the coumarin‐chromophore region and the aza‐aromatic region. The sign and intensity of the CD signal were significantly dependent on both the nature of the aza‐aromatic moiety and the enantiomeric purity of the external anion. These Ca²⁺ complexes worked as effective probes for the determination of the enantiomeric excess of the chiral anion. The cyclen? Ca²⁺ complexes also interacted with the non‐coordinative Δ‐TRISPHAT anion through an ion‐pairing mechanism to achieve chirality transfer from the anion to the metal complex; both complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺ clearly showed induced CD signals in the coumarin‐chromophore region, owing to ion‐paring interactions with the Δ‐TRISPHAT anion. Thus, the proper combination of an octadentate cyclen ligand and a metal center demonstrated effective chirality transfer.     

Photochemical reaction and diffusion of caged calcium studied by the transient grating

A photoreaction of caged calcium (Ca²⁺) was investigated by using the time-resolved transient grating (TG) method. The q²-dependent feature of the TG signal was analyzed based on a model that there are two parallel dissociation steps with different rates and Ca²⁺ is released promptly after the fracture of the caged compound. The TG signal representing the presence of Ca²⁺ was appeared by the volume contribution. Although the diffusion coefficients of Cg and the decomposed product are different without Ca²⁺, only one diffusion component was observed after the dissociation of CgCa²⁺, indicating that the caged compounds and Ca²⁺ diffuse together.     

Design,characterization and quantum chemical computations of a novel series of pyrazoles derivatives with potential anti-proinflammatory response

The synthesis and characterization of the full family of 11 pyrazoles were performed by means of UV–Vis, FTIR, ¹H NMR, ¹³C NMR, two-dimensional NMR experiments and DFT simulations. As pyrazoles are known for showing diverse biological actions, they were also tested in the NCI-60 cancer cell line panel, showing moderate to good activity against different cell lines. Furthermore, the anti-proinflammatory activity test of a set of pyrazoles of the form (E)-4-((4-bromophenyl)diazenyl)-3,5-dimethyl-1-R-phenyl-1H-pyrazole was performed, this is based on the study of the blockage of the increase in intracellular [Ca²⁺] observed in response to platelet-activating factor (PAF) treatment of four pyrazoles (i.e. 6, 8, 9 and 10), which successfully displayed [Ca²⁺] channel inhibition. Therefore, the obtained intracellular [Ca²⁺] signal results indicate that the pyrazole family characterized in this study, in particular compounds 6 and 10, are potent blockers of the PAF-initiated Ca²⁺ signaling that mediates the hyperpermeability typically observed during the development of inflammation.     

Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering

Ca²⁺ plays a pivotal role in the physiology and biochemistry of prokaryotic and mammalian organisms. Viruses also utilize the universal Ca²⁺ signal to create a specific cellular environment to achieve coexistence with the host, and to propagate. In this paper we first describe our development of a grafting approach to understand site-specific Ca²⁺ binding properties of EF-hand proteins with a helix-loop-helix Ca²⁺ binding motif, then summarize our prediction and identification of EF-hand Ca²⁺ binding sites on a genome-wide scale in bacteria and virus, and next report the application of the grafting approach to probe the metal binding capability of predicted EF-hand motifs within the streptococcal hemoprotein receptor (Shr) of Streptococcus pyrogenes and the nonstructural protein 1 (nsP1) of Sindbis virus. When methods such as the grafting approach are developed in conjunction with prediction algorithms we are better able to probe continuous Ca²⁺-binding sites that have been previously underrepresented due to the limitation of conventional methodology.