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Naomi Sakai

Publications and source records attributed to Naomi Sakai.

At least 19 recordsLinked to original sources
PubMed2006

Adhesive pi-clamping within synthetic multifunctional pores.

We report the design, synthesis, and evaluation of synthetic multifunctional pores with adhesive, that is, electron-deficient naphthalenediimide (NDI) pi-clamps at their inner surface. We find that, in lipid bilayer membranes, comparable synthetic pores with and without pi-clamps have similar, nanomolar activity. Functional relevance of adhesive pi-clamping within synthetic pores is demonstrated by means of an innovative in situ blocker screening method. The obtained line of experimental evidence includes (a) different blockage efficiency with and without pi-clamps (quantified as clamping factors), (b) increasing clamping factors with increasing blocker charge (supportive ion pairing), and, most importantly, (c) increasing clamping factors with increasing aromatic electron donor-acceptor interactions. The availability of advanced synthetic multifunctional pores with refined active sites is important for practical applications in domains such as drug discovery (enzyme inhibitor screening) and diagnostics (multianalyte sensing).

Journal Article↗
PubMed2006

Synthetic functional pi-stack architecture in lipid bilayers.

Neglected until recently, pi-stack architecture is rapidly emerging as a powerful strategy to create function in lipid bilayer membranes. Recent reports describe supramolecular rosettes acting as hosts of intercalating guests, to assemble in bilayer membranes and, in the case of stacked guanosine and folate quartets, to form ion channels. The introduction of rigid-rod pi-stack architecture allowed us to address one of the great challenges in the field, i.e. ligand gating. Inspiring pi-stack chemistry from related fields, covering rainbow coloration, conductivity, as well as the critical dependence of charge mobilities on the precision of supramolecular organization is summarized to zoom in on arguably the most promising application of functional pi-stack architecture in lipid bilayers, that is the creation of multifunctional photosystems.

Circular Dichroism↗
PubMed2006

Photoproduction of proton gradients with pi-stacked fluorophore scaffolds in lipid bilayers.

Rigid p-octiphenyl rods were used to create helical tetrameric pi-stacks of blue, red-fluorescent naphthalene diimides that can span lipid bilayer membranes. In lipid vesicles containing quinone as electron acceptors and surrounded by ethylenediaminetetraacetic acid as hole acceptors, transmembrane proton gradients arose through quinone reduction upon excitation with visible light. Quantitative ultrafast and relatively long-lived charge separation was confirmed as the origin of photosynthetic activity by femtosecond fluorescence and transient absorption spectroscopy. Supramolecular self-organization was essential in that photoactivity was lost upon rod shortening (from p-octiphenyl to biphenyl) and chromophore expansion (from naphthalene diimide to perylene diimide). Ligand intercalation transformed the photoactive scaffolds into ion channels.

Benzene Derivatives↗
PubMed2006

Direct and rapid cytosolic delivery using cell-penetrating peptides mediated by pyrenebutyrate.

Intracellular delivery of bioactive molecules using arginine-rich peptides, including oligoarginine and HIV-1 Tat peptides, is a recently developed technology. Here, we report a dramatic change in the methods of internalization for these peptides brought about by the presence of pyrenebutyrate, a counteranion bearing an aromatic hydrophobic moiety. In the absence of pyrenebutyrate, endocytosis plays a major role in cellular uptake. However, the addition of pyrenebutyrate results in direct membrane translocation of the peptides yielding diffuse cytosolic peptide distribution within a few minutes. Using this method, rapid and efficient cytosolic delivery of the enhanced green fluorescent protein (EGFP) was achieved in cells including rat hippocampal primary cultured neurons. Enhancement of bioactivity on the administration of anapoptosis-inducing peptide is also demonstrated. Thus, coupling arginine-rich peptides with this hydrophobic anion dramatically improved their ability to translocate cellular membranes, suggesting the great impact of this approach on exploring and controlling cell function.

Amino Acid Sequence↗
PubMed2006

Dendritic folate rosettes as ion channels in lipid bilayers.

The self-assembly of folate dendrimers into pi-stacked supramolecular rosettes is shown to produce ion channels in planar and spherical lipid bilayer membranes. The found ion channels are small, quite homogeneous, long-lived, ohmic, cation selective (Eisenman I), and blockable by the permeant cation.

Folic Acid↗
PubMed2006

A rivet model for channel formation by aerolysin-like pore-forming toxins.

The bacterial toxin aerolysin kills cells by forming heptameric channels, of unknown structure, in the plasma membrane. Using disulfide trapping and cysteine scanning mutagenesis coupled to thiol-specific labeling on lipid bilayers, we identify a loop that lines the channel. This loop has an alternating pattern of charged and uncharged residues, suggesting that the transmembrane region has a beta-barrel configuration, as observed for Staphylococcal alpha-toxin. Surprisingly, we found that the turn of the beta-hairpin is composed of a stretch of five hydrophobic residues. We show that this hydrophobic turn drives membrane insertion of the developing channel and propose that, once the lipid bilayer has been crossed, it folds back parallel to the plane of the membrane in a rivet-like fashion. This rivet-like conformation was modeled and sequence alignments suggest that such channel riveting may operate for many other pore-forming toxins.

Amino Acid Sequence↗
PubMed2006

Use of the exciton chirality method in the investigation of ligand-gated synthetic ion channels.

The objective of this brief highlight is to point out the central role of the exciton chirality method to gain insights on the structural basis of the recently achieved ligand gating of synthetic ion channels. This unprecedented ligand gating was achieved with an equally unprecedented transmembrane rigid-rod pi-stack architecture that is designed to adopt a closed conformation with helically stacked naphthalenediimide (NDI) acceptors. The intercalation of the complementary electron-rich dialkoxynaphthalene ligands then stimulates the untwisting of the closed pi-helices into hollow barrel-stave supramolecules. During this helix-barrel transition, the angle between the transition moments of the exciton-coupled NDI chromophores decreases toward zero. The corresponding disappearance of the split CD provides, according to the exciton chirality method, the otherwise elusive experimental support that ligand-gated ion channel formation really occurs by this rationally designed helix-barrel transition.

Circular Dichroism↗
PubMed2006

Sensing, threading, orienting, and cutting polymers with rigid-rod pores.

This short review describes synthetic pores that are made from rigid-rod molecules and can bind oligo-and polymers such as polyacetylenes, p-oligophenyls, terpenoids, polypeptides, polysaccharides, and oligonucleotides. The spotlight is on recent breakthroughs to image the longtime elusive pore-polymer host-guest complexes as single giant pseudorotaxanes.

Membrane Transport Modulators↗
PubMed2006

Comparison of larvicidal, adulticidal and acaricidal activity of two geometrical butylidenephthalide isomers.

Insecticidal and acaricidal activities of two geometrical isomers, (E)- and (Z)-butylidenephthalide isolated from Angelica acutiloba, against larvae and adults of fruit fly (Drosophila melanogaster), cat fleas (Ctenocephalides felis) and house dust mites (Dermatophagoides farinae and Tyrophagus putrescentiae) were investigated and compared with that of positive controls. (E)- and (Z)-Butylidenephthalide exhibited 50% lethal concentration (LC50) values of 2.07 and 0.94 micromol/ml of diet concentration against larvae of D. melanogaster, respectively. This indicated that two isomers of butylidenephthalide have geometrical stereoselectivity for larvicidal effect. Even though both (E)- and (Z)-butylidenephthalide also showed potent adulticidal and acaricidal activity against adults of D. melanogaster and two mites, there was no significant difference between two isomers. Insecticidal activity of both (E)- and (Z)-butylidenephthalide toward adults of C. felis was not detected even at the maximum concentration of 200 microg/cm2.

Aging↗
PubMed2005

Ligand-gated synthetic ion channels.

Supramolecular pi-stack architecture is fundamental in DNA chemistry but absent in biological and synthetic ion channels and pores. Here, a novel rigid-rod pi-stack architecture is introduced to create synthetic ion channels with characteristics that are at the forefront of rational design, that is, ligand gating by a conformational change of the functional supramolecule. Namely, the intercalation of electron-rich aromatics is designed to untwist inactive electron-poor helical pi-stacks without internal space into open barrel-stave ion channels. Conductance experiments in planar lipid bilayers corroborate results from spherical bilayers and molecular modeling: Highly cooperative and highly selective ligand gating produces small, long-lived, weakly anion selective, ohmic ion channels. Structural studies conducted under conditions relevant for function provide experimental support for helix-barrel transition as origin of ligand gating. Control experiments demonstrate that minor structural changes leading to internal decrowding suffice to cleanly annihilate chiral self-organization and function.

Crystallography, X-Ray↗
PubMed2005

Synthetic multifunctional pores that open and close in response to chemical stimulation.

Studies on synthetic multifunctional pores with external and internal active sites for ligand gating and noncompetitive blockage are presented, with emphasis on the contribution of external ligands to the characteristics of pore. A comparison between different synthetic multifunctional pores reveals that the location of functional groups in rigid-rod beta-barrel pores is precisely reflected in the function: molecular recognition at the outer barrel surface results in pore opening, while molecular recognition at the inner barrel surface results in pore closing. Negligible nonspecific leakage, disappearance of pH gating, inhibition of intervesicular pore transfer, and maybe also the flickering of currents of single open pores characterize external ligands as adhesive cushions that liberate the pore from lateral pressure exerted by the surrounding membrane. Refined molecular models show good agreement with pore design and experimental facts with regard to function.

Hydrogen-Ion Concentration↗
PubMed2005

Synthetic ion channels with rigid-rod pi-stack architecture that open in response to charge-transfer complex formation.

We describe the design, synthesis, and evaluation of synthetic ion channels with a new rigid-rod pi-stack architecture that open in response to guest binding by aromatic electron donor-acceptor interactions. Highly cooperative and highly selective ligand gating is shown to yield anion selective, small ion channels that have the characteristic plum color of the charge-transfer complexes formed between the dialkoxynaphthalene ligands and the stacked naphthalenediimide acceptors of the channel.

Journal Article↗
PubMed2005

Arginine magic with new counterions up the sleeve.

The elusive questions how arginine-rich sequences allow peptides and proteins to penetrate cells or to form voltage-gated ion channels are controversial topics of current scientific concern. The possible contributions of exchangeable counterions to these puzzling processes remain underexplored. The objective of this report is to clarify scope and limitations of certain counteranions to modulate cellular uptake and anion carrier activity of oligo/polyarginines. The key finding is that the efficiency of counteranion activators depends significantly on many parameters such as activator-membrane and activator-carrier interactions. This finding is important because it suggests that counteranions can be used to modulate not only efficiency but also selectivity. Specifically, activator efficiencies are found to increase with increasing aromatic surface of the activator, decreasing size of the transported anion, increasing carrier concentration as well as increasing membrane fluidity. Efficiency sequences depend on membrane composition with coronene > pyrene >>fullerene > calix[4]arene carboxylates in fluid and crystalline DPPC contrasting to fullerene > calix[4]arene approximately coronene > pyrene carboxylates in EYPC with or without cholesterol or ergosterol. In HeLa cells, the efficiency of planar activators (pyrene) exceeds that of spherical activators (fullerenes, calixarenes). Polyarginine complexes with pyrene and coronene activators exhibit exceptional excimer emission. Decreasing excimer emission with increasing ionic strength reveals dominant hydrophobic interactions with the most efficient carboxylate activators. Dominance of ion pairing with the inefficient high-affinity sulfate activators is corroborated by the reversed dependence on ionic strength. These findings on activator-carrier and activator-membrane interactions are discussed as supportive of arene-templated guanidinium-carboxylate pairing and interface-directed translocation as possible origins of the superb performance of higher arene carboxylates as activators.

Arginine↗
PubMed2005

Anionic fullerenes, calixarenes, coronenes, and pyrenes as activators of oligo/polyarginines in model membranes and live cells.

We report that the efflux of 5(6)-carboxyfluorescein anions from neutral egg yolk phosphatidylcholine vesicles is mediated by oligo/polyarginines only in the presence of activating amphiphilic anions. Screening of anion activators reveals best synergism for amphiphilic carboxylates (fullerene > calix[4]arene approximately coronene > pyrene > calix[6]arene > alkyl), whereas amphiphilic sulfates show less satisfactory activation despite often lower effective concentrations. The analogous alcohols and one calix[4]arene diphosphate were inactive. These results are discussed in the context of a tentative anion carrier mechanism, where interactions with bilayer (interface-directed translocation) and carrier (arene-templated carboxylate-guanidinium pairing) contribute to activator efficiencies. Applied to HeLa cells, pyrenebutyrate is shown to significantly increase the uptake of a fluorescently labeled octaarginine in a concentration-dependent manner.

Anions↗
PubMed2005

Direct observation of anion-mediated translocation of fluorescent oligoarginine carriers into and across bulk liquid and anionic bilayer membranes.

The recent hypothesis that counteranion-mediated dynamic inversion of charge and solubility might contribute to diverse functions of oligoarginines in biomembranes was tested with two fluorescently labelled oligomers, FL-R(8), one of the most active cell-penetrating peptides, and its longer version, FL-R(16). We report evidence for counteranion-mediated phase transfer from water into bulk chloroform and anionic lipid-bilayer membranes as well as reverse-phase transfer from bulk chloroform and across intact lipid-bilayer membranes into water. The differences found between FL-R(8) and FL-R(16) with regard to location in the bilayer and reverse-phase transfer from bulk and lipid-bilayer membranes into water implied that the reported results may be relevant for biological function.

Antiporters↗
PubMed2005

Rigid-rod molecules in biomembrane models: from hydrogen-bonded chains to synthetic multifunctional pores.

Synthetic ion channels and pores formed by rigid-rod molecules are summarized. This includes work on hydrogen-bonded chains installed along membrane-spanning rigid-rod scaffolds to transport protons. As a second topic, programmed assembly of p-septiphenyls with terminal iminodiacetate-copper complexes for potassium transport by cation-pi interactions is described. The third topic concerns rigid push-pull rods as fluorescent alpha-helix mimics to probe the importance of dipole-potential interactions for voltage gating, both on the functional and the structural level. Topic number four deals with p-octiphenyl staves as key scaffolds for the synthesis of rigid-rod beta-barrel pores. The description of internal and external design strategies for these rigid-rod beta-barrels covers a rich collection of pH-, pM-, voltage-, ligand-, and enzyme-gated synthetic multifunctional pores that can act as hosts, sensors, and catalysts. As far as practical applications are concerned, the possibility to detect chemical reactions with synthetic multifunctional pores appears most attractive. Recent molecular mechanics simulations are presented as a valuable approach to insights on the elusive suprastructures of multifunctional pores made from rigid rods.

Hydrogen Bonding↗
PubMed2004

Synthetic multifunctional pores with external and internal active sites for ligand gating and noncompetitive blockage.

Design, synthesis, and multifunctionality of p-octiphenyl beta-barrel pores with external LRL triads and internal HH dyads are described. Molecular recognition of anionic fullerenes > calixarenes > pyrenes by guanidinium arrays at the outer pore surface is shown to result in pore opening, whereas alpha-helix recognition within the topologically matching internal space is shown to result in noncompetitive pore blockage. This experimental evidence for multifunctionality is supported by comparison with pertinent control pores and blockers, by structural studies using FRET from p-octiphenyl donors in the pore to BODIPY acceptors in the bilayer, and by molecular mechanics simulations. Practical usefulness of ligand-gated synthetic multifunctional pores is exemplified with the continuous detection of chemical processes.

Animals↗