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Biomedical subjects

G Sugihara

Publications and source records attributed to G Sugihara.

At least 19 recordsLinked to original sources

De novo-designed peptide transforms Golgi-specific lipids into Golgi-like nanotubules.

Cellular organelles, such as the Golgi apparatus and the endoplasmic reticulum, adopt characteristic structures depending on their function. While the tubular shapes of these structures result from complex protein-lipid interactions that are not fully understood, some fundamental machinery must be required. We show here that a de novo-designed 18-mer amphipathic alpha-helical peptide, Hel 13-5, transforms spherical liposomes made from a Golgi-specific phospholipid mixture into nanotubules on the scale of and resembling the shape of the nanotubules that form the Golgi apparatus. Furthermore, we show that that the size and the shape of such nanotubules depend on lipid composition and peptide properties such as length and the ratio of hydrophobic to hydrophilic amino acids. Although the question of precisely how nature engineers organellar membranes remains unknown, our simple novel system provides a basic set of tools to begin addressing this question.

Circular Dichroism↗

Residual delay maps unveil global patterns of atmospheric nonlinearity and produce improved local forecasts.

We use residual-delay maps of observational field data for barometric pressure to demonstrate the structure of latitudinal gradients in nonlinearity in the atmosphere. Nonlinearity is weak and largely lacking in tropical and subtropical sites and increases rapidly into the temperate regions where the time series also appear to be much noisier. The degree of nonlinearity closely follows the meridional variation of midlatitude storm track frequency. We extract the specific functional form of this nonlinearity, a V shape in the lagged residuals that appears to be a basic feature of midlatitude synoptic weather systems associated with frontal passages. We present evidence that this form arises from the relative time scales of high-pressure versus low-pressure events. Finally, we show that this nonlinear feature is weaker in a well regarded numerical forecast model (European Centre for Medium-Range Forecasts) because small-scale temporal and spatial variation is smoothed out in the grided inputs. This is significant, in that it allows us to demonstrate how application of statistical corrections based on the residual-delay map may provide marked increases in local forecast accuracy, especially for severe weather systems.

Atmosphere↗

Enthalpy-Entropy Compensation Phenomenon Observed for Different Surfactants in Aqueous Solution.

Based on previously reported thermodynamic data such as changes of the Gibbs energy (DeltaG(m)( degrees )), the enthalpy (DeltaH(m)( degrees )), and the entropy (DeltaS(m)( degrees )) on micelle formation of more than 15 species of surfactants (including nonionic, anionic, and cationic surfactants), plots of DeltaH(m)( degrees ) vs DeltaS(m)( degrees ) (not of DeltaS(m)( degrees ) vs DeltaH(m)( degrees ), as is usually done) were made. For each surfactant, a linear relation having almost the same slope (1/307 K(-1)) within a small error (+/-2.3%) but a different intercept (varsigma) depending on the surfactant species was obtained, i.e., DeltaS(m)( degrees ) = (1/307)DeltaH(m)( degrees ) + varsigma, where 1/307 (K(-1)) means that the so-called compensation temperature (T(C)) is 307 K. Strictly speaking, T(C) ranges from 299 to 315 K, depending on the species. The intercept corresponds to the entropy change at a specific temperature giving DeltaH(m)( degrees ) = 0, at which the driving force of micelle formation comes only from the entropy term; this temperature is characteristic of the surfactant species. On the other hand, the compensation temperature has no significant meaning other than a mean temperature studied. Copyright 1999 Academic Press.

Journal Article↗

Episodic fluctuations in larval supply

The lack of a clear relationship between spawning output and recruitment success continues to confound attempts to understand and manage temporally variable fish populations. This relationship for a common reef fish is shown to be obscured by nonlinear processes in operation during the larval phase. Nonlinear responses of larval fish to their noisy physical environment may offer a general explanation for the erratic, often episodic, replenishment of open marine populations.

Journal Article↗

Morphological behavior of acidic and neutral liposomes induced by basic amphiphilic alpha-helical peptides with systematically varied hydrophobic-hydrophilic balance.

Lipid-peptide interaction has been investigated using cationic amphiphilic alpha-helical peptides and systematically varying their hydrophobic-hydrophilic balance (HHB). The influence of the peptides on neutral and acidic liposomes was examined by 1) Trp fluorescence quenched by brominated phospholipid, 2) membrane-clearing ability, 3) size determination of liposomes by dynamic light scattering, 4) morphological observation by electron microscopy, and 5) ability to form planar lipid bilayers from channels. The peptides examined consist of hydrophobic Leu and hydrophilic Lys residues with ratios 13:5, 11:7, 9:9, 7:11, and 5:13 (abbreviated as Hels 13-5, 11-7, 9-9, 7-11, and 5-13, respectively; Kiyota, T., S. Lee, and G. Sugihara. 1996. Biochemistry. 35:13196-13204). The most hydrophobic peptide (Hel 13-5) induced a twisted ribbon-like fibril structure for egg PC liposomes. In a 3/1 (egg PC/egg PG) lipid mixture, Hel 13-5 addition caused fusion of the liposomes. Hel 13-5 formed ion channels in neutral lipid bilayer (egg PE/egg PC = 7/3) at low peptide concentrations, but not in an acidic bilayer (egg PE/brain PS = 7/3). The peptides with hydrophobicity less than Hel 13-5 (Hels 11-7 and Hel 9-9) were able to partially immerse their hydrophobic part of the amphiphilic helix in lipid bilayers and fragment liposome to small bicelles or micelles, and then the bicelles aggregated to form a larger assembly. Peptides Hel 11-7 and Hel 9-9 each formed strong ion channels. Peptides (Hel 7-11 and Hel 5-13) with a more hydrophilic HHB interacted with an acidic lipid bilayer by charge interaction, in which the former immerses the hydrophobic part in lipid bilayer, and the latter did not immerse, and formed large assemblies by aggregation of original liposomes. The present study clearly showed that hydrophobic-hydrophilic balance of a peptide is a crucial factor in understanding lipid-peptide interactions.

Biophysical Phenomena↗

Micellization of Mixed System of Bile Salt and Nonionic Surfactant: Sodium Deoxycholate and Decanoyl-N-methylglucamide.

Micelle formation was studied for mixed surfactant systems of a nonionic surfactant, nonanoyl-N-methylglucamine (MEGA-10) with a bile salt, sodium deoxycholate (NaDC), in water at 30 degreesC. NaDC and MEGA-10 are quite different from each other in terms not only of hydrophobic but also of hydrophilic groups. Surface tension of the aqueous solution (gamma) at different mixing ratios was measured by the drop volume method, and critical micellization concentrations (CMCs) were determined from the gamma vs CMC curves at discrete mole fractions of MEGA-10 (XMEGA) in the surfactant mixture. The CMC-XMEGA curve showed a positive deviation from ideal mixing. The apparent interaction parameter (WR) upon micelle formation was evaluated by applying the Rubingh equations derived on the basis of the regular solution theory. The different theory developed by Motomura et al. has been also applied. The analysis of CMC data indicated that the properties of mixed micelles are different between the ranges below and above XMEGA congruent with 0.2 where an azeotrope exists and that the composition of mixed micelles is very similar to that of monomeric species in bulk solution. Copyright 1998 Academic Press.

Journal Article↗

Importance of hydrophobic region in amphiphilic structures of alpha-helical peptides for their gene transfer-ability into cells.

It has been showned that cationic alpha-helical peptides can be useful as nucleic acid-carrier molecules for gene transfer into cells. In order to investigate the significancemake sure of importance of the hydrophobic region in amphiphilic peptides in relation to their transfection ability, we have employed five kinds of peptides with a systematically varied hydrophobic-hydrophilic balance in the amphiphilic structures, and have evaluated the relationship between the structure and the gene transfer ability of the peptides into COS-7 cells. The peptides with a large hydrophobic region took alpha-helical structures, formed large aggregates and showed high transfection efficiency. Their high efficiency can be explained on the basis of their ability to form stable aggregates which can be internalized by endocytosis and remain resistant to digestion in lysosomal vesicles. Furthermore, it was suggested that the hydrophobic region of peptides plays an important role in the disruption of the endosomal membrane, which ca prevent the degradation of DNA in lysosomal vesicles. When peptides do not have so strong membrane-disruptive activity, but form aggregates which can be incorporated by endocytosis, the transfection efficiency can be recovered by the addition of an endosome-disruptive peptide.

Amino Acid Sequence↗

The spike trains of inhibited pacemaker neurons seen through the magnifying glass of nonlinear analyses.

This communication describes the new information that may be obtained by applying nonlinear analytical techniques to neurobiological time-series. Specifically, we consider the sequence of interspike intervals Ti (the "timing") of trains recorded from synaptically inhibited crayfish pacemaker neurons. As reported earlier, different postsynaptic spike train forms (sets of timings with shared properties) are generated by varying the average rate and/or pattern (implying interval dispersions and sequences) of presynaptic spike trains. When the presynaptic train is Poisson (independent exponentially distributed intervals), the form is "Poisson-driven" (unperturbed and lengthened intervals succeed each other irregularly). When presynaptic trains are pacemaker (intervals practically equal), forms are either "p:q locked" (intervals repeat periodically), "intermittent" (mostly almost locked but disrupted irregularly), "phase walk throughs" (intermittencies with briefer regular portions), or "messy" (difficult to predict or describe succinctly). Messy trains are either "erratic" (some intervals natural and others lengthened irregularly) or "stammerings" (intervals are integral multiples of presynaptic intervals). The individual spike train forms were analysed using attractor reconstruction methods based on the lagged coordinates provided by successive intervals from the time-series Ti. Numerous models were evaluated in terms of their predictive performance by a trial-and-error procedure: the most successful model was taken as best reflecting the true nature of the system's attractor. Each form was characterized in terms of its dimensionality, nonlinearity and predictability. (1) The dimensionality of the underlying dynamical attractor was estimated by the minimum number of variables (coordinates Ti) required to model acceptably the system's dynamics, i.e. by the system's degrees of freedom. Each model tested was based on a different number of Ti; the smallest number whose predictions were judged successful provided the best integer approximation of the attractor's true dimension (not necessarily an integer). Dimensionalities from three to five provided acceptable fits. (2) The degree of nonlinearity was estimated by: (i) comparing the correlations between experimental results and data from linear and nonlinear models, and (ii) tuning model nonlinearity via a distance-weighting function and identifying the either local or global neighborhood size. Lockings were compatible with linear models and stammerings were marginal; nonlinear models were best for Poisson-driven, intermittent and erratic forms. (3) Finally, prediction accuracy was plotted against increasingly long sequences of intervals forecast: the accuracies for Poisson-driven, locked and stammering forms were invariant, revealing irregularities due to uncorrelated noise, but those of intermittent and messy erratic forms decayed rapidly, indicating an underlying deterministic process. The excellent reconstructions possible for messy erratic and for some intermittent forms are especially significant because of their relatively low dimensionality (around 4), high degree of nonlinearity and prediction decay with time. This is characteristic of chaotic systems, and provides evidence that nonlinear couplings between relatively few variables are the major source of the apparent complexity seen in these cases. This demonstration of different dimensions, degrees of nonlinearity and predictabilities provides rigorous support for the categorization of different synaptically driven discharge forms proposed earlier on the basis of more heuristic criteria. This has significant implications. (1) It demonstrates that heterogeneous postsynaptic forms can indeed be induced by manipulating a few presynaptic variables. (2) Each presynaptic timing induces a form with characteristic dimensionality, thus breaking up the preparation into subsystems such that the physical variables in each operate as one

Action Potentials↗

Secondary structures of synthetic peptides corresponding to the first membrane-contact portion of normal band 3 and its deletion mutant (Southeast Asian ovalocytosis).

The conformations of synthetic peptides corresponding to the first membrane-contact portion from Tyr390 to Lys430 of band 3 (band 3-1a) and the counterpart portion of South-East Asian ovalocytosis (SAO) band 3 (band 3-1b) in lipid bilayers were examined by means of circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy as well as a proteolytic digestion method. The CD and FTIR studies showed that band 3-1a and band 3-1b in a membrane lipid bilayer cannot assume an alpha-helix rich structure but instead assume a beta-structure rich conformation. The proteolytic digestion experiments demonstrated that the cleavage sites of Tyr392 and Phe423 were common to both the model and erythrocyte membranes. Taken together with our previous work, which indicated that the first membrane-contact portion was the portion embedded in the erythrocyte membrane without tight lipid-peptide interactions [Hamasaki et al. (1997) J. Biochem. 122, 577-585], we imply herein that the first membrane-contact portion of band 3 by itself can not assume the ordinary alpha-helix conformation in the membrane lipid bilayers. A proteinase-resistant portion, from Ser402 to Phe423, was observed when liposomes containing band 3-1a were digested with proteinase K, while no proteinase-resistant core portion was found in the case of band 3-1b (DeltaAla400-Ala408). This suggests the crucial role of the deleted portion, from Ala400 to Ala408, in the interaction of the first membrane-contact portion of band 3 with a membrane lipid bilayer.

Amino Acid Sequence↗

Conformations and orientations of aromatic amino acid residues of tachyplesin I in phospholipid membranes.

Tachyplesin I, an antibacterial and antiviral heptadecapeptide from the hemocyte debris of Tachypleus tridentatus, contains four aromatic amino acids (Trp2, Phe4, Tyr8, and Tyr13) which have been shown to be crucial for activity. In order to investigate conformations and orientations of the aromatic amino acid residues of tachyplesin I in lipid bilayers, its analogs, [Phe8]- and/or [Phe13]-tachyplesin(s) I in which Tyr8 and Tyr13 are replaced by Phe, were synthesized. Circular dichroism spectral studies showed that three peptides are considerably different in conformation in aqueous solution at pH 8.0 whereas they take similar conformations in the presence of neutral egg yolk phosphatidylcholine (EYPC) liposomes. Energy transfer kinetics showed that the distances of Trp2-Tyr8 and Trp2-Tyr13 are 16 A (max of 18.3 A, min of 15.1 A) and 18 A (max of 20.2 A, min of 16.6 A) in buffer but are 12 A (max of 15.2 A, min of 8.6 A) and 18 A (max of 22.9 A, min of 12.9 A), respectively, in the presence of acidic EYPC/EYPG (3:1) liposomes. Decay kinetics for Trp2 fluorescence indicated that Trp2 takes at least three conformations in buffer and in acidic liposomes where fractions of three Trp2 conformers vary by changing the medium from buffer to acidic liposomes. Although tachyplesin I is not in amphiphilic structure in buffer in spite of its rigid antiparallel beta-conformation, its interaction with lipid bilayers appears to induce amphiphilic structure via minor alteration of peptide backbone and side chain orientations, resulting in shortening the distance of Trp2-Tyr8.

Amino Acid Sequence↗

De novo design, synthesis, and characterization of a pore-forming small globular protein and its insertion into lipid bilayers.

The question of how to design a water-soluble globular protein remains. We report here the synthesis of a native-like and pore-forming small globular protein (SGP, 69 amino acid residues). The protein was designed to have four helices: a Trp-containing short hydrophobic helix in the middle surrounded by three Tyr-containing long basic amphiphilic helices. Size-exclusion chromatography and CD measurements indicated that in buffer solution SGP is monomeric with a 50% helical structure. SGP did not completely denature even at high temperature (90 degrees C) and at relatively high Gu x HCl concentration so that the denaturant concentration at the midpoint of the transition is 5 M. Dye binding studies and fluorescence energy transfer experiments showed that SGP possesses a hydrophobic binding site and its Trp of the central helix is present at a relatively hydrophobic region and accepts the energy from Tyr(s) in other amphiphilic helices, indicating that SGP takes a stable globular-like structure in aqueous solution. From the depth-dependent fluorescent studies using egg PC liposomes containing n-doxyl fatty acids and brominated phospholipid as quenchers, it was found that the hydrophobic central alpha-helix is able to enter spontaneously into the lipid bilayers and the Trp in the central alpha-helix is located at about the middle of the alkyl chain in the outer layer of the phospholipid bilayer. The peptide is also able to increase the membrane permeability with two modes of current (basal current and single ion channel) in planar phospholipid bilayers, indicating the spontaneous insertion of the protein into the lipid bilayer (basal current) and then the formation of a uniform size of channel pore (14 pS). SGP is useful as a basic and starting model to find good amino acid sequences that fold to a desired protein structure and to search translocation mechanisms from aqueous solution into lipid bilayers.

Amino Acid Sequence↗

Micelle Formation of Dodecylammonium Surfactant with Mixed Counterions: Perfluorocarboxylate and Alkanesulfonate Ions

Micelle formation was studied for four mixing combinations of dodecylammonium (DA) salts having perfluorocarboxylate ions (trifluoroacetate (PA) and pentafluoropropionate (PP) and alkane sulfonate ions (methane sulfonate (MS) and ethane sulfonate (ES)) as their counterions, i.e., DAPA/DAMS, DAPA/DAES, DAPP/DAMS, and DAPP/DAES. The fluorocarbon anions as counterions exhibited that the degree of counterion binding to micelle (beta) as well as the extent of stabilizing micelles and lowering ability of critical micellization concentration (CMC) are greater than hydrocarbon anions. The "mixed micelle formation" was examined in terms of CMC as a function of mole fraction (Xi) in each surfactant mixture. The CMCs of the mixed surfactant systems studied here, correspond to those of "surfactant with mixed counterions". However, by regarding tentatively those combinations as binary mixed surfactant systems, the CMC vs Xi curves (singly dispersed phase curves) as well as CMC vs micellar composition (Yi) curves (micellar phase curves) were simulated by applying the present authors' and Rubingh's equations which have been derived respectively with and without taking into account mutual added-salt effect (or the beta value for each pure system). A negative deviation from ideal mixing was observed for each combination, indicating that mixing of fluorocarbon anion with hydrocarbon anion as counterion of DA salts results in more stabilized micelle formation. Plotting the derivative of specific conductance (kappa) by total concentration of surfactant (Ct), dkappa/dCt against Ct, the curves showed a constant value at the sufficiently higher concentration range than CMC, and the constant values were found able to be related to the degree of dissociation of micelles (alpha). Even for the mixed systems, the alpha or beta values were estimated from the conductivity data. The greater power to stabilize micelle formation by fluorocarbon ions was interpreted on the basis of concept of "contact hydrophobic interaction" proposed by Mukerjee (Mukerjee, P., Colloids Surf. A: Physicochem. Eng. Aspects 84, 49 (1994)).

Journal Article↗

Scaling regions for food web properties.

The robustness of eight common food web properties is examined with respect to web size. We show that the current controversy concerning the scale dependence or scale invariance of these properties can be resolved by accounting for scaling constraints introduced by webs of very small size. We demonstrate statistically that the most robust way to view these properties is not to lump webs of all sizes, but to divide them into two distinct categories. For the present data set, small webs containing 12 or fewer species exhibit scale dependence, and larger webs containing more than 12 species exhibit scale invariance.

Journal Article↗

Mixed Monolayer Properties of Tetradecanoic Acid with n-Perfluorocarboxylic Acids with 10, 12, 14, 16, and 18 Carbon Atoms

Surface pressure (pi) and surface potential (DeltaV)-area (A) isotherms were obtained for mixed monolayers of different perfluorocarboxylic acids (FCs) with a hydrocarbon fatty acid, tetradecanoic acid (HC14), on a substrate solution of pH 1.0 as a function of compositions in the mixture by employing the Langmuir method and the ionizing electrode method. Data for the mixed monolayers were analyzed in terms of the additivity rule. Judging from Matuo's classification of two-dimensional phase diagrams, our phase diagrams might be classified into three types. The first is a positive azeotrope type; the combinations of tetradecanoic acid (HC14) with perfluorodecanoic acid (FC10) and with perfluorododecanoic acid (FC12) seem miscible with each other. The second is a completely immiscible type; the combination of perfluorotetradecanoic acid (FC14) and tetradecanoic acid. The third might be a eutectic type, to which the combinations of HC14 with FC16 and with FC18 are assigned; they are miscible in the expanded state but immiscible in the condensed state. Furthermore, the data on the mean molecular area, the surface dipole moment, and the phase diagrams constructed enabled us to estimate the molecular orientation of the respective acids in the mixed monolayer state.

Journal Article↗

Design and synthesis of amphiphilic alpha-helical model peptides with systematically varied hydrophobic-hydrophilic balance and their interaction with lipid- and bio-membranes.

Five amphiphilic alpha-helical peptides of 18 residues containing a hydrophobic Trp residue as a fluorescence probe were designed. The peptides were made up of hydrophobic Leu and hydrophilic Lys residues of a ratio of 13:5, 11:7, 9:9, 7:11, and 5:13 (abbreviated as Hels 13-5, 11-7, 9-9, 7-11, and 5-13, respectively). These peptides generate ideal amphiphilic alpha-helical structures, which have systematically varied hydrophobic-hydrophilic balance (relative amphiphilic potential) as a result of different hydrophobicities and almost the same hydrophobic moments. Their hydrophobic-hydrophilic balance was estimated both theoretically from the calculated hydrophobicity values (or the magnitude of hydrophobic faces) and experimentally from the retention times in reverse phase high-performance liquid chromatography (RP-HPLC). Circular dichroism, liposome-lytic, and Trp-fluorescent studies in buffer and in the presence of acidic and neutral liposomes clearly showed that the increasing hydrophobic face area not only increases the affinity for lipid but also increases the trend of self-association. The structure-activity relationship estimated by means of leakage ability and hemolytic activity demonstrated that the model- and bio-membrane perturbation ability is completely parallel to the magnitude of the hydrophobic face area. The lipid-binding study in guanidine hydrochloride solution showed that the peptides with a hydrophobic face larger than the hydrophilic face (Hels 13-5 and 11-7) immerse their hydrophobic regions in lipid bilayers and that the inverse ones (Hels 7-11 and 5-13) interact only between the anionic lipid head groups and cationic peptide residues on liposome surfaces. The peptide Hel 9-9, which has exactly the same hydrophobic and hydrophilic regions, was found to be at a critical boundary among these peptides in terms of (1) behavior of peptide self-aggregation in buffer solution and membrane perturbation ability, (2) transfer from bulk solution to neutral lipid bilayers, and (3) necessity of charge interaction in lipid-peptide binding.

Amino Acid Sequence↗

Nonlinear control of heart rate variability in human infants.

Nonlinear analyses of infant heart rhythms reveal a marked rise in the complexity of the electrocardiogram with maturation. We find that normal mature infants (gestation greater than or equal to 35 weeks) have complex and distinctly nonlinear heart rhythms (consistent with recent reports for healthy adults) but that such nonlinearity is lacking in preterm infants (gestation > or = to 27 weeks) where parasympathetic-sympathetic interaction and function are presumed to be less well developed. Our study further shows that infants with clinical brain death and those treated with atropine exhibit a similar lack of nonlinear feedback control. These three lines of evidence support the hypothesis championed by Goldberger et al. [Goldberger, A.L., Rigney, D.R. & West, B.J. (1990) Sci. Am. 262, 43-49] that autonomic nervous system control underlies the nonlinearity and possible chaos of normal heart rhythms. This report demonstrates the acquisition of nonlinear heart rate dynamics and possible chaos in developing human infants and its loss in brain death and with the administration of atropine. It parallels earlier work documenting changes in the variability of heart rhythms in each of these cases and suggests that nonlinearity may provide additional power in characterizing physiological states.

Atropine↗