Circular dichroism studies of the B goes to A conformational transition in seven small DNA restriction fragments containing the Escherichia coli lactose control region.

The B goes to A conformational transition caused by high ethanol concentrations was studied for seven DNA restriction fragments with overlapping and known sequences. Since the DNAs are homogeneous and range in GC content from 44-63%, they permit an evaluation of the influence of DNA sequence and base composition on the B goes to A transition. Moreover, their small size (80-301 bp) minimizes precipitation artifacts. The B- form spectra (in low salt) and the transition toward the C- form (in ethanol concentrations below the B goes to A transition) agree with prior measurements on chromosomal DNAs and are similar for all seven DNAs. At higher ethanol concentrations (80%), all fragments undergo a transition to the A- form as judged by the large increase of the positive CD band at 270 nm. Difference spectra among the fragments reveal minor differences between the A- form spectra. The ethanol concentration necessary to cause this transition is 72 +/- 2% for all fragments, thus excluding a preference of the CAP-, E. coli RNA polymerase-, or lac repressor-binding sequences for the A- form. The kinetics of the B goes to A transition in 80% ethanol are biphasic; the initial rapid transition is an intramolecular B goes to A form shift and the slower transition is an aggregation (but not precipitation) of the DNA     

Temperature-dependent reversible transition of poly(dCdG) · poly(DcdG) in ethanolic and methanolic solutions

Using CD we investigated the transitions of poly(dCdG) · poly(dGdC) from B-to-Z form and from Z-to-Z′ form. We have found experimental conditions that allow the cooperative transition to occur as a function of temperature in ethanolic solutions. The transition is reversible and can be repeated as often as desired. There is no evidence of strand separation during the cooperative transition as monitored by absorbance. For purposes of calculation, we have assumed a two-state model for the B-to-Z transition, although the data indicate that such a model is too simplistic. The calculations allow the estimation of the change in enthalpy per mole of cooperative unit for the transition as a function of ethanol concentration. The values range from ±140 to ±200 kcal/mol for ethanol concentrations between 10 and 20%. Investigations of the noncooperative Z-to-Z′ transition show that it is a reversible two-state transition. The different forms of poly(dCdG) · poly(dGdC) give no scattering contributions to the CD as shown by fluorescent-detected CD or fluorscat techniques. This indicates that the CD spectra are true spectra, and contain no contributions from differential scattering of the polynucleotide. This is particularly significant in the case of the Z′ form, since it exists at high ethanol concentrations (80%) where condensation of polynucleotides can provide large contributions to the CD spectra. Analogous investigations using methanol show that the two transitions also occur, but the final Z′ form in methanol is qualitatively different from the ethanol form.     

Calorimetric studies of lipid tubule formation from ethanol-water solutions.

We have used differential scanning calorimetry to systematically investigate the thermal formation of hollow cylindrical crystalline microstructures or 'tubules' upon cooling a diacetylenic phosphatidylcholine (1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine) dispersed in varying volume fractions of ethanol/water. Tubule formation is characterized by a large exothermic event, observed upon cooling the lipid in 60-80% ethanol. The enthalpy of the transition was observed to be highest in this window of tubule formation (128-138 J/g) which is significantly higher than previously reported values for the enthalpy of tubule formation in water (90 -95 J/g). The enthalpy associated with the formation of tubules in 70% ethanol was also found to be strongly dependent on the efficiency of tubule formation and decreased as the number density of tubules decreased. A significant decrease in tubule number density could be brought about by increasing the lipid concentration of the 70% ethanol solution. Tubule number density was maximized at lipid concentrations between 0.5 and 2 mg/ml in 70% ethanol. Examination of the C-H stretch region from infrared spectra of the lipid below the phase transition, indicate that the intramolecular chain order-disorder is similar, regardless of the fraction of ethanol. The higher transition enthalpy for the melting of tubules in 60-80% ethanol (compared to water) implies that the high-temperature phase from which the tubules form in ethanol is more disordered than the lamellar liquid crystalline phase from which tubules form in water.     

On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule.

The degree of orientation of DNA in a flow has been studied within the interval of the B - A transition induced by ethanol. The orientation of the B DNA (60-65% ethanol, v/v) and that of the A DNA (80-82% ethanol) are nearly identical. This means that both conformations have similar persistence lengths and that there is no aggregation in the course of formation of the A form. Within the transition range (65-78% ethanol) the orientation attains a sharp minimum which coincides with the half-transition point (73% ethanol). The cooperative character of the B - A transition presupposes the existence of boundaries between the alternating sections of the A and B conformations that may entail an increased flexibility of the DNA molecule and a corresponding drop of orientation. Theory predicts an elliptical dependence of the number of boundaries on the proportion of the A form. The experimental degree of orientation follows the same pattern. Quantitative evaluation shows that the flexibility of a boundary is small, so that several dozen of boundaries are required to simulate free rotation.     

Potentiometric titration of poly-L-lysine: the coil-to-beta transition

We have performed potentiometric titrations of poly-L -lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α-helix in 10% ethanol (?120 and ?120 cal/mole) and from the random coil to the β-structure in water (?140 and 870 cal/mole) and in 10% ethanol (?180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α- helix transition in water (?78 and ?880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α-helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α-helix to β-structure, obtained by subtracting those for the coil → α-helix and coil → β-structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β-structure than in the α-helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β-structure as compared with the α-helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β-structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α-helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.     

Design and synthesis of a helix heparin-binding peptide.

Elaboration of heparin-protein-binding interactions is necessary to understand how heparin modulates protein function. The heparin-binding domain of some proteins is postulated to be a helix structure which presents a surface of high positive charge density. Thus, a synthetic 19-residue peptide designed to be alpha-helical in character was synthesized, and its interaction with heparin was studied. The peptide was shown to be 75% helix by circular dichroism (CD) spectrometry in neutral pH buffer (at 2 degrees C); helicity increased to nearly 85% under high ionic strength conditions or to nearly 100% in 75% ethanol. Increasing the temperature of the solution caused a change in the spectral envelope consistent with a coil transition of the peptide. The midpoint of the transition (i.e., the temperature at which the helix content was determined to be 50%) was 25 degrees C, and the determined van't Hoff enthalpy change (delta HvH) was 3.2 kcal/mol of peptide. By CD, heparin increases the helix content of the peptide to 100% and increases the apparent thermal stability of the peptide by about 1 kcal/mol. The melting point for the helix/coil transition of the heparin-peptide complex was 50 degrees C. The thermal coefficient of the transition (approximately 300 deg.cm2.dmol-1.degree C-1) was essentially the same for the peptide alone or the peptide-heparin complex. Dissociation of the complex under high ionic strength conditions was also observed in the CD experiment. Biological assays showed less heparin-binding activity than expected (micromolar KD values), but this was attributed to the absence of critical lysyl residues in the peptide.(ABSTRACT TRUNCATED AT 250 WORDS)     

A direct demonstration that the ethanol-induced transition of DNA is between the A and B forms: an X-ray diffraction study

DNA undergoes a reversible co-operative change in a number of its properties over a characteristic range of ethanol concentrations. This ethanol-induced transition of DNA has been studied by a number of groups, using circular dichroism as well as other assay techniques. There has been disagreement as to the species of DNA involved. We have used X-ray diffraction methods on DNA fibers exposed to an excess of solvent. The diffraction patterns serve as “fingerprints” to clearly show that the transition occurs between the B and A forms of DNA (at low and high ethanol concentrations, respectively) in agreement with the conclusions of some of the previous workers. At still higher ethanol concentrations, the diffraction pattern changes from that of the A form to that of a more disordered form.     

Irreversible formation of pseudohyphae by haploid Saccharomyces cerevisiae

Abstract Culturing haploid strains of Saccharomyces cerevisiae in liquid minimal medium with 2% ethanol and 2% leucine resulted in the formation of long anucleate pseudohyphae. This occurred only with the combination of ethanol as carbon source and leucine as nitrogen source and was independent of mating type. The transition to a pseudohyphal form observed under these conditions appears to be irreversible. These findings further extend our view of the developmental alternatives in this important model eukaryote.     

Studies on the aggregation and possible channel formation in membranes of a cyclic hexapeptide, cyclo (D-Ala-L-Pro-L-Ala)2.

The interaction of zwitterionic lipid DMPC and DPPC with cyclic hexapeptide, cyclo (D-Ala-L-Pro-L-Ala)2 was studied using circular dichroism (CD) and differential scanning calorimetry (DSC). Preliminary membrane conductance results showed that the peptide has a tendency to form channels inside the lipid bilayer. CD studies indicated that as the lipid/peptide (L/P) ratio (DMPC/peptide) was increased, the magnitude of the negative CD band having a lambda(max) around 200 nm decreased. At a L/P ratio of 210:1, this band disappeared completely, indicating dramatic conformational changes in the peptide on interaction with the lipid bilayer. Reduction of the phase transition temperature and the maximum heat capacity of the lipid bilayer (DPPC) for gel-to-liquid crystalline phase transition indicates a strong interaction of the peptide with the lipid bilayer.     

Mechanism of membrane activity of the antibiotic trichogin GA IV: a two-state transition controlled by peptide concentration

Synthetic fluorescent analogs of the natural lipopeptide trichogin GA IV were used to investigate the peptide position and orientation in model membranes. A translocation assay based on Forster energy transfer indicates that trichogin is associated to both the outer and inner leaflet of the membrane, even at low concentration, when it is not active. Fluorescence quenching measurements, performed by using water soluble quenchers and quenchers positioned in the membrane at different depths, indicate that at low membrane-bound peptide/lipid ratios trichogin lies close to the region of polar headgroups. By increasing peptide concentration until membrane leakage takes place, a cooperative transition occurs and a significant fraction of the peptide becomes deeply buried into the bilayer. Remarkably, this change in peptide position is strictly coupled with peptide aggregation. Therefore, the mechanism of trichogin action can be envisaged as based on a two-state transition controlled by peptide concentration. One state is the monomeric, surface bound and inactive peptide, and the other state is a buried, aggregated form, which is responsible for membrane leakage and bioactivity.     

Circulating neuropeptide Y in dog plasma consists of multiple peptide fragments

Neuropeptide Y-like immunoreactivity (NPY-LI) in dog plasma was characterized and quantified using three extraction methods (Sep-Pak:acetonitrile, HCl:ethanol, and ethanol). Sep-Pak extraction yields the best recovery and preserves the integrity of the peptide. Oxidized NPY is not generated during blood collection. Using two antisera of different specificities, at least three peptide forms in normal dog arterial and venous plasma were detected. A peptide with retention times similar to oxidized NPY or peptide YY is the major component of plasma NPY-LI under basal conditions, but NPY(1–36) predominates during sympathetic stimulation. The mature peptide in dog plasma is similar to human NPY. The antiserum ABII provides a more accurate measure of circulating NPY(1–36) and its oxidized form. The antiserum ABI is useful for detecting NPY-like fragments.     

Mutational analysis of designed peptides that undergo structural transition from alpha helix to beta sheet and amyloid fibril formation

BACKGROUND: Conformational alteration and fibril formation of proteins have a key role in a variety of amyloid diseases. A simplified model peptide would lead to a better understanding of underlying mechanisms whereby protein misfolding and aggregation occur. Recently, we reported the design of peptides that undergo a self-initiated structural transition from an alpha helix to a beta sheet and form amyloid fibrils. In this study, we focus on two glutamine residues in the peptide, and report a mutational analysis of these residues. RESULTS: A coiled-coil alpha-helix structure bearing a hydrophobic adamantanecarbonyl (Ad) group at the N terminus was designed (parent peptide Ad-QQ). In neutral aqueous solution, the double Gln-->Ala mutant (Ad-AA) underwent the alpha-->beta structural transition within four hours, which was similar to the case of Ad-QQ. In contrast, two kinds of single Gln-->Ala mutant (Ad-QA and Ad-AQ) required three days for the transition. Furthermore, Ad-QQ and Ad-AA formed amyloid fibrils, whereas Ad-QA and Ad-AQ did not. Interestingly, however, Ad-QA and Ad-AQ complementarily assembled into the fibrils when they were mixed. CONCLUSIONS: The Gln-->Ala substitution in the peptide significantly alters the alpha-->beta transitional properties and the ability to form amyloid fibrils. A heterogeneous assembly of two peptide species into the fibrils is also presented. These results suggest that the secondary structural transition and self-assembly into the well-organized fibril may depend strictly on the primary structure, which determines the beta-sheet packing. The results might provide insights into misfolding and fibril formation of disease-associated mutant proteins.     

Interaction of atriopeptin III with lipids and detergents

Atriopeptin III, a potent natural hypotensive agent, contains little alpha-helical structure but substantial amounts of beta-structure. The peptide can self-associate at millimolar concentrations or can associate with the anionic phospholipid, dimyristoylphosphatidylglycerol. Both of these processes are accompanied by a conformational change suggesting the formation of an increased amount of beta-structure. The peptide can broaden the transition and lower the transition enthalpy of dimyristoylphosphatidylglycerol. The results demonstrate that a peptide hormone can associate with lipid largely in the form of a beta-structure.     

The effects of ethanol on the structural stability of acetylcholine receptor and the activity of various molecular forms of acetylcholinesterase

The actions of ethanol on the structural stability of acetylcholine receptor (AchR)-enriched membrane vesicles and the activity of various molecular forms of acetylcholinesterase (AchE) were investigated, using the receptor and the enzyme isolated from the electric organ of Torpedo californica. In the presence of ethanol up to 200 mM, the thermogram of AchR-enriched membranes exhibited no significant decrease in the temperature (td) of receptor transition at 57 degrees C, but a decrease in the enthalpy change (delta Hd) indicated a slight ethanol-induced structural perturbation. The presence of 12.5 nmol alpha-bungarotoxin also caused a decrease in delta Hd. A complete loss of the receptor transition was observed at a higher concentration 500 nmol of alpha-bungarotoxin and no recovery of the transition was found with the addition of 200 mM ethanol. The results suggested a noncompetitive interaction of ethanol with the receptor. In the presence of 200-1000 mM ethanol, the activity of two soluble forms of AchE, a higher (117 S) aggregate and a lower (10 S) aggregate was not significantly affected. Comparing the activity of these two aggregates over a wide concentration range of ethanol (200-2000 mM) revealed no obvious difference in the level of ethanol effect between them. However, after removal of ethanol, the higher aggregate form of AchE exhibited a greater recoverability of the activity, suggesting a possible slightly greater structure-functional stability for it. Studies of soluble AchE and membrane-bound AchE showed that the presence of 200 or 600 mM ethanol caused a greater level of inhibition in membrane-bound enzyme than in soluble enzyme, possible due to a disruption of protein-lipid interaction needed to maintain the conformation of membrane-bound AchE. Interestingly, at a much higher concentration of ethanol (2.0 M), membrane-bound AchE became more resistant to ethanol than did the soluble forms of AchE. In this case, the effective concentration of ethanol felt by the enzyme was expected to be less for membrane-bound AchE, owing to ethanol's solubility in lipids.     

Temperature dependence of optical properties of aqueous dispersions of phosphatidylcholine

Aqueous dispersions of dipalmitoyl phosphatidyl choline exhibit a sharp decrease in turbidity at the crystal-liquid phase transition temperature of 41°C. The intensity of light scattered at 45°, 90°, and 135° also undergoes a sharp drop at the same temperature. Similarly, the refractive index of such dispersions decreases abruptly with the phase transition. Employing the relationship between light scattering intensity and specific refractive increment, it can be shown that about one half of the change in absorbancy and scattering are accounted for by the change in refractive index. The change in refractive index can be entirely accounted for by the known expansion and corresponding decrease in density of the bilayer. That part of the observed change in scattering and turbidity which is not accounted for by the observed change in average refractive index is apparently due to a decrease in the anisotropy of the bilayer during the melting process. Calculations based on a model which, although oversimplified, is consistent with the known thinning of the bilayer during the melting process, give quantitative agreement with experimental results. Below the phase transition temperature other changes in optical properties are observed; near 32°C, the light scattering envelope changes and the turbidity of dispersions drops markedly. The average refractive index remains constant in this region. For this and other reasons, it is postulated that these pre-transition changes indicate an aggregation-disaggregation phenomenon.     

Mechanochemical study of NaDNA and NaDNA-netropsin fibers in ethanol-water and trifluoroethanol-water solutions.

Highly oriented calf-thymus NaDNA fibers, prepared by a wet-spinning method, were complexed with netropsin in ethanol-water and trifluoroethanol (TFE)-water solutions. The relative fiber length, L/L0, was measured at room temperature as a function of ethanol or TFE concentration to obtain information on the B-A conformational transition. The B-A transition point and transition cooperativity of the fibers were calculated. The binding of netropsin to NaDNA fibers was found to stabilize B form and to displace the B-A transition to higher ethanol concentration, as indicated by its elongational effect on the fiber bundles. An increased salt concentration was found to reduce netropsin binding. In netropsin-free ethanol solution, the dissociation of bound netropsin from the DNA fibers was observable. Pure B-NaDNA fibers were found to be more stable in TFE solution than in ethanol solution. This was interpreted as being due to a different steric factor and a larger polarity of TFE compared with ethanol, resulting in its smaller capacity to reduce the water activity and dielectric constant of the medium in the immediate vicinity of DNA fibers. Therefore, the effect of netropsin binding on the B-A transition of NaDNA fibers became less obvious in TFE solution. In another series of experiments, L/L0 was measured as a function of temperature to obtain information on the helix-coil transition, or melting, as well as the B-A transition of NaDNA and NaDNA-netropsin fibers. The melting temperature and helix-coil transition width were calculated from the melting curves. A phenomenological approach was used to describe the melting behavior of the fibers in and around the B-A transition region. The effect of netropsin on the melting of DNA fibers was attributed mainly to the stabilization of B-DNA and to a higher melting cooperativity in the B-DNA region.     

Minimal transition state charge stabilization of the oxyanion during peptide bond formation by the ribosome

Peptide bond formation during ribosomal protein synthesis involves an aminolysis reaction between the aminoacyl α-amino group and the carbonyl ester of the growing peptide via a transition state with a developing negative charge, the oxyanion. Structural and molecular dynamic studies have suggested that the ribosome may stabilize the oxyanion in the transition state of peptide bond formation via a highly ordered water molecule. To biochemically investigate this mechanistic hypothesis, we estimated the energetic contribution to catalytic charge stabilization of the oxyanion using a series of transition state mimics that contain different charge distributions and hydrogen bond potential on the functional group mimicking the oxyanion. Inhibitors containing an oxyanion mimic that carried a neutral charge and a mimic that preserved the negative charge but could not form hydrogen bonds had less than a 3-fold effect on inhibitor binding affinity. These observations argue that the ribosome provides minimal transition state charge stabilization to the oxyanion during peptide bond formation via the water molecule. This is in contrast to the substantial level of oxyanion stabilization provided by serine proteases. This suggests that the oxyanion may be neutralized via a proton shuttle, resulting in an uncharged transition state.     

A comparison of the interaction of glucagon, human parathyroid hormone-(1-34)-peptide and calcitonin with dimyristoylphosphatidylglycerol and with dimyristoylphosphatidylcholine

The interaction of glucagon, human parathyroid hormone-(1-34)-peptide and salmon calcitonin with dimyristoylphosphatidylglycerol (DMPG) and with dimyristoylphosphatidylcholine (DMPC) was studied as a function of pH and temperature. The effect of lipid on the secondary structure of the peptide was assessed by circular dichroism and the effect of the peptide on the phase transition properties of the lipid was studied using differential scanning calorimetry. Some peptides interact more strongly with anionic than with zwitterionic phospholipids. This does not require an overall positive charge on the peptide. Increased thermal stability is observed in complexes formed between cationic peptides and anionic lipids. Particularly marked effects of glucagon and human parathyroid hormone-(1-34)-peptide on the phase transition properties of DMPG at pH 5 have been observed. The transition temperature is raised over 10 degrees C at a lipid/peptide molar ratio of less than 30:1 and the transition enthalpy is increased over 2-fold. These effects do not occur with any basic peptide and were not observed with metorphinamide, molluscan cardioexcitatory neuropeptide or myelin basic protein. The results demonstrate that certain peptides can affect the phase transition properties of lipids in a manner similar to divalent cations. The overall hydrophobicities of these peptides can be evaluated by their partitioning between aqueous and organic solvents. None of the above three peptide hormones partition into the organic phase. However, a closely related peptide, human calcitonin, does exhibit substantial partitioning into the organic phase. Nevertheless, human calcitonin has a weaker interaction with both DMPC and DMPG than does salmon calcitonin. The effects of human calcitonin on the phase transition of DMPC are qualitatively different from those of salmon calcitonin in that the human form more readily eliminates the pretransition but causes less change in the main transition. Like overall charge, overall hydrophobicity is not an overwhelming factor in determining the ability of peptides to interact with phospholipids but rather more specific interactions are required for strong complexes to form.     

Light waveguiding in bioinspired peptide nanostructures

Basic optical properties of bioinspired peptide nanostructures are deeply modified by thermally mediated refolding of peptide secondary structure from α‐helical to β‐sheet. This conformational transition is followed by the appearance in the β‐sheet structures of a wideband optical absorption and fluorescence in the visible region. We demonstrate that a new biophotonic effect of optical waveguiding recently observed in peptide/protein nanoensembles is a structure‐sensitive bimodal phenomenon. In the primary α‐helical structure input, light propagates via optical transmission window demonstrating conventional passive waveguiding, based on classical optics. In the β‐sheet structure, fluorescent (active) light waveguiding is revealed. The latter can be attributed to completely different physical mechanism of exciton‐polariton propagation, characterized by high effective refractive index, and can be observed in nanoscale fibers below diffraction limit. It has been shown that peptide material requirements for passive and active waveguiding are dissimilar. Original biocompatibility and biodegradability indicate high potential future applications of these bioinspired waveguiding materials in precise photobiomedicine towards advanced highly selective bioimaging, photon diagnostics, and optogenetics.     

Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers

Many antimicrobial peptides undergo a coil-to-helix transition upon binding to membranes. While this conformational transition is critical for function, little is known about the underlying mechanistic details. Here, we explore the membrane-mediated folding mechanism of an antimicrobial peptide, mastoparan X. Using stopped-flow fluorescence techniques in conjunction with a fluorescence resonance energy transfer (FRET) pair, p-cyanophenylalanine (donor) and tryptophan (acceptor), we were able to probe, albeit in an indirect manner, the membrane-mediated folding kinetics of this peptide. Our results show that the association of mastoparan X with model lipid vesicles proceeds with biphasic kinetics. The first step shows a large change in the FRET signal, indicating that the helix forms early in the time course of the interaction, while the second step where a further increase in tryptophan fluorescence is observed presumably reflects deeper insertion of the peptide into the bilayer. Additional kinetic studies on a double mutant of mastoparan X, designed to form a nucleation site for alpha-helix formation through coordination with a metal ion (e.g., Zn2+ or Ni2+), indicate that while the coil-to-helix transition occurs in the first step, it follows the rate-determining docking of the peptide onto the membrane surface. Taken together, these results indicate that the initial association of the peptide with the membrane occurs in a nonhelical conformation, which rapidly converts to a helical state within the anisotropic environment of the bilayer surface.