Filamentous bacteriophage Pf1 structure determined at 7 Å resolution by refinement of models for the α-helical subunit

The molecular structure of filamentous bacteriophage Pf1 has been determined to 7 Å resolution by analysis of X-ray diffraction data from partially oriented fibers of virus particles. The continuous intensity distribution along layer-lines was measured by numerically separating contributions from overlapping layer-lines. The data were phased by an iterative refinement technique that used the known spatial extent and high α-helical content of the virus particle to refine a structural model. This refinement converges to a unique structural solution that is consistent with the X-ray data and with information derived from physical and chemical studies. The coat protein consists of two α-helical segments: one, almost parallel to the particle axis, is centered at a radius of about 15 Å; the other, at about 25 Å radius, is tilted by about 25 ° to the particle axis. This structure is consistent with every generalization about α-helical packing. The inner and outer segments interlock along most of their length with a crossing angle of 20.5 °. The inner α-helical segments also interact with symmetry-related copies of themselves, as do the outer segments. The double layer of tightly packed, intricately interlocked α-helices forms a stable, 20 Å thick protein coat around the viral DNA.     

Calorimetric measurement of enthalpy change in the isothermal helix--coil transition of poly-L-lysine in aqueous solution

The heat ΔH° for converting an uncharged lysine residue from a coil to an α-helical state in poly-L -lysine in 0.1N KCl has been determined calorimetrically to be ?1200 cal/mole at both 15°C and 25°C. Essentially the same value has been obtained for the conversion of an uncharged residue from a coil to a β-pleated sheet state. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔH°, the observed Calorimetric heat was corrected for the heat of breaking the sample cell, the heal of dilution of HCl, the heat of neutralization of OH^? ion, and the heat of ionization of the ε-amino group in the random coil. The latter was obtained from similar Calorimetric measurements on poly-D ,L -lysine, which was shown to be a good model for the random coil form of poly-L -lysine. The measured transition heat was ～0.7 cal., which is only 7% of the total heat liberated when a 40 ml solution of 0.25% w/v poly-L -lysine is brought, from pH 11 to pH 7; nevertheless it could be determined with a precision of ±8%. The conformation of poly-L -lysine at pH 11 appears to be completely helical at 15°C, but a mixture of 90% α-helix, 5% β form, and 5% coil at 25°C. Since ΔH° ～ 0 for the α ? β conversion, the polymer behaves like one of 95% α-helix and 5% coil in the calorimeter at 25°C. At neutral pH, poly-L -lysine is an extended coil, like poly-D ,L -lysine.     

Pressure perturbation calorimetry of apolipoproteins in solution and in model lipoproteins

High‐density lipoproteins (HDLs) are complexes of lipids and proteins (termed apolipoproteins) that remove cell cholesterol and protect from atherosclerosis. Apolipoproteins contain amphipathic α‐helices that have high content (≥1/3) and distinct distribution of charged and apolar residues, adopt molten globule‐like conformations in solution, and bind to lipid surfaces. We report the first pressure perturbation calorimetry (PPC) study of apolipoproteins. In solution, the main HDL protein, apoA‐I, shows relatively large volume contraction, ΔV_unf = ?0.33%, and an apparent reduction in thermal expansivity upon unfolding, Δα_unf ≤ 0, which has not been observed in other proteins. We propose that these values are dominated by increased charged residue hydration upon α‐helical unfolding, which may result from disruption of multiple salt bridges. At 5°C, apoA‐I shows large thermal expansion coefficient, α(5°) = 15·10^?4 K^?1, that rapidly declines upon heating from 5 to 40°C, α(40°) ? α(5°) = ?4·10^?4 K^?1; apolipoprotein C‐I shows similar values of α(5°) and α(40°). These values are larger than in globular proteins. They indicate dominant effect of charged residue hydration, which may modulate functional apolipoprotein interactions with a broad range of their protein and lipid ligands. The first PPC analysis of a protein–lipid complex is reported, which focuses on the chain melting transition in model HDL containing apoA‐I or apoC‐I, dimyristoyl phosphatidylcholine, and 0–20% cholesterol. The results may provide new insights into volumetric properties of HDL that modulate metabolic lipoprotein remodeling during cholesterol transport. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Studies on the Polymorphism of l-Glutamic Acid

The enthalpy differences between the α- and β-crystals of l-glutamic acid were measured and ΔH_α?β of ?75, ?95, 8 and 27±20cal./mol. were obtained at temperatures of 5, 15, 30 and 40°C, respectively. From this result, it was found that the α-form is the more stable form in solid phase at temperatures lower than 30°C and vice versa when higher than 30°C, though the α-form had been found to be the less stable form as the saturating body in the aqueous solution in all range of temperature.     

Solid-state modifications of poly(γ-ethyl-L-glutamate)

Several modification of the arrangements of α-helical molecules were found in the solid films of poly (γ-ethyl-L -glutamate), depending on the casting solvent and the temperature. The helical conformation is somewhat looser than the normal 18-residue, 5-turn α-helix. Using x-ray diffraction, the types of molecular arrangements were classified into tetragonal, pseudohexagonal, and hexagonal ones. Tetragonal packing was observed in the filmm (form T) prepared by casting the solution in trifluorethanol or dichlorethane. The sample obtained from chloroform solution is a well-ordered, pseudohexagonal modification (form I). Forms I and T change into a poorly crystalline form III by annealing at temperatures above 130° C. It is particularly noteworthy that the less-ordered form III exhibits a thermoreversible transition around 110°C into a well-ordered form H with the hexagonal molecular packing.     

Interaction between chondroitin-6-sulfate and poly-L-arginine in aqueous solution

The interactions between chondroitin-6-sulfate and poly-L -arginine in aqueous salt solution have been investigated by circular dichroism techniques. In the presence of chondroitin-6-sulfate, at neutral pH, poly-L -arginine adopts the α-helical conformation rather than “charged coil” form observed in the absence of mucopolysaccharide. This interaction is at a maximum when the ratio of arginine to disaccharide residues is 2:1. Elevation of the temperature leads to a sharp melting transition at 76.0 ± 1.0°C. This behavior is in marked contrast to that for poly-L -lysine-chondroitin-6-sulfate interactions, which are at a maximum at a 1:1 residue ratio and have a melting transition at 47.0 ± 1.0°C. These results indicate a stronger interaction for poly-L -arginine than for poly-L -lysine. The positive arginine side chains appear to interact with both the negative sulfate and carboxyl residues, while those of the lysines are involved only with the sulfates. Poly-L -ornithine at neutral pH shows no conformation directing interaction with chondroitin-6-sulfate, although a small proportion of α-helix is formed on dilution of the mixture with methanol. The extent of the interaction of cationic polypeptides with chondroitin-6-sulfate increases in the order poly-L -ornithine, poly-L -lysine, poly-L -arginine, i.e., in the order of increasing side-chain length.     

Structure of -lactalbumin and its fluctuation

The kinetics of the hydrogen-deuterium exchange reaction in bovine α-lactalbumin have been followed, by infrared absorption measurement, in aqueous solutions at various pH values and at various temperatures. A thermal transition which takes place at about 60 °C has been examined by ultraviolet absorption measurement and circular dichroism measurement.Outlines of the exchange kinetics and the thermal transition are quite similar to those observed for hen egg-white lysozyme, the amino acid sequence of which is known to be very similar to that of α-lactalbumin. Between these two proteins, however, differences have been found in the following respects. (1) The number of slowly exchanging peptide hydrogen atoms (35 in α-lactalbumin compared with 44 in egg-white lysozyme). (2) Kinetic profile of the slow exchange reaction. (3) The midpoint of the thermal transition (54 °C in water and 58 °C in deuterium oxide for α-lactalbumin, compared with 76 °C in both water and deuterium oxide for egg-white lysozyme). (4) The enthalpy and entropy changes in the transition (72 kcal/mol and 220 e.u., respectively, for α-lactalbumin, compared with 127 kcal/mol and 364 e.u. for egg-white lysozyme). (5) The circular dichroic spectrum of the “unfolded” molecule. (6) The effective amount of the unfolded forms estimated from the kinetic measurement at temperatures slightly lower than the transition temperature. (7) The effect of pH on the exchange kinetics.These differences between the proteins are interpreted in terms of the molecular structures and their fluctuations.     

Conformation of poly-L-tyrosine in aqueous solution

The conformational transition of poly-L -tyrosine in 0.1M KCl was investigated by ORD and infrared spectroscopy, potentiometric titration, and sedimentation velocity experiments. It is shown that the fully ordered conformer is obtained by slow titration of the random coil with 0.1N HCl at 25°C. The charge-induced transition, at variance with other poly-α-amino acids, is completed in a narrow range of α. An aggregation process was detected both by potentiometric titration and sedimentation velocity. The polyamino acid aggregates around α = 0.7 at 25°C when the conformational transition is almost complete. Infrared spectra, in the region of the amide I band (1650 cm^?1) showed that the transition is a random coil → antiparallel β one. Evidence exists that the form is of the intramolecular type. The foregoing interpretations of ORD and CD spectra in terms of the α-helix conformation are discussed.     

Volume and sound velocity changes accompanying the -helix to -form and coil to -helix transitions in aqueous solution

The volume increment per amino acid residue for the α-helix to β-form transition of uncharged poly-L -lysine in aqueous solution was 3.8 ml in water and 4.3 ml in 0.2M and 1M NaBr solutions at 26°C, respectively. The sound velocity of the polymer solution was greater with the β-helix than with the β-form, but the difference was less in dilute salt solutions and disappeared in 1 or 2M NaBr solution. Thus, the β poly-L -lysine solution was slightly more compressible than the α-polymer solution, but this difference was diminished with increasing salt concentration. Both the volume change and the change in adiabatic compressibility of the polymer solution suggest that hydrophobic interactions among the lysyl groups in the β-form reduce the amount of “icebergs” surrounding the polymer molecules as compared with the amount originally present with the α-helix. The coil-to-helix transition of poly-L -glutamic acid in aqueous solution was also accompanied by a decrease in sound velocity. This can be attributed to the reduction of the water of hydration which is less compressible than free water.     

Hydrodynamic behavior and molecular conformation of poly(L-lysine HBr) in carbonate buffer solution

In carbonate buffer at pH 10.5, a transparent solution of poly(L -lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L -lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.     

Thermal Inactivation and Product Inhibition of Aspergillus terreus CECT 2663 α-L-Rhamnosidase and Their Role on Hydrolysis of Naringin Solutions

The kinetics of thermal inactivation of A. terreus α-rhamnosidase was studied using the substrate p-nitrophenyl α-L-rhamnoside between 50°C and 70°C. Up to 60°C the inactivation of the purified enzyme was completely reversible, but samples of crude or partially purified enzyme showed partial reversibility. The presence of the product rhamnose, the substrate naringin, and other additives reduced the reversible inactivation, maintaining in some cases full enzyme activity at 60°C. A mechanism for the inactivation process, which permitted the reproduction of experimental results, was proposed. The products rhamnose (inhibition constant, 2.1 mM) and prunin (2.6 mM) competitively inhibited the enzyme reaction. The maximum hydrolysis of supersaturated naringin solution, without enzyme inactivation, was observed at 60°C. Hydrolysis of naringin reached 99% with 1% naringin solution, although the hydrolysis degree of naringin was only 40% due to products inhibition when the initial concentration of flavonoid was 10%. The experimental results fitted an equation based on the integrated Michaelis-Menten's, including competitive inhibition by products satisfactorily.     

Subzero temperature study of the inner mitochondrial membrane and related phospholipid membrane systems with the fluorescent probe, trans-parinaric acid

The fluorescence intensity of trans-parinaric acid as a function of the temperature indicates a phase transition in bovine heart mitochondrial inner membranes below 0°C. The comparison of the dye fluorescence intensity in intact inner mitochondrial membranes and in vesicles from extracted phospholipids of mitochondria revealed a similar intensity increase with decreasing temperature. A synthetic phospholipid system of dioleoyl phosphatidylcholine was investigated because of its low phase transition temperature and showed a very definite intensity change at ?25°C. trans-Parinaric acid in membrane systems probes an environment of intermediate polarity; this was found from the excitation and emission spectra and from fluorescence decay.     

Hormones and liver mitochondria: Influence of growth hormone,thyroxine, testosterone,and insulin on thermotropic effects of respiration and fatty acid composition of membranes

The effects of hypophysectomy and subsequent administration of growth hormone, thyroxine, insulin, and testosterone were examined in rat liver for the relationship between the thermotropic effects on State 3 respiration (ADP induced) and fatty acid composition of the phospholipid fraction of intact mitochondria as well as of inner membrane vesicles. The Arrhenius profile for energy-linked (succinate) State 3 respiration of mitochondria from hypophysectomized rats lacked the discontinuity at 23.5 °C seen with mitochondria from normal rats. After injections of the hormones the discontinuity representing the transition temperature from gel to liquid crystalline state of lipids occurred at different temperatures: 18.5 °C for growth hormone, 26.0 °C for thyroxine, 19.5 °C for growth hormone + thyroxine, 27.6 °C for insulin, and 25.3 °C for testosterone. The energy of activation between 37.5 and 23.5 °C was 1.9 times greater for hypophysectomy than for controls. Growth hormone was the most effective in restoring the energy of activation to normal, above as well as below transition temperature. The effect of thyroxine appears to be due to a larger stimulation of the State 4 respiration than that of growth hormone, insulin, or testosterone, especially at higher temperatures. Phospholipids extracted from intact mitochondria or inner membrane vesicles of hypophysectomized rats contained less arachidonic acid (20:4) and more linoleic acid (18:2) than those of normal rats. In addition, the contents of some of the minor fatty acids were also changed. Calculated unsaturation index showed an 18.8 and 14.9% depletion in unsaturation in whole mitochondria and inner membranes, respectively. Among the different hormones used to treat the hypophysectomized rats, growth hormone was the most effective in restoring the transition temperature and fatty acid composition to normal levels and increasing the gain in body weight. Although the other hormones increased total unsaturation index to some extent, some of the individual fatty acids were affected differently. Good correlation exists between the unsaturation index of mitochondrial fatty acids and transition temperature of State 3 respiration. These results strongly suggest a role for the hormones, particularly growth hormone, in the control of mitochondrial membrane fluidity of hypophysectomized rat liver, through fatty acid composition of phospholipids.     

Temperature-dependent stomatal movement in tulip petals controls water transpiration during flower opening and closing

Temperature‐dependent tulip petal opening and closing movement was previously suggested to be regulated by reversible phosphorylation of a plasma membrane aquaporin ( Azad et al., 2004a ). Stomatal apertures of petals were investigated during petal opening at 20°C and closing at 5°C. In completely open petals, the proportion of open stomata in outer and inner surfaces of the same petal was 27 ± 6% and 65 ± 3%, respectively. During the course of petal closing, stomatal apertures in both surfaces reversed, and in completely closed petals, the proportion of open stomata in outer and inner surfaces of the same petal was 74 ± 3% and 29 ± 6%, respectively, indicating an inverse relationship between stomatal aperture in outer and inner surfaces of the petal during petal opening and closing. Both petal opening and stomatal closure in the outer surface of the petal was inhibited by a Ca²⁺ channel blocker and a Ca²⁺ chelator, whereas the inner surface stomata remained unaffected. On the other hand, sodium nitroprusside, a nitric oxide donor, had no effect on stomatal aperture of the outer surface but influenced the inner surface stomatal aperture during petal opening and closing, suggesting different signalling pathways for regulation of temperature‐dependent stomatal changes in the two surfaces of tulip petals. Stomata were found to be differentially distributed in the bottom, middle and upper parts of tulip petals. During petal closing, water transpiration was observed by measuring the loss of ³H₂O. Transpiration of ³H₂O by petals was fivefold greater in the first 10 min than that found after 30 min, and the transpiration rate was shown to be associated with stomatal distribution and aperture. Thus, the stomata of outer and inner surfaces of the petal are involved in the accumulation and transpiration of water during petal opening.     

Melting behaviour of a triple helical polysaccharide schizophyllan in aqueous solution

Two sonicated samples of schizophyllan in aqueous solution at temperatures from 20 to 160°C were investigated by viscometry. The temperature dependence of the viscosity coefficient η showed that schizophyllan in water undergoes an irreversible thermal transition at about 135°C. The values of $\text{(ln η}{}_{\mathrm{r}}\text{)}\text{c}$ (ηr is the relative viscosity and c is the polymer concentration (w/v)) at 25°C determined after preheating aqueous schizophyllan indicated that the major conformations of schizophyllan in water at 120 and 150°C are triple helix and single random coil, respectively. Thus, it was concluded that the change in η at about 135°C with an increase in temperature is due to the melting of triple helices to single chains. Schizophyllan denatured to single chains at about 150°C did not restore the intact triple helix, but formed aggregates, when the solution was cooled to 25°C. It was also found that the aggregates form a gel when c is higher than a certain value.     

Flow-induced conformational changes and phase behavior of aqueous poly-L-lysine solutions

Poly-L -lysine exists as an α-helix at high pH and a random coil at neutral pH. When the α-helix is heated above 27°C, the macromolecule undergoes a conformational transition to a β-sheet. In this study, the stability of the secondary structure of poly-L -lysine in solutions subjected to shear flow, at temperatures below the α-helix to β-sheet transition temperature, were examined using Raman spectroscopy and CD. Solutions initially in the α-helical state showed time-dependent increases in viscosity with shearing, rising as much as an order of magnitude. Visual observation and turbidity measurements showed the formation of a gel-like phase under flow. Laser Raman measurements demonstrated the presence of small amounts of β-sheet structure evidenced by the amide I band at 1666 cm⁻¹. CD measurements indicated that solutions of predominantly α-helical conformation at 20°C transformed into 85% α-helix and 15% β-sheet after being sheared for 20 min. However, on continued shearing the content of β-sheet conformation decreased. The observed phenomena were explained in terms of a “zipping-up” molecular model based on flow enhanced hydrophobic interactions similar to that observed in gel-forming flexible polymers. © 1998 John Wiley & Sons, Inc. Biopoly 45: 239–246, 1998     

Radioreceptor Assay for α;-Msh Using Mouse B16 Melanoma Cells

Abstract

A radioreceptor assay for α;-MSH is described which is based on cultured mouse B16 melanoma cells and bioactive monoiodinated [Nle⁴]-α;-MSH tracer. The assay was used (1) to study the binding characteristics of α;-MSH to B16 cells, (2) to determine the relative binding activity of MSH peptides, and (3) to measure MSH in tissue extracts. The association of α;-MSH to B16 cells reached a stable plateau after 3 h at 15°C. At 25° or 37°C, the binding was transient and at 0-1°C, the association was very slow. The hormone-receptor complex was relatively stable between 0° and 15°C whereas a 50% dissociation was reached after 90 min at 25°C and after 35 min at 37°C. The mean K_D for α;-MSH of four saturation experiments was 1.3 nM and the number of receptors 9570 per cell. 1,10-Phenanthroline had a stabilizing effect in the binding assay when used at a 0.3 mM concentration. From the MSH peptides tested in the binding assay, some showed similar potencies in three bioassays (tyrosinase, melanin and Anolis skin), whereas others displayed considerably     

Oxidative properties of swollen rat liver mitochondria.

Rat liver mitochondria undergo extensive swelling when they are incubated in hypotonic sucrose medium containing 5 mm P_i. After 30 min of swelling at 25 °C, a three- to fourfold increase in volume has occurred, accompanied by gross disorganization of the matrix as observed by electron microscopy. Succinate-supported respiration was unchanged, but the respiration of NAD-linked substrates was reduced and there was a complete and irreversible loss of phosphorylation in both cases. β-Hydroxybutyrate-supported respiration was regained completely on addition of NAD to the swollen mitochondria. α-Ketoglutarate- and malate + pyruvate-supported respiration was only partially restored by the addition of NAD. This inhibition of respiration in swollen mitochondria may be due to a disorganization of a putative complex of Krebs cycle enzymes on the inner surface of the inner membrane.     

Temperature effect on retrogradation rate and crystalline structure of amylose

Commercial potato amylose was used to study temperature effects on the retrogradation of amylose solutions (3.5mg/ml). The retrogradation rate decreased as incubation temperature increased (5 to 45 °C). The degree of retrogradation within 24 h decreased from 58.8 to 7.1% as incubation temperature increased from 5 to 45 °C. In the amylose solution, different-sized molecular subfractions retrograded at different rates. After incubating at 5 °C for 100 days, the majority of the amylose molecules retrograded and precipitated from the solution; at 45 °C, only amylose of the small-molecular subfraction (number average, DP_n = 110; weight average, DP_w = 150) retrograded and precipitated. Entanglement of molecules was observed in size exclusion chromatograms. The morphology of retrograded amylose observed by using a scanning electron microscope differed with the retrogradation temperature. The chain length of amylose crystalline segments, prepared by hydrolysis of retrograded amylose, showed a narrow distribution (polydispersity from 1.21 to 1.67). The chain lengths of resistant segments increased DP_n from 39 to 52 and DP_w from 47 to 72 for α-amylolysis and DP_n from 34 to 40 and DP_w from 48 to 67 for 16% sulfuric acid hydrolysis, when incubation temperature increased from 5 to 45 °C.     

Comparison of the enthalpy state of vesicles of different size by their interaction with α-lactalbumin

The characteristics of small unilamellar, large unilamellar and large multilamellar vesicles of dimyristoylphosphatidylcholine and their interaction with α-lactalbumin are compared at pH 4. (1) By differential scanning calorimetry and from steady-state fluorescence anisotropy data of the lipophilic probe 1,6-diphenyl-1,3,5-hexatriene it is shown that the transition characteristics of the phospholipids in the large unilamellar vesicles resemble more those of the multilamellar vesicles than of the small unilamellar vesicles. (2) The size and composition of the lipid-protein complex formed with α-lactalbumin around the transition temperature of the lipid are independent of the vesicle type used. Fluorescence anisotropy data indicate that in this complex the motions of the lipid molecules are strongly restricted in the presence of α-lactalbumin. (3) The previous data and a comparison of the enthalpy changes, $\text{ΔH}$, of the interaction of the three vesicle types with α-lactalbumin allow us to derive that the enthalpy state of the small unilamellar vesicles just below 24°C is about 24 kJ/mol lipid higher than the enthalpy state of both large vesicle types at the same temperature. The abrupt transition from endothermic to exothermic $\text{ΔH}$ values around 24°C for large vesicles approximates the transition enthalpy of the pure phospholipid