Studies of NAD(H) conformations in solution: A new method using the PMR spectra of cobalt ion—dinucleotide complexes

In aqueous solutions of NAD(H), there is an equilibrium between two different conformations : a “folded” conformation in which adenine and nicotinamide are staked together and an “unfolded” conformation in which the two rings are without interaction.The folded conformation is the more stable in aqueous solution whereas in organic solution it is the unfolded one.As we have previously shown, the PMR spectra of Co²⁺—NAD(H) complexes may be related with the coenzyme conformation giving suggest to a new method for NAD(H) conformational analysis.The results of this method applied to methanol ²H₂O and dioxane/²H₂O solutions are reported in this paper: they are in good accordance with those of spectrofluorimetric analysis.     

Beta-turns in bridged proline-containing cyclic peptide models

The synthesis, CD, ir spectroscopic, and conformational studies of a series of bridged cyclic peptides of the general formula, cyclo[NH-(CH₂)_n-CO-Gly-Pro-Y-Gly] (2a–d, Y = Gly or Ser(OBu^t), n = 4 or 2) is reported. As indicated by difference nuclear Overhauser enhancement and Fourier transform ir experiments, the tetrapeptide sequence of cyclo[NH-(CH₂)₄-CO-Gly-Pro-Gly-Gly] (2a) and cyclo[NH-(CH₂)₂-CO-Gly-Pro-Gly-Gly] (2b) adopts a 1 ← 4 hydrogenbonded type II β-turn conformation in solution, while cyclo[NH-(CH₂)₄-CO-Gly-Pro-Ser(OBu^t) -Gly] (2c) features a type I β-turn, fixed by 1 ← 4 and O^γ … NH intramolecular H bonds. In aqueous solution 2a and 2c show class B and class C CD spectra, respectively. This is the first case reported of a typical class C CD pattern in aqueous solution for a conformationally mobile system having a type I β-turn. Based on the comparison of the band intensities of the bridged models with those of linear and cyclic model systems reported earlier, a set of subspectra with reduced band intensities is suggested for use in the CD analysis of the conformation of polypeptides in solution.     

Conformation of amylose in water. I. Light-scattering and sedimentation-equilibrium measurements

The conformation of amylose in aqueous solution has been found to be dependent on its molecular weight. When the molecular weight of amylose is outside of the so-called “dissolving gap” described by Burchard (6500<M_r<160,000) it behaves as a random coil, whereas when its molecular weight is within the “dissolving gap,” it easily aggregates forming a rigid coil which is the B-type (retrograded) amylose. The conformation of this rigid coil is suggested to be a double helix.     

Conformational properties of Eu(III) complexes of 3,3′; 5,3″-polymethylene bridged derivatives of 2,2′; 6,2″-terpyridine

The complex [Eu(tpy)₃](ClO₄)₃ where TPY=2,2′; 6,2″-terpyridine, has been prepared and reexamined. The complex appears to be stable in acetonitrile solution with respect to decomplexation of the ligands but the addition of water does cause partial replacement of tpy. Analogous complexes have been prepared with 3,3′; 5,3″-polymethylene bridged derivatives of tpy having two or three carbons in the bridge. The bridging enforces a cisoid geometry of the ligand and prohibits its replacement by added water. An X-ray determination was carried out for [Eu(3b)₃](ClO₄)₃, where 3b=3,3′; 5,3″-dimethylene tpy, which crystallizes in the monoclinic space group P2₁/c with a=11.908(4), b=15.768(5), c=29.513(9) Å, β=93.60(2)°, μ=13.5 cm⁻¹ and Z=4. The complex forms a tricapped trigonal prism with each of the ligands adopting the same dl conformation. Variable temperature NMR analysis of the bridged ligand complexes indicates that conformational inversion of the bound ligand is not a concerted process and barriers for inversion of individual methylene units can be estimated from coalescence of the signals from the geminal methylene protons. The luminescence properties of the bridged tpy complexes are similar to the parent unbridged system.     

A 13C-NMR study on the conformational and dynamical properties of a cereal seed storage protein,C-hordein,and its model peptides

We have recorded the ¹³C CP-MAS and DD-MAS nmr spectra of dry and hydrated barley storage protein, C-hordein, as a model for wheat S-poor prolamins, together with those of model synthetic peptides (Pro)₂(Gln)₆(I) and (Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln)₃(II) under dry or hydrated conditions. The spectral features of C-hordein as well as these peptides were appreciably different from each other depending on the extent of hydration, reflecting different domains that adopt different types of conformations as well as dynamics. In particular, considerable proportions of the peak intensities were lost in the CP-MAS spectra, and well-resolved ¹³C-nmr signals emerged in DD-MAS nmr spectra owing to acquisition of molecular motions by swelling. It was shown that local β-turn or (Pro)_n type II conformation is more preferable for individual Pro residues and β-sheet type conformation is dominant for individual Gln residues in the dry and hydrated systems. In addition, two types of Gln environments are originated in C-hordein that differ in their mobility. Further, ¹³C spin-lattice relaxation times (T₁'s) of C- hordein and peptide II were reduced by more than one order of magnitude by hydration, reflecting the presence of well-swollen molecular chains. In contrast, theT₁ values of peptide I upon hydration remained one third of those in the dry state. Carbon-resolved proton spin-lattice relaxation times in the rotating frame (T_1ρ's) were also decreased by about 50% upon hydration, although these parameters were less sensitive as compared to T₁ values. In addition, the ¹³C-nmr signals of the aromatic side chain of Phe residues disappeared on hydration owing to interference between the frequency of the acquired flip-flop motion and the proton decoupling frequency. This information gives a new insight into establishing the structural properties of the studied protein system. A model may be put forward for a gel-type structure in which the more rigid part of the system involves intermolecular hydrogen-bonded Gln side chains as well as some hydrophobic “pockets” involving Pro and Phe residues. The liquid-like domain is characterized by considerable backbone and side-chain motion as well as rapid ring-puckering motion in Pro residues. © 1997 John Wiley & Sons, Inc.     

Intrachain reactions of a pair of reactive groups attached to polymer ends. V. Formation of disulfide linkages in the air-oxidation of sulfhydryl groups attached to ends of polysarcosine chain

Polysarcosine having sulfhydryl groups attached to both ends was synthesized by the NCA method and its air-oxidation was investigated in aqueous solution with cupric-ion or ferric-ion catalysts. Air-oxidation was also conducted for a polysarcosine having one terminal sulfhydryl group. The product of the air-oxidation was fractionated by gel chromatography. The product analysis of the fully oxidized monofunctional polymer showed that the sulfhydryl groups were converted into disulfide bonds exclusively. There was no evidence for the interchange between two disulfide linkages or between a disulfide linkage and a sulfhydryl group during the air-oxidation. The analysis of the products from the bifunctional polysarcosine showed that they were composed of a series of cyclic “monomer,” “dimer,” “trimer,” and higher “oligomers.” The cyclic structure was characterized by the larger elution volume in the gel chromatogram than that for a linear homologue having the same molecular weight. The weight fraction of each cyclic oligomer was determined by gel chromatography. The fraction of cyclic monomer F₁ decreased monotonously with increasing the chain length. Smaller values of F₁ were observed with cupric-ion catalyst than with ferric-ion catalyst. The dependence of F₁ on the polymer concentration was much smaller than that expected from a simple competition mechanism between intra- and intermolecular reactions. These results indicate that the choice between intra- and intermolecular reactions is governed by the mode of the coordination of sulfhydryl groups to transition metal ions.     

Spin Labeled Nucleoside Analogues: 4′-Hydroxymorpholin-2′-Ylpurines and Pyrimidines

Abstract

Upon borane-pyridine reduction, a series of nucleoside dialdehyde dioximes 2 underwent cyclization to the corresponding 4′-hydroxymorpholin-2′-ylpurines or pyrimidines 3 from which the peracetyl derivatives 4 were prepared. At room temperature, compounds 3 and 4 exist as a mixture of invertomers in which the 4′S (equatorial 4′-OH or 4′-OAc) predominates. A 14 kcal/mol, nitrogen inversion barrier was estimated from variable temperature experiments. N.O.E. and ³J_CH measurements established the anti conformation of the base-“sugar” bond. Compounds 3 spontaneously oxidized to the corresponding aminoxyl free radicals, EPR spectra of which showed that they existed in a chair conformation.     

Conformational interconversions in peptide β-turns: Discrimination between enantiomeric conformations by chiral perturbation

The crystal structure of the model tripeptide Boc-Aib-Gly-Leu-OMe ( 1 ) reveals two independent molecules in the asymmetric unit that adopt “enantiomeric” type I and type I′ β-turn conformations with the Aib and Gly residues occupying the corner (i + 1 and i + 2) positions. ¹³C cross polarization and magic angle sample spinning spectra in the solid state also support the coexistence of two conformational species. ¹³C-nmr in CDCl₃ establishes the presence of a single species or rapid exchange between conformations. 400 MHz ¹H-nmr provides evidence for conformational exchange involving a major and minor species, with β-turn conformations supported by the low solvent exposure of Leu(3) NH and the observation of N_iH ↔ N_i+1H nuclear Overhauser effects. CD bands in the region 190–230 nm are positive, supporting a major population of type I′ β-turns. The isomeric peptide, Boc-Gly-Leu-Aib-OMe ( 2 ), adopts an “open” type II′ β-turn conformation in crystals. Solid state and solution nmr support population of a single conformational species. Chiral perturbation introduced outside the folded region of peptides may provide a means of modulating screw sense in achiral sequences. © 1998 John Wiley & Sons, Inc. Biopoly 45: 191–202, 1998     

Synthesis and carbon-13 nuclear magnetic resonance spectra of Cyclo(D-leucyl-L-leucine) and Cyclo(L-leucyl-L-leucine)

Cyclo(D -Leu-L -Leu) and cyclo(L -Leu-L -Leu) were synthesized, and their carbon-13 nmr spectra at 65 MHz were examined in dimethylsulfoxide and trifluoroacetic acid solutions. The chemical shift data are consistent with a boat or “twisted” boat conformation of the diketopiperazine ring in both solvents. There was no indication of protonation of the cyclic dipeptides by trifluoroacetic acid. Attempts at polymerizing the cyclic dipeptides were unsuccessful.     

Optical and conformational properties of the 7-(beta-D-ribofuranosyl) purines

The optical and conformational properties of certain 7-ribosyl purines have been studied using several experimental and theoretical methods. The CD, MCD, and absorption spectra of the 7-ribosyl purines and their cations have been determined experimentally with some solvent effects being noted. Theoretically we have used the SCF-CI and CNDO molecular orbital calculations to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the ribose moiety; the optical activity was determined by the dipole coupling and electricmagnetic coupling equations; and the conformational energy calculations are included as a basis for excluding highly improbable conformations. On the basis of these calculations, we concluded that the oxy derivatives and the amino derivatives are predominately in the “extreme anti” conformation and “standard anti” conformation, respectively. However, the conclusions are tentative since at the present time the band assignments are not unequivocal. At least one n-π* transition has been identified in the spectra which is not notably sensitive to pH and solvent effects. Several implications of this observation are discussed.     

Calcite-forming Bacillus licheniformis Thriving on Underwater Speleothems of a Hydrothermal Cave

The underwater environment of Grotta Giusti (Monsummano Terme, Italy) is a suggestive setting with different types of speleothems including “leafy” and “cauliflower” concretions along the walls and roof, and conical pseudo-stalagmites on the floor. Very high calcium and dissolved CO₂ levels, and massive calcium carbonate precipitation characterize this cave environment. Yet, life thrives on the leafy concretion surfaces with loads of cultivable heterotrophic microorganisms around 10⁵ colony-forming units per cm². Bacillus licheniformis appeared to be the prevalent cultivable microorganism on a low-nutrient medium that was used for screening. 16S rRNA gene-based polymerase chain reaction–single strand conformation polymorphism profiling indicated that Group VI Bacillaceae species was well represented in the bacterial community of underwater speleothems. Interpretation of X-ray diffraction spectra and Raman spectroscopy data indicated that the B. licheniformis isolate produced in vitro abundant calcite microcrystals that were also characterized by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. Production of calcite microcrystals was analyzed in different media (Christensen’s urea agar and B4 calcium carbonate precipitation medium) and incubation conditions, and it was found to be enhanced by nitrate supplement in B4 medium under low-oxygen conditions. B4 and B4-nitrate media also stimulated antibiotic production by the B. licheniformis isolate, which was analyzed by microbiological assays.     

Vibrational circular dichroism spectra of three conformationally distinct states and an unordered state of poly(L-lysine) in deuterated aqueous solution

Fourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L-lysine) in D₂O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right-handed α-helix, the antiparallel β-sheet, an extended helix conformation previously referred to as the so-called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β-sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.     

Involvement of Delta and Nodal signals in the specification process of five types of secondary mesenchyme cells in embryo of the sea urchin, Hemicentrotus pulcherrimus

Secondary mesenchyme cells (SMCs) of the sea urchin embryo are composed of pigment cells, blastocoelar cells, spicule tip cells, coelomic pouch cells and muscle cells. To learn how and when these five types of SMCs are specified in the veg₂ descendants, Notch or Nodal signaling was blocked with γ‐secretase inhibitor or Nodal receptor inhibitor, respectively. All types of SMCs were decreased with DAPT, while sensitivity to this inhibitor varied among them. Pulse‐treatment revealed that five types of SMCs are divided into “early” (pigment cells and blastocoelar cells) and “late” (spicule tip cells, coelomic pouch cells and muscle cells) groups; the “early” group was sensitive to DAPT up to the hatching, and the “late” group was sensitive until the mesenchyme blastula stage. Judging from timing of the shift of Delta‐expressing regions, it was suggested that the “early” group and “late” groups are derived from the lower and the middle tier of veg₂ descendants, respectively. Interestingly, numbers of SMCs were also altered with SB431542; blastocoelar cells, coelomic pouch cells and circum‐esophageal muscles decreased, whereas pigment cells and spicule tip cells increased in number. Pulse‐treatment showed that the “early” group was sensitive up to the mesenchyme blastula stage, while the “late” group up to the onset of gastrulation. Thus, it became clear that precursor cells of the “early” and “late” groups, which are located in different regions in the vegetal plate, receive Delta and Nodal signals at different timings, resulting in the diversification of SMCs. Based on the obtained results, the specification processes of five types of SMCs are diagrammatically presented.     

Untersuchung der 13c-kernresonanz-spektren der acht isomeren 1,6-anhydro-β-D-hexopyranosen

The signals of the ¹³C-n.m.r. spectra of the eight isomeric 1,6-anhydro-β-D-hexopyranoses having the ¹C₄ conformation were assigned by comparison with the spectra of selectively deuterated derivatives and by observation of the substituent effect of the O-isopropylidene derivatives. Of the two substituted C atoms in the O-isopropylidene derivatives, the signal of the equatorially substituted C atom was shifted to a lower field more strongly than that of the carbon atom bearing an axial substituent. The chemical shifts and their calculation with empirical parameters are discussed.     

Quasielastic light scattering by biopolymers. IV. Tertiary collapse of calf thymus DNA in 5.5M LiCl

Circular dichroism has been commonly employed to infer the conformation of DNA in solution. The basis of the conformational assignments is the work of Tunis-Schneider and Maestre, wherein CD spectra of DNA were obtained under conditions comparable to those employed in the x-ray diffraction studies of A-, B-, and C-DNA. It has recently been suggested that the CD spectrum of DNA in chromatin, which is similar to the CD spectrum of the C-form DNA, is a superposition of the normal B-DNA spectrum and a single negative band, centered at 275 nm. This negative band is qualitatively identical to the spectrum for condensed Ψ-form DNA. We have employed the hydrodynamic methods of quasielastic light scattering and sedimentation velocity to determine the extent of DNA tertiary structural alteration in 5.5M LiCl as a possible explanation of the C-form CD spectrum. These studies suggest an eightfold contraction of the Stokes hydrodynamic volume for calf thymus DNA in going from 0.4M NH₄Ac to 5.5M LiCl, with no change in molecular weight. The estimated maximum presistence length of DNA in 5.5M LiCl is estimated to be 20.0 nm compared to the “minimum” value of 44.7 nm in NaCl solutions. The value 20.0 nm corresponds to a maximum radius of 16.7 nm for a “continuously coiled” cylinder of DNA, which compares with the value 5.0 nm of DNA in the nucleosome unit of chromatin.     

Effects of Chain-length of Alkane Substrate on Fatty Acid Composition and Biosynthetic Pathway in Some Candida Yeasts

Cellular fatty acid compositions of Candida tropicalis pK 233 and Candida lipolytica NRRL Y -6795 and the time-course changes during yeast growth were studied using individual n-alkanes of various chain lengths (from C₁₁ to C₁₈) and a mixture of n-alkanes (C₁₁ to C₁₈) as a sole carbon source. Observed relationships of the chain-length of n-alkane substrate to time-course changes and final patterns of the fatty acid compositions of these yeasts, especially those of the cells grown on odd-carbon alkanes, indicated that “intact incorporation mechanism,” that is, accumulation of the fatty acid having the same chain-length as that of the alkane substrate used was predominant in the yeasts cultivated on a longer alkane such as n-heptadecane and n-octadecane. On the other hand, “chain elongation pathway” and “de novo synthesis pathway” following β-oxidation of substrate were simultaneously operative in the cells growing on a relatively shorter alkane such as undecane and dodecane.     

Interruption of aggregation pheromone in Ips typographus (L.) (Col. Scolytidae) by non-host bark volatiles

Abstract 1 The antennally active nonhost bark volatiles (NHVs): trans‐conophthorin (tC), C₆‐alcohols (green leaf volatiles; GLVs) and C₈‐alcohols, were tested for their ability to reduce attraction of the spruce bark beetle Ips typographus (L) (Col. Scolytidae) to its pheromone sources in both laboratory walking bioassy and field trapping experiments. 2 In the walking bioassay with I. typographus females, individual NHVs such as tC, 3‐octanol and 1‐octen‐3‐ol, and the unsuitable host signal, verbenone (Vn), were inactive at the doses tested. However, the blend of C₆‐alcohols (3GLVs) and all the binary, ternary, or quarternary blends significantly reduced the female attraction to the pheromone sources. 3 In the field trapping experiments, individual NHV signals (tC, C6‐alcohols and C₈‐alcohols) all reduced catch of I. typographus in pheromone‐baited traps, with their inhibitory effects similar to that of the known inhibitor, Vn. The binary, ternary or quarternary combinations of these NHV signals or Vn, all caused significantly stronger reductions in trap catches than the individual signals. The blends showed similar levels of interruption, except the binary blend of C₈‐alcohols (2C8OH) and Vn. 4 Difference in trapping mechanism between pipe traps (attraction and landing) and Lindgren funnel traps (attraction) did not affect the pattern of inhibition of these active NHV signals and Vn. 5 These behaviourally active nonhost volatiles and Vn might be used effectively to protect spruce trees or stands against attacks by I. typographus.     

A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules

A novel scheme for the parameterization of a type of “potential energy” function for protein molecules is introduced. The function is parameterized based on the known conformations of previously determined protein structures and their sequence similarity to a molecule whose conformation is to be calculated. Once parameterized, minima of the potential energy function can be located using a version of simulated annealing which has been previously shown to locate global and near-global minima with the given functional form. As a test problem, the potential was parameterized based on the known structures of the rubredoxins from Desulfovibrio vulgaris, Desulfovibrio desulfuricans, and Clostridium pasteurianum, which vary from 45 to 54 amino acids in length, and the sequence alignments of these molecules with the rubredoxin sequence from Desulfovibrio gigas. Since the Desulfovibrio gigas rubredeoxin conformation has also been determined, it is possible to check the accuracy of the results. Ten simulated-annealing runs from random starting conformations were performed. Seven of the 10 resultant conformations have an all-C_α rms deviation from the crystallographically determined conformation of less than 1.7 Å. For five of the structures, the rms deviation is less than 0.8 Å. Four of the structures have conformations which are virtually identical to each other except for the position of the carboxy-terminal residue. This is also the conformation which is achieved if the determined crystal structure is minimized with the same potential. The all-C_α rms difference between the crystal and minimized crystal structures is 0.6 Å. It is further observed that the “energies” of the structures according to the potential function exhibit a strong correlation with rms deviation from the native structure. The conformations of the individual model structures and the computational aspects of the modeling procedure are discussed. © 1993 Wiley-Liss, Inc.     

The solution behavior of poly-L-proline: I. Light scattering studies in water and concentrated aqueous neutral salt solutions

The solution bebavior of poly-L -proline Form II has been studied in water and aqueous salt solutions by both elastic and quasi-elastic light -scattering techniques. The results of this study suggest that polyproline Form II can exist in water at 24 °C as an associated polymer complex and that certain salts which do not appear to affect the helix integrity, e.g., guanidinium-HCl, resutl in dissociation of the aggregate. Other neutral salts, of the variety effective in mediating unfolding of the Form II helix (e.g., 4M NaClO₄) also induce aggregate dissociation, but 4M CaCl₂ results in enhanced aggregation of polyproline. Kinetic experiments indicate that a time of 20 hours is necessary for the completion of the “large” to “small” transformation (at 22°C) which is induced by the addition of 4M NaClO₄. Thus it appears that neutral salts additives in aqueous solutions of polyproline influence both the state of aggregation and the conformation of this polymer.     

Conformations of model compounds of proteins. I. Acetylglycine N-methylamide

Infrared spectra in the region 4000–60 cm^?1 have been measured for acetylglycine N-methylamide and its deuterium homologs, CD₃CONHCH₂CONHCH₃, CH₃-CONHCD₂CONHCH₃, CH₂CONHCH₂CONHCD₃, and CH₃CONDCH₂CONDCH₃. Normal frequencies have also been calculated for these molecules with various conformations. The spectra show that this compound has two crystalline modifications, form A and form B. The frequencies and their isotope shifts show that the molecular conformation (Ψ, ?) of form B is near (0, 120) and that of form A near (180, 120). The short-range factors determining the conformation of peptide backbone having glycine residues are discussed.