bluuebunny/crossref_metadata_2025 huggingface dataset:
Enantiomer selection in the reaction of N‐methyl‐α‐amino acid N‐carboxyanhydride and 3‐methyl‐5‐substituted hydantoin: A model reaction for the stereoselective polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio
Published: December 2004

The addition reaction to N‐methyl‐(S)‐alanine or N‐methyl‐(S)‐phenylalanine N‐car‐boxyanhydride (NCA) of 3‐methyl‐5‐substituted hydantoin (HDT) catalyzed by a tertiary amine was investigated as a model reaction for the propagation reaction of NCA according to the activated‐NCA mechanism. Several activated HDTs having the (S)‐configuration of the asymmetric carbon atom were found to react more rapidly than their activated enantiomers. This experimental result indicates that the enantiomer selection by terminal‐unit control takes place in the propagation reaction according to the activated‐NCA mechanism in which an activated NCA is added to a terminal acylated NCA ring of the growing chain. The enantiomer excess of the HDT recovered from the reaction mixture of N‐methyl‐(S)‐phenylalanine NCA and racemic HDTs activated by a tertiary amine was determined. The extent of the enantiomer selection in the polymerization was found to be 3–10 times as large as that in the model reaction. From these results, it was concluded that the chirality of the penultimate unit, as well as that of the terminal NCA ring, plays an important role in determining the enantiomer selection in the NCA polymerization.
Analysis of high‐resolution melting (thermal dispersion) of DNA. Methods
Authors: Yen W. S. , Blake R. D.
Published: December 2004

We describe the capabilities of a method for obtaining high‐resolution melting profiles of short, homogeneous DNAs using a thermo‐differential absorbance technique. The absorbance difference of two identical DNA solutions, raised linearly in temperature and maintained at a constant temperature difference, is monitored using a double‐beam spectrophotometer. A specially constructed temperature controller and cell holder enable the temperature of the DNA samples to be controlled and monitored directly. A heating rate of 6.75°C/hr has been found to give reproducible results at ionic strengths > 0.01M. A method of reconstructing the true derivative from experimental data using a Taylor series expansion is described and shown to work well when the difference in temperature between samples is in the range of 0.2°C. Reconstructed derivative profiles are further analyzed by deconvolution into distinct Gaussian components. The melting profile of PM‐2 DNA is shown to consist of 14 components, while the much longer lambda DNA yields 55. Related techniques such as data management and analysis for the fractional G·C content of specific domains are also described.
Intra‐ and intermolecular charge‐transfer interactions between terminal electron donor and acceptor attached to poly(γ‐benzyl‐L‐glutamate) in solution
Authors: Sisido Masahiko , Shimizu Toshimi , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

Poly(γ‐benzyl‐L‐glutamate) having a terminal dimethylaminoanilide group as an electron donor (D) and a terminal 3,5‐dinitrobenzoyl group as an electron acceptor (A) (A‐[Glu(OBzl)]n‐D) was synthesized by the N‐carboxyanhydride method. Polymer samples were fractionated by gel chromatography and their number‐average degrees of polymerization n were determined by the absorbances of the terminal chromophores. These polymers in chloroform and dimethylformamide solutions showed a charge‐transfer (CT) absorption band around 455 nm, and the fraction of the polymer forming the CT complex was evaluated as a function of the chain length. CT absorption for short chains (n = 5 ∼ 20) was attributed to intramolecular CT complex in which the A‐[Glu(OBzl)]n‐D chain takes cyclic conformations. An optimum chain length for the intramolecular CT was found to be n ≅ 10, where the [Glu(OBzl)]n chain may most easily bend back to form cyclic conformations. Stronger CT absorption observed for longer chains than n = 20 was shown to be intermolecular, and an intermolecular head‐to‐tail aggregation was found to be a cause of the strong CT interaction. All helical A‐[Glu(OBzl)]n‐D chains were found to form the head‐to‐tail dimers in chloroform solution.
Fluorescence‐detected circular dichroism of dinucleoside phosphates. A study of solution conformations and the two‐state model
Authors: Reich Charles , Tinoco Ignacio
Published: December 2004

Three fluorescent dinucleoside phosphates containing 1,N6‐ethenoadenosine (εA), εApεA, εApεC, and εApU were studied using fluorescence‐detected circular dichroism (FDCD), circular dichroism (CD), and absorption measurements. The FDCD data indicate that εApεC and εApU can be described as two‐state systems consisting of a fluorescent species and a stacked, nonfluorescent species. Thermodynamic stacking parameters are calculated for these molecules using the van't Hoff equation. εApεA is found to be a more complicated system with a fluorescent CD which is different in shape, but comparable in magnitude, to the conventional CD of the dimer. This molecule, unlike the other two dinucleoside phosphates, cannot be characterized as a two‐state system; it is described as consisting of at least three states at temperatures above 35°C. The CD data were subjected to a linear analysis in order to determine the minimum number of states present. In agreement with the FDCD data, εApεC and εApU are found to consist of a minimum of two states, while εApεA is indicated to have at least three. The more complicated behavior of the latter dimer is also indicated by the values of the unstacked CD obtained in the van't Hoff analysis.
Calorimetric determination of the enthalpy of ionization of oxidized and reduced horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Berger R. L.
Published: December 2004

The heats of ionization of protons, ΔHi, of oxidized and reduced horse heart cytochrome c in 0.15M KCl at 20°C were determined using a titration calorimeter which simultaneously afforded the potentiometric titration curve. Reproducibility of the thermal titrations is within 2%, and evaluation of the heats observed after the heat loss corrections is estimated to be within 5%. A single titration of oxidized cytochrome c from pH 11 to 3 is in excellent agreement with the thermal titration of this protein obtained with flow calorimetry. The thermal titration, however, is not reversible, due in part to the loss of titratable group(s) in this pH region and to the heat contribution of the acid and alkaline conformational changes which occur. Although of lesser magnitude, the reduced form also indicates similar thermal transitions. These differences are due solely to conformational contributions to the thermal process, since the potentiometric curves are reversible. The nature of the irreversibility for oxidized cytochrome c appears to involve the loss of a group with pK′ 8.9 and the shift of two groups from pK′ 5.6 to 4.8. Thermal difference curves for this process indicate that heats of −7.8 and −24.1 kcal/mol are liberated which are centered at pH 9.3 and 3.9, respectively.
A quantitative test of Zimm's model for the rotor‐speed‐department sedimentation of linear DNA molecules
Authors: Clark Roger William , Lange Christopher S.
Published: December 2004

In 1974, Zimm described a theory which predicts that the sedimentation coefficient of high‐molecular‐weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed‐dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well‐defined sucrose‐gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T‐even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild‐type phage (T4D+) was also used in some experiments.

In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.

The results show that in the range of 25,000–50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed‐dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
Unwinding of DNA induced by fluorescein mercuric acetate
Authors: Takeuchi Shintaro , Maeda Akio
Published: December 2004

Fluorescein mercuric acetate causes the unwinding of DNA and binds to the separated bases. This unwinding process can be followed by measuring absorption changes of this reagent. For untreated calf thymus DNA, the initial rate was very slow, and the shape of the kinetic curve was sigmoidal. When double‐strand breaks of DNA were produced by DNase II treatment or sonication, the initial rate increased and the sigmoidal character disappeared. The initial rate was shown to be proportional to the concentration of helix ends. From this relation the rate of unwinding was estimated to be 2.0 base pairs/sec at 1.0 × 10−5M fluorescein mercuric acetate and 25°C. DNase I treatment, which produces single‐strand breaks and a smaller number of double‐strand breaks, also increased the initial rate. However, this increase was due only to the double‐strand breaks, that is, single‐strand breaks had no significant effect on the initial rate. Also, uv irradiation increased the initial rate linearly with uv dose, at least up to 2 × 105 erg/mm2, suggesting that this increase is due to photoproducts other than usual pyrimidine dimers. We discuss the usefulness of this kinetic method in structural studies of DNA.
Fluorescent‐labeled collagen: Age‐related differences and fluorescence changes during the lag phase of fibril formation
Authors: Crabtree Donald V. , Fujimori Eiji
Published: December 2004

Acid‐soluble collagens isolated from young and old rat tail tendon were fluorescent‐labeled with dansyl hydrazine, which is capable of reacting with aldehyde groups in collagen. The dansyl fluorescence of aged collagen exhibited a weak peak at 525 nm, whereas that of young collagen had a stronger broad peak at 500 nm. Fibril formation in vitro was partially inhibited in these dansylated collagens. During the turbidity lag phase, the dansyl fluorescence was found to increase (30–50%), also shifting to 485 nm. These changes reveal the telopeptide conformation changes occurring during this period. A new fluorescence peak at 420 nm also increased during fibril formation. When the dansylated collagen was irradiated in air with uv light (340 nm), a rapid decrease of the dansyl fluorescence with a concurrent shift to 490 nm occurred. Also, the formation of fibrils was further inhibited. With increasing temperature, the dansyl fluorescence of young collagen decreased, whereas that of old collagen substantially increased, particularly at the denaturation temperature around 38°C. After denaturation, both fluorescences became similar in their intensity and position (490 nm). These findings are discussed in connection with both age‐related structural changes of collagen and the mechanism of fibril formation.
Conformation of poly(L‐homoarginine)
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo
Published: December 2004

Poly(L‐arginine) assumes the α‐helix in the presence of the tetrahedral‐type anions or some polyanions by forming the “ringed‐structure bridge” between guanidinium groups and anions which is stabilized by a pair of hydrogen bonds and electrostatic interaction [Ichimura, S., Mita, K. & Zama, M. (1978) Biopolymers 17, 2769–2782; Mita, K., Ichimura, S. & Zama, M. (1978) Biopolymers 17, 2783–2798]. This paper describes the parallel CD studies on the conformational effects on poly (L‐homoarginine) of various mono‐, di‐, polyvalent anions and some polyanions, as well as alcohol and sodium dodecylsulfate. The random coil to α‐helix transition of poly(L‐homoarginine) occurred only in NaClO4 solution or in the presence of high content of ethanol or methanol. The divalent and polyvalent anions of the tetrahedral type (SO, HPO, and P2O), which are strong α‐helix‐forming agents for poly(L‐arginine), failed to induce the α‐helical conformation of poly(L‐homoarginine). By complexing with poly(L‐glutamic acid) or with polyacrylate, which is also a strong α‐helix‐forming agent for poly(L‐arginine), poly(L‐homoarginine) only partially formed the α‐helical conformation. Monovalent anions (OH−, Cl−, F−, and H2PO) did not change poly(L‐homoarginine) to the α‐helix, and in the range of pH 2–11, the polypeptide remained in an unordered conformation. In sodium dodecylsulfate, poly(L‐homoarginine) exhibited the remarkably enlarged CD spectrum of an extended conformation, while poly(L‐arginine) forms the α‐helix by interacting with the agent. Thus poly(L‐homoarginine), compared with poly(L‐arginine), has a much lower ability to form the α‐helical conformation by interacting with anions. The stronger hydrophobicity of homoarginine residue in comparison with the arginine residue would provide unfavorable conditions to maintain the α‐helical conformation.
Quasielastic light scattering by biopolymers. IV. Tertiary collapse of calf thymus DNA in 5.5M LiCl
Authors: Parthasarathy Nambi , Schmitz Kenneth S. , Cowman Mary K.
Published: December 2004

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.
Local conformations of ends of α‐helical poly[Glu(OBzl)] studied by circular dichroism of terminal chromophores
Authors: Shimizu Toshimi , Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

Conformations of terminal peptide units of α‐helical poly(γ‐benzyl‐L‐glutamate), poly‐[Glu(OBzl)], were examined by an induced circular dichroism (CD) of chromophores which were covalently attached to both ends of the chain. In chloroform, where the helical poly‐[Glu(OBzl)] exists as a head‐to‐tail‐type dimeric associate, the chromophores showed a strong CD induced by an asymmetric perturbation from the helical structure. The induced CD almost disappeared by an addition of a few percent of dichloroacetic acid, which has been reported as a powerful breaker of the associate. These results are explained by an incorporation of terminal peptide units into a helical conformation in the head‐to‐tail associate and a local unfolding of the terminal portions by the addition of acid. An induced CD of a charge‐transfer complex between the two terminal chromophores was also observed and the structure of the helix–helix junction of the head‐to‐tail dimer is discussed.
Proton NMR study of the interaction of cis‐dichloro‐diamine‐platinum(II) with poly(I) and poly(I)·poly(C)
Authors: Fazakerley G. Victor , Hermann Dominique , Guschlbauer Wilhelm
Published: December 2004

The fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07–0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05–0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
The nonplanar peptide unit. IV. Geometry and nonplanar distortions of the cis‐peptide unit
Authors: Kolaskar A. S. , Sarathy K. P.
Published: December 2004

Semiempirical quantum chemical calculations were carried out using the CNDO/2 and the INDO methods on the model compound cis‐N‐methylacetamide in order to get an insight into the problem of possible nonplanar distortions of the cis‐peptide unit. In addition, the crystal structure data of cyclic peptides containing cis‐peptide units were analyzed. These studies have indicated that the dihedral angles θN and Δω are correlated approximately by the relation Δω = −θN, whereas θC is small and is uncorrelated with Δω, as was found in the case of the trans‐peptide unit. Both theory and crystal data suggest that out‐of‐plane distortions at the nitrogen atom of the peptide unit were quite likely to occur and should be included in the conformational calculations. The average geometry for the planar cis‐peptide unit has also been obtained from the observed examples.
Dynamics of tyrosine ring rotations in a globular protein
Authors: McCammon J. A. , Karplus M.
Published: December 2004

The dynamics of activated rotations of a tyrosine ring inside the bovine pancreatic trypsin inhibitor have been studied by computer simulation. The simulation method consists of two parts. In the first part, typical transition‐state configurations of the protein atoms are prepared. In the second part, the classical equations of motion for the protein atoms are solved to yield trajectories which pass through these transition‐state configurations. Analysis of the trajectories shows that the ring is driven over the rotational potential barrier by nearly impulsive collisions with atoms of the surrounding protein matrix. The collisions are similar to those that occur while the ring oscillates about its equilibrium orientation. The frequency and strength of the collisions are such that transition‐state theory is approximately valid for this simple reaction. The enthalpy of activation is substantially reduced by bond‐angle deformations which occur rapidly on the time scale of the barrier crossing. Small, transient packing defects in the protein appear to play a role in initiating the ring rotation.
The linear relationship between iodine staining and average chain length of the unbranched amyloglucans
Authors: Fales Frank W.
Published: December 2004

A simple straight‐line relationship between iodine staining and the average chain length (CL) of the linear amyloglucans has been derived utilizing the published data of Baldwin et al. [J. Am. Chem. Soc. 66, 111 (1944)], Bailey and Whelan [J. Biol. Chem. 236, 939 (1961)], Szejtli et al. [Biopolymers 5, 5 (1976)], Pfannemüller et al. [Biopolymers 10, 243 (1971)], and Banks et al. [Carbohydr. Res. 17, 25 (1971)]. The iodine staining characteristics—the wavelength of maximal optical absorbance (λM); the maximal absorbance (AM); and the iodine binding capacity (Ib) per chain—are all linearly related to the chain length. As an example, Ib per chain is linearly related to the CL and in the formula of a straight line: Y = nX − c where Y equals Ib per chain (or Ib × CL); X equals the CL, n is the slope, and c is the intercept of the Y‐axis by the straight line. Thus, CL and Ib are related as follows: CL = c/(n − Ib) Using the data of Banks et al., it was found that the slope was not affected by changes in temperature, but the Y‐intercept became less negative with decreasing temperature. Thus, the number of glucose residues per iodine molecule in the helix did not change, but shorter chain length species could complex with the iodine, and a larger fraction of each chain could form the helical configuration with iodine as the temperature was reduced. These findings suggest that the CL and therefore the number‐average degree of polymerization and the number‐average molecular weight of the unbranched amyloglucans could be determined by AM, Ib or λM measurements after standardization under precise experimental conditions.
Influence of methanol on the rotational diffusion of poly(L‐lysine) in the helix–coil transition
Authors: Hanssum H. , Rüterjans H.
Published: December 2004

13C spin‐lattice relaxation times of poly(L‐lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin‐lattice relaxation times of the 13Cα and the side‐chain carbon resonances reflects the diffusional motion in the random‐coil conformation, in the helix–coil transition, and in the conformation of the α‐helix. In the mixed solvent the reorientational correlation time of the Cα‐Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α‐helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side‐chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
Cation effects on the nonlinear electrical properties of DNA solutions
Authors: Marion C. , Hanss M.
Published: December 2004

The nonlinear electrical properties of DNA solutions were measured when different monovalent cations were added to DNA. The influence of different parameters has been examined: fundamental frequency, field strength, and concentration. A linear relationship between the harmonic current Ih and the DNA concentration is shown, even for higher concentration values (400 mg/l.). The frequency dispersion of Ih has the same shape for all the cations and the low‐frequency amplitude of Ih increases in the following order: Li+ < Na+ < K+ < NH < Cs+. The nonlinear polarizability values are compared with the linear ones determined using the very low field electric birefringence technique. Both linear and nonlinear values are of the same order of magnitude. It is thought that the nonlinear electrical property of high‐molecular‐weight DNA mainly results from the deformation of the DNA coils by the electric field.
Dependence of the internal relaxation time for DNA on salt type as inferred by quasielastic light scattering
Authors: Parthasarathy Nambi , Schmitz Kenneth S.
Published: December 2004

Quasielastic light scattering methods were used to study calf thymus DNA in solutions of LiCl, NaCl, NH4Ac, and NH4Cl. Plots of the reciprocal relaxation time (1/τ) vs sin2(θ/2), where θ is the scattering angle, exhibit two linear regions, in accordance with theories for semiflexible polymers based on the t → 0 approximation. In these theories the slope of the linear region at low angles is associated with the translational diffusion coefficient (Dt), whereas the slope of the linear region at high angles is associated with the segmental diffusion coefficient (Ds = kT/ƒs). The midpoint of the “transition” between these two linear regions is associated with the mean displacement between segments (b). Data presented here indicate that the Rouse‐Zimm parameters b and ƒs are significantly different for DNA in 0.4M NH4Cl relative to the other salts at comparable ionic strengths. It is suggested that this difference reflects local solvent structure and that both b and Ds are sensitive to the local water structure.
Laser Raman spectroscopic studies of poly(r‐cytidylic acid) and poly(r‐adenylic acid) complexes with poly(L‐lysine) and poly(L‐arginine)
Authors: Hernández Luis A. , Vieta René S. , Jao Tze‐Chi
Published: December 2004

Complexes of polyribocytidylic acid and polyriboadenylic acid with poly(L‐lysine) and poly(L‐arginine) were studied by Raman spectroscopy. The backbones of both polynucleotides are distorted by poly(L‐arginine). On the other hand, poly(L‐lysine) could distort the backbone of polyriboadenylic acid but not that of polyribocytidylic acid. In general, poly(L‐arginine) can increase the order of the base stacking, while poly(L‐lysine) causes disordering in the base stacking.
Sodium counterion activity of poly(S‐carboxymethyl‐L‐cysteine) and the beta–random‐coil transition
Authors: Ooi Kenta , Maeda Hiroshi , Ikeda Shoichi
Published: December 2004

Sodium ion activity was measured using a Na‐glass electrode in a solution of poly(S‐carboxymethyl‐L‐cysteine) with no added salt at various degrees of neutralization and various concentrations for samples of different molecular weights. The conformational change from random coil to the β‐structure was detected from the activity coefficient of counterions, as well as from CD. At a constant degree of neutralization, the activity coefficient is insensitive to a concentration change not only in the random‐coil state, but also in the range of conformational change if the concentration is below about 3 × 10−2 monomolal. At high concentrations of about 5 × 10−2 monomolal, however, the activity coefficient becomes low, probably due to the occurrence of the stacking of the pleated sheets.
Triple helix–coil transition of covalently bridged collagenlike peptides
Authors: Roth Werner , Heidemann Eckhart
Published: December 2004

The thermal triple helix–coil transition of covalently bridged collagenlike peptides with repeating sequences of (Ala‐Gly‐Pro)n, n = 5–15, was studied optically. The peptides were soluble in water/acetic acid (99:1) and were found to form triple‐helical structures in this solvent system beginning with n = 8. The thermodynamic analysis of the transition equilibrium curves for n = 9–13 yielded the parameters ΔH°s = −7.0 kJ per tripeptide unit, ΔS°s = −23.1 J deg−1 mol−1 per tripeptide unit for the coil‐to‐helix transition, and the apparent nucleation parameter σ ≃ 5 × 10−2. It was suggested through double‐jump temperature experiments that the rate‐limiting step during refolding is not only influenced by the difficulties of nucleation, but also by cis–trans isomerization of the Gly‐Pro peptide bond.
Experimental characterization of poly(hydroxyalkyl‐L‐glutamine) conformations in aqueous calcium chloride and sodium perchlorate solutions
Authors: McCord Robert W. , Madison Edwin L. , Mattice Wayne L.
Published: December 2004

Poly(hydroxyalkyl‐L‐glutamine) (alkyl = ethyl, propyl, butyl) solutions have been studied by CD as functions of temperature and activity of calcium chloride and sodium perchlorate. Helical content is altered by changes in salt activity and temperature. The helicity of poly(hydroxybutyl‐L‐glutamine) and poly(hydroxypropyl‐L‐glutamine) falls to zero in a monotonic fashion with increasing calcium chloride activity. A nonzero helicity reappears at activities in excess of 5–50 mol kg−1. Poly(hydroxypropyl‐L‐glutamine) is much more sensitive to calcium chloride than is poly(hydroxybutyl‐L‐glutamine), and both polypeptides are more sensitive to calcium chloride than are typical proteins. Markedly different behavior is observed with sodium perchlorate. This salt acts as a helix stabilizer at low activities but becomes a destabilizer at activities higher than 0.3–1.0 mol kg−1. In this respect the effect of sodium perchlorate on nonionic poly(hydroxyalkyl‐L‐glutamines) resembles that seen with cationic poly(L‐lysine) and poly(L‐arginine). Helix stabilization at low sodium perchlorate activity is moderate for poly(hydroxybutyl‐L‐glutamine) and large for poly(hydroxypropyl‐L‐glutamine) and poly(hydroxyethyl‐L‐glutamine).
Influence of uracil photohydrate formation on the conformational properties of heterodinucleoside monophosphates
Authors: Ezra Fouad S. , Maccoss Malcolm , Danyluk Steven S.
Published: December 2004

The structural properties of uracil photohydrates at the monomer and dimer level in aqueous solution have been examined in detail by nmr spectroscopy. Based on such evidence, the absolute configurations of the two possible diastereomers have been assigned, and the conformational perturbations induced by photohydration have been evaluated. In all instances, photohydration shifts the 2E ⇌ 3E puckering equilibrium of the sugar ring of the uridylyl fragment towards 2E (from 12–18%). In addition, for both dimers examined in detail, ho6UpA and Apho6hU, the effect of dimerization on sugar pucker is such that the 3′‐terminal unit shows a clear increase in the percentage of 3E (relative to the appropriate 5′‐mononucleotide), whereas the percentage 3E of the 5′‐terminal unit shows no change. This is contrary to the findings in the normal dinucleoside monophosphates, where an increased preference for 3E pucker occurs in both residues on dimerization and increased base stacking. Significant base–base interactions were observed in both hydrated dimers despite the loss of the planar π‐system in the uracil fragment. In addition, the rate of photohydration for a particular dimer pair (e.g., ApU and UpA or GpU and UpG) is shown to be inversely dependent on the amount of base stacking in the parent dimer. This latter parameter has also been correlated with the ratio of the two possible diastereomers formed in the reaction and is associated with a preferential attack at one face of the pyrimidine base ring. The shift of the sugar puckering equilibrium towards 2E has been compared with similar shifts observed when adenosine and guanosine are methylated at N(1) and N(7), respectively. The possible biological significance of the above‐mentioned conformational aspects is discussed.
A general multistate model for the analysis of hydrogen‐exchange kinetics
Authors: Krishna N. Rama , Goldstein Gideon , Glickson Jerry D.
Published: December 2004

In proton nmr, the chemical exchange rates of slowly exchanging labile hydrogens (with lifetimes in the range ∼ 10 msec – ∼ 1 sec) of peptides, proteins, and nucleic acids can be measured in H2O by a combination of two separate experiments: (1) the transfer of solvent saturation and (2) saturation‐recovery experiments. When these molecules exist in a dynamic equilibrium among different conformations, the experiments cannot be analyzed in a straightforward manner to derive the intrinsic exchange rates. In the present study we have derived analytical expressions for the above two experiments on a biomolecule under certain limiting conditions: (1) the extreme low‐motility limit, where each of the conformational transitions is much slower than the corresponding hydrogen exchange rate with the solvent; (2) the high‐motility limit (EX2 mechanism), which is the opposite extreme of the previous limit; and (3) the low‐motility limit (EX1 mechanism), which is a mixture of limits (1) and (2), i.e., for some of the conformations, the exchange rate with the solvent is much faster than their conformational transition rates, while for the remaining conformations the reverse situation is realized. The results may be considered as a generalization to an arbitrary number of states of the two‐state model treated by Hvidt. Equations have also been derived that are applicable to the iostope exchange method of measuring very slow exchange rates (with life‐times of the order of minutes and longer) in biomolecules. The saturation recovery experiments performed in H2O on the active pentapeptide fragment of thymopoietin serve to illustrate the high‐motility limit. The theoretical formulation presented in this study can be easily adapted to other double‐resonance techniques and also to situations where the kinetics of an arbitrary system existing in a multistate equilibrium are of interest.
Study of the influence of NH ⃛S hydrogen bonds on the reduction potential in Clostridium pasteurianum 2(4Fe‐4S) ferredoxin using deuterium exchange
Authors: Sweeney William V. , Magliozzo Richard S.
Published: December 2004

The effect of deuterium substitution of exchangeable hydrogen atoms on the reduction potential of Clostridium pasteurianum 2(4Fe‐4S) ferredoxin has been studied. The studies were conducted to determine if NH ⃛S hydrogen bonds to the iron–sulfur cluster are dominant in the mechanism of influence of the protein on cluster reduction potential, as has been proposed [Carter, C. W. (1977) J. Biol. Chem. 252, 7802–7811]. Deuteration of the slowly exchangeable hydrogen atoms, however, yields essentially no shift in the reduction potential (−0.2 ± 0.8 mV), suggesting that NH ⃛S bonds are not important modifiers of cluster reduction potential in this protein.
Structural and conformational investigation of carrageenans
Authors: Rochas Cyrille , Rinaudo Marguerite , Vincendon Marc
Published: December 2004

A detailed assignment of the 13C chemical shifts of κ‐ and ι‐carrageenans in their Na+ and K+ forms in D2O and dimethylsulfoxide is given. Evidence of the conformational transition induced by temperature variation in the absence of any gel formation on κ‐carrageenans is also presented. This evidence is based on 13C‐nmr and optical rotation experiments.
The chiroptical properties of proteins. II. Near‐ultraviolet circular dichroism of lysozyme
Authors: Goux Warren J. , Hooker Thomas M.
Published: December 2004

A study of the near‐uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri‐N‐acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme‐inhibitor complex were performed. The results of these calculations indicate that the near‐uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293–300 nm) and the disulfide n‐σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near‐uv transitions arises primarily from coupling interactions involving other side‐chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri‐N‐acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active‐site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
Effects of pD on ring‐stacking interactions between dinucleoside phosphates and tryptamine
Authors: Kolodny N. H. , Neville A. C.
Published: December 2004

Complex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
Cation binding cyclic peptides composed of imino acid residues
Authors: Shimizu Toshimi , Fujishige Shoei
Published: December 2004

Cyclo(L‐Pro‐Sar)n (n = 2–4) with moderate flexibility and hydrophobicity of molecular structure was synthesized, and the characteristics of these cyclic peptides and their metal complexes in acetonitrile were investigated in connection with the residual properties using 13C‐nmr measurements. The cyclic tetrapeptide cyclo(L‐Pro‐Sar)2 showed a sterically hindered phenomenon in acetonitrile in which the amide backbone adopted a cis‐trans‐cis‐trans sequence. The cyclic hexapeptide cyclo(L‐Pro‐Sar)3 existed as a mixture of several conformers whose interconversion is slow on the nmr time scale, including cis‐cis‐trans and/or cis‐trans‐trans arrangement of the Sar‐Pro bond. Finally, it was demonstrated that the cyclic octapeptide cyclo(L‐Pro‐Sar)4 behaved as a mixture of multiple conformers which allowed for cis‐trans isomerism about the Pro‐Sar peptide bond, of which 20–30% had the all‐cis Sar‐Pro bond isomer and the remaining 70–80% had one (or more) cis Sar‐Pro bond isomer. 13C‐nmr spectra also demonstrated that cyclo(L‐Pro‐Sar)n (n = 3,4) formed a 1:1 ion complex whose conformation was characterized by an all‐trans peptide bond in the presence of excess metal salt. Cation binding studies, using CD measurements, established that the ion selectivity of cyclo(L‐Pro‐Sar)4 in acetonitrile decreased in the order, Ba2+ > Ca2+ > Na+ > Mg2+ > Li+.
Kinetic studies of spin interconversion in ferric mixed‐spin derivatives of myoglobin
Authors: Sano Takayuki , Ishibashi Joji , Ikeda Naoki , Yasunaga Tatsuya , Ogawa Satoshi , Morishima Isao
Published: December 2004

Kinetic studies of spin interconversion in various derivatives of metmyoglobin such as the fluoride, aquo, hydroxide, azide, imidazole, and cyanide were performed by the coaxial‐cable temperature‐jump method. For all these derivatives, except fluoride and aquomyoglobin, a single relaxation was observed around 3 μsec. The rate constants and activation parameters for the spin interconversion were estimated and are discussed in comparison with those reported for the reaction of synthetic iron complex. Other hemoproteins such as cytochrome c and human hemoglobin were also examined, and the results were compared with those for myoglobin. The effect of buffer solution is also discussed.
Conformational studies of peptides: Crystal and molecular structures of L‐3,4‐dehydroproline and its t‐butoxycarbonyl and acetyl amide derivatives
Authors: Benedetti Ettore , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo , Felix Arthur , Goodman Murray
Published: December 2004

The crystal structures of L‐3,4‐dehydroproline, t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide, and acetyl‐L‐3,4‐dehydroproline amide have been determined. L‐3,4‐Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl‐L‐3,4‐dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L‐3,4‐dehydroproline is 0.046 based on 529 reflections; for t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide, 0.050 based on 792 reflections; and for acetyl‐L‐3,4‐dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t‐Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl‐L‐3,4‐dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present ϕ and ψ values corresponding to those of a right‐handed α‐helical conformation (conformation A), the t‐Boc and acetyl derivatives both have ϕ and ψ values corresponding to a collagenlike conformation (conformation F).
Contribution from the chirality of the growing chain to the enantiomer selectivity in activated‐NCA polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio
Published: December 2004

As a model compound for the growing chain in the activated‐NCA type of polymerization of α‐amino acid N‐carboxyanhydride (NCA), 3‐[ω‐acetylglycyl‐poly(α‐amino acid) acyl]‐α‐amino acid NCA (called the prepolymer) having various degrees of polymerization (DPs) was synthesized by the polymerization of Phe, Val, Glu(OEt), and Asp(OBzl) NCA in the presence of AcGly NCA by the tertiary amine. Activated (S)‐Phe, Val, Glu(OEt), and Asp(OBzl) NCA were added to the terminal cyclic group of the corresponding (S)‐ or (R)‐ prepolymer, and the enantiomer selectivity in the reaction was investigated. With prepolymers having DPs ranging from 1 to 15, the addition reaction always took place preferentially between species having the same configuration, and the degree of the enantiomer selection increased with increasing DP of the prepolymer. With prepolymers having DP = 1 and 2, we found contributions from the chiral terminal unit and the chiral penultimate unit to the enantiomer selection, respectively. Prepolymer having DP = 5 was shown to take a β‐type conformation, which led to higher enantiomer selection; and prepolymers having DP = 10 and 15 were shown to take an α‐helix conformation, which led to much higher enantiomer selection than did the β‐type conformation. In the present investigation the mechanisms of terminal‐unit control, penultimate‐unit control and conformational control of the enantiomer selection in the activated‐NCA type of polymerization were clearly observed.
Intrachain end‐to‐end charge transfer interaction in oligosarcosines
Authors: Sidido Masahiko , Kanazawa Yoshihiro , Imanishi Yukio
Published: December 2004

Oligosarcosines with two to seven sarcosine units terminated by an electron donor (p‐dimethylaminoanilide group) and an electron acceptor (3,5‐dinitrobenzoyl group) were synthesized by a liquid‐ or solid‐phase method. The oligomers showed a distinct charge‐transfer (CT) absorption in chloroform and ethanol solutions at low enough concentrations to eliminate the contribution of intermolecular CT interaction. Fractions of the oligomers which form the intrachain CT complex were evaluated at infinite dilution and plotted as a function of the number of sarcosine units n. The plot showed an alternating higher and lower tendency with the increase of n from n = 3 to 7; the total maximum was found at n = 4. The maximum reached 0.24 in chloroform, which is higher than that expected for an unperturbed oligosarcosine chain free from the end‐to‐end interaction, by an approximate factor of 50. The alternating chain‐length dependence was found to be governed by an alternating tendency in the conformational enthalpy required for cyclization.
Three‐dimensional structure of actinoxanthin. III. A 4‐Å resolution
Authors: Pletnev V. Z. , Kuzin A. P. , Trakhanov S. D. , Kostetsky P. V. , Popovich V. A. , Tsigannik I. N.
Published: December 2004

The protein actinoxanthin (molecular weight 10,300) crystallizes in space group P212121, with cell dimensions a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and z = 4. The three‐dimensional structure of actinoxanthin at 4‐Å resolution was determined by x‐ray methods on the basis of experimental data from the native protein and five isomorphous derivatives. At the stage of solving the phase problem, the heavy atoms in the derivatives were located using direct methods. The actinoxanthin molecule can be described as an oblate ellipsoid with approximate dimensions 20 × 30 × 40 Å and consists of two different sizes of folded units separated by a well‐defined cleft. The larger unit, including the N‐ and C‐terminals of the protein chain, is characterized by a significant content of β‐sheet structure. The smaller unit, containing two deca‐ and hexapeptide cycles closed by disulfide bonds, has a mainly irregular structure.
Structural conformations of nucleosomes at low ionic strength from flow birefringence and intrinsic viscosity
Authors: Harrington Rodney E.
Published: December 2004

The shape and structure of nucleosomes from chicken erythrocytes as a function of ionic strength in solution using the complementary techniques of streaming birefringence and intrinsic viscosity were studied. As characterized by both rotational diffusion and optical anisotropy, three distinct conformational levels were observed. Above ∼8 mM ionic strength, the particles are oblate ellipsoids or discs with axial ratio of ∼0.5. Below ∼8 mM, two structural variants were observed: a relatively more symmetrical particle which exists between ∼8 and ∼0.5 mM, and a relatively asymmetric structure below ∼0.5 mM. Birefringence data are consistent with an “opened clamshell” type of model for the first of these and with a somewhat compacted form of linear DNA for the latter. The results provide insights into possible conformational states of transcriptionally active chromatin at the nucleosomal level of structure.
Kinetics of activation and desensitization in receptor proteins
Authors: Kanehisa Minoru I.
Published: December 2004

Receptors are functional membrane proteins on the cell surface that recognize external signals and trigger biological responses by generating intracellular signals. Due to prolonged exposure to external signals, receptors are often desensitized and no longer produce intracellular signals. This simple control mechanism may work without negative‐feedback regulation from another molecule if the active state of a receptor reflects a transient metastable molecular structure. A theoretical framework is developed to identify a metastable state associated with a conformational transition of protein molecules, in which a transient state can be observed somewhat above the equilibrium transition point. The conducting state of the acetylcholine receptor may thus represent a metastable state associated with a conformational transition from the resting state to the desensitized state. Similarly, the conducting state of the voltage‐sensitive sodium channel may represent a metastable state associated with a conformational transition from the resting state to the refractory state. The rates of appearance and disappearance of the transient state, as well as the equilibrium ratio of the two preexisting states, can be estimated from the free energy of protein structure. The appearance of the transient state is generally a multirelaxation process and may show a time lag, while the disappearance is a slower single‐relaxation process.