bluuebunny/crossref_metadata_2025 huggingface dataset:
Block sequential polypeptides of L‐alanine and glycine with D, L‐glutamic acid
Authors: Iio Takayoshi I
Published: May 2005

Sequential polypeptides of L‐alanine(A) and glycine(G), which were incorporated between two blocks of poly(D,L‐glutamic acid) (DL), were synthesized by applying Merri‐field's solid‐phase method. On the basis of optical rotatory dispersion criteria, DL(A)38‐DL was found to assume the α‐helix in the whole range of the water‐methanol system; whereas other block sequential polypeptides were found to assume the random‐coiled conformation in water and partly the α‐helix at the high methanol content. The stability of the α‐helix decreased in the order: DL(A)38DL, DL(A2G)10DL, DL(A2G)6DL, and DL(A3G)7DL. This phenomenon may be explained in terms of the dependence of hydrophobic bonding between the C3H group of the ith L‐alanine regularly arranged on the surface of the α‐helix and the C2H group of the (i + 3)th residue on whether the residue is alanine or glycine. The role which the methanol plays in stabilizing the α‐helix is also discussed.
The infrared spectrum and water binding of collagen as a function of relative humidity
Authors: Susi H. , Ard J. S. , Carroll R. J.
Published: May 2005

The infrared spectra of undenatured bovine tendon collagen were investigated at 25°C and relative humidities from 0 to 95%. Suitable samples were prepared by forcing frozen suspensions of the material in distilled water through a stainless steel capillary. The samples were investigated by electron microscopy before and after the spectra were obtained to ascertain that no denaturation had taken place while the sample was exposed to infrared radiation. Temperature controlled absorption cells were constructed which permitted the passing of air with a known water content over the sample film. Gradual changes were observed in the frequencies and intensities of characteristic amide bands over the relative humidity range of 0 to 75%. These changes are particularly pronounced for the amide II band, associated with bending motions of peptide NH bonds. They lead to the conclusion that water molecules are gradually attached to peptide NH bonds within the triple helix over a wide range of relative humidity. Changes in CH deformation bands suggest that CH to O hydrogen bonding does occur and that it is more pronounced in collagen exposed to high relative humidity.
Conformation of poly‐S‐carboxyethyl‐L‐cysteine in aqueous solutions
Authors: Makda Hiroshi , Ikeda Rhoichi
Published: May 2005

Poly‐S‐carboxyethyl‐L‐cysteine, a higher side‐chain homolog of poly‐S‐carboxymethyl‐L‐cysteine, has been prepared from poly‐S‐carbobenzoxyethyl‐L‐cysteine with hydrogen bromide in chloroform or acetic acid. The polymer is found to be in the β‐conformation of an antiparallel arrangement of polypeptide chains in solid films, both in acid and salt forms, when examined by infrared spectra. Aqueous solutions of t he polymer have been investigated by measurements of rotatory dispersion and circular dichroism as well as by infrared spectra in D2O. These properties show sharp changes around pH 5.5, as the pH of solution is varied. At higher ionization the polymer is randomly coiled, but at lower ionization it is in the β‐conformation. Dependence of the rotatory properties upon polymer concentration as well as on ionic strength has been observed even at the lowest degree of ionization attained, and this has been attributed to the formation of intermolecular β‐conformation in solutions. The β‐structure is characterized by a negative circular dichroic band at 223 mμ and a positive dichroic band at a wavelength lower than 200 mμ, and furt her by a negative bo value, −140°. The pH‐induced coil‐β transition of the polymer is compared with that of poly‐S‐carboxymethl‐L‐cysteine.
Molecular orbital calculations on the conformation of polypeptides and proteins. VIII. The conformational energy maps and stereochemical rotational slates of the asparaginyl, glutaminyl aspartyl and glutamyl residues
Authors: Maigret Bernard , Perahia David , Pullman Bernard
Published: May 2005

Quantum‐mechanical calculations on the conformational energy map and stereo‐chemical rotational states of aminoacid residues by the PCILO method are extended to the asparaginyl, glutaminyl, aspartyl and glutamyl residues in their neutral form. One of the most outstanding features of the results is the occurrence of the global minimum (or of one of a few equivalent global minima) in the region of the left handed α‐helix for the first three of the above mentioned residues. The results of the calculations are compared with experimental data from eight, globular proteins which confirm that these residues may exist, in fact, in this conformation. They also enable to understand the experimentally observed possibility of helix reversal in esters of poly‐L‐aspartic acid as a function of substitutions in the side chain.
Calorimetry of rat tail tendon collagen before and after denaturation: the heat of fusion of its absorbed water
Authors: Haly A. R. , Snaith J. W.
Published: May 2005

The specific heat, of rat tail tendon at various water contents was measured as a function of temperature. The resulting graphs showed peaks arising from the melting, near 50°C, of helical material in the collagen, and from the melting of absorbed water in the range ‐40°C to 0°C. The heat of melting of helical material was 11.7 cal per gram of dry tendon. Determination of the heat and temperature of fusion of the absorbed water allowed resolution of the water into four states in the case of tendon before denaturation, and three states after denaturation. The four states are (1) water not freezable on cooling to ‐ 70°C, (2) freezable water with‐both heat and temperature of fusion different from the values for ordinary water, (3) freezable water with the heat of fusion of ordinary water, but a different temperature of fusion, and (4) water not distinguished from ordinary water. The fourth state was absent in denatured tendon. The results are discussed in terms of increasing size of clusters of absorbed water molecules.
Charge effects in the sedimentation of polyelectrolytes
Authors: Ziccardi Robert , Schumaker Verne
Published: May 2005

The theory for sedimentation of macromolecular polyelectrolytes in solutions of low‐ionic strength has been modified for the case of a supporting low molecular weight electrolyte possessing a partial specific volume close to unity. The final equations simplify greatly, allowing sedimentation data to be plotted in a linear fashion. These data then may be readily extrapolated to infinite dilution, yielding a value, So, simply related to size and shape. From the initial slope of such plots, the net charge on the macro‐molecular polyelectrolyte may be determined. It is suggested that tetramethyl‐ammonium chloride may prove to be a satisfactory supporting electrolyte for such studies.
Synthesis and optical studies of isoleucine oligopeptides in solution
Authors: Toniolo Claudio
Published: May 2005

In this paper we have successfully applied the dicyclohexylcarbodiimide and the acylazide coupling methods to the synthesis of a series of L‐isoleucine peptides from dimer to octamer. In the course of our synthetic, approach we employed t‐butyloxycarbonyl as the N‐protecting and methyl ester as the C‐protecting end groups. Peptide coupling reactions known to give products of high optical purity in good yields were used in these researches. Finally, we described preliminary stereochemical investigations on these homo‐oligopeptides using polarimetric and ultraviolet, absorption techniques. The con‐formational properties of high molecular weight poly‐α‐amino acids have attracted considerable attention as protein model compounds. In addition, investigations performed on oligopeptides have yielded important information concerning the dependence of secondary structure on chain length. Goodman and co‐workers2–5 have conducted extensive studies on the critical size for helix formation in L‐alanine, L‐aspartate and L‐glutamate oligomers and cooligomers. By a variety of techniques, they demonstrated that the onset of secondary structure is dependent both on the solvent and the nature of the side chain. In this and in the accompanying6 paper we report the extension of this approach to homo‐oligopeptides derived from L‐isoleucine, which is considered to be disruptive of α‐helices for steric reasons7 in proteins and polypeptides. In particular this manuscript will describe the synthesis of the homologous series of BOC‐L‐(Ileu)n‐OMe* (n = 2–8) and preliminary stereochemical investigations by means of polarimetry and ultraviolet (UV) spectroscopy. In the accompanying paper a much more detailed analysis of the stereochemistry of these oligopeptides will be reported.
Polyelectrolyte complexes of glycol chitosan with some polysaccharides. I. Mixing ratio and dielectric properties
Authors: Srinivasan R. , Kamalam R.
Published: May 2005

The formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1–100 kHz at different temperatures above and below room temperature. The GlChi–DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi–CMC and GlChi–(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell‐Wagner interfacial polarization. In the case of GlChi–AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456–1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double‐layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636–2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi–AlgA film.
Comparative microcalorimetric and dilatometric analysis of the interactions of quinacrine, chloroquine, and ethidium bromide with DNA
Authors: Delben Franco , Quadrifoglio Franco , Giancotti Vincenzo , Crescenzi Vittorio
Published: May 2005

The enthalpies of binding of chloroquine and quinacrine to DNA at different molar ratios of drug to DNA and at different ionic strengths have been measured. The limiting values obtained with quinacrine fall in the range found for typical intercalating agents (e.g., ethidium, proflavin, adriamycin), whereas the value obtained with chloroquine is always zero, independent of the ratio of drug to DNA and ionic strength. The dilatometric measurements performed on the same systems and on the ethidium–DNA system show that when ethidium and quinacrine bind to DNA at low drug/DNA ratios, a volume decrease of about 16 mL/mol of bound drug occurs. No change in volume is observed when the two drugs bind to DNA through external, electrostatic forces. The volume change can be attributed to the loss of structured water around hydrophobic moieties of the drug molecules, following intercalation. In contrast, chloroquine binding to DNA at low drug/DNA ratios is characterized by a volume change distinctly smaller than that shown by quinacrine. The low ΔVB and ΔHB values shown by chloroquine are discussed in terms of the mechanism of interaction with DNA.
Chromatin structure studied by linear dichroism at different salt concentrations
Authors: Tjerneld Folke , Nordén Bengt , Wallin Håkan
Published: May 2005

We have studied the linear dichroism (LD) of rat liver chromatin oriented by flow. Soluble chromatin, prepared by brief nuclease digestion, is found to exhibit a positive LD at low ionic strength (1 mM NaCl), with a constant LD/A over the absorption band centered at 260 nm (A, isotropic absorbance). Several previous dichroism studies on soluble chromatin have been performed on sonicated materials and have given negative LD, probably due to the presence of uncoiled DNA. The positive dichroism can be interpreted in terms of a supercoil of DNA in chromatin with a pitch angle larger than 55°, and is, for example, consistent with a model where the cylindrical nucleosome core particles are stacked face to face in the chromatin filament. In contrast to the nuclease‐digested chromatin, sonicated chromatin was confirmed to exhibit negative LD. This difference can be attributed to a partial uncoiling of the linker regions between the nucleosomes due to the shearing. The structural transition of chromatin to a compact form can be observed as a reduction of the positive LD of the nuclease‐digested chromatin to almost zero in 0.1 M NaCl or in 0.1 mM MgCl2. This transition is due to a decreased electrostatic repulsion between negative phosphate groups on the DNA chain. In the case of Na+, this can be explained as a screening effect due to the bulk concentration of Na+. With Mg2+ a considerably stronger effect may indicate a more localized binding to the phosphates. At ionic strengths higher than 0.5M NaCl, the dissociation of the histones from DNA leads to uncoiling of chromatin. The change in LD during this process shows that histone H1 contributes only to a small degree to the coiling of the DNA chain, whereas histones H3 and H4 play the major role in the coiling.
Thermodynamic functions of biopolymer hydration. I. Their determination by vapor pressure studies, discussed in an analysis of the primary hydration process
Authors: Lüscher‐mattli Madeleine , Rüegg Max
Published: May 2005

The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer–water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06–0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption–desorption scanning experiments were performed on a globular protein (α‐chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.
Thermodynamic functions of biopolymer hydration. II. Enthalpy–entropy compensation in hydrophilic hydration processes
Authors: Lüscher‐mattli Madeleine , Rüegg Max
Published: May 2005

The thermodynamic functions of biopolymer hydration were investigated by multitemperature vapor pressure studies. Desorption measurements were performed that allowed determination of reversible isotherms in the hydration range of 0.1 to 0.3–0.5 g H2O/g dry polymer. These isotherms are accessible to thermodynamic interpretation and are relevant to the interaction of water with biopolymers in their solution conformation. The results obtained on a series of different biopolymers (lysozyme, α‐chymotrypsin, apo‐lactoferrin, and desoxyribonucleic acid), show the following common features of interest: (1) The differential excess enthalpies (ΔHe) and entropies (ΔSe) are negative, and exhibit pronounced anomalies in a well‐defined low‐humidity range (approx. 0.1 g H2O/g dry polymer). These initial extrema are interpretable by structural changes, induced in the native biopolymer structures by water removal below a critical degree of hydration. (2) The ΔHe and ΔSe terms exhibit statistically significant linear enthalpy–entropy compensation effects in all biopolymer–water systems investigated. The compensation temperatures \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta = \overline {\Delta H} ^e /\overline {\Delta S} ^e $\end{document} are approximately identical for all biopolymers, ranging from 360 to 500 K. The compensation effects are attributable to phase transitions of water molecules between the bulk liquid and the inner‐sphere hydration shell of native biopolymers. (3) The negative excess free energies (ΔGe) decrease monotonically with increasing water content and are close to zero at 0.3 to 0.5 g H2O/g polymer. This result indicates that only transitions between the bulk liquid and the inner‐sphere hydration shell are associated with significant net free energy effects. The outer‐sphere hydration water is thermodynamically comparable to bulk water. The importance of the proportionality factor \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta $\end{document} in the control of the free energy term is discussed.
Physicochemical properties of pectic acid. I. Thermodynamic evidence of a pH‐induced conformational transition in aqueous solution
Authors: Cesàro A. , Ciana A. , Delben F. , Manzini G. , Paoletti S.
Published: May 2005

On the basis of measurements of enthalpy of dissociation and of dilution, an interamolecular conformational transition induced by pH change is shown for pectic acid in aqueous solution. Additional evidence is given by potentiometic, viscometric, and chiroptical results. The transition from a more rigid, probably H‐bonded, structure prevailing at low pH to a more extended one at around neutrality is accompanied by a ΔH value of about 500 cal/equiv and a ΔS value of 1.6 cal/equiv K in water at 25°C. The addition of salts increases the stability of the rigid conformation without changing the general features of the phenomenon. Dilatometric measurements suggest that the transition is accompanied by practically no change in the overall solvation of the polymer chain.
Borate complexes of amphotericin B: Polymeric species and aggregates in aqueous solutions
Authors: Strauss George , Kral Frank
Published: May 2005

Amphotericin B, a polyene macrolide antibiotic, exists in aqueous solution as a poorly soluble, high‐molecular‐weight aggregate. A borate complex of this polyene was prepared that has greater solubility and is less aggregated. In aqueous solution this borate complex exists as a mixture of several molecular species differing in borate content, molecular weight, and molecular conformation. The solubility varied with pH and was minimal at neutrality. Throughout the pH range it was one to two orders of magnitude higher than that of the parent compound. The molecular size distribution, as determined by differential ultrafiltration, showed a progressive increase in the weight fraction of aggregates going from acid to alkaline solutions. The sizes of aggregates ranged from under 25 to over 100 molecules. The borate content of the complexes increased with increasing pH. No borate was complexed in acid solutions. This indicated that amphotericin B and borate ions can complex to form copolymer chains of varying length in which these species alternate, since both are bifunctional. The complexation equilibrium is favored by high pH. Absorption and CD spectra indicated that the polyene molecules can stack reversibly to form dimers. Dimerization constants calculated from the spectra were highest in neutral solution and declined with increasing acidity or alkalinity. In alkaline solutions the polymer chains are long and extended, with minimal stacking. In neutral solution the chains are shorter and extensively stacked. In acid solutions no borate complexes are formed, and the polyenes are stacked to an intermediate degree. The very different effects of pH and concentration on the degree of complexation with borate and on the degree of dimerization of the polyenes shows that these equilibria are independent of each other.
Semiflexibility of collagens in solution
Authors: Saito Takahide , Iso Naomichi , Mizuno Haruo , Onda Nobuhiko , Yamato Hideyuki , Odashima Hiroshi
Published: May 2005

The persistence length of lugworm cuticle collagen in 0.1M acetic acid was evaluated as 1600 ∼ 1800 Å by Yamakawa‐Fujii's model for a wormlike chain from the sedimentation constant and the intrinsic viscosity. The persistence length was further examined for a series of sample “collagen sonicates” produced by varying the duration of sonic irradiation. To estimate the salt effect on the persistence length, measurements were made over a range of NaCl concentrations from 0 to 0.1M. The results showed that the cuticle collagen and collagen sonicates had identical values of persistence length and that the neutral salt effect for the cuticle collagen was far smaller than that for DNA.
Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure
Authors: Clementi Enrico , Corongiu Giorgina
Published: May 2005

We report on a computer experiment in which, using Monte Carlo techniques, we considered a three‐turn (30‐base‐pairs) B‐DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B‐DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B‐DNA strands are fully analyzed and described in detail. A model for base‐pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.
Interactions of DNA with divalent metal ions. IV. Competitive studies of Mn2+ binding to AT‐ and GC‐rich DNAs
Authors: Granot Joseph , Assa‐Munt Nuria , Kearns David R.
Published: May 2005

It has been inferred from previous studies that Mn2+ ions bind preferentially to G·C base pairs in DNA, and it has even been suggested that this preference for G·C pairs might be responsible for some of the Mn2+ specific effects observed in various biochemical reactions. In this paper we investigate the AT/GC preference of Mn2+ by direct competition studies in which AT‐rich DNA was dialyzed against GC‐rich DNA in the presence of varying amounts of Mn2+. Analysis of these results demonstrates that over a wide range of Mn2+/DNA(P) molar ratios, Mn2+ binds to A·T and to G·C base pairs with virtually identical affinity, although in a somewhat different mode. Both the present and previous nmr, uv, CD, and melting studies are discussed in terms of the different modes of binding of Mn2+ to single‐ and double‐stranded DNA.
Influence of surfactants on the conformation of β‐lactoglobulin B using circular dichroism
Authors: Damon Amy Jo Hillquist , Kresheck Gordon C.
Published: May 2005

The effect of several surfactants on the secondary structure of bovine β‐lactoglobulin B was determined from the circular dichroism spectra. The spectra were measured at several concentrations of surfactant ranging from 1 mg/mL to the critical micelle concentration. The surfactants studied were sodium dodecyl, decyl, and octyl sulfate, sodium dodecyl sarcosinate, dodecyltrimethylammonium bromide. The data were analyzed using the method of Chen et al. [Biochemistry (1974) 13, 3350–3359] to determine the percentage of α‐helix, β‐sheet, and unordered form at each surfactant concentration. In every case, an increase in structured form and a 20–25% decrease in the amount of unordered form was noted when the surfactant concentration reached the critical micelle concentration. However, the relative amounts of the two structured forms present depend on the surfactant used. The profile of the secondary structure of the protein also varied from surfactant to surfactant as the protein was titrated, probably reflecting the delicate balance between ionic and nonionic forces that governs the secondary structure of β‐lactoglobulin and most other globular proteins in aqueous solution.
Flow birefringence of T7 phage DNA: Dependence on salt concentration
Authors: Cairney Kim L. , Harrington Rodney E.
Published: May 2005

We have determined extinction angles and flow birefringence of T7 bacteriophage DNA over a wide range of shear, polymer concentration, and solvent ionic strength. From these data, information on the simple salt dependence of coil permeability to solvent and on short‐range intrachain interactions (persistence length) was obtained. At all ionic strengths, our results are consistent with a partially draining coil in the Gaussian subchain dynamical theory of Rouse‐Zimm‐Tschoegl‐Bloomfield. Salt dependence of persistence length is comparable to, although somewhat less than, that obtained previously using similar methods with a fivefold higher‐molecular‐weight DNA (T2 bacteriophage DNA). Possible reasons for observed discrepancies are analyzed, and the results of this work are compared in detail to other current studies of solvent ionic strength dependence in persistence length and hydrodynamic properties of DNA.
Conformational dependence of the vicinal proton coupling constant for the CαCβ bond in peptides
Authors: Cung M. T. , Marraud M.
Published: May 2005

We use the nmr data concerning the CαHCβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHαCβHβHβ′, the three‐dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation,

which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating CαCβ bonds in peptides.
Interaction of poly C with cis‐ and trans‐diamminedichloroplatinum (II): Secondary structure effects
Authors: Strommen Dennis P. , Peticolas Warner L.
Published: May 2005

The interactions of the ribonucleotide poly C with cis‐ and trans‐diamminedichloroplatinum (II) were probed with Raman spectroscopy. Both platinum compounds attack the N‐1 position of the cytosine residue, while the trans form appears to attack the PO2− as well. Raman difference spectra obtained from samples of poly C containing similar amounts of the respective Pt compounds indicate that the trans form is able to disrupt the secondary structure of poly C to a greater degree than the cis form. This latter observation may be a contributing factor in the low therapeutic index exhibited by the trans form.
Polynucleotide folding in yeast tRNAPhe: Elucidation of short‐, medium‐, and long‐range interactions of sugar–phosphate–sugar backbone and base using a “blocked” nucleotide probe
Authors: Malathi R. , Yathindra N.
Published: May 2005

It has recently been proposed that the repeating backbone nucleotide may be regarded as consisting of two blocks of equal magnitude representable by two virtual bonds. Implicit consideration of the nucleotide (ψ,ψ) and internucleotide (ω′,ω) geometry that generate variety in polynucleotide conformations, and of the constancy of the repeating structural moieties (P‐C4′ and C4′‐P) independent of the above rotations, has enabled us to utilize this scheme in the study of ordered structures such as di‐, oligonucleotides and, most significantly, tRNA. The polynucleotide folding dictated by short‐, intermediate‐, and long‐range interactions in the monoclinic and orthorhombic forms is described and compared through circular plots depicting the virtual bond torsions and distance plots constructed independently for backbone as well as bases. The torsions and the bond angles associated with the virtual bonds afford a clear distinction between ordered helical segments from loops and bends of tRNA. Lower virtual bond torsions (−60° to 60°) concomitant with higher values of virtual bond angles characterize various bend regions, while torsions around 160°–210° typify ordered helical strands. The distance plot elucidates the type of interaction associated with various sub‐structures (helix–helix, helix–loop, and loop–loop) that form the constituents of different structural domains. Several other features such as the manifestation of the P10 loop and the approximate twofold symmetry in the tRNA molecule are conspicuous on the distance plot.
Theory of DNA condensation: Collapse versus aggregation
Authors: Post Carol Beth , Zimm Bruno H.
Published: May 2005

In an unfavorable solvent environment, DNA (and other polymers) undergo a conformational transition to a collapsed form, accompanied by a dramatic reduction in the effective volume of the molecule. Solvent conditions leading to the collapse are the same as those that cause aggregation. We give here a thermodynamic description of the collapse and its relations to aggregation (or precipitation). This is formulated in terms of the Flory‐Huggins theory of the thermodynamics of polymer solutions. The results show that it is possible for three different states of DNA to be stable under different conditions: (1) the extended random coil, (2) the collapsed coil, and (3) a concentrated phase of aggregated random coils. The collapsed coil is predicted to be stable against aggregation only at high dilutions, of the order of parts per million. For DNA the transition between the extended coil and the collapsed coil is predicted to be discontinuous, in the sense that intermediate states are not present, because of the relatively high stiffness of the chain. The transition should appear diffuse because of the small size of the single molecule in comparison to macroscopic systems.
A fully nonequilibrium concerted model for enzymes
Authors: Shiner J. S.
Published: May 2005

The concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.
Conformational studies of diastereoisomeric cyclo(alanyl‐phenylalanyl) with the coupling constants 1H–1H, 15N–1H, 13C–1H, and 13C–15N
Authors: Vicar Jaroslav , Blaha Karel , Piriou François , Juy Michel , Lam‐thanh Hung , Fermandjian Serge
Published: May 2005

The cyclodipeptides cyclo(L‐alanyl‐L‐phenylalanyl) and cyclo(D‐alanyl‐L‐phenylalanyl) were synthesized with various atoms substituted by the isotopes 15N and 13C. Thus, the coupling constants 15N–1H, 13C–1H, and 13C–15N could be obtained, in addition to the commonly used 1H–1H constants. The applicability of these coupling constants for obtaining conformational information on side chains and substituted 2,5‐piperazinedione rings is discussed.
Linear dichroism studies of nucleic acids. II. Calculation of reduced dichroism curves of A‐and B‐form DNA
Authors: Matsuoka Yukio , Nordén Bengt
Published: May 2005

We have calculated the uv linear dichroism for the A‐ and B‐forms of DNA using π‐π* transition moments and band components determined from the free DNA bases. The reduced dichroism (LDR) as a function of wavelength is estimated is in the 220–300‐nm region, for both the oriented‐gas model and a simple exciton model. For B‐form DNA, LDR is obtained to −1.48S (S being the orientation factor) over the whole wavelenth region by both models. For A‐form DNA, LDR is not constant, but changes monotonically from about −1.15S at 220 nm to about −1.35S to −1.45S at 300 nm, depending on base combination and degree of interaction (−1.35S for the oriented gas). It is emphasized that a common assumption of a single “effective” transition moment of the principal band at 260 nm may not generally be made because of the extensive overlap of differently polarized bands. The possibility of using the reduced dichroism curve for characterizing the secondary structure of DNA is discussed.
Molecular structure of t‐butyloxycarbonyl‐Leu‐Aib‐Pro‐Val‐Aib‐methyl ester, a fragment of alamethicin and suzukacillin: A 310‐helical pentapeptide
Authors: Rao Ch. Pulla , Balaram P.
Published: May 2005

The pentapeptide Boc‐Leu‐Aib‐Pro‐Val‐Aib‐OMe, a fragment of alamethicin and suzukacillin, crystallizes in the space group P21, with a = 11.034 (2), b = 10.894 (2), c = 15.483 (2) Å, β = 104.80 (2)° and Z = 2. The crystal structure has been solved by direct methods and refined to an R value of 0.069. The peptide backbone folds into a right‐handed 310‐helical conformation, stabilized by two intramolecular 4 → 1 hydrogen bonds between the Leu(1) CO and Val(4) NH and Aib(2) CO and Aib(5) NH groups. The solid‐state conformation is consistent with results of spectroscopic analysis in solution.
Structure of a cellulose II‐hydrazine complex
Authors: Lee David M. , Blackwell John , Litt M. H.
Published: May 2005

The structure of a crystalline cellulose II‐hydrazine complex has been determined by x‐ray diffraction methods as part of an investigation of cellulose‐solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x‐ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked‐atom least‐squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen‐bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen‐bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an NH…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter‐staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.
Multinuclear magnetic resonance studies of monomers and diemrs containing 2′‐fluoro‐2′‐deoxyadenosine
Authors: Cheng Doris M. , Kan Lou‐Sing , Ts'o Paul O. P. , Uesugi Seiichi , Takatsuka Yoko , Ikehara Morio
Published: May 2005

A series of 2′‐fluorinated adenosine compounds, dAfl, dAflp, pdAfl, dAfl‐A, A‐dAfl, and dAfl‐dAfl, have been investigated by nmr spectroscopies. The 1H‐, 19F‐, and 31P‐nmr data provide structural information from different parts of these moleucles. The pKa of the phosphate group of these two 2′‐fluoro‐2′‐deoxyadenosine monophosphates was found to be the same as that of hte parent adenosine monophosphate. As for the pentose conformation, the 3E population is greatly increased as a result of the fluorine substitution at the C2′ position. However, the populations of conformers of gg (C4′‐C5′) and g′g′ (C5′‐O5′) and the average angle ϕ′(C3′‐O3′) of the 2′‐fluoro compounds remain unchanged as compared to the natural riboadenosine monomer and dimer (A‐A). Thefefore, the backbone conformation of the 2′‐fluoro‐2′‐deoxy‐adenosine, its monophosphates and dimers, resembles that of RNA. The extent of base‐base overlapping in these 2′‐fluoro‐2′‐deoxy‐adenosine‐containing dimers is also found to be similar to or even greater than A‐A. Thus, the conformations of these compounds can be considered as those in the RNA family.

These fluorocompounds also serve as models for a careful study on the 19F‐nmr in nucleic acid. The 19F chemical‐shift values are sensitive to the environment of the fluorine atom such as ionic structure of the neighboring group(s) (phosphate of base), solvation, and ring‐ruccent anisotropic effect from the base(s). Qualitatively, the change of the 19F chemical‐shift values (up to 2 ppm) is much larger than that of 1H‐nmr (up to 0.5 ppm) in the dimers. Using dAfl·poly(U), poly(dAfl)·poly(dAfl), and poly(dAfl)·poly(U) helix–coil transition as model systems, the linewidth of 19F in dAfl‐ residues reflects effectively the mobility of the unit in the nucleic acid complex as calibrated by uv data and by 1H‐nmr. Therefore, application of 19F‐nmr spectroscopy on fluorine‐substituted nucleic acid can also be used to detect nucleic acid‐nucleic acid interaction in complicated systems.
Laser light scattering of PBLG in DMF
Authors: Kubota K. , Chu B.
Published: May 2005

We report measurements of static and dynamic properties of poly(γ‐benzyl‐L‐glutamate) (PBLG) in dimethyl formamide at 25 °C using laser light scattering. Correlation‐function profile analyses were performed using the histogram method. The resultant average linewidth and dispersion were reconfirmed using the cumulants method. We were able to determine the molecular‐weight distribution of PBLG using the histogram method and to confirm the polydispersity for rod polymers in solution to be roughly Mw/Mn ∼ 1 + μ2/Γ2. In our analysis of the Rayleigh linewidth, we used both the rigid‐rod model and the Fujime approach involving rod flexibility. We obtained very reasonable agreement between the Fujime theory and our experiments and concluded that for most stiff polymers of interest, it would be more appropriate to use the Fujime approach, which could also yield a rod‐flexibility parameter. In semidilute solutions, we observed two effects, namely, a maximum in the diffusion coefficient and a broadening of the linewidth distribution function at both low and high frequencies, which were not predicted by the Doi‐Edwards theory.
Conformational analysis of acetyl‐L‐phenylalanine p‐acetyl and p‐valeryl anilides
Authors: Petkov D. D. , Ivanov P. M. , Stoineva I. B.
Published: May 2005

Empirical force‐field calculations and ir and 1H‐nmr spectra indicate that five‐membered (C5) and seven‐membered (C) hydrogen‐bonded rings are the preferred conformations of acetyl‐L‐Phe p‐acetyl and p‐valeryl anilides in nonpolar media. The C5/C ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational‐energy calculations suggest that a molecule of water participates in the stabilization of the C conformation.
Crystal structure of Boc‐Ala‐Aib‐Ala‐Aib‐Aib‐methyl ester, a pentapeptide fragment of the channel‐forming ionophore suzukacillin
Authors: Francis A. K. , Iqbal M. , Balaram P. , Vijayan M.
Published: May 2005

t‐Buthyoxycarbonyl‐L‐alanyl‐α‐aminiosobutyryl‐L‐alanyl‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester (t‐Boc‐L‐Ala‐Aib‐L‐Ala‐Aib‐Aib‐OMe), C24H43N5O8, an end‐protected pentapeptide with a sequence corresponding to the 6th through the 10th residues in suzukacillin, crystallizes in the orthorhombic space group P212121 with a = 11.671, b = 14.534, c = 17.906 Å and z = 4. The molecule exists as a right‐handed 310‐helix with a pitch of 6.026 Å. The helix is stabilized by three 4 → 1 hydrogen bonds with the NH groups of Ala(3), Aib(4), and Aib(5) hydrogen bonding to the carbonyl oxygens of t‐Boc, Ala(1), and Aib(2), respectively. The helical molecules arrange themselves in a head‐to‐tail fashion along the a direction in such a way that the NH groups of Ala(1) and Aib(2) hydrogen bond to the carbonyl oxygens of Aib(4) and Aib(5), respectively, of a translationally related molecule. The helical columns thus formed close‐pack nearly hexagonally to form the crystal.
X‐Ray conformational study of the DNA duplex in solution
Authors: Grassian V. , Brady G. W. , Benham C. J.
Published: May 2005

Earlier x‐ray studies on dissolved linear DNA molecules were interpreted on the assumption that the molecules scattered as rigid rods. Improvement in equipment and advances in theory of the scattering from randomly oriented helices prompted us into a reinvestigation of this problem. Careful measurements were made on the scattering from both linear calf thymus DNA and from circular plasmid C0P608 superhelical DNA. Contrary to the earlier work, we find that the scattering patterns show a helical character, with maxima corresponding to those of a helix with pitch angle of 62°, close to that of the C‐W helix. The patterns for both types of DNA, although similar, show a 5% displacement of the maximum in the superhelical form, just that expected when the C‐W helix is superimposed on a superhelix axis. Introduction of intercalators (PtTS) causes a progressive extension of the helix, as shown by a shift to larger angles and a fading out of the maximum. In the concentration range of 40 mg/mL, interfernce peaks develop, the result of an apparent stacking of the chains, with an interchain distance of ∼35 Å.
Total intensity light scattering from short, optically anisotropic wormlike chains
Authors: Allison Stuart A.
Published: May 2005

Simple exact equations are derived for intensity light scattering from optically anisotropic wormlike chains in the absence of excluded volume. The results are valid at low scattering angles (q2 〈R2G〉 ≲ 1) for all sormilke chains from rigid rods to random couils. The present work and an earlier theory [Nagai, K. (1972) Polym. J. 3, 67–83] appear to be equivalent, although they were both derived using different methods. The present work is primarily concerned with short wormlike chains, since intensity light scattering from short fragments may provide valuable information about DNA flexibility. By using the results of this work to reanalyze some older light‐scattering studies [Godfrey, J. E. & Eisenberg, H. (1976) Biophys. Chem. 5, 301–318], it is shown that anisotropy corrections to polarized light‐scattering measurements have been overcorrected in the past. It can be anticipated that future light‐scattering experiments will determine the base‐pair anisotropy.
Monomolecular condensation of λ‐DNA induced by cobalt hexammine
Authors: Widom Jonathan , Baldwin Robert L.
Published: May 2005

Measurements of static and dynamic light scattering have been used to distinguish between monomolecular DNA condensation and aggregation of condensed molecules. In low salt, using Co3+(NH3)6 as the condensing agent, and at λ‐DNA concentrations below 0.2 μg/mL, the transition curves for monomolecular condensation and aggregation are well separated for times of 16 h. In these conditions, the intensity of scattered light (90°) and also the diffusion coefficient of the condensed DNA show reasonable values for monomolecular condensation that are independent of DNA concentration and also of Na+ Co3+(NH3)6 concentrations for which monomolecular condensation is complete. At higher Co3+(NH3)6 concentrations, which produce aggregation (as judged by the intensity of scattered light), the diffusion coefficient decreases sharply.

The transition curve for monomolecular condensation is independent of DNA concentration but shows a hysteresis loop. The kinetics of condensation are slow in the forward direction and fast in the reverse direction, indicating that the actual transition curve is measured closely by reversal experiments. Aggregation is blocked kinetically in both the forward and reverse directions when Co3+(NH3)6 is the condensing agent at low Na+ concentrations. When spermine or spermidine is the condensing agent and observations are made at 16 h, it is not possible to separate the transition curves for monomolecular condensation and for aggregation in conditions that are successful with Co3+(NH3)6.

Some interesting properties of monomolecular condensation are noted. (1) The transition is not a two‐state reaction, as judged by measurements of the diffusion coefficient through the transition zone. (2) The transition for monomolecular condensation is diffuse. (3) The dimensions of the monomolecular condensates have been calculated from the translational diffusion coefficient for an assumed toroidal shape by the formula derived by Allison and coworkers [(1981) Biopolymers 20, 469–488]. These dimensions are in reasonable agreement with ones deduced from electron microscopy by Chattoraj and coworkers [(1978) J. Mol. Biol. 121, 327–337]. (4) The phase diagram relating the Na+ to the Co3+(NH3)6 concentrations needed for condensation has a slope of 0.6 in a log–log plot. According to numerical solutions of Manning's theory for the atmospheric binding of competing cations to DNA, this means that condensation occurs at a late stage in the replacement of Na+ by Co3+(NH3)6 around the DNA. The fraction of DNA phosphate charge neutralized at condensation is computed to be in the neighborhood of 0.9, as found by Wilson and Bloomfield [(1979) Biochemistry 18, 2192–2196], but to vary with the Na+ concentration.
Inhibition of cation‐induced DNA condensation by intercalating dyes
Authors: Widom Jonathan , Baldwin Robert L.
Published: May 2005

Several intercalating dyes are shown to inhibit the cation‐induced condensation of λ‐DNA when Co3+(NH3)6 is the condensing agent. The dyes that have been studied are ethidium, propidium, proflavin, quinacrine, and actinomycin D. Earlier work has shown that intercalating dyes inhibit ψ‐DNA condensation. [Lerman, L. S. (1971) Prog. Mol. Subcell. Biol. 2, 382–391; Cheng, S. & Mohr, S. C. (1975) Biopolymers 14, 663–674.] Dye‐induced decondensation of intramolecularly condensed DNA has been studied by making use of conditions in which Co3+(NH3)6 produces intramolecular condensation without significant aggregation. Some aggregation is caused, however, during dye‐induced decondensation. Dye titration curves of DNA decondensation have been measured by excess light scattering to monitor decondensation and by fluorescence to monitor intercalation. All of the dyes studied act as competing cations in displacing the condensing cation Co3+(NH3)6 from the DNA. Competition occurs both in and below the transition zone for condensation. The effectiveness of a dye as a competing cation increases with its net positive charge. Before decondensation begins, no intercalated dye can be detected, suggesting that intercalation might be incompatible with the proper helix packing needed for cation‐induced DNA condensation. To test this last point, methidium–spermine was synthesized: it contains an intercalating methidium head group combined with a polyamine tail. Methidium–spermine is found to cause λ‐DNA condensation, but aggregation accompanies condensation, as has been found earlier for spermine and spermidine. Fluorescence and absorption spectra indicate that the methidium group is intercalated when the DNA is condensed, indicating that intercalation need not be incompatible with DNA condensation. The presence of aggregates among the condensed DNA molecules makes this last conclusion tentative.