bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Study of stepwise conformational changes in poly(β‐benzyl‐L‐aspartate) with the helix–coil transition by means of proton and carbon‐13 NMR
Authors: Sase Shigeru , Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô 
Published: May 2005

AbstractThe helix–coil transition for poly(β‐benzyl‐L‐aspartate) [poly(Asp[OBzl])] in solvent mixtures of trifluoroacetic acid/deuterated chloroform (F3AcOH/CDCl3) was studied by means of proton and carbon‐13 nmr. Conformational fixation of the side chain occurs before the coil–helix transition of the backbone, when neighboring phenyl rings face each other. Another type of conformational fixation occurs in the side chain after the coil–helix transition of the backbone. These conformational changes of the side chain are due to the changes of the strength of the interaction between the side‐chain ester group and the F3AcOH molecule. In the absence of F3AcOH (coil‐forming solvent), the polymer has a rather rigid structure in which the side chain may wrap around the backbone. These conformational changes of the polymer are closely related to the changes of the interaction between the polymer and F3AcOH molecules.
Intermolecular indole–imidazolium complexes. II. Interaction of a block copolymer (L‐tryptophan)n–(γ‐ethyl‐DL‐glutamate)m with imidazolium hydrochloride and poly(L‐histidine hydrochloride)
Authors: Palumbo Manlio , Cosani Alessandro , Terbojevich Maria , Peggion Evaristo 
Published: May 2005

AbstractThe charge‐transfer complexes of a poly(L‐tryptophan) sequence with imidazolium hydrochloride and poly(L‐histidine hydrochloride) have been investigated in 2,2,2‐trifluoroethanol by ultraviolet (uv), circular dichroism (CD), and fluorescence techniques. Both complexes exhibit absorption maxima centered at around 275 nm, whereas hypochromism with respect to the combined spectra of the constituents can be observed below 250 nm. All complexes show optical activity in the near uv and in the peptide absorption region, which is discussed in terms of the conformational properties of the donor. A marked decrease of the fluorescence intensity of the L‐tryptophan sequence is observed upon addition of imidazolium hydrochloride and poly(L‐histidine hydrochloride). From the fluorescence data the formation constant of the charge‐transfer complex between the L‐tryptophan sequence and imidazolium ions is also evaluated.
Statistical theory of chain scission and concurrent damage not associated with chain scission in linear polymers
Authors: Hawkins Roland B. 
Published: May 2005

AbstractA statistical theory of the parallel accumulation of randomly placed breaks and damage not associated with breaks in linear polymers is presented. Expressions for the weight fraction of polymer in the form of chains that bear n or more sites of nonbreak damage (markers) are developed, and results of numerical computations with them presented. The effects of polydispersity in the undamaged sample are discussed. The relation of the computed quantities to experimental methods used in the study of damage to nucleic acids due to radiation and chemical exposure is discussed.
On the B to A conformation change of the double helix
Authors: Eyster James M. , Prohofsky E. W. 
Published: May 2005

AbstractWe have investigated the B to A conformation change of DNA double helices by a new method “soft‐mode analysis.” We find theoretically that a mode does soften when the vibration normal modes are perturbed by increasing the electrostatic interaction between the unbalanced charges on atoms in the double helix. The same mode also softens for enhanced van der Waals interactions. The mode softening indicates the onset of conformation change. The enhancing of the electrostatic and van der Waals interaction mimic the effect of decreasing the polar nature of the solvent or water of hydration associated with the B conformation DNA. We discuss qualitatively the concept of soft modes and their relation to conformation change as well as their applicability to macromolecules. We discuss previous work in which the normal vibrational modes have been calculated. We also discuss the displacement which comes from the soft mode and show that it correlates very well with that expected for the B to A conformation charge.
Helix coil transitions of d (A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n; evaluation of parameters governing DNA stability
Authors: Oliver Adrian L. , Wartell Roger M. , Ratliff Robert L. 
Published: May 2005

AbstractThe thermally induced helix‐coil transitions of three A‐T DNAs, d(A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n, were studied. Experimental transition curves of the DNAs were analyzed using the loop entropy model of DNA melting. The calculation of the melting curve of d(A‐A‐T)n·d(A‐T‐T)n is presented using the integral equation formalism of Goel and Montroll. The aim of this work was to evaluate thermodynamic parameters which govern DNA stability and to test the theoretical model employed in the analysis. Our results show (1) an excellent over‐all agreement between theory and experiment, (2) a loop entropy exponent k = 1.55 ± 0.05 provided the best fit to all the polymer transition curves, (3) the evaluated stacking free energies reflect the relative stability of the DNAs, and (4) the stacking energies of the ApA·TpT dimer evaluated from d(A)n·d(T)n and d(A‐A‐T)n·d(A‐T‐T)n differ. The last result is consistent with different conformations for the dimer in these two polymers.
DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions
Authors: Orosz Jerry M. , Wetmur James G. 
Published: May 2005

AbstractDNA melting temperatures and renaturation rates have been determined for Me2Et2NBr and a series of RMe3NBr and REt3NBr solvents where R is a linear hydrocarbon chain. The point of independence of DNA melting temperature on base composition has been investigated for each solvent system. Renaturation rates are compared with those found in other concentrated salt solutions. Solvent mixtures which accelerate DNA renaturation have also been investigated.
Analysis of periodic patterns in amino acid sequences: Collagen
Authors: McLachlan A. D. 
Published: May 2005

AbstractMethods are given for analyzing regularly spaced patterns of amino acids in proteins and applied to the α1 chain of collagen. Fourier methods use the transform of the sequence either embedded in a very long array or folded onto a fundamental base period. Filtering through a moveable “window” of definite width is used to display almost regular features at any chosen frequency. A pattern detection method is described for patterns of general shape. Collagen has statistically significant periodicities at fractions of the stagger distance D = 670 Å. Hydrophobic groups show strong orders of 5, 6, 11; proline 5; charged groups 6, 18, 21. Charged residues mostly occur as neutral pairs. Their distribution has strong 6th and 21st orders which also appear in the changes which are paired at multiples of D. Charge pairs separated by (D + 3) residues show a strong 5D/89 pattern and may form a system of salt bridges across the fibril. There is no sign of any regular pattern of amino acids over the triple helix with a period close to its natural pitch of 30 residues. Supercoiled models with six relative turns of the contact edge between paired triple‐helical strands are examined.
Circular dichroism evidence for G·U and G·T base pairing in poly[r(G‐U)] and poly[d(G‐T)]
Authors: Gray Donald M. , Ratliff Robert L. 
Published: May 2005

AbstractWe have measured the circular dichroism (CD) and absorption properties of poly[r(G‐U)] and poly [d(G‐T)] over a wide range of Na+ concentrations and temperatures. We find evidence for self‐complexed forms of these polymers at lower temperatures and/or higher Na+ concentrations than generally needed for double‐strand formation in other DNA and RNA polymers. These self‐complexes could be composed of double‐stranded regions with weak G·U or G·T base pairs.
Cis‐Trans equilibrium and kinetic studies of acetyl‐L‐proline and glycyl‐L‐proline
Authors: Cheng H. N. , Bovey F. A. 
Published: May 2005

AbstractBy means of carbon‐13 nmr (at 25 MHz) the trans/cis conformer ratio in glycyl‐L‐proline has been measured in aqueous (D2O) solution over the temperature range 33–96°C. It is found that ΔH0 = −4.2 kJ/mole and ΔS0 = −9.7 J/mole/K.Measurements of the T1 values for the proline ring carbons yielded values consistent with a fast puckering process involving both the β‐ and γ‐carbons.Measurements of the rate of cis‐trans conformational interconversion in glycyl‐L‐proline, using complete line‐shape analysis for the glycyl α‐carbon resonance, gave values for the trans → cis isomerization as follows: ΔH≠ = 83.5 ± 0.2 kJ/mole; ΔS≠ = 0.0 ± 10 J/mole/K. A more approximate determination from coalescence temperature observations gave a value of ΔG≠ of 82.0 ± 0.4 kJ/mole for this process in acetyl‐L‐proline in aqueous solution. The presence of 12M NaSCN lowered this barrier by ca. 2.6 kJ/mole.Such measurements are relevant to present theoretical models of the denaturation‐renaturation processes in proteins, in which proline residues may play a key role.
Circular dichroism of adenine and thymine containing synthetic polynucleotides
Authors: Greve J. , Maestre M. F. , Levin A. 
Published: May 2005

AbstractCircular dichroism (CD) spectra of poly(dA), poly(dT), poly(dA)·poly(dT), and poly[d(A‐T)]·poly[d(T‐A)] have been measured as a function of temperature. From these data difference spectra have been calculated by subtracting the spectrum measured at low temperature from the spectra measured at higher temperatures. The CD difference spectra obtained upon melting of the two double‐stranded polymers are very similar. From a comparison of these difference spectra with calculated ones it is shown that optical transitions near 272 nm (on A) and 288 nm (most probably on T) are present. The premelting changes of the CD spectrum of poly[d(A‐t)]·poly[d(T‐A)] are due to a change in conformation in which the secondary structure goes from a C‐ to B‐type spectrum by increasing the A‐type nature of the polymer. Such a change is not observed for poly(dA)·poly(dT). Instead, a transition between two different B‐type geometries occurs.
Calorimetric investigation of some elastin‐solvent systems
Authors: Ceccorulli Giuseppina , Scandola Mariastella , Pezzin Giovanni 
Published: May 2005

AbstractThe interaction of ox ligamentum nuchae elastin (native, purified, and soluble) with different solvents (water, ethylene glycol, methanol, and 2,2,2‐trifluoroethanol) was investigated by means of differential scanning calorimetry. The unfreezable solvent content and the corresponding solvent to elastin residue molar ratio were determined from the melting endotherms of the freezable solvent present in these systems. The molar ratio obtained in the case of water and ethylene glycol agrees with hypothesis of a direct solvation of the main chain peptide group and is interpreted according to a model previously proposed for polyamides. Quite different molar ratios are obtained in the case of the two monofunctional solvents and no model can be proposed at present to explain their interaction with the protein.
Poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid). II. Conformational studies
Authors: Goren H. Joseph , McMillin Carl R. , Walton Alan G. 
Published: May 2005

AbstractThe solution characterization of poly(Lys‐Ala‐Glu) is described. This polytripeptide is zwitterionic at neutral pH and is shown to take on a conformation which is dictated by the state of ionization, molecular weight, temperature, and solvent. The polypeptide is almost entirely α‐helical at low pH and temperature for polymers of greater than 25,000 molecular weight. Melting profiles for these conditions show tm ∼ 20°C. Analysis of circular dichroism curves shows the α‐helical content to vary in a linear manner with molecular weight in the range 3000–30,000. At neutral pH the charged polypeptide is essentially random, but substantial α‐helix could be induced by addition of methanol or trifluoroethanol. At temperatures where the sequential polypeptide is a random coil, addition of trifluoroethanol produces a polymer which is mostly α‐helical but also contains an appreciable ammount of β‐structure. The infrared spectrum of a low‐molecular‐weight fraction assumed to be cyclo(Lys‐Ala‐Glu)2 was tentatively assigned a β‐pleated sheet structure.A comparison of this polytripeptide in various ionization states with other polytripeptides containing L‐alanine and L‐glutamate or L‐lysine shows the α‐helix directing properties for the (uncharged) residues to lie in the order Ala > Glu > Lys.
Viscosity and potentiometric measurements of poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid) and poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid)
Authors: Goren H. Joseph , Grandan Loretta , Jay Alfred W. L. , Lotan Noah 
Published: May 2005

AbstractPoly(His‐Ala‐Glu) and poly(Lys‐Ala‐Glu) were examined by viscosity and potentiometric titration. These measurements were interpreted in terms of the hydrodynamic size of the above sequential polypeptides. Effects of polymer, size and concentration, and solution‐salt concentration were demonstrated. Although the sequential polypeptides generally behave like polyampholytes, they do demonstrate some differences. These differences my be attributed to the ability of ionized side chains three residues apart to repel themselves, in the order His < Glu < Lys.
Kinetics of the renaturation of yeast tRNA3Leu
Authors: Hawkins E. R. , Chang S. H. , Mattice Wayne L. 
Published: May 2005

AbstractYeast tRNA3Leu is one of several tRNA molecules which can adopt a stable, biologically inactive, denatured conformation. The circular dichroism of the native and denatured conformers differs, providing the basis for the present study of the mechanism for the renaturation process. Conversion of the denatured structure to the native takes place in two steps: a rapid change occurring immediately on addition of Mg++, followed by a slower, strongly temperature‐dependent step which returns the molecule to its biologically active state. Optimal kinetic data for the second step could be obtained at 285 nm. Analysis of the time dependence of Δε285 by the Guggenheim method demonstrated that this step follows first‐order kinetics. The temperature dependence of the rate constants over the range 32–41°C yielded the following parameters for the rate‐limiting step: Ea = 69 kcal/mole, ΔH‡ = 69 kcal/mole, and ΔS‡ = 146 cal/mole deg. Values of this magnitude are typical of order—order transitions in nucleic acids.
Synthesis and conformational study of poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine)
Authors: Yamamoto Hiroyuki , Hayakawa Tadao 
Published: May 2005

AbstractHigh‐molecular‐weight poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine) was prepared by the N‐carboxyanhydride method. From the results obtained by a study of the optical rotation, nuclear magnetic resonance, and solution infrared absorption, the conformation of poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine) depended greatly on the solvent taking a right‐handed helix with [θ]225 = −13,600 ∼ −18,900 in alkyl halides, a left‐handed helix with [θ]228 = 22,100 ∼ 24,800 in cyclic ethers or trimethylphosphate, and a random coil structure in dichloroacetic acid, trifluoroacetic acid, or hexafluoroacetone sesquihydrate. The polypeptide underwent a right‐handed helix‐coil transition in chloroform/dichloroacetic acid (or trifluoroacetic acid) mixed solvents and a left‐handed helix‐coil transition in dioxane/dichloroacetic acid (or trifluoroacetic acid) mixed solvents. The results were compared with those of poly(0‐carbobenzoxy‐L‐tyrosine).
Unsaturated amino‐acid residues as probes for the conformation of polypeptides in solution
Authors: Pieroni Osvaldo , Fissi Adriano , Montagnoli Giorgio , Ciardelli Francesco 
Published: May 2005

AbstractAcetyl‐(dehydro‐Phe) and acetyl‐bis(dehydro‐Phe) groups have been attached to the ε‐amino group of the lysine residues of the copolymer poly(Glu92Lys8) by reacting this last with acetyl‐(dehydro‐Phe)‐azlactone and acetyl‐bis(dehydro‐Phe)‐azlactone, respectively.In the latter case induced CD is observed between 250 and 330 nm, due to the relative dissymmetric disposition of the two dehydro‐Phe groups under the chiral field of the polypeptide chain.pH dependence of the induced CD, observed for the copolymer and lacking in the lowmolecular‐weight structural model, is related to the α‐helical and random coiled conformation of the polypeptide chain.
Nuclear magnetic resonance study of the impact of ribose 2′‐O‐methylation on the aqueous solution conformation of cytidylyl‐(3′ → 5′)‐cytidine
Authors: Cheng Doris M. , Sarma Ramaswamy H. 
Published: May 2005

AbstractIn order to obtain information about the conformational characteristics at the nearestneighbor level in the 2′‐O‐methylated region of t‐RNA, as well as in the bizarre 5′‐terminus of eucaryotic mRNA, a detailed nuclear magnetic resonance study of 2′‐O‐methyl‐cytidylyl‐(3′ → 5′)‐cytidine (CmpC) was conducted. Proton spectra were recorded at 270 MHz in the Fourier mode in D2O solutions, 0.01M, pD 7.3 in the temperature range 5–80°C. Complete accurate sets of nmr parameters were derived for each of the nucleotidyl units by a combination of homo‐nuclear decouplings and simulation iteration methods. The data were translated into conformational parameters using procedures developed in earlier studies from these laboratories.It is shown that the ribofuranose ring exists at a 2E ⇄ 3E equilibrium with clear preference [(75–80)%] for the 3E mode. The C(4′)‐C(5′) and C(5′)‐O(5′) bonds form a stable conformational network with outspoken preference for conformers in which Ψ1, Ψ2 ≃ 60° and ϕ2 ≃ 180°. The orientation of the 3′‐phosphate and 2′‐O‐methyl groups is such that ϕ1′ ≃ 210° and ϕ″ ≃ 60°. The phosphodiester bonds are flexible and shift trends for base, H(1′), and H(5″) suggest the existence of a conformational blend of right‐handed stack (g−g−), left‐handed stack (g+g+), and unstacked arrays (tg− and tg+).Elevation of temperature perturbs the 2E ⇄ 3E equilibrium accompanied with modest depopulation of ψ1, ψ2 ≃ 60° and ϕ2 ≃ 180° conformers. The major effect of elevation of temperature is in the increase of unstacked arrays at the expense of g−g− and g+g+ conformers. The shift trend of Cmp‐H(3′) with temperature shows that torsional variation about O(3′)‐P is facilitated by increase in temperature and the preferred rotamer about O(3′)‐P in the unstacked form is t (ω1′ = 180°).A detailed comparison of the aqueous solution conformations of CpC and CmpC reveals that 2′‐O‐methylation causes: (i) a reduction in the magnitude of χ1; (ii) an increase in the population of 3E pucker at the 3′‐nucleotidyl unit; and (iii) modest perturbations in the O(3′)‐P and P‐O(5′) bond conformations. Comparison of the aqueous solution conformations of AmpA and CmpC makes clear that the conformational properties of pyrimidine‐pyrimidine and purine‐purine dimers which carry a 2′‐O‐methylated 3′‐nucleotidyl unit are significantly different.
Hydrodynamic properties of macromolecular complexes. I. Translation
Authors: De La Torre Jose Garcia , Bloomfield Victor A. 
Published: May 2005

AbstractWe have developed an improved theory for calculating the translational frictional coefficients of rigid macromolecular complexes composed of unequal spherical subunits. The Yamakawa hydrodynamic interaction tensor, which improves on the Oseen tensor by taking account of the finite sizes of the frictional subunits, has been generalized to accomodate nonidentical subunits. Iterative numerical methods are described for solving the set of simultaneous hydrodynamic interaction equations, thus avoiding preaveraging. The theory is applied to prolate ellipsoids of revolution, to lollipops, and to dumbbells, and comparison is made with earlier, more approximate theories.
Conformational properties of L‐leucine, L‐isoleucine, and L‐norleucine side chains in L‐lysine copolymers
Authors: Arfmann H.‐A. , Labitzke R. , Wagner K. G. 
Published: May 2005

AbstractThe structure inducing properties of L‐leucine, L‐isoleucine, and L‐norleucine residues incorporated into poly(L‐lysine) were investigated by the observation of the circular dichroism of the respective random copolypeptides. The comparison involves the coil‐helix transition in water/methanol mixtures, the formation of ordered structures at higher pH, and the kinetics of the α‐helix to β‐conformation transition of the leucine and norleucine copolymers induced by temperature changes at pH 10.5. The results confirm the known properties of the leucine residue, strongly supporting the α‐helix conformation. They also support the idea that the isoleucine residue is one of the most powerful candidates for β‐structure formation, and they show that the unbranched norleucine residue has intermediate properties. The results are discussed on the basis of steric and hydrophobic properties of the three side chains.
Low velocity gradient flow birefringence and viscosity changes in hyaluronate solutions as a function of pH
Authors: Barrett T. W. , Harrington R. E. 
Published: May 2005

AbstractThe flow birefringence and extinction angle over a velocity gradient range of approximately 5–100 sec−1, and the zero shear‐viscosity have been obtained from human umbilical cord hyaluronic acid at concentrations of 0.25, 0.125 and 0.0625%, and pHs 6.0, 6.5, 7.0, 7.5, 8.0, and 8.5 and constant ionic strength 0.1. The data indicate a large change in optical anisotropy as a function of pH, with most of the transition in the pH range 7.0–7.5, i.e., across the physiological range. The sign of the anisotropy changes between pH 8.0 and 8.5. These results, together with changes in the extinction angle and intrinsic viscosity as a function of pH, suggest a pH‐dependent structural change in the system. Due to the abruptness of the transition, as evidenced by the intrinsic viscosity and flow birefringence, it is probable that the structural transition is cooperative. If the data are interpreted in terms of the Rouse‐Zimm Gaussian subchain theory, a modification of the model in terms of the Haller‐Cerf concept of internal viscosity is required. Thus, the demonstrated properties of hyaluronate solutions indicate a system with memory of stress. Due to the presence of large concentration effects discernible in the extinction angle measurements, hyaluronic acid probably exists as a network in solution. The results are discussed with respect to the mechanoelectrical transducing properties of hyaluronates and stress‐dependent changes in ORD already reported.
Pyrene derivatives as fluorescent probes of conformation near the 3′ termini of polyribonucleotides
Authors: Koenig Paul , Reines Scott A. , Cantor Charles R. 
Published: May 2005

AbstractWhen pyrene butyric acid hydrazide or pyrene acetic acid hydrazide is attached to single‐strand RNA 3′ termini a red shift in absorbance and substantial hypochromicity are observed. A strong induced CD is seen and the fluorescence intensity is quenched by an order of magnitude. In double‐stranded samples, a further 10‐fold quenching of fluorescence is seen. Several lines of evidence suggest that the residual fluorescence of pyrene butyric acid hydrazide‐duplex conjugates arises from a minor species. The most likely possibility is dye reacted at a site other than the 3′ end. Some indication exists that 3′‐attached pyrene may perturb the relative stability of nearby duplex. Within the limits of this reservation, it appears that 3′‐pyrene conjugates may be rather useful for detecting the existence of duplex regions accessible to a dye at the 3′ end of complex RNAs.