bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of aggregates and helix–coil transition of polypeptides by dielectric measurements. I. Poly‐γ‐benzyl‐L‐glutamate in dioxane and dioxane–dichloroacetic acid
Authors: Gupta A. K. , Dufour C. , Marchal E. 
Published: December 2004

AbstractDielectric dispersion measurements on poly‐γ‐benzyl‐L‐glutamate (PBLG) in dioxane and dioxane–dichloroacetic acid (DCA) mixtures in the frequency range 200 Hz–2 MHz were made in order to study the structure of molecular aggregates. The structure of aggregates is explained on the basis of the variation of dipole moment and relaxation time with degree of aggregation. PBLG was found to form linear head‐to‐tail‐type aggregates in dioxane. These aggregates gradually reduce in size without loosing their α‐helical structure during the process of disaggregation obtained by either adding DCA to the solution in dioxane or by heating. It was confirmed that the addition of 30 wt % DCA completely destroys the aggregation of PBLG in dioxane at 30°C. Thermal disaggregation, however, was not complete even at a temperature approaching the boiling point of the solvent.A reaction scheme for aggregation is proposed and equilibrium constants are calculated at various stages of aggregation. The enthalpy of aggregate formation is found to be −3 kcal/mol. Results of optical rotatory dispersion measurements of the helix–coil transition in this system are also presented.
Conformational studies on the hypothalamic thyrotropin releasing factor and related compounds by 1H nuclear magnetic resonance spectroscopy
Authors: Donzel B. , Rivier J. , Goodman M. 
Published: December 2004

AbstractProton magnetic resonance studies at 220 MHz were carried out on the hypothalamic thyrotropin releasing factor (TRF) and a variety of synthetic analogs designed to yield specific information about side chain–side chain and side chain–backbone interactions. The results show that the very low field resonance position of one of the carboxamide protons observed for TRF dissolved in dimethylsulfoxide is neither caused by a seven‐membered nor by a ten‐membered hydrogen bonded ring, but rather is due to a short range interaction between the unprotonated histidyl side chain and the carboxamide residue. A systematic study of the preferred histidyl side chain conformation in various TRF analogs is in good agreement with this interpretation. It was demonstrated that this interaction is not strong enough to cause significant changes in the preferred back bone conformation of the hormone. The possibilities for typical dipole–dipole interaction are discussed. No such interaction has been detected in TRF dissolved in water. We conclude that the tertiary structure of TRF in polar solvents is determined primarily by the steric characteristics of the bulky side chains which maintain the molecule preferentially in an extended conformation.
Random copolymers of α‐benzyl‐L‐aspartate with ortho‐ and para‐nitrobenzyl‐L‐aspartates. Intrinsic and extrinsic dichroic bands and the left‐to‐right‐handed α‐helical transition
Authors: Loucheux‐Lefebvre Marie‐H. , Duflot Catherine , Weill Gilbert 
Published: December 2004

AbstractCopolymers of benzylaspartate with the corresponding para‐nitro and ortho‐nitro derivatives are known to undergo, at increasing nitro content, a transition from a left‐handed α‐helical conformation to a right‐handed α‐helical conformation. The circular dichroism associated with the n, π* transition of the amide group, as well as the extrinsic bands associated with the nitrobenzyl chromophore, have been studied for these copolymers as a function of the nitro content. The circular dichroism associated with the 330‐nm extrinsic band is shown to present an abrupt change, which parallels the change in the 222‐nm band characteristic of the left‐ to right‐handed helix transition. The intensity of the 222‐nm CD band seems unaffected by the interaction with the side‐band chromophore. The circular dichroism associated with the 330‐nm band is much stronger in the right‐handed conformation and is unaffected by increasing interactions between side chains. Interpretation in the light of the possible mechanism for optical activity of helical molecules seems to indicate that the 330‐nm extrinsic effect is essentially due to the Condon, Altar, and Eyring (CAE) mechanism and μ‐m perturbation (in Schellmann terminology) on the side‐chain chromophore n, π* transition.
Equilibrium studies on neutral red–DNA binding
Authors: Walz Frederick G. , Terenna Barry , Rolince David 
Published: December 2004

AbstractSpectrophotometric binding studies were undertaken on the interaction of neutral red with native and heat‐denatured, sonicated, calf thymus DNA in a 0.2M ionic strength buffer containing Tris–sodium acetate–potassium chloride at 25°C. The pKA of neutral red was found to be 6.81. At pH 5 the binding of protonated neutral red was complicated even at low concentration ratios of dye to DNA. In the pH range 7.5–8.5 the tight binding process could be studied and it was found that both protonated and free base species of neutral red significantly bind with DNA having association constants (in terms of polynucleotide phosphate) of 5.99 × 103 M−1 and 0.136 × 103 M−1, respectively, for native DNA and 7.48 × 103 M−1 and 0.938 × 103 M−1, respectively, for denatured DNA. The pKA value of the neutral red–DNA complexes were 8.46 for native DNA and 7.72 for denatured DNA. These results are discussed in terms of possible binding mechanisms.
Conformational states of poly(L‐tyrosine) in aqueous solution
Authors: Patton Elizabeth , Auer Henry E. 
Published: December 2004

AbstractPoly(L‐tyrosine) [(L‐Tyr)n] has been characterized in aqueous solution using circular dichroism (CD) and infrared (ir) spectroscopy, and ultracentrifugal analysis. Most of the experiments were carried out at 0.01% polymer or less to avoid the complications caused by precipitation previously encountered by others. This permitted us to study solutions of (L‐Tyr)n at lower pH values than had been attained previously. Our results show that a transition to an antiparallel‐β conformation occurs at pH 11.32 upon titration from higher pH. The β structure is intramolecular when first formed and aggregates with time or upon titration below pH 11. Ultracentrifugal analysis of the intramolecular β conformation shows that it is quite compact, with a frictional coefficient ratio, f/fmin, of 1.09. In addition to the β structure, a nonordered form of the polymer has been obtained below pH 11 by rapid titration of the ionized polyelectrolyte. This form is nonaggregated and was found to have an f/fmin of 1.01, and is therefore almost spherical. The aggregated β form was found to be thermodynamically more stable than the nonordered form at pH 10.7.
Assignment of the histidine 12‐threonine 45 hydrogen‐bonded proton in the nmr spectrum of ribonuclease A in H2O
Authors: Patel Dinshaw J. , Canuel Lita L. , Woodward Clare , Bovey Frank A. 
Published: December 2004

AbstractDescribed herein are proton nmr experiments on chemically modified derivatives of ribonuclease A designed to elucidate the origin of an exchangeable resonance, assigned previously to a histidine ring N proton that titrates between 11 to 13 ppm with a pKa of 6.1 in H2O solution. Histidines 48 and 105, which are distant from the active site, are eliminated as candidates for this resonance from inhibitor binding studies on the enzyme in acetate–water solutions. This exchangeable resonance titrates with modified pKa's and constant area over the above pH range in His‐119‐N1‐carboxymethylated‐RNase A and des‐(121–124)‐RNase A, thus eliminating the imidazole N3 proton in the His 119‐Asp 121 hydrogen bond. In His‐12‐N1‐carboxymethylated‐RNase A, this resonance is also observable, but broadens on raising the pH above 7 and at elevated temperatures above neutrality. It exhibits a pH‐independent chemical shift characteristic of the protonated state of histidine. On the basis of these findings, this exchangeable resonance, designated a, is assigned to the imidazole N1 proton of His 12, which is hydrogen‐bonded to the carbonyl oxygen of Thr 45 in the crystal.
Correlation of exchangeable (NH) and nonexchangeable (C2H) histidine resonances in the proton nmr spectrum of ribonuclease A in aqueous solution
Authors: Patel Dinshaw J. , Woodward Clare , Canuel Lita L. , Bovey F. A. 
Published: December 2004

AbstractThe ionization characteristics of the hydrogen‐bonded His 12 N1 proton observed to titrate between 11 to 13 ppm in the nmr spectrum of ribonuclease A in H2O solution are compared with the ionization characteristics of the four histidine C2 protons in the enzyme. Comparison of the pKa's of the enzyme in H2O and D2O in the absence and presence of cytidine monophosphate (−5′, −3′, and −2′) inhibitors, line widths in the presence of Cu II at pH 3.6 and 5.6, and chemical shifts in the presence of AgNO3 permit a correlation of the exchangeable His 12 N1 proton with the active site histidine C2 proton exhibiting the lower ionization pKa. The histidines with pKa of 5.1 and 5.6 in ribonuclease A in the absence of salt are assigned in this study to His 12 and His 119, respectively.
Reassignment of the active site histidines in ribonuclease A by selective deuteration studies
Authors: Patel Dinshaw J. , Canuel Lita L. , Bovey Frank A. 
Published: December 2004

AbstractThe C2H resonance of the active site histidine residue designated AS‐2, which has the lower pKa of the two active site histidines, has been correlated in both RNase A and RNase S by comparing the pH 3 to 5.5 regions of the chemical shift titration curves, the effect of the inhibitor CMP‐3′ on the chemical shifts at pH 4.0, and the effect of Cu II on the line widths at pH 3.6. It has been demonstrated that resonance AS‐2 is absent in the spectrum of RNase S′ reconstituted using S‐peptide deuterated at the C2 of His 12, and in that of the RNase S′‐CMP‐3′ complex. We thus demonstrate that histidine AS‐2 is in fact His 12 in both enzymes. This finding is in agreement with out previous assignment of the exchangeable NH proton in RNase A to His 12, but reverses the assignments of the active site histidine C2H resonances made earlier by other authors.
Magnetic susceptibility of ferrihemoglobin in water and 5% t‐butanol
Authors: Anusiem A. C. I. 
Published: December 2004

AbstractThe molar magnetic susceptibility of ferrihemoglobin solutions, as a function of pH and temperature using the nmr technique of Evans, in water and 5% t‐butanol has been determined. Results suggest that within a small pH region, the conventional analysis of magnetic susceptibility in terms of high‐spin and low‐spin contributions breaks down. The implication of this is discussed in terms of possible conformational change involving two subspecies. The effect of t‐butanol is also discussed in terms of the t‐butanol effect on water.
Adsorption behaviour of globular proteins at the water/mercury interface
Authors: Scheller Frieder , Jänchen Michael , Prümke Hans‐Jörg 
Published: December 2004

AbstractThe adsorption of globular proteins at solid/liquid or liquid/liquid interfaces provides evidence of unfolded molecular conformation. Proteins with high apolar character are strongly unfolded, while those with high polar character are generally incompletely unfolded. Structural changes of globular proteins at adsorption on mercury electrodes were studied by ac polarography and capacity–time curves. The surface area per molecule of nine globular proteins was determined from the adsorption kinetics at the dropping mercury electrode. For all the proteins investigated, this value was greater than the maximal molecular cross section of the native proteins. The surface area was about 19 Å2 per amino acid residue, which coincides with the value for unfolded proteins at the water/air interface. Differences between dropping mercury electrode and hanging drop mercury electrode occurred only with lysozyme and phosphorylase; for the other proteins, the structure of the adsorption layer was independent of the time of interaction at the electrode. Since not all of the reducible groups of the adsorbed proteins come into contact with the electrode, the flattening should be incomplete.
The random coil → β transition of copolymers of L‐lysine and L‐valine: Potentiometric titration and circular dichroism studies
Authors: Mandel Richard , Fasman Gerald D. 
Published: December 2004

AbstractA series of copolymers of L‐lysine and L‐valine [poly(L‐lysinef L‐valine100‐f)] containing 0–13% L‐valine have been studied, in 0.10M KF solution, using potentiometric titration and circular dichroism spectroscopy. Incorporation of increasing amounts of valine into the copolymers favors β‐sheet formation over α‐helix formation at high pH and room temperature. The titrations were analyzed using the method of Zimm and Rice and the partial free energy (ΔG0cβ) for the coil‐to‐β‐sheet transition for valine is estimated at 900 cal/mole at 25°C. From the temperature dependence of the free energy, the partial enthalpy, ΔH0cβ, and entropy, ΔS0cβ, of the transition for valine is estimated to be 854 cal/mole and 6.0 e.u., respectively. The corresponding partial thermodynamic parameters for L‐lysine are in agreement with published results. The fraction of β‐sheet versus pH has been calculated for poly(L‐lysine86.8 L‐valine13.2) at 25.0°C using the titration data; data obtained from circular dichroism spectroscopy for the same copolymer are in good accord. It is concluded from these results that L‐valine is a very strong β‐sheet forming amino acid. Furthermore, these results indicate that the Zimm–Rice method is applicable to transitions between the coil and β‐sheet states for a polypeptide containing two different residues.
Sedimentation of generalized systems of interacting particles. II. Active enzyme centrifugation—theory and extensions of its validity range
Authors: Cohen René , Claverie Jean‐Michel 
Published: December 2004

AbstractThe first detailed application of a recently published very general approach to chemical equilibria during sedimentation is presented. As a consequence of the very extensive theoretical treatment, made possible by this approach, the active enzyme analytical centrifugation method can now be used under a far wider set of conditions than before, including the study of many interacting active molecule systems. It has also been shown that this method is as precise as the more conventional ones.
Configuration‐dependent properties of randomly coiling polynucleotide chains. I. A comparison of theoretical energy estimates
Authors: Olson Wilma K. 
Published: December 2004

AbstractVarious theoretical estimates of the conformational energy associated with polynucleotides in solution have been compared with each other and also with the experimentally observed conformations found in X‐ray crystallographic investigations of low‐molecular‐weight nucleic acid analogs. In view of the disparities between these data, certain configuration‐dependent properties (i.e., the mean‐square unperturbed end‐to‐end distance 〈r2〉0 and the average vicinal nmr coupling constant 〈J〉) appropriate to randomly coiling polynucleotides described by either the energy estimates or by the crystallographically preferred conformations have also been calculated and compared with the known solution behavior of polynucleotide chains. Both the theoretical energy surfaces and the X‐ray data show good agreement with the nmr coupling constant indications of the preferred rotations about the O‐C and C‐C bonds of the chain backbone. The principal discrepancies between the theoretical methods and X‐ray data arise in their ability to predict successfully the preferred rotations about the two phosphodiester bonds of the chain backbone and the unperturbed dimensions of randomly coiling polynucleotide chains.
Estimation of the zero shear rate viscosity for dilute solutions of rigid macromolecules with complex configurations
Authors: Abdel‐Khalik S. I. , Bird R. Byron 
Published: December 2004

AbstractA method for estimating the zero shear rate viscosity for dilute solutions of rigid macromolecules with complex configurations is proposed; this method is based on the macromolecular kinetic theory of Curtiss, Bird, and Hassager. Macromolecular models constructed from a collection of spheres, cylindrical rods, circular discs, and parallelepipeds with arbitrary dimensions and relative orientations can be easily handled by this method. Comparison with available experimental data for several biopolymers shows excellent agreement. As an application to this method, we investigate the effect of surface roughness on the intrinsic viscosity of spherical particles.
The use of nanosecond fluorometry in detecting conformational transitions of an allosteric enzyme
Authors: Tung Ming S. , Steiner Robert F. 
Published: December 2004

AbstractAnalysis of the time decay of fluorescence of 1‐anilino‐naphthalene‐8‐sulfonate bound to phosphorylase b reveals the presence of two components with different decay times. In glycylglycine buffer, pH 7.0, the addition of the activators AMP or IMP, or the conversion to phosphorylase a results in a preferential decrease in the amplitude of the component of longer decay time, arising probably from a preferential dissociation of 1‐anilino‐naphthalene‐8‐sulfonate from the corresponding site as a consequence of a change in molecular state.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. II. Ultraviolet absorption and circular dichroism properties of co‐oligopeptides of tryptophan and glycine
Authors: Luisi Pier Luigi , Rizzo Vincenzo , Lorenzi Gian Paolo , Straub Barbara , Suter Ulrich , Guarnaccia Rocco 
Published: December 2004

AbstractThe uv absorption and circular dichroism (CD) properties in water (pH 5.9) and trifluoroethanol of several co‐oligopeptides of glycine and tryptophan have been investigated. These compounds contain one tryptophyl residue, such as H‐Gly‐Trp‐OH, H‐Trp‐Gly‐OH, and H‐Gly‐Trp‐Gly‐OH; or two, such as H‐Trp‐Trp‐OH, H‐Gly‐Trp‐Trp‐OH, H‐Trp‐Trp‐Gly‐OH, and H‐Gly‐Trp‐(Gly)n‐Trp‐Gly‐OH (I, n = 0,1,2). Furthermore, the case of some protected derivatives, such as Z‐Trp‐Gly‐OMe, Z‐Gly‐Trp‐Gly‐OMe, and Z‐Trp‐Trp‐OMe, Z‐Trp‐Trp‐Gly‐OMe, Z‐Gly‐Trp‐Trp‐Ome were investigated. The extinction coefficients in H2O in the region of the L bands, referred to one mole of tryptophyl residue, are essentially the same for all compounds within the limit of experimental error, thus indicating that no strong chromophoric interaction takes place in the oligopeptides containing two aromatic residues. However, in the far uv region, anomalies in the absorption properties cannot be excluded. The investigated compounds show marked differences in their CD properties. Whereas in the case of lower molecular‐weight peptides (e.g., H‐Trp‐Gly‐OH and H‐Gly‐Trp‐OH), these differences can be ascribed, at least in part, to the influence of the charge end groups on the indole chromophore, in the case of the compounds containing two tryptophyl residues, the differences in CD properties are assumed to reflect the different structures and conformations of the oligopeptides. In particular, we observed a negative dichroic band at ∼225 nm in H‐Gly‐Trp‐Trp‐OH and I(n = 0) in water. In trifluoroethanol, this band has a much larger intensity, and it is present also in Z‐Gly‐Trp‐Trp‐OMe, Z‐Trp‐Trp‐Gly‐OMe, and Z‐Trp‐Trp‐OMe. It is argued that such a negative band is characteristic of the sequence ‐CO‐Trp‐Trp‐, and the possibility that it derives from intramolecular chromophoric interaction is discussed. It is also pointed out, particularly in view of the high ellipticity values found in some cases (up to 100,000 deg cm2 dmol−1), that this feature may reflect a high degree of conformational rigidity connected with the sequence ‐CO‐Trp‐Trp‐.
Stereochemistry of the D and L copolymerization of valine N‐carboxyanhydride
Authors: Akaike Toshihiro , Aogaki Yukio , Inoue Shohei 
Published: December 2004

AbstractIn the D and L copolymerization of valine N‐carboxyanhydride (NCA) with various D/L ratios initiated by n‐butylamine, the stereoselection of monomer NCA by the growing polymer chains, which take a β‐like conformation, does not take place. This result is in remarkable contrast to that in the D and L copolymerization of alanine NCA and of γ‐benzyl glutamate NCA where the growing α‐helical polymer chains participate in the stereoselection of the monomer antipodes.
Photon correlation spectroscopy, total intensity light scattering with laser radiation, and hydrodynamic studies of a well fractionated DNA sample
Authors: Jolly Douglas , Eisenberg Henryk 
Published: December 2004

AbstractA Malvern laser light‐scattering instrument has been modified for use at scattering angles down to 5° and both total intensity and quasi‐elastic scattering experiments. A sample of sheared, length‐fractionated calf‐thymus DNA was characterized by sedimentation, viscosity and electron microscopy. Quasi‐elastic scattering and absolute intensity determinations were performed with the laser instrument and intensity determinations only with a Fica conventional light‐scattering photometer. The total intensity experiments gave M̄w = (3.75 ± 0.15) × 106 and 〈R2〉1/2z = (206.9 ± 10.3) nm which yielded a value for the persistence length, allowing for polydispersity, of 66 ± 6nm. The quasi‐elastic experiments at scattering angles below 20° gave D020, w = (2.23 ± 0.06) × 10−8 cm2/sec which combined with S020, w = 15.6 in the Svedberg equation gave M̄w = (3.73 ± 0.18) × 106. In addition, from the higher angle data we extracted a value of the longest intramolecular relaxation time, τ1 of 17.5 msec. This is not in particularly good agreement with τ1 predicted by the Zimm–Rouse theory using our other experimental parameters. The disagreement may be due to the restricted applicability of the Zimm–Rouse spring‐bead model as a quantitative representation of DNA molecules. Alternatively, it may be due to present difficulties in the unambiguous interpretation of molecular motions from the experimental autocorrelation functions.
The two β forms of poly (L‐glutamic acid)
Authors: Itoh Koichi , Foxman Bruce M. , Fasman Gerald D. 
Published: December 2004

Abstractβ‐Helical poly(L‐glutamic acid) in a gel state was found to be easily converted to the antiparallel β form by heating. Two β forms were obtained, depending on the temperature of heating. Temperatures between 40° and 85°C produced a β form with a spacing between pleated sheets (d001) of 9.03 Å, termed β1. If the heating was carried out at temperatures higher than 85°C, the β1 form underwent another conformational transition reducing the d001 value from 9.03 to 7.83 Å (termed β2) without any prominent change in the fiber repeat distance (i.e., the polypeptide backbone conformation). The time course of these two transitions was followed by measuring the infrared spectra of the samples, and it was concluded that the α → β1 transition in its initial stage obeys a pseudo‐first order rate process with activation enthalpy and entropy of 54 kcal/mol and 92 eu, respectively. On the other hand, the typical sigmoidal conversion curves observed for the transition between the two types of β forms (β1 → β2) indicate that this transition proceeds via a socalled “nucleation and growth” process. The kinetic theory of phase transitions developed by Avrami can be applied with success to explain this transition. The infrared spectra, in the region from 1800 to 200 cm−1, were measured for these two β forms and the results showed that the conformation of the side chains and the mode of the hydrogen bonding between the side‐chain carboxyl groups undergo appreciable change during the transition.The heat‐induced conformational transition of poly(L‐Glu78 L‐Val22) was also studied. The copolymer was transformed from the α‐helical conformation directly to the β2 form. The reason for this was thought to be due to the fact that the L‐valine residues and the L‐glutamyl residues near the L‐valine residues have a strong tendency to take the more compact β2 form.