bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequential oligopeptides. Conformational studies of the oligopeptides and a polypeptide with the repeating sequence L‐norvalyl‐glycyl‐L‐proline
Authors: Bonora Gian Maria , Toniolo Claudio
Published: December 2004

Conformational studies of a series of oligopeptides (from the tripeptide to the octadecapeptide) with the repeating sequence L‐norvalyl‐glycyl‐L‐proline and a polytripeptide with this sequence are reported. By means of chiroptical techniques, unordered conformations are found for all oligopeptides in water, trifluoroethanol, and ethylene glycol and for the water‐insoluble polymer in trifluoroethanol. In ethylene glycol the polymer assumes a collagen‐like structure. Infrared studies indicate that all the oligomers, in contrast to the polymer, are unordered in the solid state.
Spin‐labeled polyuridylic acid. Formation of an intermediate structure
Authors: Pan Yu‐Ching E. , Bobst Albert M.
Published: December 2004

Temperature‐dependent conformational transitions of spin‐labeled poly(U) at low temperature in spermidine and cesium chloride buffer have been measured by electron spin resonance spectroscopy. The Arrhenius plot shows the existence of the order‐disorder transition at a temperature close to that obtained from absorbance temperature profiles. However, in addition the formation of an intermediate state is observed during the melting of the ordered poly(U) to its random coil.
Conformation and packing analysis of polysaccharides and derivatives. I: Mannan
Authors: Zugenmaier P.
Published: December 2004

A previously described procedure for simultaneous optimization of bond lengths and angles was used to test different models for mannan I. Potential hydrogen bonds and the glycosidic angle were included in the optimization. A conformational model with bifurcated intramolecular hydrogen bonds of the type observed in the methyl cellobioside methanol complex showed the best agreement with available exprerimental data. The coordinates of this model were provided by computer calculations. The available X‐ray data, however, were not sufficient for selecting this model; rather, ir data were necessary to furnish the needed information. The different conformational models tested all showed an almost constant virtual bond length O(1)–O(4) of the β‐pyranose residue. This was in contrast to the previously obtained results for the α‐pyranose residues.
Interaction of ethidium bromide with DNA. Optical and electrooptical study
Authors: Houssier Claude , Hardy Bernadette , Fredericq Eugene
Published: December 2004

The binding of ethidium bromide to DNA has been studied by various optical methods. From fluorescence polarization studies, and film, electric linear dichroism, and circular dichroism spectra, we propose assignments of the absorption bands of the dye, which are discussed in connection with wave‐mechanical calculations recently reported.

The optical activity induced in the dye absorption bands upon binding to DNA was attributed to various origins depending on the electronic transition considered. The visible absorption band displayed a circular dichroism due to the asymmetry of the binding site and independent of the amount of binding. The transition identified at 378 nm from the circular dichroism and electric dichroism observations was thought to be due to a magnetic‐dipole transition. It remained constant with increasing amounts of dye bound. The main ultraviolet band showed circular dichroism characteristics corresponding to exciton interactions between dye molecules bound to neighboring sites.

The electric dichroism observed for the strongly bound dye molecules indicated that the phenanthridinium ring of ethidium bromide was probably not perfectly parallel to the DNA base planes. When the amount of dye bound to DNA exceeded the maximum amount compatible with the exclusion of adjacent binding sites, the electric dichroism decreased owing to the appearance of externally bound dye molecules with no contribution to the dichroism.

Sonicated DNA was used to study the lengthening of the DNA molecule upon complexation. Although the viscosity of the complexes increased with the amount of binding, the rotational diffusion coefficient measured by the electric birefringence relaxation was not detectably affected. The absence of variation in the electric birefringence with the binding indicated that the DNA base stacking remained unaltered.
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

Dielectric 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

Proton 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

Copolymers 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

Spectrophotometric 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

Poly(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

Described 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

The 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

The 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

The 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

The 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

A 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

The 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

Various 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

A 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

Analysis 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

The 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

In 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

A 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

β‐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.
The structure of triple‐stranded G·2C polynucleotide helices
Authors: Hattori Masao , Frazier Joe , Miles H. Todd
Published: December 2004

The thermal stability of a new polynucleotide complex has been used to establish the hydrogen‐bonding structure of three‐stranded C‐G·CH+ helices. In the Hoogsteen structure, the 8NH2 group of 8NH2GMP can form a third hydrogen bond to the CH+ strand, but in the alternative structure, the 8NH2 group can form no interbase hydrogen bonds. For the new complex, 8NH2GMP·2 poly(C), a transition temperature of 80°C is observed under conditions in which the corresponding complex formed with 5′‐GMP has a Tm of 20°C. We conclude from this 60° elevation of transition temperature that a third hydrogen bond is formed by the 8NH2 group and that the structure must have Hoogsteen bonding. In order to be compatible with this structure in regular helices formed by U,C copolymers, A·2U bonding would also have to have a Hoogsteen structure.
Intermediates in the strand‐separation transition of T7 DNA
Authors: Wensley C. Glen , Record M. Thomas
Published: December 2004

Sedimentation velocity runs as a function of temperature in the region of the alkaline helix‐coil transition have enabled us to demonstrate the existence of stable two‐stranded intermediates in the strand‐separation process for T7 DNA. The strand‐separation transition under these conditions has an intrinsic breadth of ∼1°C, and within this temperature range (Tm + 2°C < T < Tm + 3°C) the intermediate forms are progressively converted (as a function of temperature) to single‐stranded DNA. Parallel characterizations of the strand‐separation transition by viscosity and absorbance–renaturation studies in the alkaline solvent are entirely consistent with the sedimentation experiments. Comparison of the experimental mean sedimentation coefficient of the intermediate forms with theoretical predictions for branched structures suggests that in these molecules the two strands are connected at a single point, not centrally located with respect to the ends of the molecule.
Thermal properties of collagen in helical and random coiled states in the temperature range from 4° to 300°K
Authors: Andronikashvili E. L. , Mrevlishvili G. M. , Sh. Japaridze G. , Sokhadze V. M. , Kvavadze K. A.
Published: December 2004

The low‐temperature heat capacity of collagen (in the hydrated and dehydrated states) and the large entropy of collagen in the coiled state relative to the same protein in the helical state were investigated. The heat capacity for collagen in the solid state in the temperature range 4°–50° K changes proportionally to the square of temperature (Cp ∼ T2). Above 50°K there is a linear dependence (Cp ∼ T). The differences in the character of temperature dependence of heat capacity for the hydrated and dehydrated collagen show the importance of the specific interaction of water molecules with polypeptide chains of this protein. The peculiarities of the temperature dependence of the heat capacity difference (ΔCp) of hydrated denatured (random coiled) and hydrated native (helical) collagen are observed at 15°, 120°, and 240°K. These differences are caused by the varying degree of ordering of the hydrate water molecules in native and denatured collagen macromolecules. At all temperatures (4°–300°K) the entropy of the random coiled state is higher than that of collagen in the native state and at 298°K ΔS = ∫ (ΔCp/T)dT = 0.8 cal/100 g °K.
Electronic energy transfer between tyrosine and tryptophan in the peptides trp‐(pro)n‐Tyr
Authors: Chiu H. C. , Bersohn R.
Published: December 2004

A series of peptides, Trp‐(Pro)n‐Tyr, n = 0,…,5 were synthesized. Details of the synthetic method using the Merrifield method are given. The initial objective was to determine the characteristic distance R0 for energy transfer from tyrosine to tryptophan. This objective became submerged in the question of the structure of the chain of prolyl spacers. The efficiency of the energy transfer diminishes as the number of intervening prolines increases. Quantitatively the fit is much better if we assume that the peptides have a polyproline I structure (cis) than if we assume a trans polyproline II structure. Proton nmr spectra on the other hand suggest that the n = 1,3,5 peptides are mixtures of rotamers. Our conclusions are similar to those of previous workers, i.e., that in water there is a transition from a mixture of structures for small n to an all‐trans structure at some n > 5. This means that in water, at least, proline is a dubious spacer for energy‐transfer studies.
Influence of local interactions on protein structure. I. Conformational energy studies of N‐acetyl‐N′‐methylamides of pro‐X and X‐pro dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A.
Published: December 2004

Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N‐acetyl‐N′‐methylamides of Pro‐X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X‐Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low‐energy single‐residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low‐energy single‐residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low‐energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low‐energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro‐X dipeptides because ϕPro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X‐Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.
A nuclear magnetic resonance study of the helix–coil transition of poly(L‐glutamic acid)
Authors: Lader H. J. , Komoroski R. A. , Mandelkern L.
Published: December 2004

There have been many reports that the nuclear magnetic resonance (nmr) spectra of a large number of polypeptides exhibit peak doubling of the α‐carbon and the α‐carbon proton in the helix–coil transition region. One apparent exception to this generalization has been polypeptides with ionizable side chains, where the helix–coil transition is induced by changes in pH in aqueous solution. Because it is important to establish the proper theoretical reason for the peak doubling and its relation to the rate of conformational change of amino acid residues, we have reexamined the proton and carbon‐13 nmr spectra, at high field, for two polydisperse samples of poly(L‐glutamic acid). Doubling of the α‐carbon proton resonance as well as those of the α‐ and β‐carbon, and backbone carbonyl are observed for a low‐molecular‐weight sample (DP = 54), while a higher molecular weight sample (DP = 309), exhibits only single resonances. Thus, polydispersity by itself is not sufficient to observe peak doubling; low‐molecular weight is also required.
Architecture of chitin gel as examined by scanning electron microscopy
Authors: Hirano Shigehiro , Yamaguchi Ryuji , Matsuda Noriaki
Published: December 2004

An architecture of the solid phase of chitin gel was examined by scanning electron microscopy. The ultrastructure of the xerogel was microporous with parallel channels surrounded with membranous walls. The pore shapes at cross section were polyhedral with three walls at the junctions. The pore was 30–50 μm in diameter and 80–300 μm in length, and the thickness of the walls was less than 1.5 μm. The gel is considered to be a polyphasic gel, consisting of small droplets of water held up in these pores.
The concentration dependence of transport processes: A general description applicable to the sedimentation, translational diffusion, and viscosity coefficients of macromolecular solutes
Authors: Rowe A. J.
Published: December 2004

The transport coefficients of macromolecular solutes are normally extrapolated to “infinite dilution” to remove the effects of concentration‐dependence terms, for which no satisfactory general treatment has been available. It is shown that a simple general treatment for the concentration‐dependence effect can be derived, applicable to limiting concentrations in the absence of charge effects or other forms of specific interactions between the solute particles. The relationships derived are of considerable practical significance for the characterization of the size and conformation of natural and synthetic polymers.
Scattering correction to the absorbance, wavelength dependence of the refractive index increment, and molecular weight of the bovine liver glutamate dehydrogenase oligomer and subunits
Authors: Eisenberg Henryk , Josephs Robert , Reisler Emil , Schellman John A.
Published: December 2004

The wavelength dependence of the refractive index increments of bovine serum albumin and bovine liver glutamate dehydrogenase solutions was determined in the range 650–300 nm. It was shown, by measuring the extinction coefficients of glutamate dehydrogenase under conditions of widely differing molecular weights, that a significant scattering correction need not be applied to correct extinction measurements in the absorbtion band. The molecular weight of glutamate dehydrogenase oligomer determined by light scattering and sedimentation equilibrium agrees with the value calculated from the primary structure, if a recently reported value of the extinction coefficient is used.
Light‐scattering and depolarization in biopolymers: Distinction between flexible chain models
Authors: Shkorbatov A. G. , Verkin B. I. , Kulik I. O.
Published: December 2004

The general formulas describing the low‐angular dependence of polarized (Vv) and depolarized (Hv) light‐scattering intensity by a chain macromolecule of arbitrary form with anisotropic polarizability are derived. It is shown that the value dHv/dtHvo (where t = [〈R2〉S/L]2, S being the scattering vector) is an indication of the chain‐flexibility mechanism. This permits one to distinguish between the models of a wormlike chain, regular zigzag, or statistical zigzag. The results of numerical calculations useful for the interpretation of experimental data are presented.
The analysis of circular dichroism spectra of natural DNAs using spectral components from synthetic DNAs
Authors: Gray Donald M. , Hamilton Frederick D. , Vaughan Marilyn R.
Published: December 2004

We have tested 21 different basis sets of synthetic DNA circular dichroism spectra and have slected one for use in spectral analyses of natural DNAs. This “standard” set consists of spectra of eight polymers: poly[d(A‐A‐T)·d(A‐T‐T)], poly[d(A‐G‐G)·d(C‐C‐T)], poly[d(A‐T)·d(A‐T)], poly[d(G‐C)·d(G‐C)], poly[d(A‐G)·d(C‐T)], poly[d(A‐C)·d(G‐T)], poly[d(A‐T‐C)·d(G‐A‐T)], and poly[d(A‐G‐C)·d(G‐C‐T)]. This basis set, applied according to the first‐neighbor polymer procedure of Gray and Tinoco, allows a more uniformly accurate spectral analysis of six natural complex DNAs and eight (A+T)‐rich satellite DNAs for base composition and first‐neighbor frequencies than was previously possible. We find that spectra of poly[d(A)·d(T)] and/or poly[d(A‐C‐T‐)·d(A‐G‐T)] are not generally required for good analysis results but we show in this and the following paper that these spectra are needed for the most accurate analyses of some satellite DNAs.
Cooligopeptides containing aromatic residues spaced by glycyl residues. IX. Fluorescence properties of tryptophan‐containing peptides
Authors: Wiget Peter , Luisi Pier Luigi
Published: December 2004

The fluorescence properties of several cooligopeptides of glycine, phenylalanine, and tryptophan, containing one or two aromatic residues, are investigated. In particular, a detailed analysis is made of the influence of pH upon the quantum yield and the position of the emission maximum (λmax) in H‐Trp‐Trp‐OH, H‐Trp‐Gly‐OH, H‐Gly‐Trp‐OH, H‐Gly‐Trp‐Gly‐OH, H‐Trp‐Trp‐OH, H‐Trp‐Trp‐Gly‐OH, H‐Gly‐Trp‐Trp‐OH, H‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, H‐Gly‐Phe‐Trp‐OH, and H‐Gly‐X‐(Gly)n‐Trp‐Gly‐OH, with X = Phe or Trp, and n = 0,1,2. It is shown that raising the pH from ca. 2 to 11 results in a red shift of λmax, and an increase in the quantum yield. These changes, mostly structure dependent, are in most cases attributable to electronic perturbations acting directly upon the λmax of the fluorophore(s) and upon the quenching efficiency of the free amino and carbonyl groups. For the compounds having two adjacent tryptophyl residues, it is shown that the two fluorophores do not appear to have the same emission properties and the quantum yield is lower than expected. The causes of this behavior are discussed in terms of conformational effects, stacking interactions, and radiationless energy transfer. Finally, an attempt is made to correlate fluorescence data with previous circular dichroism data which had indicated the occurrence of a conformationally rigid structure for some of the compounds having two adjacent aromatic residues.
Conformational studies on Cu(II) polycomplexes of pyridoxal Schiff bases of polypeptides
Authors: Dentini M. , Savino M. , De Santis P. , Verdini A. S.
Published: December 2004

Structures of Cu(II) complexes of pyridoxal Schiff bases with poly(L‐lysine), poly(L‐ornithine), and poly(L‐α,γ‐diaminobutyric acid) were investigated by absorption spectra, CD, and conformational analysis.

Although the polypeptides retain their typical right‐handed α‐helical conformation, opposite Cotton effects were found for the poly(L‐lysine) and poly(L‐ornithine) polycomplexes in the whole range of wavelengths from 600 to 250 nm. As in the analogous derivatives of salicyladehyde, this effect seems to be due to a stereospecific binding of the square planar Cu(II)‐bis‐pyridoxylideneimine group to the α‐helical matrix. Circular dichroism spectrum of poly(L‐α,γ‐diaminobutyric acid) polycomplex is similar to that found for poly(L‐lysine) derivative, but indicates large tetrahedral distortion of the square‐planar coordination of copper ion.
Vectorial interpretation of spectra for the study of associations
Authors: Marck Ch. , Schneider Ch. , Brehamet L.
Published: December 2004

If one considers CD spectra as vectors, then a CD spectrum may be treated as a single parameter, every wavelength entering with the same weight. The representation of a set of spectra as a vector space and the problem of the linear independence of the concentrations are discussed. Three examples of vectorial interpretation are given: determination of the number of independent molecular species; determination of the stoichiometry of a complex; and graphical representation of the overall variation of a spectrum as a function of an external parameter.
Theory of ligand binding to heterogeneous receptor populations: Characterization of the free‐energy distribution function
Authors: Thakur Ajit K. , Delisi Charles
Published: December 2004

We present a method for characterizing the free‐energy and affinity distributions of a heterogeneous population of molecules interacting with a homogeneous population of ligands, by driving expressions for the moments as functions of experimental binding curve characteristics, and then constructing the distribution as an expansion over a Gaussian basis set. Although the method provides the complete distribution in principle, in practice it is restricted by experimental noise, inaccuracies in data fitting, and the severity with which the distribution deviates from a Gaussian. Limitations imposed by experimental inaccuracies and the requirement of an appropriate analytic function for data fitting were evaluated by Monte Carlo simulations of binding experiments with various degrees of error in the data. Thus a distribution was assumed, binding curves with random errors were generated, and the technique was applied in order to determine the extent to which the characteristics of the assumed distribution could be recovered. Typical inaccuracies in the first two moments fell within experimental error, whereas inaccuracies in the third and fourth were generally larger than standard deviations in the data. The accuracy of these higher‐order moments was invarient for experimental errors ranging from 2 to 10% and may thus be limited, within this range, primarily by the curve fitting procedure. The other aspect of the problem, accurate inference of the distribution, is limited in part by inaccuracies in the moments but more importantly by the extent to which the distribution deviates from a Gaussian. The extensive statistical literature on the problem of inference enables the delineation of specific criteria for estimating the efficiency of construction, as well as for deciding whether certain features of the inferred distribution, such as bimodality, are artifacts of the procedure. In spite of the limitations of the method, the results indicate that the mean and standard deviation are obtainable with greater accuracy than by a Sipsian analysis. This difference is particularly important when the distribution is narrow and width detection is beyond the sensitivity of the Sips plot. The method should be more accurate than the latter as an assay for homogeneity as well as for characterizing the moments, though equally easy to apply.
Lysinonorleucine cross‐link formation in alpha amino heptenoic acid‐substituted peptide derivatives
Authors: Karwoski Gene , Galione Michael , Starcher Barry
Published: December 2004

Studies on the cross‐linking of a tripeptide (t‐butyloxycarbonyl‐L‐alanyl‐D,L‐2‐amino‐6‐heptenoyl‐L‐alanine methyl ester) have shown that it is possible to form specific cross‐links in good yields through Schiff base formation of the ε amino group of lysine. The heptenoic acid residue has been ozonized to an aldehyde and condensed with the ε amino of lysine in the compounds alpha‐t‐butyloxycarbonyl‐L‐alanyl‐L‐lysine methyl ester and alpha‐t‐butyloxycarbonyl‐L‐lysine methyl ester to form the cross‐link, lysinonorleucine. This compound has been stabilized by reduction with sodium borohydride and quantitated on the amino acid analyzer. This technique converts from 60 to 98% of the available aldehyde to lysinonorleucine.
The flow linear dichroism of DNA: Comparison with the bead‐spring theory
Authors: Wilson Robert W. , Schellman John A.
Published: December 2004

The flow linear dichroism if T7 bacteriophage DNA has been obtained as a function of velocity gradient in neutral aqueous solutions containing 0.15M Na+ or K+. The data are compared with the hydrodynamic bead‐spring theory of Rouse and Zimm using currently available spectroscopy, structural, and hydrodynamic parameters. Good agreement between theoretical and experimental isocline angle behavior is found. The magnitude of the measured linear dichroism is not in exact agreement with theory when presently accepted stiffness and optical parameters are used. Agreement is improved either by assuming a shorter persistence length or a less negative value for the limiting dichroism of DNA.
Solvent denaturation
Authors: Schellman John A.
Published: December 2004

Solvent denaturation is developed along thermodynamic lines rather than from multiple‐binding theory. Almost all the relations derivable from site‐binding theory have their counterparts in the thermodynamic formulation showing that the details of binding models may be sufficient but are not necessary for the general description of solvent denaturation. Equations are derived for the effect of denaturant concentration on stability at constant temperature and on tm. It is recommended that the thermodynamic treatment be used instead of binding models unless stoichiometric interactions are demonstrable experimentally.