bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman spectrum of the right‐handed α‐helix of poly‐L‐alanine
Authors: Koenig J. L. , Sutton P. L. 
Published: May 2005

AbstractThe laser‐excited Raman vibrational spectrum of poly‐L‐alanine has been obtained. The Raman spectrum is compared with the infrared spectrum and vibrational frequencies calculated from normal coordinate analysis. The symmetric modes of the α‐helix appear with strong intensity in the Raman spectrum. A large number of skeletal modes are obtained in this Raman spectrum for the first time.
Helix–random coil phase transitions in polypeptide systems with random defects: A statistical mechanical model
Authors: DuPré Donald B. , Salsburg Zevi W. 
Published: May 2005

AbstractThe statistical mechanics of the effect of a small number of randomly occurring defects on the melting of a polypeptide chain is developed by using a perturbation of Boltzmann factors technique. The method is illustrated by an example where a second‐component impurity contributes more to the energy of the hydrogen‐bonded superstructure of the polypeptide chain than does the dominant amino acid residue, resulting in the overall destabilization of the helical conformation.
Conformational studies of β‐D‐1,4′‐xylan
Authors: Sundararajan P. R. , Rao V. S. R. 
Published: May 2005

AbstractThe nonbonded interaction energy was computed for xylobiose and xylan as a function of the dihedral angles (ϕ,ψ). The energy maps indicate that interactions higher than the second neighbor are negligible. Of the four possibilities, the left‐handed helical conformation with (ϕ,ψ) = (63°,25°) is of the lowest energy. The hydrogen bond search and the energy maps reveal that the xylan helix is stabilized mainly by van der Waals forces. The allowed region map shows that the freedom of rotation of the monomer units in cellulose is more restricted than that of the monomer units in xylan, because of the presence of the CH2OH group in the former. The intramolecular hydrogen bond of the O5 ⃛O3′ type is stronger in cellulose.
Temperature dependence of CD spectra of DNA from various sources
Authors: Usatyi A. F. , Shlyakhtenko L. S. 
Published: May 2005

AbstractThe CD spectra of DNA from various sources (T2; T4; Cd; Escherichia coli; calf thymus; Streptomyces chrysomalis) were investigated. A new band Δε210 in the CD spectra of glucosylated DNA of the T even phages was found. The temperature dependence of the CD spectra of DNA was obtained over a wide range of temperatures, including those of the helix–coil transition.The band Δε275 for all DNAs does not appreciably change in the range of the helix–coil transition. The monotonic increase of this band before melting, and its decrease after melting is observed with an increase in temperature.The amplitude of the CD band Δε245 for all the DNAs studied and Δε210 (glucosylated DNA) parallels the change of E260 absorbance.
Investigation of the effect of amylose/iodine complexation on the conformation of amylose in aqueous solution
Authors: Senior Marilyn B. , Hamori Eugene 
Published: May 2005

AbstractUsing a potato amylose fraction of 8 × 105, molecular‐weight viscosity studies were carried out at 25°C on solutions containing 0.176–0.042% polymer, 8.67 mM KI, 1% ethanol, and different concentrations of iodine. By a novel extrapolation method, the intrinsic viscosities of the amylose/iodine complex were determined under various conditions of iodine binding (0–0.133 g I2/g amylose). Contrary to the view long held in this research area, it was found that the intrinsic viscosity of amylose solutions decreases significantly upon complex formation with iodine. Taking into account the results of our previous kinetic studies, the present findings are interpreted in terms of an amylose model characterized by loose, extended helical regions which are interrupted by short disordered regions. It is proposed that the intrinsic viscosity decrease observed is due to a shortening of the linear dimension of the polymer chain. This conformation change is apparently caused by the contraction of loose helical regions of the amylose macromolecule due to the entrapment of iodine (and perhaps other) atoms inside the helical cavities.
Intrachain hydrolysis in sarcosine–γ‐p‐nitrophenyl‐L‐glutamate copolymers
Authors: Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu 
Published: May 2005

AbstractRandom copolymers of sarcosine and small amounts of γ‐p‐nitrophenyl‐L‐glutamate (poly(Sar,pNPGlu)) were synthesized and their hydrolyses were investigated in buffer solutions. The reaction courses of their spontaneous hydrolyses consisted of two parts; the initial fast reaction and the subsequent slow reaction. Since the former became shorter as the chain length of copolymer increased, it was attributed to a faster hydrolysis of ester groups near the chain ends.The hydrolysis was considerably accelerated by the introduction of a pyridyl group to a chain end of the copolymer. This was explained by the intrachain catalysis, since the contribution of interchain catalysis was found to be very small. The extent of acceleration was much smaller than in the reaction along the polyacrylamide chain reported by Morawetz et al. The lesser flexibility of polysarcosine chain may account for the difference. Also in the intrachain hydrolysis a large deviation from the first‐order kinetics was observed, which indicated the different reactivities of each ester group positioned at the different separation along the chain from the terminal pyridyl group. Kinetic calculations were carried out using rate constant ki, for the hydrolysis of an ester group attached to the ith residue by the terminal puridyl group. It was found that the dependence of ki on i, Which is the distance between an ester group and the terminal pyridyl group, was more specific than that of intrachain rate constants for the chain effect polymerization of DL‐phenylalanine NCA previously investigated.
Electrical conduction in hydrated collagen. I. Conductivity mechanisms
Authors: Bardelmeyer G. H. 
Published: May 2005

AbstractThe electrical conductivity of bovine Achilles tendon with various amounts of adsorbed water was measuredas a function of temperature. The conduction appeared to be fully determined by the water of hydration. The current is probably primarily carried by protons at water contents up to 45% and by small ions at water contents beyond 65%. In both ranges of water content, a linear relation between activation energy and water and content was found. As to the lower range, this is explained by the action of Coulombic forces during the separation of proton–hydroxyl ion pairs. In two regions of water content a linear relation between the logarithm of the pre‐exponential factor and the activation energy was found. There are, however, indications that at certain water contents the dissociation constant of the adsorbed water is several orders of magnitude higher than in liquid water.
Electrical conduction in collagen. II. Some aspects of hydration
Authors: Bardelmeyer G. H. 
Published: May 2005

AbstractDeterminations of the amount of bound water in hydrated proteins yield strongly diverging values. The cause of this is the continuity of the transition from bound to free water, and the diffeernt sensitivities to water structure of the measuring techniques. Only the methods that aim at the determination of the amount of water, whose phase remians unchanged duing freezing, yield similar values. The value for collagen as deduced from conductivity data is about 50% water of the dry weight. It is believed that this water interacts with adsorptive groups on the macromolecules, whereas the freezable water occurs in capillaries.
The effects of salts on the nmr spectra of D2O in collagen fibers
Authors: Dehl R. E. 
Published: May 2005

AbstractThe effects of two salts, MgCl2 and MgSO4 on the wide‐line nmr spectrum of D2O in oriented, undernatured collagen fibers have been examined at four different D2O contents. MgCl2 was found to decrease the nmr doublet splitting, as compared with equal quantities of pure D2O while the major effect of MgSO4 was to inhibit the adsorption of D2O without significantly affecting its nmr spectrum. The results, together with a few observations of KCl and LiCl solutions, indicate that even fairly high concentrations of salt have only small effects on the nmr spectrum of D2O in fibrous collagen. It is considered unlikely that either “two‐state” or “structured‐water” models can satisfactorily account for the D2O‐nmr doublet spectrum or the effects of salts on it, over the entire range of observed D2O content.
Temperature dependence of partial volumes of proteins
Authors: Bull Henry B. , Breese Keith 
Published: May 2005

AbstractThe change of the apparent partial specific volumes of egg albumin, bovine serum albumin, bovine methemoglobin, β‐lactoglobulin, and lysozyme with temperature through the thermal transitions of the proteins have been measured with dilatometers. Four regions in the plot of the apparent partial specific volumes against temperature can be recognized: (1) linear sections extending from 25°C up to 45–50°C: (2) a decrease in slope between 50°C and 60°C; (3) a sharp increase in slope with increasing temperature coinciding with the appearance of heat coagulation of the protein and followed by (4) a decrease in the slope. The return of the protein samples to 25°C yields linear relations between the apparent partial specific volumes of the heat‐denatured proteins and the decreasing temperature.
Determination of the molecular conformation of β‐D‐O2,2′‐cyclouridine in aqueous solution by proton magnetic resonance spectroscopy
Authors: Cross Bradford P. , Schleich Thomas 
Published: May 2005

AbstractThe solution conformation of β‐D‐O2,2′‐cyclouridine has been determined at 27 and 88°C in D2O by proton magnetic resonance spectroscopy. The conformation is described in terms of a fixed syn‐like sugar‐base torsional angle, a type S furanose ring conformation (similar to 2′‐endo), and a temperature‐dependent exocyclic C(4)′–C(5′) rotamer population containing approximately 50% of the gauche‐gauche form at 27°C. β‐D‐O2,2′‐Cyclouridine 5′‐phosphate likewise possesses a type S furanose ring conformation.
Intramolecular distances determined by energy transfer. Dependence on orientational freedom of donor and acceptor
Authors: Dale Robert E. , Eisinger Josef 
Published: May 2005

AbstractThe dependence of Förster long‐range resonance energy transfer efficiency on the orientational freedom of donor D and acceptor A molecules attached to a macromolecular substrate is examined. The usefulness of polarized emission measurements in determining the mutual orientation as well as the degree of orientational freedom of D and A and thereby deriving maximum and minimum values for the D–A separation from the transfer efficieny is demonstrated.
The calculated circular dichroism of polyproline ii in the polarizability approximation
Authors: Ronish E. W. , Krimm S. 
Published: May 2005

AbstractThe circular dichroism (CD) spectrum of polyproline II (PPII) has heretofore been moderately well calculated from exciton theory only at the expense of assuming unreasonable chain conformations and accepting a conservative spectrum in the 180–250‐nm region (which is not observed). We have incorporated far uv transitions in the polarizability approximation and, together with the π2π* transition, have calculated the resulting correction to the exciton model. This has been accompanied by a modified assignment of the ππ* transition in PPII, and a simultaneous calculation of the absorption and CD spectra of the α‐helix, β structure, PPI, and PPII. We obtain good agreement with the observed CD spectrum of PPII in the 180–250‐nm region for acceptable chain conformations. In addition, we predict a negative CD into the far uv, in agreement with recent experimental observations. Our calculations also reproduce features of the far uv CD spectrum of the α‐helix, and are in agreement with the CD spectra of the β chain and PPI. The calculated CD of the unordered polypeptide chain is not significantly influenced by far uv contributions, indicating that our previous calculation is valid for such a system. These results demonstrate the importance of incorporating far uv transitions in order to achieve an adequate theoretical explanation of the CD spectra of polypeptides.
Helix–coil transition in nucleoprotein. Effect of ionic strength on thermal denaturation of polylysine–DNA complexes
Authors: Li Hsueh Jei , Brand Benjamin , Rotter Arnold , Chang Catherine , Weiskope Manuel 
Published: May 2005

AbstractThermal denaturation of direct‐mixed and reconstituted polylysine–DNA complexes in 2.5 × 10−4 M EDTA, pH 8.0 and various concentrations of NaCl has been studied. For both complexes, increasing ionic strength of the solution raises Tm, the melting temperature of free base pairs. The linear dependence of Tm on log Na+ indicates that the concept of electrostatic shielding on phosphate lattice of an infinitely long pure DNA by Na+ can be applied to short free DNA segments in a nucleoprotein. For a direct‐mixed polylysine–DNA complex, the melting temperature of bound base pairs Tm′ remains constant at various ionic strengths. On the other hand, the Tm′ in a reconstituted polylysine–DNA complex is shifted to lower temperature at higher ionic strength. This phenomenon occurs for reconstituted complex with long polylysine of one thousand residues or short polylysine of one hundred residues. It is shown that such a decrease of Tm′ is not due to a reduction of coupling melting between free and bound regions in a complex when the ionic strength is raised. It is also not due to intermolecular or intramolecular change from a reconstituted to a direct‐mixed complex. It is suggested that this phenomenon is due to structural change on polylysine‐bound regions by ionic strength. It is suggested further that Na+ may replace water molecules and bind polylysine‐bound regions in a reconstituted complex. Such a dehydration effect destabilizes these regions and lowers Tm′. This explanation is supported by circular dichroism (CD) results.
Theoretical investigation of semiconductive properties in proteins. I. Electrical conductivity, charge carrier mobilities, and free paths in β‐polyglycine
Authors: Suhai Sándor 
Published: May 2005

AbstractTheoretical values are reported for the specific conductivity, charge carrier mobilities, and delocalized free paths in β‐polyglycine using the parallel‐chain pleated sheet conformation and the all‐valence electron energy band structure obtained previously. The mobilities are found to be much larger along the polypeptide backbones than in the direction of the hydrogen bonds. This indicates a mechanism of conduction in which the former path is favored for electronic delocalization. The preexponential factor of the specific conductivity obtained theoretically agrees well with experimental results.
Circular dichroism studies of complexes of the antibiotics daunomycin, nogalamycin, chromomycin, and mithramycin with DNA
Authors: Dalgleish D. G. , Fey G. , Kersten W. 
Published: May 2005

AbstractThe circular dichroism spectra of complexes of the antibiotics daunomycin, nogalamycin, chromomycin, and mithramycin with calf thymus DNA have been measured over a range of drug/DNA ratios. The similarity of the CD spectra of bound chromomycin and mithramycin suggests that they have very similar binding sites, which produce strong effects on the CD spectra of the bound drugs, and remove the differences arising from local stereochemistry in the free drugs. It was found that it was not possible to predict whether the antibiotics intercalated, from studies of the CD spectra alone, even when comparisons were made with the CD spectra of aminoacridine–DNA complexes with intercalating or nonintercalating ligands.
Theory of dipolar relaxation in aqueous macromolecular solutions
Authors: South G. P. , Grant E. H. 
Published: May 2005

AbstractRecent advances in dielectric theory are applied to two models representing an aqueous solution of dipolar macromolecules. In one model the water is treated as a dielectric continuum and the macromolecule as a finite‐sized sphere; in the other both components are represented as point dipoles suspended in a background dielectric. The predicted frequency dependences of the complex permittivity in these two cases agree and the validity of the dielectric technique for estimating macromolecular size and shape is established. The model in which water is treated as a dielectric continuum predicts a larger dielectric dispersion in the radio frequency region, which is consistent with the experimental data available for myoglobin. The validity of the Debye formula for relaxation time and the effect of “dielectric friction” in macromolecular solutions are also discussed.
Molecular visualization of pectin and DNA by ruthenium red
Authors: Hanke D. E. , Northcote D. H. 
Published: May 2005

AbstractApple fruit pectin was visualized in the electron microscope by the Kleinschmidt technique with Pt/Pd rotary shadowing, and also on benzalkonium‐treated, especially thin carbon films using ruthenium red stain. Apple pectin molecules formed reticulate associations, which were partly dispersed after increasing the charge density of the molecules by enzymatic demethylation. Sycamore callus pectin molecules were visualized by the benzalkonium‐ruthenium red technique as short rows of intensely electrondense dots, 3 nm across. Using the same technique, short sections of the ϕX174 RF DNA double helix were visualized and the existence of the B conformation in solution directly confirmed. These observations confirm the nature of chromotropism as indicated by physical studies and provide new evidence on the staining reactions of ruthenium red.
Self‐association of β‐lactoglobulin A in acid solution. I. Translational diffusion coefficients
Authors: Chu B. , Yeh A. , Chen F. C. , Weiner B. 
Published: May 2005

AbstractWe report measurements of the diffusion coefficient of β‐lactoglobulin A (βLG‐A) at pH = 5.60 and 4.58 in 0.10 ionic strength acetate buffer by the techniques of analog photocurrent signal correlation and digital single‐clipped photon correlation. At a concentration of 21 mg/ml and a pH of 4.58, the self‐association of β‐lactoglobulin can be represented by a simple dimer–octamer equilibrium model. We determined the translational diffusion coefficient of the dimer and that of the octamer using the scattering results of Kumosinski and Timasheff in a dimer–octamer mixture. Our analysis shows that the dimer βLG‐A does not change its size if the pH is varied from 5.60 to 4.58 and both species remain constant in size for temperature changes from 3.5° to 25°C Hydrodynamically, the octamers behave like closed‐packed spheres with an effective radius of about 45 Å according to the Stokes‐Einstein relation.
Transient electric birefringence of T‐even bacteriophages. II. T4B in the Presence of tryptophan and T4D
Authors: Greve J. , Blok Joh. 
Published: May 2005

AbstractMeasurements of electric birefringence, sedimentation velocity, and biological adsorption rate are used to study the properties of bacteriophage T4B in the presence of excess tryptophan. The adsorption rate determined in borate buffer pH 9 (at 25°C) increases from 0.003 × 10−8 ml min−1 (0.025 M) to 0.130 × 10−8 ml min−1 (0.150 M). The Kerr coefficient, rotational diffusion coefficient, and the sedimentation coefficient of the phage are also dependent on buffer concentration and reach plateau values above 0.12 M given by Ksp = −(275 ± 18) × 10−9 OD−1 cm2 statvolt−2, D25,w = 133 ± 4 sec−1, and s20,w = 818 ± 11 S. From a comparison of electric birefringence measurements of T4B and T4D it is concluded that T4D and T4B (in the presence of excess tryptophan) exhibit a similar hydrodynamic behavior. The change in physical parameters is solely due to a shift in fiber configuration. At high buffer concentrations the fibers make an angle of approximately 3π/4 with the sheath and the permanent dipole moment is about 200,000 D. This dipole moment is roughly ten times as large as that of a phage particle with nonextended fibers. This difference may be due to a change in hydrodynamic center upon fiber extension or to the presence of positive charges on the fiber tips, or both. At intermediate buffer concentrations the phage population behaves as if it were monodisperse. Probably not all six fibers are extended under such conditions.
Optical activity of polypeptides in the infrared. Predicted CD of the amide I and amide II bands
Authors: Snir Joseph , Frankel Richard A. , Schellman John A. 
Published: May 2005

AbstractThe Miyazawa‐Blout‐Krimm (M‐B‐K) treatment of polypeptide absorption in the infrared is extended to the calculation of circular dichroism (CD), linear dichroism, and oriented CD for the amide I and amide II transitions. Matrix methods are applied to the α helix and β structures using measured values for the strengths and directions of the transition dipole moments and empirical values from M‐B‐K for the coupling constants.Relatively small aggregates, a 36‐residue helix, and 8‐chain × 4‐residue β sheets, are large enough to show calculated absorption agreeing with M‐B‐K results, which are based on infinite lattices.In all cases the predicted CD is an approximately conservative couple. The strongest CD should appear in the α helix, Δε/ε ≃± 10−3 for both transitions. The amide II transition should show moderate CD couples in both β structures, Δε/ε ≃ (+2 to −1) × 10−4. The amide I transitions in β structures should show weak CD couples, Δε/ε = (+3 to −2) × 10−5, except that the negative branch in the antiparallel structure may be detectable (Δε/ε ≃ −2 × 10−4) because absorption is very low at its wavelength peak.CD on oriented samples should be enhanced over the unoriented cases, giving values as large as Δε/ε = 3 × 10−3 because particular directions of observation allow the light to avoid much of the absorption in the sample.If all three structures are considered as helices, then the larger distance of the transition dipoles from the axis in the α helix, and the orientations of the transitions in the different structures, are the factors that, in terms of our previous theoretical work [Snir and Schellman (1973) J. Phys. Chem. 77, 1653] satisfactorily explain the calculated results. Simple dipole–dipole interaction is calculated to make a substantial contribution to the coupling between groups.
Ethidium bromide–dinucleotide complexes. Evidence for intercalation and sequence preferences in binding to double‐stranded nucleic acids
Authors: Krugh Thomas R. , Wittlin Frederick N. , Cramer Stephen P. 
Published: May 2005

AbstractThe solution complexes of ethidium bromide with nine different deoxydinucleotides and the four self‐complementary ribodinucleoside monophosphates as well as mixtures of complementary and noncomplementary deoxydinucleotides were studied as models for the binding of the drug to DNA and RNA. Ethidium bromide forms the strongest complexes with pdC‐dG and CpG and shows a definite preference for interaction with pyrimidine–purine sequence isomers. Cooperativity is observed in the binding curves of the self‐complementary deoxydinucleotides pdC‐dG and pdG‐dC as well as the ribodinucleoside monophosphates CpG and GpC, indicating the formation of a minihelix around ethidium bromide. The role of complementarity of the nucleotide bases was evident in the visible and circular dichroism spectra of mixtures of complementary and noncomplementary dinucleotides. Nuclear magnetic resonance measurements on an ethidium bromide complex with CpG provided evidence for the intercalation model for the binding of ethidium bromide to double‐stranded nucleic acids. The results also suggest that ethidium bromide may bind to various sequences on DNA and RNA with significantly different binding constants.