bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laser‐Raman spectroscopy of biomolecules. XI. Conformational study of poly(L‐valine) and copolymers of L‐valine and L‐alanine
Authors: Fasman Gerald D. , Itoh Koichi , Liu Christopher S. , Lord Richard C. 
Published: December 2004

AbstractRaman spectroscopic studies have been carried out on polymers of L‐valine ranging in degree of polymerization (DP) from 2 to 930. The spectrum of the hexapeptide (DP = 6) is closely similar over the entire range 40–1750 cm−1 to those of polymers with much higher DP, and the structure is clearly shown to be that of the antiparallel pleated sheet (β‐structure) by the amide I and III frequencies. The formation of a little α‐helical structure occurs in polymers with DP above 500, although the amount does not appear to be a linear function of DP. The α‐helical structure is unstable and readily destroyed in samples cast from trifluoroacetic acid solution. It is stabilized by the incorporation of L‐alanine, a strong helix‐former; polymers of the latter may in turn be forced into a α‐structure in copolymers sufficiently rich in L‐valine.
Determination of the number of cross‐links in a protein gel from its mechanical and swelling properties
Authors: Van Kleef F. S. M. , Boskamp J. V. , Van Den Tempel M. 
Published: December 2004

AbstractThe relation between the chemical structure of a protein and the physical properties of a heat‐set gel of that protein has been investigated. The physical properties of the gel are determined by means of mechanical experiments in which the viscoelastic properties of the gel are determined in terms of the storage shear modulus, the loss modulus and the stress‐strain curve. The storage shear modulus defined the solid (elastic) character of the gel. The chemical structure of the protein and the nature of the solvent determine the nature and number of cross‐links in the gel. The cross‐links in gels formed by heating concentrated solutions of ovalbumin in 6M urea solutions were found to be disulfide bridges and the mechanical properties of these ovalbumin/urea gels approximated those of an ideal rubber. The latter finding enables one to calculate the number of cross‐links per ovalbumin molecule from the value of the storage modulus, using the classical theory of rubber elasticity. This theory, together with the Flory‐Huggins lattice model, can also be used to calculate the number of cros‐links per ovalbumin molecule from the swelling behavior of ovalbumin/urea gels. The number of cross‐links per ovalbumin molecule calculated from these two types of experiments are in mutual agreement and correspond with the number of thiol groups in ovalbumin. We conclude, thereforee, that theories of polymer physics can be used to relate the chemical structure of a protein to the physical properties of its gel.
Structures and populations of conformers of nucleoside monophosphates in aqueous solution. I. General methods of conformation search with lanthanide‐ion probes and spin‐coupling constants and application to uridine‐5′‐monophosphate
Authors: Inagaki Fuyuhiko , Tasumi Mitsuo , Miyazawa Tatsuo 
Published: December 2004

AbstractThe Ln(III)‐induced shifts and Gd(III)‐induced changes of the spin‐lattice relaxation times were observed for the 1H and 13C resonances of uridine‐5′‐monophosphate (5′‐UMP) in 2H2O solutions at pH 1.7–2.0. The vicinal spin‐coupling constants changed little by the addition of lanthanide cations, indicating that the conformations of this mononucleotide remained almost the same upon complex formation.A general method was worked out for conformation studies of flexible molecules with lanthanide‐ion probes and spin‐coupling constants. This method was applied in an extensive computer search for 5′‐UMP, and it was concluded that the observed Ln(III)‐induced shifts, Gd(III)‐induced changes of relaxation times, and vicinal spin‐coupling constants could only be accounted for by a mixture of conformers. The populations of the major conformers, gg‐3′‐endo‐anti, and gg‐2′‐endo‐anti, amount to 46 ± 12% and 29 ± 11%, respectively. The correlation between local conformations are discussed on the basis of the present results.
Empirical calculations of dinucleotide optical activity
Authors: Johnson Neil P. , Switkes Eugene 
Published: December 2004

AbstractIn this paper we present calculations of dinucleotide optical activity based on the exciton‐coupled oscillator and generalized susceptibility theories of CD. Our application of these methods utilizes experimental transition moment data for the nucleic acids and does not require explicit wavefunctions for the monomers. In addition to near‐uv π‐π* states, the calculations include n‐π* and far‐uv π‐π* transitions recently characterized by Clark. We also show that correlated motions of electrons in the ground state of a system is reflected in the net CD summed over all transitions. Sample calculations for dinucleotides in several conformations illustrate the methods.
Magnesium ion effect on the helix‐coil transition of DNA
Authors: Blagoi Yu. P. , Sorokin V. A. , Valeyev V. A. , Khomenko S. A. , Gladchenko G. O. 
Published: December 2004

AbstractThe effect of magnesium ions on the parameters of the DNA helix‐coil transition has been studied for the concentration range 10−6–10−1M at the ionic strengths of 10−3M Na+. Special attention has been given to the region of low ion concentrations and to the effect of polyvalent metallic impurities present in DNA. It has been shown that binding with Mg++ increases the DNA stability, the effect being observed mainly in the concentration range 10−6–10−4M. At[Mg++]>10−2M the thermal stability of DNA starts to decrease. The melting range extends to concentrations ∼10−5M and then decreases to 7–8°C at the ion content of 10−3M. Asymmetry of the melting curves is observed at low ionic strengths ([Na+] = 10−3M) and [Mg++] ⩽ 10−5M. The results, analyzed in terms of the statistical thermodynamic theory of double‐stranded homopolymers melting in the presence of ligands, suggest that the effects observed might be due to the ion redistribution from denatured to native DNA. An experimental DNA–Mg++ phase diagram has been obtained which is in good agreement with the theory. It has been shown that thermal denaturation of the system may be an efficient method for determining the ion‐binding constants for both native and denatured DNA.
Base stacking in A fluorescent dinucleoside monophosphate: εApεA
Authors: Baker B. M. , Vanderkool J. , Kallenbach N. R. 
Published: December 2004

AbstractThe optical properties of the 1,N6 ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo4>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.
Aromatic side‐chain contributions to the far ultraviolet circular dichroism of peptides and proteins
Authors: Woody Robert W. 
Published: December 2004

AbstractThe rotational strength of the La transition in phenylalanine and tyrosine side chains has been calculated for dipeptides with various backbone and side‐chain conformations. Similar calculations have also been performed for tripeptides in the β‐turn conformation with aromatic residues at the corners of the turn. The interaction of the aromatic ring with neighboring peptides generates rotational strengths in the La transition of the order of 0.1 Debye‐Bohr magneton. When the preferred backbone and side‐chain conformations are considered, it is found that the most probable conformations have positive La bonds. This result accounts for the observation that the N‐acyl amino acid amides of L‐Tyr and LPhe have positive La bands. It also suggests that, although other interactions may affect the numerical value and even the sign, there will be a significant positive contribution to the rotational strength of aromatic residues in globular proteins from nearest‐neighbor interactions. Calculations on proteins of known conformation at the nearest‐neighbor level confirm the tendency toward positive La contributions for Phe and Tyr residues. This contribution can be of the order of 10% of the observed CD even in proteins with rather strong amide contributions. In some proteins, such as the gene 5 protein from bacteriophage fd and many snake‐venom toxins, side‐chain contributions from Tyr and Trp residues manifest themselves as positive CD bands in the 225–250‐nm region. The magnitude of the nearest‐neighbor contributions and the trend toward positive contributions are consistent with the observation of such CD bands in globular proteins. No special stacking interaction among aromatic side chains needs to be invoked.
Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT
Authors: Broyde S. , Wartell R. M. , Stellman S. D. , Hingerty B. 
Published: December 2004

AbstractMinimum energy conformations have been calculated for the deoxydinucleoside phosphates dGpdC, dApdA, dCpdC, dGpdG, and dTpdT. In these potential energy calculations the eight diheldral angles and the sugar pucker were flexible parameters. A substantial survey of conformation space was made in which all staggred combination ofthe dihedral angles ω′,ω, and ψ, in conjuction with C(2′)‐endo puker, were used as starting conformers for the energy minimization. The most important conformations in the C(3′)‐endo‐puckering domain have ψ = g+; ω′,ω = g−,g−(A‐form),g+, g+, and g−,t. With C(2′)‐endo‐type puker the most important conformations have ψ = g+; ω′,ω =g_,g_(B‐form) and g+,t; and ψ =t; ω′,ω =g_,t(Watson‐Crick from) and t,g+ (skewed). Stacked bases are a persistent feature of the low‐energy conformations, the g+ conformer being an exception. Freeing the suger puker allowed this conformation to become low energy, with C(3′)‐exo puker. It also caused other low‐energy forms, such and the Waston‐Crick conformation, to become more favourable. Conformation flexibility in the sugar puker and in ψ, as well as the ω′,ω angle pair, is indicated for the dimeric subunits of DNA.
Dielectric relaxation of DNA solutions. II
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku 
Published: December 2004

AbstractReal and imaganiry parts of complex dielectric constant of dilute solutions of DNA in 10−3M NaCl with molecular weight ranging from 0.4 × 106 to 4 × 106 were measured at frequencies from 0.2 Hz to 30 kHz. Dielectric increments Δε were obtained from Cole‐Cole plots and relaxation times τD from the loss maximum frequency. The τD of all samples agrees well with twice of the maximum viscoelastic relexation time in the Zimm theory, indicating that the low‐frequency dielectric relaxiation should be ascribed to be the rotation of DNA. The rms dipole moment, which was obtained from Δε, agree well with that calculated from the counterion fluctuation theory. The dielectric increment was found to be greatly depressed in MgCl2, which is resonably interpreted in terms of a strong binding of Mg++ ions with DNA.
Linear dichroism and radial flow birefringence of stream‐oriented hyaluronate solutions as a function of system pH
Authors: Barrett T. W. 
Published: December 2004

AbstractThe linear dischroism in the radial direction of solution flow over a velocity gradient of approximately 10–850 sec−1 has been obtained for human umbilical cord hyaluronic acid at concentrations of 0.1, 0.0666, and 0.0333%, and pHs 6.0, 6.5, 7.0, 7.5, 8.0, and 8.5, at constant ionic strength 0.1. The redial flow briefingenece has also been obtained for these solutions by a Kroing‐Kramers transformation. The data indicate a change in linear dichroism and optical anisotrophy as a function of pH, with most of the transition across the physiological range: 7.0–7.5. Previously reported axial flow birefringence and extinction angles indicating a similar pH‐dependent structural change in hyaluronate solutions across the same pH range are thus confirmed with other instrumentation. The radial birefringence measurements reported here, together with the axial measurements previously reported, permit a complete description of the refractive index tensor for each of the six solutions. The interpretation of these tensors in terms of the Peterlin modification of the Rouse‐Zimm Gaussian subchain theory results in a description of entropy production induced by changes in system pH.
Electric dichroism of poly(riboadenylic acid)
Authors: Charney Elliot , Milstien Julie B. 
Published: December 2004

AbstractElectric dichroism measurements on poly(A) in low‐ionic‐strength solution demonstrate that below a molecular weight of 130,000 the double‐stranded polymer is hydrodynamically rigid and above that molecular weight becomes increasingly flexible. At 500,000 it is considerably more flexible than DNA of the same molecular weight, with a mean end‐to‐end distance of about 1150 Å compared to approximately 1600 Å for DNA. The fully extended length for both DNA and poly(A) of this molecular weight is about 2750 Å. It is further shown that the orientation of these polyelectrolytes in an electric field is consistent with theoretical treatments of the counter‐ion distribution and a preliminary model based on the additivity of classical valence charge anisotropy and counter‐ion polarization is postulated for the orientation mechanism. Single‐stranded pol (A) is shown not only to retain its base stacking in the presence of the electric field but to extend the persistent regions of stacked bases so that it attains a rodlike structure very similar to the one in the double‐stranded polymer is found to be less than that expected from consideration of the x‐ray structure. An explanation for this result is sought in the electric asymmetry of the helical polymer.
Measurement of the strongly held water of myoglobin by drying
Authors: Rao P. Bhaskara , Bryan William P. 
Published: December 2004

AbstractThe karl Fischer reagent method has been used to study the drying of whale skeletal muscle myoglobin. Drying curves for metmyglobin were obtained by mechanical pumping (moderate vacuum) and diffusion pumping (high vacum) at 20, 10, 0, −10, and −20°C. Strongly held water is present in about the same amounts as were previously observed with lysozyme. Nearly all of this strongly held water is still present during the drying of acid denatured metmyoglobin. This suggest that a core structure containing strongly held water is still present at pH 4.0. Comparison of the drying of metmyoglobin, deoxymyoglobin, and oxymyoglobin indicates that the iron‐coordinated water of methyoglobin is the second most strongly held water of the molocule.
Carbon‐13 NMR chemical shifts of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐ X‐L‐ Ala‐OH
Authors: Richarz René , Wüthrich Kurt 
Published: December 2004

AbstractThe 13C nmr chemical shifts of the common amino acid residues were measured in D2O solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH. For Asp, Glu, Lys, Tyr and His, the titration shifts arising from the ionization of te amino acid side chains were also obtained. These data are compared with the corresponding 13C chemical shifts in the protected tetrapeptides CF3CO‐Gly‐Gly‐X‐L‐Ala‐OCH3, the linear pentapeptides H‐Gly‐Gly‐X‐Gly‐Gly‐OH, and the free amino acids. On this basism the selection of suitable “random coil” 13C chemical shifts for conformational studies of polypeptides chain is discussed.
A general method for the evaluation of diffusion constants, dilute‐solution viscoelasticity, and the complex dielectric constant of a rigid macromolecule with an arbitrary configuration. II
Authors: Nokajima Haruhiko , Wada Yasaku 
Published: December 2004

AbstractAs a continuation of a previous paper [Biopolymers 16, (1977)], in which we described a general method for the evaluation of the diffusion constants of a rigid macromolecule with an arbitrary configuration, this paper presents a theory for evaluating the relaxational behavior of the molecule in solution. The diffusion equation of a molecule subjected to hydrodynamic or electric forces is solved and both a complex viscosity and a complex dielectric constant are obtained by assuming that the molecule is composed of Tokes spheres and, in the dielectric property, the molecule possesses a fixed charge distribution. The viscoelasticity of a rigid rod is calculated and compared with the analytical results.
Nonradiative energy transfer in oligopeptide chains generated by a monte‐cralo mehod including long‐range interactions
Authors: Leclerc Marc , Prémilat Samuel , Englert Anne 
Published: December 2004

AbstractA Monte‐Carlo method including long‐range interactions is used to oligopeptide chains in random‐coil state. The chains are composed of 4, 9, or 14 repeating units and are labeled with the luminopheres tyrosine or tryptophan. Interactions with a solvent (water) are taken into account in the calculations through modifications of the semiempirical potential‐energy functions. The chains represent oligopeptides composed of hydrophobic or hydrophilic amino acid residues. Various properties relavent to the interpretaiton of nonradiative enrgy‐transfer experiments, such as the average value of the orientation factor for dipole‐dipole interaction of the luminophores, 〈k2〉, the distribution function of the distances between the luminophores f(rl), the efficiences of energy transfer in the static and dyamic averaging regimes, 〈T〉s amnd 〈T〉d, as well as the fluorescence decay I(t) of the donor luminophore in various averaging conditions, are computed. It is shown that, for all chains considered, 〈k2〉 is not vary far form 0.67 and that 〈T〉s and 〈T〉d have completely different values. Due to the small extent of correlation between the distances rl and the mutual orientations of the lumninophores, the decay kinetics 〈I(t)s corresponding to a static averaging regime can be expressed in terms of distribution functions f(rl). These results are in agrrement with those obtained previously for the unperturbed chain model.
A Monte Carlo study of the amylosic chain conformation
Authors: Jordan Robert C. , Brant David A , Cesàro Attilio 
Published: December 2004

AbstractMonte Carlo studies of the unperturbed amylosic chain conformation have been carried out in the approximation of separable chain configuration energies. Sample chains of arbitrary chain length have been generated so as to be distributed consistent with refined estimates of the configuration energy and thus suitable for evaluation of averages of the desired configuration‐dependent properties. Perspective drawings of representative chains from the Monte Carlo sample have been made for comparison with standard idealizations of amylosic chain conformation. He molecular model employed generates a randomly coiling chain possessing perceptible regions of left‐handed pseudohelical backbone trajectory. Distribution functions for the end‐to‐end distance of short amylosic chains disclose some propensity for the chain to suffer self‐intersections at sort range in the chain sequence, which may vitiate the usual amylosic chain models based on the assumed independence of sets of glycosidic linkage torsion angles. The amylosic persistence vector and persistence length have been calculated as a function of chain length for the chain model employed.
1H‐15N Spin–spin couplings in alumichrome
Authors: Demarco Antonio , LlináS Miguell , Wuthrich Kurt 
Published: December 2004

AbstractWe report the determination of two‐ and three‐bond 1H‐15N spin–spin couplings in the nmr spectra of a polypeptide. The 1H‐ and 15N‐nmr spectra of 99.2% 15N‐enriched alumichrome have been studied at 360 MHz and 10.1 MHz, repectively. While some 2J and 3J coupling are of the order of 5 Hz, most splitting resulting from the heteronuclear interaction are ≲2 Hz, which introduces strigent requirements of spectral resolution. In the 1H spectra these requirements were met by digital deconvolution with a sine bell routine combined with positive exponential filtering. Although the 15N spectra clearly exhibit features of fine structure, mainly because of the intrinsic higher nmir sensitivity of protons, observation of 1H‐15N spin–spin couplings was found to be more practical in the 1H than in the 15N spectra. We find that the alumichrome data do not satisfy a simple cyclic relationship linking the heteronuclear couplings to the crystallographic ψ dihedral angles. It is suggested that a formal treatment of the ψ‐related interresidue 1H‐15N coupling might have to take into account a more complex dependence of the intervening 3J on the overall local electronic structure, which is dependent on ϕ,ψ, and ω simultaneoulsy. In contrast, our analysis indicates that χ1 can be readily determined from the measurement of the corresponding heteronuclear 3J coupling in the 1Hβ or in the amide 15N resonances. Karplus relationships are proposed that relate this heteronuclear 3J to the corresponding dihedral angle θ and which, on average, yield
Conformation of poly(L‐arginine). I. Effects of anions
Authors: Ichimura Sachiko , Mita Kazuei , Zama Mitsuo 
Published: December 2004

AbstractThe conformational transition of poly(L‐agrignine) by binding with various mono‐, di‐, and polyvalent anions, especially with SO, was studied by CD measurements. The intramolecular random coil‐to‐α‐helix conformational transition and the subsequent transition to the β‐turn‐like structure was caused by binding with SO. The binding data obtained from equilibrium dialysis experiments showed that the α‐helical conformation of poly(L‐arginine) is stabilized at a 1:3 stoichiometric ratio of bound SO to arginine residue; at higher free SO concentrations, the α‐helix converts to the β‐turn‐like structure accompanied by a decrease in amount of bound SO. The same conformaitonal transition of poly(L‐arginine) also occurred in the solutions of other divalent anions (SO, CO, and HPO) and polyvalent anions (P2O, P3O). Among the monovalent anions examined, CIO and dodecyl sulfate were effective in including α‐helical conformation, while the other monovalent anions (OH−, Cl−, F−, H2PO, HCO and CIO) failed to induce poly(L‐arginine) to assume the α‐helical conformation. Thus, we noticed that, except for dodecyl sufate, the terahedral structure is common to the α‐helix‐forming anions. A well‐defined model to the α‐helical poly(L‐arginine)/anion complex was proposed, in which both the binding stoichiometry of anions to the arginine residue and the tetrahedral structure of anions were taken into consideration. Based on these results, it was concluded that the tetrahedral‐type anions stabilize the α‐helical conformation of poly(L‐arginine) by crosslinking between two guanidinium groups of nearby side chains on the same α‐helix through the ringed structures stabilized by hydrogen bonds as well as by electrostatic interaction. Throughout the study it was noticed that the structural behavior of poly(L‐arginine) toward anions is distinct from that of poly(L‐lysine).