bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation of poly‐L‐tyrosine in trimethyl phosphate solution
Authors: Damle Vinayak N. 
Published: December 2004

AbstractAbsorption, circular dichroism (CD), and optical rotatory dispersion (ORD) measurements were carried out on poly‐L‐tyrosine in trimethyl phosphate solution over the spectral range 185–600 mμ. There is evidence in the CD spectrum for side chain‐side chain interactions in poly‐L‐tyrosine. ORD and CD data in dimethylformamide and pyridine closely parallel those in trimethyl phosphate, indicating a similarity in conformation of the polymer in all three solvents. In the polarized infrared spectrum both position and polarization of amide A, I, and II bands are characteristic of α‐helical polypeptides. Bands corresponding to side chain also exhibit dichroism, suggesting that the side chains are not randomly oriented. Viscosity and light‐scattering studies are consistent with α‐helical structure for the polymer that, remains rigid over a temperature range of 15–50°C and becomes somewhat flexible at higher temperatures. Optical rotatory properties were found to vary gradually and continuously with temperature over the range of −30 to +100°C. This suggested that all three electronic transitions of tyrosyl side chain are optically active, and that the side chains have some freedom of motion that decreases with decreasing temperature, disappearing only at about −30°C.
Characterization of acid‐denatured DNA by low‐angle light scattering
Authors: Krasna Alvin I. , Dawson Jeffrey R. , Harpst Jerry A. 
Published: December 2004

AbstractLow‐angle light scattering results reported previously demonstrated that measurements on high molecular weight native DNA must be made at angles below 30° in order to obtain correct molecular weights. Earlier light‐scattering data obtained on denaturated DNA at angles above 30° showed no change in molecular weight upon denaturation, even though other techniques clearly showed that strand separation occurred. This paper reports low‐angle measurements on solutions of calf thymus and T7 DNA denatured under acidic conditions. The results demonstrate that a halving of molecular weight consistent with strand separation is detected by light scattering only when low‐angle data are used to obtain correct molecular weights for native material. As expected from theoretical considerations, the scattering from denatured DNA is a linear function of sin2(θ/2), where θ is the angle of observation. This result shows that anticipated experimental artifacts have no significant effect on the low‐angle measurements and demonstrates that the curvature in the scattering envelope observed for native DNA below 30° is an inherent property of the native molecule.
Low‐angle light‐scattering studies on alkali‐ and heat‐denatured DNA
Authors: Krasna Alvin I. 
Published: December 2004

AbstractThe molecular weight of native DNA is shown to decrease by at least a factor of two on denaturation by heat or alkali. This result is obtained only if low‐angle (<30°) light‐scattering measurements are used. High‐angle measurements (>30°) do not reveal a decrease in molecular weight on denaturation due to the incorrect value for native DNA. The dn/dc value for both native and denatured DNA is 0.166 ml/g ± 0.003 ml/g. Methods are described for the clarification of native and denatured DNA solutions for light scattering by the use of membrane filters.
Potentiometric titration of poly‐S‐carboxymethyl‐L‐cysteine in aqueous NaCl solution
Authors: Makino Shio , Sugai Shintaro 
Published: December 2004

AbstractpH titration measurements of poly‐ S‐carboxymethyl‐L‐cysteine were undertaken in the aqueous Nacl solution in relation to the β form–random coil transition. The titration curves show a marked molecular weight dependence because of the shortened chain length of materials. Comparison of the optical rotatory dispersion parameter a0 with the titration curve reveals that the titration curve apparently reflects a β structure–random coil transition. The β form of this polymer is assumed to be an intramolecular β form, rather than a β structure stabilized by an intermolecular hydrogen bond, at least in the polymer concentration range considered here. The standard free energy change per amino acid residue for the transition from un‐ionized random coil to un‐ionized β form is estimated to be about −750 cal/mole residue in the range of 0.005–0.2M NaCl concentration.
Optical activity of aromatic chromophores. I. o, m, and p‐tyrosine
Authors: Hooker Thomas M. , Schellman John A. 
Published: December 2004

AbstractThe optical activity and the conformational energy of the amino acids tyrosine, o‐tyrosine, and m‐tyrosine have been calculated as a function of molecular conformation. A new graphic technique, rotatory strength–conformational energy maps, was developed for the presentation of these calculations. Experimental circular dichroism spectra were determined by utilization of a new experimental technique that involves complete computer control of a Cary spectropolarimeter. This permitted repetitive scanning with signal averaging over extended time periods and resulted in a greatly enhanced signal to noise ratio. On the basis of these calculations, it, was concluded that the Kirkwood “coupled oscillator” mechanism is capable of explaining the observed optical activity of the aromatic chromophores of the molecules that were investigated.
The influence of single‐strand breaks on the kinetics of denaturation of DNA
Authors: Hoff A. J. , Blok Joh. 
Published: December 2004

AbstractThe influence of single‐strand breaks on the kinetics of the relaxation of DNA in a solution of low ionic strength has been investigated by a temperature jump method. The relaxation of DNA after a jump of 0.7 °C in the melting region has been monitored by measuring the extinction at 260 nm. For essentially monodisperse T4 DNA (M = 130 × 106) two distinct relaxation times have been observed, that depend markedly on the initial extent of denaturation 1 − θ. The larger relaxation time decreases from 450 sec to about 300 sec, the smaller one from 55 see to 30 when 1 − θ increases from 0.03 to about 0.8. The dependence of these relaxation times on the average number of single‐strand breaks per molecule (p) appears to be very small up to p = 100. However, the relative contribution of the slow process decreases sharply when p increases from 0.6 to 30 and remains nearly constant for larger p. The observations are discussed in the light recent theories of the kinetics of denaturation.
Electro‐optic scattering studies on deoxyribonucleic acid
Authors: Jennings B. R. , Plummer H. 
Published: December 2004

AbstractMeasurements have been made of the intensity of light scattered from aqueous solutions of calf thymus DNA with and without the application of electric fields. For fields approaching 150 V/cm and frequencies below 2.5 KHz, changes (ΔI) of up to 10% in the residual scattered intensity were observed. In agreement with previous dielectric and electric birefringence measurements, a low frequency dispersion of ΔI was observed, from which a rotary diffusion constant (D) of 1200 s−1 was determined. Interpreting the electric field data in terms of the classical dipolar orientation theory led to values of 2.4 × 10−25 cm (7.4 × 10−14 esu) and 4.3 × 10−25 cm (13 × 10−14 esu) for the permanent dipole moment and the anisotropy of the electric polarisabilities respectively. Furthermore the permanent dipole moment was along the major molecular axis and the particles orientated in the field as rigid entities. The zero field data indicated a molecular shape which was not rodlike but corresponded to the Kratky‐Porod “stiffness” parameter of x = 24 for the wormlike coil model. Although curved, the molecules appeared to orientate in low‐intensity electric fields as rigid, but not rodlike molecules. The implications of this on recent discrepancies in D determined by two or more dynamic relaxation methods is briefly discussed.
Studies on bacteriophage MS2. VIII. Evidence for dimer formation of MS2 RNA by reaction with formaldehyde at acidic pH
Authors: Slegers H. , Fiers W. 
Published: December 2004

AbstractReaction of 27 SMS2 RNA with formaldehyde normally results in an unfolded, 13.4 S form. At acidic pH, however, and under the proper ionic conditions, a compact component sedimenting at 36–40 S was obtained. The molecular weight of this species corresponds to a dinner. The formaldehyde concentration was not critical, and approximately the same number of base pairs had been opened in the compact and in the unfolded form. Presumably dimers, which had been specifically formed under defined conditions, were stabilized by formaldehyde‐induced crosslinks. Similar dimers were formed by 16 S and by 23 S ribosomal RNA, but not by tRNA.
Buoyant density and solvation of magnesium DNA
Authors: Vijayendran B. R. , Vold R. D. 
Published: December 2004

AbstractThe buoyant density of T‐4 DNA was determined by equilibrium sedimentation in a density gradient, of mixed solutions of cesium and magnesium chlorides and bromides. The preferential hydration was calculated from these data, allowing appropriately for the exchange equilibrium of DNA with Cs+ and Mg++ ions. The charge and intrinsic solvation of the counterions were found to have no appreciable effect on the hydration of the DNA, the extent of solvation depending only on the thermodynamic, activity of the water. Various reasonable hypotheses are discussed to account for these results.
Theory of interaction of polymer and small molecules which can aggregate in solution
Authors: Damle Vinayak N. 
Published: December 2004

AbstractThe theory of interaction of small molecules with polymers is extended to the case where the small molecules can aggregate in solution to form dimers, trimers, etc., and where the aggregates can also interact with the polymer. The secular equation is found to be identical in form with that obtained for the binding of nonaggregating monomer to the polymer. Thus, all formulas derived for the latter case apply to the present one also, except that, now the concentration of the free monomer is the relevant factor. It is shown how the experimental data can be analyzed by using information on the molal activity coefficients of the small molecules. As an illustration these formulas are applied to data on the interaction of purines and nucleosides with poly(uridylic acid) in concentrated solutions.
Dielectrophoresis of macromolecules
Authors: Eisenstadt Maurice , Scheinberg I. Herbert 
Published: December 2004

AbstractDilute solutions of rigid helical macromolecules with permanent dipole moments have been studied with dielectrophoresis. The polymers used were poly‐γ‐benzyl‐L‐glutmate and poly‐n‐butyl isocyanate, both fractions of average molecular weight 120,000. In this phenomenon dipolar molecules migrate in an inhomogeneous electric field towards the region of maximum field strength. The field gradient is produced by a 10‐μm diameter Pt wire serving as the inner electrode of a cell, and a 2.5‐mm diameter cylinder as the outer electrode. An equilibrium exponential concentration gradient is achieved within a few wire radii of the inner electrode in a matter of minutes, making both kinetic and equilibrium measurements feasible. The concentration gradient is monitored by measuring the change in capacitance ΔC of the cell from its value for a uniform solute concentration. The time dependences of ΔC for the build‐up of the concentration gradient towards the equilibrium value, and the decay to a uniform concentration after the field is removed have been calculated, using a frictional coefficient and a Boltzmann factor, β1, as the sole adjustable parameters.For low voltages (β1 small), the measured build‐up and decay are completely symmetrical, in agreement with theory, and yield the same frictional coefficient. For larger β1, the build‐up is faster, reflecting a reduced frictional coefficient due to partial alignment of the long axes of the polymers in the direction of migration. In either case, the decay determines a diffusion constant of randomly aligned molecules, identical to classical diffusion measurement.The value of ΔC at equilibrium, for β1 small, determines μ2F2, where μ is the dipole moment and F is the internal field at the polymer. Combined with a classical dielectric constant measurement, which gives μ2F, both μ and F may be determined, independent of assumptions about cavity shapes.Dielectrophoresis works in alternating as well as constant fields, provided the dipolar orientation can follow the field reversals. The dispersion of dielectrophoresis with frequency is a sensitive measure of the molecular‐weight distribution of a given sample.
A carbon‐13 magnetic resonance study of the helix–coil transition in polyuridylic acid
Authors: Govil Girjesh , Smith Ian C. P. 
Published: December 2004

AbstractThe temperature‐dependent conformations of poly(U) in 0.5M CsC1 have been studied by carbon‐13 nuclear magnetic resonance. The transition from random coil to an ordered structure results in broadening of lines in the 13C spectra, due to intramolecular 1H–13C dipolar interactions and restricted motions in the ordered state. Changes in the chemical shifts suggest that the bases are interacting below the transition temperature. The random coil form shows conformation preferences for internal rotation about C4′–C5′, C5′–O5′, and C3′–O 3′ bonds. The statistical randomness of the coil arises mainly because of flexibility about O–P bonds. The results are analyzed in conjunction with theoretical calculations and light‐scattering data.
Transient electric birefringence of T‐even bacteriophages. I. T4B in the absence of tryptophan and fiberless T4 particles
Authors: Greve J. , Block Joh. 
Published: December 2004

AbstractMeasurements of the electric birefringence of suspensions of T4B in the absence of tryptophan and of fiberless T4 particles show that both kinds of particles are hydrodynamically equivalent. Their rotational diffusion coefficients corrected to 25°C and water viscosity (D25,w) are 280 ± 9 sec−1 and 295 ± 10 sec−1, respectively. These corrected rotational diffusion coefficients are almost independent of buffer concentration and temperature. The sedimentation coefficient (s20,w) of T4 B is equal to 1023 ± 12 S, a value which is likewise independent of buffer concentration.By analysis of the field strength dependence of the steady‐state birefringence and by reversing pulse experiments it could be shown that the orientation in an electric field is largely due to a permanent dipole moment. This dipole moment is somewhat dependent on buffer concentration and amounts to about 24,000 debye for T4B and 95,000 debye for fiberless T4. An approximate calculation shows that the difference in dipole moment may be ascribed to positive charges on the fiber tip (at least ten per fiber), to negative charges along the fiber or (and) positive charges on the fiberless particle at those places where the fibers are attached in normal particles.
Conformational characteristics of dApdA, dApdT, dTpdA, and dTpdT from energy minimization studies
Authors: Thiyagarajan P. , Ponnuswamy P. K. 
Published: December 2004

AbstractThe conformational characteristics of the deoxydinucleoside monophosphates with adenine and thymine bases in all possible sequences, namely, dApdA, dApdT, dTpdA, and dTpdT have been studied using an improved set of energy parameters to calculate the total potential energy and an improved set of energy parameters to calculate the total potential energy and an improved version of the minimization technique to minimize the total energy by allowing all seven dihedral angles of the molecular fragment to vary simultaneously. The results reveal that the most preferred conformation in all these units usually corresponds to one of the four helical conformations, namely, the A‐DNA, B‐DNA, C‐DNA, and Watson‐Crick DNA models. These helical conformations differ in energies by about 3 kcal/mol with respect to one another. The conformations which could promote a loop or bend in the backbone are, in general, less stable by about 3.5 kcal/mol with respect to the respective lowest‐energy helical conformation. The results indicate that there is a definite influence of bases and their actual sequences on the preferred conformations of the deoxydinucleoside monophosphates. The lowest‐energy structure, although corresponding to one of the four helical conformations, differ with the type of the deoxydinucleoside monophosphate. Good or reasonable base stacking is noted in dApdA and dTpdA with both C(3′)‐endo and C(2′)‐endo sugars and in dApdT and dTpdT with only C(3′)‐endo sugar. The inversion of the base sequence in deoxydinucleoside monophosphates alters the order of preference of low‐energy conformations as well as the base‐stacking property of the unit. The paths linking the starting and final states in the (ω′, ω) plane show interesting features with regard to the energy spread, thus providing insight into the path of conformational movement ofthe molecule under slight perturbation. The stabilities of the A and B forms, including the internal energies of the C(3′)‐endo ans C(2′)‐endo sugar systems, indicate that for dTpdT the B → A transition is less probable. For dApdA, dApdT, and dTpdA this transition is probable in the same order of preference. We propose that the T‐A sequence in the polynucleotide chain might serve as the site accessible for B ⇄ A transitions. The theoretical predictions are in good agreement with the experimental observations.
Prediction of β‐sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest‐neighbors on conformations of middle amino acids in proteins
Authors: Wu Tai Te , Szu Shousun C. , Jernigan Robert L. , Bilofsky Howard , Kabat Elvin A. 
Published: December 2004

AbstractThe extraordinarily large number of immunoglobulins renders them an intriguing class of molecules for attempts to predict their conformations. The predictive method applied, using a 20 × 20 table of the observed effects of nearest‐neighboring amino acids on the conformation (Φ,Ψ angles) of the middle residue in known proteins, indicates positions of tri‐peptides that tend to break α‐helices or regular β‐sheets. This 20 × 20 table is derived from data on 19 proteins, as compared with the earlier version based on 12 proteins, and includes a separate listing of residues of β‐turns that have helical Φ,Ψ values. Secondary conformations predicted by methods of Chou and Fasman, Lim and Burgess, Ponnuswamy, and Scheraga have also been compared; for all three methods, wrong predicitons of residues in β‐sheet conformation exceed correct ones. Better predictions are obtained when there is agreement with two or three of the methods. If there is consistent overprediction of β‐structure, as with the Chou and Fasman method, the use of the β‐sheet‐breaking tripeptides can improve pre‐dictability somewhat.
Synthesis of polymeric models of elastin: Polyhexapeptides and an insoluble, hybrid cross‐linked polypeptide
Authors: Okamoto K. , Rapaka R. S. , Urry D. W. 
Published: December 2004

AbstractThe polymer of the hexapeptide sequence, Val‐Ala‐Pro‐Gly‐Glu‐Gly, was synthesized and demostrated of exhibit a reversible, pH‐dependent coacervation in low‐pH aqueous solution. In addition, the synthesis of an insoluble, hybrid, cross‐linked polypeptide matrix is described. The cross‐linking was achieved in the coacervate state during flow orientation of the polymers. The chemical means of covalent cross‐linking was intermolecular primary amide bond formation between the lysyl side chains in one polypentapeptide unit and the glutamyl side chains in another polyhexapeptide unit. The carboxyl activating reagent was a water‐soluble carbodiimide. The key intermediates in the syntheses, the hexamers and their high polymers, were analyzed by carbon‐13 magnetic resonance to verify the correctness of synthesis and to obtain information on conformation.
Analysis of the 1H‐NMR spectra of ferrichrome peptides. II. The amide resonances
Authors: Demarco Antonio , Llinás Miguel , Wüthrich Kurt 
Published: December 2004

AbstractThe high‐resolution 1H‐nmr study of the ferrichrome cyclohexapeptides, in d6‐DMSO solutions, has been extended to the amide NH spectral region. A total of ten diamagnetic analogues of ferrichrome that differ in the coordinated metal ion (Al3+, Ga3+ or Co3+), the primary structure, the nature of the bidentate hydroxamate moiety, or the isotope compositions (14N, 15N) have been investigated. The 3JαNH values reflect regiorous conformational isomorphism throughout the complete suite of analogues, quite independent of the residue occupancy of each site. Totally resolved amide multiplets have been obtained in most cases and the four‐line (doublet of doublets) appearances of glycyl NH resonances has been observed for the first times; these data enabled stereospecific assignment and accurate analysis of the NH‐CαH proton spin systems. The high resolution was made possible by the use of a suitable spectral deconvolution shceme at 360 MHz. The fine structure, extraordinarily well displayed in the 15N‐peptide spectra, provides a series of parameter values whose consistency has been checked by computer simulation. Since the crystallographic structure for two of the ferric peptides is known to 0.002‐Å resolution, a 3J vs θ correspondence could be confidently established. A Karplus curve was derived from the combined x‐ray and nmr data:

It is suggested that seriously nonplanar amides can exhibit 3JαNH values higher than predicted by the ferrichrome curve.
Solution properties of synthetic polypeptiedes. XXI. Solvent effect on the helix‐coil transition of poly(e‐carbobenzoxy L‐lysine)
Authors: Nishioka Noboru , Maekawa Akio , Teramoto Akio 
Published: December 2004

AbstractHelix‐coil transitions of poly(ϵ‐carbobenzoxy L‐lysine) in mixtures of dichloroacetic acid and 1,2‐dichloroethane were investigated by optical rotatory dispersion (ORD) measurements. The ORD data were analyzed according to the statistical mechanical approaches developed by Sayama et al. (1970) (Ref. 10) and by Karasz and Gajnos (1973) (Ref. 4) to obtain the enthalpy chage associated with the unfolding of helix in the inert solvent 1,2‐dichloroethane, ΔHo, and that for the solvation of the peptide backbone with the dichloroacetic acid dimer, ΔHa. The results were: ΔHo = −(340 ∼ 620) cal/mol and ΔHa = ‐(2.4 ∼ 3.6) kcal/mol. These values are favorably compared with those for poly(γ‐benzyl L‐glutamate) and poly(β‐benzyl L‐aspartage) in the same solvent system. On the other hand, the equilibrium constant for the solvation and hte cooperativity parameter in the inert solvent 1,2‐dichloroethane depended appreciably on the chemical structure of hte side chain. In terms of the Zimm‐Bragg parameter, s, which varied from 1.3 to 1.7 with polypeptied species, the helices of these three polypeptieds are far from complete even in the typical helix‐supporting solvent 1,2‐dichloroethane.