bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time‐dependent fluorescence depolarization and Brownian rotational diffusion coefficients of macromolecules
Authors: Tao Terence 
Published: December 2004

AbstractUsing a distribution function formalism, we have derived relations between the time‐dependent fluorescence polarization anistropy r(t) = [I‖(t) − I⟂(t)]/[I‖(t) + 2I⟂(t)] and the Brownian rotational diffusion coefficients of macromolecules. It is shown that in the most general case of a completely asymmetric body, five exponentials appear in r(t). Reduction to previously obtained simpler expressions are presented and discussed. Experiments were performed to measure r(t) for the complex of 1‐anilino‐8‐naphthalene sulfonate (ANS) and apomyoglobin. The results revealed a spherical geometry, with a radius of 20.8 Å. Similar experiments were performed on the ANS–apohorse radish peroxidase complex. The results were inconclusive towards the geometry of the complex, but when assumed to be spherical, the radius was estimated to be 29.6 Å, consistent with the larger molecular weight of horse radish peroxidase.
In vitro incorporation of tritium into native DNA
Authors: Doppler‐Bernardi Françoise , Felsenfeld Gary 
Published: December 2004

AbstractAn exchange method is described for producing tritium‐labeled native DNA in vitro with minimal physical damage to the DNA. Tritium‐labeled calf thymus DNA prepared in this way has a specific activity of about 100 μCi/mmole of nucleotide (i.e., about 2 × 108 dpm/mmole). Sedimentation velocity at neutral and alkaline pH indicate that the product has an average of two single strand breaks per duplex molecule of molecular weight 6 × 106 daltons. The optical and thermal denaturation properties of the product are those of native DNA. The method should be particularly useful for labeling DNA from organisms that cannot be labeled conveniently in vivo.
Bindings of RNAse to denatured and native deoxyribonucleic acids
Authors: Raju E. V. , Davidson N. 
Published: December 2004

AbstractThe binding of pancreatic ribonuclease‐A by denatured DNA, native DNA, poly‐dA, and poly‐dT, has been studied by a gel filtration method. With denatured DNA at pH 7.5, ionic strength 0.053M, there is one binding site per 12 nucleotides and the equilibrium binding constant per site is 9.7 × 104 l./mole. The binding constant increases by a factor of 8 as the pH is decreased from 8 to 7. The strength of the binding of denatured DNA increases with decreasing ionic strength. At pH 7.5, native DNA binds about ⅛ as strongly as does denatured DNA. The binding affinity increases in the order poly‐dA, denatured DNA, and poly‐dT. These results support the view that the binding of denatured DNA involves both electrostatic interactions between the negatively charged polynucleotide and the positively charged protein, and an interaction of the protein with a pyrimidine residue of the denatured DNA, and thus that the binding is basically similar to that between RNAse and its substrate RNA.
Theoretical evaluation of polytripeptide collagen models
Authors: Hopfinger A. J. , Walton A. G. 
Published: December 2004

AbstractThe influence of inserting certain residues (X) into a polytripeptide sequence conformed into a poly‐L‐proline II helix is examined theoretically. It is found that for sequences such as ‐Gly‐Pro‐X‐ and ‐Gly‐X‐Pro‐, the introduction of glycyl, L‐alanyl or L‐seryl residues in the X position destabilizes the helix so that it is no longer the most stable intramolecular form. On the other hand, L‐prolyl and L‐hydroxyprolyl residues cause the PP II helix to be most stable. Of the many stable intramolecular forms, the majority will not pack efficiently to form fiber or solid‐state structures. The Rich‐Crick and Ramachandran collagen model structures were examined in terms of a Gly‐Pro‐Ala sequence, the Ramachandran, one‐hydrogen‐bond structure, being the most stable. However, another triple‐strand structure for (Gly‐Pro‐Ala)n, is much more energetically favorable. Hence, it may be concluded that none of the aforementioned is an entirely satisfactory collagen model. The new triple helix conformation proposed by Traub, Yonath, and Segal for (Gly‐Pro‐Pro) is found to give a more favorable intramolecular conformation for (Gly‐Pro‐Ala)n than those derived from other collagen models. It is concluded that the collagen molecule derives its stability from interchain interactions in proline‐sparse regions and intrachain stability in proline‐rich regions.
Syntheses of poly[γ‐(l)‐menthyl L‐ and D‐glutamates] and their secondary structures
Authors: Yamamoto Hiroyuki , Kondo Yoshiyuki , Hayakawa Tadao 
Published: December 2004

Abstractγ‐(l)‐Menthyl L‐ and D‐glutamates were prepared by a fusion reaction of N‐phthalyl‐L‐ and D‐glutamic anhydrides with l‐menthol, followed by hydrazinolysis. The monomers were polymerized to poly[γ‐(l)‐menthyl L‐ and D‐glutamates] by the N‐carboxyanhydride method. These polymers were soluble in many organic solvents, such as ethyl ether, chloroform, tetrahydrofuran, and n‐hexane. From the results obtained by a study of the infrared absorption spectra, the x‐ray photographs, the optical rotatory dispersions and the circular dichroisms, poly[γ‐(l)‐menthyl L‐glutamate] was found to be a right‐handed α‐helix in the solid state and in solution. Similarly, poly[γ‐(l)‐menthyl D‐glutamate] was a left‐handed α‐helix. The helix‐coil transition of these polymers was observed in the vicinity of 40% dichloroacetic acid in a chloroform–dichloroacetic acid mixture.
Diamide model for the optical activity of collagen and polyproline I and II
Authors: Madison Vincent , Schellman John 
Published: December 2004

AbstractA diamide, N‐acetyl‐L‐proline‐N,N‐dimethylamide (AcProDMA), in water solution has optical rotatory dispersion (ORD) and circular dichroism (CD) spectra very similar to those of poly‐L‐proline II and the fibrous protein collagen. In contrast, AcProDMA in cyclohexane solution has optical activity resembling that of poly‐L‐proline I. Conformational analysis shows that AcProDMA is confined by steric constraints to either of two narrow regions of conformational space. The trans isomer of AcProDMA assumes conformations near those of polyproline II and collagen nearest neighbors, while cis‐AcProDMA assumes conformations near that of polyproline I nearest neighbors. Nuclear magnetic resonance (NMR) experiments show that an equilibrium mixture of the cis and trans isomers of AcProDMA is present in solution. The trans isomer predominates in aqueous solution, but the equilibrium shifts to favor the cis isomer in nonpolar organic solvents such as cyclohexane. Analysis of the ORD spectra in terms of two basic spectra reveals a solvent dependent isomerization which parallels that observed by NMR. The optical activity of the pure isomers of AcProDMA can be derived from the ORD, CD and NMR data. A comparison of component cotton effects confirms the similarity in optical activity of trans‐AcProDMA, polyproline II, and collagen on the one hand, and of cis‐AcProDMA and Polyproline I on the other.
Cooperative transition between two helical conformations in a linear system: Poly‐L‐proline I ⇌ II. I. Equilibrium studies
Authors: Ganser V. , Engel J. , Winklmair D. , Krause G. 
Published: December 2004

AbstractThe solvent‐induced conformational transition between the two helical forms of poly‐L‐proline is studied as a model for cooperative order ⇌ order transitions. The chain length dependent equilibrium data in two solvent systems are described by Schwarz's theory, which is based upon the most general formulation of the linear Ising model with nearest neighbor interactions. The parameter σ which describes the difficulty of nucleation of a I (II) residue in an uninterrupted II (I)‐helix is 10−5 in both solvent systems. The ratios of the nucleation difficulties of states I and II at the ends of the chains β′ and β″ are very different in the two systems. Nucleation difficulty within the chain is interpreted as being due to unfavorable excess interaction energies at the I–II and II–I junctions, which add up to 7 kcal/mole of nuclei as calculated from the σ value. A similar value is computed from the atomic interactions at the junctions. In contrast to this intrinsic properly of poly‐L‐proline, the energies of I and II residues at the ends are heavily influenced by interactions of the endgroups with the solvent. The above values of the nucleation parameters are determined by a new least‐square fitting procedure which does not necessitate the assumption of the dependence of the equilibrium constant s for propagation upon the external parameters, but yields this function from the experimental transition data. A quantitative explanation of this experimental s function through the binding of solvent is attempted. In the transition region a very small free energy change (about 0.1 kcal/mole), arising from a preferential binding of solvent molecules to one of the conformational states, is sufficient for a complete conversion from one helical form to the other.
Simplified quantitative electron microscopy of biopolymers
Authors: Lang D. , Mitani Michiko 
Published: December 2004

AbstractShape and molecular weight of DNA can be obtained with a new method involving spontaneous surface adsorption of DNA or of other macromolecules from a solution which contains formaldehyde and a critical amount of cytochrome c. Subsequent transfer to specimen grids and electron microscopy shows individual molecules suitable for quantitative evaluation. Adsorption of DNA and fd bacteriophages is proportional to (time)0.75. Contour lengths of double‐stranded DNA are not influenced by formaldehyde. A modification of this method requires only 2 × 10−5 μg DNA.
Chemical fixation of chymotrypsin to water‐insoluble crosslinked dextran (Sephadex) and solubilization of the enzyme derivatives by means of dextranase
Authors: Axén Rolf , Myrin Per‐Åke , Janson Jan‐Christer 
Published: December 2004

AbstractCatalytically active chymotrypsin derivatives can be synthesized from cyanogen bromide‐activated Sephadex G200. In most cases the apparent catalytic activity of the covalently fixed enzyme appears to be considerably decreased in comparison to the activity of the free enzyme. However, by proper choice of the reaction conditions for the activation, enzyme conjugates with high activity, even toward a high molecular substrate, can be synthesized. These latter derivatives may be of practical value for the digestion of proteins. Crosslinked dextran as carrier was chosen because of the possbility, of digesting it enzymatically by dextranase. Sephadex G200, if activated at or below pH 10.3, will combine with chymotrypsin to yield digestable products. Changes of apparent kinetic properties of the fixed enzyme can accordingly be studied during the degradation process. On the solubilization of the insoluble conjugate, a total recovery of activity of the fixed enzyme can be obtained in cases the carrier has been activated by a sufficiently mild procedure. The high apparent Michaelis constant Km of insoluble chymotrypsin–Sephadex toward N‐acetyl‐L‐tyrosine ethyl ester shifts back on solubilization to the value of free chymotrypsin. We therefore propose that the decreased activity of an insoluble chymotrypsin–Sephadex is due to diffusional effects shown by the gel matrix toward the substrate. Similarly observed shifts in optimum pH are explained by accumulation of hydrogen ions in the gel. The organic chemical reaction used for coupling the enzyme to the polymer can therefore be performed without decreasing the inherent catalytic activity of the enzyme. The route described for fixing chymotrypsin to Sephadex followed by solubilization of the products may be useful as a synthetic method for binding proteins, peptides, and other amino group‐containing substances to soluble carriers, e.g., for the modification of pharmaceuticals.
Stability of the helical conformation of random L‐alanine–L‐lysine copolymers in aqueous solution
Authors: Sugiyama Hiroyuki , Noda Haruhiko 
Published: December 2004

AbstractThe potentiometric titration of random copolymers of L‐lysine and L‐alanine containing 0–35% alanine was carried out. The standard free‐energy change for the transition of coil to helix was calculated from the titration curve, and was treated by taking account of first‐neighbor interactions. For uncharged lysine ΔG° = −140 cal/mole, and for alanine ΔG° = −50 cal/mole in 0.06M NaBr at 25°C, indicating that the alanine helix is thermodynamically less stable than the lysine helix. The randomness in co‐polymerization was confirmed by trypsin treatment.
Raman spectra of L‐alanine oligomers
Authors: Sutton P. , Koenig J. L. 
Published: December 2004

AbstractThe Raman spectra have been obtained of di‐, tri‐, tetra‐, penta‐, and hexa‐L‐alanine in the solid state. Raman spectra of the dimer and trimer in aqueous solution are also reported. The oligomers of alanine exist as zwitterions in the solid state and aqueous solution. Spectral differences between the dipeptide, and other oligomers arise primarily from the conformationally sensitive amide modes. The dipeptide exists as a nonplanar structure in the solid state and the other oligomere as β conformations. Comparison of Raman spectra of tri‐L‐alanine in the solid state and in aqueous solution suggests a conformational change to a random coil upon dissolution.
Cooperative binding of adenosine by polyuridylic acid: A further analysis
Authors: Schmitz Kenneth S. , Schurr J. Michael 
Published: December 2004

AbstractThe dialysis data of Huang and Ts'o for the cooperative binding of adensine to polyuridylic acid are analyzed here using a grand‐partition function Ising model method similar to that originally employed for polyelectrolytes by Rice and Nagasawa. An appropriate modification permitting the treatment of the sliding degeneracy of the two polyuridylic acid strands is also included. In addition to the previously estimated stacking energy of about −6 kcal/mole one also obtains the free energy change F̄ for the transfer of a single adenosine molecule from a fixed site in solution to a fixed site on the polyuridylic acid. This binding energy falls in the range F̄ = −140 to +620 cal/mole, indicating that binding in the 1:2 (purine: pyrimidine) complex is either very weak or repulsive. The absence of any comparable cooperative stacking of adenosines in solution at the same concentration together with the likely repulsive character of the binding implies that the stacking energy must contain a significant contribution from other processes than simple stacking of adenosines. A generalization of the theory to treat multicomponent binding and longer‐range interactions is effected, and the form applicable to simultaneous binding of both adenosine and guanosine by polyuridylic acid is presented.
Interaction of nucleic acids. VI. Interaction of purine with nucleic acids
Authors: Sander Christian , Ts'o Paul O. P. 
Published: December 2004

AbstractThe interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly‐nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de‐naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic‐costacking mechanism. Results from studies on optical rotation and helix‐coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg++ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20–40°C lower) in the presence of purine (0.2–0.6M).
Configurational statistics of polysaccharide chains. Part II. Cellulose
Authors: Yathindra N. , Rao V. S. R. 
Published: December 2004

AbstractThe characteristic ratio of unperturbed cellulose chain was computed as a function of the angle τ at, the bridge oxygen atom and the degree of polymerization. Very high values of the order of 40 or more, depending on the angle at the bridge oxygen atom, have been obtained for this ratio, indicating that cellulose chains are highly extended. The average dimensions of cellulose chains are found to be sensitive even for small changes in the angle at the bridge oxygen, and these chains attain the character of a random coil in very high molecular weight range (degree of polymerization greater than 2000). The large differences in the unperturbed dimensions of cellulosic chains observed in different solvents have been attributed to the possible small changes in the angle τ caused by specific solvent, interactions.
Ionic polysaccharides. IV. Free‐rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid
Authors: Cleland Robert L. 
Published: December 2004

AbstractThe root‐mean‐square end‐to‐end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order‐of‐magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non‐ionic synthetic polymers. A double logarithmic plot of the product of [η] and M̄w, the weight‐average molecular weight, against the degree of polymerization in the range for M̄w of 104 to 2 × 104 permits a straight‐line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short‐chain hydrodynamic behavior of these polymers.
Experimental thermodynamics of the helix–random coil transition. III. Determination of the transition enthalpies of the helical complexes poly(I + C) and poly I in solution
Authors: Hinz H.‐J. , Haar W. , Ackermann Th. 
Published: December 2004

AbstractThe enthalpies of the helix‐coil transitions of the ordered polynucleotide systems of poly(inosinic acid)–poly(cytidylic acid) [poly(I + C)], (helical duplex), and of poly (inosinic acid) [poly(I + I + I)], (proposed secondary structure: a triple‐stranded helical complex), were determined by using an adiabatic twin‐vessel differential calorimeter. Measuring the temperature course of the heat capacity of the aqueous polymer solutions, the enthalpy values for the dissociation of the helical duplex poly (I + C) and the three‐stranded helical complex poly(I + 1 + 1), respectively, were obtained by evaluating the additional heat capacity involved in the conformational change of the polynucleotide system in the transition range. The ΔH values of the helix‐coil transition of poly (I + C) resulting from the analysis of the calorimetric measurements vary between the limits 6.5 ± 0.4 kcal/mole (I + C) and 8.4 ± 0.4 kcal/mole (I + C). depending on the variation of the cation concentration ranging from 0.063 mole cations kg H2O to 1.003 mole cations/kg H2O. The calorimetric investigation of an aqueous poly I solution (cation concentration 1.0 mole/kg H2O) yielded the enthalpy value ΔH = 1.9 ± 0.4 kcal/mole (I), a result which has been interpreted qualitatively following current models of inter‐ and intramolecular forces of biologically significant macromolecules. Additional information on the transition behavior of poly(I+ C)Was obtained by ultraviolet and infrared absorption measurements.
Enthalpy of helix–coil transitions from heats of solution. II. Poly‐ε‐carbobenzoxy‐L‐lysine and copolymers with L‐phenylalanine
Authors: Giacometti Giovanni , Turolla Angklo , Boni Renzo 
Published: December 2004

AbstractThe heal of solution of Poly‐ε‐carbobenzoxy‐L‐lysine and of a series of its copolymers with phenylalanine was measured as a function of solvent composition. The enthalpy change of the helix‐to‐coil transition was estimated for the various cases. The previous findings that side chains do not greatly affect the transition enthalpy is confirmed also in cases having much larger differences in helix stability.
X‐Ray diffraction of ethylenediamine–amylose complex
Authors: Simpson T. D. 
Published: December 2004

AbstractSolutions of amylose in ethylenediamine yield a crystalline film complex upon evaporation of solvent. The x‐ray analysis indicates the presence of a tetragonal‐shaped cell with a symmetry approximating that of space group P212121. The amylose sixfold helix has a diameter of 13.3 Å and a translation period of 8.0Å. Chemical and physical analyses support a complexing ratio of one ethylenediamine molecule to every two glucose units. The structure is nearly identical to any amylose–dimethyl sulfoxide complex previously examined. The square mode of packing arrangement appears to result from complexation between amylose chains. Such complexing indicates a much greater degree of amylose interaction than is observed in amylose complex structures having a hexagonal close‐packing arrangement.
Oligonucleotide interactions. IV. Conformational differences between deoxy‐ and ribodinucleoside phosphates
Authors: Warshaw Myron M. , Cantor Charles R. 
Published: December 2004

AbstractThe circular dichroism spectra of all 16 ribodinudeoside phosphates containing the bases adenine, uracil, cytosine, and guanine have been measured at room temperature and neutral pH. These results are compared with the circular dichroism spectra of the corresponding deoxy compounds. From the optical properties it is clear that the geometry of the base‐stacked conformation of ribo compounds must differ substantially from that of deoxy compounds. Because of this, it is not possible to draw firm conclusions about the relative extent of stacking in most ribo and deoxy compounds. The optical rotatory dispersion of about a dozen deoxy and ribodinucleoside phosphates has been studied as a function of temperature. These results confirmed the conclusions drawn earlier from measurements at a single temperature. Several dinucleoside phosphates containing a 2′ → 5′ phosphodiester bond have also been examined. These compounds have a substantial degree of base stacking at room temperature. The geometry of the stacked conformation is different from that of either the normal ribo dimer or the deoxy dimer. The role of the 2′‐hydroxyl group in stabilizing base stacked geometries has been examined by studies on C‐2′‐O‐methyl‐pC. This compound has optical properties almost identical to those of CpC. This suggests that the effect of the 2′ hydroxyl is felt indirectly through its perturbation of the geometry of the sugar ring rather than directly by hydrogen bonding. It is not possible at present to identify precise conformational differences among deoxy‐, ribo‐and 2′ → 5′ ribodinucleoside phosphates.
Raman spectra of poly‐L‐lysines
Authors: Koenig J. L. , Sutton P. L. 
Published: December 2004

AbstractThe Raman spectra of poly‐L‐lysine hydrochloride and poly‐ϵ‐carbobenzoxy‐L‐lysine in the solid state have been obtained and are consistent with the presence of an α‐helical structure. The Raman spectrum of poly‐L‐lysine in aqueous solution suggests the presence of random coil structures.