bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of telopeptide on the morphology and physicomechanical properties of reconstituted collagens
Authors: Chien James C. W. , Chang E. P.
Published: December 2004

The morphology and physicomechanical properties of two types of collagen membranes, one of which does not have telopeptides, were compared with small‐angle light scattering, rheo‐optical, dynamic mechanical, and dynamic rheo‐optical techniques. The presence of telopeptides in native collagen allows the formation of larger rod‐like superstructures; it renders the membrane more resistant to irreversible deformation yet more responsive to dynamic mechanical perturbation. Telopeptides are also responsible for relaxation at room temperature, and impart more linearly elastic properties to the material as compared to membranes derived from enzyme‐treated collagens.
Buoyant and potentiometric titrations of synthetic polypeptides. I. Six ionizable homopolypeptides in CsCl solutions
Authors: Almassy Robert , Zil John S. V. , Lum Lawrence G. , Ifft James B.
Published: December 2004

The buoyant density and potentiometric titrations of six ionizable homopolypeptides in concentrated CsCI solutions have been studied. These six homopolypeptides were chosen as models of the behavior of ionizable residues in proteins. Their buoyant and potentiometric results will be of value in interpreting the buoyant and potentiometric results observed for proteins.

The buoyant densities for all six homopolypeptides were found to increase sigmoidally as the pH is increased. These density changes are interpreted in terms of changes in the hydrations and ion binding which are associated with the titration of the residues. Preferential hydrations for the homopolypeptides are calculated. The buoyant density titrations are combined with the potentiometric titrations to determine the relationship between the buoyant density and the degree of ionization.

A better method of computing buoyant densities of proteins is described. The slope of β(ρ) has been computed for CsCl using least‐squares curve fitting and this is used in calculating the isoconcentration position. This method has been found to be more accurate than calculating the isoconcentration position from the normalized isoconcentration ratio, which is known only under limited conditions.
Polarography of polynucleotides. IV. Effect of the molecular weight of poly(U) on its adsorption at a charged surface
Authors: Janik Borek , Sommer Ronald G.
Published: December 2004

Effects of molecular size on the adsorption properties of poly(U) were studied using alternating current polarography as a technique and a dropping mercury electrode (d.m.e.) as a model interface. The measurements were carried out on fractions (by molecular weight) of poly(U) characterized by sedimentation and viscosity measurements. The data indicate that the rate of poly(U) adsorption is controlled by diffusion. The adsorption equilibrium can be established during the drop‐life at higher concentrations of poly(U) where the electrode is fully covered, while at low concentrations corresponding to the linearized isotherm, the time τ for the establishment of the adsorption equilibrium is much longer than can be obtained with d.m.e. The time τ increases with increasing chain length, n (in monomeric units). From the concentration dependence of the course of current time, I ∼t, curves, or of the current values at the end of the drop life, a constant K was calculated which depends on n. In the range of molecular weights studied (25 × 103 to 564 × 103) the data obeys the relationship log n = a + b log K (where a and b are constants). Area, A, occupied by the monomer of an adsorbed poly(U) molecule was calculated from experimental values of K and D (diffusion coefficient). The decrease of A with increasing n was explained in terms of the looping of longer poly(U) chains out from the electrode surface.
Studies on cyclic peptides. I. Cyclodisarcosyl–metal salts complexes
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

The complexes of cyclodisarcosyl (N,N′‐dimethyldiketopiperazine) have been synthesized with copper perchlorate, lithium perchlorate, barium perchlorate, silver perchlorate, silver nitrate, and boron trifluoride. It has been shown by infrared absorption spectra that the metal cations coordinate to carbonyl groups of the peptide to form insoluble complexes. It has been suggested that the complexation takes place by ion–dipole interaction. Since a linear analog of the peptide formed no insoluble complex with the metal salts, conformation of cyclodisarcosyl seems to play an important role in the complex formation. Examination of the molecular model and X‐ray analysis suggest that the copper perchlorate complex of the cyclic peptide has a “2:1‐sandwich” structure.
Synthesis and electron microscopic investigation of model polyacryloylnucleosides
Authors: Mosevitsky M. I. , Panarin E. F.
Published: December 2004

Using the interaction of polyacrylic anhydride with uridine or N‐acetyl derivatives of adenosine, cytidine, and guanosine, the water‐soluble copolymers, polyacryloylnucleosides, were obtained. The acryloylnucleoside units to acrylic acid units ratio in the copolymer was usually about 1:20. The attaching of nucleosides to the polymer occurs mostly through the 5′‐hydroxyl group of the sugar.

The prominent feature of all polyacryloylnucleosides obtained is their fibrous structure at an ionic strength 0.2 and neutral pH. At concentrations <200 μg/ml the separate strands with a length of 0.2–1.0 μ and diameter of 30–40 Å are distinguishable. Evidently they are formed by side association of two molecules of copolymer or by folding of one molecule on itself. At higher concentrations branched multistranded structures are formed. In the same conditions polyacrylic acid alone does not form the fibrous structures.

Heating of polyacryloylnucleoside solutions at 100°C and fast cooling in ice water, or raising of the pH to 12 turned the stranded structures to coils. After annealing or neutralization the stranded structures reformed. These transformations are similar to those which occur with nucleic acids. The results show that the fibrous structure of the copolymers depends on the hydrogen bonds formed by purine and/or pyrimidine bases.
Macromolecular structure and organization of alpha keratin
Authors: Harget P. J. , Krimm S.
Published: December 2004

The small‐angle equatorial X‐ray scattering of alpha keratin (African porcupine quill) was studied using a direct type of analysis, which allows the separation of the intermicro‐fibrillar interference effects from those of the intramicrofibrillar scattering without the use of prior assumptions. X‐ray data were obtained from 470–21 Å; their analysis by the above method resulted in a z‐axis projection of the microfibrillar electron density, which extends over a diameter of 80 Å and has a core region surrounded by a peak located at a radius of 28 Å. The macromolecular organization of the 80‐Å‐diameter microfibrils was found to be an arc‐like layer type of aggregation and not a pseudohexagonal packing. When the specimen was subjected to silver staining the aggregation of the microfibrils did not change except for a slight contraction. The z‐axis projection of the stained microfibril, however, was significantly different. The silver appears to build up slightly around the outer periphery of the microfibril, stains the peripheral region very little, deposits on the inside of the peripheral region, and outlines the core area.
Isothermes de partage de DNA, rRNA et RNA rapidment marqués dans un système solvant salin
Authors: Garel Jean‐Pierre
Published: December 2004

Partition isotherms of DNA, rRNA, and rapidly labeled RNA in a salt solvent system are determined. In the salt solvent system PMB (potassium phosphate buffer 1.50 M pH 7.0:2‐methoxyethanol:2‐butoxyethanol; 3:1:variable volume), equilibrated at the temperature T, the partition isotherms of animal ribosomal RNA and DNA form a series of straight lines according to the basic relation log k = B − AT(BuO), where k is the partition coefficient, B and AT are parameters depending upon the base composition, the molecular weight, the helix content, and conformation of nucleic acids, and (BuO) refers to the 2‐butoxyethanol amount in volume percent. This relation is also valid for other nucleic acid compounds (bases, nucleosides, nucleotides, oligoribonucleotides, and transfer RNA). For RNA fractions distributed in different Kirby salt solvent systems, log k is proportional to the relative levels of adenine and guanine expressed as the A/(A+G) ratio.

Partition isotherms of high molecular weight RNA from mouse plasmocytoma, labeled during a few hours, are not straight lines. This behavior indicates a heterogeneous RNA population. By plotting the specific activity of this mixture (rRNA and rapidly labeled RNA) determined in the top phase of our salt solvent system as a function of the 2‐but‐oxyethanol content, we obtained a sigmoidal curve, which characterizes the nature of the RNA population investigated. Formulas are given for the calculation of the specific activities of rRNA and rapidly labeled RNA and for the calculation of their relative ratio.
Sequential oligopeptides. Synthesis and characterization of the oligopeptides and a polypeptide with the repeating sequence L‐norvalyl‐glycyl‐L‐proline
Authors: Bonora Gian Maria , Toniolo Claudio
Published: December 2004

The synthesis and characterization of a series of oligopeptides (from the tripeptide to the octadecapeptide) with the repeating sequence L‐norvalyl‐glycyl‐L‐proline and a polytripeptide with this sequence are reported. The oligomers were synthesized step by step using the mixed anhydride method. All the products were chemically and optically pure. The polymer was prepared by the active ester method, using the p‐nitrophenyl ester as the polymerizable tripeptide derivative. Good yield of relatively high average molecular‐weight polymer was obtained. In the accompanying paper conformational investigations, both in solution and in the solid state, on the oligomers and the polymer are described.
Solution properties of synthetic polypeptides. XVIII: Helix–coil transition of poly‐N5‐(2‐hydroxyethyl)L‐glutamine
Authors: Miyake Michihisa , Akita Shuichi , Teramoto Akio , Norisuye Takashi , Fumita Hiroshi
Published: December 2004

The helix–coil transition of poly‐N5‐(2‐hydroxyethyl)L‐glutamine (PHEG) in aqueous isopropanol was examined by means of optical rotatory dispersion (ORD) and intrinsic viscosity [η] measurements. The Zimm–Bragg parameters σ and s for the transition were determined from the ORD data as a function of molecular weight. It was found that the transition was characterized by a relatively low cooperativity; the values of \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt \sigma $\end{document} were in the range from 0.039 to 0.066, depending on the solvent composition. These σ values are much larger than those reported for other polypeptide–solvent systems. The transition enthalpy was negative and its magnitude varied with the solvent composition, with a maximum of 620 cal/mol at 40 wt% isopropanol. The curve of [η] versus helical content for a high‐molecular‐weight sample exhibited a very broad minimum, and this behavior was attributed to the low cooperativity of the transition.
Conformational change of poly‐Nε‐glutary‐L‐lysine and poly‐Nε‐succinyl‐L‐lysine in aqueous salt solutions
Authors: Murai Norio , Sugai Shintaro
Published: December 2004

The conformational changes of poly‐Nε‐glutaryl‐L‐lysine (PGL) and poly‐Nε‐succinyl‐L‐lysine (PSL) in various salt solutions were studied by use of ORD and potentiometric titration measurements. The addition of alkali metal salts to the fully ionized PGL or PSL solution caused helix formation. The helical content of the polymers increases in the following sequences: at salt concentration 0–2 M, CsCl < KCl < LiCl < NaCl; and at 2–3 M, LiCl < CsCl < KCl ∼ NaCl. The preferential binding of the solvent components with various alkali metal salts of PGL or PSL was measured in LiCl, NaCl, and KCl solutions by means of equilibrium dialysis and differential refractometry. It was found that with increasing salt concentration, the polymers were preferentially hydrated in NaCl and KCl soultions; however the salt was preferentially bound to the polymers in LiCl solution. Such preferential binding was suggested to be closely related to conformational change. The addition of CaCl2 to polymer solutions led to the stabilization of the helical structure of PGL or PSL.
Polymerization of optical isomers of phenylalanine N‐carboxyanhydride by poly (N‐methylalanine) diethylamide
Authors: Imanishi Yukio , Kugimiya Kazuya , Higashimura Toshinobu
Published: December 2004

In the polymerization of phenylalanine N‐carboxyanhydride (NCA) using poly(N‐methyl‐L‐or DL‐alanine) diethylamide as initiator, the polymerization rate was L‐NCA ≃ D‐NCA > DL‐NCA. This is a new type of selective polymerization and indicates the incompleteness of earlier investigations to study the asymmetrically selective polymerization without D‐NCA. Neither secondary structure nor optical activity of the polymeric initiator is a reason for the selectivity. Hence the cause for the selectivity was sought in the properties of the NCA's in solution. However, the selectivity was not observed in the polymerization initiated by poly(L‐phenylalanine) dimethylamide. The importance of the initiator being a secondary amine type was suggested. The experimental results are discussed on the basis of these considerations.
Dielectric studies of electrolytic poly(α‐amino acid)s in aqueous solutions
Authors: Aiuchi Toshihiro , Murai Norio , Sugai Shintaro
Published: December 2004

The dependence of the dielectric constant and dielectric loss of aqueous solutions of poly‐ε, N‐succinyl‐L‐lysine on its degree of polymerization, degree of neutralization, concentration of the polymer, and counterion type was studied in a frequency range from 300 Hz to 5 MHz. Regardless of the conformation, a low‐frequency dispersion in a frequency range lower than 10 kHz and a high‐frequency dispersion in a range higher than 100 kHz were found. The large value of the dielectric increment, its nonlinear dependence on concentration, its remarkable dependence on counterion type, and its dependence on the degree of polymerization suggest that the low‐frequency dispersion is mainly due to the polarization of loosely bound counterions. These data were found for both the helical and coiled forms. The rotational motion of the electric dipole on the molecule could not have been primarily responsible for these results. On the other hand, the high‐frequency dispersions may be attributable to the Maxwell–Wagner‐type effect.

The results were compared with the dispersions of poly(L‐glutamic acid), poly(L‐lysine), and their salts reported previously.
Intermolecular orientations of adenosine‐5′‐monophosphate in aqueous solution as studied by fast fourier transform 1H nmr spectroscopy
Authors: Evans Frederick E. , Sarma Ramaswamy H.
Published: December 2004

Proton magnetic resonance spectra of 5′AMP were taken in the concentration range of 0.001–2.2M. The concentration profiles of all the nonexchangeable protons were determined. The data for 5′AMP was compared to those of adenine, adenosine, and poly(A). Theoretically computed isoshielding lines of the adenine moiety were used to qualitatively predict a preferred stacking geometry of 5′AMP in aqueous solution. It is concluded that 5′AMP at pH 8 forms multistacked aggregates at high concentration levels and that a preferred orientation is such that the bases are aligned face to back with considerable, though less than 100%, base overlap; and that the ribose moieties of adjacent molecules are near one another with the phosphate groups well separated. Mn(II) ion binding studies show that the stacks are not restricted to one unique orientation type. Specific evidence is given showing that base‐stacking orientations in the solid state may in some cases be considerably different from that in aqueous solution, due in part to numerous hydrogen bonding differences, and this is shown to be the case for base‐stacked adenosine. In the case of 5′AMP the stacking orientations between the solid and liquid states are also different, except in this comparison the solid‐state structure carries a positive charge.
Conformational properties of methionine homo‐oligopeptides in solution
Authors: Bonora Gian Maria , Toniolo Claudio
Published: December 2004

A conformational analysis was carried out in solution on a series of L‐methionine oligomers having the general formula \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm BOC\rlap{--} (L - Met\rlap{--})}_n {\rm OMe (}n = 2 - 7)$\end{document}. We examined these oligopeptides in TFE, HFIP, EG, and mixed organic–water media. The critical size for helix formation was found to be seven residues in TFE, whereas the β‐associated structure appears at the pentamer in EG and TFE–water (20 : 80, v/v). In HFIP, however, the oligomers exist essentially in an unordered conformation.
Optical activity of doubly ordered macromolecules
Authors: Tenenbaum A. , Triolo L.
Published: December 2004

In order to analyze the optical activity of poly‐N‐γ‐carbobenzoxy‐L‐α,γ‐diaminobutyric acid, the microscopic model we have previously worked out is here further developed. Comparison with experimental data allows us to formulate a hypothesis on the stereochemical interaction between the side chains and the backbone of the macromolecule, and on the dependence of the optical activity on the conformational state of the backbone itself. Finally, the thermodynamic parameters concerning the side chains are estimated.
Conformational change of the triple‐helical structure. II. Conformation of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n in an aqueous solution
Authors: Sutoh Kazuo , Noda Haruhiko
Published: December 2004

Measurements of the molecular weight of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n, which were synthesized by the solid‐phase method, revealed that they formed a trimer in an aqueous solution, and dissociated into single‐stranded chains on warming. Accompanying the transition, a large decrease of optical rotation was observed, like the collagen–gelatin transition. The shape of the trimeric molecule was rodlike, and the dimensions were 12 Å in diameter and 2.8 Å per residue in length, regardless of the length of Ala‐Pro‐Gly sequences in a peptide chain. The data indicate that both Pro‐Pro‐Gly sequences and Ala‐Pro‐Gly sequences from the triple‐helical structure similar to that of collagen in aqueous solution. All optical rotational dispersion (ORD) curves of solutions of the peptides were represented by a single‐term Drude equation, and the Drude constant λc was 200 nm for all peptides regardless of the length of Ala‐Pro‐Gly sequences. The resemblance between the helical structure formed by Pro‐Pro‐Gly sequences and that by Ala‐Pro‐Gly sequences was also suggested by the formation of the hybrid triple helix from two kinds of peptide chains with different lengths of Ala‐Pro‐Gly sequences.
The precipitation of poly‐L‐glutamic acid. I. α‐Precipitation
Authors: Zimmerman S. S. , Mandelkern L.
Published: December 2004

Studies have been made of the precipitation of poly‐L‐glutamic acid from dilute aqueous solutions, over the pH range where the α‐helical conformation is maintained. The major purpose is to establish the molecular conformation in the precipitate and to outline the mechanism of the precipitation. Utilizing molecular‐weight fractions, it is shown that there are two distinctly different precipitation regions, which depend on temperature, concentration, and pH. In one of these regions, the α‐region, a variety of physical properties demonstrate that precipitation occurs without any conformational change. The temperature coefficient of the precipitation process in this region indicates that it is nucleation‐controlled.
Conformation of tetranactin in solution
Authors: Kyogoku Yoshimasa , Ueno Masaharu , Akutsu Hideo , Nawata Yoshiharu
Published: December 2004

The conformation of tetranactin, an ionophore, in chloroform was investigated by infrared and Raman spectra and by proton and 13C magnetic resonances. The infrared spectra show that the structure of its K+ complex in the solution is quite similar to that in crystals. The proton spin–spin coupling constants are explained well by assuming that the crystalline structure is retained in solution. The spin–lattice relaxation times of the 13C nuclei of the K+ complex indicate that its framework is rigid. The correlation time of the overall reorientation of the molecule was calculated to be 9 X 10−11 sec. On the other hand, the conformation of the complexed form in chloroform differs from that in crystals. Despite the geometrical nonequivalence of the four subunits in the crystalline state, the nuclear magnetic resonance spectra show their magnetic equivalence in the solution. The proton spin–spin coupling constants have values that are averaged by rapid internal rotation. The spin–lattice relaxation times of the 13C nuclei in its framework are unexplained by the overall reorientation of the molecule, and reveal the existence of internal motion in the framework. The rate of the local motion of the framework is between 102–1010 sec−1. By comparison of the infrared spectra, it can be said that the mean conformation of the fluctuated framework of the uncomplexed tetranactin in the solution is similar to that of nonactin in the crystalline form, which has an S4 symmetry axis through the center of the macrocyclic ring.
The structure of V amylose dehydrate: A combined X‐ray and stereochemical approach
Authors: Murphy Vincent Gerard , Zaslow Bert , French Alfred Dexter
Published: December 2004

Visually integrated, flat‐plate film data were collected from oriented filaments of V amylose dehydrated made from dimethyl sulfoxide–amylose; and X‐ray diffraction and stereochemical methods were used to search a multidimensional parameter space for the most satisfactory description of the crystal and molecular structure. Results indicate that the helical chains are left‐handed and that they pack into the unit cell in an antiparallel arrangement conforming to space group P212121. Packing is very compact with several O …. O contacts in the range 2.70–2.85 Å between both parallel and antiparallel pairs of chains. Other characteristics of the final model are residue geometry similarity to residue 3 from potassium acetate–cyclohexamylose, O(2)i–O(3)i+1 distance of 2.75 Å, O(6) gg, and O(6)i–O(2)i–6 distance of 2.84 Å. Proton magnetic resonance studies of dried, crystalline V amylose dehydrate powder showed only 0.15 water per glucose residue.
Estimation of the circular dichroism exhibited by statistical coils of poly(L‐alanine) and unionized poly(L‐lysine) in water
Authors: Mattice Wayne L. , Harrison William H.
Published: December 2004

The circular dichroism of Ac‐(Ala)x‐OMe and H‐Lys‐(Lys)x‐OH with x = 1, 2, 3, and 4 has been measured in aqueous solutions. The oligomers with x = 4 show similar circular dichroism spectra in water when the lysyl amino groups are protonated, and they respond in similar fashion to heating and to sodium perchlorate. Both oligomers at 15°C exhibit a positive circular dichroism band at 217–218 nm, which is eliminated by the isothermal addition of 4 M sodium perchlorate or by heating. The positive circular dichroism of the lysine oligomer is also eliminated when the pH is elevated to deprotonate the amino groups. Positive circular dichroism is still observed for Ac‐(Ala)4‐OMe at elevated pH. Circular dichroism spectra have been estimated for poly(L‐alanine) and poly(L‐lysine) as statistical coils under the above conditions, based on the trends established with the oligomers. Poly(L‐lysine) and poly(L‐alanine) are predicted to exhibit similar circular dichroism behavior in aqueous solution so long as the lysyl amino groups are protonated. The circular dichroism of the statistical coil of poly(L‐lysine), but not poly(L‐alanine), is predicted to change when the pH is elevated sufficiently to deprotonate the lysyl amino groups. These results suggest that the unionized lysyl side chains participate in interactions that are not available to poly(L‐alanine). Hydrophobic interactions may occur between the unionized lysyl side chains. Protonation of the lysyl amino groups is proposed to disrupt these interactions, causing poly(L‐alanine) and protonated poly(L‐lysine) to have similar circular dichroism properties.
The conformational analysis of adenosine triphosphate by classical potential energy calculations
Authors: Millner O. E. , Andersen Jon A.
Published: December 2004

The conformational analysis of adenosine triphosphate was conducted by using classical potential energy calculations. All rotatable bonds were examined, i.e., no dihedral angles were fixed at predetermined conformations except for the ribofuranose ring, which was held in the C(3′)‐endo conformation—the conformation observed for adenosine in the crystal state.

The energy terms included in the total energy expression consist of nonbonded pairwise interaction, electrostatic pairwise interaction, free energy of solvation, and torsional bond potentials.

Two separate approaches were used in the conformational analyses. The first consisted of a sequential fragment approach were four bonds were rotated simultaneously at 30° increments. Each fragment overlapped the preceding one by at least one bond. All rotors were then simultaneously examined at their minima and at ±15°. The second approach consisted of a coarse grid search where all rotors were examined simultaneously, but only at staggered positions. The low‐energy conformations thus obtained were then used as starting conformations for a minimization routine based on the method of conjugate directions. The first approach required about 40 hr of central processing unit (CPU) computer time, while the coarse grid/minimization approach required about 4 hr of CPU time.

Both the sequential fragment approach and the minimization approach yielded lowest‐energy conformations which are remarkably similar to the solid‐state conformation of C(3′)‐endo ATP.
Nonactin, monactin, dinactin, trinactin, and tetranactin. A Raman spectroscopic study
Authors: Phillies George D. J. , Asher Irvin M. , Stanley H. Eugene
Published: December 2004

Raman spectra are reported for crystalline nonactin, monactin, dinactin, trinactin, and tetranactin and their solutions in CCl4, CHCl3, CH3OH, and 4:1 (v/v) CH3OH:CHCl3. The macrotetrolide nactins selectively bind a wide variety of cations, and are important model compounds for the study of ion complexation. The conformations of nonactin, monactin, and dinactin in solution are similar. Their conformations are found to be sufficiently open to permit the ester carbonyl groups to form hydrogen bonds with CH3OH; this gives rise to characteristic changes in the vibration frequencies associated with the ester groups. Nonactin, which is the least soluble of the nactins in CH3OH, is also the least effective at forming hydrogen bonds with CH3OH. The greater ability of the higher nactins to form hydrogen bonds with CH3OH may be due to the increased inductive effect of ethyl over methyl side chains, which may increase the dipole moment of the ester carbonyl groups. Spectra of crystalline nonactin, monactin, and tetranactin are fairly similar, while the spectra of dinactin and trinactin comprise a second, distinct family. This is consistent with X‐ray crystallographic studies, which show that nonactin and tetranactin form monoclinic crystals, while trinactin is triclinic.
A triple‐helical model for (Gly‐Pro‐Hyp)n with cis peptide units
Authors: Bansal M. , Ramakrishnan C. , Ramachandran G. N.
Published: December 2004

Synthetic regular polytripeptides of the type (Gly‐R2‐R3) where R2, R3, or both, are imino acids have been widely studied as model compounds for collagen. One such polytripeptide is poly(Gly‐Pro‐Hyp), since triplets with this sequence constitute about 10% of collagen. Recently, a new model has been proposed for this polytripeptide in which one of the three peptide bonds in the tripeptide unit is in the cis conformation, and the γ‐hydroxyl group of hydroxyproline forms a direct interchain hydrogen bond within the triple helix. We have confirmed this structure by model building using computer techniques, and the helical parameters obtained by us are close to the experimentally observed values. The model is also found to be comparable in stability with other models from energy considerations.
The interaction of glutaraldehyde with poly(α,L‐lysine), n‐butylamine, and collagen. I. The primary proton release in aqueous medium
Authors: Blauer G. , Harmatz D. , Meir E. , Swenson M. K. , Zvilichovsky B.
Published: December 2004

The interaction between poly(α,L‐lysine) (DP = 180) and glutaraldehyde was investigated in dilute aqueous solution by measurement of the kinetics of proton release at constant pH and temperature and at various concentrations of the reaction components. Under various conditions, the release of protons at constant pH appeared kinetically to be composed of at least two steps: an initial zero‐order reaction, followed by a slower reaction.

At excess of polylysine amino groups, the pH optimum for the rates of reaction was at pH 9–10 (24–25°C). Under the conditions used and at pH 8, the initial rate of the second kinetic step was proportional to the glutaraldehyde concentration and was practically independent of polylysine concentration at pH 8 and 8.6, at an excess of amino groups. At pH values of 7, 8, and 8.6 the apparent overall energy of activation for the second kinetic step was 18–19 kcal/mole (temp. range 4–40°C). Comparing acetaldehyde with the difunctional glutaraldehyde, it was found that the rate of proton release was much smaller in the case of acetaldehyde. Comparing n‐butylamine with the macromolecular polylysine at equal concentrations of amino groups, the rates of proton release were much smaller in the case of n‐butylamine. Collagen in aqueous medium also interacted with glutaraldehyde in a manner analogous to polylysine, although the conditions were not quite comparable. In the case of collagen, the initial fast proton liberation step was relatively much larger than in the case of polylysine.

A reaction scheme for the initial reaction steps is being proposed which includes primary complex formation between glutaraldehyde and polylysine. This dialdehyde–polyamino acid system is considered to serve as a model for tanning processes of hides and for fixation procedures.
Kinetic studies on the cyclization of T7 and T1 DNA's
Authors: Lee C. S. , Pyeritz R. E. , Thomas C. A.
Published: December 2004

The rates of cyclization of two terminally repetitious phage DNA molecules, T7 and T1, were determined and compared with earlier studies of λ DNA. Though differing over 200‐fold in the number of complementary nucleotides in the single‐chain terminals, these three DNA's cyclize at about comparable rates, suggesting that excluded volume effects are significant. The first order rate constants for T7 and T1 are strictly dependent on solvent viscosity, consistent with a diffusion limitation of the rate determining step. Whole molecules with exposed single‐chain terminals were shear‐broken to half‐molecules and the second order rate constants for joining were measured. The rates for T7 and T1 were nearly equivalent and some tenfold slower than predicted, suggesting that the long double‐helical region appended to the renaturing regions and perhaps other undetermined factors retard the rate of joining of half‐molecules.
Polypeptide models of collagen. Solution properties of (Gly‐Pro‐Sar)n and (Gly‐Sar‐Pro)n
Authors: Ananthanarayanan V. S. , Brahmachari Samir K. , Rapaka Rao S. , Bhatnagar Rajendra S.
Published: December 2004

Our studies on the solution conformation of (Gly‐Pro‐Sar)n and (Gly‐Sar‐Pro)n synthesized as polypeptide models for collagen are reported. It is found that, while (Gly‐Pro‐Sar)n exists in ordered triple‐helical conformation, (Gly‐Sar‐Pro)n remains as a disordered random coil in water. Addition of certain helix‐promoting solvents seems to generate order in (Gly‐Sar‐Pro)n.
Buoyant and potentiometric titrations of synthetic polypeptides. II. Five copolypeptides and two nonionizable homopolypeptides in CsCl solutions
Authors: Sharp Dan S. , Almassy Robert , Lum Lawrence G. , Kinzie Kathleen , Zil John S. V. , Ifft James B.
Published: December 2004

The buoyant density titrations of five ionizable copolypeptides in concentrated CsCl solutions have been determined. The results are used to formulate models for predicting the buoyant density titration behavior of copolypeptides and proteins using the previously reported homopolypeptide buoyant density titration curves. It was determined for these copolypeptides that the best predictive model must include not only the buoyant densities of the constituent amino acid residues and the relative composition, but also hydration and salt binding.

Hydrations determined for the homopolypeptides are used in the copolypeptide predictive model. The hydrations of the neutral homopolypeptides were readily calculable since their buoyant densities are thermodynamically defined in terms of their partial specific volumes and hydrations. For the case of a charged macromolecule, an expression for the buoyant density as a function of the number and nature of the bound ions, its partial specific volume, and its relative hydration has also been available for some time. This heretofore intuitive relationship is now derived from thermodynamic principles and allows calculations of hydrations to charged macromolecules which bind either cations, anions, or both.

The potentiometric titrations of three of the five copolypeptides in concentrated CsCl solutions were determined in order to study the effect of residue interaction and solvation effects on their ionization behavior. The potentiometric results are also combined directly with the buoyant density titration results to determine the correlation of the buoyant density with the degree of ionization. As in the cases of poly(Glu) and poly(His), the buoyant density of the copolypeptides changed linearily with the degree of ionization.

The buoyant density titrations of two nonionizable homopolypeptides, poly(Gly) and poly(Ala), were determined in concentrated CsCl solutions. The buoyant density was found to increase with increasing pH, despite the fact that side chains do not contain ionizable groups. This is the first evidence from homopolypeptide or copolypeptide data that buoyant density changes can be observed from effects other than side‐chain ionizations.
Proton magnetic resonance investigation of interactions between L‐tryptophan and dinucleoside phosphates at low pD
Authors: Kolodny N. H. , Neville A. C. , Coleman D. L. , Zamecnik P. C.
Published: December 2004

Interactions between mononucleoside and dinucleoside phosphates containing adenine and/or cytosine and L‐tryptophan have been studied at low pD by proton magnetic resonance (pmr) spectroscopy. The results of those studies indicate that, despite extensive protonation of ring positions, and resulting electrostatic repulsion, ring stacking does occur between both like and unlike molecules. Geometries for stacked complexes are proposed and the extent of complex formation between L‐tryptophan and adenosine or cytidine in 3′ or 5′ esterified positions is discussed qualitatively.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. V. pH‐Dependent conformational changes in peptides containing two adjacent tryptophyl residues as evidenced by circular dichroism studies
Authors: Rizzo Vincenzo , Luisi Pier Luigi
Published: December 2004

The influence of pH upon CD spectra of H‐Trp‐Trp‐OH, H‐Trp‐Trp‐Gly‐OH, and H‐Gly‐Trp‐Trp‐OH is investigated and data are compared with those obtained for peptides containing only one tryptophyl residue. A negative Cotton effect at around 225 nm, which in previous work has been related to an increase of the conformational rigidity in compounds having the sequence ‐CO‐Trp‐Trp, is also observed in the case of H‐Trp‐Trp‐OH and H‐Trp‐Trp‐Gly‐OH upon deprotonation of the terminal α‐amino group. These data, together with observations arising from solvent and temperature effects, give evidence that H‐Trp‐Trp‐OH undergoes a conformational change upon going from acid to alkaline conditions, where the two aromatic side chains become conformationally more rigid relative to each other. This rigidity generates an exciton coupling between the Bb transitions of the two indoles. Hydrophobic forces, including stacking interactions, do not appear important in stabilizing this conformationally rigid structure. Rather, intramolecular electrostatic interactions (e.g., hydrogen bondings or polar interactions between the aromatic side chain and the peptide backbone) as well as interactions with the OH group(s) of the solvent, are suggested to be the salient forces. Possible structures which obey these requisites are discussed.
Enzymic activity and conformational properties of native and crosslinked glucose oxidase
Authors: Solomon Beca , Lotan Noah , Katchalski‐Katzir Ephraim
Published: December 2004

Glucose oxidase has been modified by reacting it with glutardialdehyde. The products obtained are water soluble and merely intramolecularly crosslinked; they exhibit high enzymic activity and good stability towards denaturing agents. Comparative circular dichroism studies have been performed with the native and crosslinked enzymes, as well as with the corresponding apoenzymes. The results suggest that the FAD coenzyme is not a gross structural determinant of glucose oxidase.
Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid
Authors: Suurkuusk J. , Alvarez J. , Freire E. , Biltonen R.
Published: December 2004

The heat capacities of the single‐stranded and double‐stranded forms of polyadenylic acid, polyuridylic acid, and poly(uridylic and adenylic acid) were determined with a drop heat capacity calorimeter. In addition, the temperature dependence of the apparent partial heat capacity (ϕCp) was measured with a newly developed differential scanning calorimeter. The calculated ΔCp at 28°C for the transition poly(A)·poly(A) ⇄ 2 poly(A) was found to be 165 ± 24 cal/Kmol‐base pair, compared with a value of 140 ± 28 for the transition poly(A)·poly(U) ⇄ poly(A) + poly(U). The temperature dependence of ϕCp of single‐stranded poly(U) was consistent with the conclusion that it is totally unstacked at temperatures above 15°C. The temperature dependence of ϕCp of single‐stranded poly(A) was used to determine the base‐stacking parameters for poly(A). The experimental results are consistent with a stacking enthalpy change of −8.5 ± 0.1 kcal/mol bases and a cooperativity parameter σ of 0.57 ± 0.03 for the stacking of adenine bases. These results demonstrate that the heat capacity of single‐stranded polynucleotides is greater than that of the double‐stranded forms. This increased heat capacity is mainly the result of the temperature dependence of the base‐stacking interactions in the single‐stranded form.
Conformation of adenosine 5′‐monophosphate in aqueous solution as studied by nmr‐DESERT method
Authors: Imoto Toshiaki , Shibata Susumu , Akasaka Kazuyuki , Hatano Hiroyuki
Published: December 2004

The molecular conformation of adenosine‐5′‐monophosphate (5′‐AMP) in D2O (pH 8.1) has been investigated by the method of “DESERT” proposed earlier by Akasaka et al. [J. Magn. Reson. 18, 328 (1975)]. The reciprocal sixth‐power‐averaged distances r̄i′8 between H(8) of the adenine ring and H(i′) (i′ = 1′, 2′, and 3′) of the ribose moiety have been deduced directly from the differential spin‐lattice relaxation rates of these ribose protons upon deuterium substitution for H(8) and the rotational correlation times of the molecule estimated from carbon‐13 T1 values, by utilizing the pulse Fourier transform nmr method. The r̄i′8 values have been found to change significantly with the concentration of 5′‐AMP. The values of r̄1′8, r̄2′8, and r̄3′8 at infinite dilution have been determined to be 3.14, 2.45, and 3.37 Å, respectively, whereas those corresponding to the infinite concentration have been determined to be 3.84, 2.80, and 3.01 Å, respectively.

The interproton distances obtained for infinite dilution are not consistent with any single conformation with respect to the rotation about the glycosidic torsional angle and to the ribose puckering, but can be explained well by approximately an equal mixture of three groups of conformers showing an intercorrelation between the ribose puckering and the glycosidic torsional angle, i.e., 3′‐endo‐anti, 2′‐endo‐syn, and 2′‐endo‐intermediate. The increase of r̄1′8 and r̄2′8 and the decrease of r̄3′8 with increasing concentration of 5′‐AMP can be explained well quantitatively by the preferential stabilization of anti conformers for both ribose states with formation of a base‐stacked dimer. The present results are compared with those obtained previously by other workers using a variety of methods.
Proton magnetic resonance and model peptides conformations
Authors: Forchioni A. , Abillon E. , Thiéry J. M. , Le Barny P. , Loucheux‐Lefebvre M. H.
Published: December 2004

Derivatives and peptides of β‐nitrobenzyl‐L‐aspartates were studied with high‐field nmr. Differences were observed between the chemical shifts of protons located near the extremity of the principal chain as a function of the terminal group. These differences are explained by conformational calculations which exclude the existence of an hydrogen bond and demonstrate the influence of the aromatic ring position on the protons of the main chain. Both nmr experiments and conformational analysis indicate that conformations are nearly the same for ortho, meta, and para nitro substitution. These conclusions are in good agreement with Karplus relationship applied to the α and β protons.
Block oligopeptides (L‐lysyl)m‐(L‐alanyl)n‐L‐Tyrosyl‐(L‐Alanyl)n‐(L‐Lysyl)m. II. Circular dichroism and pulsefluorimetry conformational studies
Authors: Mayer R. , Gauduchon P. , Spach G. , Wahl Ph.
Published: December 2004

The conformation of chromatographically pure block oligopeptides (L‐lysyl)m‐(L‐alanyl)n‐ L‐tyrosyl‐(L‐alanyl)n‐(L ‐lysyl)m with n = 3 and m = 6 or 3 is investigated. By circular dichroism it is shown that these peptides may exhibit a partially α‐helical structure depending upon pH, ionic strength, solvent, and temprerature. An attempt is made to describe the helical content of these small peptides by utilizing the data obtained on high‐molecular‐weight poly(L‐lysine). By measurement of the quantum yield and the decays of the peptides fluorescence, it is shown that, in aqueous solution, at neutral pH, the fluorescence of the peptides is quenched by interactions with the peptide carbonyl groups. The decays are multiexponential, which shows the presence of several conformations of the phenolic chromophore relative to the peptide chain. The addition of methanol, which induced the helix formation, decreases the quenching of the fluorescence and the multiexponential character of the decays. In presence of sodium hydroxide, which further increases the helical content of the peptides, a dynamic quenching occured that can be attributed to interactions between the phenol hydroxyl group of tyrosine (ith residue) and the ε‐amino groups of the (i+4)th and (i ‐4)th lysyl residues.
Different families of double‐stranded conformations of DNA as revealed by computer calculations
Authors: Zhurkin V. B. , Lysov Yu. P. , Ivanov V. I.
Published: December 2004

An algorithm has been developed that permits one to find all possible conformations of the sugar‐phosphate backbone for any given disposition of DNA base pairs. For each of the conformations thus obtained, the energy of the helix was calculated by the method of atom‐atom potentials. Several isolated regions in the space of the bases′ parameters (Arnott's parameters) have been found for energetically favorable helical structures. Two parameters, the distance of a base pair from the helix axis, D, and the windling angle, τ, allow one to subdivide possible conformations into the families of closely related forms. Two regions (ravines) on the (D, τ) map correspond to the know A and B families. In the B family a continuous transition has been obtained in which the double helix undergoes increasing winding, while the base pairs are moving toward the major (nonglycosidic) groove.

Interrelationships between the variables, characterizing the spatial structure of the double helix, D, τ, TL and χ, when going along the bottom of the B ravine, were also obtained.

Besides the Known A and B families, several new ones were found to be energetically possible. Among these the strongly underwound helices with the negative D values, as well as the forms with the C4‐C5 angle in a trans position, should be mentioned.

Biological roles of the different double‐stranded conformations, in particular, in protein‐nuclei acid interaction are discussed.
Statistical mechanical deconvolution of thermal transitions in macromolecules. II. General treatment of cooperative phenomena
Authors: Freire Ernesto , Biltonen Rodney L.
Published: December 2004

In the preceding article1 we demonstrated that the partition function of a system is experimentally accessible from scanning calorimetric data. In this article the general results of the deconvolution theory are applied to the general case of cooperative transitions in macromolecules. It is demonstrated that, in the limit of very large systems, all the relevant molecular averages and molecular distribution functions can be directly obtained from the experiment. In doing this, the method of the grand partition function is used. It is shown that in the case of homopolymers, only one parameter, the stability constant, needs to be explicitly specified for a complete description of the system. Since the partition function is directly evaluated from the experiment, no special assumptions or artificial constraints directed to obtain a mathematically solvable model are required. This result offers the unique opportunity of having direct experimental access to statistical averages of systems in which the partition function cannot analytically be solved. Consequently, the theory can be extended to cooperative transitions occurring in two and three dimensions by introducing cluster distribution functions.
Statistical mechanical deconvolution of thermal transitions in macromolecules. III. Application to double‐stranded to single‐stranded transitions of nucleic acids
Authors: Freire Ernesto , Biltonen Rodney L.
Published: December 2004

The statistical mechanical deconvolution theory for macromolecular conformational transitions is extended to the case of nucleic acids transitions involving strand separation. It is demonstrated that the partition function, Q, as well as all the relevant thermodynamic quantities of the system, can be calculated from experimental scanning calorimetric data. In particular, it is shown that important thermodynamic parameters such as the size of the average cooperative unit during strand separation, the mean helical segment length, and the mean coil‐segment length can be calculated from the average excess enthalpy function 〈ΔH〉. The theory is applied to the double‐stranded to single‐stranded transition of the system poly(A)·poly(U) at different salt concentrations. It is shown that the mean helical segment length is a monotonically decreasing function of the temperature well before strand separation occurs. On the other hand, the mean coil segment length remains practically constant until temperatures very close to Tm. Both experimental findings clearly indicate that the unfolding of poly(A)·poly(U) proceeds through the formation of many short helical sequences. The cooperative unit for the strand separation is calculated to be about 120 base pairs and essentially independent of the salt concentration. The existence of a minimum helical segment length of 10 ± 2 base pairs within the double‐stranded form is calculated.