bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical reactivity of protonated aziridine with nucleophilic centers of DNA bases
Authors: Kikuchi O. , Hopfinger A. J. , Klopman G.
Published: December 2004

A series of molecular orbital calculations, using MINDO/3 and CNDO/2L methods, have been used to characterize the chemical reaction of protonated aziridine with DNA nucleophilic base sites. The N‐7 atom of guanine is found to be the preferred alkylation site only when the O‐6 atom of guanine is involved in base‐pair hydrogen bonding. Otherwise O‐6 is the predicted major site of alkylation. This indirectly suggests that protonated aziridine alkylation processes involve base‐paired DNA structures, since N‐7 guanine is the observed major site of alkylation. Alkylation of N‐3 adenine is predicted to be more favorable than chemical attack of the N‐7 adenine position. Both of these sites, however, are predicted to be less reactive than N‐7 of guanine. These chemical reactivity studies resolve alkylation specifically not achieved in the DNA–alkylator physical association calculations reported in the preceding paper.
Conformational analysis of somatostatin and selected analogs in oriented polyoxyethylene by infrared dichroism
Authors: Gilon C. , Simmons D. , Goodman M. , Rivier J.
Published: December 2004

Infrared dichroic studies and deuterium exchange measurements of somatostatin and some of its analogs incorporated in uniaxially oriented polyoxyethylene are described. Band positions and dichroic ratios in the N‐H stretching and amide I and II regions are similar to those of flexible and nonordered peptides like valinomycin and poly[Glu(ONa)]. This information, together with fast deuterium exchange rates, suggests that somatostatin exists in a flexible nonordered conformation in polyoxyethylene. One analog, di‐S3,14‐acetamidomethyl dihydrosomatostatin, was found to exist in both nonordered and β‐like conformations.
Study of salt effects on adenosine–polyuridylic acid interaction
Authors: Gukovskaya A. S. , Gukovsky I. Ya. , Chikh V. P. , Sukhorukov B. I.
Published: December 2004

Complex formation between poly(U) and adenosine in solutions of salts that stabilize (Na2SO4), destabilize (NaClO4), or have little effect on the water structure (NaCl), as well as the poly(U)·poly(A) interaction in NaClO4, was studied by equilibrium dialysis and uv spectroscopy. At 3°C and neutral pH, Ado·2 poly(U) is formed in 1M NaCl and 0.33M Na2SO4. In NaClO4 solutions under the same conditions, an Ado·poly(U) was found over the whole range of salt concentration investigated (10 mM−1M), which has not been previously observed under any conditions. The Ado‐poly(U) was also found in a NaCl/NaClO4 mixture, the transition from the triple‐ to the double‐helical complex occurring within a narrow range of concentration of added NaClO4. In the presence of 1M NaCl this transition is observed on adding as little as 10 mM NaClO4, i.e., at a [ClO]/[Cl−] ratio of about 1:100. However, when NaClO4 is added to a 1M solution of the stabilizing salt Na2SO4, no transition occurs even at a [ClO]/[SO] ratio of 1:4. Investigation of melting curves and uv spectra has shown that in an equimolar mixture of the polynucleotides, only a double‐helical poly(U)·poly(A) exists in 1M NaClO4 at low temperatures; this also holds for 1M NaCl. This changes to a triple‐helical 2 poly(U)·poly(A) and then dissociates as the temperature increases. At low temperatures and the poly(U)/poly(A) concentration ratio of 2:1, a mixture of 2 poly(U)·poly(A) and poly(U)·poly(A) was observed in 1M NaClO4, in contrast to the case of 1M NaCl. Thus, sodium perchlorate, a strong destabilizer of water structure, promotes formation of double‐helical complexes both in the polynucleotide–monomer and the polynucleotide–polynucleotide systems.

Beginning with a sufficiently high ionic strength (μ ≃ 0.9), a further increase in the salt molarity results in an increase of the poly(U)·adenosine melting temperature in both stabilizing and neutral salts and a decrease in the destabilizing salt. In Na2SO4 concentrations higher than 1.2M Ado·2 poly(U) precipitates at room temperature. Analysis of the binding isotherms and melting profiles of the complexes between poly(U) and adenosine according to Hill's model shows that the cooperativity of binding, due to adenosine stacking on poly(U), increases in the order NaClO4 < NaCl < Na2SO4. The free energy of adenosine stacking on the template is similar to that of hydrogen bonding between adenosine and poly(U) and ranges from −1 to −2 kcal/mol. The values of ΔHt [the effective enthalpy of adenosine binding to poly(U) next to an occupied site, obtained from the relationship between complex melting temperature and free monomer concentration at the midpoint of the transition] are −14.2, −18.3, and −16.8 kcal/mol for 1M solutions of NaClO4, NaCl, and Na2SO4, respectively. The results indicate that the effects of anions of the salts studied are related to water structure alterations rather than to their direct interaction with the complexes between poly(U) and adenosine.
Application of band centrifugation to the study of the assembly of alfalfa mosaic virus
Authors: Driedonks René A. , Joe Michael K. K. Tjok , Mellema Jan E.
Published: December 2004

A band‐centrifugation method for the analysis of an assembly reaction of a simple virus from its RNA and protein is described. The experiment was carried out by sedimenting a band of viral RNA through a solution of depolymerized coat protein. The resulting radial distribution of the reaction products, followed as a function of time, was analyzed by a computer simulation of the series of reaction. This method is based on a numerical solution of the continuity equation for the sedimentation–diffusion process [Claverie, J.‐M., Dreux, H. & Cohen, R. (1975) Biopolymers 14, 1685–1700; Cohen, R. & Claverie, J.‐M. (1975) Biopolymers 14, 1701–1716]. A numerical method for the simulation of the chemical reaction is derived. From the simulated reaction series, equilibrium constants emerge for the successive addition of protein subunits to the growing nucleoprotein particle.

The method is applied to the assembly of alfalfa mosaic virus. If the reaction between RNA and protein is carried out in 0.32M CsCl, pH 7.0, two stages during particle growth are resolved, each characterized by an equilibrium constant K. The determined values for K range from 5 × 105 to 3 × 106 l. mol−1. The existence of these two stages may have a structural implication in the assembly, as they likely represent an elongation and a termination stage. If the reaction is carried out under more favorable conditions (0.25M CsCl, pH 7.0), a kinetic constant of at least 105 l. mol−1 sec−1 is derived for each reaction step. Under these conditions the assembly appears to be completed within 1 min, which is too fast to detect distinct stages by band sedimentation.
Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA
Authors: Le Bret Marc
Published: December 2004

Closed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types—0, 31, 41, 51, and 52—the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1/4 (w/N)2, and therefore depends on the writhing density and on the length of the DNA.
Measurement of preferential solvation of some glucans in mixed solvent systems by gel‐permeation chromatography
Authors: Straub Peggy R. , Brant David A.
Published: December 2004

Preferential solvation of the glucans amylose, pullulan, and dextran in binary dimethyl‐sulfoxide/water (DMSO/H2O) solvent mixtures has been measured using gel‐permeation chromatography. The preferential solvation behavior of the three glucans in DMSO/H2O solvent mixtures is indistinguishable in the experiments reported. In solvent mixtures with mol ratio DMSO/H2O less than 1:2, all three glucans are solvated preferentially by H2O. The maximum extent of preferential solvation by H2O is about 2.5 mol H2O/mol of glucose residues. When the DMSO/H2O mol ratio exceeds 1:2, DMSO solvates the glucans preferentially to a maximum extent of about 1 mol DMSO/mol of glucose residues. An interpretation of the change in preferential solvation with mixed solvent composition is suggested in terms of the known characteristics of the binary solvent system, and the relationship of preferential solvation, reported here, to the absolute solvation of the glucan chains is discussed.
Electrical conductivity of single crystals of lysozyme
Authors: Ataka Mitsuo , Tanaka Shoji
Published: December 2004

The dc electrical conductivity of large single crystals of hen egg‐white lysozyme has been measured. The samples were grown from aqueous solution and dried in air with silica gel. The temperature dependence of the conductivity obeyed the relation σ = σ0 exp(− ΔE/kT), with ΔE = 1.2 eV. The ΔE value agreed with most of the previous results for various proteins in the form of lyophilized powder. On the other hand, log σ0, being between 7 and 11, was much larger than the previously reported values and differed among the samples. An irreversible decrease in σ0, without affecting ΔE, was observed on heating the samples above 85°C. It was shown that the set of results can be explained if the charge carriers responsible for the observed conduction are regarded as protons, originating from residual water molecules. Photoresponse of the samples to uv radiation below 305–315 nm was also observed. Reproducible and reliable results were obtained relatively easily in the present experiments, which is thought to be the main advantage of using single‐crystalline samples.
Transport properties and hydrodynamic centers of rigid macromolecules with arbitrary shapes
Authors: Bernal José M. García , De La Torre José García
Published: December 2004

A general formalism, which includes translation–rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational–rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation–rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length‐to‐diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.
Effects of glycosaminoglycans and proteoglycan on the in vitro assembly and thermal stability of collagen fibrils
Authors: Snowden John McK. , Swann David A.
Published: December 2004

The effects of three glycosaminoglycans (chondroitin 6‐sulfate, dermatan sulfate, and hyaluronate) and a proteoglycan on the kinetics of fibril formation and on the thermal stability of the in vitro assembled collagen fibrils, under physiological conditions of ionic strength and pH, have been examined. The glycosaminoglycans were found to influence the kinetics of collagen precipitation but not the thermal stability of the in vitro assembled fibrils. The proteoglycan was found to influence the kinetics of collagen precipitation and to reduce the thermal stability of the in vitro assembled fibrils. Comparison of the interaction occurring between chondroitin 6‐sulfate and collagen under acidic conditions (0.05M acetic acid) and that occurring under physiological conditions showed that markedly different interaction products were formed under the different conditions.
NMR evidence for a type I β‐turn in (Pro2)‐tetrapeptides and interdependence of cis:Trans isomerism, ring flexibility, and backbone conformation
Authors: Toma Flavio , Lam‐Thanh Hung , Piriou François , Heindl Marie‐Christine , Lintner Karl , Fermandjian Serge
Published: December 2004

Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N‐terminal side, were studied in their various ionic states in 2H2O and in Me2SO‐d6 by 1H‐ and 13C‐nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H‐1H, 13C‐13C, and 13C‐1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β‐turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3J and the 3J coupling constants, which both furnish a dihedral angle of ϕ3 = −90°, and from the positive value of the temperature coefficient of the glycine‐4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side‐chain rotamer fractions of the residue in position 3. In the β‐turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β‐turn.
Potentiometric titration curves of oxidized and reduced horse heart cytochrome c
Authors: Marini M. A. , Marti G. E. , Berger R. L. , Martin C. J.
Published: December 2004

Potentiometric titration curves of oxidized and reduced horse heart cytochrome c in 0.15M KCl at 20°C have been obtained by timed titration (0.125–0.500 μmol/sec) from the isoionic points (pH 10.2–10.4) to pH 3 and back to the isoionic point. Computer‐assisted (PROPHET) data acquisition and blank corrections give curves with good precision with a maximum standard deviation of 0.3 groups for an average error of 1%. The potentiometric titration curve of reduced cytochrome c is reversible within the precision of the method and for the pH range studied. The potentiometric curves for oxidized cytochrome c titrated upscale (pH 3–10) and downscale (pH 10–3) are not reversible. However, they show the same ionization behavior after the initial downscale titration. This is probably the result of a conformational change. Comparison of the data herein reported with the titration curves of oxidized cytochrome c already published by others indicates good agreement on the basis of a normalization of the concentration of protein or on the basis of 25 titrable groups between the acid end point and the isoionic pH.

Titration of the 2 μmol imidazole in the upscale or downscale direction gives the correct analytical concentration and pK′ after correction for the solvent titration. Titration of reduced cytochrome c in the presence and absence of an additional equivalent of imidazole gave a difference titration curve, which indicates that a group on the protein shifts from pK′ 5.8 to pK′ 5.3 in the presence of imidazole. The pK′ of imidazole, in the presence of the protein, remains at a nearly normal value of 7.34.
Effects of pH and ionic strength on the structure of collagen fibrils
Authors: Ripamonti A. , Roveri N. , Braga D. , Hulmes D. J. S. , Miller A. , Timmins P. A.
Published: December 2004

The roles of pH and ionic strength on the structure and stability of collagen fibrils have been investigated by means of x‐ray and neutron diffraction techniques. High‐angle x‐ray diffraction shows that a salt concentration of 0.5M KCl is sufficient to reduce the osmotic swelling and related disordering in the pH range 1–3. The relative intensities of the low‐angle meridional x‐ray and neutron diffraction Bragg reflections vary with pH. Difference Fourier syntheses between pH 7 and 1.6 data indicate, for both x‐ray and neutron diffraction, a reduced scattering contribution from the telopeptides at low pH. Lyotropic relaxation is a crucial step in the appearance at low pH of a doubling of the 668‐Å axial periodicity (D) of collagen fibrils. These results suggest that electrostatic interactions are essential for the structural stability of the telopeptide regions and of the 1D and 3D intermolecular staggers between collagen molecules.
Linked and threaded loops in proteins
Authors: Connolly Michael L. , Kuntz I. D. , Crippen Gordon M.
Published: December 2004

Tertiary structure of globular proteins has traditionally been analyzed in terms of the organization of secondary structure elements. This paper presents a method for systematically identifying different topological features of the convolutions of the backbone. We define a loop as a segment of chain whose end residues are in contact. We find some loops which are threaded by another segment of chain passing through the loop or actually linked with another loop. Fifty‐six loop threadings were found among the 20 proteins studied, all of them occurring in a subset of seven proteins. In our sample, threadings and linkings were generally found if and only if the protein has more than 200 residues. To account for the existence of these topological features, despite their apparent entropic unfavorability, we have proposed a number of kinetic mechanisms by which they may form without a thread actually passing through a loop. We have found that almost all loop threadings possess structural features that would make one of these mechanisms plausible.
Physicochemical studies of amylose and its derivatives in aqueous solutions: Thermodynamics of the iodine–triiodide complex
Authors: Cesàro Attilio , Jerian Edvino , Saule Silvano
Published: December 2004

Thermodynamic properties of the amylose–iodine–triiodide complex have been studied by spectrophotometry and by calorimetry using previously studied samples of amylose ionic derivatives, carboxymethylamylose and diethylaminoethylamylose. The ratio of triiodide to total molecular iodine ([I3]b/[I]b + [I2]b) in the complex is ca. 0.3 over a range of iodide concentration from 10−5 to 10−4M, and there is no evidence for an increasing charge at slightly higher iodide concentration. Direct calorimetric experiments have been carried out in different conditions of polymer, iodine, and iodide concentration in order to study the dependence of the heat of the complexation as a function of the above parameters. It is shown that the dependence of the measured ΔH on the iodide concentration simply derives from the rearrangement of the triiodide equilibrium because of the uptake of a fixed ratio of iodine and triiodide molecules in the complex.
Ultraviolet Raman spectroscopy of polyribouridylic acid: Excitation profile of the hypochromism induced by order–disorder transition
Authors: Chinsky L. , Turpin P. Y.
Published: December 2004

Raman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength—its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order–disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order‐disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O‐O transition of uracil and a vibronic linewidth of 2200 cm−1.
Interactions of molecules with nucleic acids. III. Steric and electrostatic energy contours for the principal intercalation sites, prerequisites for binding, and the exclusion of essential metabolites from intercalation
Authors: Miller Kenneth J. , Macrea Joseph , Pycior Joseph F.
Published: December 2004

Based on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6‐n (n = 14) potential. This method is a soft potential analog of an excluded‐volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B‐DNA via a tetramer‐duplex unit, and the unconstrained dimer‐duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base‐pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
Interactions of molecules with nucleic acids. IV. Binding energies and conformations of acridine and phenanthridine compounds in the two principal and in several unconstrained dimer‐duplex intercalation sites
Authors: Miller Kenneth J. , Brodzinsky Richard , Hall Stephen
Published: December 2004

The binding positions and relative minimum binding energies are calculated for complexes of 9‐aminoacridine, proflavine, N‐methylphenanthridinium, and ethidium in theoretically determined intercalation sites in B‐DNA (sites I and II) and in unconstrained dimer‐duplex sites. The selection of site I in B‐DNA by these compounds agrees with the theoretical interpretation of studies of unwinding angles in closed circular DNA in all cases but ethidium, which is predicted to select site II. The most stable binding positions of the acridines and ethidium in unconstrained dimer‐duplex units agree with experimental results of intercalation complexes of dinucleoside monophosphate units. Base‐pair specificity for Watson‐Crick pairing is examined. The energy of an intercalation complex is partitioned into ΔE23, the energy required to open base pairs BP2 and BP3 in B‐DNA to a site, and ΔEIn, the energy change when a free molecular intercalates. ΔE23 depends strongly on the base‐pair sequence, whereas ΔEIn for the four molecules studied does not. The three most stable sequences contain (pyrimidine)p(purine) units, and this provides a rationale for the exclusive formation of crystals of intercalation complexes with these units. In spite of this selectivity, the distribution of GṁC and AṁT base pairs is equal for these three units and persists as the more unstable sequences are included. Therefore, specificity arises from the interaction between the base pairs and the 2′‐deoxyribose 5′‐monophosphate backbone for the opening of B‐DNA to an intercalation site and not from the interaction between the chromophore and the DNA.
Rǒle des electrons π des fonctions amide et ester dans les peptides et depsipeptides
Authors: Boussard G. , Marraud M.
Published: December 2004

The IR data for the R1 CO‐O‐CHR2‐CO‐NHR3 derivatives are interpreted in terms of a H…π interaction involving the NH bond and the π orbitals of the ester function and giving rise to a high ν(CO) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values ϕ # −90°, ψ # 0°. The H…π interaction in MeCO‐L‐Lac‐NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(CO) ester or amide frequency of the middle function in β‐folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
Polyelectrolyte contribution to the persistence length of DNA
Authors: Schurr J. M. , Allison S. A.
Published: December 2004

The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double‐strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
Hydrodynamic behavior and molecular conformation of poly(L‐lysine HBr) in carbonate buffer solution
Authors: Kakiuchi Kinji , Akutsu Hideo
Published: December 2004

In carbonate buffer at pH 10.5, a transparent solution of poly(L‐lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β‐structure and α‐helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α‐helix and β‐structure was observed as a function of either poly(L‐lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
Viscoelastic properties of protein crystals: Triclinic crystals of hen egg white lysozyme in different conditions
Authors: Morozov V. N. , Morozova T. Ya.
Published: December 2004

A technique for the measurement of the dynamic Young's modulus E and logarithmic decrement 𝓋 of protein crystals and other microscopic samples by the resonance method modified to a microscale is described. Monoclinic crystals of horse hemoglobin and sperm whale myoglobin; triclinic hen egg white lysozyme crystals, crosslinked by glutaraldehyde; and native and crosslinked needlelike lysozyme crystals were studied, as were amorphous protein films. The E of wet protein crystals is shown to be in the range (3–15) × 103 kg/cm2, 𝓋 = 0.3–0.7. The crosslinking does not significantly affect the values. General elastic properties were analyzed for triclinic lysozyme crystals. No frequency dependence of E and 𝓋 was found over the frequency range of 2.5–65 kHz. The temperature dependence was found to be characteristic for glassy polymers; the decrement of Young's modulus was −2.4 ± 0.1%/°C. The guanidine HCl denaturation caused a 1000‐fold decrease of E, its temperature dependence becoming similar to that of rubberlike materials. Studies of pH and salt effects showed E to be influenced by ionization of the acidic groups at pH 3–4.5. A humidity decrease from 100 to 30% caused a three‐ to fourfold increase of E and a decrease of 𝓋. The final values of E = (40–60) × 103 kg/cm2 and 𝓋 ≃ 0.1 were the same for dry crystals and amorphous films, whether crosslinked or not. These values may be attributed to the protein globular material.
Monte Carlo simulation on the intrachain end‐to‐end charge‐transfer interaction on oligosarcosines
Authors: Sisido Masahiko , Imanishi Yukio
Published: December 2004

Monte Carlo conformational calculations for oligosarcosines having terminal electron‐donor (D) and ‐acceptor (A) chromophores [A‐(Sar)n‐D, n = 2–8] were carried out. The bulkiness of the terminal chromophores, the conformational energies, and the charge‐transfer (CT) interaction energy were taken into account in the calculation. The equilibrium constant for the intramolecular end‐to‐end CT interaction was evaluated, and the result was compared with the experimental data. The alternating chain‐length dependence of the equilibrium constant observed experimentally was reproduced by the simulation and the solvent dependence of the equilibrium constant was also reasonably explained.
Interaction of Mn2+ with DNA as studied by proton‐relaxation enhancement of solvent water
Authors: Van Steenwinkel Raymond , Campagnari Francesco , Merlini Margaret
Published: December 2004

The binding of Mn2+ to double‐stranded DNA in solution has been studied by measuring the proton‐relaxation enhancement of solvent water. The nmr experiments were carried out on DNAs of different base composition and showed the existence of weak and tight binding sites for Mn2+. The former sites are related to the electrostatic binding of the divalent cation with two contiguous phosphate groups, and the latter appear to vary almost proportionally with the number of G·C base pairs in the DNAs. Our results agree, in general, with the emerging evidence for a specific interaction of Mn2+ with the G·C residues of DNA. Competition experiments with Mg2+ suggested that this binding of Mn2+ in DNA also involves the phosphate groups. More definitely, our data conform with the hypothesis made by Clement et al. of Mn2+ chelation between the phosphate and the nitrogen N7 of a deoxyguanyl unit of DNA.
Molecular‐weight dependence of the low‐frequency dielectric properties of aqueous solutions of gel‐fractionated DNA
Authors: Molinari Robert J. , Cole Robert H. , Gibbs Julian H.
Published: December 2004

Combined three‐ and four‐terminal AC bridge measurements have been made at frequencies from 10 Hz to 100 KHz on samples of DNA with different molecular weight in aqueous solution under varying conditions of DNA concentrations and added salt. A method is described for the separation of large quantities of DNA fractionated according to size. A complicated pattern of dependence of the specific dielectric increment on concentration is found, and the difficulties of comparing the results from sample to sample are discussed. The dielectric properties of the fractionated samples of DNA in aqueous solution are reported for solutions sufficiently dilute that specific dielectric increment is independent of concentration. The specific dielectric increment of the solutions (with concentration measured in moles of DNA molecules/liter) is found to increase as the square of the molecular weight. The results are compared with results of polyelectrolyte theories which deal explicitly with counterion fluctuations and interactions. The frequency dependence of the dispersion is much broader than for simple Debye relaxation. It is satisfactorily fitted by the empirical Cole–Cole circular are function and the breadth of the dispersion is found to be, if anything, less for the fractionated samples than for native DNA in solution.
Noninteracting local‐structure model of folding and unfolding transition in globular proteins. II. Application to two‐dimensional lattice proteins
Authors: Abe Haruo , GŌ Nobuhiro
Published: December 2004

The noninteracting local‐structure model of the folding and unfolding transition in globular proteins, the formulation of which was given in the preceding paper, is applied to the analysis of the two‐dimensional lattice model of proteins. The lattice model of proteins is a theoretical tool designed to study the statistical‐mechanical aspect of the folding and unfolding transition. Its dynamics have been studied by a method of Monte Carlo simulation. The noninteracting local‐structure model reproduces the equilibrium properties of the lattice model obtained previously by computer simulation remarkably well, when the specificity of the long‐range interactions is strong. This observation indicates that the basic assumption of the noninteracting local‐structure model is equivalent to the assumption of strong specificity of intramolecular interactions. It is argued that by assuming this strong specificity, we can emphasize the correct main paths of folding and unfolding transition. The way local structures grow and/or merge along the most probable path of folding in the lattice model is discussed by the noninteracting local‐structure model.
Relationship between proton–proton nmr coupling constants and substituent electronegativities. III. Conformational analysis of proline rings in solution using a generalized Karplus equation
Authors: Haasnoot C. A. G. , De Leeuw F. A. A. M. , De Leeuw H. P. M. , Altona C.
Published: December 2004

The relationship between published vicinal proton–proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L‐proline, 4‐hydroxy‐L‐proline, 4‐fluoro‐L‐proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton–proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least‐squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x‐ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well‐defined N‐ and S‐type forms. Introduction of an amide group at the C‐terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S‐type form which is roughly 1.1 kcal/mol more stable than its N‐type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N‐type state, but N‐acetylation results in the appearance of a minor (S‐type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77–88%) corresponds to the N‐type conformer observed in the solid state; the minor S‐form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°–8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
Optical second‐harmonic scattering in rat‐tail tendon
Authors: Roth Shmuel , Freund Isaac
Published: December 2004

The angular dependence of optical second‐harmonic generation by native, wet, rat‐tail tendon is found to display a sharp, intense, forward peak superimposed on a broad background. The sharp peak is shown to imply long‐range polar order, while the broad background corresponds to that predicted for the random “up”/“down” array of collagen fibrils seen with the electron microscope. The degree of polar order is determined, and the dependence of the fibril diameter distribution on age and state of hydration is measured. The coherence length of tendon for harmonic generation and the absolute magnitude of the nonlinear susceptibility of the collagen fibril are also determined. The biological significance of these various findings is discussed.
Conformation of amylose–iodine–iodide complex in aqueous solution
Authors: Handa Takashi , Yajima Hirofumi
Published: December 2004

The conformational characteristics of the amylose–iodine–iodide complex in aqueous solution, particularly for a rapidly mixed system, were studied by resonance polarized scattering measurements using a He‐Ne laser at low concentrations of the complex and by viscosity measurements at high concentrations of the complex. For the scattering measurements, the following results were obtained: the depolarization ratios ρu and ρv showed a pronounced increase with the degree of saturation of the bound iodine (q) in amylose, depending on KI concentration. At q ≃ 0.7, the increase in these values appeared to be suppressed. However, the ρh value was approximately 1, irrespective of q. Additionally, the dissymmetry Z decreased appreciably with increasing q. The conformational change of the complex with q was characterized by the changes in the contour and persistence lengths of the chain and in the optical anisotropy of the scattering segments, which were obtained from numerical computations based on the polarized scattering equation for a wormlike‐chain model with a restriction by the entropy force of the chain. The viscosity of the complex solution decreased with increasing q; above q ≃ 0.7 it increased strikingly. The conformational change of the complex with q was characterized by the change in exponent α in the Houwink‐Mark‐Sakurada equation [η] = KMα. It was concluded that the iodine‐saturated complex has the characteristics of a rod, regardless of the complex concentration.
The equivalent conductivity of aqueous salt‐free solutions of DNA: Influence of univalent counterions
Authors: Kuznetsov I. A. , Apolonnik N. V.
Published: December 2004

The equivalent conductivity of salt‐free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10−4 to 4 × 10−3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where Cp is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10−4 Sm m2 equiv.−1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H+‐DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.
Excluded volume as a determinant of macromolecular structure and reactivity
Authors: Minton Allen P.
Published: December 2004

The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard‐particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi‐spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self‐ and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi‐spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme‐catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self‐association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self‐association of larger macromolecules.
Effects of some organic cosolvents on the functional properties of hemoglobin: Kinetics of O2 displacement by CO
Authors: Cordone Lorenzo , Cupane Antonio
Published: December 2004

We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso‐propanol, n‐propanol, formamide, acetamide, N‐methyl‐formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
Interaction of calcium ions with α‐elastin: An equilibrium dialysis, circular dichroism, and microcalorimetric study
Authors: Terbojevich M. , Palumbo M. , Cosani A. , Peggion E. , Gotte L. , Garbisa S.
Published: December 2004

The interaction of calcium ions with α‐elastin has been investigated by equilibrium dialysis, CD, and microcalorimetric techniques. Consistent with literature data, it was found that the interaction in water is very poor. In trifluoroethanol (TFE), equilibrium dialysis experiments showed that calcium ions bind to ∼‐elastin with an association constant of ∼250 L × mol−1. Such a figure is not consistent with highly specific, highly selective binding. It was also found that the CD response is not directly proportional to the amount of bound calcium but depends on the protein concentration. From microcalorimetric experiments it was found that the heat effect relative to the binding process is of the order of 1.9 kcal/g ion. From this figure and from the binding constant, a positive ΔS value of about 17 e.u. was evaluated, leading to the conclusion that the binding process is entropy driven. From microcalorimetric measurements a ΔH of 1.5 kcal/residue was found for the calcium‐induced conformational transition of the protein.
Quasielastic light‐scattering study of polyadenylic acid solutions. II
Authors: Mathiez P. , Mouttet C. , Weisbuch G.
Published: December 2004

Quasielastic light scattering is used to study saline solutions of polyadenylic acid with varying polymer concentrations and molecular masses. These experiments clearly show the existence of two relaxation times. For dilute solutions, when the chains are mutually independent, the fast mode is due to the free diffusion of the polymer chains. For concentrations above the overlap concentration C*, the fast mode is due to the propagation of collective excitations of the pseudolattice of polymer chains. The slow modes are observed when the polymer concentration is in the vicinity of the overlap concentration C*. A series of experiments shows that both their relaxation time and amplitude depend only on the polymer concentration and not on the polymer molecular mass. This result rules out any previous explanation based on individual chain motion. Furthermore, since the amplitudes depend on the time elapsed from the preparation of the solution, the slow modes are due to the diffusion of concentration inhomogeneities in the pseudolattice.
Determination of molecular weight by neutron scattering
Authors: Jacrot Bernard , Zaccai Giuseppe
Published: December 2004

Theoretical and practical advantages of neutron scattering for the determination of molecular weights of particles in solution are discussed. The method presented does not use known particles for calibration and is applicable to a wide molecular weight range (104–109); it is not sensitive to assumptions about the partial specific volume of the particles, and the experiments are performed quite easily in standard spectrophotometer cells using 100–500 μg of material. The method is nondestructive and the sample can be recovered totally. The use of D2O in solvents has particular advantages especially for multicomponent particles, for which the in situ molecular weight of each component can be determined separately.
Condensed states of nucleic acids. III. Ψ(+) and Ψ(−) Conformational transitions of DNA induced by ethanol and salt
Authors: Huey Ruth , Mohr Scott C.
Published: December 2004

The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro‐molecule with unusually large positive ellipticity in the 250–300‐nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples—via a series of intermediate forms with CD spectra resembling those of A‐DNA, then B‐DNA—into Ψ(−) states having anomalously large negative ellipticity similar to the well‐known Ψ(−) forms produced by above‐critical concentrations of poly‐(ethylene oxide) and salt. These ethanol/salt‐induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B‐form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(−) interconversion has been reported. A “skein‐of‐yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.