bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA bis‐intercalation: Application of theory to the binding of echinomycin to DNA
Authors: Shafer Richard H. , Waring Michael J.
Published: December 2004

The statistical mechanical model for the binding of bifunctional intercalating ligands to duplex DNA described in the preceding paper is applied to the example of echinomycin–DNA interactions. This is the only system for which binding curves have been obtained under conditions leading to binding by both bis‐intercalation and mono‐intercalation simultaneously. Binding parameters and Scatchard plots are calculated for a variety of conditions. A detailed comparison of these calculations with the results from the previous analysis of the same binding data in terms of the McGhee‐Von Hippel theory, assuming only one mode of binding, is presented. The results of our calculations are consistent with the model of bis‐intercalation requiring the two bound chromophores of a bifunctional ligand to be separated by two base pairs. It is not necessary to assume violation of the nearest‐neighbor exclusion principle, as occurred in the original analysis.
Conformational flexibility of peptides containing α,β‐unsaturated amino acid residues. I. Conformational analysis of N‐acetyl‐N′‐methylamides of dehydroalanine and N‐methyldehydroalanine
Authors: Ajò David , Granozzi Gaetano , Tondello Eugenio , Del Prà Antonio
Published: December 2004

Conformational energy calculations on the N‐acetyl‐N′‐methylamides of dehydroalanine and N‐methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x‐ray and nmr investigations on peptides containing α,β‐unsaturated residues are discussed on the basis of these theoretical results.
Spectroscopic and equilibrium dialysis studies of poly(α‐L‐glutamic acid)–Cu(II) complexes in the pH range 4–7
Authors: Masujima Tsutomu , Yamaoka Kiwamu
Published: December 2004

The formation of complex between the Cu2+ ion and poly(α‐L‐glutamic acid) [poly(Glu)] in 150 mM NaCl solutions was studied by uv–visible absorption and equilibrium dialysis methods at the mixing ratios of Glu residues to Cu2+, R, of 32, 16, and 8 and in the pH range 4–7. The results showed that more than 90% of Cu2+ ions bind to the poly(Glu) at pH > 4.9, but the bound Cu(II) begins to dissociate with a decrease in pH. The absorption spectra of bound Cu(II) varied with pH and R in a complicated manner. Three different component spectra were disclosed from the analysis of the pH dependence of the bound spectra. We concluded that poly(Glu)–Cu(II) complexes fall into three classes in the pH range 4–7, with the proportions of these complexes varying with both pH and R. The three complexes predominate either in the helix or extended‐coil region, in the helix–coil transition region, or in the helix‐aggregate region. The stability constant and binding mode of each Cu(II)–Glu complex were estimated from the dialysis data. With these results, the possible structure of each complex is discussed.
NMR relaxation processes of 31P in macromolecules
Authors: Shindo Heisaburo
Published: December 2004

31P‐Nmr relaxation parameters (spin‐lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well‐defined (145 ± 3 base‐pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of 31P chemical shift anisotropy as well as by 1H‐31P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least‐square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ0 = 6.5 × 10−7 sec for the end‐to‐end motion, (2) the ratio of diffusion constants D∥/D⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log − χ2 distribution function of correlation times [Scheafer, J. (1973) Macromolecules 6, 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10−9 sec and a distribution parameter p = 14.
Adsorption of polypeptides on the solid surface. II. Effect of secondary chain structure and helix–coil transition
Authors: Zhulina E. B. , Birshtein T. M. , Skvortsov A. M.
Published: December 2004

The theory of adsorption of semistiff chains on a planar surface developed by the authors previously has been used to consider the helix–coil transition in single‐stranded macromolecule interacting with an adsorbent plane. The cases of nonselective interaction when the adsorption energy is independent of the unit conformation (a) and selective interaction with only helical (b) or coiled (c) sequences active in adsorption were investigated. In case (b) the existence of secondary structure favors chain bonding to the surface. This leads to the increase in the stability of the helical state and complete polypeptide chain spiralization. The profile of the conformational helix–coil transition acquires an asymmetrical shape inherent to the second‐order phase transition.

In case (c) the bonding of a partially helical chain to the surface is similar to the adsorption of Gaussian coils and is accompanied by the destruction of secondary structure, this destruction being appreciable even if the helical state in space was favorable.
Dielectric relaxation of DNA solutions. IV. Effects of salts and dyes
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku
Published: December 2004

The effects of salts (NaCl, LiCl, Me4NCl, AgNO3, MgCl2, CuCl2 and MnCl2) and dyes (acridine orange and methylene blue) on the low‐frequency dielectric relaxation (0.1 Hz–30 kHz) of dilute aqueous solutions of DNA were investigated with varying salt or dye concentrations. Both the dielectric relaxation time τD and the rotational relaxation time τ estimated from the reduced viscosity decrease in quite parallel ways with increasing M/P (M/P being the normality ratio of cation to phosphate residue), reflecting the contraction of DNA molecule due to electrostatic shielding and cation binding. The agreement between τD and τ through the whole range of M/P supports our previous conclusion that the low‐frequency relaxation of DNA arises from rotation of the molecule. The dielectric increment Δε also decreases with increasing M/P on account of both the contraction of DNA and the decrease in effective degree of dissociation of DNA. Δε as a function of M/P is interpreted in terms of a quasi‐permanent dipole due to counterion fluctuation. These effects of cations are the strongest for divalent cations and rather weak for Na+, Li+, and Me4N+. Effects of dye on τD and Δε are also well explained by the rotation of DNA molecule with a quasi‐permanent dipole due to counterion fluctuation on the basis of intercalation of dye at D/P < 0.2 (D/P being the molarity ratio of dye to phosphate residue) and external binding at 0.2 < D/P < 1.0.
Characterization of multiple bends in proteins
Authors: Isogai Y. , Némethy G. , Rackovsky S. , Leach S. J. , Scheraga H. A.
Published: December 2004

The concept of bends or chain reversals [nonhelical dipeptide sequences in which the distance R3 (i,i+3) between the Cα atoms of residues i and i+3 is ≦ 7.0 Å] has been extended to define double bends as tripeptide sequences, not in an α‐helix, in which two successive distances R3(i,i+3) and R3 (i+1, i+4) are both ≦7.0 Å, with analogous definitions for higher‐order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher‐order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well‐defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution of R3 distances does not differ in single and multiple bends. However, R4 (the distance between the Cα atoms of residues i and i+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value of R4 in many multiple bends is near those for α‐helices. In some other multiple bends, R4 is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cα atoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right‐handed (like an α‐helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single‐bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α‐helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual‐bond dihedral angles differ, have conformations that are very different from an α‐helix. They act as chain reversals occuring over three residues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain.
Heavy‐atom effects associated with methylmercury (II) binding to rabbit glyceraldehyde‐3‐phosphate dehydrogenase
Authors: Hershberger Martin V. , Maki August H.
Published: December 2004

The complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde‐3‐phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)–GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy‐atom effect. Based on the x‐ray diffraction structure of the lobster enzyme, it is proposed that the heavy‐atom effect results from the interaction of tryptophan‐310 with CH3Hg(II) bound to cysteine‐281 in the rabbit muscle enzyme.
Interaction of spermine with different forms of DNA. A conformational study
Authors: Zhurkin Victor B. , Lysov Yury P. , Ivanov Valery I.
Published: December 2004

The energy of interaction of a spermine molecule with the A‐ and B‐forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom–atom potentials method was used. Optimal structures for the A‐DNA–spermine and B‐DNA–spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A‐DNA is energetically more favorable than that with the B‐DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A‐DNA (which is about 1 Å less than that in B‐DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A‐DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B‐DNA. These conclusions are further confirmed by the calculations for DNA–propane diamine complexes.
The translational friction of toroids
Authors: Allison Stuart A. , Easterly Russell A. , Teller David C.
Published: December 2004

An approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell‐model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high‐viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5–3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2–3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent–electrolyte systems and polyamines.
Conformational analysis of the milk oligosaccharides
Authors: Biswas Margaret , Rao V. S. R.
Published: December 2004

Possible conformations of lacto‐N‐tetraose, lacto‐N‐neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy‐minimization procedure using empirical potential functions. Lacto‐N‐tetraose favors a “curved” conformation, while lacto‐N‐neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto‐N‐neotetraose compared with lacto‐N‐tetraose in its ability to inhibit the cross‐reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto‐N‐tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto‐N‐neotetraose (active) differs. The favored conformations for the disaccharides galactose‐β(1‐4)‐N‐acetylglucosamine, galactose‐β(1‐3)‐N‐acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto‐N‐fucopentaose I over that of lacto‐N‐tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1‐4)‐linked galactose residue alone.
Toroidal elastic supercoiling of DNA
Authors: Calladine C. R.
Published: December 2004

Covalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double‐helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear‐elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
Fluorine nmr studies of poly(N‐acryloyl‐β‐alanine)–α‐chymotrypsin conjugates
Authors: Gerig J. T. , Loehr D. T.
Published: December 2004

Fluorine nmr experiments carried out at 51.0 and 94.1 MHz have been used to explore the interaction of the probe molecule p‐fluorocinnamate with conjugates formed from α‐chymotrypsin and poly(N‐acryloyl‐β‐alanine). The data obtained include enzyme‐induced chemical‐shift effects, spin‐lattice (R1) and transverse (R2) relaxation rates, and the rate constant for dissociation of the fluorocinnamate–enzyme complexes. Analysis of the results indicates that while overall molecular tumbling of the enzyme molecule is not greatly changed by attachment of polymers of various sizes, conjugated polymer can appreciably affect the structure of the p‐fluorocinnamate binding site. The important variable involved in such structural changes appears to be the amount of polymer present per mole of protein.
Concentration distribution and spatial moments of moving macromolecules undergoing isomerization
Authors: Killalea M. K. , McCoy B. J.
Published: December 2004

Expressions for zeroth, first, and second spatial moments are obtained for diffusing macromolecules A and B that move due to an external field and undergo reversible isomerization, switching back and forth according to first‐order kinetics. In addition, expressions for third and fourth moments are derived for the special case of equal diffusion coefficients, equal rate constants, and equal but opposite velocities. The initial conditions are arbitrary amounts of A or B concentrated in an infinitesimally narrow region. The moments are computed from derivatives of the Fourier‐transformed concentration profiles of A and B. The moments are used in an expansion in term of Hermite polynomials, the Gram‐Charlier expansion, to construct the concentration profiles of A or B or A and B together. The examples presented show that a few terms of the expansion, for which explicit expressions are given, can give tolerable accuracy if the velocity is not too large and the rate constants and diffusion coefficient are not too small. The expansion can be used to determine when the profiles are unimodal.
Circular dichroism of N‐phenylnaphthylamine derivatives complexed with the β‐form of poly(L‐lysine)
Authors: Sato Yukio , Woody Robert W.
Published: December 2004

Complex formation of 1‐anilinonaphthalene‐8‐sulfonate (ANS) and 2‐p‐toluidinonaphthalene‐6‐sulfonate (TNS) with the β‐form of poly(L‐lysine) [(β‐Lys)n] has been studied by circular dichroism (CD) and absorption spectra measurements. Not only hydrophobic interactions but also hydrogen‐bonding and electrostatic interactions contribute to complex formation. The relative importance of these stabilizing factors depends on the relative position of the arylamino group and the sulfonate. For example, ionic interactions play a significant role in the binding of 1,8‐ANS and 1,8‐TNS, but not in the case of 2,6‐TNS. The induced CD of the complexes of (β‐Lys)n with 1,8‐ANS and 1,8‐TNS is consistent with theoretical calculations for nonplanar conformations of these dyes, twisted in a left‐handed sense. As expected for steric reasons, the dominant isomer is one in which the arylamino group is oriented away from the 8‐sulfonate (α1). The induced CD of complexes with 2,6‐TNS can be accounted for by an equimolar mixture of left‐handed isomers in which the arylamino group is oriented toward the 1‐position (β2) and toward the 3‐position (β1). Our results demonstrate that (β‐Lys)n is capable of chiral discrimination and suggest its general utility for CD studies of racemic anionic dyes.
New synthesis of somatostatin according to the S‐tert‐butylthiocysteine procedure
Authors: Moroder L. , Gemeiner M. , Goehring W. , Jaeger E. , Thamm P. , Wünsch E.
Published: December 2004

To exemplify the usefulness of the S‐tert‐butylthio group for a reversible blocking of the cysteine thiol function in peptide synthesis, fully protected dihydrosomatostatin was prepared by the fragment‐condensation procedure. The experimental results confirm the excellent stability of the asymmetric disulfide under the normal conditions of peptide synthesis and prove that the selective, acid‐catalyzed nucleophil removal—as well as by mercaptans—of the 2‐nitrophenylsulfenyl group proceeds smoothly in the presence of this thiol protection. Thus, the strategy of overall acid‐labile side‐chain protection in combination with the Nα‐2‐nitrophenylsulfenyl group for the chain‐elongation steps can be successfully applied to the synthesis of cysteine‐containing peptides using their S‐tert‐butylthio derivatives. Removal of the acid‐labile groups, followed by reductive cleavage of the asymmetric disulfides and successive air oxidation, allowed a clean conversion of protected dihydrosomatostatin into somatostatin at a high degree of purity and in good yields.
Laser light‐scattering analysis of the dimerization of transfer ribonucleic acids with complementary anticodons
Authors: Wang Chun‐Chen , Ford Norman C. , Fournier Maurille J.
Published: December 2004

Photon‐correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M−1 in the absence of magnesium to 1.5 × 106M−1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
Interaction of the antimalarial drug fluoroquine with DNA, tRNA, and poly(A): 19F‐NMR chemical‐shift and relaxation, optical absorption, and fluorescence studies
Authors: Bolton Philip H. , Mirau Peter A. , Shafer Richard H. , James Thomas L.
Published: December 2004

The interaction of the fluorinated antimalarial drug fluoroquine [7‐fluoro‐4‐(diethyl‐amino‐1‐methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F‐nmr chemical‐shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well‐known analog chloroquine. At low drug‐to‐base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F‐nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F‐nmr relaxation experiments were carried out to measure the spin‐lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off‐resonance intensity ratio (R), off‐resonance rotating‐frame spin‐lattice relaxation time (T), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton‐fluorine dipolar and chemical‐shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine–DNA complex can be well described by a motional model incorporating long‐range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
A theory of aggregation in the thermal denaturation region of multistrand biopolymers
Authors: Shibata John H. , Schurr J. Michael
Published: December 2004

A theory explicitly allowing the possibility of aggregation of multistrand biopolymers is proposed. It is found that the same secondary bonds responsible for stabilizing the native structure at low temperature will promote aggregation in the thermal denaturation region for sufficiently long chains. A requirement for both open and zippered regions dictates that the aggregation region does not extend far below Tm. However, its width, or extension on the high‐temperature side of Tm, is a strongly increasing function of chain length and also of the cooperativity parameter. The present theoretical results obtained for DNA and collagen with almost no adjustable parameters are in good qualitative agreement with a number of previously poorly understood experimental observations. The significance of such a spontaneous aggregation phenomenon for genetic recombination is noted.
Calculated microwave absorption of double‐helical B‐conformation poly(dG)·poly(dC)
Authors: Kohli M. , Mei W. N. , Prohofsky E. W. , Van Zandt L. L.
Published: December 2004

We have estimated the absorption of microwave radiation by the four acoustic modes of poly(dG)·poly(dC) in B conformation. The eigenvectors used in this calculation are those obtained from a refined normal coordinate analysis by fitting the velocity of the longitudinal acoustic mode to that observed by Brillouin scattering. The acoustic modes couple to the radiation field when translational invariance is broken such as for finite segments of helix and as may be the case in vivo. Calculations for various helix lengths show that the estimated absorption is greater than that of water by at least two to three orders of magnitude in some cases.
Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles
Authors: Gotoh Osamu , Tagashira Yusaku
Published: December 2004

Melting profiles were calculated for restriction fragments of ϕX174 and fd phage DNAs and compared with experimental profiles. The algorithm of Fixman and Freire was slightly modified so that a stability parameter was assigned not to a base pair but to each nearest‐neighbor doublet. Stabilities of the 10 kinds of nearest‐neighbor doublets were estimated by fitting the calculated profiles to the observed ones. Agreement of the calculated and observed profiles was much improved by this modification. The most interesting finding was that purine (3′‐5′) pyrimidine stackings are much more stable than their respective reverses. The order of nearest‐neighbor stabilities is in excellent agreement with that of negative stacking energies calculated by Rein and coworkers by a quantum‐chemical method.
Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition
Authors: Brian A. A. , Frisch H. L. , Lerman L. S.
Published: December 2004

Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard‐core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
Early stages of fibrinogen to fibrin conversion studied by static and dynamic light scattering
Authors: Wiltzius P. , Känzig W. , Hofmann V. , Straub P. W.
Published: December 2004

The early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end‐to‐end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
Influence of the telopeptides on type I collagen fibrillogenesis
Authors: Brennan Maureen , Davison Peter F.
Published: December 2004

Preparations have been made of acid‐soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
Influence of water structure and of hydrophobic interactions on the strength of side‐chain hydrogen bonds in proteins
Authors: Némethy George , Steinberg Izchak Z. , Scheraga Harold A.
Published: December 2004

The thermodynamic properties derived earlier for the formation of side‐chain hydrogen bonds were re‐evaluated, taking into account medium effects and interactions of the side chains with nearby nonpolar groups. In determining the enthalpy of formation of the hydrogen bond, competitive hydrogen bonding with water has to be considered, except for “buried” groups, i.e., groups surrounded entirely by nonpolar groups. For such buried groups, the earlier estimate of ΔH = −6 kcal./mole is still valid, but for groups exposed to water, a lower value has to be used, estimated to be −1.5 kcal./mole. The internal bond rotations of side chains involved in hydrogen bonding are not restricted completely; therefore, ΔS is only −2 to −5 e.u. per side chain, instead of the much higher values estimated earlier. As a result, the new estimated value of ΔF is 0 to −0.5 kcal./mole, not much different from the earlier estimate. The ease of hydrogen bond formation may be changed by cooperative or competitive hydrophobic bonding of the nonpolar portions of the polar side chains with the backbone or nearby nonpolar side chains. Various cases of such interactions are discussed, including the burying of polar groups and the formation of hydrogen bonds between buried groups. It is shown that, in aqueous environment, the polar groups form more than one hydrogen bond with water, an effect to be taken into account when considering buried groups. Medium effects due to the presence of nonpolar groups and the effects of changes in the water structure on the ease of formation of the α‐helix are mentioned. Estimates for the thermodynamic parameters of the various hydrogen‐bonding and hydrophobic interactions are given. It is shown that hydrophobic interactions will, in general, enhance the strength of hydrogen bonds. The net free energy of formation of a simple structure involving both interactions may range from about −0.5 to −2.4 kcal./mole. It may reach much more highly negative values for large structures. The corresponding ranges of the net enthalpy and entropy of formation are −1.5 to −0.5 kcal./mole and −3 to +7 e.u., respectively.
Absorption spectra of nucleotides, polynucleotides, and nucleic acids in the far ultraviolet
Authors: Voet D. , Gratzer W. B. , Cox R. A. , Doty Paul
Published: December 2004

Ultaviolet absorption spectra down to 185 mμ are presented for a number of nucleic acids and synthetic polynucleotides in the helical and random forms, and of their constituent mononucleotides, as well as the corresponding nucleosides and free bases. A short wavelength absorption band is in all cases observed with a maximum varying between about 187 and 201 mμ. These bands are more intense than those near 260 mμ. The helical polymers show a hypochromic effect in this region of a somewhat similar magnitude to that in the 260 mμ region. Other spectral phenomena accompanying denaturation and degradation are described.
Infrared spectra and molecular conformations of D,L‐copoly‐γ‐benzylglutamates
Authors: Tsuboi Masamichi , Mitsui Yukio , Wada Akiyoshi , Miyazawa Tatsuo , Nagashima Nobuya
Published: December 2004

Infrared absorption and x‐ray diffraction measurements have been made of D,L‐copoly‐γ‐benzylglutamate fibers (cast from dioxane solutions) with various D/L ratios and with various degrees of polymerization. It was found that each chain of these copolymers consists of a random coil portion and an α‐helix portion and that the conformation of the latter is similar to the α‐helix of pure poly‐γ‐benzyl‐L‐glutamate. It was also found that the fraction of the α‐helix portion increases with the degree of polymerization of the copolymer. A simplified polymerization mechanism has been proposed for mixtures of D‐ and L‐amino acid N‐carboxyanhydrides. A model of the molecular conformation of the D,L‐copolypeptide chains derived from this proposed polymerization mechanism is in good agreement with infrared, x‐ray, and other measurements. Based on the results of these observations, we discuss the number of L‐ or D‐residues linked in succession that is required for initiating the formation of an α‐helix during the course of polymerization.
Sedimentation and diffusion of polyelectrolytes. Part I. Theoretical description
Authors: Alexandrowicz Z. , Daniel Ezra
Published: December 2004

The effect of charges on sedimentation and diffusion of macroions is treated along the lines adopted by Svedberg‐Pedersen for the description of sedimentation, with the difference that the virtual electrophoretic motion of the macroions which gives rise to the charge effect is not equated to the real electrophoretic mobility. Furthermore the activity correction is introduced through the recently established representation, according to which a constant fraction of the counter‐ions may be considered to be permanently immobilized. Lastly, for the sake of simplicity, it is assumed that the frictional coefficient of the macroions does not depend on the ionic strength. On this basis a relatively simple description in terms of readily accessible parameters is obtained. The charge effects in sedimentation and diffusion are closely related, one to another, and to other polyelectrolyte properties. The physical significance of the results is discussed. The description is compared to experimental data in the literature and also to the second experimental part of this work: it is found that the main features of the charge effect are satisfactorily described under widely differing conditions, although some deviations indicate the limitations of the approximate treatment.
Sedimentation and diffusion of polyelectrolytes. Part II. Experimental studies with poly‐L‐lysine hydrohalides
Authors: Daniel Ezra , Alexandrowicz Z.
Published: December 2004

The sedimentation, diffusion, and osmotic behavior of poly‐L‐lysine hydrochloride is examined over a wide range of ionic strengths and in solutions which range in relative composition from a swamping excess of added salt (suppression of charge effect) to salt‐free solutions (maximum effect). The charge effect is found to essentially obey the theoretical treatment proposed in Part I of this work. The frictional coefficient of the macroion in salt‐free solutions is comparable to that of the fully stretched chain. In excess of salt the friction is appreciably smaller, its magnitude not varying greatly with ionic strength. The molecular weight is determined osmotically and also from diffusion‐sedimentation, with the charge effect suppressed by addition of salt or eliminated through the use of non‐ionized forms of the polymer; a reasonable agreement is obtained between the methods. The influence of small ions on sedimentation is also examined. The secondary salt effect is found to be much smaller than that predicted theoretically; on the other hand, the substitution of different counterions in the absence of secondary salt effect gives rise to changes of the expected magnitude.
Synthesis of poly‐L‐lysine and poly‐L‐lysyl albumin via ϵ,N‐trifluoroacetyl‐α,N‐carboxy‐L‐lysine anhydride
Authors: Sela Michael , Arnon Ruth , Jacobson Israel
Published: December 2004

Free poly‐L‐lysine base has been synthesized from ϵ,N‐trifluoroacetyl‐α,N‐carboxy‐L‐lysine anhydride via poly‐ϵ,N‐trifluoroacetyl‐L‐lysine (IV). No racemization occurred during the removal of trifluoroacetyl groups from IV with 1M piperidine. Measurements of optical rotatory dispersion suggest that IV exists in methanol in a helical form. The synthesis of poly‐L‐lysyl rabbit serum albumin is also described.
Properties of poly‐β‐hydroxybutyrate. I. General considerations concerning the naturally occurring polymer
Authors: Alper R. , Lundgren D. G. , Marchessault R. H. , Cote W. A.
Published: December 2004

Poly‐β‐hydroxybutyric acid has been isolated from two bacterial sources by two different procedures. Molecular weight and intrinsic viscosity for the two samples were vastly different. This was blamed on degradation occurring during polymer isolation. An optical rotatory dispersion curve for the high molecular weight sample showed a sharp increase in specific rotation at wavelengths less than 450mμ. From this fact and the reported optical activity of the monomer it is concluded that the polymer is stereo‐regular. X‐ray examination of the “native” and “regenerated” polymer yielded the same crystalline pattern. Electron diffraction and x‐ray data on single crystals of the polymer indicate a fiber repeat of 5.9 A. The value can only be reconciled with some kind of helical conformation in the solid state.
Reduced sedimentation equilibrium time by two‐step initial loading
Authors: Todd G. Peter , Haschemeyer Rudy H.
Published: December 2004

Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two‐step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
Electric dichroism studies on ferriheme– and ferroheme–poly(L‐lysine) complexes at pH 9–12
Authors: Yamagishi Akihiko , Watanabe Fumiyuki
Published: December 2004

Transient electric dichroism has been measured for the ferriheme–poly(L‐lysine)[(Lys)n], ferroheme–(Lys)n, and ferroheme–(Lys)n–carbon monoxide (CO) solutions at pH 9–12. The Soret absorption maximum in electronic spectrum (λ), the reduced linear dichroism (ρ∞) at complete orientation and the calculated angle (ϕ) between the porphyrin plane of a bound heme and the oriented polymer axis are determined for the following complexes: a ferriheme–(Lys)n complex at pH 9.5–10.5 (λ = 420 nm, ρ∞ = 0.50, and ϕ = 19°), a ferroheme–(Lys)n complex at pH 9.5–10.2 (λ = 432 nm, ρ∞ = 0.77, and ϕ = 0°), and a ferroheme–(Lys)n–CO complex at pH 9.25 (λ = 430 nm, ρ∞ = 0.38, and ϕ = 24°). Based on the above data, the validity of the structures of heme–(Lys)n complexes proposed by other investigators is discussed.
The δ‐function counterion condensate around a line charge derived from the Fuoss, Katchalsky, and Lifson polyelectrolyte theory
Authors: Lampert Murray A.
Published: December 2004

It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson‐Boltzmann theory, is an encapsulating δ‐function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson‐Boltzmann equation.
Interactions of DNA with divalent metal ions. III. Extent of metal binding: Experiment and theory
Authors: Granot Joseph , Kearns David R.
Published: December 2004

DNA with Mn2+ as the only counterion has been prepared, and the extent of the Mn2+ binding was determined under a variety of conditions through measurements of the proton relaxation enhancement of water. The total extent of Mn2+ binding per DNA phosphate is found to be 0.43 ± 0.04, independent of the metal ion concentration in the experimental range of 2.8 × 10−5 to 2.1 × 10−3M. The predictions of Manning's condensation theory and those obtained from solution of the generalized Poisson‐Boltzmann equation regarding the extent of divalent ion binding to polyelectrolytes, in the presence and absence of monovalent counterions, are compared with one another and with the experimental results. Good agreement between the two theoretical approaches is found, with less than 14% variance in the predicted extent of binding over a large range of mono‐ and divalent ion concentrations. While the predictions of both theoretical approaches generally agree with the experimental results, some discrepancies are noted and their possible origins discussed.
Conformational study of poly(α‐L‐aspartic acid)
Authors: Saudek V. , Štokrová Š. , Schmidt P.
Published: December 2004

The conformation of poly(α‐L‐aspartic acid) was investigated on a sample in which β‐bonds were not detected. CD and ir spectroscopy showed that poly(α‐L‐aspartic acid) passes through a conformational change induced by changes of the degree of ionization that is accompanied by precipitation; the precipitate is probably highly helical. The change was also detected by potentiometric titration.
Binding of ligands to a one‐dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides
Authors: Sturm Jean
Published: December 2004

A temperature‐jump relaxation study of the interaction of tilorone with different polynucleotides and DNA has been performed. A single relaxation time, attributed to the intercalation step, has been observed in the case of poly[d(A‐T)]·poly[d(A‐T)], poly[d(A‐C)]·poly[d(G‐T)], poly[d(G‐C)]·poly[d(G‐C)], and poly(dG)·poly(dC). No intercalation into poly(dA)·poly(dT) occurs, and the interaction with poly(dG)·poly(dC) is different from what is observed with the other intercalating homopolymers. Refinement of the binding model is suggested from the analysis of the kinetic data. The relaxation curves obtained with DNA are well simulated based on a binding mechanism where DNA is considered a heterogeneous lattice and each type of site behaves as if it were located in the corresponding homopolymer. Poly(dA)·poly(dT) shows a unique behavior: studies of the effects of concentration and temperature indicate that tilorone acts as a probe of a process involving the polynucleotide alone. This process appears to be related to the dynamic structure of the nucleic acid and is detectable only when the bound dye is not intercalated.
Equilibrium folding and unfolding pathways for a model protein
Authors: Miyazawa S. , Jernigan R. L.
Published: December 2004

The folding–unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only Cα and Cβ atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (ϕ,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding–unfolding transition for this idealized model is an “all‐or‐none” type; this is attributable to the specific long‐range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding–unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium‐range contacts at a β‐turn and at the α‐helix. (2) These grow to include the native pair of interacting β‐strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long‐range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.