bluuebunny/crossref_metadata_2025 huggingface dataset:
Infrared spectra of transfer ribonucleic acids. III. Fragments of formyl‐methionine tRNA from Escherichia Coli
Authors: Katsura Tatsuo , Morikawa Kosuke , Tsuboi Masamichi , Kyogoku Yoshimasa , Seno Takeshi , Nishimura Susumu
Published: May 2005

Four fragments (named K, L, M, and N) of Escherichia coli formylmethionine transfer RNA have been prepared by a partial digestion with ribonuclease T1 followed by a chromatographic separation with a DEAE–Sphadex (A‐25) column and then a DEAE–cellulose column. The fragment K is the anticodon fragment with 19 nucleotides (previously reported). L is a fragment with 57 nucleotides involving the 3′‐terminal (CCA). M is a fragment with 51 nucleotides which is equal to L except that M lacks 6 nucleotides at the 3′‐terminal. N is a fragment with 20 nucleotides which involved the 5′‐terminal and corresponds to the complementary half to L. The infrared absorption spectrum has been observed of each of these fragments and two equimolar mixtures L + N and M + N in D2O solutions at several temperatures. The results indicate that at 37°C, K has about 4 hydrogen‐bonded base‐pairs, L about 11, and M about 13. On the other hand, fragment N is found to have only three weak G‐C pairs. For both L + N and M + N, 15–17 strong base pairs are found. The observations give direct support to the clover‐leaf structure and at the same time provide information on the stability of each of the four arms in the structure.
Infrared investigation of poly‐L‐histidine structure dependent on protonation
Authors: Muehlinghaus J. , Zundel G.
Published: May 2005

Poly‐L‐histidine (PLH) films at different degrees of protonation were produced mid subjected to infrared spectroscopic investigation (range 4000‐650 cm−1). In addition, the N‐deuterated film spectra were plotted. The amide II and III bands show that the peptide group is present in the trans form. The amide I and II bands show that at 0% and 50% protonation the PLH occurs as an α‐helix and at 100% protonation as a random coil with some ranges in β structure. At 0% and 50% protonation, no hydration water is bound to the backbone. At 0% protonation all NH groups are linked to each other or to water molecules via hydrogen bonds. At 50% protonation NH+ċN bonds form between the imidazole rings. These protons are present in continuous energy level distribution. Such bonds with tunneling protons are extremely polarizable and between these bonds may act proton dispersion forces. The Cl− ions are bonded to the NH groups of the imidazole groups. The hydration water is bonded to the Cl−− ions and to the NH groups. At 100% protonation, hydration water is bonded also to the CO groups of the backbone. The NH groups of the backbone, like those of the rings, endeavor especially in the dry state to bond to the Cl− ions. This leads to a strong steric constraint of the random coil.
X‐Ray diffraction by amorphous polymers: Models for biological systems
Authors: Balyuzi H. H. M. , Burge R. E.
Published: May 2005

The x‐ray scattering method has been used to investigate the structure in two amorphous crosslinked polymers which are regarded as test systems to establish the power of the method as applied to amorphous biologically significant polymer associations. It is shown that structural information can be determined about the rigid regions within the polymer systems, i.e., those regions held in particular configuration by stereochemical effects. Models of such regions extending over distances with dimensions of ca 18 Å are proposed for an Araldite polymer and for crosslinked poly (methyl/butyl methacrylate). The results allow some general statements about the usefulness and limitations of the amorphous x‐ray method.
Optical Rotatory Dispersion of Polypeptides in the Near‐Infrared Region
Authors: Chirgadze Yu. N. , Venyaminov S. Yu. , Lobachev V. M.
Published: May 2005

For the first time ORD measurements in the near‐infrared region from 0.7 to 2.0 μ for well‐known polypeptides, namely, poly(γ‐benzyl L‐glutamate), poly(L‐glutamic acid), poly‐L‐lysine·HCl, poly‐S‐carbobenzoxymethyl‐L‐cysteine, and Bombyx mori silk fibroin, were carried out. It was found that the value of the optical activity infrared term, which is proportional to the sum of rotational strengths of vibrational transitions, depends on polypeptide conformation. The optical activity infrared term value is equal to zero for the random‐coil conformation, it is small but exceeds the measurement error for the α‐helical state, and finally, for the β conformation it is an order of magnitude higher than for the α‐helical state. The obtained results permit one to hope that on the basis of ORD measurement in the near‐infrared region it will be possible to suggest a method of determining the β‐form content in polypeptides and proteins
Sedimentation analysis of the ionic strength dependence of the tertiary structure of native DNA in solution
Authors: Triebel H. , Reinert K. E.
Published: May 2005

Sedimentation experiments have been performed on a polydisperse bacterial DNA sample over a wide range of ionic strength (8 × 10−4M to 2M Na+), at very low DNA concentrations (5–30 μg ml). True sedimentation constant distributions were obtained by careful analysis of experimental data and extrapolation to infinite dilution. In order to give a quantitative description of macromolecular shape, the changes of the exponent as in the general equation, s0 = ksM, have been determined by comparing sedimentation constant distributions obtained at different ionic strengths. as has been found to vary from 0.419 at 2M Na+ to 0.200 at 8 × 10−4M Na+. As well as the decrease of the mean sedimentation constant, this result indicates a pronounced expansion of DNA molecules with decreasing ionic strength. A discussion of the distinct mechanism responsible for the expansion behavior of DNA is given. Furthermore, the dependence of the Mandelkern‐Flory parameter β on ionic strength has been calculated by combining the s0 data with the corresponding [η] values of the sample.
Tautomerism in cytidine
Authors: Johnson W. C. , Vipond P. M. , Girod J. C.
Published: May 2005

The large change in the electronic absorption spectrum of cytidine on going from an aqueous to an aprotic medium is attributed to the existence of a hydrogen bonded solvent‐solute complex in solvents capable of donating a proton. The spectrum of cytidine in a variety of solvents and the spectra of a number of nontautomerising model compounds are presented. The tautomerisin of cytidine and its biological implications are discussed.
Time‐dependent model for hemoglobin and allosteric enzymes. I. General formulation
Authors: Bush Robert Ter , Thompson Colin J.
Published: May 2005

A previous equilibrium model is generalized to study time‐dependent behavior of hemoglobin and allosteric enzymes. An exact solution for two interacting subunits (e.g., diheme) is given, and a general method for solving the resulting set of differential equations is outlined. At half saturation (equilibrium) concentration, the model takes a particularly simple form which suggests an experiment to determine the number of subunits of an allosteric enzyme, or in particular to distinguish diheme from ordinary hemoglobin. The relation between the present model and other kinetic models is also discussed.
Microscopic model for the study of fluctuations and the kinetics of conformational changes of polypeptides. I. Diglycine
Authors: Simon Eliot M.
Published: May 2005

In this paper a microscopic model is developed which considers conformational changes in polypeptides. The model applied here to diglycine involves calculation of torques due to pairwise interatomic forces acting about the two single bonds (NC and CC′) of the peptide unit. Account is taken of Brownian motion and rotational frictional resistance in addition to a van der Waals 6–12 potential, a classical electrostatic potential and a torsional potential. The rates of the conformational transition from an initial α‐helical position are computed. The mechanism of Conformational change is a random walk within the minimum well followed by a jump out of the minimum into another portion of the energy surface. The latter process occurs when a fluctuation carries the dipeptide into a high energy region of the potential surface. Correlation times for the process are computed. Estimates are made for the relaxation times for the process. A first passage‐time treatment is developed and used to compute internal diffusion coefficients for the relaxation process.
Sedimentation studies of DNA in concentrated solutions of magnesium salts
Authors: Vijayendran B. R. , Vold R. D.
Published: May 2005

The sedimentation coefficient of calf thymus and of T7 DNA was determined at several concentrations up to saturation in solutions of each of the following salts: MgCl2, MgBr2, and MgSO4. Under certain conditions, a plot of the product of the relative viscosity and sedimentation coefficient against the density of the solution has been found to be linear and to extrapolate to zero at a density corresponding to that of the solvated molecule. This behavior was realized in MgSO4 solutions, the zero intercept occurring at a density of 1.41 g/cc, corresponding to a wafer activity of 0.89. The preferential solvation of DNA in MgSO4 solutions calculated for this value is 10.5 moles water/mole of nucleotide, in good agreement with published values of solvation of DNA at the same water activity in univalent salt solutions. Since linear plots were not obtained in MgCl2 and MgBr2 solutions, buoyant densities could not be determined in these cases. The nonlinear behavior observed in MgCl2 and MgBr2 solutions may be due to a change in shape of the DNA molecule at the lower water activities reached in these solutions. The possibility of increased DNA–solute interactions in MgBr2 and MgCl2 solutions is also considered as an explanation for the difference in behavior between MgSO4 and the two magnesium halides.
Distorted α‐helix for poly (γ‐benzyl L‐glutamate) in the nematic solid stale
Authors: Samulski E. T. , Tobolsky A. V.
Published: May 2005

A strong magnetic field has been utilized to orient the liquid crystalline phase of concentrated polypeptide solutions enabeling the preparation of nematic solid films. The uniaxially oriented nematic films are suitable for x‐ray studies of the polypeptide backbone chain conformation. A distorted α‐helix with 3.5 residues per turn is observed in nematic films of the L‐isomer of poly (benzyl glutamate) when the film is cast from chloroform. The normal α‐helix (3.6 residues per turn) is found in similarly prepared films cast from dichloromethane.
Size and shape determination of apotransferrin and transferrin monomers
Authors: Rosseneu‐motreff M. Y. , Soetewey F. , Lamote R. , Peeters H.
Published: May 2005

Dielectric dispersion and viscosity measurement, s were performed on apotransferrin and transferrin monomers in aqueous solutions so as to check the influence of iron binding on the overall conformation of the molecule. Iron saturation by two iron atoms per transferrin molecule modifies the parameters of the equivalent ellipsoid. The molecule becomes more spherical while its hydration value remains high.
Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates
Authors: Hermans Jan , Ferro Dino
Published: May 2005

The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.
Physicochemical studies of oligodextran. I. Molecular weight dependence of intrinsic viscosity, partial specific compressibility and hydrated water
Authors: Gekko Kunihiko , Noguchi Hajime
Published: May 2005

The number average molecular weight, Mn, of low molecular weight dextran was determined through endgroup analysis, and the intrinsic, viscosities of these materials in aqueous solution were determined at 25°C. The ultrasonic velocities in their aqueous solutions were also measured at 25 and 45°C. As concerns the molecular weight dependence of the intrinsic viscosity, partial specific compressibility of solute and the hound water around the solute, the following results were obtained. (1) log [η]‐log Mn and [η]/Mn0.5 – Mn0.5 plots were in accord with the Mark‐Houwink and Stockmayer‐Fix‐man equations respectively for Mn > 2, 000, but these plots deviated from the equations for Mn < 2, 000. (2)The partial specific compressibility, β1°, of dextran is expressed by following equation for Mn < 2,000: β1° = 10−12 × (13.6 log Mn ‐ 51.7) (cm2/dyne). In contrast, it, becomes the constant value, ‐‐ 7.3 × 10−12 cm2/dyne, for Mn > 2,000. (3) The amount of bound water of dextran calculated from the sound velocity measurement lakes constant value of 0.17 ml g for Mn > 2, 000, but the amount of hydration increase with decreasing molecular weight for Mn < 2,000. From these results, a dextran molecule in aqueous solution is expected to change its conformation from random coiling to uncoiling stretched form at the molecular weight of around 2, 000 or about 12 glucose units.
Elude dielectrique de la transconformation thermique du Na DNA en solution
Authors: Grassi Hexri , Vasilescu Dane
Published: May 2005

A dielectric method is presented to measure the ejection of counterion during the thermal fusion of Na DNA solutions. The dielectric conductivity behavior at fixed frequency versus temperature is a measure of the molar concentration of counterfoils formed from the macromolecules. A linear dependence between Na+ cations released and DNA concentration was verified. We consider the variation of sodium activity coefficient Δ during thermal transconformation to be in good agreement with other experimental data.
Conformational energy calculations on alginic acid. II. Conformational statistics of the copolymers
Authors: Whittincjton S. G.
Published: May 2005

Conformational energy maps have been calculated for α‐D‐mannuronic acid (1–4) α‐L‐guluronic acid and for α‐L‐guluronic acid (1–4) β‐D‐mannuronic acid. These have been used, together with maps previously calculated for the homomonomeric dimers, to estimate the characteristic ratios and Kuhn lengths of the alternating copolymer and of a stochastic copolymer similar in composition to that extracted from L. digitata.The results show that the alternating copolymer is less extended than either homopolymer. Kuhn lengths calculated for the stochastic copolymer agree well with experimental results on high ionic strength solutions of alginate isolated from L digitata.
Conformational Changes in the Reassembly of MS2 Protein Subunits
Authors: Oriel P. J. , Lindsey Pamela , Schueneman Cheryl
Published: May 2005

Conformatioiial changes during the reassembly of bacteriophage MS2 coat proteiii from guanidiiie hydrochloride have been investigated by optical rotatory dispersion. Optical rotatory dispersion aid circular dichroism data of the reassembled particles are interpreted as those of β structure. Refolding of the subunit with increasing temperature demonstrated in 2 M guauidine hydrochloride. The stabilization of this structure by hydrophobic bonds and its role in reassembly is discussed.
Polyelectrolyte complexes of glycol chitosan with some polysaccharides. II. Electrical conductivity
Authors: Srinivasan R. , Kamalam R.
Published: May 2005

The dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high‐temperature region vary from 0.85 to 1.18 eV and in the low‐temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current–voltage relation is almost linear in the GlChi–DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi–DS and GlChi–CMC complexes. The nonlinear current–voltage relation is ascribed to a space‐charge‐limited conductivity.
15N‐nmr spectroscopy. 33. Assignments of isotactic and syndiotactic sequences in poly(D,L‐amino acids)
Authors: Kricheldorf Hans R. , Hull William E.
Published: May 2005

15N‐enriched (D,L‐Leu)n, (γ‐OMe‐D,L‐Glu)n, (D,L‐Val)n, and (D,L‐Phe)n were prepared, 40.55‐MHz 15N‐nmr spectra were measured in various solvents. The signal patterns depend strongly on the nature of the solvent, yet in most cases at least four signals are resolved, representing the four enantiomeric pairs of triads L‐L‐L (D‐D‐D), L‐D‐L (D‐L‐D), L‐L‐D (D‐D‐L), and D‐L‐L (L‐D‐D). Numerous copolypeptides of the general structure (A)n‐B*‐(A)m (the asterisk denotes 40–50% 15N enrichment) were synthesized and measured as models for syndiotactic sequences in the spectra of poly(D,L‐amino acids). In this way unambiguous assignments for both isotactic and syndiotactic trials were obtained. A spectroscopic rule was established: “isotactic sequences absorb downfield of syndiotactic ones.” Furthermore, the spectra of various types of stereocopolypeptides such as (L‐Leu/L‐Val)n and (L‐Leu/D‐Val)n were investigated, including the ternary systems (L‐Leu/L‐Ala/D‐Ala)n (L‐Leu/L‐Ala/Gly)n, (L‐Leu/D‐Ala/Gly)n, (L‐Val/L‐Ala/Gly)n, and (L‐Val/D‐Ala/Gly)n. All copolymerization of D‐ and L‐amino acid NCAs investigated in this work showed a low degree of stereoselectivity.
Spin‐label studies of the pH‐induced random coil to α‐helix conformational transition in poly(L‐lysine)
Authors: Skinner James F. , Calkins Hugh H. , Liles W. Conrad , Kaplan Lawrence J.
Published: May 2005

Poly(L‐lysine) of various molecular weights between 2700 and 475,000 was spin‐labeled. From the electron spin resonance spectra, the degree of freedom of the nitroxide was determined by calculation of the rotational correlation time as the poly(L‐lysine) underwent the pH‐induced random coil to α‐helix conformational transition. In general, the rotational correlation time of the nitroxide increased as the pH was increased, indicating a more restricted environment for the spin label when poly(L‐lysine) is deprotonated. For the high‐molecular‐weight poly(L‐lysine) this corresponds to the formation of the α‐helix and indicates that the side chain–side chain interaction and decreased segmental motion of the backbone (slightly) restricts the motion of the spin label. For the 2700‐molecular‐weight poly(L‐lysine), previously shown not to assume a helical conformation at high pH, the increase in the rotational correlation time of the spin label indicates that the side chain–side chain interaction takes place after deprotonation but without helix formation. This may indicate that helix formation per se is not needed to produce the observed effect even with the high‐molecular‐weight polymers. The rotational correlation time of the spin label at a particular pH did not depend on the molecular weight of the poly(L‐lysine) over the 200‐fold range of molecular weights. This indicates that the rotational correlation time reflects the rotational mobility of the spin label in a localized environment and not the rotational diffusion of the entire macromolecule.
Circular dichroism study of modified nucleosides
Authors: Gałat Andrzej , Jankowski Aleksander
Published: May 2005

CD study of four modified nucleosides, constituents of tRNA molecules, revealed that 2‐thio‐5‐methyluridine and 5‐methyluridine in aqueous solution, 0.1N HCl, and organic solvents essentially occur in an anti‐conformation. 5‐Methylcytidine also occurs in an anti‐conformation similar to cytidine in aqueous solution and organic solvents, while 2‐thiocytidine dihydrate appears to occur in an anti‐conformation. It is stressed that the CD data of thionucleosides might be applied to the successfully conformational analysis of tRNA molecules.
Calculated compression, bending, shearing, torsion, and base‐tilting force constants of B‐ and A‐form poly(dG)·poly(dC)
Authors: Putnam B. F. , Prohofsky E. W. , Zandt L. L. Van
Published: May 2005

Force constants associated with large‐scale motions of the DNA double‐helical homopolymer poly(dG)·poly(dC) are projected out of a long‐range atom–atom Coulomb force field. Force constants for both B‐ and A‐conformations have been calculated. Using the Coulomb interaction as previously incorporated into our DNA normal mode calculations, we obtain the forces determined by this long‐range interaction. These include compression, bending, shearing, torsion, and base tilting. We show, quantitatively, how the shearing and torsional transverse interactions fall off with intercell distance more rapidly than the compressional (longitudinal) interactions. Reasonable values for the elastic moduli of B‐ and A‐DNA are calculated. An important prediction of the present interaction theory is that although the single adjustable strength parameter in the Coulomb force field was chosen so as to reproduce an experimental value for the longitudinal sound velocity, the transverse torsional potential resulting from this fitted force field is in excellent agreement with results reported from supercoiling data and fluorescence measurements.
Cooperative binding of n‐mers with steric hindrance to finite and infinite one‐dimensional lattices
Authors: Tsuchiya Takashi , Szabo Attila
Published: May 2005

The cooperative binding of n‐mers to a finite ring, a finite open chain, and an infinite chain is treated in a unified way using the matrix method. For an infinite chain, the implicit closed‐form expression (“Scatchard formula”) for the fraction of bound sites obtained by McGhee and von Hippel, is simply rederived using a procedure involving implicit differentiation of the characteristic equation. A variety of models for n‐mer binding that incorporate steric hindrance for formulated, and corresponding Scatchard formulas are derived using our procedure.
Energy embedding of trypsin inhibitor
Authors: Crippen Gordon M.
Published: May 2005

Energy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake‐Crippen residue–residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake‐Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary structure.
Molecular‐mechanical studies of Z‐DNA: A comparison of the structural and energetic properties of Z‐ and B‐DNA
Authors: Kollman Peter , Weiner Paul , Quigley Gary , Wang Andrew
Published: May 2005

Molecular‐mechanical studies of the left‐handed Z‐DNA polymers have been carried out and the results compared with similar calculations on B‐DNA polymers. We have studied d(CGCGCG)2, d(GCGCGC)2 (and their 5‐methyl cytosine analogs), dG6·dC6, d(ATATAT)2, and d(TATATA)2 in both B‐ and Z‐forms. For the left‐handed Z helices, we considered the ZI and ZII model of Quigley and co‐workers [Wang, A. H., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979) Nature (London) 282, 680–686], the actual “Z spermidine” and “Z spermine” structures of Quigley and the model‐built structure of Chandresekharan et al. [Arnott, S., Chandresekharan, R., Bindsall, D. L., Leslie, A. G. W. & Ratliff, R. L. (1980) Nature 283, 743–745]. The major conclusions of this study are as follows. (1) The stabilization of Z‐DNA relative to B‐DNA occurs as one increases the “effective” dielectric constant or adds counterions, consistent with observations of Z‐DNA only under high salt conditions. (2) The ZII polymer is calculated to be more stable than the ZI polymer. It is not yet clear whether the greater stability of ZII than ZI is a real effect or an artifact caused by the lack of inclusion of specific solvation effects in these calculations. (3) The greater tendency of the 5‐methyl cytosine analog of poly(dG‐dC)·poly(dG‐dC) to undergo the B → Z transition is found in our calculations and is due to destabilizing base–base and base–phosphate interactions, which are greater in the B‐ than in the Z‐form of the 5‐methyl cytosine polymer. (4) There are no large sequence‐dependent effects on the relative stabilities, and the AT polymers are calculated to be as likely to form Z‐helices as the GC polymers. In addition, the relative stability of a nonalternating sequence in the conformation is only slightly less than that found for alternating sequences.
Crystal structure and solution conformation of 1‐N‐acetyl‐β‐D‐glucopyranosyl amine: A model for the glycopeptide linkage
Authors: Bush C. Allen , Blumberg Karl , Brown Joe N.
Published: May 2005

The crystal structure of the title compound, a model for the glycosyl linkage between the asparagine side chain and N‐acetyl glucosamine in glycoproteins, has been determined and compared to other model structures. The pyranose ring in the crystal is in the 4C1 chair conformation and the amide functions at C1 and at C2 are both oriented such that the amide protons are nearly trans to their respective sugar‐ring protons. Coupling constants determined from the fully assigned proton nmr spectrum in aqueous solution are consistent with the conformation in the crystal.
Flow dichroism of capsid DNA phages. II. Effect of DNA deletions and intercalating dyes
Authors: Hall Stephen B. , Schellman John A.
Published: May 2005

The flow linear dichroism of bacteriophage λ and its deletion mutants, λ b2 and λ b221, was determined. The hydrodynamic behavior of the three phages differed slightly, but the magnitude of the dichroism was substantially the same with 〈cos2θμp〉 = 0.364, 0.368, and 0.372, respectively. The dichroism of intercalating dyes combined with bacteriophage was used as a further probe of phage structure. The reduced dichroism from proflavin with T4 showed no change with time during the reaction, but the interpretation of the ligand dichroism is complicated by an alteration of the hydrodynamic behavior of the phage–dye complex relative to the phage alone. Ethidium with λ also produced a stable reduced dichroism, but the signal indicated an average orientation of intercalated dye that is different from the average base orientation. The reduced dichroism of ethidium changes with time as it penetrates λ b2, eventually approaching the dichroism of the nucleotide bases. The implication of these findings on the plausibility of various simple DNA packing models is discussed.
Pulsed field gradient nmr determination of the temperature dependence of the tracer diffusion coefficient of hemoglobin
Authors: Everhart Cherie H. , Johnson Charles S.
Published: May 2005

We have studied the temperature dependence of the tracer diffusion coefficient of carbonmonoxy hemoglobin A (HbA‐CO) by means of pulsed‐field gradient nmr (PFG‐nmr). Measurements were made over the temperature range from 15 to 35°C for samples having concentrations 7.4 and 16.7 g/dL. No significant deviations were found from the predictions of the Stokes‐Einstein relation. Thus, this work does not corroborate the recently proposed conformational change in hemoglobin at 22°C. The advantages of PFG‐nmr for the study of hemoglobin are discussed.
Effect of water on piezoelectric, dielectric, and elastic properties of bone
Authors: Maeda Hideatsu , Fukada Eiich
Published: May 2005

The complex piezoelectric constant (d = d′ − id″), elastic constant (c = c′ + ic″), and dielectric constant (ε = ε′ − iε″) were measured at a frequency of 10 Hz over the temperature range from −150 to 50°C and for a range of hydration up to 0.26 g/g for decalcified bone and up to 0.084 g/g for bone. For decalcified bone, ε′ and ε″ increased with increasing hydration with a deflection at the critical hydration hc = 0.08 g/g;d′ at −150°C increased below hc but decreased above hc with increasing hydration; c′ increased below −60°C but decreased above −60°C with increasing hydration; and the peak temperatures of ε″, d″, and c″ below −50°C agree with each other and decreased with increasing hydration with a deflection at hc. For bone, similar hydration and temperature dependences were observed for ε and c. However, the dependence of d on hydration and temperature was different from that of decalcified bone, reflecting a two‐phase structure consisting of collagen fibers and mineral hydroxyapatite. The critical hydration for bone was 0.04 g/g.
New polymer syntheses. IV. Polypeptides of lysine and ornithine with pending pyrimidine bases
Authors: Kricheldorf Hans R. , Fehrle Martin
Published: May 2005

Starting with β‐methoxy methacryloylisocyanate, β‐methoxy methacrylisothiocyanate, and β‐isocyanatopropionyl chloride, on the one hand, and Nα‐Z‐lysine or Nα‐Z‐ornithine, on the other hand, Nα‐Z‐amino acids with pyrimidine bases in the side chain were synthesized. These Z‐protected nucleoamino acids were converted to the corresponding N‐carboxyanhydrides (NCAs) via the silylester method. In the case of 2‐thiothymine derivatives, the reaction intermediate of the NCA synthesis caused benzylation of the thioxo‐ group, so that a new class of 2‐mercaptopyrimidine derivatives was isolated unexpectedly. The poly(nucleoamino acids) obtained by polymerization of the nucleoamino acid NCAs were characterized by elemental analyses, optical rotations 1H‐nmr and 13C‐nmr spectra. Vapor pressure osmometry revealed that the DPs were in the range of 20–30. Their spectra suggest a helical secondary structure. While all homopolypeptides are insoluble in water, copolypeptides containing L‐lysine Nε‐hydrobromide possess good solubility in water.
Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides
Authors: Lal Brij B. , Nafie Laurence A.
Published: May 2005

Vibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (NH stretch) and amide I (predominantly CO stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D2O. Our results for poly(γ‐benzyl‐L‐glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers 20, 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α‐helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β‐benzyl‐L‐asparate) and poly(im‐benzyl‐L‐histidine), that form left‐handed as opposed to right‐handed α‐helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the NH stretching mode has been identified as a weak shoulder on the low‐frequency side of the amide A band near 3200 cm−1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D2O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen‐bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.
Fibrin polymerization studied by static and dynamic light‐scattering as a function of fibrinopeptide A release
Authors: Wiltzius P. , Dietler G. , Känzig W. , Häberli A. , Straub P. W.
Published: May 2005

The polymerization of fibrin induced by the enzyme thrombin was investigated in the pregelation phase by combining measurements of the release of the fibrinopeptides A with static and dynamic light‐scattering at scattering angles ranging from 5°–150°. Without making any assumptions about the polymer distribution, one is led to the following conclusions: The aggregates are rodlike; the Flory‐Stockmayer model is to be preferred over the percolation model, i.e., cyclic bonds are infrequent; in the early stages the experiments indicate a functionality f = 2 (number of reactive binding sites per monomer) that increases with increasing release of fibrinopeptides A, eventually approaching the value f = 4; the number of binding sites involved in a bond is about twice the number of the released fibrinopeptides A; and in the polymers the monomer units aggregate end‐to‐end in the very early stage and then in a staggered overlap.
1H‐nmr studies of polyoxyethylene‐bound homo‐oligo‐L‐methionines
Authors: Ribeiro Anthony A. , Saltman Robert P. , Goodman Murray , Mutter Manfred
Published: May 2005

The use of 1H‐nmr spectroscopy is demonstrated to be a useful analytical method to characterize the structure of synthetic peptides attached to soluble, macromolecular polyoxyethylene (POE) supports in the liquid‐phase method (LPM) of peptide synthesis. We report an extensive 360‐MHz 1H‐nmr study of POE‐bound homo‐oligo‐L‐methionine peptides. A combination of high field and selective saturation or Redfield pulse methods allows resolution of individual backbone NH and α‐CH resonances of dilute peptides in the presence of strong resonances from macromolecular POE and/or protonated solvents. The nmr spectra for the POE‐bound peptides in CDCl3 are qualitatively similar to those of the low‐molecular‐weight Boc‐L‐Metn‐OMe peptide esters. This corroborates other observations that POE has little effect on peptide stucture. The backbone α‐CH region of peptides is overlapped by signals from the terminal oxyethylene group of POE, but the peptide side‐chain and low‐field backbone NH resonances are well resolved. In trifluoroethanol the Boc‐(L‐Met)n‐NH‐POE heptamer and octamer adopt the right‐handed α‐helical structure, and the present nmr studies provide evidence for two strong intramolecular hydrogen bonds to stabilize the helices. In water, the N‐deblocked derivatives, (L‐Met)n‐NH‐POE oligomers adopt β‐sheet structure and manifest well‐resolved nonequivalent NH resonances with 6–7 Hz 3JNH‐CH coupling constants.
Kinetics of formation of fibrin oligomers. I. Theory
Authors: Janmey Paul A.
Published: May 2005

The course of formation of fibrin oligomers is treated theoretically for the condition that self‐assembly of fibrin monomers is rapid compared with the loss of A peptides by the enzymatic action of thrombin. The rate constant for removal of the second A peptide is taken to be larger than that for the first by an arbitrary factor q; the association of activated A sites with their complementary a sites is assumed to be random and independent of oligomer size. Two types of oligomers are considered: noncovalently bonded protofibrils formed by the staggered overlap of thrombin‐activated monomers and covalently bonded linear oligomers formed by factor XIIIa‐mediated end‐to‐end ligation of adjacent monomers within protofibrils. Oligomers of the first type, if ligated, are dissociated to oligomers of the second type by solubilization in SDS–urea. Theoretical curves are presented for xw and x′w (weight‐average degree of polymerization of staggered overlap and linear ligated oligomers, respectively) and for the weight fractions of monomer, dimer, and decamer of both ligated and unligated species as functions of y, the fraction of A peptide removed; and also for wx and w′x, the weight fractions of x‐mer of the respective oligomer types, as a function of x at y = 0.5. With increasing q, the maximum wx or w′x that a low oligomer will reach during the reaction decreases and the size distribution is broadened toward larger oligomers. Comparison with experiment is made in a companion paper.
On the theory of Ψ‐condensation
Authors: Grosberg A. Yu. , Erukhimovitch I. Ya. , Shakhnovitch E. I.
Published: May 2005

We suggest a theory of Ψ‐condensation, based on the assumption that a compact DNA particle is a globule, and specifically that a polymer solution is a strongly fluctuating system and that double‐stranded DNA is a stiff homopolymer single‐stranded chain. We show the DNA globule as it appears in a dilute poly(ethylene oxide) (PEO) solution. The corresponding phase transition is investigated in detail. Growth of the PEO concentration should lead to a decrease in the size of the compact particle and to an increase in its optical rotatory power. Conditions are defined at which drastic compaction of DNA takes place, accompanied by the loss of its optic rotatory power, in regions of high PEO concentrations.
Microwave absorption of DNA between 8 and 12 GHz
Authors: Swicord Mays L. , Davis Christopher C.
Published: May 2005

The microwave absorption of aqueous solutions of DNA extracted from E. coli has been studied between 8 and 12 GHz by the use of an optical heterodyne technique. By measuring optically the temperature rise produced in an absorbing sample by pulsed microwave radiation, unambiguous, direct measurement of the microwave absorption is possible. Our results show that E. coli DNA absorbs microwaves in the 8–12‐GHz region substantially more efficiently than water, which is itself an extremely efficient absorber. The observed absorption is featureless and decreases slightly with increasing frequency. These observations are consistent with an explanation involving direct absorption by longitudinal acoustic modes of the double helix.
Raman spectra and normal vibrations of dipeptides. II. Glycyl‐L‐proline
Authors: Lagant P. , Loucheux‐Lefebvre M. H. , Huvenne J. P. , Vergoten G. , Fleury G. , Legrand P.
Published: May 2005

Raman and ir spectra of the glycyl‐L‐proline (GP) dipeptide were recorded. A normal‐coordinate treatment was performed on the basis of the experimental spectra, using a modified Urey‐Bradley force field (MUBFF). Cyclic redundancies were eliminated, and those due to the ring methylene groups, particularly distorted in regard to the tetrahedral conformation, were treated. An assignment of the experimental frequencies is proposed on the basis of the normal treatment.
Vacuum‐ultraviolet circular dichroism of sodium hyaluronate oligosaccharides and polymer segments
Authors: Cowman Mary K. , Bush C. Allen , Balazs Endre A.
Published: May 2005

The CD spectrum of an enzymatically derived sodium hyaluronate (NaHA) segment preparation with chain length 18 ± 3 disaccharide units [NaHAseg, ( NaGlcUA GlcNAc)15–20°. NaGlcUA, sodium D‐glucuronate; GlcNAc, 2‐acetamido‐2‐deoxy‐D‐glucose] in H2O was recorded to 180 nm using a computer‐controlled vacuum‐uv CD instrument. Near 190 nm the spectrum is of low intensity, similar to the sum of the free monosaccharide contributios, attributed to the π–π* transitions of the acetamido and carboxylate substituents. In contrast, much smaller oligosaccharides, also derived from high‐molecular‐weight NaHA by enzymatic digestions, show CD spectra in H2O with prominent bands centered near 190 nm. The oligosaccharide spectra can be matched as linear combinations of interior sugar residue ( NaHAseg) and end sugar residue CD contributions. End residues from oligosaccharides of the type (NaGlcUA‐GlcNAc)n show a negative CD band near 190 nm. End residues from oligosaccharides of the reverse sequence (GlcNAc‐NaGlcUA)n show a positive CD band near 190 nm. Averaging of the two end‐residue spectral contributions yields an approximate match for the spectrum of NAHAseg below 200 nm. It is proposed that the low intensity CD of NaHA in the π–π* region is the result of large‐magnitude, oppositely signed contributions, which can be visulized by studying oligosaccharides.
Peptaibol antibiotics: Conformational preferences of synthetic emerimicin fragments
Authors: Toniolo Claudio , Bonora Gian Maria , Benedetti Ettore , Bavoso Alfonso , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo
Published: May 2005

The ir absorption and CD conformational analyses of solutions of the protected 2–9 fragment of the peptaibol antibiotics emerimicins III and IV \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - L - Leu\rlap{--} (Aib_2 \rlap{--} ) $\end{document} and related short sequences are consistent with the presence of a right‐handed α‐helix for the octapeptide, while the tri‐, tetra‐, and pentapeptides adopt a 310‐helix, either right‐ or left‐handed, depending on the amino acid sequences. The structural preferences of solid‐state \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - OMe $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - OMe $\end{document} have been determined by x‐ray diffraction. In accord with the solution data, incipient 310‐helices, formed by two and three β‐turns, have been found for the tetra‐ and pentapeptides, respectively. The tetrapeptide helix has the left‐handed screw sense, while that of the pentapetide is right‐handed, thus confirming the conclusions of the CD analysis of the solution.
Molecular structure by the constrained damped least‐squares (CDLS) method
Authors: Subhasini S. , Sundaram K.
Published: May 2005

A method for simulating three‐dimensional molecular structure is presented. The method can satisfy any number of constraints on the molecular structure. The constraints can pertain to the constancy of individual distances and angles or be related to point‐group symmetry. A simulated three‐dimonsional model is forced to satisfy the required constraints in the least‐squares sense. The least‐squares optimization is damped to guard against convergence failure. This method is suggested as a tool to obtain approximate molecular structure in situations where a number of quantitative features are known about a molecular structure from preliminary crystallographic results but not the full molecular structure. An application to the structure of enniatin B–K+ complex is given to illustrate such a use.
Band structure of electronic circular dichroism spectra and the born‐oppenheimer approximation
Authors: Dewey T. G.
Published: May 2005

Theory is presented for determining the effects of band structure on electronic CD spectra. In this development, the effect of the first‐order correction to the Born‐Oppenheimer approximation is considered. This removes the unrealistic feature of identical CD and absorbance spectral band structures present in previous models. The predicted order of magnitude of this correction is consistent with experimentally observed differences in CD and absorbance band structure. A Green function formalism is used to determine the contribution of the intrinsic CD to the total CD of an aggregate of chromophores. The intrinsic CD can be determined from the monomeric CD that has been corrected for effects of the intermolecular interactions in the aggregate.
Comparative flexibility, extension, and conformation of some simple polysaccharide chains
Authors: Burton Bruce A. , Brant David A.
Published: May 2005

Realistic polymer chain models are developed for several polysaccharides to illustrate, using perspective drawings of representative chain conformations, the wide range of configuration, extension, and flexibility found in chains of the polysaccharide class. A method for incorporating the gauche or exo‐anomeric effect into polysaccharide conformational energy functions is described, and a novel measure of directional correlation and pseudohelical persistence is utilized to help distinguish the differences in chain configuration observed among the polysaccharides compared.
Description of collagen fibril formation by a theory of polymer crystallization
Authors: Wallace Donald G. , Thompson Andrea
Published: May 2005

A well‐known nucleation‐growth model, used extensively to describe the crystallization of synthetic polymers, has been applied to collagen. The model gives (1) a general representation of the effect of temperature on the rate of collagen fibril formation, (2) a semi‐quantitative description of the effect of collagen concentration on growth rate, and (3) an estimate of fibril diameter that is in agreement with observations made by electron microscopy. The mechanism described is apparently that of the early stages of fibril growth, in which microfibrils are formed. An important parameter required in this approach is the free energy of fibril formation. The free energy was approximated by use of an expression derived by Flory for rodlike polymers. Flory's equation plus experimental data on collagen solubility permitted calculation of the free energy over a range of temperature. The resultant expression was of the same form as one commonly used in describing crystallization of synthetic polymers.
Computer simulation of the conformational properties of retro–inverso peptides. I. Empirical force field calculations of rigid and flexible geometries of N‐acetylglycine‐N′‐ methylamide, bis(acetamido) methane, and N, N′‐ dimethylmalonamide and their corresponding Cα‐methylated analogs
Authors: Stern P. S. , Chorev M. , Goodman M. , Hagler A. T.
Published: May 2005

Rigid and flexible geometry calculations are described for N‐acetylglycine‐N′‐methylamide, N‐acetylalanine‐N′‐methylamide, and their retro‐inverso analogs, bis(acetamido) methane, 1,1‐bis(acetamido) ethane, N,N′‐dimethylmalonamide, and N,N′‐dimethyl‐2‐methyl‐malonamide. The significance of relaxing all degrees of freedom, especially angular flexibility is demonstrated. The flexible geometry approach yields energy maps similar to those from rigid geometry, but the energy barriers between minima are substantially reduced, leading in general, to more probable transitions and a higher volume of accessible conformational space. Whereas the glycine and alanine derivatives exhibit their lowest energy minima in the C region, the gem‐diaminoalkyl and malonyl residues show their lowest minima in the “α‐helical” regions. With respect to the effect of side chains (H versus CH3), the greatest conformational influence appears with the gem‐diaminoalkyl residues. These results indicate significantly different conformational behavior of retro peptides and the implications of these pairwise incorporations of retro‐inverso residues in peptide chains, are discussed.