bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship between the energy of superhelix formation, the shear modulus, and the torsional brownian motion of DNA
Authors: Bret Marc Le
Published: December 2004

The torsional energy of a DNA is the energy involved when the average angle between adjacent base pairs is modified under applied constraints. A relationship is established between the energy of superhelix formation of a upercoiled DNA and its torsional energy. This relationship, valid when the number of the tertiary turns of the supercoiled DNA is small, contains the ratio of the bending to the torsional elastic paramaters of the DNA. From this relationship, the fluctations of the number of tertiary turns of the supercoiled DNA may be compared to those of the DNA with only one sinle‐strand scission. An expression for the shear modulus of the DNA is derived from the anisotropy of the fluorescnece of the intercalated ethidium [Wahl et al. (190) Proc. Natl. Acad. Sci. USA 65, 417–421.]. The value of te torsional elastic parameter deduced from these computations is very close to the parameter of the energy of the superhelix formation determined on supercoiled DNAs by different authors. The energy that must be given to twist it. Consequently, the number of crossovers determined using the EM technique should be much less than the value deduced from the amount of ethiium necessary words, the first ethidium cations intercalating into a relaxed, closed double‐standard DNA change the twist of the DNA but not its tertiary structure.
An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking
Authors: Ornstein Rick L. , Rein Robert , Breen Donnal L. , Macelroy Robert D.
Published: December 2004

An optimized potential function for base‐stacking interaction is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole‐monopole approximation (MMA) is compared to the more refined segmented multipole–multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima. The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima. The attractive part of the Lennard‐Jones 6–12 potential is compared to and parameterized against the expression for the second‐order interaction terms composed of multipole‐bond polarizability for the polarization energy and transition‐dipole bond polarizabilities for approximation of the dispersion energy. The repulsive part of the Lennard‐Jones potential is compared to a Kitaygorodski‐type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function. Stacking minima calculated with the optimized potential method are compared with various perturbation‐type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.
15N‐NMR spectroscopy. IV. Comparison of poly(L‐lysine) and isopoly(L‐lysine)
Authors: Hull William E. , Kricheldorf Hans R. , Fehrle Martin
Published: December 2004

The natural abundance 15N‐nmr spectroscopy has been used to characterize the isomeric polymers (L‐Lys)n and iso (L‐Lys)n in aqueous solution. Although the peptide nitrogens of the two polymers have nearly equivalent shifts at pH < 10, the amino nitrogens differ by 5–6 ppm at pH < 7 and provide an easy means of identification. Furthermore, the polymers are distinguishable by the pKa of the amino group and the basicity of the peptide nitrogen. At pH 10.3 and 25°C, (Lys)n exhibits line broadening and an upfield chemical shift of the peptide nitrogen, indicative of the coil → helix transition. The formation of 100% helix may produce a shift as large as 5 ppm, which probably makes 15N‐nmr spectroscopy more suitable for studies of this transition.
Polyelectroyte behavior of a bacterial polysaccharide from Xanthomonas campestris: Comparison with carboxymethylcellulose
Authors: Rinaudo M. , Mils M.
Published: December 2004

The main physicochemical properties of the polysaccharide called Xanthan produced by Xanthomonas compestris are discussed: the activity coefficient of the counter‐ion, the pK(α), and the ionic selectivity are investigated and compared to those of a carboxymetholcellulose. The weight‐average molecular weight (Mw = 2 × 106), the intrinsic viscosity and the constant of sedimentation are determined as a function of the ionic strength. It is proved that in dilute solution, there is no intermolecular association, whatever the ionic strength. The conformation is proposed to be a rigid rodlike molecule whose length is 6000 Å, independent of ionic strength > 10−2N.
Solid‐state modifications of poly(γ‐ethyl‐L‐glutamate)
Authors: Sasaki Shintaro , Miyamoto Misao , Nakamura Takao , Uematsu Ichitaro
Published: December 2004

Several modification of the arrangements of α‐helical molecules were found in the solid films of poly (γ‐ethyl‐L‐glutamate), depending on the casting solvent and the temperature. The helical conformation is somewhat looser than the normal 18‐residue, 5‐turn α‐helix. Using x‐ray diffraction, the types of molecular arrangements were classified into tetragonal, pseudohexagonal, and hexagonal ones. Tetragonal packing was observed in the filmm (form T) prepared by casting the solution in trifluorethanol or dichlorethane. The sample obtained from chloroform solution is a well‐ordered, pseudohexagonal modification (form I). Forms I and T change into a poorly crystalline form III by annealing at temperatures above 130° C. It is particularly noteworthy that the less‐ordered form III exhibits a thermoreversible transition around 110°C into a well‐ordered form H with the hexagonal molecular packing.
The random copolymerization of γ‐benzyl‐L‐glutamate and L‐valine N‐carboxyanhydrides: Reactivity ratio and heteogeneity studies
Authors: Sederel W. , Deshmane S. , Hayashi T. , Anderson J. M.
Published: December 2004

The random copolymerization of the N‐carboxyhydrides of γ‐benzyl‐L‐glutamate and L‐valine using triethylamine as the initiator in low dielectric media reults in high‐molecular‐weight copolymers at low convenrson. This behavior makes it possible to apply the monomer reactivity ration theory, which was dervied for addition polymerizations, and from the use of the copolymer composition equation, the respective monomer reactivity ratios, the average and incremental copolymer compositions, and the monomer feed ratio at any conversion can be determined. A comparison of the reactivity ratios for the copolymerization of γ‐benzyl‐L‐glutamate NCA and L‐valine NCA in benzene/methylene chloride (rG = 2.1, rV = 0.6) with those obtained using dioxane (rG = 2.7, rV = 0.3) indicates that the interchain compositional heterogeneity is greater for copolymers prepared in the dioxane. For Example, at 100% conversion of the monomeric NCAs, Poly[Glu(OBzl)50Val50] prepared in dioxance has an interchain composition ranging from 74 to 0 mol % γ‐benzyl‐L‐glutamate, whereas in benzene/methylene chloride the interchain composition of γ‐benzyl‐L‐glutamae ranges from 65 to 0 mol %. Once the reactivity ratios are obtained for any pair of α‐amino and N‐carboxyanhydrides, the use of the aforementioned parameters relating to interchain composition can give insight into the compositional heterogeneity between chains as a function of conversion and provide a basis for the preparation of random α‐amino acid copolymers that are homogeneous.
Dielectric relaxation of collagen in aqueous solutions
Authors: Umemura Shin'ichiro , Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku
Published: December 2004

The complex dielectric constant of collagen in aqueous solutions (polymer concentration, Cp = 0.02–0.2%) was measured at 10°C in the frequency range from 3 Hz to 30 kHz. The loss peak for Cp = 0.02% is located at 90 Hz and the dielectric relaxation time τD is estimated to be 1.8 ± 0.3 msec. The τD agrees well with the rotational relaxation time estimated from the reduced viscosity, and the relaxation is ascribed to the end‐over‐end rotation of the molecule. The Cp dependence of τD and the dielectric increment Δε are interpreted in terms of the aggregation of molecules. The dipole moment of a molecule, obtained from Δε at Cp = 0.02% and pH 6.5, is (5.2 ± 0.2) × 104D, which is explained by the asymmetrical distribution of the ionized side chains of the molecule.
Urease oligomerizes in a linear pattern: Further hydrodynamic evidence from intrinsic viscosity theories and measurement
Authors: Tirrell Matthew , Middleman Stanley
Published: December 2004

Measurements of the intrinsic viscosity of the urease “monomer” and of a mixture of oligomers are shown to lead to the conclusion that urease oligomerizes in a linear fashion, when viewed in the light of several available theories of intrinsic viscosity of rigid protein macromolecules. This conclusion is also consistent with previously reported work on the sedimentation coefficients of the urease oligomers. The use of a detailed subunit structure for the urease “monomer” and oligomers is explored and found to give quantitatively good results for all hydrodynamic properties of all urease oligomers. The realm of validity of the intrinsic viscosity theories proposed by Garcia de la Torre and Bloomfield, by Tsuda, and by Abdel‐Khalik and Bird is explored in this context.
Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions
Authors: Havel Timothy F. , Crippen Gordon M. , Kuntz Irwin D.
Published: December 2004

By generating classes of random structures for trypsin inhibitor and carp myogen, each consistent with a given set of experimental or theoretical information, we have assessed the relative utility of various experiments and theories in deducing the conformation of macromolecules. We compare the calculated structures with known x‐ray coordinates and compute for each class an average error. Small errors mean that the experimental or theoretical constraints limit the structures to the vicinity of the crystal structure, whereas large errors show that the constraints permit a wide variety of tertiary conformations. We find the following points to hold true: (1) Qualitative information on all the distances, as might be obtained from the correct prediction of interresidue contacts, effectively determines the structure (error approximately 1 Å). (2) Quantitative information on a limited number of distances, as might be obtained from nmr or crosslinking experiments, significantly restricts the range of possible structures only when the number of distances given is comparable to the number of residues (error approximately 3 Å). (3) Quantitative information on the distances of each residue to the center of mass of the molecule, as might in part be obtained from solvent accessibility and solution x‐ray studies, is not particularly restrictive by itself (error approximately 5 Å). (4) Complete qualitative local distance information, as might be obtained from secondary prediction and CD/ORD studies, is clearly consistent with a wide variety of tertiary structures (error approximately 7 Å).
Accelerated deacylation of acyl salicylates and neighboring group effects in derivatives of poly(ethylenimine)
Authors: Johnson Ronald S. , Klotz Irving M.
Published: December 2004

The deacylation of acetylsalicylate and of adipoyldisalicylate in the presence of modified and unmodified poly(ethylenimine)s has been investigated. The kinetics of these reactions have been analyzed in terms of an initial binding step followed by one or two aminolysis steps, and the relevant kinetic parameters have been evaluated. The polymers markedly accelerate the rate of deacylation. Second‐order rate constants based on total primary amine concentration for aminolysis by the polymers are 103–105 times larger than those for methylamine. The most striking effect of the polymer has been observed in the two successive aminolysis steps of adipolydisalicylate where the second rate constant is approximately 20‐fold greater than the first, presumably because of local proximity factors.
Circular dichroism and the pH‐induced β‐coil transition of poly(S‐carboxymethyl‐L‐cysteine) and its side‐chain homolog
Authors: Ikeda Shoichi , Fukutome Akira , Imae Toyoko , Yoshida Tomohiko
Published: December 2004

The CD of aqueous solutions of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine) has been measured at different pH, and the pH‐induced β‐coil transition is observed by changes in residue ellipticity of dichroic bands around 200 and 225 nm. The residue ellipticity at 200 nm of the former polypeptide is twice as large as that of the latter, when the β‐conformation is formed in solution. However, the β‐conformation of the latter polypeptide is more stable against electrostatic repulsion than that of the former. The transition curve of poly(S‐carboxymethyl‐L‐cysteine) has also been determined for different molecular weights. The curves were found to be completely coincident with one another if the degree of polymerization were higher than about 100. Such a transition curve is generally divided into three steps: initiation, cooperative formation, and rearrangement of hydrogen bonds. The cooperative step is very sharp, occurring at a constant pH. These steps become agglomerated into two or one when the polypeptide concentration or added salt concentration is increased.
31P nmr spin‐lattice relaxation studies of deoxyoligonucleotides
Authors: Davanloo Pari , Armitage Ian M. , Crothers Donald M.
Published: December 2004

Temperature‐dependent conformational transitions of deoxyoligonucleotides have been monitored by measuring 31P chemical shifts, spin‐lattice relaxation times (T1), and 31P‐{H} nuclear Overhauser enhancements (NOEs). The measured NOE ranged from 30 to 80%, compared to the theoretical maximum of 124% for a dipolar relaxation mediated by rapid isotropic rotation. The observed 3′‐5′ phosphate diester 31P T1 showed a similar temperature dependence over the range 2–75°C for both double‐ and single‐stranded oligonucleotides, and for dinucleotides. The results show that dipole–dipole interactions dominate the internucleotide phosphate relaxation rate in oligonucleotides. The same is true of terminal phosphate groups at low temperature; but at higher temperature another process, possibly due to contamination by paramagnetic ions, becomes dominant. The rotational correlation time τR calculated from the dipole–dipole relaxation rate of the internucleotide phosphate in d(pA)2 at 16°C is τR = 5.0 × 10−10 sec, implying a Stokes radius for isotropic rotation of 7.6 Å. The T1 and NOE values for the double‐helical octanucleotide d(pA)3pGpC(pT)3 are consistent with dominance of dipole–dipole relaxation and isotropic rotation of a sphere of radius 14 Å, a reasonable dimension for the double helix. Activation energies for the rotation of dinucleotides range from 4 to 6 kcal/mol, close to the value of 4 kcal/mol expected for isotropic rotation. In order to test the possible effect of internal motion of correlation time τG on the results, we considered a model in which the nucleotide chain rotates about the P‐O bonds. Comparison of the calculation with our experimental results shows that internal motion with τG ≅ 10−9 sec, as found from other studies to be present for large nucleic acids, would not influence out T1 and NOE values enough to be distinguished from isotropic rotation. However, we can conclude that τG cannot be as fast as 10−10 sec, even for dinucleotides.
Disorder–order transitions induced in anionic homopolypeptides by cationic detergents
Authors: Mattice Wayne L. , McCord Robert W. , Shippey Patrice M.
Published: December 2004

CD spectra have been obtained for poly(L‐glutamic acid) and poly(L‐aspartic acid) as functions of temperature and concentration of cationic detergents. Dodecylammonium chloride induces a coil–helix transition in fully ionized poly(L‐glutamic acid). The interaction of the monomeric detergent with the polypeptide is responsible for the conformational transition. The detergent concentration required to produce the transition is independent of temperature. The CD of fully ionized poly(L‐aspartic acid) is nearly unaffected by dodecylammonium chloride, in marked contrast to the situation found with poly(L‐glutamic acid). However, these results do not imply that dodecylammonium chloride interacts differently with aspartyl and glutamyl residues. The observed results can be accounted for by the well‐known fact that the glutamyl residue has a higher helix‐forming tendency that the aspartyl residue. Cetyltrimethylammonium chloride destabilizes the helical form of poly(L‐glutamic acid). This detergent presents an exception to the usual ability of ionic detergents to promote formation of ordered structures in oppositely charged homopolypeptides.
Mean‐square amplitudes of the longitudinal vibrational of helical polymers
Authors: Peticolas Warner L.
Published: December 2004

A simple model for the longitudinal acoustical vibrations of helical polymers has been developed. This model consists of a linear string of masses, M, connected by springs. The mass must be taken as that of one helical turn of the true helix. It has been found that all of the previously observed or calculated frequencies for the longitudinal acoustical modes of helical polymers can be calculated from this model using only one adjustable parameter, the force constant f, between the turns, for each type of helix. Using this simplified model it has been possible to obtain the rms amplitudes of the changes in the overall end‐to‐end length of helical polymers as a function of their chain length and temperature. At room temperatures the rms end‐to‐end length is found to vary from a few tenths of an angstrom for hydrocarbon chains of the length found in phospholipid membrane bilayers to several angstroms in a rigid α‐helix of 100 peptide residues. The damping of these α‐helical modes is not considered but may be appreciable in solution.
A model for the simulation of an aqueous dipeptide solution
Authors: Rossky Peter J. , Karplus Martin , Rahman Aneesur
Published: December 2004

A model for the simulation of a solution of an alanine dipeptide in water is presented that combines a previous model for bulk water (ST2) with that used in conformational energy studies on small molecules and proteins. The results of a pilot molecular dynamics study indicate that the model leads to reasonable solvent–solute interactions. No evidence is found for substantial changes in the structure or dynamics of the dipeptide in solution as compared to in vacuo. Furthermore, at the elevated temperature examined, there appear to be no significant effects on the dynamics or intermolecular bonding of the water molecules in contact with the solute.
Conformation and circular dichroism of DNA
Authors: Sprecher Cindy A. , Baase Walter A. , Johnson W. Curtis
Published: December 2004

CD spectra of calf thymus, C. perfringens, E. coli, and M. luteus DNA have been measured in the vacuum‐uv region to about 168 nm for the A‐, B‐, and C‐forms. The positive band at about 187 nm and the negative band at about 170 nm found for each type and form of DNA are sensitive to the source of the DNA and the base–base interactions of the double‐stranded helix. The A‐form spectra confirm that these bands are indeed sensitive to secondary structure. In the near‐uv, the CD of B‐form DNA is well analyzed as a linear combination of 27% A‐form and 78% C‐form. However, an analysis of the extended spectrum demonstrates that the near‐uv analysis is not correct. The extended analysis shows that the base–base interactions are similar for B‐ and C‐forms in solution, which implies that these two forms have nearly the same number of base pairs per turn. Various types of CD difference spectra are also discussed.
High‐resolution NMR of exchangeable protons in arginine, oligoarginines, and the arginine‐rich histone tetramer
Authors: Klavan Leonard , Crothers Donald M.
Published: December 2004

High‐resolution nmr of exchangeable protons in the side chain of arginine reveals two distinct resonances arising from restricted rotation about the N(1)–C(ε) bond. Spectral assignments based upon pH‐dependent proton‐exchange behaviour identified each resonance as arising from one of the magnetically distinct guanidinium amino groups in the molecule. Computer simulation of the temperature‐dependent coalescence of these peaks defines an activation energy of 14.3 kcal/mol for internal rotation about this bond. Similar results to those observed in monoarginine are reported for diarginine, triarginine, and the arginine‐rich histone tetramer. Based on these findings, a nonsymmetric mode of arginine–ligand interaction is suggested, and the molecular dynamics of proton exchange in the arginine side chain is discussed.
A Raman difference spectroscopic investigation of ovalbumin and S‐ovalbumin
Authors: Kint Saima , Tomimatsu Yoshio
Published: December 2004

Raman spectra from 800 to 1850 cm−1 of aqueous solutions of ovalbumin and its more heat‐stable form, S‐ovalbumin, are presented. A Raman difference spectrum (ovalbumin minus S‐ovalbumin) shows differences in intensity in the amide I and III regions. These intensity differences lead us to postulate that the conversion of ovalbumin to S‐ovalbumin involves a conformation change of a small part (∼3–4%) of the protein from α‐helix to antiparallel β‐sheet geometry. This small difference in the three‐dimensional arrangement of the peptide chain may contribute to the large difference in the thermodynamic stability between ovalbumin and S‐ovalbumin.
Hydrodynamic properties of macromolecular complexes. V. Improved calculation of rotational diffusion coefficient and intrinsic viscosity
Authors: Wilson Robert W. , Bloomfield Victor A.
Published: December 2004

In our previous calculations of rotational diffusion coefficients and intrinsic viscosities of macromolecular complexes modeled by arrays of spherical subunits [J. G. de la Torre & V. A. Bloomfield, Biopolymers 16, 1765, 1779 (1977); 17, 1605 (1978)], results were poor when the dominant subunit was located near the center of frictional resistance. A simple means of correcting this flaw, which gives satisfactorily accurate results with little increase in computation time, is to replace the single large subunit with an array of smaller ones. We have examined trigonal bipyramidal, octahedral, and cubic arrays of spheres whose radii were chosen to give the same total volume or the same rotational diffusion coefficient as the parent sphere. These all give similar results, so the details of the modeling are not important. Results obtained using this stratagem are in much better agreement with the theories of Perrin and Simha for short prolate ellipsoids of revolution, and with experimental measurements of rotational diffusion coefficients of T‐even bacteriophage without fibers or with fibers retracted. We have also extended our previous calculations to consider phage with various numbers of fibers attached.
Conformational studies of proteoglycans: Theoretical studies on the conformation of heparin
Authors: Nagarajan M. , Rao V. S. R.
Published: December 2004

Various models proposed for heparin have been examined by a stereochemical approach involving contact distance criteria and potential energy calculations. The present study suggests that the model favored by Atkins and coworkers [Biochem. J. (1973) 135, 729–733 and (1974) 143, 251–252] is not stereochemically satisfactory. An alternative model has been proposed with N‐acetyl‐D‐glucosamine and one of the uronides in the 4C1 conformation and the other uronide (probably sulfated) in the 1C4 conformation. The observed variations in the tetrasaccharide periodicities (16.5–17.3 Å) in different crystalline modifications of heparin have been attributed to possible changes in the rotational angles about the interunit glycosidic bonds rather than a change in the pyranose ring conformation. The proposed model is also independent of the observed variation in the relative composition of uronic acid residues in heparin. These conclusions are in disagreement with those of earlier workers.
Alkylated poly(amino acids). I. Conformational properties of poly(Nε‐trimethyl‐L‐lysine) and poly(Nδ‐trimethyl‐L‐ornithine)
Authors: Granados Edward N. , Bello Jake
Published: December 2004

Poly(Nε‐trimethyl‐L‐lysine), [Lys(Me3)]n, and poly(Nδ‐trimethyl‐L‐ornithine), [Orn(Me3)]n, in sodium dodecylsulfate do not assume the β‐structure or α‐helix, respectively, of their parent polymers. In 0.5M Ca(ClO4)2 both [Lys(Me3)]n and [Orn(Me3)]n are aggregated and display CD spectra indicative of a regular, perhaps helical, structure. For [Lys]n and [Lys(Me3)]n, the T1 of the α‐hydrogens are 0.379 and 0.230 sec, respectively, indicating greater rigidity for [Lys(Me3)]n. The CD spectrum of [Lys(Me3)]n at pH 8 is more heat resistant than that of [Lys]n. It is suggested that apolar interactions are more important in the methylated polymers than in the parent polymers.
Internal condensation of a single DNA molecule
Authors: Post Carol Beth , Zimm Bruno H.
Published: December 2004

We report a theoretical description of the collapse of a single chain molecule, such as DNA, from a voluminous random coil to a condensed state. With the polymer lattice theory developed by Flory as a starting point, the configurational free energy of a single polymer molecule in solution is expressed as a virial expansion in the polymer segment volume fraction. We have extended the series by one term beyond Flory's analysis and have evaluated the third virial coefficient. Whenever the potential of interaction between two chain segments is attractive, the addition of this new term causes a new minimum to appear in the free energy. The new minimum represents a polymer configuration in which the chain occupies a very small solution volume; we identify this minimum with the collapsed state. There is a critical point for the transition to the collapsed state; above a certain value of the rms end‐to‐end distance, the change in the polymer solution volume is a sudden one, whereas below this value the transition is gradual. An example of the results of the free energy calculation using parameters from T2 DNA is presented. DNA should show a sudden collapse, but synthetic polymers such as polystyrene should show a gradual collapse.
Direct differential absorbance profiles of denaturing transitions in ribosomal and mRNA
Authors: Kallenbach Neville R. , Brentani Maria Mitzi , Brentani Ricardo R.
Published: December 2004

A direct method for measuring the derivative of thermal transition profiles (ΔA/ΔT), first described by Pavlov and Lyubchenko [Biopolymers 17, 795–798 (1978)], is applied to the secondary structure of several eukaryotic ribosomal and messenger RNAs. The method consists of generating an effective ΔT between a sample and reference cuvette by altering the Tm (midpoint denaturation temperature) of one of the solutions with respect to the other. This can be done by changing salt concentration, solvent, pH, or ligands. Scanning the two cuvettes by varying the wavelength at different temperatures permits detailed examination of the base composition of differentially melting domains. We report here the ΔA/ΔT profiles generated by monovalent ion concentration differences for a number of high‐molecular‐weight natural RNAs, as well as the synthetic polynucleotides poly(rA) and “random” poly[r(A,G,U,C)].

The 18S and 28S rRNAs from chick embryos exhibit a reproducible series of peaks in the ΔA/ΔT profiles at low salt with ΔT = 4K. The high‐temperature transitions in 28S rRNA appear to contain G·C base pairs exclusively, in contrast to those in 18S rRNA or any natural mRNA. Each mRNA we have examined (bacteriophage MS2, globin mRNA from rabbit reticulocytes, and procollagen mRNA from chick embryos) exhibits a distinctive ΔA/ΔT profile in low salt. The stability of many of the transitions in each of the mRNAs is no greater than that of the secondary structure in random poly(A,G,U,C) in low salt. More than 50% of the base pairing in procollagen mRNA actually “melts” below the mean for the random copolymer, indicating that despite its high G·C content, this mRNA contains a secondary structure that is exceptionally low in stability.
Quasielastic light scattering from solutions of lollipop‐shaped particles
Authors: Koopmans G. , Van Der Meer B. J. , Hopman P. C. , Greve J.
Published: December 2004

An expression is derived for the field correlation function of the light scattered from a solution of lollipop‐shaped particles. Such particles are a tractable model of certain bacteriophages. They are assumed to consist of an ellipsoidal head containing optically anisotropic scattering material and a tail which does not scatter. Because of the tail, Brownian rotational movement occurs around a center of rotational friction which is at a distance r0 from the center of the head. The dependence of the field correlation function C(τ) on the rotational diffusion coefficient DR is given by the factor ΣlBl exp[−l(l + 1)DRτ]. It is shown that the tail causes the coefficients Bl to be different from zero for all values of l. Therefore, C(τ) contains a term proportional to exp(−2DRτ), which is not present when r0 = 0. We give plots of Bl for various combinations of parameters. It turns out that dynamic light scattering may be used to measure r0.
Rotational effects in quasielastic laser light scattering from T‐even bacteriophage
Authors: Wilson Robert W. , Bloomfield Victor A.
Published: December 2004

We have applied a theory of dynamic light scattering from large anisotropic particles, developed by Aragón and Pecora [J. Chem. Phys. 66, 2506–2516 (1977)] to calculate the scattering expected from T‐even phage models. The results indicate that the off‐center rotation of the massive virus head with respect to the center of frictional resistance introduces significant rotational contributions to the light‐scattering time autocorrelation function. The effect is particularly important when the fibers of the phage are extended. Reanalysis of previously published data [J. B. Welch III and V. A. Bloomfield, Biopolymers 17, 2001–2014 (1978)], taking into account rotational corrections, confirms the equality of molecular weights of the slow‐ and fast‐sedimenting forms of T2L bacteriophage.
Self‐association of hemoglobin: A dielectric dispersion study
Authors: Desnica D.
Published: December 2004

The concentration dependence of the dielectric dispersion between 1 kHz and 0.5 MHz was investigated for dense hemoglobin solutions. The concentration was varied between 4 and 26 mM/l. per heme. From the characteristic changes in dielectric parameters at some threshold concentration, we observe that the association of hemoglobin macromolecules occurs. This statement is also confirmed by viscosity measurement data.
Particular structural role of H1 in complexes with DNA and comparison with H2A– and H4–DNA complexes investigated by IR linear dichroism
Authors: Taillandier E. , Taboury J. , Liquier J. , Gadenne M. C. , Champagne M. , Brahms J.
Published: December 2004

The particular role of H1 in the structure of histone–DNA associations is shown by means of ir linear dichroism. H1–, H2A–, and H4–DNA complexes are studied for different histone: DNA input ratios and various relative humidities (r.h.). The measurement of the dichroic ratios allows one to determine the secondary structure of DNA in the complexes. It is shown that the progressive addition of histone H2A or H4 to DNA inhibits the structural B → A transition and DNA remains in a B‐type form at low r.h. It is found that the B → A transition is inhibited for 19 or 26 base pairs of DNA per molecule of H2A or H4. The stabilization of DNA in a B‐conformation by H2A and H4 has been also observed by H2B and H3 but with a different efficiency. In contrast, histone H1, which does not belong to the core of the nucleosomes in chromatin, leaves the DNA in H1–DNA complexes free to adopt an A conformation at low r.h. for H1/DNA ratios below 0.6/1. Thus a major difference in the structural role between histone H1 and histones belonging to the nucleosomal core with respect to the conformational flexibility of DNA in the histone–DNA complexes is demonstrated.
Light scattering of aqueous solutions of DNA, poly(acrylic acid), and tobacco mosaic virus under alternating electric field
Authors: Fujikado Takashi , Hayakawa Reinosuke , Wada Yasaku
Published: December 2004

Two new techniques, amplitude modulation (AM) and frequency modulation (FM) of an electric field, are developed for the light‐scattering study of polymer solutions under ac electric fields. The AM technique makes it possible to observe accurately the frequency dependence of the intensity changes of scattered light due to the electric field. The FM one allows us to obtain directly the frequency derivative of the intensity change. The techniques are applied to DNA, poly(acrylic acid), and tobacco mosaic virus in the frequency range from 10 Hz to 100 kHz. A low‐frequency relaxation is found for both DNA and poly(acrylic acid). The obsersved relaxation time of DNA agrees with that in the dielectric relaxation of DNA, which has been attributed to the rotation of the molecule with a quasipermanent dipole. In the case of poly(acrylic acid), the relaxation strength increases with increasing degree of neutralization. TMV at a concentration of 0.1% exhibits a negative relaxation at low frequencies, which indicates the rotation of TMV aggregate with a permanent dipole along its minor axis.
Structure of strand‐separted DNA in different environments studied by linear dichroism
Authors: Nordén Bengt , Seth Stefan
Published: December 2004

We have studied the denaturation of DNA by linear dichroism (LD) techniques in the following systems: (1) in aqueous solution at low pH, (2) in 90% (w/w) ethylene glycol and in 90% glycerol solutions, and (3) in a matrix of polyvinyl alcohol (PVA). We report that denatured DNA at low ionic strength can be oriented by shear forces in all these systems and that it exhibits positive LD with markedly varying LD/A over the absorption band centered at 260 nm (A being the ordinary absorbance) as compared to the negative LD with approximately constant LD/A of ordinary native DNA. These results are interpreted in terms of a large tilt of the planes of the DNA bases. DNA adopts denatured forms in (1) aqueous solutions at pH < 3.5, (2) ethylene glycol and glycerol at low Na+ concentrations, and (3) PVA after heating. If the denaturation is done in dry PVA, a complete re‐formation of the double helix is obtained after humidifying (60% w/w) the matrix. This shows that the matrix can keep the two strands in a position allowing a perfect fitting on reassociation. Previous attempts to determine any intrinsic LD of denatured DNA have failed, probably due to the fact that, unless a very low ionic strength is used, the flexibility of the single strands prevents the orientation required to give a detectable LD signal even with recently developed high‐sensitivity measurement techniques.
Cation‐binding cyclic peptides with lipophilic tails
Authors: Deber C. M. , Adawadkar P. D.
Published: December 2004

We have synthesized and characterized a series of cation‐binding cyclic octapeptides which may function as potential ionophoric substances. The materials contain varying degrees of hydrophobic character, which was controlled systematically through the incorporation of N‐alkylglycine residues where N‐alkyl = methyl, n‐hexyl, cyclohexyl, or n‐decyl. The peptides reported include cyclo(Phe‐Sar‐Gly‐Sar)2, cyclo(Glu(OBzl)‐Sar‐Gly‐Sar‐Glu(OBzl)‐Sar‐Gly‐(N‐decyl)Gly), cyclo(Glu(OBzl)‐Sar‐Gly‐(N‐decyl)Gly)2, cyclo(Glu(OBzl)‐Sar‐Gly‐(N‐hexyl)Gly)2, cyclo(Glu(OBzl)‐Sar‐Gly‐(N‐cyclohexyl)Gly)2, and the corresponding free diacid forms of the Glu‐containing compounds. Using 13C‐ and 1H‐nmr spectra, we demonstrated that the mixture of cis/trans peptide bond‐isomer conformers, characteristic of the free‐peptide benzyl esters in solution, was converted to unique C2‐symmetric, presumably all‐trans conformers on complexation with calcium ions. Cation‐transport experiments, using the thick‐liquid model of transport in a Pressman cell, established that these compounds transport a variety of cations and that one peptide examined in detail, cyclo(Glu(OBzl)‐Sar‐Gly‐(N‐decyl)Gly)2 (selectivity Ca2+ > Na+ > K+ > Mn2+ > Cu2+ > Mg2+ > Co2+ > Zn2+), transports calcium about an order of magnitude more efficiently than magnesium.
Interaction of Water with DNA Single‐Helix in the A Conformation
Authors: Clementi E. , Corongiu G.
Published: December 2004

The interaction energy between water and the DNA single helix in the A conformation is computed at a number of planar cross sections perpendicular to the long axis of the helix and for cylindrical surfaces enclosing the helix. In addition, Monte Carlo simulations are presented for a small cluster of water around regions of energy minima. On the basis of these simulations, the structure of water for the DNA (single helix in the A conformation) is proposed and discussed.
Hydrogen‐bond cooperativity in protein secondary structure
Authors: Sheridan Robert P. , Lee Richard H. , Peters Nancy , Allen Leland C.
Published: December 2004

Hydrogen bonding in the α‐helix and β‐sheet has been studied by ab initio molecular orbital calculations carried out on complexes of formamide. Hydrogen‐bond geometries were taken from x‐ray crystallography of polypeptides. Positive cooperativity is found in all cases. The limiting value for infinite chains is obtained by use of a double‐reciprocal plot and indicates an increase in the effective bond strength of 25% over that of a single isolated bond. Parallel calculations based on a classical electrostatic model yield qualitatively similar trends but underestimate the cooperativity by half. Charge redistribution accompanying cooperativity is characterized by a new type of charge‐density difference plot, the cooperativity map. The magnitude and distance over which cooperativity acts suggest several significant biological consequences. Thus the average of α‐helices and the number of β‐sheet strands found in protein may be influenced by cooperativity. Cooperativity in the interpeptide hydrogen bond may also be partly responsible for the rapid formation of secondary structure in renaturing proteins and help stabilize secondary structure relative to the random‐coil conformation.
Enzymatic degradation of β(1 → 4) xylan single crystals
Authors: Chanzy H. , Comtat J. , Dube M. , Marchessault R. H.
Published: December 2004

The enzymatic degradation of β(1 → 4) xylan single crystals with xylanases was investigated by electron microscopy and electron diffraction. The enzyme attack takes place at the edge of the crystals and progresses towards their centers. This is consistent with an endo‐enzyme mechanism, where the enzyme interacts essentially with the accessible xylan chains located at the crystal periphery.
Quasielastic light scattering from solutions of filamentous viruses. I. Experimental
Authors: Loh Eugene , Ralston Edward , Schumaker Verne N.
Published: December 2004

Intensity fluctuations of laser light scattered from filamentous viruses Pf1 [length L (Å) × diameter d (Å) = 20,000 × 90], M13 (9000 × 90), potato virus X (5150 × 130), and tobacco mosaic virus (3000 × 180) in sucrose density gradients were measured with a photon correlation spectrometer over a range of scattering angles from 15° to 120°. The experimental data can be approximated by two exponential decays, “slow” and “fast.” The slow decay rate constant t corresponds to the translational diffusion D of the virus, i.e., t = K2D, where K is the magnitude of the scattering vector. The amplitude of the slow component, i.e., translational diffusion, remains greater than that of the fast component, even at high KL. The fast decay rate constant t is also proportional to K2 for viruses such as Pf1, M13, and even potato virus X. In the companion paper, we shall attribute the amplitude enhancement of the translational diffusion to the coupling of its anisotropy to the rotational diffusion modes. In order to explain the excessive decay rates in the fast component, we need to consider the bending mode of rodlike viruses, especially in the longer viruses such as M13 and Pf1, in addition to the usually expected rotational diffusion modes.
Brownian motion of the wormlike chain and segmental diffusion of DNA
Authors: Berg Otto G.
Published: December 2004

The dynamics of the wormlike chain model for a polymer in solution is investigated in the case of free torsional and no longitudinal variations. A Langevin equation is derived and solved for circularly closed chains, neglecting hydrodynamic interactions. The local diffusion behavior of particular segments is described, and it is found that the mean‐square displacements are proportional to t3/4 at short times. Also, the equilibrium correlation functions for the closed chain are derived from the dynamic model in both the discrete and wormlike cases.
Theory of H1‐mediated control of higher orders of structure in chromatin
Authors: Manning Gerald S.
Published: December 2004

It is known that the lysine‐rich histone H1 induces both higher orders of folding in chromatin and donut shapes in DNA. However, these phenomena occur only on the high‐salt side of a narrow transition range located at about 0.02M salt. Previous theoretical analyses of the ionic‐strength dependencies of DNA persistence length and denaturation rate have provided the information that the basic rigid‐rod unit in high‐molecular‐weight DNA is a segment 60 base pairs in length and that if the phosphate charge is neutralized, this segment will spontaneously adopt a bent conformation with radius of curvature 170 Å. On the assumption that an H1 molecule does not completely neutralize the DNA charge in its vicinity, the theory has been extended here to determine the onset of spontaneous bending as a function of salt concentration and extent of phosphate neutralization. A salt transition of the kind observed has been found for the realistic value of 82% charge neutralization, with the actual value likely to be in the neighborhood of 90%, as suggested by the measurements of Wilson and Bloomfield.1 It is recalled that the spacer DNA length in chromatin is of about the same length as the DNA rigid‐rod unit. If binding of H1 to the spacer induces, as predicted, a bent conformation of radius about 170 Å, then the observed value of about 150 Å for the outer radius of the solenoid presently thought to be the basic mode of folding for a nucleosome chain can be understood as a reflection of the inherent maximum curvature of DNA in aqueous salt solution.
Flexibility of the pyranose ring in α‐ and β‐D‐glucoses
Authors: Joshi N. V. , Rao V. S. R.
Published: December 2004

Conformational energies of α‐ and β‐D‐glucopyranoses were computed by varying all the ring bond angles and torsional angles using semiempirical potential functions. Solvent accessibility calculations were also performed to obtain a measure of solvent interaction.

The results indicate that the 4C1 (D) chair is the most favored conformation, both by potential energy and solvent accessibility criteria. The 4C1 (D) chair conformation is also found to be somewhat flexible, being able to accommodate variations up to 10° in the ring torsional angles without appreciable change in energy. Observed solid‐state conformations of these sugars and their derivatives lie in the minimum‐energy region, suggesting that the substituents and crystal field forces play a minor role in influencing the pyranose ring conformation. Theory also predicts the variations in the ring torsional angles, i.e., CCCC < CCCO < CCOC, in agreement with the experimental results. The boat and twist‐boat conformations are found to be at least 5 kcal mol−1 higher in energy compared to the 4C1 (D) chair, suggesting that these forms are unlikely to be present in a polysaccharide chain. The 1C4 (D) chair has energy intermediate between that of the 4C1 (D) chair and that of the twist‐boat conformation. The calculated energy barrier between 4C1 (D) and 1C4 (D) conformations is high—about 11 kcal mol−1.
Relaxational contributions to protein compressibility from ultrasonic data
Authors: Sarvazyan A. P. , Hemmes Paul
Published: December 2004

The ultrasonic absorption spectra of proteins in solution generally show relaxational behaviour. There will be a corresponding dispersion of sound velocities accompanying each relaxation. The compressibility of the protein as measured by sound velocity techniques will therefore include a relaxational contribution. We have evaluated this contribution for a number of proteins and found that in some cases the relaxational contribution is a significant fraction of the total compressibility. The relaxational contribution will be large only if the molecule has a large number of degrees of freedom with low force constants. However, such motions are likely to be those involved in the biological functioning of the molecule. Care is needed in interpreting the relaxation spectrum since proton transfer processes give large apparent relaxational compressibilities.
Temperature dependence of macromolecular interactions in dilute and concentrated hemoglobin solutions
Authors: Veldkamp Wilfrid B. , Votano Joseph R.
Published: December 2004

We studied the temperature‐dependent effects of intramolecular interactions on the mutual diffusion coefficient of normal human oxygenated hemoglobin in salt solution. We used photon correlation spectroscopy to observe this temperature dependence of the mutual diffusion coefficient of two protein concentrations (1.25 and 17.0 g %) between 13 and 37°C. This coefficient was our probe for monitoring temperature‐dependent structural changes of hydrated hemoglobin in solution. Comparison of our measured diffusion coefficient with that predicted by the Stokes‐Einstein relationship in terms of solvent or solution viscosity showed a clear transition in the conformation of hemoglobin at approximately 22°C, independent of the hemoglobin concentration. We postulated that at this physiological temperature, a considerable quaternary rearrangement of the hemoglobin chains takes place. We believe this rearrangement changes the effective volume and the hydration sphere of the hemoglobin macromolecule.
Conformation of sequential and random lysine–phenylalanine copolypeptides
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G.
Published: December 2004

The sequential copolypeptides (Lys‐Phe‐Lys)n and (Lys2‐Phe‐Lys)n and a series of related random copolypeptides were investigated with respect of their ability to adopt the α‐helix or β‐conformation. Conformational transitions were induced by increasing the pH or by addition of NaClO4 or methanol and were observed by recording the CD spectra. In contrast to the respective alternating copolypeptide (Phe‐Lys)n with its strong tendency for the β‐structure reported previously, (Lys‐Phe‐Lys)n can adopt either secondary structure, whereas (Lys2‐Phe‐Lys)n strongly favors the α‐helix. Together with the random copolypeptides, whose composition varied from 20 to 50 mol % phenylalanine and whose average molecular weights ranged from 10,000 to 90,000, the influence of the phenylalanine content and of the chain length on conformational stability and the rotatory strength of the respective secondary structures were elaborated.