bluuebunny/crossref_metadata_2025_split huggingface dataset:
A model for the simulation of an aqueous dipeptide solution
Authors: Rossky Peter J. , Karplus Martin , Rahman Aneesur 
Published: December 2004

AbstractA 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

AbstractCD 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

AbstractHigh‐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

AbstractRaman 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

AbstractIn 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

AbstractVarious 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

AbstractPoly(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

AbstractWe 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

AbstractA 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

AbstractAn 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

AbstractWe 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

AbstractThe 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

AbstractThe 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

AbstractTwo 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

AbstractWe 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

AbstractWe 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

AbstractThe 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

AbstractHydrogen 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

AbstractThe 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

AbstractIntensity 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

AbstractThe 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.