bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA conformational kinetics
Authors: Szu Shousun C. , Jernigan Robert L.
Published: December 2004

A model for the time dependence of DNA conformational state probabilities is formulated in the form of first‐order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 104 min−1 as the step rate for melting a single base pair.
Local order in polyelectrolytic solutions detected by magnetic birefringence measurements on the (Tyr‐Glu)n copolymer
Authors: Maret G. , Domard A. , Rinaudo M.
Published: December 2004

The local electrostatic order in polyelectrolytic solutions has been studied by magnetic birefringence measurements on short segments (n ∼ 34) of the (Tyr‐Glu)n polypeptide in high magnetic fields up to 13 T. We give evidence that only above a critical polymer concentration do small domains exist within which the polymers show a parallel ordering. This structural order disappears suddenly at ionic strengths above about 5 × 10−2 M and above a melting temperature of about 50°C.
Conformational studies on polynucleotide chains. IV. Backbone structure of ribonucleic acids
Authors: Tosi Camillo , Pescatori Emilio , Clementi Enrico
Published: December 2004

In preceding papers the energies associated with the internal rotations in the sugar–phosphate–sugar complex were described with an analytical potential consisting of a Lennard‐Jones 6–12 term and an intrinsic torsional term and representing the best fit to a large number of energies computed with a quantum mechanical ab initio technique. The complex considered there (of 37 atoms and with the chemical formula C10H18O8P) is repesentative of deoxyribonucleic acids. In this paper we apply our potential to evaluating the intramolecular energies of the 39‐atom complex C10H18O10P, representative of the ribonucleic acids. The potential energies for the internal rotations (considered independent from one another) and the energy maps for rotations about consecutive bonds of the backbone chain are critically compared, both with those obtained for the deoxy system and with those obtained from different theoretical approaches as available from literature. It is shown that, at least for certain combinations of the internal rotation angles, the choice of the starting geometry for the sugarphosphate–sugar molecule (bond lengths and valence angles) strongly affects the value of the computed energy. If a proper geometry is used, very low energies are predicted by our potential in correspondence of the sets of torsional angles found in various RNAs by x‐ray crystallography.
Unperturbed dimensions of crosslinked histones evaluated using random‐flight statistics and rotational isomeric state theory
Authors: Mattice Wayne L.
Published: December 2004

Unperturbed dimensions have been computed via rotational isomeric state theory for approximately 700 dimers obtained from histones 2A, 2B, and 4. Dimers result from a crosslink joining either lysyl or tyrosyl residues in different histones. Sets of statistical weights were chosen that yield either a low helicity or a helical content near 40%. These extremes correspond to helicities of histones in the commonly used acid/urea and sodium dodecyl sulfate systems, respectively. Many features of the rotational isomeric state results can be sucessfully reproduced by much simpler expressions based on random‐flight statistics. For example, the two methods are about equally effective in predicting how the radius of gyration of a given type of crosslinked dimer should vary from that of the analogous linear polypeptide chain. This result is in marked contrast to that attained using crosslinked, partially helical homopolypeptides. The unexpected success of random‐flight statistics with partially helical crosslinked histones is due to the suppression of long helical segments by helix‐breaking amino acid residues. Random‐flight statistics should be applicable to other crosslinked, partially helical proteins if their amino acid sequences contain the usual representation of helix‐breaking amino acid residues.
Phase transitions of the starch–water system
Authors: Donovan John W.
Published: December 2004

When purified potato starch granules are heated in the presence of limited amounts of water (less than 1.5 H2O: starch, w/w), two endothermic transitions are observed by differential scanning calorimetry. The lower temperature endotherm is always observed at a fixed temperature, 66°C; it is the only endotherm observed when excess water is present. The higher temperature endotherm is observed at increasing temperatures as the water content is decreased. The size of this endotherm decreases with water content. The appearance of the higher temperature endotherm allows the determination of the stoichiometry for full hydration of starch, 14 H2O/hexose unit. The shift of the higher temperature endotherm is interpreted as the lowering of the melting point of starch crystallites by solvent water.
Density‐gradient‐sedimentation velocity of solvated macromolecules: Theoretical considerations about the buoyancy factor
Authors: Nieuwenhuysen Paul
Published: December 2004

The solvation of macromolecules lowers their sedimentation velocity in a density gradient. Some consequences of this effect are pointed out. Overlooking the solvation results in the understimation of the standard sedimentation coefficient of the macromolecules. (The error increases with partial specific volume, solvation, and the density in the gradient.) The construction of an isokinetic density gradient also requires that solvation be taken into account. This can be done when the solvation parameter, relevant in this context, is known.
Changes in the refractive index ellipsoid isotropies, symmetric anisotropies, and depolarization ratios of potassium hyaluronate solutions as a function of pH
Authors: Barrett T. W.
Published: December 2004

A new method is presented for studying the tertiary and possibly the secondary structure of a biopolymer, which is applied to the pH‐dependent structural transition of potassium hyaluronate solutions. The method involves a new application of Dirac dispersion theory polarization dependence measures to isotropic and anisotropic components of the refractive index ellipsoid. Changes in the dipole moment may also be observed by this method. The pH‐induced changes in viscosity and optical properties of hyaluronic acid previously reported appear to be dependent on changes in secondary and tertiary structure.
4‐Phenoxy‐3,5‐dinitrobenzoylpolyethyleneglycol: Reversible attachment of cysteine‐containing polypeptides to polymers in aqueous solutions
Authors: Glass John D. , Silver Lester , Sondheimer James , Pande Chandra S. , Coderre Jeffrey
Published: December 2004

Polyethyleneglycol of molecular weight 6000 was treated with 4‐phenoxy‐3,5‐dinitrobenzoyl chloride in warm toluene. The product of this reaction is a white crystalline solid containing 0.1–0.2 mmol of labile phenoxy groups per gram of polymer derivative. In aqueous buffers of pH 7, the phenoxydinitrobenzoyl polymer reacts rapidly with side‐chain sulfhydryl groups of cysteine, but very slowly with other functional groups found in polypeptides, yielding peptide‐polymer compounds in which the peptide and polymer are linked by a thiol‐sensitive dinitrophenylene bridge. Both small synthetic peptides and the B‐chain of bovine insulin thus linked to polyethylene glycol are soluble in water and in some organic solvents. An arginine‐containing peptide bound to the polymer was hydrolyzed by trypsin at the arginyl bond, indicating that the linear polyethyleneglycol support does not restrict access of enzymes to bound peptides. Release of peptides from the polymer is rapidly accomplished by treatment with thiols at pH 7 in aqueous solutions.
Circular dichroism of helical polynucleotides calculated by the linear response method
Authors: Redmann Stephen M. , Rhodes William
Published: December 2004

Linear response theory in the decorrelation or random‐phase approximation is used to calculate the absorption and CD spectra of model helical polymers, including single‐stranded polyadenylic acid. The method, which makes use of infinite polymer selection rules for the linear response tensor, has the advantages that (1) only a few three‐dimensional matrices need be inverted; (2) spectral band shapes of the polymer arise naturally from those of the monomer, as well as from the geometry‐dependent interactions in the helix; and (3) the spectral dependence on geometrical factors of the helix is made transparent. It is found that the structure of the polymer CD spectrum depends critically on monomer bandshape. An asymmetric CD spectrum, similar to some experimental spectra, arises from either a Gaussian or a composite monomer band. Single‐stranded polyadenylic acid spectra are sensitive to helix geometry in the region 200–240 nm, in reasonable agreement with experimental spectra. This sensitivity arises from the 207‐nm monomer transition, and the results suggest that this region of the spectrum should be more fully exploited as a tool for helix geometry studies.
Infrared and Raman study in the solid state of fully protected, monodispersed homooligopeptides of L‐valine, L‐isoleucine, and L‐phenylalanine
Authors: Baron M. H. , De Loze C. , Toniolo C. , Fasman G. D.
Published: December 2004

An ir‐absorption and Raman‐scattering study, in the solid state, has been carried out on monodispersed, N‐ and C‐protected homooligopeptides (number of residues, n, from 2 to 7) of L‐valine, L‐isoleucine, and L‐phenylalanine. The amide I, II, III, V, and vNH regions have been examined. Some deuterated (ND) samples have been examined to complete the assignments. L‐Phenylalanine dipeptide displays spectral characteristics compatible with the parallel β‐structure; L‐isoleucine and L‐valine dipeptides are probably in a distorted structure. A mixture of parallel and antiparallel extended chains cannot be excluded for the peptides with n = 3. In the amide I region the spectra of peptides with n ≥ 4 show the existence of the β‐conformation. The problem of chain orientation within the pleated‐sheet structure is discussed on the basis of a recent theoretical treatment of vibrational interactions of the amide I mode.
Crystal structure of putrescine diphosphate: A model system for amine‐nucleic acid interactions
Authors: Woo Nancy H. , Seeman Nadrian C. , Rich Alexander
Published: December 2004

The three‐dimensional structure of putrescine diphosphate has been solved by x‐ray diffraction analysis. The structure reveals the detailed interaction between the amino groups of putrescine and the phosphate residues in which hydrogen bonding and electrostatic forces play a predominant role. The structure serves as a useful model for understanding the interaction of amines with nucleic acids both in a sequence‐specific and non‐sequence‐specific fashion. In particular, a model is proposed for the interaction of the E‐amino group of lysine with regions of DNA containing adenine–thymine sequences.
Stereochemical studies on cyclic peptides. IX. Conformational studies on cyclic tetrapeptides containing alternating cis and trans peptide units
Authors: Manjula G. , Ramakrishnan C.
Published: December 2004

Conformational analyses of cyclic tetrapeptides consisting of alternating cis and trans peptide units have been made using contact criteria and energy calculations. This study has been restricted to those structures having a symmetry element in the backbone ring, such as a twofold axis (d) or a center of inversion (i). There are five main results. (1) There are two distinct types of conformations, which are stereochemically favorable corresponding to each of twofold and inversion‐symmetrical structures, designated as d1, d2 (for twofold symmetrical) and i1, i2 (for inversion‐symmetrical). Among these, the i1 type has the lowest energy when glycyl residues occur at all four α‐carbon atoms. (2) With the glycyl residue at all four α‐carbon atoms, methyl substitution at the cis peptide nitrogen atoms is possible in all the four types, whereas the substitution at trans peptide nitrogen atoms is possible only for the i1 type. Thus only in the i1 type can all the nitrogen atoms be methylated simultaneously. The conformation of the molecule in the crystal structure of cyclotetrasarcosyl belongs to the i1 type. (3) When alanyl residues occur at all four α‐carbon atoms, the possible symmetrical type is dependent on the enantiomorphic form and the actual sequence of the alanyl residues. (4) The methyl substitution at peptide nitrogen atoms for cyclic tetrapeptides having alanyl residues causes more stereochemical restriction in the allowed conformations than with glycyl residues. (5) The prolyl residue can be incorporated favorably at the cis‐trans junction of both d and i types of structures. The results of the present study are compared with the data on cyclic tetrapeptides available from the crystal structure and nmr studies. The results show an overall agreement both regarding the type of symmetry and the conformational parameters.
Kinetic studies of the helix–coil transition in aqueous solutions of poly(L‐lysine)
Authors: Inoue S. , Sano T. , Yakabe Y. , Ushio H. , Yasunaga T.
Published: December 2004

The rate of conformational change of aqueous poly(α‐L‐lysine) solutions was measured using the electric field pulse relaxation method with conductivity detection. The relaxation time as a function of pH exhibits two maxima. One is assigned to a proton transfer reaction and the other to the helix–coil conformational transition. The helix nucleation parameter and the maximum relaxation time yield the rate constant of helix growth process (kF) according to Schwarz's kinetic theory as kF = 2 × 107 sec−1, which is comparable to that of the poly(glutamic acid) solution. The thermodynamic parameters of the helix growth process are compared with those of poly(glutamic acid).
Conformational characteristics of the trinucleoside diphosphate d(ApApA) from energy‐minimization studies
Authors: Thiyagarajan P. , Ponnuswamy P. K.
Published: December 2004

Energy‐minimization studies were carried out on the trinucleoside diphosphate d(ApApA). The potential energy contributions from nonbonded, electrostatic, hydrogen‐bonding, and torsional interactions were minimized by treating the 13 relevant dihedral angles as simultaneous variables. For the C(3′)‐endo trimer, 14 low‐energy conformations are within 10 kcal/mol above the lowest energy found, compared to only 3 in the case of the C(2′)‐endo trimer. This result shows the flexible character of the C(3′)‐endo unit. The hairpin‐type, loop‐promoting conformer with (ω′,ω) = (101°, 59°) was found to be the most favored structure at the 3′‐terminus of d(ApApA).

The predicted U‐ and L‐type bend conformers were found to lie within 5 kcal/mol, compared to the lowest energy B‐DNA structure. The A‐DNA and Watson‐Crick DNA types of helical conformers also lie within very small energy barriers. The phosphate group at the 5′‐end of the nucleotide residue has a definite influence on the base of the corresponding nucleotide, keeping it in the normal anti‐region, and hence on the base‐stacking property. The results are compared with the presently available experimental data, mainly with the tRNAPhe crystal.
Thermal denaturation of chromatin and lysine copolymer–DNA complexes. Effects of ethylene glycol
Authors: Schwartz Arnold M. , Fasman Gerald D.
Published: December 2004

Chromatin was thermally denatured in the presence and absence of 1M ethylene glycol using a technique whereby both the hyperchromism and ellipticity are monitored simultaneously. Model complexes containing poly(L‐Lys) or poly(L‐Lys, L‐Ala, Gly) and DNA were similarly melted in order to assist in interpreting the chromatin results. In both cases a general pattern emerged whereby ethylene glycol perturbed the resultant melting profile, showing increased hyperchromicity, ellipticity, and premelt slope. In addition, ethylene glycol destabilizes and reduces the high melting region of polypeptide‐bound DNA and the extent of higher ordered structure in model complexes and chromatin. These results emphasize the importance of hydrophobic forces in polypeptide–polypeptide and polypeptide–DNA interactions.
Quasielastic light‐scattering studies on human fibrinogen and fibrin. I. Fibrinogen
Authors: Palmer G. R. , Fritz O. G. , Hallett F. R.
Published: December 2004

A quasielastic light‐scattering system has been constructed to study human fibrinogen. The first phase of the investigation was an attempt to clarify the shape of the firbinogen molecule using diffusion methods. The translational diffusion coefficient was measured as 2.04 ± 0.09 × 10−7 cm2 sec−1. Aggregation is suggested as the reason for a lower value previously obtained using this technique. Diffusion indicated the molecule was rigid and did not dissociate at low concentration, low ionic strength, or 37°C. Thermal denaturation was observed at 40°C. At 3°C, a second thermal instability was discovered.
Quasielastic light‐scattering studies on human fibrinogen and fibrin. II. Fibrin polymerization
Authors: Palmer G. R. , Fritz O. G.
Published: December 2004

The shape of fibrin intermediate polymers as well as the rate of fibrinogen polymerization was studied using diffusion measured by quasielastic light scattering. After their length distribution was narrowed by gel filtration, the polymers yielded translational and rotational diffusion coefficients of 0.37 ± 0.05 × 10−7 cm2 sec−1 and 142 ± 32 sec−1, respectively. Theoretical considerations indicated the polymers to be rigid rods. The rate of polymerization of fibrinogen monitored by diffusion paralleled that provided by simulataneous intensity measurements. Both monitors indicated polymerization occurs most rapidly at 30°C.
Hemoglobin aggregation in oxygenated sickle cells studied by carbon‐13 rotating frame spin–lattice relaxation in the presence of an off‐resonance radiofrequency field
Authors: James Thomas L. , Matthews Roberta , Matson Gerald B.
Published: December 2004

Evidence is presented which shows that hemoglobin S in sickle cells has a tendency to aggregate even in the oxygenated state. The basis for that conclusion is derived from 13C‐nmr rotating‐frame spin–lattice relaxation studies in the presence of an off‐resonance radiofrequency field in which the carbonyl resonances of hemoglobins in erythrocytes are examined. The experiments indicate that the rotational correlation time of hemoglobin S in oxygenated sickle cells at 38°C is 130 nsec compared to a value of 95 nsec for hemoglobin A in normal erythrocytes at the same temperature and the same mean cell hemoglobin content.
Comparisons between oriented film and solution tertiary structure of various nucleic acids
Authors: Priore Douglas R. C. , Allen Fritz S.
Published: December 2004

We have considered whether or not the tertiary structure of a biomolecule is the same in a crystal (or an oriented film) as it is in solution. A methodology has been developed for comparing polarized absorption spectra obtained from a solid‐state sample with those obtained from an oriented solute to further resolve this question. An electric dichroism instrument built in our laboratory was used to measure the solution dichroism signal which, along with the ordinary solution uv absorption spectra, yields polarized absorption spectra in the directions parallel and perpendicular to the applied electric field. These were then compared to polarized absorption data from oriented films of nucleic acids to determine whether the two sets of data could be rotated into coincidence. This rotation was accomplished using a computer program based on a nonlinear programming method. Four nucleic acids were studied and the film and solution data for three of these were found to be equivalent, requiring rotation through an angle of 3°−20°, depending on film humidity, to bring them into coincidence. For the fourth sample we were unable, perhaps because of signal‐to‐noise ratio limitations, to find a correlation. Flow dichroism and electric dichroism data were also found to be quite similar. Thus it is clear that the induced dipole moment is along the helical axis and that the physical, hydrodynamical, and electrical axes of the nucleic acid molecules are equivalent.
Geometry of experimentally observed RNA residues in tRNA and dinucleoside monophosphates: The effect of small variations in the backbone angles
Authors: Hingerty B.
Published: December 2004

The polymerization of various experimentally observed conformers of RNA from tRNA and some dinucleoside monophosphates have been examined with a program that computes the basic helix parameters directly from the six backbone torsion angles ω′, ϕ′, ψ′, ψ, ϕ, ω to give n (= 360/θ), the number of residues per turn; h, the rise per residue; and r, the radius of the phosphate atoms from the helix axis. The single‐stranded regions of tRNA that have A‐form residues have a notably lower value of n than the double‐stranded regions. The G‐U “wobble” base pair is shown to be an energetically strained left‐handed form. The A‐form dinucleoside monophosphates also have a low value of n. A model of UpAl polymerized as a fourfold left‐handed helix with the bases on the outside and phosphates on the inside is investigated for its sharp 90° turn angle characteristics. UpA2 cannot be polymerized due to a low values of h (1.31 Å) and r (2.72 Å), which cause steric hindering. An eightfold model of poly(rA) is discussed as are the nonhelical residues of tRNA. Finally, the effects of small changes in dihedral angles and bond lengths and angles on the helical parameters are investigated and discussed by way of explaining this behavior.
Melting curves, denaturation maps, and genetic map of ϕX174: Their relations and applications
Authors: Tong B. Y. , Battersby Stephen J.
Published: December 2004

In this paper we analyze theoretically the observable details of the differential melting curves (DMC) and the denaturation maps (DM) of a DNA. With the help of a mathematical model, we explore their implications, their relation with each other and with the genetic map of the molecule, and discuss possible future applications. ϕX174 is used as the example, since its sequence and genetic map are available. We find that each gene section of ϕX174 has a characteristic DMC. A reconstruction scheme to get the DMC of a whole piece from those of its constituent genes is shown to be fairly successuful. The relations between the melting curve and the denaturation maps are clarified. We observe that nearly always, the beginning and end of a gene melt at lower temperatures. The sharp features in the DM indicate that despite the long‐range cooperative interactions, the DM do reflect the local sequence effect. Denaturation maps (theoretical) of ϕX174 and SV40 are presented. From available data of other authors, we estimate that the dependence of the melting temperature tm on GC, the fraction of (G+C)‐content, and on x, the ionic concentration in fractions of the standard saline citrate solution, can be expressed as tm(x, GC) = ‐5.2 (log x)GC + 18.4 log x + 41.0GC + 69.4. The first two coefficients are less certain.
Theoretical drug design: 6‐Azauridine‐5′‐phosphate—its X‐ray crystal structure, potential energy maps, and mechanism of inhibition of orotidine‐5′‐phosphate decarboxylase
Authors: Saenger Wolfram , Suck Dietrich , Knappenberg Marianne , Dirkx Jaques
Published: December 2004

The cytostatic drug 6‐azauridine is converted in vivo to 6‐azauridine‐5′‐phosphate (z6Urd‐5′‐P), which blocks the enzyme orotidine‐5′‐phosphate decarboxylase (Ord‐5′‐Pdecase) and therefore inhibits the de novo production of uridine‐5′‐phosphate (Urd‐5′‐P). In order to relate the structure and function of z6Urd‐5′‐P, it was crystallized as trihydrate, space group P212121 with a = 20.615 Å, b = 6.265 Å, c = 11.881 Å, and the structure established by Patterson methods. Atomic parameters were refined by full‐matrix least‐squares methods to R = 0.066 using 1638 counter measured x‐ray data. The ribose of z6Urd‐5′‐P is in a twisted C(2′)‐exo, C(3′)endo conformation, the heterocycle is in extreme anti position with angle N(6)‐N(1)‐C(1′)‐O(4′) at 86.3°, and the orientation about the C(4′)‐C(5′) bond is gauche, trans in contrast to gauche, gauche found for all the other 5′‐ribonucleotides. Conformational energy calculations show that z6Urd‐5′‐P may adopt an extreme anti conformation not allowed to Urd‐5′‐P, and they also predict the same unusual trans, gauche conformation about the C(4′)‐C(5′) bond in orotidine‐5′‐phosphate (Ord‐5′‐P) and in z6Urd‐5′‐P, which renders the distances O(2)…O(5′) in z6Urd‐5′‐P and O(7)…O(5′) in Ord‐5′‐P comparable. On this basis the function of z6Urd‐5′‐P as an Ord‐5′‐Pdecase inhibitor can be explained as being due to its structural similarity with the substrate Ord‐5′‐P and further clarifies the inhibitory action of 5′‐nucleotides bearing the heterocycles oxipurinol, xanthine, or allopurinol [J. A. Fyfe, R. L. Miller, and T. A. Krenitsky, J. Biol. Chem. 248, 3801 (1973)]. With this in mind, new inhibitors for Ord‐5′‐Pdecase may be designed.
Kinetics of nucleic acid–large ligand interactions: Exact Monte Carlo treatment and limitingl cases of reversible binding
Authors: Epstein Irving R.
Published: December 2004

Many ligands, including basic polypeptides, histones, and other proteins bind nonspecifically to DNA in such a way as to render unavailable for further binding several contiguous sites (generally bases or base pairs). An accurate description of the kinetics of such large ligand binding requires a more complex theoretical analysis than does the study of the binding of small ligands to DNA. An exact analytical solution of the problem does not appear feasible. Instead, a Monte Carlo approach is developed which provides an essentially exact numerical solution by simulating the binding experiment using a model one‐dimensional lattice to represent the DNA molecule. For the limiting cases of totally irreversible binding and of instantaneous redistribution of bound ligands along the lattice, relatively simple equations can be written and solved for the binding kinetics. These solutions and their realms of applicability are discussed in some detail.
Protonation and quaternization of 1, N6‐ethenoadenosine: What are the species responsible for the fluorescence of 1, N6‐ethenoadenosine?
Authors: Inoue Yasuo , Kuramochi Takao , Imakubo Keiichi
Published: December 2004

Methylation of 1,N6‐ethenoadenosine (εAdo) gives a mixture of N1‐ and N9‐quaternized methyl‐3‐β‐D‐ribofuranosylimidazo[2,1‐i] purinium salts (m1εAdo+ and m9εAdo+, respectively). The ratio of the two forms of the protonated εAdo [H1εAdo+]/[H9εAdo+] has been estimated to be approximately 0.10 by comparing the uv absorption spectra of the protonated species of εAdo and the two nontautomerizable model compounds. In relation to a study on the protonation effect on the fluorescence of εAdo, we have now determined the effect of quaternization on the fluorescence spectra at 293 and 77 K. We have found that m1εAdo+ and m9εAdo+ are both fluorescent, and the high degree of coincidence between the fluorescence spectra of εAdo and m1εAdo+ at pH 7 is noted. The m1εAdo+ singlet form is a more efficient fluorescer than the m9εAdo+ ion at room temperature (quantum yields of 0.43 and 0.11, respectively). All the results which are presented in this paper are consistent with the picture that there exist more than one species responsible for the fluorescence of εAdo, depending on the environment of the molecule in aqueous solution (temperature and pH of solvent).
Conformational studies of BSA using laser light scattering
Authors: Harvey John D. , Geddes Robert , Wills Peter R.
Published: December 2004

The usefulness of laser light scattering as a technique for determining protein conformation has been investigated by studying the self‐association and drug binding of bovine serum albumin (BSA). The diffusion coefficients of BSA monomers and dimers have been measured and the ratio of these two quantities indicates that in the dimer, the subunit separation is 2.2 times the monomeric hydrodynamic radius. The binding of salicylate to BSA causes an increase in its diffusion coefficient corresponding to a reduction in the frictional drag of the solvent on the protein molecules. It has been found that data obtained using laser light scattering may be interpreted confidently only when proper care has been taken in sample preparation and the scattered intensity autocorrelation function has been appropriately analyzed.
On the possibility of true phase transition in heterogeneous DNA during thermal denaturation under conditions close to equal stability of A+T and G+C pairs
Authors: Blagoi Yu. P. , Sorokin V. A. , Valkeev V. A. , Gladchenko G. O. , Khomenko S. A. , Galkin V. L.
Published: December 2004

The DNA helix–coil transition has been studied in the presence of high concentrations of manganese ions (about 10−3M), which corresponds to the conditions close to equal stability of the A+T and G+C pairs, at the ionic strengths of 10−1, 10−2, and 1.6 × 10−3M Na+. With the Mn2+ ion effect, the transition range is significantly reduced to not more than 0.2°C at 1.2 × 10−3M Mn2+ and 1.6 × 10−3M Na+. The melting curves display a sharp kink at the end of the helix–coil transition, which is interpreted as an indication of the second‐order phase transition. It is shown that the melting curves obtained can be approximated by a simple analytical expression 1 – θ = exp[–a(tc ‐ t)], where θ is the DNA helix fraction, tc is the phase transition temperature, and a is an empirical parameter characterizing the breadth of the melting range and responsible for the magnitude of a jump of the helicity derivative with respect to the temperature at the phase transition point.
Quasielastic light scattering from solutions of filamentous viruses. II. Comparison between theories and experiments
Authors: Loh Eugene
Published: December 2004

We have compared four theoretical effects of rodlike macromolecules with the fast components, i.e., components other than translational diffusion, of our experimental data, which are presented as amplitude autocorrelation functions of electric field scattered from dilute solutions of monodisperse rodlike viruses with lengths from 3300 Å for tobacco mosaic virus to 20,000 Å for Pf1. The four effects are (1) the optic anisotropy treated by Aragón and Pecora, (2) coupled translational–rotational diffusion due to anisotropy in translational mobility recently reformulated by Gierke, (3) anisotropic rotational diffusion with respect to the direction of translational displacement first discussed by Berne and Pecora, and (4) the bending mode of a rod by Fujime and Maruyama. We show that both the first and second effects are required to explain the enhancement of amplitude of the translational diffusion at the expense of fast components. The experimental decay rates of the fast component exceed that of the rotational diffusions. In order to explain the excessive decay rate in the fast component, we need to include a minute amount (∼1%) of bending mode of rodlike viruses, especially in longer viruses such as M13 and Pf1.
Enthalpy of Mixing Glycosaminoglycans with Aqueous NaCl
Authors: Cleland Robert L.
Published: December 2004

Calorimetric measurements of ΔH, the enthalpy of mixing with NaCl solutions per mole of polymer charge equivalent, have been made for the sodium salts of hyaluronate, chondroitin 4‐sulfate, and chondroitin over the range msf = 0–0.5 (where msf is final NaCl molality); corrections were made for the enthalpy of dilution of NaCl. Values of ΔH for the range msf = 0–0.1 agree reasonably well with a theoretical estimate from the infinite line charge theory of polyelectrolytes. In order to apply the latter, calculations of several average short‐range atomic spacings in hyaluronate were made from a statistical model with use of energy parameters which provide a good fit to experimental values of unperturbed dimensions.
Motion of myosin fragments during actin‐activated ATPase: fluorescence correlation spectroscopy study
Authors: Borejdo Julian
Published: December 2004

The rates of the translational motion of myosin fragments, heavy meromyosin (HMM), and heavy meromyosin subfragment‐1 (HMM S‐1) were measured during actin‐activated ATPase reaction by the method of fluorescence correlation spectroscopy. This technique monitors the random fluctuations in the concentration of fluorescent molecules in an open volume which result from the translational diffusion of the molecular species under observation. The statistical behavior of the fluctuations is represented in the form of the autocorrelation function, which is related to the translational diffusion coefficient of the fluorescent molecules. The translational motion of fluorescently labeled myosin fragments was progressively slowed down after additions of increasing amounts of actin in the presence of excess MgATP. When these results are interpreted according to a simple binding scheme, the extent of the retardation can be used to obtain the apparent association constant for binding of S‐1 and HMM to actin in the presence of MgATP. In 0.1M KCl and at 23°C, the apparent association constants were determined as KappHMM = 2.2 × 104M−1 and KappS‐1 = 8.8 × 103 for HMM and S‐1, respectively.
Denaturation of cobalt–carbonic anhydrase B from bovine erythrocyte
Authors: McCoy Leslie F. , Wong Kin‐Ping
Published: December 2004

We have attempted to elucidate the mechanism of the acquisition of active‐site conformation in enzymes by studying the unfolding and refolding of Co(II) carbonic anhydrase. This enzyme possesses characteristic absorption and CD spectra in the visible region, which reflect primarily the local conformational environment of the active site where the Co(II) is bound. The conformation of the cobalt–protein is found to be almost the same as the native zinc–protein. It has lower thermal stability and unfolds at a lower concentration of guanidinium chloride, even though a single‐phase transition is observed in these denaturations. The unfolding to the random‐coiled protein was followed by various spectroscopic methods which reflect different conformational changes. The results show that separable stages of unfolding are observable for the cobalt–protein. It appears that the collapse of the active‐site conformation, as followed by changes in visible absorption and CD parameters, occurs immediately after the loosening of the molecule. This is followed by the exposure of buried aromatic residues and the unraveling of the backbone secondary structure. However, renaturation of the cobalt–protein results in an inactive protein which has spectroscopic properties significantly different from those of the native cobalt–protein.
Kinetic analysis of local structure formations in protein folding
Authors: Kanehisa Minoru I. , Tsong Tian Yow
Published: December 2004

The protein folding process is described by a cluster model based on the assumption that local structures or clusters are formed at an early stage in different regions of the polypeptide chain. Possible local structural elements in a globular protein are helices, bends, and hydrophobic cores whose formation is presumably determined by the interaction with the environment. Thus the tendency of local structure formation is expressed by a surface free energy of the cluster, which is assigned to the interface between the cluster and its environment. The probability of finding the chain of N residues with k clusters and m residues in the cluster is represented by a cluster distribution map. The cluster model exhibits a distinct two‐state‐like equilibrium transition, which can be seen on this map as well‐separated native and denatured populations at the midpoint of the transition. The native population is localized at k ≈ 1 and m ≈ N, while the position of the denatured population can vary significantly depending on the surface free energy of the cluster. If the surface free energy is strong, the denatured population is localized near k = 0 and m = 0. On the other hand, if the surface free energy is weak, the denatured population is localized at high k and m values. The dynamics of the cluster model are treated as a stochastic process involving the transition from a state (k,m) to one of its six neighbors. The transition probability for each transition is determined by the free energy difference between two states; thus no activation process is assumed. However, the conversion of the two macrostates, native and denatured populations, involves the free energy activation due to the cooperative interaction of the macrosystem. The dynamics are analyzed by following the time evolution of the population profile on the cluster distribution map. Kinetic schemes are proposed to describe the multistep mechanism of protein folding and unfolding.
Synthesis of sequential polypeptides containing L‐β‐3,4‐dihydroxyphenyl‐α‐alanine (DOPA) and L‐glutamic acid
Authors: Yamamoto Hiroyuki , Hayakawa Tadao
Published: December 2004

Sequential polypeptides with the repeating units L‐glutamyl‐L‐DOPA, L‐DOPA‐L‐glutamyl‐L‐DOPA, L‐glutamyl‐L‐glutamyl‐L‐DOPA, L‐DOPA‐L‐DOPA‐L‐glutamyl‐L‐DOPA, and L‐glutamyl‐L‐glutamyl‐L‐glutamyl‐L‐DOPA have been synthesized by solution polymerization of the p‐nitrophenyl esters of the corresponding di‐, tri‐, and tetrapeptides. The O, O′‐dimethyl and γ‐methyl groups were used to protect side chains of L‐DOPA and L‐glutamic acid. The monomers for the polytripeptides and polytetrapeptides were prepared by stepwise elongation, using the dicyclohexylcarbodiimide coupling method. Moderately high molecular weight sequential polypeptides were obtained. The protected groups of the side chain were removed simultaneously by use of boron tribromide in chloroform. Trimethylphosphate‐soluble sequential polypeptides containing L‐DOPA were obtained.
Polyxanthylic acid: structures of the ordered forms
Authors: Roy Kunal B. , Frazier Joe , Miles H. Todd
Published: December 2004

We present evidence for structures of two ordered forms of polyxanthylic acid based on ir spectroscopy, pH titrations, and thermal transitions. Over the pH range ∼6–9.5, the structure is a four‐stranded helix with alkali metal ions specifically complexed in the central channel. These internal counterions stabilize the structure by complexing with carbonyl oxygens and by partial screening of electrostatic repulsion caused by ionization of the xanthine residues in this pH range. Below pH 5, the structure is quite different and much more stable. Our data are consistent with a six‐stranded helix in which both carbonyl oxygens and both NH protons are hydrogen bonded.
Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of β‐turns
Authors: Krimm S. , Bandekar Jagdeesh
Published: December 2004

The normal modes have been calculated for β‐turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β‐turn frequencies can overlap with those of the α‐helix and β‐sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β‐turns are predicted at significantly higher frequencies than those of α‐helix and β‐sheet structures, and this region therefore provides the best possibility of identifying β‐turn structures. Amide V frequencies of β‐turns may also be distinctive for such structures.
DNA sequencing and helix–coil transition. III. DNA sequencing
Authors: Azbel M. Ya.
Published: December 2004

We show that the fine oscillatory structure of the DNA melting curve can be used to determine explicitly the nucleotide composition and the order of certain domains within the DNA. If DNA is specifically fragmented, the order of fragments can be learned directly from a comparison of the differential melting curves of the nonfragmented and fragmented DNA. The indicated information may complement exact methods of DNA sequencing. The proposed analysis is applied to bacteriophage ϕX‐174, whose melting curve is known. Compared to the known ϕX‐174 DNA sequence, the results of the analysis are found to be very accurate.
Viscoelastic properties of rigid and semiflexible particles in solution. II. Application to rodlike molecules such as poly(γ‐benzyl‐L‐glutamate) in the helical state
Authors: Iwata Kazuyoshi
Published: December 2004

The theory presented in Part I [Iwata, K. (1979) J. Chem. Phys. 71, 931–943] is applied to calculation of complex viscosities of the following three models which are designed to simulate various motions of polypeptides in helicogenic solvents. Model I is composed of identical spheres which are arranged regularly along a Kratky‐Porod chain and is adopted for describing flexural deformation of polypeptide helices. Model II is composed of two kinds of spheres, mobile and immobile, which are arranged in a pillar form with a multilayer structure and is adopted for estimating sidegroup motion of polypeptide helices. The mobile spheres are assumed movable in their individual intramolecular potential field under the influences of hydrodynamic resistance by solvent and of “internal friction” caused by other spheres in the same molecule. When the mobile and immobile spheres are arranged alternatively in a mosaic form (model IIa), the model exhibits a local motion of the side groups. When all the spheres are mobile (model IIb), their motions are correlated with each other through the internal friction.

The complex viscosities of these models are computed and compared with those measured by Ookubo et al. [(1976) Biopolymers 15, 929–949] for poly(γ‐benzyl‐L‐glutamate)‐[Glu(OBzl)]n in m‐cresol. The results are as follows: (1) The dynamic viscosity [η′] of [Glu(OBzl)]n with molecular weight 75,000 is explained well not by model IIa or IIb, but by model I, and the relaxational mode B observed at 760 kHz is assigned to the flexural deformation of the [Glu(OBzl)]n helix. (2) [η′] of [Glu(OBzl)]n with molecular weight 120,000 deviates largely from that predicted by model I; it is therefore deduced that the interruption of the helix becomes predominant between Mr 75,000 and Mr 120,000. (3) The persistence length of [Glu(OBzl)]n in m‐cresol is estimated to be 1600 Å and the flexural rigidity of the helix to be 6.7 × 10−19 dyn cm2 from the relaxation time of mode B. The present estimate of the persistence length is larger than the previous ones (700–1100 Å), which were obtained by neglecting the possibility of helix interruption.
Studies of the collagen fold formation in aqueous solutions of α‐gelatin. II
Authors: Eagland D. , Pilling G.
Published: December 2004

Optical rotation and density studies have been performed as a function of time on solutions of a single‐strand gelatin in salt‐free solutions and in solutions containing sodium bromide, tetramethyl and tetrabutylammonium bromide. The reversion to the collagen fold is shown to be first order in all cases but undergoes a change in magnitude as a function of an aggregation process which occurs at a concentration of approximately 0.1% w/v. The structuring effects of the electrolytes on the solvent are shown to relate to the extent of helix regeneration by the protein, in the presence of the electrolyte. The extent of helix regeneration is also shown to relate to the thickness of the electric double layer surrounding the protein molecule.
Studies on transfer ribonucleic acids and related compounds. XXVI. Circular dichroic properties of cyclic oligoribonucleotides and their linear counterparts
Authors: Markham A. F. , Nakagawa E. , Ohtsuka E. , Ikehara M.
Published: December 2004

The CD spectra of cUpUp, cCpCp, and cGpGp derived from DCC‐catalyzed polymerization of the relevant protected ribonucleoside 3′‐phosphates are described. Similar studies on Up, U > p, and cUp, as well as cUpUpUp and cUpUpUpUp, are presented. The spectral properties of the cyclic oligomers are compared with those of the corresponding linear oligomers with terminal 3′‐phosphates so as to demonstrate that disruption of normal right‐handed base stacking is considerable in these RNA loops.
Chemical synthesis of (1 → 2)‐α‐D‐mannopyranan
Authors: Yamaguchi Hidemasa , Schuerch Conrad
Published: December 2004

The polymerization of 1,2‐anhydro‐3,4,6‐tri‐O‐benzyl‐β‐D‐mannopyranose proceeds in the presence of Lewis acids, cationic coordination catalysts, and strong bases. Debenzylation of the products yields oligomeric saccharides or low polymers. Polymerization in toluene by means of potassium alkoxide complexed with crown ethers leads to essentially stereoregular (1 → 2)‐α‐D‐mannopyranan. The original derivatives have been characterized by optical rotation, viscosity, molecular weight, gel permeation chromatography, and spectrometry. The free polysaccharides have been characterized by optical rotation, molecular weight, and 1H‐ and 13C‐nmr spectrometry and compared to yeast mannan hydrolysate oligomers.
Induction of helicity in polyuridylic acid and polyinosinic acid by silver ions
Authors: Shin Y. A. , Eichhorn G. L.
Published: December 2004

Silver ions binding to poly(U) and poly(I) produce highly ordered multistranded helices under conditions which would otherwise lead to random coils. Evidence for helicity comes from the hypochromicity and high ellipticity generated in the polymers by Ag+ binding, as well as from x‐ray studies and from the cooperativity of the Ag+ complexing reaction. Continuous variation studies show that both polymers form 1:1 and 2:1 polymer–Ag+ complexes. Low pH favors the 1:1 complex with poly(U) and the 2:1 complex with poly(I); the reverse is true at high pH. Ag+ binding and proton‐release experiments make it clear that at low pH, unprotonated electron‐donor groups are complexed preferentially, but that at high pH, Ag+ readily displaces H+ from protonated groups. In poly(I) the unprotonated donor is N(7), leading at low pH to a 2:1 complex containing N(7)‐Ag‐N(7) bonds; at high pH, proton release from N(1) leads to a 1:1 complex containing N(1)‐Ag‐O bonds. In poly(U) there is no unprotonated donor; the low‐pH 1:1 complex involves deprotonation of only one N(3) per bound Ag+, leading to N3‐Ag‐O bonding, while high pH causes deprotonation of two N(3) per Ag+ and a 2:1 N(3)‐Ag‐N(3) complex. Thus silver ions react with the nucleotide bases in chemically predictable ways, and the formation of different Ag–nucleotide bonds leads to different multiple‐helix structures.