bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unperturbed dimensions of crosslinked histones evaluated using random‐flight statistics and rotational isomeric state theory
Authors: Mattice Wayne L. 
Published: December 2004

AbstractUnperturbed 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

AbstractWhen 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

AbstractThe 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

AbstractA 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

AbstractPolyethyleneglycol 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

AbstractLinear 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

AbstractAn 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

AbstractThe 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

AbstractConformational 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

AbstractThe 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

AbstractEnergy‐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

AbstractChromatin 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

AbstractA 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

AbstractThe 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

AbstractEvidence 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

AbstractWe 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

AbstractThe 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

AbstractIn 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

AbstractThe 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

AbstractMany 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.