bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of molecules with nucleic acids. II. Two pairs of families of intercalation sites, unwinding angles, and the neighbor‐exclusion principle
Authors: Miller Kenneth J. , Pycior Joseph F. 
Published: December 2004

AbstractIntercalation‐site geometries are generated for a tetramer duplex extracted from B‐DNA. Glycosidic angles and puckers of the deoxyribose sugar groups bonded to base pairs BP1 and BP4, namely, those at either end of the tetramer duplex, are assumed to be those of B‐DNA to insure continuity. All possible geometrical conformations for combinations of C(2′)‐endo, C(3′)‐endo, C(2′)‐exo, and C(3′)‐exo sugar puckers are determined for the tetranucleotide backbone. Those with minimum energy are selected as candidates for intercalation sites. Calculations reveal two pairs of physically meaningful families of intercalation sites which occur in two distinct regions, I and II, of helical angles which orient BP2 relative to BP3 and with the helical axis disjointed between these base pairs. For each site I and II within BP2 and BP3, there are two distinct backbone conformations, A and B, connecting BP3 to BP4 or BP1 to BP2 which do not disrupt backbone conformations connecting BP2 to BP3. Hence two pairs, IA and IB, and IIA and IIB, of intercalation sites exist in which the sugar puckers along the backbone of the tetramer alternate from C(2′)‐endo to C(3′)‐endo on the backbone (5′p3′) connecting BP2 to BP3. The glycosidic angles of the C(3′)‐endo sugar χ3γ are, coincidentally, 80° ± 2° for both conformations γ = A and B connecting BP3 to BP4 along the phosphate backbone (5′p3′). Consistent with the theoretical results, the experimental unwinding angles can be grouped into two categories with absolute values of 18° and 26°. The theoretical unwinding angles for sites IA and IB of 16° and for sites IIA and IIB of 20° occur for a displacement of ‐0.8 Å in the helical axes of BP2 and BP3 and for a 100% G·C composition, with a decrease depending on the amount of A·T base pairs present. Ratios of theoretical unwinding angles of sites I and II, which range from 0.75 to 0.84 for the two principal sites, compare well with the experimental value of 0.71. The theoretical results, in agreement with experimental observation, provide a new interpretation of the nature and conformation of the possible binding sites. Conformations obtained from these studies of intercalation sites in a tetramer duplex are used to rationalize the well‐known neighbor‐exclusion principle. The possibility of violation of this principle is demonstrated by the existence of two families of physically meaningful conformations. Conformations of unconstrained dimer duplexes are also obtained, one of which corresponds to the experimental crystal structure of ethidium–dinucleoside complexes, but these cannot be joined to the B‐DNA structure. Backbone conformations of the tetramer duplex can be constructed until the base‐pair separation reaches 8.25 Å, which may limit the molecules that can intercalate.
Absorption and circular dichroism spectra of methylene blue bound to alginate
Authors: Seely G. R. , Hart R. L. 
Published: December 2004

AbstractThe addition of methylene blue to certain samples of Na alginate produces a complex succession of spectrally distinguishable aggregated (metachromatic) dye species. Three of these species are active in CD; they are interpreted as aggregates of dye, but probably dimers, bound in orientations characteristic of the constituent copolymer blocks of alginate to which they are tentatively assigned. The aggregates compete with divalent metal ions and hydrogen ion for the binding sites of the polymer. Other samples of alginate give a modified succession of aggregated spectral species, which are almost devoid of CD activity. Mild treatment with acid, insufficient for hydrolysis, converts forms of alginate with CD activity into modified forms without it, the absorption spectra of which resemble those of samples originally devoid of activity. It is implied, subject to confirmation, that the chiral properties of the binding sites of the native polysaccharide are diminished or lost by acid treatment during commercial preparation.
Effect of sodium ion on the high‐resolution melting of lambda DNA
Authors: Blake R. D. , Haydock Paul V. 
Published: December 2004

AbstractA series of high‐resolution melting curves were obtained by the continuous direct‐derivative method [Blake, R. D. & Lefoley, S. G. (1978) Biochim. Biophys. Acta 518, 233–246] on lambda DNA (cI857S7 strain) under varying conditions of [Na+]. Examination of the denaturation patterns at close intervals of [Na+] indicates that frequent changes in mechanism occur below 0.04M Na+, while almost none occurs above 0.1M Na+. Changes at low [Na+] generally occur in an abrupt fashion, in most cases within a 3 mM change in [Na+], and in at least one case within 0.6 mM, indicating the balance between alternative mechanisms is frequently quite delicate. These changes involve segments of between 900 and 1500 or more base pairs in length and are therefore not insignificant. Changes at low [Na+] reflect a perturbation of the energetic balance between competing mechanisms by weakly screened long‐range electrostatic forces. Some perturbation probably also arises from variations in the linear charge density of the double helix induced by the proximity of premelted loop segments; however, this contribution cannot be evaluated without a detailed denaturation map.At high [Na+] the mechanism of melting is more conserved, permitting the dependence of subtrasitional melting temperature tm(i) on [Na+] to be examined for almost all 34 ± 2 subtransitions. The G + C composition of segments responsible for each subtransition was determined by a quantitative spectral method. Analysis according to the Manning‐Record expression [Manning, G. (1972) Biopolymers 11, 937–949; Record, M. T., Jr., Anderson, C. F. & Lohman, T. M. (1978) Q. Rev. Biophysics 11, 103–178] relating ΔHm and dtm(i)/d log[Na+] to the fraction of Na+ released during melting, appears to indicate almost 40% more Na+ is bound to the single‐stranded G and/or C residues than to A and T residues. This is consistent with a much shorter mean axial spacing and higher charge density in the former, particularly single‐stranded G residues, which have an extraordinary tendency to stack.
Thermodynamic stability theory for DNA doughnut shapes induced by charge neutralization
Authors: Manning Gerald S. 
Published: December 2004

AbstractA thermodynamic analysis of the bending free energy of DNA, initiated previously, is extended. It was demonstrated that the ionic‐strength dependence of the persistence length of DNA in aqueous NaCl can be understood by postulating (1) a rigid‐rod 60 base‐pair unit and (2) a negative contribution from nonelectrostatic sources to the bending free energy of this unit. On electrostatic neutralization of the phosphate charge, the latter term alone survives, and bending becomes a spontaneous process. In this paper it is demonstrated from a theoretical analysis of the ionic‐strength dependence of the rate of denaturation of DNA that the above statements are restricted in their validity to radii of curvature greater than 170 Å; beyond this limit, the steeply rising repulsive energy of tightly packed atoms dominates the bending free energy. Therefore, spontaneous bending on charge neutralization proceeds up to, but not beyond, this barrier to curvature. It is noted that doughnut forms of DNA induced by binding of cationic spermidine, or mixtures of Mg2+ and polyamines are observed to possess maximum curvatures, corresponding to the radius of the “hole in the middle,” in the range 1/150–1/200 Å.
13C‐1H magnetic double‐resonance study of fetal enamel matrix proteins
Authors: Termine J. D. , Torchia D. A. 
Published: December 2004

AbstractRecently developed 13C‐1H nuclear magnetic double‐resonance techniques have been used to study proteins in the intact fetal enamel matrix. Enamel protein chains undergoing rapid, almost isotropic motion were detected in scalar decoupled 13C‐nmr spectra, while motionally restricted enamel protein chains were principally observed in proton‐enhanced spectra. The latter spectra were obtained using a matched Hartmann‐Hahn contact to transfer polarization from protons to carbons (cross‐polarization). Both mobile and motionally restricted enamel protein chains were observed in dipolar decoupled 13C‐nmr spectra. A comparison of integrated intensities obtained from the scalar decoupled and dipolar decoupled spectra showed that 70% of the fetal enamel protein chains exhibit rapid, nearly isotropic molecular motion (τ ≲ 10−6 sec), while the remaining 30% are rigid or undergo only anisotropic molecular motion.
Influence of double scattering in determination of rotational diffusion coefficients by depolarized dynamic light scattering: Application to the bacteriophages T7 and T4B
Authors: Hopman P. C. , Koopmans G. , Greve J. 
Published: December 2004

AbstractDynamic light scattering experiments were performed on solutions of the bacteriophages T7 and T4B in order to obtain the rotational diffusion coefficients of these phages. Correlation functions were determined from the depolarized intensity scattered in the forward direction. The apparatus used in this study is described in detail. Particular attention is paid to the minimalization of the depolarized intensity due to double scattering. If double scattering cannot be neglected, the correlation function of the depolarized field is the sum of the correlation functions resulting from single and double scattering. It is shown that by correcting for double scattering, it is then possible to obtain the rotational diffusion coefficient of the macromolecules. Although the optical anisotropy of both T4B (retracted fibers) and T7 is very small, the experimental conditions could be chosen in such a way that no depolarized scattering due to double scattering was observed. The measured rotational diffusion coefficients for T4B and T7 are D = 258 ± 12 and 4528 ± 100 sec−1, respectively. These values compare very well with those obtained by electric birefringence experiments.
Physical aging of dry elastin
Authors: Struik L. C. E. , Pezzin G. 
Published: December 2004

AbstractDry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from −20 to +180°C. At each temperature, the small‐strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
Preferred conformations of protected homo‐oligo‐L‐glutamate peptides in CDCl3 and CDCl3/TFA mixtures
Authors: Ribeiro Anthony , Saltman Robert P. , Goodman Murray 
Published: December 2004

AbstractA conformational analysis of protected glutamate homo‐oligopeptides Z‐[Glu(OEt)]n‐OEt (n = 2–7) was carried out in chloroform solution using high‐resolution 1H‐nmr spectroscopy. At dilute peptide concentrations, the backbone NH and α‐CH resonances are well resolved and can be assigned by combining extensive homonuclear decoupling experiments with data for co‐oligopeptide derivatives. The structure of these peptides in solution was then assessed using information from chemical shifts, coupling constants, temperature coefficients, and titration of each oligomer with trifluoroacetic acid (TFA). The di‐ and tripeptides are found to be in disordered forms in deuterochloroform (CDCl3) and CDCl3/TFA mixtures. The tetrapeptide exhibits a folded structure with intramolecular hydrogen bonding at Glu2 in CDCl3 and undergoes a transition to increasingly disordered forms as TFA is added. The pentamer to heptamer show a folded structure with a strong intramolecular hydrogen bond at Glu2 and a weaker hydrogen bond at Glu3, which are disrupted as these peptides go to random coils at high TFA/CDCl3 ratios. In addition, the N‐terminal portions of these glutamate peptides appear to be involved in side chain–main chain interactions. The results support the hypothesis that protected linear homo‐oligopeptides may possess two or more segments of conformation with intramolecular folding preferred near the N‐terminal portion.
Role of aldehydes in collagen fibrillogenesis in vitro
Authors: Brennan Maureen , Davison Peter F. 
Published: December 2004

AbstractThe process of in vitro fibrillogenesis of type I collagen from bovine tendon has been studied with particular attention to the events occurring in the lag phase. From the conditions under which those events can be reversed or stabilized and from the effects of reduction on the length of the lag phase, we conclude that one event is the reaction of aldehydes on the molecules. However, we have been unable to detect the products of these reactions or any physical changes in the solution, so the change most probably involves the inter‐ or intramolecular reaction of a very small fraction of the molecules. In particular, the viscosity appears unchanged in solutions in which nucleation‐promoting structures have been stabilized, and so measurable numbers of polymers are not formed in this process.
Modification of the apparent radius of gyration of cytochrome c by the distribution of counterions in solution
Authors: Borso C. S. , Stamatoff J. B. 
Published: December 2004

AbstractSmall changes in the apparent radius of gyration of native cytochrome c were measured as a function of pH in solutions of 0 and 50 mM ruthenium hexicyanide. The forward scattering was also measured as a function of pH under the same conditions to ascertain the contribution of the Ru ion shell to the forward scattering and concomitantly to the radius of gyration. The forward scattering and small alterations in the radius of gyration were then measured as a function of Ru counterion concentration. These results are then interpreted in terms of the mechanisms which influence the measured apparent radius of gyration. It is shown that the Debye‐Hückel theory of counterion distributions can be used to describe the data in situations where scattering from the bound Ru ions contributes less significantly than scattering from the ion cloud.
Differential equation systems for heat‐loss corrections of isoperibolic microcalorimeters: A computer‐modeling approach
Authors: Martin C. J. , Sreenathan B. R. , Marini M. A. 
Published: December 2004

AbstractThe problem of adequately correcting thermal titration curves for heat losses in isoperibolic microcalorimeters during rapid reactions in small volumes has been examined. With a data‐acquisition system for the simultaneous encoding of changes in heat, pH, and time linked directly to a DEC‐20 computer, various possible mechanisms for heat‐loss corrections were tested using computer‐modeling techniques. Models expressed by series exponential terms, as commonly used in linear pharmacokinetics to describe the time‐course concentration of a drug, proved to be inadequate to reconstruct the “adiabatic” thermal curve, since its apparent magnitude increased with the time taken for its generation. However, models based on mechanisms incorporating at least two heat sinks, one of which can be equated to the surroundings, have proved successful. The differential equations descriptive of the various models examined have rate constants characteristic of the reaction cell and its inserts, the reaction volume, and the calorimeter used. These can be evaluated by a curve‐fitting algorithm (MLAB) using standard thermal‐titration data (the neutralization of HCL with KOH). Once the rate constants are known, the differential equation solver of MLAB is then used to deconvolute any time: heat‐change matrix to that which would obtain in the absence of heat loss (the “adiabatic” state). With an appropriate differential equation model, the magnitude of the corrected heat change is independent of the time taken for its production and so‐called best model(s) have been judged on the basis of Akaike's information criterion. The application of the heat‐loss correction procedure to the thermal titration of chymotrypsinogen is illustrated.
Electric dichroism and birefringence of poly(ribocytidylic acid). I. Optical properties and stability
Authors: Chen Holly Ho , Charney Elliot 
Published: December 2004

AbstractMeasurements of the uv absorption and melting profiles of poly(rC) at low‐salt conditions confirm the existence of a double‐stranded complex at low pH and imply, but do not prove, the structure proposed by Akinrimisi et al. (1963) Biochemistry 2, 340–343. Electric dichroism and birefringence provide additional supporting evidence and indicate that the complex is one in which the bases are tilted considerably from the major molecular axis. The base‐stacking tendency of single‐stranded poly(rC), unlike poly(rA), is found to be insufficient to maintain a rodlike structure; the persistence length of stacked bases in poly(rC) must be very small. The existence of an out‐of‐plane transition in poly(rC) in the vicinity of 300 nm is conclusively demonstrated by both dichroism and birefringence measurements.
Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes
Authors: Poltev V. I. , Milova L. A. , Zhorov B. S. , Govyrin V. A. 
Published: December 2004

AbstractUsing classical potential functions, we carried out potential‐energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum‐energy conformations of the complexes are close to DNA A‐ and B‐family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low‐energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.
XII. Conformational studies of histidine‐containing peptides in solution
Authors: Jäckle Hans , Luisi Pier Luigi 
Published: December 2004

AbstractThe spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200–320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first‐approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
Kinetics of nucleosome unfolding at low ionic strength
Authors: Dieterich Ann E. , Cantor Charles R. 
Published: December 2004

AbstractThe kinetics of a conformational change which occurs in nucleosome core particles at about 1 mM ionic strength have been studied by observing changes in the fluorescence of labeled histone H3. The unfolding reaction is intramolecular since no concentration dependence is observed. However, the kinetics are unexpectedly complicated and reveal evidence of at least three relaxation times. It is possible to fit the kinetics observed under several conditions to a consistent four‐state cyclic mechanism in which folded and unfolded forms can inter‐convert by two parallel pathways, each involving a distinct intermediate. While the data are not sufficient to establish this mechanism as a unique choice, they exclude many simpler possibilities. The cyclic mechanism is quite reasonable in view of what is currently known about the structures of the folded and unfolded forms.
Evidence for the binding states of copper(II)–serum albumin complexes as revealed by transient electric dichroism measurements
Authors: Yamagishi Akihiko 
Published: December 2004

AbstractTransient electric dichroism has been measured for a Cu(II)–bovine serum albumin (BSA)–2‐(2‐pyridylazo)‐1‐naphthol (αPAN) complex at pH 5.5–12. From the magnitude of the reduced linear dichroism and the disorientation rate of the oriented chromophore, at least three kinds of binding states of Cu(αPAN)+ complex exist. They are present predominantly at pH 5.5–10, 7.5–10, and 10–12, with the αPAN plane approximately parallel, vertical, and parallel with respect to the oriented axis of a BSA molecule.
Quantum‐mechanical study of model molecules in relation to collagen structure. II. (Gly‐Phe‐Pro) and (Gly‐Pro‐Phe) repeating units
Authors: Cabrol Daniel , Broch Henri , Vasilescu Dane 
Published: December 2004

AbstractA conformational quantum‐mechanical study of (Gly‐Phe‐Pro) and (Gly‐Pro‐Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple‐helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly‐Pro‐Pro and Gly‐Phe‐Pro indicates that phenylalanyl in the second position favors the triple‐helix formation.
Conformational aspects of gastrin‐related peptides: A circular dichroism study
Authors: Peggion E. , Jaeger E. , Knof S. , Moroder L. , Wuensch E. 
Published: December 2004

AbstractThe conformational properties of a series of gastrin‐related peptides in aqueous solution and in 2,2,2‐trifluoroethanol (TFE) have been investigated by CD measurements. In aqueous solution the peptides Leu32‐HG‐34 (human big gastrin), Nle15‐HG‐17 (human little gastrin), and Nle11‐HG‐13 assume a random‐coil structure in the pH range 3–7. In TFE the three hormones fold into partially ordered structures, consisting of mixtures of α‐helix, β‐form and random coil. Comparison with the CD properties of the shorter gastrin peptides HG‐4 (tetragastrin), Nα‐Boc‐HG‐5 (pentagastrin), and HG‐7 (heptagastrin) indicates that the biologically important C‐terminal sequence Trp‐Met‐Asp‐Phe‐NH2 in TFE does not maintain the same geometry upon elongation of the chain at the N‐terminus from 4 to 34 residues. Thus, the various conformations in solution of the gastrin peptides examined do not provide a structural explanation for their very similar biological activity. Therefore, we hypothesize that the C‐terminal tetrapeptide amide folds into an “active” structure only upon interaction with the receptor.