bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the effects of cationic porphyrins on DNA properties: Influence of GC content of native and synthetic polymers
Authors: Banville Debra L. , Marzilli Luigi G. , Strickland James A. , Wilson W. David 
Published: December 2004

AbstractInteractions of meso‐tetra(4‐N‐methylpyridyl)porphyrin [TMpyP(4)], meso‐tetra(2‐N‐methylpyridyl)porphyrin [TMpyP(2)], and meso‐tetra(para‐N‐trimethylanilinium)porphyrin (TMAP) with several native and synthetic DNAs were studied by a variety of physical techniques: nmr (31P and 1H), absorption spectroscopy, viscosity, and flow dichroism (FD). Of the three porphyrins studied, only the interaction of TMpyP(4) with poly [d(G‐C)2] was fully consistent with intercalation. In particular, a large increase in viscosity, a downfield 31P‐nmr signal (ca. ‐1 ppm), and upfield imino proton signals (11 to 12 ppm range) were observed. Comparison of the effects of TMpyP(4) on DNAs of different GC contents revealed larger changes in solution viscosity with increased GC content. However, the characteristic changes in 31P‐ and 1H‐nmr spectra were not observed. The viscosity increases observed in studies with poly[d(A‐C)(G‐T)] and C. Perf. DNA were much lower than with poly[d(G‐C)2], M. Lys. DNA, and calf thymus DNA. Thus, GC sequence and content are clearly important. The principal change in the 31P‐nmr signal of native DNA is the appearance of a very broad shoulder centered at ca. ‐2.0 ppm, which is larger in M. Lys. DNA than in C. Perf. DNA. FD studies indicate highly ordered TMpyP(4) cations arranged perpendicular to the DNA axis of calf thymus DNA. Together, these results suggest the major effects of TMpyP(4) on DNA properties are due to strong GC‐binding interactions that influence DNA structure. The data are consistent with combined intercalative and outside binding interactions of TMpyP(4) with GC regions of DNA. In contrast, similar studies with TMAP suggest that it influences AT regions of DNA by an outside binding mode. On the other hand, TMpyP(2) effects on DNA properties are consistent with nonselective outside binding.
Multiple denaturational transitions in fibrillar collagen
Authors: Wallace Donald G. , Condell Richard A. , Donovan John W. , Paivinen Amy , Rhee Woonza M. , Wade Susan B. 
Published: December 2004

AbstractThe heat denaturation of pepsinized bovine nonfibrillar and fibrillar collagen was studied by differential scanning calorimetry. For fibrillar preparations that had been rapidly precipitated with stirring at low ionic strength, then resuspended at physiological ionic strength, multiple denaturational transitions were observed. At heating rates of 10°C/min, melting endotherms occurred at about 44, 50, 53, and 57°C. Fibrillar collagen that was slowly gelled without stirring at physiological ionic strength exhibited a similar series of endotherms, but the lower melting transitions were less conspicuous. In contrast, nonfibrillar bovine collagen in acidic solution showed only a single denaturational transition at 40°C. Nonfibrillar solutions at pH 7, to which inhibitors of fibrillogenesis were added, showed a major endotherm as high as 46°C. These results suggest that reconstituted fibrillar collagen contains a heterogeneous fibril population, possibly including molecules in a nonfibrillar state. It was proposed that the multiple melting endotherms of such preparations were due to sequential melting of molecular and fibril classes, each with a distinct melting temperature. The fibrillar classes may represent three or more types of banded and nonbanded species that differ from each other in packing order, collagen concentration, and possibly also in fibril width and level of cross‐linking.
Elastic model of highly supercoiled DNA
Authors: Tsuru Hideo , Wadati Miki 
Published: December 2004

AbstractThe equilibrium shapes of supercoiled DNA are investigated by employing an elastic model. First, a set of Euler equations is derived to determine the equilibrium shapes under ring‐closure conditions. Two exact solutions that describe circular and figure‐8 shapes are obtained. Using these and their topological properties, the configuration change from the circular to the figure‐8 form is discussed. Second, more intricate structures of supercoiling DNA are studied by a numerical analysis. Among a class of configurations, the shape that has the minimum elastic energy is explicitly determined. Poisson's ratio, the ratio of the self‐avoiding radius to the total length, and the deficit (or excess) of the linking number ΔLk are found to be the important parameters. We conclude that the topology and the elastic theory of looped DNA explain the essential features of the supercoiling phenomena.
The dielectric constant of a folded protein
Authors: Gilson Michael K. , Honig Barry H. 
Published: December 2004

AbstractThe goal of this paper is to obtain a theoretical estimate of the dielectric constant of a folded protein. To this end, we develop a form of the Kirkwood–Fröhlich dielectric theory that applies to polar solids and folded proteins. The resulting theory incorporates a factor expressing the degree to which dipolar groups are constrained within the material's structure, as well as a generalized form of Kirkwood's correlation factor. The theory is applied to a hypothetical isotropic protein composed of randomly oriented α‐helices and having a number density of dipolar groups equal to that found in actual proteins. The factor of constraint and the generalized dipole correlation factor are calculated using normal mode analysis. Temperature factors are also computed by normal mode analysis and are in reasonable agreement with those found experimentally. The computed dielectric constant is low; the best estimate is that it falls between 2.5 and 4.
A novel peptide conformation: First unequivocal observation of the oxy‐analog of a β‐bend
Authors: Toniolo Claudio , Valle Giovanni , Bonora Gian Maria , Crisma Marco , Formaggio Fernando , Bavoso Alfonso , Benedetti Ettore , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo 
Published: December 2004

AbstractThe x‐ray diffraction analysis of the N‐benzyloxycarbonyl homo‐tripeptide from α‐amino‐isobutyric acid has shown the occurrence of an incipient 310‐helix characterized by one type‐III (or type‐III′) β‐bend followed by one oxy‐analog of the same type of β‐bend. This represents the first unequivocal observation of the latter conformation, where the O—H group of the COOH moiety present at the C‐terminus of the peptide main chain plays the role of the hydrogen‐bonding donor. These results have been compared with those of the same peptide in its monohydrate form and of its methyl ester derivative, the x‐ray diffraction structures of which are also described here.
Synthesis of fragments by classical solution methods for use in cytochrome c semisynthesis
Authors: Borin Gianfranco , Marchiori Fernando , Calderan Andrea , Corradin Giampietro , Wallace Carmichael J. A. 
Published: December 2004

AbstractWe report details of the chemical synthesis of two fragments reproducing the C‐terminal sequences 71‐108 and 70‐108 of Saccharomices cerevisiae cytochrome c. Preparation of the fragments employed classical solution methods and a fragment‐condensation strategy; they have been used, together with a third fragment (sequence 67‐108) [L. Moroder, B. Filippi, G. Borin & F. Marchiori (1975) Biopolymers 14, 2061–2074], in the semisynthesis of chimeric cytochromes [C. J. A. Wallace, G. Corradin, F. Marchiori & G. Borin (1986) Biopolymers 25, 2121–2132].
DNA polymorphism: Spectroscopic and electro‐optic characterizations of Z‐DNA and other types of left‐handed helical structures induced by Ni2+
Authors: Hacques Marie‐Françoise , Marion Christian 
Published: December 2004

AbstractCD and uv spectroscopy reveal that the synthetic polynucleotides poly(dG–dC) · poly(dG–dC) and poly(dG–m5dC) · poly(dG–m5dC) undergo a transition induced by small amounts of Ni++ cation from a right‐handed B‐form to left‐handed Z‐type conformations. We describe the application of steady‐state and transient electric birefringence to the characterization of the transition observed at very low ionic strength (10 mM Tris HCl, pH 7.4). Dialysis experiments show that the changes in spectroscopic and electro‐optic properties upon addition of Ni++ are completely reversible. The differences in shape of the inverted CD spectra suggest the existence of a family of left‐handed conformations, depending on the polymer used and on the amounts of cation added. The stoichiometry required for inducing the Z‐conformation of poly(dG–m5dC) is 1 cation/4 nucleotide phosphates. The transition is accompanied by a decrease in birefringence, an increase in length, and the more important contribution of a permanent or slowly induced dipole moment to the orientation mechanism. High concentrations of Ni++ promote the Z → Z* transition. Upon increasing the Ni++ concentration, poly(dG–dC) undergoes a biphasic transition, first to one intermediate conformation that is neither B‐ nor Z‐like and then to a left‐handed form that is probably different from Z*. These conversions are accompanied by regular decreases both in birefringence and in chain length, but no transient appears in the field‐reversal experiments.
Energy transfer in polynucleotide homopolymers and copolymers
Authors: Burns Victor W. 
Published: December 2004

AbstractUsing the fluorophore Tb3+ as a reporter, the effect of thallium (Tl+1) on the transfer of energy in polyribonucleotides and polydeoxynucleotides at room temperature has been studied. In p(G), p(G, I), and pd(G)6 thallium greatly increases the transfer of uv energy absorbed by the bases to Tb3+. In DNA, p(G, U), p(G, A), p(A, U), p(X), p(A), p(U), p(I), pd(G, A)6, and pd(G, T)5 thallium has little or no effect. Thallium increases intersystem crossing to the triplet states only in p(G), p(G, I), and pd(G)6, and the triplets overlap the excited singlet state in Tb3+. In those G‐ and X‐containing polymers showing little thallium effect, the evidence suggests that intersystem crossing is comparatively high to begin with. These polymers, including DNA, appear to transfer absorbed energy to triplet states efficiently at room temperature.
Effect of cosolvents on solubility of protein in equilibrium between different states
Authors: Arakawa Tsutomu 
Published: December 2004

AbstractThis paper describes a theoretical work on the solubility of a protein in equilibrium between different forms such as isomerization (A ⇌ B) and dimerization (2A ⇌ B). Under the assumptions that A and B have different solubilities and form their own solid phases (in the form of either precipitation or crystal), it was shownthat only either A or B precipitates at a given condition, another form being in equilibrium in solution with the precipitating form, provided that the solubility ratio of A to B is not identical to their equilibrium composition in the solution phase determined by the equilibrium constant. It follows, then, that the total concentration of the protein in the solution phase can be calculated by summing the solubility of the precipitating form and the concentration in solution of another form in equilibrium with the precipitating form. Assuming various preferential protein‐solvent interactions for the two forms in solution as well as solid phases, dependences of the total protein solubility on the additive concentration were examined. It was shown that this dependence may be complex, showing maximum, minimum, or inflection point, depending on the preferential protein interactions with solvent components.
Proton polarizability and proton transfer in histidine‐phosphate hydrogen bonds as a function of cations present: Ir investigations
Authors: Burget Ulrike , Zundel Georg 
Published: December 2004

Abstract(L‐His)n‐ dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ⇌ O−…H+N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li+ to the K+ system. In the K+−system, His‐Pi‐Pi chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ⇌ O−…H−N equilibria are determined from ir bands. With the Li+ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na+ system (41%), and amounts to only 32% with the K+ system. With the increasing degree of hydration the removal of the degeneracy of νas−PO2−3 vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ⇌ O−…H+N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.
Site specificity of binding of antitumor antibiotics to DNA
Authors: Jones Martin B. , Hollstein Ulrich , Allen Fritz S. 
Published: December 2004

AbstractThe site specificities for intercalation of steffimycin B, adriamycin, echinomycin, and ethidium bromide with DNA have been determined by CD first‐neighbor analysis. The first three, which are antineoplastic antibiotics, all exhibit preferential binding to sites comprised of guanine and cytosine (GpC, CpG, and CpC or its complement GpG). Ethidium bromide displays nonspecific intercalation. The results are compared with findings from “footprinting” studies.
Prediction of the folding of short polypeptide segments by uniform conformational sampling
Authors: Bruccoleri Robert E. , Karplus Martin 
Published: December 2004

AbstractA procedure, CONGEN, for uniformly sampling the conformational spaceof short polypeptide segments in proteins has been implemented. Because thetime required for this sampling grows exponentially with the number of residues, parameters are introduced to limit the conformational space that has to be explored. This is done by the use of the empirical energy function ofCHARMM [B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus (1983) J. Comput. Chem. 4, 187‐217] and truncating the search when conformations of grossly unfavorable energy are sampled. Tests are made to determine control parameters that optimize the search without excluding important configurations. When applied to known protein structures, the resulting procedure is generally capable of generating conformations where the lowest energy conformation matches the known structure within a rms deviation of 1 Å.
A theoretical exploration of conformational aspects of ethidium bromide intercalation into a d(CpG)2 minihelix
Authors: Chen Kai‐Xian , Gresh Nohad , Pullman Bernard 
Published: December 2004

AbstractIn order to gain insight into the structural and conformational factors involved in the binding of ethidium bromide to oligonucleotides, theoretical computations are performed on the ethidium bromide–d(CpG)2 complexes, in which the ligand–nucleotide interaction energy, the conformational energy of the ligand, and that of the nucleotide are simultaneously optimized. The intermolecular and conformational energy computations are performed with the SIBFA procedures (sum of interactions between fragments computed ab initio), which use empirical formulas based on ab initio SCF (Self Consistent Field) computations. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structure) elaborated by Miller and co‐workers. The pyrimidine sugar is held in the C3′‐endo conformation and the purine sugar in the C2′‐endo conformation in conformity with both x‐ray and nmr results for dinucleoside duplexes. Several candidate intercalation sites, selected on the basis of energy criteria, could be generated by the procedure. They were found to recur in a persistent fashion over the whole range of unwinding angles investigated, which span from −20° to −30°. Among these, a conformation closely similar to the one determined crystallographically by Sobell et al. was found to be the intrinsically most favorable and to react with the strongest interaction energy with ethidium. For this conformation, the most favorable value of the unwinding angle is −26°, close to the value in the crystal structure. Several pairwise correlations of structural parameters could be evidenced. The effect of the 2′OH groups (as in RNA duplexes as opposed to DNA duplexes) was also investigated and shown to further enhance, albeit slightly, the intrinsic stability of the Sobell‐like Δα = −26° conformation.
On the stretching of DNA in the reptation theories of gel electrophoresis
Authors: Slater Gary W. , Rousseau Jean , Noolandi Jaan 
Published: December 2004

AbstractThe reptation dynamics of DNA chains in gel electrophoresis is discussed. The differences between the Lumpkin, Déjardin, and Zimm (LDZ), and the Slater and Noolandi (SN), biased reptation models are pointed out and studied. We show that new assumptions are necessary in order to study large‐field electrophoresis, and we present preliminary results of a computer simulation of DNA gel electrophoresis.
Protofibrin clots induced by calcium and zinc
Authors: Marx Gerard 
Published: December 2004

AbstractDuring the course of studies with fibrin protofibrils, produced by adding hirudin to thrombin‐activated fibrinogen prior to the onset of gelation, turbid clots were observed to be generated merely by adding Ca(II) or Zn(II) to protofibrils. The rate of gelation (CT) and turbidity of the “protofibrin” clots increases with cation levels in a concentration‐dependent manner, with Zn(II) much more potent than Ca(II). For example, 50 μM Zn(II) generated a more turbid protofibrin clot than 0.5 mM Ca(II). In combination, levels of Zn(II) and Ca(II), which individually have no effect, induce protofibril gelation. The generation of protofibrin clots by Zn(II) is decreased at increasing ionic strength. Apparently, the underlying electrostatic forces that bind the monomers in fibrin and protofibrin gels are similar. SEM micrographs show that Ca(II)‐ or Zn(II)‐induced protofibrin clots (600–1500Å thick) are essentially indistinguishable from those formed directly from fibrinogen and thrombin with divalent cation. The protofibrin fibers induced by the cations are thicker than the fibers formed directly from fibrinogen and thrombin in the absence of divalent cation. Branching appears brought about the the divalent cation‐sensitive lateral association of different protofibril strands. These findings describe simple experimental methods for separately studying the early and late stages of fibrin gelation.
Monte carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of β‐barrel proteins
Authors: Kolinski Andrzej , Skolnick Jeffrey , Yaris Robert 
Published: December 2004

AbstractDynamic Monte Carlo studies have been performed on various diamond lattice models of β‐proteins. Unlike previous work, no bias toward the native state is introduced; instead, the protein is allowed to freely hunt through all of phase space to find the equilibrium conformation. Thus, these systems may aid in the elucidation of the rules governing protein folding from a given primary sequence; in particular, the interplay of short‐ vs long‐range interaction can be explored. Three distinct models (AC) were examined. In model A, in addition to the preference for trans (t) over gauche states (g+ and g−) (thereby perhaps favoring β‐sheet formation), attractive interactions are allowed between all nonbonded, nearest neighbor pairs of segments. If the molecules possess a relatively large fraction of t states in the denatured form, on cooling spontaneous collapse to a well‐defined β‐barrel is observed. Unfortunately, in model A the denatured state exhibits too much secondary structure to correctly model the globular protein collapse transition. Thus in models B and C, the local stiffness is reduced. In model B, in the absence of long‐range interactions, t and g states are equally weighted, and cooperativity is introduced by favoring formation of adjacent pairs of nonbonded (but not necessarily parallel) t states. While the denatured state of these systems behaves like a random coil, their native globular structure is poorly defined. Model C retains the cooperativity of model B but allows for a slight preference of t over g states in the short‐range interactions. Here, the denatured state is indistinguishable from a random coil, and the globular state is a well‐defined β‐barrel. Over a range of chain lengths, the collapse is well represented by an all‐or‐none model. Hence, model C possesses the essential qualitative features observed in real globular proteins. These studies strongly suggest that the uniqueness of the globular conformation requires some residual secondary structure to be present in the denatured state.
Time‐Resolved fluorescence polarization anisotropy of short restriction fragments: The friction factor for rotation of DNA about its symmetry axis
Authors: Wu Pengguang , Fujimoto Bryant S. , Michael Schurr J. 
Published: December 2004

AbstractThe time‐resolved fluorescence polarization anisotropy (FPA) of ethidium dye intercalated in 43 and 69 base pair (bp) restriction fragments is measured, and the friction factor per bp for rotation of DNA about its symmetry axis is determined. The same value of the hydrodynamic radius, a = 12.0 ± 0.6 Å, is obtained for both the 43‐ and 69‐bp fragments, but only when (1) the twisting correlation functions appropriate for such short filaments are used: (2) the correct amplitude is employed for the uniform tumbling mode decays: and (3) the data analysis is restricted to times after the internal bending modes have died away leaving just reduced amplitudes of the exponentially decaying uniform tumbling modes. The present value of the hydrodynamic radius is significantly larger than that implied by the cross‐sectional area perpendicular to the symmetry axis. This strongly suggests that a significant fraction of water in the major and minor groves is rotating more or less rigidly with the DNA on this time scale. The correct expression for the amplitude Dn(∞) of the uniform mode decay of the tumbling correlation function, including the average over all sites to which the dye could bind, is derived in the appendix. The present theory for Dn(∞) is compared with that of Barkley and Zimm [(1979) J. Chem. Phys. 70, 2991–3007], and with recent Brownian simulations of discrete wormlike chains by Allison and co‐workers [S. A. Allison and J. A. McCammon (1984) Biopolymers 23, 363–375; S. A. Allison (1986) Macromolecules 19, 118–124].