bluuebunny/crossref_metadata_2025_split huggingface dataset:
The europium (III)‐induced conformational transitions of poly(dG‐dC) · poly(dG‐dC) and poly(dG‐m5dC) · poly(dG‐m5dC) as studied by europium(III) luminescence, UV, and CD spectroscopy
Authors: Klakamp Scott L. , Horrocks William Dew. 
Published: December 2004

AbstractThe Eu3+ ion induces a B to Z transition in poly(dG‐dC) · poly(dG‐dC) and poly(dG‐m5dC) · poly(dG‐m5dC). Other conformations were also elicited by this ion. The conformational changes of these polynucleotides were followed by CD and uv spectroscopy. Eu3+ excitation spectra and Eu3+ excited‐state lifetimes were measured for the Eu3+ ion bound to the duplexes in various conformations. B‐form poly(dG‐dC) and poly(dG‐m5dC) appear to have a single class of the Eu3+ binding site while the Z‐form observed conformation exhibits two. The numbers of H2O molecules coordinated to the Eu3+ ion bound to the various conformations of the duplexes were determined by measuring Eu3+ excited‐state lifetimes in H2O and D2O. The first‐order rate constants for the Eu3− and [Co(NH3)6]3+ induced B to Z transitions were measured. The Eu3+ mediated conversion is much faster than the [Co(NH3)6]3+ induced conversion in both polynucleotides.
Determination of eigenvectors in DNA polymer spectroscopy by isotopic substitution
Authors: Van Zandt L. L. , Saxena V. K. 
Published: December 2004

AbstractA simple relationship between frequency shifts to be expected in molecular vibrational spectra upon isotopic substitution and component values of eigenvectors is displayed. Application of this expression to the problem of force constant refinement is discussed in terms of a refinement algorithm developed some years ago to overcome particular problems associated with large molecular systems. Calculations of expected isotopic shifts have been calculated and are tabulated here for experimental reference.
Dynamic bending rigidity of DNA
Authors: Song Lu , Schurr J. Michael 
Published: December 2004

AbstractRapidly relaxing components in the decay of the transient electric dichroism of DNA restriction fragments were reported by Diekmann et al. [(1982) Biophys. Chem. 15, 263–270] and Pörschke et al. [(1987) Biopolymers 26, 1971–1974]. These are analyzed using a new normal mode theory for weakly bending rods and assigned to bending. The longest bending relaxation times for fragments with 95–250 base pairs coincide with the theoretical curve calculated for a dynamic bending rigidity corresponding to a dynamic persistence length Pd = 2100 Å. Analysis of the relative amplitudes of fast and slow components following weak orienting pulses is also consistent with a rather large dynamic persistence length. The enhancement of the relative amplitude of the fast component in large electric fields is attributed to steady‐state bending of initially perpendicular DNAs by the field. Several reasons are proposed why the dynamic bending rigidity is 4 times larger than the apparent static bending rigidity inferred from equilibrium persistence length measurements on the same fragments.
Anomalously slow electrophoretic mobilities of DNA restriction fragments in polyacrylamide gels are not eliminated by increasing the gel pore size
Authors: Stellwagen Anne , Stellwagen Nancy C. 
Published: December 2004

AbstractThe effect of gel pore size on the anomalous mobility of certain curved DNA restriction fragments in polyacrylamide gels was studied by comparing the electrophoretic mobilities of normal and anomalous fragments in gels of varying composition but constant acrylamide concentration. Molecular weight ladders were prepared from two 147 base pair G‐C rich restriction fragments, called 12A (anomalous) and 12B (normal), obtained from the MspI digestion of plasmid pBR322. The electrophoretic mobilities of multimers of the two fragments increasingly diverged with increasing molecular weight. The anomalous mobility of fragment 12A was essentially independent of gel pore size, regardless of whether the pore size was varied by increasing the acrylamide concentration at constant cross‐linker concentration or by increasing the cross‐linker concentration at constant acrylamide concentration. The anomalous mobility of higher multimers of fragment 12A decreased with increasing gel pore size when the pore size was varied by changing the gel concentration. However, when the gel pore size was changed by varying the cross‐linker concentration at constant acrylamide concentration, the anomalous mobility of higher multimers of fragment 12A went through a maximum and then decreased as the pore size was increased. Copolymerizing acrylamide with high molecular weight linear polyacrylamides had no effect on the anomalous mobility of the 12A multimer ladder, even though the apparent absolute mobilities of all fragments increased markedly. Only by incorporating charged residues into the gel matrix or by copolymerizing acrylamide with the intercalator ethidium bromide could the difference in mobility between the 12A and 12B multimer ladders be substantially reduced or eliminated. Similar results were observed with a molecular weight ladder containing 78 base pair repeats of the bending locus of kinetoplast DNA. These results suggest that pore size alone is not responsible for the anomalously slow migration of curved DNA molecules in polyacrylamide gels.
Bond‐Optimized ring closure for proline: Comparison of conformations and semiempirical energies with small molecule X‐ray structures
Authors: Thomasson Kathryn A. , Applequist Jon 
Published: December 2004

AbstractA method is described for generating proline ring structures by successive addition of atoms, wherein ring closure is achieved by optimizing the fit to known ring bond‐angles and one closing bond‐length (“bond‐optimized ring closure”). Two ring torsion angles are fixed independently within broad, allowed ranges, and the remaining torsion angles are determined uniquely in most cases. The independent torsion angles are chosen as ϕ and χ2, and ring closure is achieved without prohibitive strain through most of the ranges −130° < ϕ < −20° and −60° < χ2 < 60°. Comparisons of predicted ring structures to 191 X‐ray diffraction structures from the literature, starting with the known values of ϕ and χ2, yielded root‐mean‐square deviations of 4.8° in χ1, 4.7° in χ3, 8.3° in χ4, and 0.3–2% in the ring bond angles and the N‐Cδ distance. Semiempirical energies were calculated for the optimized structures using three sets of energy parameters from the literature. The energy surfaces show broad minima coinciding with the torsion angle regions in which the highest concentrations of observed structures are found. Two of the sets of energy parameters produce double minima corresponding to the “up” and “down” puckered conformations.
Relation between calculated amide frequencies and solution structure in Ala‐X peptides
Authors: Williams Robert W. , Weaver James L. , Lowrey Alfred H. 
Published: December 2004

AbstractComputational techniques have been used to aid interpretation of observed systematic shifts in the amide III frequencies of Ala‐X peptides. Optimized structures and frequencies have been calculated for Ala‐X peptides using GAUSSIAN86/88 with the 4‐31G basis, MOPAC, and normal mode methods based on empirical force fields. We observe the following: (1) Frequencies calculated using scaled GAUSSIAN86 force constants correlate well with the experimental results. (2) Structures of the Ala‐X peptides optimized by GAUSSIAN show a clear trend toward lower values of the dihedral angle ϕ as the X side chain becomes larger, while structures optimized here using semiempirical and empirical force fields do not show trends. (3) Computational changes in peptide conformations from β‐sheet to α‐helix produce large changes in both amide I and amide III frequencies that are inconsistent with the experimental results. (4) Computational changes in the dihedral angle ϕ of Ala‐Ala produce a change in the amide III frequency consistent with the experimental results. (5) The experimental frequency shifts cannot be attributed directly to the effects of changing mass.
Heteronuclear two‐dimensional 15N‐ and 13C‐nmr studies of DNA oligomers and their netropsin complexes using indirect proton detection
Authors: Ashcroft Joseph , Live David H. , Patel Dinshaw J. , Cowburn David 
Published: December 2004

AbstractHeteronuclear multispin coherence proton‐detected two‐dimensional nmr spectroscopic experiments were used to obtain information on protonated carbons and nitrogens of the self‐complementary d (G‐G‐T‐A‐T‐A‐C‐C) and d (G‐G‐A‐A‐T‐T‐C‐C) duplexes, with and without the drug netropsin dissolved in aqueous solution. Many correlations of protons coupled to 13C nuclei on the base and sugar rings of the octanucleotides were detected, allowing the carbon resonances to be assigned based on previous homonuclear proton two‐dimensional nmr studies. Imino nitrogen assignments can also be made using the proton assignments from previous one‐dimensional nuclear overhauser effect experiments. Imino nitrogen shifts may be useful indicators of changes in local hydrogen‐bonding interactions to base‐pair edges.
Virtual rigid body dynamics
Authors: Head‐Cordon Teresa , Brooks Charles L. 
Published: December 2004

AbstractAn important direction in biological simulations is the development of methods that permit the study of larger systems and/or longer simulation time scales than is currently feasible by molecular dynamics. One such method designed with this objective in mind is stochastic boundary molecular dynamics (SBMD). SBMD was developed for the characterization of spatially localized processes in proteins, and has been shown to successfully reproduce structural and dynamical properties of these macromolecules, as compared to a molecular dynamics control simulation, when concerted or global motions are not present. The virtual rigid body dynamics method presented in this work extends the range of applicability of the SBMD method, by providing a framework to include these important long time scale conformational transitions. In this paper we describe the two‐step implementation of the virtual rigid body model: first, the reduction of the full atomic representation to a reduced particle (virtual bond) model, and second, the propagation of the dynamics of flexibly connected rigid bodies containing virtual atom sites.
High directional Monte Carlo procedure coupled with the temperature heating and annealing as a method to obtain the global energy minimum structure of polypeptides and proteins
Authors: Shin Jae Kwang , Jhon Mu Shik 
Published: December 2004

AbstractA high directional Monte Carlo procedure that predicts the topology of the energy hyper‐surface before it walks, is developed as a method to obtain a global energy minimum structure of polypeptides and proteins. It calculates its covariance matrix, which controls the individual trial step distribution of the next set of steps, from the second moment of the actual walk segment in the previous set. The method is successfully applied to the pentapeptide Metenkephalin system. And it is shown that some initial heating process, which provides the more flexible molecule, is necessary in order to overcome the energy barriers that can be overestimated by some biases in the empirical description of the system. The sampling efficiency, traced by an average conformational changes, is found to be at least 20 times greater than the one in the conventional Metropolis Monte Carlo methods, and it is expected that this increases in efficiency will be more prominent when the system is larger.
Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch
Authors: Guo Qiu , Lu Min , Kallenbach N. R. 
Published: December 2004

AbstractFour‐arm DNA branched junctions are stable analogues of Holliday recombinational intermediates. A number of four‐arm DNA junctions synthesized from oligonucleotides have now been studied. Gel mobility or chemical footprinting experiments on several immobile four‐arm junctions indicate that in the presence of Mg2+, they assume a preferred conformation consisting of two helical domains, each formed by stacking a particular pair of arms on each other. We show here that a junction we designate as J1c that has the same chemical composition as one we have previously studied in detail, J1, but is formed from the four strands complementary to those of the latter, exhibits the reverse stacking preference. The pattern of self‐protection of the strands of J1c exposed to Fe(II) · EDTA‐induced scission reveals that twofold symmetry is preserved, but the opposite pair of strands preferentially cross over. Moreover, the Fe(II) · EDTA scission profiles of J1c indicate that this junction exhibits a weaker bias as to which strands cross over than is observed in J1. The preference for the dominant species in J1 is 1.3 times greater than in J1c at 4°C and in the presence of 10 mM Mg2+, based on chemical reactivity data. This is confirmed by a cleavage experiment using the resolvase enzyme, endonuclease I, from bacteriophage T7. This difference could reflect either sequence‐dependent differences in the equilibrium among isomers, or in the structure of these junctions. Chemical footprinting experiments using the probes MPE · Fe(II) and (OP)2Cu(I) show that the high‐affinity ligand binding site in immobile junctions is determined by junction geometry.
An estimate of the nearest neighbor base‐pair content of 5S RNA using CD and absorption spectroscopy
Authors: Johnson Kenneth H. , Gray Donald M. 
Published: December 2004

AbstractWe analyzed the CD and uv absorption spectra of 5S RNA from Escherichia coli using the method developed in the preceding paper. The analysis of spectra of 5S RNA at 20°C in 0.1 M NaClO4, 2.5 mM Na+ (phosphate), pH 7.0, and 0.5 mM MgSO4 gave 7 ± 3.6 A · U base pairs, 25 ± 3.6 G · C base pairs, and 7.5 ± 3.6 G · U base pairs. Estimates of nearest neighbor base pairs were more consistent with the Pieler–Erdmann and the Gewirth–Moore secondary structure models than with the Fox–Woese or the Burns–Luoma–Marshall models.We also examined the structure of 5S RNA as a function of temperature. The melting profile exhibited two transitions—one at about 35°C and one above 50°C. Our spectral data showed that helices I and II were stable during the first transition, and agreed with other data that helix III was the most likely helix to have melted. The results from this in‐depth study of 5S RNA indicate that our method of analysis should be useful for studying the secondary structures of other small, unmodified RNAs.
Conformations and time‐resolved fluorescence of oligomers of (−)‐epicatechin with 4β → 8 interflavan bonds
Authors: Cho Donghwan , Porter Lawrence J. , Mattice Wayne L. 
Published: December 2004

AbstractOligomers of (−)‐epicatechin with 4β → 8 interflavan bonds, and as many as five monomer units, have been studied by conformational analysis and time‐resolved fluorescence. The conformational analysis yields 2x−1 conformations for each oligomer with x monomer units. There are two conformations accessible at each interflavan bond. These conformations are denoted by + and −. The dominant conformations for the trimer and higher oligomers have an interaction between the phenolic hydroxyl groups on monomers i and i+2. This interaction involves the hydroxyl group at C(5) on monomer i, and either C(13) or C(8) of monomer i+2, depending on whether the conformation of the two intervening interflavan bonds is + + or + −, respectively. Minor contributions to the ensemble for the tetramer and pentamer are made by conformations that contain the sequence of successive interflavan bonds denoted by −+ or −−. In −+ the interaction between monomer units i and i + 2 involves an aliphatic hydroxyl with a phenolic hydroxyl, and there are no hydroxyl‐hydroxyl interactions between units iand i + 2 in −−. The onset of a different decay law for the fluorescence when x increases from 3 to 4 may be associated with the appearance of the −+ and −− conformations as minor constituents in the ensemble.
New insights on μ/δ selectivity of opioid peptides: Conformational analysis of deltorphin analogues
Authors: Tancredi T. , Temussi P. A. , Picone D. , Amodeo P. , Tomatis R. , Salvadori S. , Marastoni M. , Santagada V. , Balboni G. 
Published: December 2004

AbstractThe message domain of dermorphin (Tyr‐D‐Ala‐Phe), a natural μ‐opioid heptapeptide, has long been considered the main cause of the high μ selectivity of this peptide and of its analogues. The recent discovery, in the skin of Phyllomedusa sauvagei (i.e., the same natural source of dermorphin) and of Phyllomedusa bicolorof deltorphins, challenges this belief. Deltorphins, in fact, are three heptapeptides characterized by a message domain typical of μ‐selective peptides, but endowed of an extremely high δ selectivity, the highest of all natural opioid peptides.A conformational analysis of dermorphin and deltorphins, based on nmr studies in DMSO and cryoprotective mixtures and internal energy calculations, showed that the enormous differences in receptor selectivity can be interpreted on the basis of receptor models for μ and δ opioids that recognize the same β‐turn in the N‐terminal part, but discriminate for the conformation and polarity of the C‐terminal part.Here we present the synthesis, biological activity, and conformational analysis in solution of three deltorphin analogues with very similar constitution, but with different net charge, different location of negative residues, or even without negative residues, which confirm these hypotheses and show that His4 can play a specific structural role.
Two‐Dimensional 1H‐nmr study of antigen–antibody interactions: Binding of synthetic decapeptides to an anti‐acetylcholine receptor monoclonal antibody
Authors: Cung Manh Thong , Demange Pascal , Marraud Michel , Tsikaris Vassilios , Sakarellos Constantinos , Papadouli Irene , Kokla Anna , Tzartos Socrates J. 
Published: December 2004

AbstractTwo‐dimensional NMR experiments [correlated spectroscopy (COSY) and two‐dimensional transferred nuclear Overhauser enhancement spectroscopy (TR‐NOESY)] have been applied to study the interactions of a monoclonal antibody (mAb) directed to the main immunogenic region (MIR) of the acetylcholine receptor (AChR), and four synthetic decapeptides from the MIR. The decapeptides were the Torpedo AChR α67‐76 fragment (W 67‐N68‐P69‐A70‐D71‐Y72‐G73‐G74‐I75‐K76) and its three [A69], [A73], and [A76] analogues. The results led to the following conclusions: (1) the magnitude of the TR‐NOE cross peaks does not depend only on the structuration of the peptide in the bound state, but also on restrictions of the mobility, i.e., on the correlation time τc, which can be different for every residue; (2) the binding capacity of the synthetic peptides to mAbs measured by radioimmunoassay is directly correlated to the NOE magnitude; and (3) the combined interpretation of the COSY and TR‐NOESY experiments gives a qualitative information about the nature and the overall conformation of the sequence which is in contact with the mAb binding site.
Time‐Resolved study of network self‐organization from a biopolymeric solution
Authors: Emanuele A. , Di Stefano L. , Giacomazza D. , Trapanese M. , Palma‐Vittorelli M. B. , Palma M. U. 
Published: December 2004

AbstractTime‐resolved studies of network self‐organization from homogeneous solutions of the representative biostructural polymer agarose are presented. Solutions are temperature quenched and observed by several techniques. Consistent with previous suggestions by the authors, experiments at concentrations up to about 1.75% w/v provide direct kinetic evidence for the occurrence of at least two distinct processes, leading, in sequence, to self‐assembly. These are as follows: (a) a liquid–liquid phase separation of the solution occurring via spinodal demixing and resulting in two sets of regions that have, respectively, higher and lower than average concentrations of random‐coiled polymers; and (b) the subsequent 2 coils → double helix transition and accompanying cross‐linking and gelation (due to branching of double helices), occurring in the high‐concentration regions. The size of the high‐concentration regions depends upon agarose concentration and quenching temperature, and is in the range from a fraction of micrometers to a few micrometers, in agreement with earlier experiments. Bundling of the double‐helical segments is known to follow self‐assembly and can be considered as a third step (gel curing). This follows from the thermo‐dynamic instability of the helical segments in the solvent, behaving as a system of rod‐like particles connected by more or less flexible joints.The two processes leading in succession to self‐assembly are discussed in terms of a phase diagram consistent with available data. Their time scales differ remarkably. At the end of the first process, all polymers remain random coiled and freely drifting. Much later coil–helix transition is observed, always in coincidence with polymer cross‐linking and gelation. The enhancement of concentration of random‐coiled polymers in specific regions of the sol caused by spinodal demixing is thus a prerequisite for self‐assembly of these biostructural gels in the concentration interval studied. Conceptually, concentration enhancements of this type can provide a new pathway for promotion of functional biomolecular interactions even at very low average concentrations. The mechanism will work identically if the region of instability is reached by varying the polymer concentration (e.g., by biosynthesis), rather than by temperature quenching.
Evidence of three distinct conformations—single chain, single helix, and triple helix—of (1 → 3)‐β‐D‐xylan in the solid and intact frond of green algae as studied by 13C‐nmr spectroscopy
Authors: Saitô Hazime , Yamada Junko , Yoshioka Yuko , Shibata Yûkô , Erata Tomoki 
Published: December 2004

AbstractHigh‐resolution solid‐state 13C‐nmr spectra of (1 → 3) ‐β‐D‐xylan from Bryopsis maxima and Caulerpa brachypus were recorded for various preparations from intact through dried frond to anhydrous and hydrated xylan, to gain insight into their secondary structures as compared with those of (1 → 3)‐β‐D‐glucans. It turned out that 13C‐nmr peaks of intact or dried frond were mainly ascribed to the peaks from (1 → 3)‐β‐D‐linked xylose residue, although some peaks were seen at the carbonyl and aliphatic regions. Dehydration of frond by either air drying or ethanol, and extraction of xylan with acid, did not result in substantial spectral change, although extraction with saturated ZnCl2 solution caused appreciable displacements of the C‐3 as well as C‐2 and C‐5 peaks. This means that no major conformational change was induced during the above‐mentioned processes of the dehydration and the extraction with acid. The extraction with ZnCl2 solution, however, induced major conformational change. Thus, we found that the above‐mentioned three distinct conformations–triple helix, single helix, and single chain–are also present in (1 → 3)‐β‐D‐xylan, as judged from the conformation‐dependent displacements of 13C chemical shifts, hydration/dehydration‐induced spectral change, and the x‐ray diffraction data on Penicillus dumetosus by Atkins et al. In particular, we found that all the preparations except for the extraction with ZnCl2 solution retain the triple helix form, whereas the anhydrous and hydrate samples of the latter preparations take the single‐chain and single‐helix form, respectively. Further, we measured the 13C spin‐lattice relaxation times of laboratory frame of the xylan to gain insight into better understanding of the role of the hydroxymethyl group as an efficient relaxation pathway in (1 → 3)‐β‐D‐glucan.