bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical studies on β‐lactam antibiotics. IV. Conformational analysis of novel β‐lactam antibiotics and the binding specificities of crosslinking enzyme(s) and β‐lactamases
Authors: Vasudevan T. K. , Rao V. S. R. 
Published: December 2004

AbstractConformational‐energy calculations were carried out on the new family of β‐lactam antibiotics (viz., thienamycin, PS‐5, 1‐oxa‐ and 1‐thiapenems, and their close analogs); these exhibit broad‐spectrum antibacterial activity and stability towards β‐lactamase‐producing strains. The bicyclic ring system in all the compounds studied was found to be highly rigid and to favor only one conformation. This is in contrast to findings in penicillins, where the five‐membered ring assumes two puckered conformations. The relative orientations of the bicyclic ring system and the nature and configuration of the substituent at C‐5 position, besides nonplanarity of the lactam peptide bond, are shown to be important for biological activity. The present study, in agreement with x‐ray studies, predicts that the lactam peptide bond in 1‐carbapenem is more nonplanar than in 1‐thiapenem. These studies also suggest that the conformational requirement of bicyclic ring system to bind to crosslinking enzyme(s) and β‐lactamases is very similar.
Mechanism of DNA denaturation in the presence of manganese ions
Authors: Yurgaitis A. P. , Lazurkin Yu. S. 
Published: December 2004

AbstractThe unwinding of DNA strands in the presence of small concentrations of Mn2+ ions (2 × 10−4−4 × 10−4M) has been studied. The process of unwinding is nonequilibrium; the DNA strands are gradually unwound at a constant temperature corresponding to the beginning of the melting curve. There is no true renaturation in the partially melted DNA. It is shown in the paper that these effects are due to the aggregation of the unwound DNA regions. The Mn2+ ions are responsible for the binding of the unwound strands. The aggregation precludes renaturation, shifts the equilibrium towards the melted state, and causes slow unwinding at a constant temperature. The binding of denaturated regions seems to occur through the guanines.
Polarized luminescence and mobility of tryptophan residues in polypeptide chains
Authors: Semisotnov G. V. , Zikherman K. Kh. , Kasatkin S. B. , Ptitsyn O. B. , Anufrieva E. V. 
Published: December 2004

AbstractPolarized luminescence was used to study the mobility of tryptophan residues in polypeptide chains of different chemical composition and structural organization. It has been shown that the luminescence depolarization of tryptophan residues in coillike, helical, and β‐structural polypeptide chains is mainly caused by “fast” torsional vibrations and “slow” rotational isomerization of indole groups of tryptophan side chains. The characteristics of these types of motions are practically the same for tryptophan residues included in coillike chains of different chemical structure. Helix–coil transitions in copolymers of glutamic acid and lysine with tryptophan (Glu, Trp) and (Lys, Trp) (where side groups of tryptophan residues weakly interact with the surrounding side groups) do not appreciably change the amplitude of torsional vibrations or rotational isomerization. At the same time, in the helical state of glutamic acid–leucine–tryptophan copolymers (Glu, Leu, Trp) and in the β‐structural state of (Lys, Trp) copolymers (where direct interactions of Trp side groups with other side groups are possible), the amplitudes of the torsional vibrations are smaller and the rotational isomerization times larger than in the coil. The transition of (Glu, Leu, Trp) polypeptide chains into a compact state is accompanied by a marked decrease of both “fast” and “slow” intra‐molecular mobility and by an increase of the contribution made by the rotation of the macromolecule as a whole, as shown by the decrease of the luminescence polarization.
Binding of multivalent ligands to mobile receptors in membranes
Authors: Dwyer John D. , Bloomfield Victor A. 
Published: December 2004

AbstractWe present a model to describe the equilibrium binding properties for the attachment of multivalent ligands to mobile receptors in membranes. The interaction is assumed to be governed by two inherently different association constants. The first of these controls the initial attachment of a ligand to its first receptor, by adsorption from bulk solution, while the second governs subsequent receptor attachments to this initially bound ligand by rearrangement of membrane‐bound species. Simple statistical mechanical expressions are used to estimate contributions to these association constants that are attributable to losses of translational and rotational degrees of freedom occurring upon binding. Suitable combinatorial expressions are combined with these association constants to derive the concentrations of bound species and the binding isotherms. Examination of these expressions leads to the conclusion that once initially bound, most multivalent ligands will be completely saturated by receptors and that partially bound species will be essentially nonexistent. This behavior is attributable to the generally high overall affinities of these ligands and to the mobility of the membrane‐bound species. Some specific comments are made, in light of this theory, about the binding of cholera toxin to its membrane receptor, the ganglioside GM1.
Transient electric birefringence study of the length and stiffness of short DNA restriction fragments
Authors: Elias John G. , Eden Don 
Published: December 2004

AbstractTransient electric birefringence measurements of the rotational diffusion constant of five short restriction fragments of the plasmid pBR322 show that the hydrodynamic length is independent of sodium ion concentration in the range of 0.2 to 2.5 mM. The fragments are too stiff to be modeled as wormlike molecules. The rotational relaxation times of the fragments, which range from 64 to 124 base pairs, have been used to calculate the rise per base pair using six different theoretical expressions for the length dependence of the rotational diffusion coefficient of straight cylinder. The best estimate for the rise per base pair of Na‐DNA in solution is 3.3 ± 0.1 Å.
Simulations of the solvent structure for macromolecules. II. Structure of water solvating Na+‐B‐DNA at 300 K and a model for conformational transitions induced by solvent variations
Authors: Corongiu Giorgina , Clementi Enrico 
Published: December 2004

AbstractThe structure of water and its interaction energy with a fragment of B‐DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen‐bonded filaments of water are reported and discussed. The stabilization of the B‐conformation induced by the solvent with counterion (“ion‐induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x‐ray and neutron beam) data on DNA insolution.
Dependence of laser light scattering of DNA on NaCl concentration
Authors: Kam Zvi , Borochov Nina , Eisenberg H. 
Published: December 2004

AbstractWe show that the persistence length a of DNA, derived from total intensity laser light scattering of linear Col E1 DNA and corrected for excluded‐volume effects, varies from about 68 nm in 0.005M NaCl to about 40 nm in 0.2M NaCl, leveling off to a constant value (about 27 nm) at high NaCl (1–4M) concentration. These observations do not agree with current views on the effect of electrostatic charge and ionic conditions on DNA dimensions. The apparent diffusion constant Dapp, determined from laser light scattering autocorrelation as a function of scattering vector q, at NaCl concentrations 0.005–4M, correctly yields the translational diffusion coefficient Dt at low values of q and scales with molecular dimensions rather than segment length at high values of q; thus, Dapp/Dt yields a universal curve when plotted against q2R, where Rg is the radius of the gyration. The sedimentation coefficients s at 0.1 and 0.2M NaCl concentration closely agree with the well‐tested empirical relations, and a combination of s, Dt, and the appropriate density increments yield correct molar masses over the whole salt concentration range. Approximate constancy of DtRg indicates limited draining in translational flow. We present some observations and thoughts on the regimes in which a dependence of the correlation decay times on q3 rather than q2 applies. We conclude that quasielastic laser light scattering discloses little information about dynamics of internal motion of DNA chains.
Investigation of structural aspects and classification of plant sulfated polysaccharides on the basis of the optical properties of their complexes with metachromatic dyes
Authors: Stone Audrey Larack , Childers Lillian G. , Bradley Dan F. 
Published: December 2004

AbstractOptical properties of complexes of plant sulfated polysaccharides with basic dyes have been examined. Spectral shifts in the dye have been used as the basis for quantitative analysis of anionic sites in these compounds. The κ‐ and λ‐carrageenans have been shown to give characteristically different titration curves. Other, similar, plant extractives have been shown to fall into one or the other of these two classes. Cotton effects in the region of the absorption spectrum of the dye have been discovered, indicating the presence of long range order and asymmetry in the λ‐C2 carrageenan. The relation of the optical effects to each other and to the structure of the polymer is discussed briefly in terms of recent developments in the theory of metachromasy.
Characterization of a second helical amylose modification
Authors: Zaslow B. 
Published: December 2004

AbstractFrom x‐ray diffraction data, a pseudohexagonal unit cell with a = b = 14.94 A. and c = 7.93 A. has been obtained for partially dried precipitate of amylose and tertiary butyl alcohol. Geometrical considerations establish a helical amylose configuration which has seven glucose residues per helix turn.
Conformational aspects of polypeptides. XI. The nitroaromatic effect
Authors: Goodman Murray , Felix Arthur M. , Deber Charles M. , Brause Allan R. , Schwartz Gerald 
Published: December 2004

Abstractβ‐ρ‐Nitrobenzyl‐L‐aspartate and γ‐p‐nitrobenzyl‐L‐glutamate were synthesized, and copolymers were prepared respectively with β‐benzyl‐D‐(and ‐L‐) aspartate and γ‐benzyl‐L‐glutamate. In chloroform there is a reversal in helical sense of poly‐β‐benzyl‐L‐aspartate to the right‐handed sense of poly‐β‐p‐nitrobenzyl‐L‐aspartate when 26–32 mole‐% of the latter is present in the copolymer. A new conformationally dependent Cotton effect was found for these copolymers at 370 mμ. In dimethylformamide there is a transition from the random conformation of poly‐β‐benzyl‐D‐(or ‐L‐) aspartate to the right‐handed helical sense of poly‐β‐p‐nitrobenzyl‐L‐aspartate. The formation of a side chain helix is proposed to explain the enhanced rotatory properties for the nitrated aspartates. In the glutamate series no helix reversal or unusual rotatory properties were observed in DMF or chloroform.
Conformational dependence of the Raman scattering intensities from polynucleotides. III. Order‐disorder changes in helical structures
Authors: Small Exoch W. , Peticolas Warner L. 
Published: December 2004

AbstractRaman spectra are presented on ordered and presumably helical structures of DNA and RNA as well as the poly A·poly U helical complex, polydAT, and the helical aggregates of 5′‐GMP and 3′‐GMP. The changes in the frequency and the intensity of the Raman bands as these structures undergo order‐disorder transitions have been measured. In general the changes we have found can be placed into three categories: (1) A reduction in the intensities of certain ring vibrations of the polynucleotide bases is observed when stacking or ordering occurs (Raman hypochromism). Since the ring vibrational frequencies are different for each type of base, we have been able to obtain some estimate of average amount of order of each type of base in partially ordered helical systems. (2) A very large increase in the intensity of a sharp, strongly polarized band at about 815 cm−1 is observed when polyriboA and polyriboU are formed into a helical complex. Although this band is not present in the separated chains at high temperature, a broad diffuse band at about 800 cm−1 is present. The 815 cm−1 band undoubtedly arises from the vibrations of the phosphate‐sugar portions of the molecule and provides a sensitive handle to the back‐bone conformation of the polymer. This band also appears upon ordering of RNA, formation of the helical aggregate of 5′‐riboGMP, and to some extent in the selfstacking of the polyribonucleotides polyA, polyU in the presence of Mg++, PolyC, and polyG. No such intense, polarized band is found, however, in ordered DNA, polydAT, or the 3′‐riboGMP aggregate, although there is a conformationally independent band at about 795 cm−1 in DNA and polydAT. (3) Numerous frequency changes occur during Conformational changes. In particular the 1600–1700 cm−1 region in D2O shows significant conformationally dependent changes in the CO stretching region analogous to the changes in this region which have been observed in these substances in the infrared. Thus, Raman scattering appears to provide a technique for simultaneously observing the effects of base stacking, backbone conformation and carbonyl hydrogen bonding in nucleic acids in moderately dilute (10–25 mg/ml) aqueous solutions.
Melting experiment concerning the topological structure of closed circular double‐stranded DNA
Authors: Giacomoni Paolo U. 
Published: December 2004

AbstractA melting experiment was performed on the whole set of populations of the replicative form of ϕX174 DNA, which can be obtained treating this DNA with rat liver nicking‐closing enzyme in the presence of ethidium bromide. Gel electrophoresis performed by loading the DNA samples at neutral and alkaline pH allows separation of these populations in discrete sets of bands, which can then be compared. The outcome of the experiments indicates that in the range of electrophoretic mobilities which can be explored, no band is formed exclusively by circular complementary strands which can be separated by alkaline denaturation. These results are compared with what would be expected if double‐stranded closed circular DNA had structures other than the canonical double helix. Under nonrestrictive hypotheses, the experiments reported allow one to obtain a minimum estimate of the absolute value of the linking number of a closed circular double‐stranded DNA: for native ϕX174 RF DNA, the linking number appears to be greater than 12 (in absolute value). Some data on the electrophoretic mobility of denatured closed circular duplexes are reported, which still wait for a physicochemical interpretation.
A stereospecific complex of poly(I) with ammonium ion
Authors: Howard Frank B. , Miles H. Todd 
Published: December 2004

AbstractWe describe conditions which lead to complete helix formation of poly(I) in the presence of NH. Binding of NH is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH–poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH. A stereospecific model is proposed for the NH–poly(I) helix in which the N of NH is located on the axis of the four‐stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
Conformations of cyclic peptide/calcium complexes in solution
Authors: Hughes Donald W. , Deber Charles M. 
Published: December 2004

AbstractSynthetic cyclic octapeptides of general structure cyclo[Glu(γOBzl)‐Sar‐Gly‐(N‐R)Gly]2 (R = n‐hexyl and cyclohexyl) transport calcium ions selectively across organic phases and phospholipid membranes. We have now used proton nmr spectroscopy (360 MHz) to study the solution conformation(s) of their calcium complexes. When Ca(ClO4)2 was added to solutions of these peptides in CDCl3, nmr spectra of the resulting calcium complexes were characteristic of a single C2‐symmetric conformer. From a Karplus‐Bystrov analysis of vicinal coupling constants in both the peptide backbone and Glu side chain (treated as an ABCC′MX spin system), in conjuction with model‐building studies, a structure was proposed in which the calcium ion is bound in an octahedral‐type complex by the four (coplanar) carbonyl groups of the (all‐trans) Glu‐Sar and Gly‐(N‐R)Gly peptide bonds. Occurrence of preferred rotamers about Glu side chain Cα–Cβ bonds indicated that restricted rotation in peptide side chains arises upon calcium binding.
Factors affecting the kinetics of DNA reassociation in phenol–water emulsion at high DNA concentrations
Authors: Wieder Robert , Wetmur James G. 
Published: December 2004

AbstractDNA reassociation kinetics using the phenol emulsion reassociation technique (PERT) [Kohne, D. E., Levison, S. A. & Byers, M. J. (1977) Biochemistry 16, 5329–5341] has been investigated at high DNA concentrations using an endonuclease S1 assay of reaction progress. Apparent second‐order rate constants fall on two intersecting straight lines when presented as a function of DNA concentrations on a log–log plot. In the low DNA concentration range, the rate constants drop about 10‐fold when concentration increases 1000‐fold. In the high DNA concentration range, the rate constants drop more than 10‐fold when concentration increases 10‐fold. The slopes of these lines are the same in different solvents and at different temperatures. The intersection between the lines occurs when the available catalytic surface is saturated. At high DNA concentrations, high‐complexity heterologous denatured DNA apparently competes 2–4 times better for the surface than homologous DNA because it does not participate in a reassociation reaction. Native and partially native DNA molecules cannot compete with single‐stranded DNA for a saturated surface. At high DNA concentrations, reactions using PERT become dependent on the single‐strand DNA length. Increasing length lowers reassociation rates.
Polydispersion in the diameter of fibers in fibrin networks: Consequences on the measurement of mass–length ratio by permeability and turbidity
Authors: Shah G. A. , Ferguson I. A. , Dhall T. Z. , Dhall D. P. 
Published: December 2004

AbstractThe diameters of the fibrin fibers in a clot are not uniform. Morphometric analysis of transmission electron micrographs show a bimodal distribution. The effect of polydispersity of fiber diameter on mass–length ratio calculated from the turbidity and permeability of a clot has been investigated with the aid of a two network model, the networks being called Major and Minor. The fibers in the Major network are many times thicker than those in the Minor network. In a model in which Major network fibers are 10 times thicker than fibers of the Minor network, the fibers in the Minor network make a negligible contribution to the turbidity of the clot. However, they may have a marked effect on its permeability. Experiments with clots made from human fibrinogen show that the Minor network is stabilized by α‐polymer and γ‐γ linkages and that without such linkages it is washed away during permeation. It remains relatively intact in crosslinked clots. In agreement with the theoretical model, when mass–length ratios calculated from the turbidity are compared with those calculated from the permeability, the latter were reduced in crosslinked clots with an intact Minor network.
Cu(II)–protamine interaction. II. The formation and structure of Cu(II) complexes of clupeine YII and of peptides mimicking clupeine N‐terminals
Authors: Salardi Sergio , Tosi Lucia , Garnier‐Suillerot Arlette , Toniolo Claudio , Bonora Gian Maria , Marchiori Fernando 
Published: December 2004

AbstractThe interaction of Cu(II) with the protamine clupeine YII (containing proline at the N‐terminal) and with four peptides (H‐Ala‐Arg‐OMe, H‐Ala‐Arg2‐OMe, H‐Pro‐Arg‐OMe, and H‐Arg4‐Tyr) has been studied by means of absorption, CD, and pH neasurements. The first two peptides mimic clupeine YI and Z N‐terminals; the third, the clupeine YII N‐terminal. At 1:1 molar ratio, clupeine YII yields two complexes: the first (I), at pH 6.6, through coordination via the N‐terminal and the contiguous peptide nitrogen forming a five‐membered chelate; the second (II), at pH 8.5, through the occupancy of the other two corners of the coordination square by amino nitrogens of the lateral chains. These complexes are strictly analogous and occur at the same pH as those formed with clupeine Z. Under the same conditions, all the peptides yield complex I in the first step, although the pH at which this complex is fully defined depends on the number of residues in the chain. It is 8.5 for dipeptides, decreases to 6.5 by the addition of a third residue to the chain, and remains constant when the number of residues is three or more. The amino nitrogens of lateral chains are unable to coordinate to the metal in a second step unless one additional peptide bond lies between the N‐terminal residue and that containing the lateral chain bound to the metal. Thus, H‐Ala‐Arg‐OMe and H‐Pro‐Arg‐OMe form hydroxyl complexes in a second step (pH 11), by deprotonation of one of the water molecules coordinated to the metal; one of the lateral chains of H‐Ala‐Arg2‐OMe is able to coordinate in a second step (pH 8.5), but it is only with H‐Arg4‐Tyr that a second complex (II) is obtained in which two amino nitrogens of lateral chains supersede the oxygens of water molecules in I, at pH 8.5.
Broadline proton magnetic resonance study of cellulose, pectin, and bean cell walls
Authors: MaCkay Alex L. , Bloom Myer , Tepfer Mark , Taylor Iain E. P. 
Published: December 2004

AbstractWe have used broadline proton magnetic resonance to study molecular motion in cellulose, a sodium pectate solution, a calcium pectate gel, and isolated bean cell walls. All samples were prepared in D2O to minimize the contribution of water to the observed signals. For each sample, a free induction decay was obtained, and the second moment, spin‐lattice relaxation, and dipolar relaxation were measured. Our results show that the large majority of protons in cellulose are immobile. Rigid and mobile domains were also observed in the pectate samples. We have shown that gelation induces large‐scale changes in the free induction decay, the second moment, and the relaxation behavior of the pectate. As with the other samples, rigid and more mobile domains were found in bean cell walls. The fraction in the rigid domains is much larger than the fraction of cellulose in the sample, suggesting that the noncellulosic wall components are also organized into rigid and mobile domains.