bluuebunny/crossref_metadata_2025_split huggingface dataset:
β‐Alanyl‐β‐alanine in cyclic β‐turned peptides
Authors: Blasio B. Di , Lombardi A. , Yang X. , Pedone C. , Pavone V. 
Published: December 2004

AbstractIn the present paper we describe the synthesis, purification, and single crystal x‐ray analysis of the cyclic pentapeptide cyclo‐(L‐Pro‐L‐Pro‐L‐Phe‐β‐Ala‐β‐Ala). The peptide was synthesized by classical solution methods and the cyclization of the free pentapeptide was accomplished in good yields in diluted methylenechloride solution using N,N‐dicyclohexylcarbodiimide. The compound crystallizes in the monoclinic space group P21 from hot water with five solvent molecules. The Pro1‐Pro2 peptide bond is cis and the molecular conformation is stabilized by an intramolecular hydrogen bond between the CO group of the β‐Ala5 and the NH of the Phe3 residue. The Pro1‐Pro2 segment occupies the relative positions 2 and 3 of a type VIa β‐turn, while the L‐phenylalanyl‐β‐alanyl‐β‐alanine segment is incorporated in a C13‐like ring structure. The crystal packing is characterized by a network of 11 intermolecular hydrogen bonds involving all the remaining CO, NH, and the water molecules.
Thermally induced conformational transition of double‐stranded xanthan in aqueous salt solutions
Authors: Kitamura Shinichi , Takeo Kenichi , Kuge Takashi , Stokke Bjørn T. 
Published: December 2004

AbstractThe thermally induced conformational transition of double‐stranded xanthans (degree of pyruvate substitution, DSP = 0.45) having Mw = 3.1, 5.7, and 20.3 × 105 has been studied in aqueous salt solutions by high‐sensitivity differential scanning calorimetry (DSC). The double strandedness of these samples in the ordered conformation was ascertained by the value of mass per unit length, ML = 2090 ± 270 g mol−1 nm−1, which was determined from the contour length obtained by electron microscopic observations and the molecular weight by light scattering measurements. The temperature at half completion of the transition T½ for these samples increased linearly with the logarithm of the cation (Na+, K +) concentration. The plot of 1/T½ vs the natural logarithm of cation (Na + ) concentration in mM for the sample with Mw = 5.7 × 105 (15‐SX) yielded the equation 103/T½ = 3.45−0.159 in[Na +]. The specific enthalpy Δhcal, for 15‐SX, essentially independent of salt concentration above 20 mM, was 8.31 ± 0.39 J/g (SD, n = 6). No systematic dependence of molecular weight on the transition temperature and the enthalpy was observed. Application of the Manning polyelectrolyte theory to the system using the DSC data suggested that the separation of the double strand of xanthan into two single chains was not completed at the temperature where the endothermic peak was finished. This suggestion is consistent with recent findings by light scattering measurements as a function of temperature. Our DSC study was extended to include four other samples from various sources. It was found that T½ and Δhcal depend on the pyruvate contents of the samples. For example, the t½(t½/° C = T½/K − 237.15) values for samples with high pyruvate content (DSp = 0.9) and depyruvated (DSp = 0.14) in 20 m Maqueous NaCl were 48.8 and 85.3°C, respectively. Two other samples showed relatively broad DSC curves having shoulders, which were resolved into two independent components. Thermodynamic parameters for each component were examined as a function of salt concentration, and the results obtained were interpreted in terms of the heterogeneity of the pyruvate content of the samples.
Determining molecular weight distributions of antigen–antibody complex by quasi‐elastic light scattering
Authors: Murphy Regina M. , Yarmush Martin L. , Colton Clark K. 
Published: December 2004

AbstractPhysiological properties of soluble antigen–antibody (Ag‐Ab) complexes depend in part on the size of the complexes. In previous work, the size distribution and structure of model Ag‐Ab complexes were determined by electron microscopy. In this study, we used constrained regularization analysis of quasi‐elastic light scattering data to estimate molecular weight distributions of model Ag‐Ab complexes. A conformational model was necessary to determine appropriate correlations between molecular weight and diffusion coefficient, and to estimate particle structure factors. Porod–Kratky theory proved to be an adequate conformational model for these purposes. The molecular weight distributions determined by constrained regularization compared favorably with distributions obtained either by electron microscopy or by thermodynamic modeling.
Dependence of the hydration shell structure in the minor groove of the DNA double helix on the groove width as revealed by monte carlo simulation
Authors: Teplukhin A. V. , Poltev V. I. , Chuprina V. P. 
Published: December 2004

AbstractThe hydration shell of several conformations of the polynucleotides poly(dA) · poly(dT), poly (dA) · poly (dU), and poly (dA‐dl) · poly (dT‐dC) has been simulated using the Monte Carlo method (Metropolis sampling). Calculations have shown that the structure of the hydration shell of the minor groove greatly depends on its width. In conformations with a narrowed minor groove, the first layer of the hydration shell of this groove has only one molecule per nucleotide pair that forms H bonds with purine N3 of one pair and pyrimidine O2 of the next pair. The second layer of the hydration shell of such conformations contains molecules that form H bonds between two adjacent molecules of the first layer. The probability of formation of hydration spine is about 20% while the bridges of the first layer are formed with a probability of about 70%.In the first layer of the minor groove of the B–DNA conformation with wide minor groove there are approximately two water molecules per base pair that form H bonds with purine N3 or pyrimidine O2 and with the sugar ring oxygen of the adjacent nucleotide. The probability of simultaneous H bonding of a water molecule with N3 (or O2) and O of sugar ring is about 30%.The results of simulation suggest that hydration spine proposed for the narrowed minor groove of oligonucleotide crystals [H. R. Drew, and R. E. Dickerson (1981) Journal of Molecular Biology, Vol. 151, pp. 535–556] can be formed in fibers of poly (dA) · poly (dT), poly (dA) · poly (dU), and poly (dA‐dl) · poly (dT‐dC) as well as in DNA fragments of these sequences in solution. The role of the hydration shell of the minor groove of DNA double helix in stabilization of certain B‐family conformations is discussed.
Anti‐insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent
Authors: Tanner John J. , Nell Laura J. , McCammon J. Andrew 
Published: December 2004

AbstractMolecular dynamics at 300 K was used as a conformation searching tool to analyze a knowledge‐based structure prediction of an anti‐insulin antibody. Solvation effects were modeled by packing water molecules around the antigen binding loops. Some loops underwent backbone and side‐chain conformational changes during the 95‐ps equilibration, and most of these new, lower potential energy conformations were stable during the subsequent 200‐ps simulation. Alterations to the model include changes in the intraloop, main‐chain hydrogen bonding network of loop H3, and adjustments of Tyr and Lys side chains of H3 induced by hydrogen bonding to water molecules. The structures observed during molecular dynamics support the conclusion of the previous paper that hydrogen bonding will play the dominant role in antibody‐insulin recognition. Determination of the structure of the antibody by x‐ray crystallography is currently being pursued to provide an experimental test of these results. The simulation appears to improve the model, but longer simulations at higher temperatures should be performed.
Quantum yield for preferential photodimerization in long pyrimidine tracts
Authors: Texter John 
Published: December 2004

AbstractThe quantum yield for cyclobutyl‐pyrimidine dimerization in DNA has been observed to increase approximately linearly with increasing pyrimidine tract length. A model without adjustable parameters for this yield is proposed based on energy delocalization, vibronic symmetry switching, and saturation statistics that describe the average number of (base pairwise) breathing modes in a given tract of pyrimidines. This average number of modes is an approximately linear function of the tract length. Monte Carlo techniques are used to simulate base sequences and photochemical events, and indicate that this model is consistent with experiment for Tetrahymena pyriformis DNA.
Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc‐Gly‐Val‐Gly‐Gly‐Leu‐Ome
Authors: Lelj F. , Tamburro A. M. , Villan V. , Grimaldi P. , Guantieri V. 
Published: December 2004

AbstractThe conformational behavior of the synthetic peptide, Boc‐Gly‐Val‐Gly‐Gly‐Leu‐OMe, containing the X‐Gly‐Gly and Gly‐Gly‐X (X = Val or Leu) repeating sequences and constituting a fragment of elastin was investigated by molecular mechanics and molecular dynamics (MD) simulation. The results suggest that, irrespective of the approximations used, the molecule shows a manifold of low energy conformations characterized by γ‐turns and type II β‐turns. Furthermore, MD simulations point out a conformational floppiness due to very low barriers between different conformations. Experimental CD measurements in a virtually apolar medium (dioxane − ε = 2.209), which better mimics the vacuum conditions of the simulation, support the theoretical results. The general emerging picture, indicating the molecule as characterized by a combination of flexibility with conformational preferences, is in agreement with previous experimental findings and enriches of new aspects the description of the microscopic behavior of this molecule suggesting more detailed interpretation of previous data.
Helix formation in poly(Nε,Nε,Nε‐trimethyl‐L‐lysine) and poly(L‐lysine): Dependence on concentration and molecular weight
Authors: Bello Jake 
Published: December 2004

AbstractHelix formation in (Lys)n · HClO4 and poly(Nε, Nε, Nε–trimethyl‐L‐lysine) · HClO4 [(LysMe3)n · HClO4] is dependent on peptide concentration and on molecular weight. For (LysMe3)n · HClO4 of degree of polymerization (DP) 2510 the midpoint of the coil‐to‐helix transition is 2 mM and for DP of 190 it is 5 mM. For (Lys)n · HC1O4 the peptide concentration for half‐helix is 30–60 times as high, and is only weakly dependent, if at all, on molecular weight. Helix formation is an intermolecular process. The use of methylated (Lys)n as the perchlorate permits study of the intermolecular coil‐helix transition at low concentration, instead of the high concentration (ca. 1–2M) required for (Lys)n · HBr. At constant peptide concentration helix content increases with added NaClO4. The higher the peptide concentration, the less NaClO4 is needed to induce helix.
Conformations of type 1 and type 2 oligosaccharides from ovarian cyst glycoprotein by nuclear overhauser effect spectroscopy and T1 simulations
Authors: Cagas Perseveranda , Bush C. Allen 
Published: December 2004

AbstractTo probe differences in conformation of the type 1 and type 2 linkages in blood group oligosaccharides, two‐dimensional nuclear Overhauser effect spectroscopy (2D‐NOESY) and 1H T1 data were obtained for two blood group A oligosaccharide alditols containing the type 1 and type 2 linkage. The NOE data were interpreted using a complete relaxation matrix approach. Simulations of NOE and T1 values were made using disaccharide and tetrasaccharide model conformations generated by a systematic variation of the glycosidic dihedral angles ϕ and ψ. NOEs from the amide protons of GlcNAc and GalNAc in the type 1 pentasaccharide alditol were obtained, and simulated in a manner similar to those from carbon‐bound protons. In addition to providing data for determining the conformation of the type 1 linkage from amide proton NOEs of GlcNAc and GalNAc to neighboring residues, amide proton NOEs also yield information on the orientation of the acetamido side chains. The amide NOE data indicated subtle differences in the orientation of the amide side chain of GlcNAc among the A type 1 pentasaccharide alditol and two previously studied blood group oligosaccharides, lacto‐N‐difucohexaose 1 and lacto‐N‐fucopentaose 1. From the NOE and 1H T1 data, and from simple rigid geometry energy calculations, it is concluded that the type 1 and type 2 linkages in the oligosaccharides studied have different conformations and that these conformations are relatively rigid in solution.
Refinement of the thrombin‐bound structure of a hirudin peptide by a restrained electrostatically driven Monte Carlo method
Authors: Ripoll Daniel R. , Ni Feng 
Published: December 2004

AbstractEnergy refinement of the structure of a linear peptide, hirudin56–65, bound to thrombin was carried out using a conformational search method in combination with restrained minimization. Five conformations originated from nmr data and distance geometry calculations having a similar global folding pattern but quite different backbone conformations were used as the starting structures. As a result of this approach, a series of low‐energy conformations compatible with a set of upper and lower bounds of interproton distances determined from transferred nuclear Overhauser effects were found. A comparison among the lowest energy conformations of each run showed that the combination of energy refinement plus distance constraints led to a very well‐defined structure for both the backbone and the side chains of the last 7 residues of the polypeptide. Furthermore, the low‐energy conformations generated with this technique contain a segment of 310‐helix involving the last 5 residues at the COOH terminal end.
Tyrosine‐derived polycarbonates: Backbone‐modified “pseudo”‐poly(amino acids) designed for biomedical applications
Authors: Pulapura Satish , Kohn Joachim 
Published: December 2004

AbstractStarting from L‐tyrosine (Tyr) and its metabolites desaminotyrosine (Dat) and tyramine (Tym), four structurally related model dipeptides were prepared: Dat‐Tym (neither N‐ or C‐terminus present), Z‐Tyr‐Tym (N‐terminus protected by benzyloxycarbonyl), Dat‐Tyr‐Hex (C‐terminus protected by a hexyl ester group), and Z‐Tyr‐Tyr‐Hex (both N‐ and C‐termini present, protected by benzyloxycarbonyl and hexyl ester, respectively). The model dipeptides were used as monomers in the synthesis of polycarbonates. The polymerization reaction in the presence of either phosgene or triphosgene proceeded via the phenolic hydroxyl groups. Polymers with molecular weights of 105,000–400,000 da (by gel permeation chromatography, relative to polystyrene standards) were obtained. The physicomechanical properties (solubility, mechanical strength, glass transition and decomposition temperature, processibility) of the polymers were determined, and an attempt was made to correlate the polymer properties with the nature of the N‐ and C‐terminus protecting groups. The presence of the urethane bond at the N‐terminus protecting group was found to reduce solubility, ductility, and processibility, probably due to interchain hydrogen bonding. The presence of a C‐terminus alkyl ester group increased solubility and processibility. Thus, the most promising candidate polymer for biomedical applications was obtained from Dat‐Tyr‐Hex, the monomer carrying a C‐terminus protecting group only. Since very similar results had recently been obtained for a series of structurally related polyiminocarbonates, the structure property correlations seem to be generally valid.
The structure of Ro 09‐0198 in different environments
Authors: Kessler H. , Mierke D. F. , Saulitis J. , Seip S. , Steuernagel S. , Wein T. , Will M. 
Published: December 2004

AbstractThe constitution and configuration of Ro 09‐0198 (cinnamycin) have been determined in DMSO. Further investigations in aqueous solution, in SDS micelles and in a lipid bilayer have been done to study the influence of different environments on the conformation of the peptide. It turned out that in spite of the polycyclic structure of the molecule, the conformation is drastically changed going from water to SDS micelles. Ro 09‐0198 orients itself in lipid bilayers as expected from its amphiphilic structure. According to a nuclear Overhauser effect spectroscopy experiment under magic angle spinning (MAS) conditions, the molecule is incorporated into the membrane with its hydrophobic part inside the bilayer.
NMR and CD studies of triple‐helical peptides
Authors: Brodsky Barbara , Li Ming‐Hua , Long Cynthia Gwynne , Apigo Josefa , Baum Jean 
Published: December 2004

AbstractTriple‐helix formation of the peptide (Pro‐Hyp‐Gly)10 was monitored by nmr and CD spectroscopy. The two‐dimensional nmr spectra indicated that the Gly Cα H and Pro CδH proton resonances shift upfield in going from the nonhelical to helical form, while hydroxyproline resonances are unchanged. The integrated areas of the helical and nonhelical resonances could be monitored in the one‐dimensional nmr spectrum, and indicate that in the (Pro‐Hyp‐Gly)10 about 90% of the residues are in a defined triple‐helical conformation. The introduction of a glycine to alanine substitution or the deletion of a single hydroxyproline residue in the stable triple‐helical peptide (Pro‐Hyp‐Gly)10 still allows trimers to be formed, but the trimers show a substantial loss of triple helix and decreased thermal stability compared with (Pro‐Hyp‐Gly)10. Two computer models were generated for the Gly → Ala peptide, one with the Ala side chains packed inside the helix and the other with the region containing the alanines forming a β‐bend that loops out from the helix. The nmr data is more consistent with the latter model.
Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide
Authors: Loncharich Richard J. , Brooks Bernard R. , Pastor Richard W. 
Published: December 2004

AbstractThe rate constant for the transition between the equatorial and axial conformations of N‐acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency γ = 2 ps−1, shows diffusive character for γ ≥ 10 ps−1, but does not approach zero even at γ = 0.01 ps−1. This behavior differs from that found for a one‐dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., γ ≈ 2 ps−1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with γ = 0) or molecular dynamics in solvent (where dynamics is largely diffusive).
Theory of delocalized ionic binding to polynucleotides: Structural and excluded‐volume effects
Authors: Ray Jolly , Manning Gerald S. 
Published: December 2004

AbstractA previously developed theory for the delocalized binding of ions to polyelectrolytes was restricted to point ions and a structurally rigid polyelectrolyte. For the binding of substances like oligolysines and polyamines to DNA, the restriction to point ions would appear not to be realistic. For the binding of ions to flexible chains like single‐stranded polynucleotides, the restriction to a rigid polyelectrolyte may not be realistic. In this article, we assess the effect of relaxation of these two restrictions. Excluded volume among bound ions is modeled by a hard‐rod potential in the context of the theory of a one‐dimensional fluid. The possibility that a flexible chain folds in some manner in the immediate vicinity of a bound ion is modeled by allowing the mean spacing between charged groups on the polymer to become smaller as the number of bound ions increases. We compare our results with recent data on the binding of a series of oligolysines to single‐stranded polynucleotides, which conflict with the predictions of the original theory of delocalized binding of point ions to rigid polyelectrolytes. Inclusion of excluded volume among bound ions does not significantly improve agreement with the data. Substantial improvement in the level of agreement is obtained when the polyion chain is assumed to be flexible. One of our conclusions is that the excluded‐site description of anticooperativity, which was designed for the binding of ligands to discrete sites on a polymer chain, and which does not include the effect of ionic forces, should not be used in cases of delocalized binding of ions.
Heavy metal binding to heparin disaccharides. I. Iduronic acid is the main binding site
Authors: Whitfield Dennis M. , Choay Jean , Sarkar Bibudhendra 
Published: December 2004

AbstractAs model compounds for Ni(II)‐binding heparin‐like compounds isolated from human kidneys (Templeton, D. M. & Sarkar, B. (1985) Biochem. J. 230 35–42.), we investigated two disaccharides—4‐O‐(2‐O‐sulfo‐α‐L‐idopyranosyluronic acid)‐2,5‐anhydro‐D‐mannitol, disodium salt (1a), and 4‐O‐(2‐O‐sulfo‐α‐L‐idopyranosyluronic acid)‐6‐O‐sulfo‐2,5‐an‐hydro‐D‐mannitol, trisodium salt (1b)—that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high‐performance liquid chromatography (HPLC) binding assay with the tracer ions 63Ni(II) 54Mn(II), 65Zn(II), and 109Cd(II). This result is in accord with the isolation of two 67Cu(II) and 63Ni(II) binding fractions from a complete pool of nitrous‐acid‐derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB‐MS, NMR and HPLC‐PAD. Similarly, two synthetic disaccharides—methyl, 2‐O‐sulfo‐4‐O‐(α‐L‐idopyranosyluronic acid)‐2‐deoxy‐2‐sulfamido‐α‐D‐glucosamine, trisodium salt [IdopA2S(α1,4)GlcNSαMe,2a], and 2‐O‐sulfo‐4‐O‐ (α‐L‐idopyranosyluronic acid)‐2‐deoxy‐2‐sulfamide‐6‐O‐sulfo‐α‐D‐glucosamine, tetrasodium salt [IdopA2S(α1,4) GlcNS6SαMe,2b]—were shown to bind tracer amounts of 63Ni and 67Cu using chromatographic assays. Subsequently, 1H NMR titrations of 1a, 1b, 2a, and 2b with Zn(OAc)2 were analyzed to yield 1:1 Zn(II)‐binding constants of 472 ± 59, 698 ± 120, 8,758 ± 2,237 and 20,100 ± 5,598M−1, respectively. The values for 2a and 2b suggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. NMR evidence for this hypothesis comes from marked 1H and 13C chemical shift changes to the iduronic acid resonances after addition of diamagnetic Zn(II) ions.