bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modified chemotactic peptides: Synthesis, conformation, and biological activity of for‐Thp‐Leu‐ΔzPhe‐OMe
Authors: Torrini I. , Zecchini G. Pagani , Paradisi M. Paglialunga , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Traniello S. , Spisani S. , Cerichelli G. 
Published: December 2004

AbstractFor‐Thp‐Leu‐ΔzPhe‐OMe (2), an analogue of the chemotactic tripeptide For‐Met‐Leu‐Phe‐OMe, containing 4‐aminotetrahydrothiopyran‐4‐carboxylic acid (Thp) and (Z)‐2,3‐didehydrophenylalanine (ΔzPhe) as achiral, conformationally restricted mimics of Met and Phe, respectively, has been synthesized. In the crystal the new formyltripeptide adopts a type I β‐turn conformation stabilized by a weak H bond between the formylic oxygen and the ΔzPhe NH. 1H‐nmr analysis based on NH solvent accessibility and nuclear Overhauser effect experiments suggests that the β‐turn is not preferred in CDCl3 solution where a γ‐turn, centered at the Thp residue, prevails. The biological activity of 2 has been determined on human neutrophils and compared to that of previously studied analogues. The tripeptide 2 is practically unable to elicit superoxide anion production and lysozyme release, while slight, but not statistically significant activity was induced in chemotaxis. The role of the orientation of the aromatic ring with respect to the backbone adjacent atoms is discussed. © 1994 John Wiley & Sons, Inc.
Molecular modeling of the conformational and sodium ion binding properties of the oligosaccharide component of ganglioside GM1
Authors: Rodgers James C. , Portoghese Philip S. 
Published: December 2004

AbstractThe receptor‐like recognition behavior of the GM1 ganglioside has been examined theoretically in terms of conformational and binding properties. Modeling was conducted at two limiting conditions of dielectric constant in order to determine sensitivity to scaling of coulombic interactions. A systematic conformational search of the GM1 oligosaccharide in the absence of explicit solvent molecules indicates that there are many inherently low energy conformational states. Up to 39 conformers were found with energies within 5 kcal/mole of the observed lowest energy conformer. Using a dielectric constant of 80, a systematic search of sodium binding sites on GM1 identified 37 sites where a positively charged group might bind, while at least 12 sites were identified using a dielectric constant of 1. Notably important binding sites include pockets formed by the proximity of glycosidic (O1), sugar ring (O5), and exocyclic methylene hydroxyl (OH6) oxygens on the sugars. The oxygens of acetyl groups attached to sugars also contribute to the binding. Direct coordination with the carboxylate of sialic acid is not a prerequisite for cationic binding. The large number of conformational states and binding sites for the GM1 oligosaccharide are paradoxical to the specific recognition behavior of the molecule. This paradox can be explained in terms of bridging ligands, which are found from molecular dynamics to be capable of stabilizing molecular conformation. © 1994 John Wiley & Sons, Inc.
Effects of DNA charge and length on the electrophoretic mobility of intercalated DNA
Authors: Reese Howard R. 
Published: December 2004

AbstractDNA molecules ranging in size from 1 to 630 kilobase pair and intercalated with either ethidium bromide (EtBr) or propidium iodide (PI) were electrophoresed in 1% agarose at four different electric field strengths. The extent of intercalation of EtBr under the conditions of our electrophoresis experiments was determined by a spectroscopic technique, whereas the extent of intercalation of PI was inferred from previous studies. The effects of the increase in DNA contour length and the concomitant decrease of linear charge density were separated based on our analysis of the mobility data. We conclude that the main factor responsible for the reduced electrophoretic mobility of intercalated DNA is the diminished linear charge density and not the increased contour length. © 1994 John Wiley & Sons, Inc.
Vibrational analysis of glutathione
Authors: Qian Weili , Krimm Samuel 
Published: December 2004

AbstractInfrared and Raman spectra have been obtained of crystalline glutathione and its deuterated derivative and interpreted by normal mode analysis. The force field consisted of our empirical force fields for the peptide group and NH and CO end groups, plus our ab initio force fields for the CH2SH and CH2COOH moieties. Observed bands are reproduced with an average error of 5 cm−1, demonstrating that the vibrational spectrum of such a complex molecule can be understood in great depth. © 1994 John Wiley & Sons, Inc.
The potential energy surface of methyl 3‐O‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside in aqueous solution: Conclusions derived from optical rotation
Authors: Stevens Eugene S. 
Published: December 2004

AbstractThe optical rotation of methyl 3‐O ‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside is calculated semiempirically as a function of the linkage dihedral angles ϕ (H1‐C1‐O1‐C3′) and ψ (C1‐O1‐C3′‐H3′). Comparison with the observed optical rotation in aqueous solution indicates the existence of at least two conformers in solution, which implies a degree of linkage flexibility. The result is in agreement with some, but not all, calculated potential energy surfaces, and with recently published nmr data. © 1994 John Wiley & Sons, Inc.
Modeling of arabinofuranose and arabinan, II. Nmr and Conformational analysis of arabinobiose and arabinan
Authors: Cros Soizic , Imberty Anne , Bouchemal Nadia , Du Penhoat Catherine Hervé , Perez Serge 
Published: December 2004

AbstractThe disaccharide arabinobiose (5‐O‐α‐L‐arabinofuranosyl‐α‐L‐arabinofuranose) constitutes the basic repeating structures found in such polysaccharides as arabinan or in the side chains of the hairy regions of pectins. The conformational behavior of aqueous arabinobiose has been investigated by high resolution nmr and computerized molecular modeling. The complete conformational analysis of the, disaccharide has been achieved with the MM3 molecular mechanics methods using the flexible residue method. In this study, both the puckering of the arabinofuranose, rings and the orientations about the glycosidic torsion angles ϕ, ψ, and ω; were considered. Some insights into conformational transitions were obtained through molecular dynamics simulation using the CHARMM force field. In parallel, transient nuclear Overhauser effects at 400.13 MHz and long‐range vicinal homonuclear and heteronuclear coupling constants have been measured. The theoretical nmr data were calculated taking into account all accessible conformations and using averaging methods for both slow and fast internal motions models. The data do not support a single conformational model, and only conformational averaging yields the excellent agreement between the observed and simulated parameters. Within the potential energy surfaces computed for the disaccharide, several low energy conformers can be identified. When these conformations are extrapolated to regular polysaccharide structures, they generate chains of arabinan displaying right‐ and left‐handed chirality and a wide range of repeating units per turn of helix. © 1994 John Wiley & Sons, Inc.
Redox‐active bis‐cysteinyl peptides. I. Synthesis of cyclic cystinyl peptides by conventional methods in solution and on solid supports
Authors: Musiol Hans‐Jürgen , Siedler Frank , Quarzago Daniela , Moroder Luis 
Published: December 2004

AbstractCyclic mono‐cystinyl active‐site fragments of thioredoxin and thioredoxin reductase were synthesized as N‐acetyl and C‐amide octapeptides by conventional methods of peptide synthesis in solution and on solid supports. Using a side‐chain protection based on acid‐labile tert‐butanol‐derived groups and on the S‐tert‐butylthio unsymmetric disulfide for the thiol functions, in combination with Nα‐Z‐ or Nα‐Nps derivatives in the chain elongation steps, the synthesis in solution was carried out in straightforward manner yielding the fully protected octapeptides as well characterized compounds. Upon deprotection with trifluoroacetic acid and reduction of the unsymmetrical disulfides with tri‐butylphosphine, the resulting bis‐cysteinyl‐octapeptides were oxidized in dimethylformamide with azodicarboxylic acid di‐tert‐butyl ester to produce the desired cyclic compounds in good overall yields. For the synthesis on solid supports a similar acid‐labile side‐chain protection was applied in combination with the Nα 9‐flourenylmethyoxycarbonyl derivatives in the chain elongation steps. Thereby acylations were performed with the related amino acid N‐car‐boxyanhydrides (UNCAs) or by the O‐(1H‐benzotriazol‐1‐yl)‐N,N,N′,N′‐tetramethyl‐uronium‐tetrafluoroborate/1‐hydroxybenzotriazole (TBTU/HOBt) procedure. The solid phase synthesis of the two octapeptides led to unexpected difficulties in terms of recovery of peptidic material from the resins in the final acidolytic cleavage step as well as of racemization at the level of the cysteine residues by the TBTU/HOBt coupling method. Racemization was efficiently suppressed by employing the related pentafluorophenyl ester and this method led to crude octapeptide products of a degree of purity comparable to those obtained by the synthesis in solution. However, the recovery of the peptides from the resin, i.e., irreversible reattachment of cleaved peptidic material via alkylation of various side‐chain functions, could not be avoided even using the most efficient scavengers or their cocktails. © 1994 John Wiley & Sons, Inc. © 1994 John Wiley & Sons, Inc.
Nmr study of collagen‐water interactions
Authors: Renou J. P. , Bonnet M. , Bielicki G. , Rochdi A. , Gatellier P. 
Published: December 2004

AbstractA proton magnetic resonance study of different cross‐linked collagens was performed as a function of water content and temperature. Collagens from three connective tissues (calf, steer, and cow) were chosen according to the different number of nonreducible multivalent cross‐links, which increases during the life of animal. Samples were hydrated under five well‐defined water activities (Aw) ranging from 0.44 to 0.85. The transverse and cross‐relaxation times of water protons were studied as a function of temperature from −20 up to 100°C. From the temperature dependence of relaxation rates, the dynamics of water molecules can be described according to different processes: exchange of protons at the higher temperatures and dipole‐dipole interactions that prevail at the lower temperatures. The exchange processes are analyzed as a function of the residence lifetime of water molecules at the protein interface and of the transfer of spin energy from water protons to macromolecule protons. The proton dipole‐dipole interactions are related to the relaxation parameters of protein and water protons. All the relaxation parameters showed specific behavior for the 0.44 water activity for every tissue. The collagen tissue from calf also showed distinct behavior in comparison with other tissues. © 1994 John Wiley & Sons, Inc.
Predicting immunoglobulin‐like hypervariable loops
Authors: Vasmatzis George , Brower Richard , Delisi Charles 
Published: December 2004

AbstractA two‐stage method is developed to search the conformational space of small protein segments for low energy structures. Central features of the method are efficient procedures for generating small, eight‐backbone atom, local moves in Cartesian coordinates and for introducing geometric constraints in adaptable Monte Carlo procedures. This allows natural implementation of an adaptive simulated annealing algorithm, which achieves an effective trade‐off between speed and acceptance ratio. The method is applied to the calculation of various immunoglobulin loops. We also develop data base derived rules for identifying constraint conditions, and show that the incorporation of an identified side‐chain constraint allows a 1.2 Å all‐backbone atom rms deviation prediction of a 9 residue long L1 loop. © 1994 John Wiley & Sons, Inc.
Characterization of β‐bend ribbon spiral forming peptides using electronic and vibrational CD
Authors: Yoder Gorm , Keiderling Timothy A. , Formaggio Fernando , Crisma Marco , Toniolo Claudio 
Published: December 2004

AbstractTerminally blocked (L‐Pro‐Aib)n and Aib‐(L‐Pro‐Aib)n sequential oligopeptides are known to form right‐handed β‐bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 310‐helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260‐180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750‐1500 cm−1) regions. The critical chain length for full development of the β‐bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration‐induced stabilization of the structures of the longer peptides were seen in the resolution‐enhanced FTIR spectra. Comparison to previous studies of (Aib)n and (Pro)n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 310‐helix. © 1995 John Wiley & Sons, Inc.
Molecular dynamics simulations of the effects of ring‐saturated thymine lesions on DNA structure
Authors: Miaskiewicz Karol , Miller John , Ornstein Rick , Osman Roman 
Published: December 2004

AbstractThe effect of thymine lesions produced by radiation or oxidative damage on DNA structure was studied by molecular dynamics simulations of native and damaged DNA. Thymine in position 7 of native dodecamer d(CGCGAATTCGCG)2 was replaced by one of the four thymine lesions 5‐hydroxy‐5,6‐dihydrothymine, 6‐hydroxy‐5,6‐dihydrothymine (thymine photohydrate), 5,6‐dihydmxy‐5,6‐dihydro‐thymine (thymine glycol), and 5,6‐dihydmthymine. Simulations were performed with Assisted Model Building with Energy Refinement force field. Solvent was represented by a rectangular box of water with periodic boundary conditions applied. A constant temperature and constant volume protocol was used, the observed level of distortions of DNA structure depends on the specific nature of the lesion. The 5,6‐dihydrothymine does not cause distinguishable perturbations to DNA. Other lesions produce a dramatic increase in the rise parameter between the lesion and the 5′ adjacent adenine. These changes are accompanied by weakening of Watson–Crick hydrogen bonds in the A6‐T19 base pair on the 5′ side of the lesion. The lesioned bases also show negative values of inclination relative to the helical axis. No changes in the pattern of backbone torsional angles are observed with any of the lesions incorporated into DNA. The structural distortions in DNA correlate well with known biological effects of 5,6‐dihydrothymine and thymine glycol on such processes as polymerase action or recognition by repair enzymes. © 1995 John Wiley & Sons, Inc.
Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations
Authors: Beglov Dmitrii , Roux Benoît 
Published: December 2004

AbstractA simple approximation is developed to account for the dominant effects of solvation in molecular dynamics simulations of biopolymers. A small number of water molecules are included explicitly in the primary hydration shell around the biopolymer. A nonspherical confining potential responding dynamically to the conformational changes of the biopolymer is applied to prevent evaporation and to approximate the conditions of constant pressure of a bulk solution. Simulations of a spherical system of 25 water molecules are lined to adjust the empirical restraining potential to yield a uniform density distribution close to that in the bulk liquid. The primary hydration shell approach is tested with molecular dynamics simulations of simple hydrated peptides. The conformational equilibrium of alanine dipeptide and alanine tripeptide is examined using umbrella sampling calculations. The relative free energies of the C7ax (ϕ = 60, ψ = −80) and αL (ϕ = 60, ψ = 60) conformations of the alanine dipeptide and the opened and closed conformations of a reversed β‐turn modeled with the alanine tripeptide were calculated. The results indicate that the primary hydration shell can reproduce the influence of solvent on small peptides that was observed in simulations involving a much larger number of water molecules. © 1995 John Wiley & Sons, Inc.
Gel electrophoresis measurement of counterion condensation on DNA
Authors: Ma Chenglie , Bloomfield Victor A. 
Published: December 2004

AbstractWe used agarose gel electrophoresis to measure the effective charge neutralization of DNA by counterions of different structure and valence, including Na+, Mg2+, Co(NH3), and sperinidine3+, which competed for binding with an excess of Tris acetate buffer. Linear DNA molecules ranged in size from 1 to 5 kilobases, and supercoiled plasmid pUC18 was also measured. In all cases, the results were in good agreement with theoretical predict ions from counterion condensation theory for two‐counterion mixtures. © 1995 John Wiley & Sons, Inc.
Modeling of long‐range electrostatic interactions in DNA
Authors: Vologodskii Alexander , Cozzarelli Nicholas 
Published: December 2004

AbstractWe used a Monte Carlo approach to compute the statistical properties of closed DNA chains with different descriptions of the electrostatic interactions. We compared these computed results with experimentally measured knotting probabilities, which are very sensitive to intersegment interactions. The calculated results based on the Debye‐Hückel approximation of the solution of the Poisson‐Boltzmann equation agreed very well with the published experimental data, while potential based on counterion condensation theory was clearly less satisfactory. We then compared the simpler hard‐core approximation of electrostatic interactions to the Debye‐Hückel potential. The hard‐core approximation, specified in terms of a DNA effective diameter, gives the same conformational properties of random coils as the Debye‐Hückel approximation. We found clear but relatively small differences between the two potentials for the conformational properties of supercoiled DNA. © 1995 John Wiley & Sons, Inc.
1H‐, 13C‐, and 113Cd‐nmr study of the Cd(II) complex of a blocked peptide, Z‐Cys‐Ala‐Pro‐His‐OMe, in organic solvents
Authors: Zaima Hiroaki , Ueyama Norikazu , Adachi Hayamitsu , Nakamura Akira 
Published: December 2004

AbstractThe Cd(II) complex of a peptide, Z‐Cys‐Ala‐Pro‐His‐OMe was prepared and characterized by absorption, CD, 1H‐, 13C‐, and 113Cd‐nmr, and nuclear Overhauser effect spectroscopy (NOESY) spectra to show the coordination of cysteine thiolate and histidine imizazole to Cd(II) ion. The NOESY spectra in dimethyl formamide showed that the cysteine residue was in proximity to the histidine residue. These results reveal the dictation of Z‐Cys‐Ala‐Pro‐His‐OMe to Cd(II) ion in solution. Temperature‐dependent dissociation equilibrium of histidine imidazole in solution was observed in this complex. Structural features of the chelating peptide are discussed. © 1995 John Wiley & Sons, Inc.
The osmotic sensitivity of netropsin analogue binding to DNA
Authors: Sidorova Nina Yu. , Rau Donald C. 
Published: December 2004

AbstractThe binding of a netropsin analogue to random sequence DNA, monitored by CD, is seen dependent on the concentration of neutral solutes. The binding free energy decreases linearly with solute osmolal concentration and the magnitude of the effect is insensitive to the chemical identity of the solute fur betaine, sorbitol, and triethylene glycol. These solutes appear to modulate binding through their effect on water activity and changes in the hydration of the drug and DNA in the complex reaction, not through a direct interaction with the reactants or the product. The dependence of binding constant on solute concentration can be interpreted as an additional binding of some 50–60 extra solute excluding water molecules by the complex. A water sensitivity of drug binding is further seen from the dependence of binding constants on the type of anion in solution. Anions in the Hofmeister series strongly affect bulk water free energies and entropies. The differences in netropsin analogue binding to DNA with Cl−, F−, and CIO are consistent with the effect observed with neutral solutes. The ability to measure changes in water binding associated with a specific DNA interaction is a first step toward correlating changes in hydration with the strength and specificity of binding. © 1995 John Wiley & Sons, Inc.
Quasielastic light scattering, electrophoresis, and fluorescence studies of lysozyme‐poly(2‐acrylamido‐methylpropylsulfate) complexes
Authors: Xia Jiulin , Dubin Paul L. , Morishima Yotaro , Sato Takeshi , Muhoberac Barry B. 
Published: December 2004

AbstractComplexation between lysozyme and sodium poly(2‐acrylamido‐2‐methylpropanesulfonate) (PAMPS) was studied by quasielastic light scattering, electrophoretic light scattering, fluorescence, and turbidimetry in electrolyte solution. These techniques show that complexation occurs at pH 9.6 in an ionic strength buffer of 0.25M NaCl + 25 mM Na2B4O7. At constant lysozyme concentration (Cpro). The structure of the complex depends on the polymer concentration. At low polymer concentration (relative to Cpro), an intrapolymer complex is formed. This intrapolymer complex aggregates to an interpolymer species upon increase in polymer concentration. Complex formation was also studied by fluorescence using pyrene‐labeled PAMPS (Py‐PAMPS). Energy transfer from singlet‐excited tryptophan residues in lysozyme to the pyrene label occurs when the complex is formed. Fluorescence and turbidity data indicate that lysozyme interacts with Py‐PAMPS preferentially at pyrene sites, which leads to static quenching of tryptophan fluorescence via energy transfer to the pyrene label. © 1995 John Wiley & Sons, Inc.
Solution behavior of α‐chymotrypsin dissolved in nonpolar organic solvents via hydrophobic ion pairing
Authors: Meyer Jeffrey D. , Matsuura James E. , Kendrick Brent S. , Evans Emily S. , Evans Gabriel J. , Manning Mark C. 
Published: December 2004

AbstractDissolution of α‐chymotrypsin in nonpolar organic solvents can be achieved using hydrophobic ion pairing, whereby the polar counterions are replaced by a stoichiometric number of detergent molecules. Using Aerosol OT[AOT, sodium bis(2‐octyl)sulfosuccinate], it is possible to partition significant amounts of the enzyme into alkanes and chlorocarbons. Apparent solubility in isooctane is greater than 1 mg/mL (80 μM). Necessary conditions for achieving effective partitioning of α‐chymotrypsin into these solvents are described. Using CD spectroscopy, it can be shown that the AOT–α‐chymotrypsin (CMT) complex retains its native secondary and tertiary structure when dissolved in alkanes, and that the globular structure is stable to more than 100°C. In contrast, α‐chymotrypsin unfolds at 54°C in aqueous solution. The relative solubility of the AOT–CMT complex in a variety of alkanes and chlorocarbons is also reported. The native structure of α‐chymotrypsin is maintained in carbon tetrachloride, but not in methylene chloride or chloroform. © 1995 John Wiley & Sons, Inc.