bluuebunny/crossref_metadata_2025_split huggingface dataset:
A thermodynamic analysis of calcium–alginate gel formation in the presence of inert electrolyte
Authors: Nilsson Svante 
Published: December 2004

AbstractThe effect of mixed salt (1:1 and 2:1 electrolyte) on alginate (a charged polysaccharide) gel formation is analyzed within the Poisson‐Boltzmann cell model utilizing experimental data from the literature. The concentration of calcium ions needed to induce gelation of alginate goes through a minimum as 1 : 1 electrolyte is added. The theoretical model can account for this in a qualitative manner. According to the theoretical model, however, it is only in terms of concentrations that the minimum exists. In terms of chemical potentials for the ions (or salt) the curve is monotonic. The effect is due to the highly nonideal interactions in polyelectrolyte solutions when the total salt content is low. © 1992 John Wiley & Sons, Inc.
Stacking interactions of ApA analogues with modified backbones
Authors: Kang Hunseung , Chou Ping‐Jung , Johnson W. Curtis , Weller Dwight , Huang Sung‐Ben , Summerton James E. 
Published: December 2004

AbstractCD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus‐linked morpholino analogues are at least as strong as those found in d (ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters. © 1992 John Wiley & Sons, Inc.
A synthetic analogue for the active site of plant‐type ferredoxin: Two different coordination isomers by a four‐Cys‐containing [20]‐peptide
Authors: Ueyama Norikazu , Ueno Satoru , Nakamura Akira , Wada Keishiro , Matsubara Hiroshi , Kumagai Shin‐Ichiro , Sakakibara Shumpei , Tsukihara Tomitake 
Published: December 2004

AbstractThe (Fe2S2)2+ complex of an artificial 20‐peptide ligand, Ac‐Pro‐Tyr‐Ser‐Cys‐Arg‐Ala‐Gly‐Ala‐Cys‐Ser‐Thr‐Cys‐Ala‐Gly‐Pro‐Leu‐Leu‐Thr‐Cys‐Val‐NH2, containing an invariant Cys‐A‐B‐C‐D‐Cys‐X‐Y‐Cys (A, B, C, D, X, Y = amino acid residues) fragment of plant‐type ferredoxins was synthesized by a ligand exchange method with [Fe2S2(S‐t‐Bu)4]2−. 1H‐nmr spectroscopic and electrochemical data of the complex indicate the presence of two coordination isomers. One of them having a Cys‐X‐Y‐Cys bridging coordination to the two Fe(III) ions, has the (Fe2S2)2+ core environment similar to those of the denatured plant‐type ferredoxins and exhibits a positive shifted redox potential at −0.64 V vs saturated colonel electrode (SCE) in N,N‐dimethylformamide (DMF). Another isomer with the Cys‐A‐B‐C‐D‐Cys bridging coordination shows a negative redox potential at −0.96 V vs SCE in DMF. © 1992 John Wiley & Sons, Inc.
Peptide hormone–membrane interactions: The aggregational and conformational state of lipo‐gastrin derivatives and their receptor binding affinity
Authors: Romano R. , Musiol H.‐J. , Weyher E. , Dufresne M. , Moroder L. 
Published: December 2004

AbstractThe (2RS) −1,2‐dipalmitoyl−3‐mercaptoglycerol/‐, (2RS) −1,2‐dimyristoy1–3‐mercaptogly‐cerol/−, and (2RS)‐1‐myristoy1–2‐palmitoy1–3‐mercaptoglycerol/maleoyl‐β‐alanyl‐[Nle15]‐human‐gastrin‐(2–17) adducts were prepared as lipo‐gastrin derivatives of explicitly primary amphiphilic properties. As representative of this class of lipo‐gastrins, the dimyristoyl derivative has been thoroughly characterized in its aggregational state since, among the three compounds, theoretically it should exhibit the lowest degree of lipid character. It aggregates in aqueous solution to form monodispersed unilamellar spherical vesicles with dislocation of the peptide moiety at the bilayer surface in predominantly unordered structure. The liposomes are remarkably stable toward solubilization with trifluoroethanol and toward vesicle to micelle transition with neutral and negatively charged surfactants even above their critical micellar concentrations. Asymmetric fusion with the detergent micelles induces pplydispersion of the liposomes in terms of shape and size without affecting in significant manner the mode of display of the gastrin portions at the bilayer surface. Only the positively charged hexadecyltrimethylammonium hydroxide provokes the collapse of the vesicles into mixed micelles with concomitant altered dislocation of the gastrin‐peptide in the new aggregational state. Despite the lipid properties of the gastrin derivatives, i.e., formation of lipocomes, they retain remarkable receptor affinities (IC50 = 1.5· 10−9M for myristoyl‐palmitoyl‐gastrin, IC50 = 2.0 · 10−9M for dimyristoyl‐gastrin and IC50 = 3.1 · 10−9 M for dipalmitoylgastrin vs IC50 = 2.8− 10−10M for Nle15‐gastrin). Since the displacement of radiolabeled Nle15‐gastrin from rat pancreatic acinar cell line membrane preparations by both the parent gastrin hormone and the three lipogastrins occurs in parallel manner, the data support a mechanism of receptor occupancy via accumulation of the gastrins at the membrane surface and their two‐dimensional diffusion to the target receptor. Thereby the differentiated decrease of affinity in function of fatty acid chain length has to be attributed to the energetically more or less favored transfer of the monomers from the donor vesicles to the acceptor membranes. Moreover, according to this model migration of the lipogastrins with their interdigitating difattyacyl moieties should be delayed, again in lipid structure‐dependent manner, in comparison to the parent gastrin molecule, which is free to float in the membrane interfacial phase. © 1992 John Wiley & Sons, Inc.
Combined use of molecular dynamics simulations and NMR to explore peptide bond isomerization and multiple intramolecular hydrogen‐bonding possibilities in a cyclic pentapeptide, cyclo (Gly‐Pro‐D‐Phe‐Gly‐Val)
Authors: Liu Zhi‐Ping , Gierasch Lila M. 
Published: December 2004

AbstractThe conformational behavior of a model cyclic pentapeptide—cyclo(Gly‐L‐Pro‐D‐Phe‐Gly‐L‐Val)—has been explored through the combined use of in vacuo molecular dynamics simulations and a range of nmr experiments (preceding paper). The molecular dynamics analysis suggests that, despite the conformational constraints imposed by formation of the pentapeptide cycle, this pentapeptide undergoes conformational transitions between various hydrogen‐bonded conformations, characterized by low energy barriers. An inverse γ turn with Pro in position i+1 and a γ turn with D‐Phe in position i+1 are two alternatives occurring frequently. Like other DLDDL cyclic pentapeptides, cyclo (Gly‐Pro‐D‐Phe‐Gly‐Val) is also stabilized by an inverse γ‐turn structure with the β‐branched Val residue in position i + 1, and this hydrogen bond is retained in the different conformational families. The γ‐turn around D‐Phe3 and the inverse γ turn around Val5 are consistent with the nmr observations. 3JNH—CHα coupling constants of the all‐trans forms were calculated from one of the molecular dynamics trajectories and are comparable to nmr experimental data, suggesting that the conformational states visited during the simulation are representative of the conformational distribution in solution. In addition to the equilibrium among various hydrogen‐bonded all‐trans conformers, the observation in nmr spectra of two sets of resonances for all peptide protons indicated a slow conformational interconversion of the Gly‐Pro peptide bond between trans and cis isomers. The activation energy between these two conformers was determined experimentally by magnetization transfer and was calculated by high temperature constrained molecular dynamics simulation. Both methods yield a free energy of activation of ca. 20 kcal/mol. Furthermore, the free energy of activation is dependent on the direction of rotation of the Gly‐Pro peptide bond. © 1992 John Wiley & Sons, Inc.
Impact of a micellar environment on the conformations of two cyclic pentapeptides
Authors: Bruch Martha D. , Rizo Josep , Gierasch Lila M. 
Published: December 2004

AbstractIn an effort to explore the influence of interfacial environments on reverse turns, we have performed a detailed analysis by nmr of the solution conformations of two cyclic pentapeptides in sodium dodecyl sulfate (SDS) micelles. The first peptide, cyclo (D‐Phe1‐Pro2‐Gly3‐D‐Ala4‐Pro5), adopts a single rigid conformation in solution (either chloroform or dimethylsulfoxide) and in crystals, whereas the second, cyclo (Gly1‐Pro2‐D‐Phe3‐Gly4‐Val5), is much more flexible and adopts different conformations in the crystal and in solution. Both of these peptides are solubilized by SDS micelles, and nmr relaxation rates indicate that they are both partially immobilized by interaction with the micelles. Furthermore, some amide protons in both peptides participate in hydrogen bonds with water. In the presence of micelles, the former peptide retains a conformation essentially the same as that found in crystals and in solution, which consists of a β turn and an inverse γ turn. However, the micellar environment has a significant effect on the latter peptide. In particular, the population of a conformer containing a cis Gly‐Pro peptide bond is increased significantly. The most likely conformation of the cis isomer, determined by a combination of nmr and restrained molecular dynamics, contains a Gly1‐Pro2 δ turn and a γ turn about D‐Phe3. The nmr data on the trans isomer indicate that this isomer is averaging between two conformations that differ mainly in the orientation of the D‐Phe3‐Gly4 peptide bond. © 1992 John Wiley & Sons, Inc.
Conformational analysis of met‐enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling
Authors: Graham William H. , Carter Eugene S. , Hicks Rickey P. 
Published: December 2004

AbstractProton and 13C chemical shift assignments are reported for the neuropeptide Met‐enkephalin (ME) in both aqueous solution and in the presence of 50 mM sodium dodecyl sulfate (SDS). Rotating frame nuclear Overhauser enhancement spectroscopy was used to qualitatively describe interproton distances. These distances were then used as restraints in the distance geometry based molecular modeling program Dspace, developed by Hare Research to generate sets of conformations of ME. The resulting aqueous solution conformations of ME were determined to exhibit characteristic of an extended random‐coil polypeptide with no distinguishable secondary structure. The resulting set of solution conformations of ME in the presence of 50 m M SDS exhibited characteristics of an amphiphilic type IV β turn that are stabilized by hydrophobic aromatic‐aromatic interactions between the side chains of Tyr1 and Phe4. © 1992 John Wiley & Sons, Inc.
Crystal structure, conformational analysis, and molecular dynamics of tetra‐O‐methyl‐(+) ‐catechin
Authors: Fronczek Frank R. , Hemingway Richard W. , Mcgraw G. Wayne , Steynberg Jan P. , Helfer Carin A. , Mattice Wayne L. 
Published: December 2004

AbstractThe structure of tetra‐O‐methyl‐ (+) ‐catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a = 4.8125(2) Å, b = 12.9148(8) Å, c = 13.8862(11) Å, α = 86.962(6) °, β = 89.120(5)°, γ = 88.044(5)°, Z = 2, Dc = 1.336 g cm−3, R = 0.033 for 6830 observations. The heterocyclic rings of the crystal structures are compared to previous results for 8‐bromotetra‐O‐methyl‐(+)‐catechin, penta‐O‐acetyl‐(+)‐catechin, and (−) ‐epicatechin. One of the two molecules has a heterocyclic ring conformation similar to that observed previously for (−)‐epicatechin, and the other has a heterocyclic ring conformation similar to one predicted earlier in a theoretical analysis of dimers of (+)‐catechin and (−) ‐epicatechin. Both structure A and structure B in the crystal have heterocyclic ring conformations that place the dimethoxyphenyl substituent at C(2) in the equatorial position. However, this heterocyclic ring conformation does not explain the proton nmr coupling constant measured in solution. Molecular dynamics simulations show an equatorial ⇌ axial interconversion of the heterocyclic ring, which can explain the nmr results. © 1993 John Wiley & Sons, Inc.
Vibrational CD study of the thermal denaturation of poly(rA) · poly(rU)
Authors: Yang Ligang , Keiderling Timothy A. 
Published: December 2004

AbstractThe vibrational cd (VCD) of a double‐stranded RNA, poly(rA) ‐ poly(rU), at pH 7 and moderate added salt concentration (0.1M) has been measured in both the base‐stretching and phosphate‐stretching regions of the ir as a function of temperature. The data in both cases show two distinct phase transitions. The first is from double‐ to a triple‐stranded form, and the second is from triple‐ to single‐stranded forms, which still retain substantial local order even up to 80°C. The nature of these transitions has been identified by comparison of the VCD and ir absorption spectra of the initially double‐stranded samples with those of single‐stranded poly(rA) and poly(rU) and with triple‐stranded poly‐(rA) ‐poly‐(rU) poly (rU). The large differences in the VCD band shapes allows positive identification of the intermediate and final states. Thus under VCD‐concentration conditions, a simple helix‐to‐coil transition can be eliminated for poly (rA ) ‐ poly (rU) while such a two‐step transition can be seen at low salt conditions. All of these observations are consistent with previous studies of the phase transitions of poly (rA) ‐ poly (rU) under various salt conditions. Additionally, the VCD is indicative of premelting for all the triple‐, double‐, and single‐strand complexes studied. The triple‐strand complex did not show disproportionation to double strand on heating under these added salt conditions. The unusual VCD pattern for low temperature poly (rA) ‐ poly (rU), as compared to high GC content RNAs and DNAs, is qualitatively, but not quantitatively, explained using exciton coupling of localized dipolar transitions in each type of base within the strand. © 1993 John Wiley & Sons, Inc.
Exhaustive conformational search and simulated annealing for models of lattice peptides
Authors: Brower R. C. , Vasmatzis George , Silverman Michael , Delisi Charles 
Published: December 2004

AbstractWe consider simple lattice models for short peptide chains whose states can be exhaustively enumerated to find the lowest energy conformation. Using these exact results and numerical simulations, we compute the distributions for the mean time tN, required to find the global minimum energy state by simulated annealing (SA), as a function of N, the number of units in the chain. On the basis of scaling arguments, the time tN, to find the global minimum energy of longer chains, beyond the range covered by exhaustive enumeration, can be estimated. On the basis of the observed exponential increase in folding time of the standard SA algorithms, it is imperative that better algorithms be found for minimizing longer chains. © 1993 John Wiley & Sons, Inc.
A cooperative self‐consistent microscopic theory of thermally induced melting of a repeat sequence DNA polymer
Authors: Chen Y. Z. , Prohofsky E. W. 
Published: December 2004

AbstractWe attempt to extend the modified self‐consistent phonon theory to describe thermal fluctuational base‐pair opening of repeat sequence DNA polymers in the helix–coil transition region as well as in the premelting region. A microscopic base‐pair open state is introduced and the effect of this open state is taken into account self‐consistently in a mean field system that models the DNA polymer. Our analysis indicates the structure of this open state changes with temperature in such a manner that on average a base pair opens and unstacks with its neighbors more completely as temperature increases. We apply this theory to a homopolymer—poly(dG) · poly(dC) to evaluate the base‐pair opening probability in a temperature range from 273 to 366.5 K. At 366.5 K the system undergoes cooperative melting. Our calculated base‐pair opening probabilities are in general agreement with several experimental estimates at room temperature. The calculated probabilities show typical melting curve behavior at temperatures close to the observed melting temperature. The cooperative modified self‐consistent phonon approximation approach becomes a viable microscopic theory of melting. © 1993 John Wiley & Sons, Inc.
The influence of hydration on the conformation of lysozyme studied by solid‐state 13C‐nmr spectroscopy
Authors: Gregory Roger B. , Gangoda Mahinda , Gilpin R. K. , Su Wen 
Published: December 2004

Abstract13C proton decoupled cross‐polarization magic‐angle spinning nmr spectra of lysozyme are reported as a function of hydration. Increases in hydration level enhance the resolution of the spectra, particularly in the aliphatic region, but has no significant effect on either the rotating frame proton spin–lattice relaxation time or the cross‐relaxation time. The enhancement in spectral resolution with hydration is attributed to a decrease in the distribution of isotropic chemical shifts, which reflects a decrease in the distribution of conformational states sampled by the protein. Changes in the distribution of isotropic chemical shifts occur after the addition of water to the charged groups as coverage of the polar side chains and peptide groups takes place. The onset of this behavior occurs at a hydration level of about, 0.1–0.2 g water/g protein and is largely complete at about 0.3 g water/g protein, the same hydration range where changes in the heat capacity are observed. That hydrogen exchange of buried protons can occur at hydration levels significantly lower than those at which changes in the distribution of conformational states are first observed suggests that some motions that mediate exchange are already present in the dry protein. The preservation of efficient dipolar coupling indicates that the conformational rearrangements that do‐occur on hydration are small and do not involve any significant overall expansion of free volume or weakening of interactions that would increase the reorientational freedom of protein groups. © 1993 John Wiley & Sons, Inc.
Reversible effects of medium dielectric constant on structural transformation of β‐lactoglobulin and its retinol binding
Authors: Dufour Eric , Bertrand‐Harb Catherine , Haertlé Tomasz 
Published: December 2004

AbstractThe secondary structure transformation of β‐lactoglobulin from a predominantly β‐structure into a predominantly α‐helical one, under the influence of solvent polarity changes is reversible. Independent of the alcohol used — methanol, ethanol, or 2‐propanol — the midpoints of the observed structural transformation occur around dielectric constant ε ≈ 60. The structural change destroying the hydrophobic core formed by the β‐barrel structure leads, at room temperature, to the dissociation of the retinol/β‐lactoglobulin complex in the neighborhood of dielectric constant ε ≈ 50. However, when the dielectric constant of the medium is raised back to ε ≈ 70 by the decrease of the temperature, both the refolding of BLG into a β‐structure and the reassociation of the retinol/β‐lactoglobulin complex are observed. The esterification of β‐lactoglobulin carboxyl groups has two effects: on the one hand it accelerates the β‐strand → α‐helix transition induced by alcohols. On the other hand, the esterification of β‐lactoglobulin strengthens its interaction with retinol as it may be deduced from the smaller apparent dissociation constant of retinol/methylated β‐lactoglobulin complex. The binding of retinol to modified or unmodified β‐lactoglobulin has no influence (stabilizing or destabilizing) on the folding changes induced by alcohol. © 1993 John Wiley & Sons, Inc.
The effect of intrinsic curvature on supercoiling: Predictions of elasticity theory
Authors: Tobias Irwin , Olson Wilma K. 
Published: December 2004

AbstractElasticity theory of naturally curved rods is employed to study the effects of intrinsic curvature on the properties of the equilibrium conformations of supercoiled DNA. The results stand in sharp contrast to those obtained when the molecule is viewed as being straight in its relaxed form. Starting from very fundamental principles of the theory, we show that the torsion of an open segment with a curved duplex axis can vary when the temperature, and along with it, the intrinsic twist is changed. Conversely, an imposed helicity, such as might be associated with binding to a histone, can change the intrinsic twist. It is also shown that another consequence of the presence of naturally curved sequences is that the twist density will, in general, vary with position along the chain in all equilibrium states. Then portions of the molecule will be more or less susceptible to interaction with other agents sensitive to such a variation. Finally, some closed equilibrium global structures uniquely associated with intrinsic curvature are discussed. © 1993 John Wiley & Sons, Inc.