bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution conformation of a pectic acid fragment by 1H‐nmr and molecular dynamics
Authors: Di Nola A. , Fabrizi G. , Lamba D. , Segre A. L. 
Published: December 2004

Abstract1H‐NMR and molecular dynamics simulations in vacuo and in water of (1 → 4)‐α‐D‐galacturono‐disaccharide were performed. The results of the molecular dynamics simulations showed that the molecule fluctuates between two conformations characterized by different values of torsion angles around the glycosidic linkage and two different intramolecular hydrogen bonds. When these conformations are extrapolated to a regular polymeric structure, they generate pectic acid compatible with a 21‐ or a right‐handed 31‐helix. © 1994 John Wiley & Sons, Inc.
Unusually stable β‐sheet formation in an ionic self‐complementary oligopeptide
Authors: Zhang Shuguang , Lockshin Curtis , Cook Richard , Rich Alexander 
Published: December 2004

AbstractA 16‐residue amphiphilic oligopeptide (EAK16) with every other residue alanine and also containing glutamic acid and lysine (Ac‐NH‐AEAEAKAKAEAEAKAK‐CONH2) is able to form an unusually stable β‐sheet structure. The β‐sheet structure is stable at very low concentrations in water and at high temperatures. Various pH changes at 1.5, 3, 7, and 11 had little effect on the stability of the β‐sheet structure. The β‐sheet structure was not altered significantly even in the presence of 0.1% SDS, 7 molar guanidine hydrochloride, or 8 molar urea. One of the structural characteristics of the EAK16 is its ionic self‐complementarity in that ionic bonds and hydrogen bonds between Glu and Lys can form readily between two oligopeptide β‐sheet structures. This structural feature is probably one of the factors that promotes its extreme stability. This is the first example of such an extended ionic self‐complementarity in a protein structure. EAK16 and its related peptides may have applications as useful biomaterials. It also offers a good model for studying the mechanism of β‐sheet formation. Because the oligopeptide can self‐assemble to form a membranous structure, it may have relevance to origin of life research. © 1994 John Wiley & Sons, Inc.
Nmr investigation of CYCLO7,10[C7,X9,C10,Nle12] analogues of the α‐factor from saccharomyces cerevisiae
Authors: Gounarides J. S. , Xue C.‐B. , Becker J. M. , Naider F. 
Published: December 2004

AbstractThe cyclo7,10[Cys7,Cys10,Nle12], cyclo7,10[Cys7,D‐Ala9,Cys10,Nle12], and cyclo7,10[Cys7,L‐Ala9,Cys10,Nle12] analogues of the α‐factor mating pheromone (WHWLQLKPGQPMY) of the yeast Saccharomyces cerevisiae were studied in DMSO/water (80 : 20) and aqueous solution by nmr spectroscopy. In addition, the cyclo7,10[Cys7,D‐Val9,Cys10,Nle12] α‐factor was examined in DMSO/water. Nuclear Overhauser effect (NOE) and NH dδ/dT data indicate that the cyclo7,10[Cys7,D‐Val9,Cys10,Nle12] α‐factor adopts a type II β‐turn in DMSO/water and that the cyclo7,10[Cys7,D‐Ala9,Cys10,Nle12] ‐ and cyclo7,10‐[Cys7,L‐Ala9,Cys10,Nle12] α‐factor analogues adopt type II and type I/III β‐turns, respectively, in both DMSO/water and aqueous solutions. In aqueous solution, residues 8 and 9 of the cyclo7,10[Cys7,Cys10,Nle12] α‐factor appear to adopt at least two distinct conformations, one of these being identified as a type I/III β‐turn. In contrast, the cyclo7,10[Cys7,Cys10,Nle12] α‐factor appears to adopt predominately a type II β‐turn in DMSO/water. Quantitative NOE measurements of the cyclo7,10[Cys7,Cys10,Nle12]‐, cyclo7,10[Cys7,D‐Val9,Cys10,Nle12]‐, and cyclo7,10[Cys7,L‐Ala9,Cys10,Nle12] α‐factors in DMSO/water were used to derive three‐dimensional structures of the cyclo7,10[Cys7,Pro8,X9Cys10] portion of these analogues. © 1994 John Wiley & Sons, Inc.
A new approach for determining low‐frequency normal modes in macromolecules
Authors: Durand Philippe , Trinquier Georges , Sanejouand Yves‐Henri 
Published: December 2004

AbstractA new method for calculating a set of low‐frequency normal modes in macromolecules is proposed and applied to the case of proteins. In a first step, the protein chain is partitioned into blocks of one or more residues and the low‐frequency modes are evaluated at a low‐resolution level by combining the local translations and rotations of each block. In a second step, these low‐resolution modes are perturbed by high‐frequency modes explicitly calculated in each block, thus leading to the exact low‐frequency modes. The procedure is tested for three cases–decaalanine, icosaleucin, and crambin–using a perturbation‐iteration scheme in the second step. Convergence properties and numerical accuracy are assessed and tested for various partitions. The low‐resolution modes obtained in the first step are always found to be good starting approximations. Potential advantages of the method include a central processing unit time roughly N2 dependent on the size of the problem (N being the number of degrees of freedom), the possibility of using parallel processing, the nonrequirement for loading the complete mass‐weighted second‐derivative input matrix into central memory, and the possibility of introducing in the procedure further structural hierarchy, such as secondary structures or motifs. In addition, any improvement or refinement of the algorithm benefits from the efficient formalism of the effective Hamiltonian theory. © 1994 John Wiley & Sons, Inc.
A CD study of the α‐helix nucleation hypothesis
Authors: Toumadje Arazdordi , Johnson W. Curtis 
Published: December 2004

AbstractOne of the dilemmas in predicting the secondary structure of proteins from their amino acid propensity for a given conformation is the presence of all amino acids in all types of secondary structure, regardless of their propensity for that specific structure. One explanation is the nucleation hypothesis that only a few residues with a strong propensity for the secondary structure, such as the α‐helix structure, initiates its formation and propagates the structure through indifferent sequences until strong breakers terminate the growth on both ends. Eight 15‐mer peptides were studied to examine the α‐helix nucleation hypothesis. The nucleation sequence of VAEAK, with high helix propensity, was mixed with an indifferent sequence of TSDSR in all possible permutations. From the percent α‐helix structure derived from the CD at 222 nm, it appears that helicity does not propagate through the indifferent sequence. © 1994 John Wiley & Sons, Inc.
Interaction of water‐soluble porphyrins with single‐ and double‐stranded polyribonucleotides
Authors: Bustamante Carlos , Gurrieri Sergio , Pasternack Robert F. , Purrello Roberto , Rizzarelli Enrico 
Published: December 2004

AbstractCD and uv‐visible absorption studies with several tetracationic water‐soluble porphyrin derivatives show that some of these species can serve as probes to discriminate between A‐ and B‐conformational forms of single‐stranded polynucleotides. It is also observed that these porphyrins can participate in the formation of double helices by forming transient intermediate complexes enroute to duplex formation. © 1994 John Wiley & Sons, Inc.
Flow linear dichroism and fourier transform IR spectra reveal geometry for X‐form DNA
Authors: Riazance‐Lawrence Jeannine H. , Kang Hunseung , Chou Ping‐Jung , Johnson W. Curtis , Vorlíc̆ková Michaela 
Published: December 2004

AbstractFlow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21° for dA and 40° for dT in the X‐form of poly (dAdT) · poly (dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen‐bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B‐form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z‐form DNA. Clearly, X‐form DNA has a unique geometry. © 1994 John Wiley & Sons, Inc.
Nuclear overhauser effect spectroscopy (NOESY) detection of the specific interaction between substituents in cellulose and amylose triacetates
Authors: Tezuka Yasuyuki 
Published: December 2004

AbstractNuclear Overhauser effect spectroscopy measurements on cellulose triacetate and on amylose triacetate with a mixing time of 500 ms, on the order of T1, of acetyl protons, were performed to detect the specific through‐space interaction between acetyl groups arising from their helix structures in solution. For cellulose triacetate, cross peaks were detected in CDCl3 between acetyl proton signals at 3 and 6 positions on an anhydroglucose unit. In DMSO‐d6, on the other hand, correlation peaks were observed not only between the 3 and 6 positions but also the 2 and 6 positions. For amylose triacetate, cross peaks were detected in CDCl3 between the acetyl proton signals at the 2 and 6 positions. The through‐space interaction of acetyl groups in cellulose triacetate and in amylose triacetate in solution was then interpreted based on their three‐dimensional structures in solid state determined by x‐ray crystallography. © 1994 John Wiley & Sons, Inc.
Redox‐active bis‐cysteinyl peptides. II. Comparative study on the sequence‐dependent tendency for disulfide loop formation
Authors: Siedler Frank , Quarzago Daniela , Rudolph‐Böhner Sabine , Moroder Luis 
Published: December 2004

AbstractBis (cysteinyl) octapeptides related to the active sites of the oxidoreductases protein disulfide isomerase (PDI), thioredoxin reductase (trr), glutaredoxin (grx), and thioredoxin (trx) were analyzed for their propensity to form the intramolecular 14‐membered disulfide ring in oxidation experiments. The rank order of percentage of cyclic monomer formed in aqueous buffer (pH 7.0) at 10−3 M concentration was found to be very similar, but opposite to that of the Kox and, correspondingly, of the redox potentials of the native enzymes. Attempts to induce intrinsic conformational preferences of the peptides by addition of trifluoroethanol led to enhancements of β‐turn structures as reflected by the CD and Fourier transform ir spectra. The induced secondary structure, instead of aligning the tendencies of the excised fragments for loop formation with those of the intact proteins, was found to suppress the differences by significantly increasing the preference for cyclic monomers (≈ 90%). Similarly, operating under denaturing conditions, i.e., in 6M guanidinium hydrochloride, only for the trx peptide was the statistical product distribution obtained. For the remaining peptides, again a strong increase of cyclic monomer contents was observed that could not be correlated with dissolution of β‐sheet type aggregates. The CD spectra are more consistent with the presence of ordered structure to some extent, possibly resulting from an hydrophobic collapse of the sparingly soluble peptides. The results of the oxidation experiments further support previous findings from thiol disulfide interchange equilibria, which clearly revealed a decisive role of the characteristic thioredoxin structural motif in dictating the redox properties of the enzymes. Point mutations in the active sites of the oxidoreductases allowed us to affect their redox potentials strongly, but apparently only in the constraint form of the three‐dimensional structure as similar exchanges in the excised fragments did not produce the expected effect. This observation contrasts with numerous reports that the conformation of short disulfide loops is mainly dictated by the amino acid sequence. © 1994 John Wiley & Sons, Inc. © 1994 John Wiley & Sons, Inc.
Peptide libraries: Determination of relative reaction rates of protected amino acids in competitive couplings
Authors: Ostresh John M. , Winkle James H. , Hamashin Vince T. , Houghten Richard A. 
Published: December 2004

AbstractIn the solid phase preparation of synthetic peptide libraries, equimolarity of the resultant peptides in the mixture simplifies the identification of active compounds. Two primary methods for the preparation of combinatorial peptide mixtures are currently used. In the first method, the starting resin is divided into equal aliquots, individual amino acids are coupled to each aliquot, and the resin is then recombined. This process is repeated for each position. However, due to the physical process, each resin bead contains only one peptide sequence. Statistically, for mixtures of longer sequences, an ever‐increasing amount of resin is necessary to ensure complete representation of each peptide in the library. Thus, each peptide will be represented in the library if a sufficient number of resin beads are used. In addition, the concentration of each peptide in the library depends on both the number of mixture positions in the library and the amount of resin used. In the second method, mixtures of amino acids are coupled simultaneously at each addition step. The proportion of each amino acid in the reaction mixture is varied inversely to its reaction rate such that, ideally, an equimolar mixture of each peptide is synthesized. An advantage of this method over the previous method is that each peptide is ensured to be represented in the library, although not necessarily in equimolar amounts. It is known that not only do the coupling rates of each amino acid vary, but the coupling rates of individual amino acids also change when coupled to different amino acid resins. Consequently, in order to obtain equimolar peptide mixtures through the use of mixtures of protected amino acids, the ratio of reaction rates of one amino acid over another must be constant irrespective of the resin‐bound amino acid. If this premise is true, this method of synthesis offers a significant advantage over the previous method since, theoretically, equimolar peptide libraries could be synthesized. The influence of the resin‐bound amino acid on the relative reaction rates of incoming amino acids was investigated in the current study. © 1994 John Wiley & Sons, Inc.
The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl α‐lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations
Authors: Asensio Juan Luis , Jimenez‐Barbero Jesus 
Published: December 2004

AbstractThe solution conformation of methyl α‐lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements hot It in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady‐state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [ε = 1 * r and 80 Debyes (D)] in an exhaustive way, and have been complemented with specific calculations at intermediate ε values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. The experimental results indicate that the β(1 → 4)‐glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its lime in the region close to the global minimum. It is shown that the over estimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when Used at low dielectric constant (ε < 20 D). The matching between the expected and observed facts increases for ε > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides. © 1995 John Wiley & Sons, Inc.
Synthesis, and crystal and molecular structure of the 310‐helical α,β‐dehydro pentapeptide Boc‐Leu‐Phe‐Ala‐ΔPhe‐Leu‐Ome
Authors: Rajashankar K. R. , Ramakumar S. , Mal T. K. , Jain R. M. , Chauhan V. S. 
Published: December 2004

Abstractα,β‐Dehydro amino acid residues are known to constrain the peptide backbone to the β‐bend conformation. A pentapeptide containing only one α,β dehydrophenylalanine (ΔPhe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc‐Leu‐Phe‐Ala‐ΔPhe‐Leu‐OMe (C39H55N5O8, Mw = 721.9) was crystallized from aqueous methanol. Monoclinic space group was P21, a = 10.290(2)°, b = 17.149(2)°, c = 12.179(2) Å, β = 96.64(1)° with two molecules in the unit cell. The x‐ray (Mo Kα, λ = 0.7107A) intensity data were collected using a CAD4 diffractometer. The crystal structure was determined by direct methods and refined using least‐squares technique. R = 4.4% and Rw = 5.4% for 4403 reflections having |F0| ≥ 3σ(|F0|). All the peptide links are trans and the pentapeptide molecule assumes 310‐helical conformation. The mean ϕ,ψ values, averaged over the first four residues, are −64.4°, −22.4° respectively. There are three 4 → 1 intramolecular hydrogen bonds, characteristic of 310,‐helix. In the crystal, the peptide helices interact through two head‐to‐tail. NHO intermolecular hydrogen bonds. The peptide molecules related by 21, screw symmetry form a skewed assembly of helices. © 1995 John Wiley & Sons, Inc.
Viscoelastic properties of human tracheobronchial mucin in aqueous solution
Authors: McCullagh C. M. , Jamieson A. M. , Blackwell J. , Gupta R. 
Published: December 2004

AbstractHuman tracheobronchial mucin isolated from cystic fibrosis patients (CF HTBM) was purified using a combination of gel filtration and density gradient centrifugation. The resulting mucin was fractionated to reduce polydispersity and to facilitate studies of the molecular weight dependence of mucin viscoelasticity in concentrated solution. The viscoelastic properties of CF HTBM were examined in distilled water, 0.1M salt solutions and chaotropic solvents. In controlled strain experiments (strain ≥ 5%) with increasing mucin concentration, a crossover from sol to gel behavior is observed. The gel strength, as measured by the magnitude of the storage modulus at comparable mucin concentrations, is greatest for distilled water, intermediate for 0.1M NaCl, and lowest far 6M GdnHCl. In distilled water, high molecular weight mucin undergoes a sol‐gel transition at ∼ 12 mg/mL, and shows evidence of a plateau modulus at higher concentrations. The storage and loss moduli of concentrated high molecular weight fractions in 6M GdnHCl exhibit a power law dependence on frequency typical of weak gels near the sol–gel transition at 20 mg/mL. Similar rheology is observed in 0.1M NaCl and 0.091M NaCl/3 mM CaCl2, but with evidence for additional weak associations at low frequency. The power law exponent in these systems is 0.70 ± 0.02, in good agreement with prediction for networks formed by a percolation mechanism. Low molecular weight fractions in these solvents exhibit a fluid‐like viscoelastic response. However, low molecular weight mucin in distilled water shows a strain‐dependent increase in elasticity at low frequency indicative of weak intermolecular associations. Comparison of the rheological behavior of CF HTBM with our earlier studies of ovine submaxillary mucin lends support to the idea that carbohydrate side‐chain interactions are important in the gelation mechanism of mucins. © 1995 John Wiley & Sons, Inc.
Kinetic and thermodynamic characterization of DNA duplex–hairpin interconversion for two DNA decamers: d(CAACGGGTTG) and d(CAACCCGTTG)
Authors: Avizonis Daina Z. , Kearns David R. 
Published: December 2004

AbstractThe duplex–hairpin interconversion of two DNA decamers, d(CAACGGGTTG) and d(CAACCCGTTG), has been characterized thermodynamically and kinetically by using uv‐melting and nmr relaxation methods. Separately, each decamer shows slow exchange between hairpin and duplex conformations. The hairpin conformations have melting points of 47 and 50°C, respectively, and exhibit similar thermodynamic stabilities. The enthalpies of duplex formation, measured by nmr, were found to be very similar (ΔHDH = 26 ± 3 kcal/mole) for both decanters at low salt concentrations (< 50 mM NaCl). However, as the salt concentration was increased the behavior of ΔHDH, and kinetics is significantly different for each decamer. The d(CAACGGGTTG) decamer forms a duplex containing two central G·G mismatches at high salt and DNA concentration. Based upon the measurement of high interconversion activation energies and a decrease in hairpin formation rate with increasing salt, the interconversion between hairpin and duplex was concluded to proceed by complete strand dissociation. In contrast, the d(CAAC‐CCGTTG) decamer was determined to form a duplex with two centrally located C·C mismatches at pH values less than 6.2, consistent with the formation of a hemiprotonated C+·C mismatch. At pH values greater than 6.4, the hairpin–duplex equilibrium is almost completely shifted toward the hairpin conformation at DNA concentrations of 0.5–7.0 mM and salt concentrations of 10–100 mM. The interconversion of duplex and hairpin conformations was ascertained by means of both kinetic and thermodynamic measurements to proceed by a slightly different mechanism than its complementary decamer. Although the interconversion proceeds by complete strand separation as suggested by high duplex‐hairpin interconversion activation enthalpies, the increasing hairpin formation rate with increasing ionic strength as well as the ΔHDH, dependence on sail indicate that an intermediate internally bulged duplex (no C+·C formation) is stabilized by increasing ionic strength. These data support an interconversion mechanism where an intermediate internally bulged duplex may be the rate limiting step before strand separation. © 1995 John Wiley & Sons, Inc.