bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helix propagation in trifluoroethanol solutions
Authors: Storrs Richard W. , Truckses Dagmar , Wemmer David E. 
Published: December 2004

AbstractHelix propagation of the S‐peptide sequence (residues 1–19 of ribonuclease A) in 2,2,2‐trifluoroethanol (TFE) solutions has been investigated with CD and nmr Overhauser effect spectroscopies. In this study, the S‐peptide helix is covalently initiated at the N‐terminus through disulfide bonds to a helix scaffold derived from the N‐terminal sequence of the bee venom peptide apamin. The entire S‐peptide sequence of this hybrid sequence peptide becomes helical at high proportions of TFE. Residues 14–19 of the S‐peptide are not helical in the free peptide in TFE, nor are they helical in ribonuclease A. The “helix stop” signal encoded by the S‐peptide sequence near residue 13 does not persist at high TFE with this hybrid sequence peptide. The helix‐stabilizing effects of TFE are due at least in part to facilitated propagation of an extant helix. This stabilizing effect appears to be a general solvation effect and not due to specific interaction of the helical peptide with TFE. Specifically these data support the idea that TFE destabilizes the coil state by less effective hydrogen bonding of the peptide amide to the solvent. © 1992 John Wiley & Sons, Inc.
Solution structure of peptides containing two dehydro‐phenylalanine residues: A CD investigation
Authors: Pieroni Osvaldo , Fissi Adriano , Pratesi Claudio , Temussi Pier Andrea , Ciardelli Francesco 
Published: December 2004

AbstractThe peptides Ac‐ΔPhe‐Ala‐ΔPhe‐NHMe (1), Ac‐ΔPhe‐Val‐ΔPhe‐NHMe (2), Ac‐ΔPhe‐Gly‐ΔPhe‐Ala‐OMe (3), and Boc‐Ala‐ΔtPhe‐Gly‐ΔPhe‐Ala‐OMe (4), containing two dehydro‐phenylalanine (ΔPhe) residues, were synthesized and the solution structure investigated in various solvents. The nmr and CD measurements indicate that all the dehydropeptides examined adopt 310‐helical conformations in solution. The tripeptides 1 and 2 exibited an intense negative CD exciton couplet, which was assigned to the right‐handed screw sense, while the tetrapeptide 3 displayed a CD couplet having opposite sign, which was assigned to the left‐handed helical sense. In the pentapeptide 4 the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum. The right‐handed sense dominates in hexafluoro‐2‐propanol, whereas a left‐handed helix prevails in chloroform, acetonitrile and methanol. A crucial role for this behavior is likely to be played by the two alanine residues positioned respectively at the head and tail of the sequence, which favor conformations having opposite screw senses. © 1993 John Wiley & Sons, Inc.
Physicochemical properties of (1 → 6)‐branched (1 → 3)‐β‐D‐glucans. 1. Physical dimensions estimated from hydrodynamic and electron microscopic data
Authors: Stokke Bjørn T. , Elgsaeter Arnljot , Hara Chihiro , Kitamura Shinichi , Takeo Kenichi 
Published: December 2004

AbstractThe physical dimensions of several (1 → 6) branched (1 → 3) ‐β‐D‐glucan samples obtained from different organisms and their derivatives have been studied by electron microscopy, light scattering measurements, viscometry, and gel permeation chromatography. The electron micrographs indicate that in most samples these biopolymers are adequately described as linear worm‐like coils. A sample reconstituted from alkaline media appeared as a blend of the linear, circular, and aggregated polymer morphologies. The average mass per unit length, ML = Mw/Lw for the macroscopically linear samples, was estimated to be 2100 ± 200 g mol−1 nm−1. The parameter mL was determined from the contour lengths obtained by electron microscopy and the molecular weight by light scattering measurements. The observed ML was consistent with the triple‐helical structure reported from x‐ray diffraction studies and observed degree of side‐chain substitution. From the molecular snapshots shown in the electron micrographs, the persistence lengths of these β‐D‐glucans were determined to be 140 ± 30 nm. The experimentally determined intrinsic viscosities were consistent with these estimates of ML and persistence length. Comparison of the molecular weight distributions obtained from gel permeation chromatography and those deduced from the electron micrographs indicates that number and weight average contour lengths are more reliable than z and z + 1 averages. © 1993 John Wiley & Sons, Inc.
Molecular dynamics study of iduronate ring conformation
Authors: Forster Mark J. , Mulloy Barbara 
Published: December 2004

AbstractMolecular dynamics (MD) simulations of the conformation of the iduronate ring in a methyl glycoside and as the central residue in a trisaccharide have been carried out. Separate simulations were carried out with initial 1C4, 2S0, and 4C1 iduronate ring conformations. Simulations were followed by observing the time development of the Cremer–Pople ring puckering parameters θ,ϕ2. Starting with chair geometries gave trajectories showing only ring oscillations close to the initial geometry. Simulations were performed with a 2S0 starting geometry using explicit water and in vacuum with dielectric constants (ε) of 1 and 80, as well as with distance‐dependent dielectric functions of 2r and 4r. In both the explicit water simulation and the vacuum (ε = 80) simulations, extensive pseudorotational motion was observed in which boat and twist‐boat ring conformers interconvert. The overall range of ϕ22 variation in the trisaccharide was about half of that observed in the methyl glycoside. The Haasnoot procedure for calculating H‐H coupling constants in saccharides was applied to structures obtained from MD trajectories. Using MD time averaged couplings along with experimental data allowed the relative fractions of chair and boat/twist‐boat forms to be derived. © 1993 John Wiley & Sons, Inc.
Diagonalization in a mixed basis: A method to compute low‐frequency normal modes for large macromolecules
Authors: Mouawad Liliane , Perahia David 
Published: December 2004

AbstractLow‐frequency collective motions in proteins are generally very important for their biological functions. To study such motions, harmonic dynamics proved most useful since it is a straightforward method; it consists of the diagonalization of the Hessian matrix of the potential energy, yielding the vibrational spectrum and the directions of internal motions. Unfortunately, the diagonalization of this matrix requires a large computer memory, which is a limiting factor when the protein contains several thousand atoms.To circumvent this limitation we have developed three methods that enable us to diagonalize large matrices using much less computer memory than the usual harmonic dynamics. The first method is approximate; it consists of diagonalizing small blocks of the Hessian matrix, followed by the coupling of the low‐frequency modes obtained for each block. It yields the low‐frequency vibrational spectrum with a maximum error of 20%. The second method consists, after diagonalizing small blocks, of coupling the high‐ and low‐frequency modes using an iterative procedure. It yields the exact low‐frequency normal modes, but requires a long computational time with convergence problems. The third method, DIMB (Diagonalization in a Mixed Basis), which has the best performance, consists of coupling the approximate low‐frequency modes with the mass‐weighted cartesian coordinates, also using an iterative procedure. It reduces significantly the required computer memory and converges rapidly. The eigenvalues and eigenvectors obtained by this method are without significant error in the chosen frequency range. Moreover, it is a general method applicable to any problem of diagonalization of a large matrix.We report the application of these methods to a deca‐alanine helix, trypsin inhibitor, a neurotoxin, and lysozyme. © 1993 John Wiley & Sons, Inc.
Self‐assembly of bioelastomeric structures from solutions: Mean‐field critical behavior and Flory–Huggins free energy of interactions
Authors: Sciortino F. , Prasad K. U. , Urry D. W. , Palma M. U. 
Published: December 2004

AbstractElastic and quasi‐elastic light scattering studies were performed on aqueous solutions of poly (Val‐Pro‐Gly‐Gly), a representative synthetic bioelastomer that differs from the previously studied poly (Val‐Pro‐Gly‐Val‐Gly) by the deletion of the hydrophobic Val in position four. When the spinodal line was approached from the region of thermodynamic stability, the intensity of light scattered by fluctuations, and the related lifetime and correlation length, were observed to diverge with mean‐field critical exponents for both systems. Fitting of the experimental data allowed determining the spinodal and binodal (coexistence) lines that characterize the phase diagrams of the two systems, and it also allowed a quantitative sorting out of the enthalpic and entropic contributions to the Flory–Huggins interaction parameters. The contribution of valine is derived by comparison of the two cases. This can be viewed as sorting out the effect of a modulation of the solute. The same approach may allow sorting out the entropic and enthalpic effect of modulations of the solvent by cosolutes (or by cosolvents). This could be of particular interest in the case of small osmolytes, affording important adaptive roles in nature, at the cost of very limited changes in genetic information.Finally, the suggestion is further supported that statistical fluctuations of anomalous amplitude, such as those occurring in proximity of the spinodal line, have a role in promoting the process of self‐assembly of extended supramolecular structures. On the practical side, the present approach appears useful in the design of novel synthetic model systems for bioelastomers. © 1993 John Wiley & Sons, Inc.
A proton magnetic resonance study of two synthetic agonist–antagonist pairs of bradykinin analogues
Authors: Otter Albin , Bigler Peter , Stewart John M. , Kotovych George 
Published: December 2004

AbstractThe conformation of two agonist–antagonist pairs of bradykinin (Arg1‐Pro2‐Pro3‐Gly4‐Phe5‐Ser6‐Pro7‐Phe8‐Arg9) analogues were studied in CD3OH/H2O solution by 1H‐nmr techniques. The first agonist peptide studied, D‐Arg0‐Arg1‐Pro2‐Hyp3‐Gly4‐Thi5‐Ser6‐Pro7‐Thi8‐Arg9, differs from the bradykinin sequence by the addition of D‐Arg0, the replacement of the Phe moieties in positions 5 and 8 by Thi (Thi = β‐(2‐thienyl)‐L‐alanine), and Hyp3 (Hyp = L‐4‐hydroxy‐L‐proline) in position 3. In the corresponding antagonist sequence, Pro7 is replaced by D‐Phe7. The second agonist–antagonist pair studied does not contain the D‐Arg0 residue, which is present only to slow down the rate of metabolism. Based on complete resonance assignments from two‐dimensional total correlation spectroscopy and rotating frame nuclear Overhauser effect spectroscopy spectra at 500 MHz, the peptides were analyzed in terms of intraresidue, sequential, and medium‐range nuclear Overhauser effects, amide proton temperature coefficients, and vicinal coupling constants. Both agonist peptides show clear evidence for the existence of a type I β‐turn comprising the C‐terminal residues Ser6‐Pro7‐Thi8‐Arg9 in fast conformational equilibrium with extended structures throughout. Although the conformational space is dominated by extended structures, the presence of the β‐turn is spectroscopically clearly discernible. The two antagonist peptides, on the other hand, do not show evidence of turn formation but rather the presence of an extended conformation with some irregularities in the N‐terminal region of the peptide. While the existence of a turn at the C‐terminal end of bradykinin and its analogues with agonist activity has been predicted by empirical calculations and measurements in very apolar solvents, this study, for the first time, provides evidence based on physical data in a polar solvent environment that the turn is present, that it is type I and that it is essential for agonist activity. In the particular solvent used in these studies, the Pro7 to D‐Phe7 substitution precluded the formation of the turn for the C‐terminal residues of the antagonist. © 1993 John Wiley & Sons, Inc.
Differential binding of the enantiomers of chloroquine and quinacrine to polynucleotides: Implications for stereoselective metabolism
Authors: Scaria P. V. , Craig John C. , Shafer Richard H. 
Published: December 2004

AbstractInteraction of the antimalarial drugs quinacrine and chloroquine with DNA has been studied extensively in order to understand the origin of their biological activity. These studies have shown that they bind to DNA through an intercalative mode and show little sequence specificity. All previous experiments were carried out using the racemic form of these drugs. We have investigated the binding of the enantiomeric forms of quinacrine and chloroquine to synthetic polynucleotides poly (dA‐dT) · poly(dA‐dT) and poly (dG‐dC) · poly(dG‐dC), and found interesting differences in their binding parameters.Quinacrine enantiomers have a much higher binding affinity for the two polynucleotides compared to those of chloroquine. The negative enantiomers were found to have higher binding affinity than the positive ones. The binding constant for the binding of quinacrine (−) to poly(dG‐dC) · poly(dG‐dC) was found to be about 3 times that of quinacrine (+). The differences in these binding affinities were further confirmed by equilibrium dialysis of the complexes of the polynucleotides with the racemic form of the drugs, which resulted in the enrichment of the dialysate with the positive enantiomer. CD spectra of the enantiomers and their polynucleotide complexes are reported. Changes in the fluorescence properties of quinacrine in the presence of the two polynucleotides are also described. Biological implications of these findings are discussed. © 1993 John Wiley & Sons, Inc.
A reexamination of the conformational transitions of T4 thioredoxin
Authors: Shalongo William , Jagannadham Medicherla , Stellwagen Earle 
Published: December 2004

AbstractThe unfolding and refolding of T4 thioredoxin was observed by equilibrium and kinetic size exclusion chromatographic measurements in guanidine hydrochloride at 4°C and pH 7.0. All the observed chromatographic profiles can be simulated by a cubic mechanism using a consistent set of equilibrium and kinetic parameters describing each of the coupled transitions. The four components in the folded protein and in the unfolded protein are interrelated by configurational transitions having parameters characteristic for proline peptide isomerizations. Only two of the four folded conformations are significantly populated at equilibrium. Each of the four unfolded components can refold by a unique Conformational transition. No transiently populated folding intermediates are detected having hydrodynamic volumes intermediate between those characteristic for the folded and unfolded protein. © 1993 John Wiley & Sons, Inc.
Enhanced solubility of proteins and peptides in nonpolar solvents through hydrophobic ion pairing
Authors: Powers Michael E. , Matsuura James , Brassell James , Manning Mark C. , Shefter Eli 
Published: December 2004

AbstractA new technique for enhancing the solubility of peptides and proteins in organic solvents is described. Complexation of polypeptides with stoichiometric amounts of an anionic detergent, such as sodium dodecyl sulfate (SDS), produces diminished aqueous solubility, but enhanced solubility in organic solvents. Consequently, the partitioning of a polypeptide into a nonpolar solvent can be increased by two to four orders of magnitude. In the case of an insulin–SDS complex, the solubility in 1‐octanol is more than tenfold greater than in water. In 1‐octanol, the native structure of insulin remains intact, as determined by CD spectroscopy, and the thermal denaturation temperature (Tm) is increased by approximately 50°C relative to unfolding in water. Finally, peptides and proteins can be extracted back into an aqueous phase provided the chloride concentration is sufficient to displace bound detergent molecules. © 1993 John Wiley & Sons, Inc.
A model of the rabies virus glycoprotein active site
Authors: Rustici Mauro , Bracci Luisa , Lozzi Luisa , Neri Paolo , Santucci Annalisa , Soldani Patrizia , Spreafico Adriano , Niccolai Neri 
Published: December 2004

AbstractThe glycoprotein from the neurotropic rabies virus shows a significant homology with the α neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the α neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side‐chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194‐Ser195‐Arg196‐Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection. © 1993 John Wiley & Sons, Inc.
CD of proline‐rich polypeptides: Application to the study of the repetitive domain of maize glutelin‐2
Authors: Rabanal F. , Ludevid M. D. , Pons M. , Giralt E. 
Published: December 2004

AbstractAn overview of CD of proline‐rich peptides is reported. First, structural characteristics, theoretical CD studies, and the biological relevance of polyproline II structure in such peptides are discussed. Second, a CD study of peptides belonging to the repetitive domain of maize glutelin‐2, H‐(Val‐His‐Leu‐Pro‐Pro‐Pro)n‐OH (n = 3, 5, 8), is described. This series of peptides displayed the CD features of polyproline II structure in water (5°C, pH5). Moreover, it was shown that the addition of increasing amounts of the polyanionic molecule heparin forced a displacement of the conformational equilibrium of those peptides toward higher proportions of the polyproline II structure. In contrast, when the temperature is raised such a structure gradually disappears, leading to more disordered conformations. © 1993 John Wiley & Sons, Inc.
Bioactive peptides: Conformational study of a cystinyl cycloheptapeptide in its free and calcium complexed forms
Authors: Zanotti Giancarlo , Maione Annamaria , Rossi Filomena , Saviano Michele , Pedone Carlo , Tancredi Teodorico 
Published: December 2004

AbstractThe disulphide bridged heptapeptide magnified image has been synthesized by classical solution methods. An ion binding study showed the peptide's ability to complex calcium ions with definite stoichiometry. The solution conformation of the peptide in its free and calcium‐complexed form has been investigated by CD and nmr. The model structure derived from nmr data has been energy minimized and the resulting structure investigated by molecular dynamics simulation in water.The structure of the equimolar peptide/Ca2− complex in acetonitrile at room temperature shows the presence of two transannular hydrogen bonds, with the formation of two ring structures of the C10 (type VIa) and C14 type. One peptide unit (Pro‐Pro) is cis, all others are trans. © 1993 John Wiley & Sons, Inc.
Modifications of the amide bond and conformational constraints in pseudopeptide analogues
Authors: Marraud Michel , Dupont Virginie , Grand Vincent , Zerkout Said , Lecoq Alain , Boussard Guy , Vidal Joelle , Collet Andre , Aubry Andre 
Published: December 2004

AbstractWe have investigated the conformational effects of modifying the amide group in model dipeptides. The N‐methyl amide ψ[CO‐NMe], N‐hydroxy amide ψ[CO‐N(OH)], N‐amino amide ψ[ CO‐N (NH2)], retro amide ψ[ NH‐CO], reduced amide in the neutral ψ[CH2‐NH] and protonated ψ[CH2‐N + H2] state, and hydrazide ψ[CO‐NH‐NH] have been introduced as surrogates of the amide link in pseudopeptide derivatives of the Pro‐Gly or Ala‐Gly model dipeptides protected on both termini by an amide group. These compounds have been studied in solution by proton nmr and ir spectroscopy, and in the solid state by x‐ray diffraction, giving an extended data set of experimental structural and conformational information on pseudopeptide sequences. The conformational effects depend both on the nature and the position of the modified amide link. Some modifications appear to have no intrinsic conformational induction (N‐amino and retro amide), but destabilize any local folded structure by hydrogen‐bond breaking. Because of the formation of strong intramolecular interactions, others are capable of stabilizing a β‐turn (for example protonated reduced amide), or of inducing a particular local conformation such as a β‐ or γ‐like turn (for example N‐hydroxy amide). The particular geometry of the cis N‐methyl amide and of the “hydrazino” proline favors the formation of a sharp turn of the main chain. All these structural data are of interest to the design of bioactive peptide mimics. © 1993 John Wiley & Sons, Inc.
Crystal structures of Boc‐D‐ and L‐Iva‐L‐Pro‐OBZl: Unturned conformation of Aib‐Pro sequence unaffected by replacement of Me with Et in Aib
Authors: Kawai Masao , Omori Yoshimasa , Yamamura Hatsuo , Butsugan Yasuo , Taga Tooru , Miwa Yoshihisa 
Published: December 2004

AbstractThe crystal structures of the isovaline (Iva) containing dipeptides, Boc‐D‐Iva‐L‐Pro‐OBzl and Boc‐L‐Iva‐L‐Pro‐OBzl, were determined by x‐ray diffraction. The diastereomeric peptides were shown to adopt unturned conformations closely similar to each other (ϕIva 52°, ψIva 46°, ϕPro–65°, and ψPro 143° for D‐Iva‐L‐Pro sequence and ϕIva 52°, ψIva 44°, ϕPro −63°, and ψpro 148° for L‐Iva‐L‐Pro sequence). The Pro ring of each peptide was in Cγ‐endo conformation. The unusually large ∠CIva‐NPro‐C values (131° in both peptides) were observed, that was due to steric repulsion between the δ‐methylene of Pro and the alkyl side chain of Iva residue. These conformations were essentially the same as that of the corresponding α‐aminoisobutyric acid (Aib)‐containing peptide Boc‐Aib‐L‐Pro‐OBzl. The result has demonstrated that replacement of either one of the two methyl groups of the Aib residue in Boc‐Aib‐L‐Pro‐OBzl with an ethyl group does not cause any significant change in the unturned conformation of the dipeptide. © 1993 John Wiley & Sons, Inc.
Statistics of RNA secondary structures
Authors: Fontana Walter , Konings Danielle A. M. , Stadler Peter F. , Schuster Peter 
Published: December 2004

AbstractA statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and free ends. Statistical properties of these elements are computed for small RNA molecules of chain lengths up to 100. The results of RNA structure statistics depend strongly on the particular alphabet chosen. The statistical reference is compared with the data derived from natural RNA molecules with similar base frequencies.Secondary structures are represented as trees. Tree editing provides a quantitative measure for the distance dt, between two structures. We compute a structure density surface as the conditional probability of two structures having distance t given that their sequences have distance h. This surface indicates that the vast majority of possible minimum free energy secondary structures occur within a fairly small neighborhood of any typical (random) sequence.Correlation lengths for secondary structures in their tree representations are computed from probability densities. They are appropriate measures for the complexity of the sequence‐structure relation. The correlation length also provides a quantitative estimate for the mean sensitivity of structures to point mutations. © 1993 John Wiley & Sons, Inc.