bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depolarization of Raman scattering from some nucleotides of RNA and DNA
Authors: Ueda Toyotoshi , Ushizawa Koichi , Tsuboi Masamichi 
Published: December 2004

AbstractDepolarization ratios of Raman bands, excited at 488.0 nm, of guanosine‐5′‐monophosphoric 4 acid, cytidine‐5′‐monophosphoric acid, adenosine‐5′‐monophosphoric acid, thymidine‐5′‐monophosphoric acid, and uridine‐5′‐monophosphoric acid have been measured in their H2O and D2O solutions in the spectral region from 300 to 1800 cm−1. For comparison, the disodium salt of 2′‐deoxyadenosine‐5′‐monophosphoric acid was also subjected to the depolarization measurement in its H2O solution. The results have been correlated with possible orientations of the principal axes of the Raman scattering tensors as well as with the relative magnitudes of the tensor components. Results should be useful for future polarized Raman studies of synthetic and natural DNA. © 1993 John Wiley & Sons, Inc.
Bioactive peptides: Solid state, solution and molecular dynamics studies of a cyclolinopeptide A‐related cystinyl cyclopentapeptide
Authors: Rossi Filomena , Saviano Michele , Di Blasio Benedetto , Zanotti Giancarlo , Maione Anna Maria , Tancredi Teodorico , Pedone Carlo 
Published: December 2004

AbstractThe conformational analysis of
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the disulphide cyclopeptide‐related cyclolinopeptide A, has been carried out by solid state methods using x‐ray diffraction techniques, in solution by nmr, CD, ir spectroscopies, and by molecular dynamics (MD) analysis. The structure of the monoclinic form, obtained from ethanol (a = 11.303(2) Å, b = 14.467(8) Å, c = 12.355(2) Å, β(°) = 109.40(1), space group P21, Z = 2) presents two transannular H bonds with the formation of one type VIa β‐turn involving the C  O of the urethane moiety and the Phe3 NH, and an intramolecular H bond between the C  O of urethane group and the Phe4 NH.In the solid state all the peptide bonds are in the trans configuration with the exception of a cis peptide bond occurring between the Cys1 and Pro2 residues; the linkage S—S assumes right‐handed chirality. The conformational study in solution by nmr spectroscopy indicates that the peptide is very flexible and that some conformer families are present at room temperature both in polar and apolar solvents.CD studies confirm that this cyclic system tends to give rise to a complex mixture of quasi‐isoenergetic conformations, favored by the flexibility of the disulphide bridge and by the isomerism of the Xxx‐Pro bond.MD studies carried out in vacuo and in solution shows that the structure determined by solid state represents a energy minimum. All hydrogen conds found in the crystalline state are correctly reproduced in vacuo and in solution simulations. © 1994 John Wiley & Sons, Inc.
The amplitude of local angular motion of purines in DNA in solution
Authors: Nuutero Sirkku , Fujimoto Bryant S. , Flynn Peter F. , Reid B. R. , Ribeiro N. S. , Schurr J. Michael 
Published: December 2004

AbstractNuclear magnetic resonance and optical experiments are combined to determine the rms amplitude of local angular motion of purines in DNA in solution. A 12 base‐pair duplex DNA with the sequence d (CGCGAATTCGCG)2 is deuterated at the H8 positions of adenine and guanine by exchange with solvent dklstwxzat 55°C. The deuterium nmr spectrum of this DNA is measured at 30 mg/mL at 30°C in an 11.76 Tesla magnet (76.75 MHz). The time‐resolved fluorescence polarization anisotropies (FPA) of this same sample and also a greatly diluted sample (0.215 mg/mL) were measured after addition of ethidium. FPA measurements of the dilute sample yield the hydrodynamic radius, RH = 9.94 ± 0.2 Å, while those at the nmr concentration are employed to characterize the collective motions in terms of either an enhanced viscosity or dimer formation. The rms amplitude of local angular motion was determined by analyzing the 2H‐nmr spectrum, in particular the line width, using recently developed theory for the transverse relaxation rate (R) together with essential information about the collective motions from these and other optical studies. When the principal‐axis frame of the electric field gradient tensor is assumed to undergo overdamped libration around each of its three body‐fixed axes in an isotropic deflection potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10°–11°, provided the high DNA concentration acts to enhance the viscosity, and is about 9°–11°, if it acts to produce end‐to‐end dimers. The proton nmr relaxation data of Eimer et al. are reanalyzed and shown to yield an rms amplitude of angular motion of the cytosme H5–H6 internuclear vector of 9°–10°, depending upon its orientation with respect to the helix axis. In all of these analyses, full account is taken of the collective twisting and bending deformations, which have a small but significant effect on the results. It is shown that the rms amplitudes of local angular motion do not depend strongly on the model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the same dimensionality. The rms amplitudes of local angular motion in solution are comparable to those observed for the same sequence at low levels of hydration in the solid state. © 1994 John Wiley & Sons, Inc.
The interaction of ellipticine derivatives with nucleic acids studied by optical and 1H‐nmr spectroscopy: Effect of size of the heterocyclic ring system
Authors: Behravan G. , Leijon M. , Sehlstedt U. , Nordén B. , Vallberg H. , Bergman J. , Gräuslund A. 
Published: December 2004

AbstractThe DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly [(dA‐dT) · (dA‐dT)], or poly [(dG‐dC) · (dG‐dC)] showed a 10 nm bathochromic shift of the light absorption bands of the pentacyclic and tetracyclic compounds upon binding to the nucleic acids, which indicates binding by intercalation. For the tricyclic compound a smaller shift of 1–3 nm was observed upon binding to the nucleic acids.Flow linear dichroism studies show that the geometry of all complexes is consistent with intercalation of the ring system, except for the DNA and poly [(dG‐dC) · (dG‐dC)] complexes of the tricyclic compound, where the average angle between the drug molecular plane and the DNA helix axis was found to be 65°.One‐dimensional 1H‐nmr spectroscopy was used to study complexes between d(CGCGATCGCG)2 and the tricyclic and pentacyclic compounds. The results on the pentacyclic compound show nonselective broadening due to intermediate chemical exchange of most oligonucleotide resonances upon drug binding. The imino proton resonances are in slow chemical exchange, and new resonances with upfield shifts approaching 1 ppm appear upon drug binding, which supports intercalative binding of the pentacyclic compound. The results on the tricyclic compound show more rapid binding kinetics and very selective broadening of resonances. The data suggest that the tricyclic compound is in an equilibrium between intercalation and minor groove binding, with a preference to bind close to the AT base pairs with the side chain residing in the minor groove. © 1994 John Wiley & Sons, Inc.
Biophysical studies on fragments of the α‐factor receptor protein
Authors: Reddy A. P. , Tallon M. A. , Becker J. M. , Naider F. 
Published: December 2004

AbstractThe receptor for the α‐factor mating pheromone of the yeast Saccharomyces cerevisiae consists of 431 amino acid residues and is a member of a family of membrane proteins predicted to have seven transmembrane helices. Fragments of the receptor corresponding to two of the transmembrane helices [residues 246–269 (M6) and 273–302 (M7)], two of the interhelical loops [residues 107–125 (E2) and 191–206 (E3)], and to a portion of the carboxyl terminus [residues 350–372 (CT)] were synthesized using solid‐phase methodologies and purified to near homogeneity. CD was used to characterize the secondary structure of these peptides in trifluoroethanol (TFE), in TFE/water mixtures, in sodium dodecyl sulfate (SDS), and in the presence of dimyristoyl phosphatidylcholine (DMPC) liposomes. In TFE, M6 and M7 exhibited CD spectra consistent with highly helical peptides, whereas CT was partially helical. In contrast, E2 and E3 were either disordered or aggregated in this solvent. M6 did not partition well into DMPC vesicles whereas M7 remained helical. Both M6 and M7 assumed helical conformations in 25 mM SDS. The loop neptides and the carboxyl terminus peptide were either in a β‐structure or disordered in the presence of lipid. These findings represent the first biophysical evidence for conformations assumed by specific segments of the STE2 receptor protein. © 1994 John Wiley & Sons, Inc.
Computer simulation of the free energy of peptides with the local states method: Analogues of gonadotropin releasing hormone in the random coil and stable states
Authors: Meirovitch Hagai , Koerber Steven C. , Rivier Jean E. , Hagler Arnold T. 
Published: December 2004

AbstractThe Helmholtz free energy F (rather than the energy) is the correct criterion for stability; therefore, calculation of F is important for peptides and proteins that can populate a large number of metastable states. The local states (LS) method proposed by H. Meirovitch [(1977) Chemical Physics Letters, Vol. 45, p. 389] enables one to obtain upper and lower bounds of the conformational free energy, FB (b, l) and FA (b, l), respectively, from molecular dynamics (MD) or Monte Carlo samples. The correlation parameter b is the number of consecutive dihedral or valence angles along the chain that are taken into account explicitly. The continuum angles are approximated by a discretization parameter l; the larger are b and l, the better the approximations; while FA can be estimated efficiently, it is more difficult to estimate FB. The method is further developed here by applying it to MD trajectories of a relatively large molecule (188 atoms), the potent “Asp4‐Dpr10” antagonist [cyclo(4/10)‐(Ac‐Δ3Pro1‐D‐pFPhe2‐D‐Trp3‐Asp4‐Tyr‐5‐D‐Nal6‐Leu7‐Arg8‐Pro9‐Dpr10‐NH2)] of gonadotropin releasing hormone (GnRH). The molecule was simulated in vacuo at T = 300 K in two conformational states, previously investigated [J. Rizo et al. Journal of the American Chemical Society, (1992) Vol. 114, p. 2860], which differ by the orientation of the N‐terminal tail, above (tail up, TU) and below (tail down. TD) the cyclic heptapeptide ring. As in previous applications of the LS method, we have found the following: (1) While FA is a crude approximation for the correct F, results for the difference, ΔFA = FA(TD) – FA(TU) converge rapidly to 5.6(1) kcal/mole as the approximation is improved (i.e., as b and l are increased), which suggests that this is the correct value for ΔF; therefore TD is more stable than TU. (The corresponding difference in entrophy. TΔSA = 1.3(2) kcal/mole, is equal to the value obtained by the harmonic approximation.) (2) The lowest approximation, which has the minimal number of local states, i.e., based on b = 0 (no correlations) and l = 1 (the angle values are distributed homogeneously), also leads to the correct value of ΔF, within the error bars. This is important since the lowest approximation can be applied even to large proteins. (3) The method enables one to define the entropy of a part of the molecule and thus to measure the flexibility of this part. We have verified that the results for T[SA(TU) – SA(TD)] of the tail alone converged to 2.4(1) kcal/mole, which demonstrates the relatively high flexibility of the tail in the TU state. In order to study the random coil state, the Asp4‐Dpr10 analogue and its linear version were simulated by MU at 1000 K. We have been able to calculate a lower bound, ∼ 25 kcal/mole for T[S(linear) – S(cyclic)], which is the reduction in the conformational entropy caused by the ring closure. © 1994 John Wiley & Sons, Inc.
Ir and Raman spectra of L‐aspartic acid and isotopic derivatives
Authors: Navarrete J. T. López , Hernández V. , Ramírez F. J. 
Published: December 2004

AbstractThe ir and Raman spectra of L‐aspartic acid, L‐aspartic‐d4 acid, and L‐aspartic‐15N acid as solid samples have been recorded and measured. The data obtained were used to propose a general assignment of the fundamental vibrational modes in the basis of the isotopic shifts measured and correlations with previous data reported for other amino acids and related molecules. A MNDO‐scaled semiempirical force field was obtained, and vibrational frequencies and descriptions were used to support the previous assignments based on experimental features. © 1994 John Wiley & Sons, Inc.
Molecular dynamics simulation and nmr study of a blood group H trisaccharide
Authors: Widmalm Göran , Venable Richard M. 
Published: December 2004

AbstractMolecular dynamics simulations in vacuum and solution have been carried out on 2′‐α‐L‐fucosyllactitol, a model for blood group H in conjunction with two‐dimensional nmr measurements on the same compound. Three independent starting conformations for the dynamics were chosen from low energy conformations obtained by a ϕ/ψ grid search. Nine 5 ns vacuum simulations of the trisaccharide were performed, employing three different ways to treat electrostatic interactions for each starting conformation: distance‐dependent dielectric with ε = r, constant dielectric with ε = 1, or constant dielectric with ε = 80. In vacuum, transitions of ϕ and ψ for the α‐L‐Fuc‐(1 → 2)‐β‐D‐Gal element occur in a cooperative manner. The virtual distance obtained for H1 in fucose to H2 in galactose from nuclear Overhauser effect spectroscopy experiments agree with one of the conformations of the trisaccharide in one of the three 100 ps aqueous simulations (ϕ/ψ ca. −100°/150°), indicating this may be a dominant solution conformation. The rms fluctuations of the ϕ‐ and ψ‐dihedral angles were ∼ 10° for a conformational state, both in the vacuum and the aqueous simulations. For the simulations in vacuum, the agreement with experimental NOE data is reasonable when a constant dielectric of 1 is used (major conformers having ϕ/ψ ca. −100°/150° and −140°/100°), whereas the agreement was poor with a constant dielectric of 80. Translational diffusion coefficients calculated from the simulation of the oligosaccharides were 0.12–0.18 × 10−5 cm2/s and from nmr measurements 0.27 × 10−5 cm2/s. © 1994 John Wiley & Sons, Inc.
Solution conformation of a cyclic neurokinin antagonist: A nmr and molecular dynamics study
Authors: Zhang Min , Quinn Thomas P. , Wong Tuck C. 
Published: December 2004

AbstractThe solution structure of a hexapeptide, cyclo(Gln‐Trp‐Phe‐Gly‐Leu‐Met), which is a selective NK‐2 antagonist, has been studied by a combination of two‐dimensional nmr and molecular dynamics (MD) techniques. The simulation based on nmr and MD data resulted in the convergence to a family of structures. Free molecular dynamics for 50 ps in the presence of DMSO solvent molecules shows that the structure is energetically stable. One intramolecular hydrogen bond between the amide proton of Gin and the carbonyl oxygen of Gly was revealed. This result is consistent with the results from the measurement of the temperature coefficient of the amide protons. The extent of intermolecular hydrogen bonding between the amide protons of the peptide and DMSO was also revealed by the free MD simulation. The resulting structure of the cyclic peptide contains a variation type I′ β‐turn in the Gly‐Leu‐Met‐Gln segment. Comparison of the structure of this peptide with that of other NK‐2 antagonist cyclic hexapeptides was made, and the activity of cyclic antagonists appears to be inversely related to the conformational rigidity of the cyclic peptides. © 1994 John Wiley & Sons, Inc.
Detection of monodisperse aggregates of a recombinant amelogenin by dynamic light scattering
Authors: Moradian‐Oldak J. , Simmer J. P. , Lau E. C. , Sarte P. E. , Slavkin H. C. , Fincham A. G. 
Published: December 2004

AbstractRecombinant murine amelogenins M179 and M166 were expressed in Escherichia coli and purified. The aggregation properties of these amelogenins have been investigated in aqueous solutions as well as acetonitrile‐containing solutions using dynamic light scattering. Dynamic light scattering provides direct measurement of the translational diffusion coefficient and hydrodynamic radius, and of an estimate of the molecular weight. Polydispersity and statistical parameters of how to interpret the analysis are also provided. Amelogenin aggregation was examined in solutions of a range of pH, ionic strengths, and protein concentrations. It was shown that at pH 7.8–8 and ionic strength of 0.02–0.05M the M179 molecules form monodispersed aggregates with hydrodynamic radii ranging from 15 to 19 nm. Analysis of hydrodynamic radii and size distribution of M179 aggregates in acetonitrile‐containing solvents compared to that in aqueous solutions indicated a primary role for hydrophobic interactions in the association process of amelogenin molecules to form aggregates. Comparison between the aggregates formed by M179 and M166, which lacks the hydrophilic carboxy‐terminal 13 residue sequence of M179, suggested that the self‐assembly of amelogenin molecules to form stable and monodisperse aggregates requires the presence of the hydrophilic carboxy‐terminal sequence of M179. © 1994 John Wiley & Sons, Inc.
Defect peptide chemistry: Perturbations in the structure of a homopentapeptide induced by a guest residue interrupting side‐chain regularity
Authors: Benedetti Ettore , Pedone Carlo , Pavone Vincenzo , Di Blasio Benedetto , Saviano Michele , Fattorusso Roberto , Crisma Marco , Formaggio Fernando , Bonora Gian Maria , Toniolo Claudio , Kaczmarek Krzysztof , Redlinski Adam S. , Leplawy Miroslaw T. 
Published: December 2004

AbstractThe fully blocked pentapeptide Tfa‐(Deg)2‐L‐Abu‐(Deg)2‐OtBu (Tfa:triflouroacetyl; Deg: Cα,α‐diethylglycine; OtBu: tert‐butoxy) adopts in the crystal state a regular, right‐handed 310‐helical structure stabilized by three N  H …︁ O  C intramolecular 1 ← 4 (or C10) H bonds, as determined by an x‐ray diffraction analysis. However, a Fourier transform ir absorption and 1H‐nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C5 forms. A comparison with the stable, fully developed, multiple C5 conformation of Tfa‐(Deg)5‐OtBu indicates that incorporation of an Abu guest residue, interrupting the side‐chain uniformity of the host (Deg)5 homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal‐state structure. © 1994 John Wiley & Sons, Inc.
A conformational study of agarose by vacuum uv CD
Authors: Arndt Edward R. , Stevens Eugene S. 
Published: December 2004

AbstractAgarose films were prepared using a variety of casting conditions, heat treatments, and solvation treatments. Films represented the high temperature sol, the room temperature gel, and a high temperature state with cross‐links intact. The vacuum uv CD of the film samples varies considerably, but the similarities between the film CD and the previously reported solution CD show that dehydration per se does not affect the CD. Combining the CD results for the dried sol with the x‐ray results of Foord and Atkins leads to a description of the high temperature sol in terms of locally extended chain conformations. The CD of the gel and its peculiarly high uv absorption are satisfactorily, albeit not uniquely, interpreted in terms of the double‐helix model of the gel, in agreement with previous conformational studies based on chiroptical properties. © 1994 John Wiley & Sons, Inc.
Helix formation in model peptides based on nucleolin TPAKK motifs
Authors: Xu Xiaobing , Cooper Laura G. , DiMario Patrick J. , Nelson Jeffrey W. 
Published: December 2004

AbstractThe structures formed by peptide models of the N‐terminal domain of the nucleolar protein nucleolin were studied by CD and nmr. The sequences of the peptides are based on the putative nucleic acid binding sequence motif TPAKK: The peptides TP1 and TP2 have the sequence acetyl‐G(ATPAKKAA)nG‐amide, with n = 1 and 2, respectively. CD measurements indicate structural changes in both peptides when the lysine side chains are uncharged by increasing the pH or acetylation of the side‐chain amines. When trifluoroethanol (TFE) is added, more extensive structural changes are observed, resembling helical structure based on nmr nuclear Overhauser effect (NOE) and Cα proton chemical shift changes, and CD spectra. The structure formed in 0.5M NaClO4 as observed by nmr is similar to that when the lysine side chains are acetylated, due presumably to interactions of perchlorate ion with side‐chain charges on lysines. The helical structure observed in TPAKK motifs may be stabilized via N‐capping interactions involving threonine. The structures observed in TFE suggest that the Thr‐Pro sequence initiates short helical segments in TPAKK motifs, and these helical structures might interact with nucleic acids, presumably via interactions between lysines and threonines of nucleolin. © 1995 John Wiley & Sons, Inc.
Normal mode calculation of a netropsin–DNA complex: Effect of structural deformation on vibrational spectrum
Authors: Chen Y. Z. , Prohofsky E. W. 
Published: December 2004

AbstractCalculations of the normal mode spectrum of a netropsin‐DNA complex, an isolated DNA helix of the same sequence, and a free netropsin molecule were carried out and compared with observations. We find that the frequency of modes of the complex that are primarily vibrations localized to the helix are relatively unchanged from the frequencies found for similar modes of the isolated helix. On the other hand, the frequencies of those modes of the complex that are found to be primarily in the netropsin are found to change significantly in the complex from that of the free netropsin. Further analysis indicates that the changes in the “netropsin modes” are primarily due to the conformational deformation induced in the netropsin by formation of the complex. All the frequencies and shifts in frequency are in good agreement with recent Raman measurements. © 1995 John Wiley & Sons, Inc.
Molecular conformational analyses of dehydroalanine analogues
Authors: Alemán Carlos , Casanovas Jordi 
Published: December 2004

AbstractThe conformational preferences of dehydroalanine (ΔAla) were examined through ab initio calculations. The geometries of the minimum energy conformations for N‐formyldehydro alanilamide and N‐acetyl‐N′‐methylamide of dehydroalanine were determined by gradient optimization at the HF/6‐31G* level, and correlation corrections were examined with MP2 single‐point energy calculations. Furthermore, HF/3‐21G ab initio geometry optimizations were performed on nine conformations of the model tripeptide N‐acetyl‐N′‐methylamide of didehydroalanine. The results indicate that the C5 is the lowest energy conformation at all levels of theory. However, the relative energy of the helix conformation decreases when the number of ΔAla residues in the peptide chain increases. On the other hand, significant variations of the geometry upon conformational change were observed for the three compounds investigated. These results permit to extract important conformationally dependent geometry trends. The results of this study were compared to x‐ray diffraction data on single crystals of dehydroalanine‐containing peptides. © 1995 John Wiley & Sons, Inc.