bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure and molecular conformation of N‐boc‐L‐pro‐dehydro‐leu‐OCH3
Authors: Narula Punit , Patel H. C. , Singh T. P. , Chauhan V. S. , Sharma Ashwani K. 
Published: December 2004

AbstractThe peptide N‐Boc‐L‐Pro‐dehydro‐Leu‐OCH3 was synthesized by coupling dehydroleucine methyl ester with Boc‐Pro‐OH. It was crystallized from its solution in a methanol–water mixture at 4°C and the crystals belong to the orthorhombic space group P212121 with a = 10.239(1) Å, b = 19.276(4) Å, c = 20.319(3) Å, V = 4010(1) Å3, and Z = 8. The structure was solved by direct methods using MULTAN 80. The structure was refined to an R value of 0.095 for 1871 observed reflections. There are two crystallographically independent molecules in the unit cell. The molecular dimensions of the two molecules are very similar. The backbone conformation angles of these molecules are as follows: θ1 = −176(1)°, ω0 = −2(2)°, ϕ1 = −72(1)°, ψ1 = 141(1)°, ω1 = 169(1)°, ϕ2 = −98(1)°, ψ2 = −179(1)°, θT = 179(1)°, θ = 174(1)°, ω10 = −3cm−1, ϕ11 = −64(1)°, ψ11 = 148(1)°, ω11 = 167(1)°, ϕ12 = −67(1)°, ψ12 = 175(1)°, and θ1T = 172(1)°, respectively. Other torsion angles such as θ = 86(1)°, χ2 = −5(2)°, = 131(1)°, and χ12 = −16(2)° are interesting to define the backbone conformation together with the dehydro‐Leu side chain as a conformation similar to that of the β‐bend type II. The central amide bond of Pro‐dehydro‐Leu segment is deviated from the planarity. The Boc group adopts a trans–cis conformation. The side‐chain torsion angles χ1, χ2, χ3, χ4, and χ0 for Pro‐residue in the two molecules are 11(2)°, −11(2)°, 6(2)°, 2(1)°, −9(1)° and −18(1)°, 31(1)°, −31(1)°, 21(1)°, and −1(1)° respectively. The side chain of the Pro residue of molecule A is in the flattened Cγ‐endo conformation while the pyrrolidine ring in miolecule B adopts the well‐known Cγ‐exo conformation. The side‐chain torsion angles χ, χ2,1, and χ2,2 in the leucyl residues of molecules A and B are −5(2)°, −111(2)°, 126(2)° and −16(2)°, −110(2)°, and 133(2)°, respectively. The molecular packing is stabilized by intermolecular hydrogen bonds and van der Waals interactions.
Nmr studies on the presence of domain structures in polysaccharides. II. 1H spin‐‐lattice relaxation time dispersion
Authors: Lacelle Serge , Gerstein Bernard C. 
Published: December 2004

AbstractThe behavior of 1H‐nmr spin–lattice relaxation times as a function of frequency is examined for powders of α‐ and β‐cyclodextrins, dextran B512F, and their “deuterated” analogues, where deuterium replaces exchangeable protons. A crossover from two‐ to one‐component relaxation decays is observed with increasing frequency (ν). By considering the effect of spin diffusion in spin–lattice relaxation measurements as a function of the frequency, estimates of domain sizes (∼ 7–10 Å) consistent with the lower limit of spatial resolution of the Goldman–Shen experiments are obtained.
Dynamic coupling between DNA and its primary hydration shell studied by brillouin scattering
Authors: Tao N. J. , Lindsay S. M. , Rupprecht A. 
Published: December 2004

AbstractWe have measured the dispersion of phonon line widths between frequencies of about 2 and 10 GHz in DNA films at relative humidities between 0 and 95%. The results show that the relaxation mode of the primary hydration shell retains its basic characteristics even in samples with very high water content. A modified mode coupling model is used to include both the collective nature of the sound wave and to describe the change in hydration explicitly. It enables us to describe the coupling between the phonons and the water relaxation mode at various water contents, and allows us to extract values for the primary shell relaxation time and coupling constants over the range of hydration studied. The primary shell relaxation time (∼ 40 ps) and coupling parameters remain nearly constant over the entire range of hydration. We have reanalyzed our earlier Brillouin data (taken as a function of temperature) in terms of two relaxation processes (primary plus a secondary shell contribution of about 2 ps at room temperature). This new analysis indicates that both processes follow a simple Arrhenius behavior with activation energies of 5 kcal mole−1 for the primary relaxation and 7 kcal mole−1 for the secondary relaxation. We also observe a rather broad central mode that can be fitted by a Lorentzian, and that may arise from direct (as opposed to coupled‐mode) scattering from the primary relaxation mode.
Conformational behavior of α,α‐dialkylated peptides: Ab initio and empirical results for cyclopropylglycine
Authors: Barone Vincenzo , Fraternali Franca , Cristinziano Pier Luigi , Lelj Francesco , Rosa Angela 
Published: December 2004

AbstractThe preferred conformations of model cyclopropylglycine peptides have been investigated by means of ab initio and empirical methods. Empirical computations performed with fixed bond lengths and valence angles using two well‐known force fields show that only values of ϕ in the ranges ±70° ± 20° are sterically allowed, and that the C7‐conformation corresponds to the absolute energy minimum irrespective of the terminal groups used. Also, ab initio computations give similar results, but suggest greater stabilities for bridge and, especially, extended structures. These discrepancies can be removed, adding to the empirical force field a twofold torsional potential on ψ and using softer steric repulsive potentials. Complete geometry optimization using both ab initio and empirical methods does not affect the relative stabilities of folded conformations, but leads to a further significant stabilization of the fully extended structure via large modifications of some valence angles.
Dielectric relaxation studies on bovine ligamentum nuchae
Authors: Luan Chi‐Hao , Harris R. Dean , Urry Dan W. 
Published: December 2004

AbstractDielectric relaxation studies of bovine ligamentum nuchae are reported over the frequency range of 1 MHz to 1 GHz and over the temperature range of 23–48°C. A temperature‐dependent relaxation process was observed at low megahertz‐frequency with the correlation time of around 40 ns. The result is quite similar to that of a synthetic polypentapeptide (VPGVG) and of α‐elastin. The relaxation is proposed to arise in part from the peptide libration within the polypentapeptide of bovine ligamentum nuchae.
Molecular structure of L‐lysyl‐L‐alanyl‐L‐alanine: A tripeptide found in histone H1
Authors: Verdaguer N. , Urpí L. , Fita I. , Subirana J. A. 
Published: December 2004

AbstractThe crystal structure of L‐lysyl‐L‐alanyl‐L‐alanine hydrochloride has been determined by x‐ray diffraction. The peptide is in zwitterionic form with the carboxylic group deprotonated, and with positive charges both in the amino terminal and ϵ‐amino groups of lysine. Crystals are monoclinic, space group P21 and Z = 4, with two peptide molecules in the asymmetric unit, which show different conformations. While one molecule has torsional angles for the Lys‐Ala peptide bond (φ2, φ2) in the β‐pleated sheet region, the values for the other molecule are close to those for the α‐helix. This molecular flexibility is of interest for the study of H1 histone, which contains this sequence repeated several times. The two lysine residues show fully extended side chains. Two methanol molecules and two acetonitrile molecules are also present in the unit cell. An extensive network of hydrogen bonds and ionic interactions stabilize the crystal structure.
Secondary structure of the human growth hormone releasing factor (GRF 1–29) by two‐dimensional 1H‐nmr spectroscopy
Authors: Theriault Y. , Boulanger Y. , Saunders J. K. 
Published: December 2004

AbstractThe secondary structure of the human growth hormone releasing factor (GRF 1‐29) in a solution mixture of 60% aqueous phosphate buffer:40% 2,2,2‐trifluoroethanol‐d3 has been investigated by two‐dimensional 1H‐nmr spectroscopy. Sequential resonance assignments and elements of secondary structure were obtained from phase‐sensitive correlation spectroscopy, relayed coherence spectroscopy, and nuclear Overhauser spectroscopy experiments. The observation of a large number of α‐amide and amide‐amide interresidual nuclear Overhauser effect connectivities as well as the existence of 11 slowly exchanging amide protons indicates that the peptide adopts a well‐defined secondary structure most likely constituted of a single long helix. This conclusion is consistent with the CD measurements.
Conformational analysis and molecular dynamics simulations of maltose
Authors: Ha S. N. , Madsen L. J. , Brady J. W. 
Published: December 2004

AbstractConstrained conformational energy minimizations have been used to calculate an adiabatic (Φ, ψ) potential energy surface for the disaccharide β‐maltose. The inclusion of molecular flexibility in the conformational energy analysis of the disaccharide was found to significantly lower the barriers to conformational transitions, as has been observed previously for other systems. Several low energy wells were identified on the adiabatic surface which differ in energy by small amounts and with low absolute barriers separating them, indicating the possibility of a non‐negligible equilibrium population distribution in each well. If such a distribution of conformations existed in the physical system, the conformation observed by NMR NOE measurements would thus be a “virtual” conformation. Molecular dynamics simulations of the motions of this molecule in vacuum were also conducted and indicate that the rate of relaxation of the molecule to the adiabatic surface may be slower than the typical timescale of conformational fluctuations. This effect is apparently due to an unphysical persistence of hydrogen bond patterns in vacuum which does not occur in aqueous solution. Trajectories undergoing transitions between wells were calculated and the effects of such conformational transitions upon the ensemble mean structure, such as might be observed in an NMR experiment, were demonstrated.
A crystal molecular conformation of leucine‐enkephalin related to the morphine molecule
Authors: Aubry A. , Birlirakis N. , Sakarellos‐Daitsiotis M. , Sakarellos C. , Marraud M. 
Published: December 2004

AbstractLeucine‐enkephalin (Try1‐Gly2‐Gly3‐Phe4‐Leu5) has been crytallized as a trihydrate from water solution. X‐ray diffraction reveals a tightly folded molecular conformation with two fused βIII‐ (Gly2‐Gly3) and βI‐ (Gly3‐Phe4) turns. The Tyr1 and Phe4 aromatic rings have a close orthogonal arrangement analogous to the tyramine and cyclohexenyl rings in morphine. This suggests that the conformation found in the trihydrate crystal structure could be required for recognition by μ‐receptor sites.
1H‐nmr studies of receptor‐selective substance P analogues reveal distinct predominant conformations in DMSO‐d6
Authors: Levian‐Teitelbaum Dina , Kolodny Nancy , Chorev Michael , Selinger Zvi , Gilon Chaim 
Published: December 2004

AbstractProton nmr parameters are reported for DMSO‐d6 solutions of two receptor‐selective substance P analogues: Ac[Arg6, Pro9]SP6‐11, which is selective for the NK‐1 (SP‐P) receptor and [pGlu6, N‐MePhe8]SP6‐11, which selectively activates the NK‐3 (SP‐N) receptor. Full peak assignments of both analogues were obtained by COSY experiments. The chemical shifts, coupling constants, and temperature coefficients of amide proton chemical shifts as well as NOESY effects and calculated side‐chain rotamer populations of Phe side chains are reported for both peptides. Analysis of coupling constants and temperature coefficients together with the nuclear Overhauser enhancement spectroscopy effects suggest that Ac[Arg6, Pro9]SP6‐11 has a trans configuration about the Phe8‐Pro9 amide bond and the preferred conformation of this analogue has a type I β‐turn. The nmr data for [pGlu6, N‐MePhe8]SP6‐11 suggest that this peptide exists as a mixture of cis–trans isomers in which the cis isomer can preferably adopt a type VI β‐turn conformation, and the trans isomer can adopt a γ‐turn conformation. There are indications that the two last turns are stabilized by a hydrogen bond between the syn carboxamide proton and the pGlu ring carbonyl.
Selective agonists for receptors of substance P and related neurokinins
Authors: Regoli D. , Dion S. , Rhaleb N.‐E. , Rouissi N. , Tousignant C. , Jukic D. , D'Orleans‐Juste P. , Drapeau G. 
Published: December 2004

AbstractNeurokinins and their receptors are a complex system consisting of at least three endogenous agents—substance P (SP), neurokinin A (NKA), and neurokinin B (NKB)—and their corresponding receptor types, respectively, NK‐1, NK‐2, and NK‐3. Investigations on receptors have been made using sensitive and fairly selective pharmacological preparations (the dog carotid artery for the NK‐1, the rabbit pulmonary artery devoid of endothelium for the NK‐2, and the rat portal vein for the NK‐3 receptor), and some natural peptides of mammalian and nonmammalian origin. Because of the nonselectivity of the natural peptides, analogues of the neurokinins have been found that act on one receptor only and show therefore high selectivity. The selective agonists [Sar9, Met(O2)11]SP, [Nle10]NKA (4–10), and [MePhe7]‐NKB have been used successfully for (a) characterizing the three neurokinin receptors, (b) identifying isolated organs whose responses to neurokinins depend on the activation of a single (monoreceptor systems) or of more than one (multireceptor systems) receptor, and (c) elucidating some of the physiological function of the three receptor types. It is suggested that NK‐1 mediate peripheral vasodilatation and exocrine secretions, NK‐2 stimulate bronchial muscles and facilitate the release of catecholamines, and NK‐3 promote the release of acetylcholine in peripheral organs.
Bioactive conformation of linear peptides in solution: An elusive goal?
Authors: Temussi Piero A. , Picone Delia , Castiglione‐Morelli Maria A. , Motta Andrea , Tancredi Teodorico 
Published: December 2004

AbstractBioactive peptides of natural origin have, in general, short linear sequences, and are characterized by a large conformational flexibility. It is very difficult to study their conformation in solution since they exist, almost invariably, as a complex mixture of numerous conformers, most of which are extended. The so‐called bioactive conformation may be one of them, although the solvents used in solution studies often have properties drastically different from those of the biological system in which the peptide acts. There is, however, no simple way of identifying the bioactive conformation amid the many existing conformers.It is possible to approach a solution to this problem using two distinct strategies: (a) Limiting the conformational freedom of the peptide, e.g., by increasing the viscosity of the solution and decreasing the temperature, in the assumption that the bioactive conformation is, even slightly, more stable than the others. (b) Trying to mimic in solution the physicochemical features of the more reliable receptor models.These two approaches will be illustrated with examples taken mainly from oploid peptides.
Regularly alternating L,D‐peptides. I. The double‐stranded left‐handed antiparallel β‐helix in the structure of Boc‐(L‐Val‐D‐Val)4‐OMe
Authors: Di Blasio Benedetto , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo , Spiniello Ottavia , Lorenzi Gian Paolo 
Published: December 2004

AbstractThe structure of Boc‐(L‐Val‐D‐Val)4‐OMe has been determined by x‐ray single‐crystal diffraction analysis. The octapeptide crystallizes in the trigonal system, space group P3221 with a = b = 12.760 Å, c = 63.190 Å and Z = 6. The independent unit is represented by one octapeptide chain. The structure has been solved by direct methods and it was anisotropically refined by least‐squares procedures to a final R value of 0.08 for the 3018 “observed” reflections. One molecule of water was also located in the unit cell. Two octapeptide chains, related by a crystallographic binary axis, wind up around each other giving rise to a double‐stranded left‐handed antiparallel ↑↓ β5.6‐helix. The dimer, stabilized by 14 interstrand NH ⃛OC hydrogen bonds, can be regarded as a cylinder with an hydrophilic inner core represented by the peptide units and an hydrophobic exterior of isopropyl groups. The inner diameter of the cylinder is 5.1 Å.
Mono and two‐dimensional 500‐MHz characterization of synthetic bombesin and related peptides in DMSO and DMSO–water,
Authors: Di Bello Carlo , Gozzini Luigia , Tonellato Mauro , Corradini Maria Grazia , D'Auria Gabriella , Paolillo Livio , Trivellone Enrico 
Published: December 2004

AbstractThe proton nmr characterization of bombesin (BBS) and of two peptide fragments corresponding to the (1–6) and (6–14) sequences has been carried out at 500 MHz in dimethyl sulfoxide (DMSO‐d6) using two‐dimensional (2D) homo and 1H‐13C heterocorrelated techniques. All resonances in the nmr spectra have been assigned and several coupling constants have been measured. The backbone JαCHNH coupling constants are quite similar and around 7.8–8.2 Hz, pointing to an unfolded structure in DMSO‐d6. The possibility of secondary structures in highly viscous mixtures of DMSO‐d6–water was investigated. The existence of sequential nuclear Overhauser enhancement (NOE) effects in the C‐terminal nonapeptide section may indicate a preferential site for secondary structuring.
Conformational analysis of peptide T and of its C‐pentapeptide fragment
Authors: Motta Andrea , Picone Delia , Temussi Piero A. , Marastoni Mauro , Tomatis Roberto 
Published: December 2004

AbstractThe synthetic peptide of sequence H‐Ala‐Ser‐Thr‐Thr‐Thr‐Asn‐Tyr‐Thr‐OH, termed peptide T, a competitor of the Human Immunodeficiency Virus in the binding to human T cells, and its C‐terminal pentapeptide fragment, were studied by 1H‐nmr in DMSO solution to determine conformational preferences. The observation of nuclear Overhauser enhancements (NOEs) for both peptides, and unusual finding for small linear peptides, allowed complete sequence‐specific resonance assignments. Long‐range NOEs, ring‐current shifts, and the very small temperature coefficient of the Thr8 NH chemical shift suggest, for the zwitterionic form of peptide T, the presence in solution of a β‐turn involving Thr5, Asn6, Tyr7 and Thr8. This conformational feature is consistent with previous structure–activity relationship studies indicating the invariance of the same residues in several potent pentapeptide analogues. The studied pentapeptide fragment, although less structured, shows some tendency to fold even in a polar solvent such as DMSO.Preliminary chemotaxis data on some pentapeptide analogues are consistent with our structural model.
Computer simulations of a tumor surface octapeptide epitope
Authors: Reid Robert H. , Hooper Charles A. , Brooks Bernard R. 
Published: December 2004

AbstractMolecular dynamics using CHARMM and GEMM programs with the Star Technologies ST 100 array processor functioning at the speed of super computers was used as a searching algorithm for conformational exploration of the octapeptide Gly‐Asn‐Thr‐Ile‐Val‐Ala‐Glu. This poorly soluble octapeptide is the N‐terminal epitope of an 11 KD glycoprotein antigen residing on human ductal carcinoma (breast) cells. Very long (nanoseconds) simulations were required. Both an α‐helix and the N‐acetyl‐N1‐methylamide derived minimized starting structures gave the same lowest potential energy conformation with simulations at 600 K. The same conformation was found only when using the latter starting conformation with simulations at 300 K. The lowest potential energy conformation was stabilized by 4 hydrophobic contacts and 13 H bonds completing one turn of a left‐handed helix.
Molecular mechanics studies on poly(purine) · poly(pyrimidine) sequences in DNA: Polymorphism and local variability
Authors: Bansal Manju , Pattabiraman N. 
Published: December 2004

AbstractEnergy minimization has been carried out on three poly(purine) · poly(pyrimidine) sequences—d(G)10 · d(C)10, d(A)10, d(T)10 and d(AG)5 · d(CT)5—using the molecular mechanics program AMBER (Assisted Model Building and Energy Refinement). In order to extensively scan the conformational space available, five different helical models were studied, three of them being right‐handed helices while the other two were left helical. For all three sequences the right‐handed A‐ and B‐type helices are energetically slightly preferred over the left helices, but the energy difference between the various right‐handed helices is only marginal. A detailed analysis has been carried out to characterize the local structural variability in the refined structures, both in terms of torsion angles as well as other parameters such as base‐pair tilt, wedge roll, and wedge tilt, etc. All three sequences exhibit similar structural features for a particular form, but both the forms A and B show significant deviations from fiber models. In particular, the A‐form structures have higher unit rise (2.7 Å), and lower unit twist (31°) and base‐pair tilt (12°), compared to the fiber model, which has corresponding values of 2.56 Å, 32.7°, 20°, respectively. All these changes indicate that the refined models are closer to the A‐form structure observed in crystals of oligonucleotides. In the refined B‐for models, the helical parameters are close to the fiber B‐form, although the torsion angles show considerable variations. None of the three sequences examined, including the d(A)n · d(T)n sequence, show any pronounced curvature for the B‐form structure.
A differential scanning calorimetric study of the conformational transitions of schizophyllan in mixtures of water and dimethylsulfoxide
Authors: Kitamura Shinichi , Kuge Takashi 
Published: December 2004

AbstractThe thermal conformational transitions of two sonicated samples of schizophyllan were studied in water‐dimethylsulfoxide (DMSO) mixtures by high‐sensitivity differential scanning calorimetry (DSC). Two transitions were observed over most of the range of solvent compositions. These were assigned to an internal change of the triple helix [T. Itou et al. (1986) Macromolecules 19, 1234–1240] and a triple‐helix–single‐coil transition [T. Sato et al. (1981) Carbohydr. Res. 95, 195–204], respectively. In water, the former transition observed at lower temperature for a low molecular weight sample, U‐1, is centered at 3°C and characterized by the specific enthalpy, Δhcal = 3.29 J g−1. A higher molecular weight sample, M‐2, showed this transition at 7°C with Δhcal = 4.39 J g−1. The transition temperature for both samples increased with increasing DMSO concentration up to about 50°C at 70 weight % DMSO, and then rapidly decreased with increasing DMSO concentration, with about 3°C higher for M‐2 than for U‐1 over the DMSO concentration. The transition was not observed when the concentration of DMSO exceeded 87%. It was found that Δhcal for both samples was a linear function of t1/2, the temperature of half‐completion in °C, Δhcal = 0.177t + 2.96. The triple helix‐coil transition was observed at around 127°C for U‐1 and above 130°C for M‐2 in the range of DMSO composition below about 70%. The transition temperature decreased with increasing DMSO concentration at above 70%, and the transition finally disappeared when the DMSO concentration exceeded 90%. The plot of Δhcal vs. t1/2 for the transition of both samples gave a linear relation, Δhcal = 0.253t – 10.58. The reversibility of the transition at lower temperature was demonstrated by the reversibility of the curves when the first heating was stopped before the second transition. Once the heating was performed over the second transition, the reheating DSC curves showed several endothermic peaks, indicating the irreversibility of the transition and heterogeneity in the conformation of the heated schizophyllan.