bluuebunny/crossref_metadata_2025_split huggingface dataset:
PAPQMD/AM1 Parametrization of the bonded term of aromatic biomolecules
Authors: Alemán Carlos , Orozco Modesto 
Published: December 2004

AbstractThe suitability of the PAPQMD/AM1 (Program for Approximate Parametrization from Quantum Mechanical Data/based on AM1 calculations) strategy to provide force‐field parameters for large heteroaromatic compounds was studied. For this purpose, PAPQMD/AMI stretching and bending parameters for adenine, cytosine, thymine, guanine, and uracil were computed and compared with experimentally derived force‐field parameters. Furthermore, equilibrium geometries and vibrational spectra for the five nucleic acid bases obtained from molecular mechanical calculations using both PAPQMD/AM1 and AMBER (Assisted Model Building with Energy Refinement) All Atoms force fields were compared with the available experimental data. © 1994 John Wiley & Sons, Inc.
IR and Raman spectroscopic studies of the interaction of trehalose with hen egg white lysozyme
Authors: Belton P. S. , Gil A. M. 
Published: December 2004

AbstractInfrared and Fourier transform Raman spectra are reported for dried mixtures of trehalose and lysozyme. The Raman spectra show effects on the protein amide I band and some sugar bands that are not present when the components are dried separately. Comparison of ir spectra with those published previously show significant differences. It is concluded that these arise because of differences in the extent of drying of the moisture, and that, contrary to some claims, vibrational spectroscopy does not so far show any clear evidence of specific trehalose/protein interactions and that results may be interpreted in terms of entrapment of water within the mixture. © 1994 John Wiley & Sons, Inc.
Design, synthesis, and conformation of a model peptide of endothelin with cystine‐stabilized α‐helix motif
Authors: Mihara Hisakazu , Tomizaki Kin‐Ya , Nishino Norikazu , Fujimoto Tsutomu , Tamaoki Haruhiko , Kobayashi Yuji 
Published: December 2004

AbstractA model 16‐peptide of endothelin‐1 (MET‐1), which has the minimized sequence homology to the corresponding pan of endothelin‐1 (ET‐1), was designed to confirm the cystine‐stabilized α‐helix motif. The model structure consists of an extended structure, a β‐turn part, and an α‐helix structure that is stabilized by two disulfide bonds. The α‐helix segment was designed to emphasize the amphiphilic nature. In order to combine the extended structure and the α‐helix segment, a D‐Ala‐Pro sequence was selected to fix the β‐turn. The model endothelin 16‐peptide amide was synthesized by solid‐phase synthesis on a 4‐methylbenzhydrylamine resin. Its conformation was examined by CD and two‐dimensional (2D) 1H‐nmr measurements. MET‐1 showed similar CD patterns to ET‐1 in both buffer and 50% aqueous trifluoroethanol solution. The 2D nmr experiments in 50% aqueous ethylene glycol revealed that MET‐1 closely resembles the conformation of ET‐1 with an extended structure, an α‐helix, and a β‐turn unit in the same position of the sequence. Furthermore, model peptides without disulfide bond(s) could not assume a stable structure in aqueous solution, while they did have similar α‐helical content in 50% trifluoroethanol with MET‐1. When the two disulfide bridges were simultaneously formed, the peptide with the correct disulfide bonds (MET‐1) was obtained in threefold excess to the isomer (apamin type. MET‐2). These findings obtained by the modeling of ET‐1 showed an important role for the stabilization of peptide conformation with disulfide bonds. © 1994 John Wiley & Sons, Inc.
Conformation of CD4‐derived cyclic hexapeptides by nmr and molecular dynamics
Authors: Ma Sougen , McGregor Malcolm J. , Cohen Fred E. , Pallai Peter V. 
Published: December 2004

AbstractTwo cyclic hexapeptides, cyclo[Ala1‐D‐Ala2‐Ser3‐Phe4‐Gly5‐Ser6] and cyclo[Ala1‐Gly2‐Ser3‐Phe4‐Gly5‐Ser6], derived from the loop portion of the C′C″ ridge of CD4, were characterized by high‐resolution nmr spectroscopy and simulated annealing studies. In DMSO‐d6 both of these peptides display a single conformer on the nmr time scale with two intramolecular H‐bond (1 ← 4) stabilized β‐turns at positions 2–3 and 5–6. The nmr derived distance constraints were used in simulated annealing calculations to generate the solution structures. These structures adopt energetically comparable conformational substates that are not resolvable on the nmr time scale. In aqueous solution, the H‐bond stabilized β‐turn conformation for cyclo [Ala‐D‐Ala‐Ser‐Phe‐Gly‐Ser] is no longer the predominant structural form. Structures generated using molecular dynamics simulations with no experimental constraints were compared with those from nmr analysis. The correlation between these two sets of structures allows the use of molecular simulations as a predictive tool for the conformational analysis of small peptides. © 1994 John Wiley & Sons, Inc.
Crystal structure of cyclo(Pro‐Gly)3: Li complex: A model for ion transport by cyclo(Pro‐Gly)3
Authors: Thomas L. M. , Ramasubbu N. , Bhandary K. K. 
Published: December 2004

AbstractThe crystal structure of cyclo(Pro‐Gly)3 (PG3) complex with LiSCN (C22H30N7O6SLi) has been solved by x‐ray diffraction. The crystals belong to the space group R3 in the hexagonal setting with unit cell parameters of a = 12.581(1), c = 29.705(3) Å, V = 4072.0 Å3, Z = 6, Mr = 527.53, Dc = 1.23 g/cm3. The crystal structure was solved by direct methods using the program SHELXS‐86 and refined to an R value of 5.3% for 1645 reflections (I > 2σI). There are two conformers in the crystal structure. One conformer has three carbonyls on one side and three on the other side of the peptide plane. The other conformer has all six of the carbonyls on the same side of the peptide plane. Both of these conformers bind independently to a Li ion. Based on the conformers of the Li complex and other reported ion complexes formed by PG3, we propose a model for the transport of ions across the lipid membrane. The features of the model are as follows: (1) PG3 forms a hexameric stack in a lipid bilayer when complexing and transporting metal ions. (2) It undergoes a conformational flipping in order pass the ion along the channel. The energy required for the conformational change involved in the flipping of the PG3 molecule may be provided by the applied potential during ion transport. © 1994 John Wiley & Sons, Inc.
Molecular dynamics simulation of a leucine zipper motif predicted for the integrase of human immunodeficiency virus type I
Authors: Wang C. Y. , Yang C. F. , Lai M. C. , Lee Y. H. , Lee T. L. , Lin T. H. 
Published: December 2004

AbstractWe have used the molecular dynamics (MD) simulation package AMBER4 to search the conformation of a peptide predicted as a leucine zipper motif for the human immunodeficiency virus type I integrase protein (HIV IN‐LZM). The peptide is composed of 22 amino acid residues and its location is from Val 151 to Leu 172. The searching procedure also includes two known α‐helices that served as positive controls—namely, a 22‐residue GCN4‐p1 (LZM) and a 20‐residue poly(L‐alanine) (PLA). A 21‐residue peptide extracted from a cytochrome C crystal (CCC‐t) with determined conformation as a β‐turn is also included as a negative control. At the beginning of the search, two starting conformations—namely, the standard right‐handed α‐helix and the fully stretched conformations—are generated for each peptide. Structures generated as standard α‐helix are equilibrated at room temperature for 90 ps while structures generated as a fully stretched one are equilibrated at 600 K for 120 ps. The CCC‐t and PLA helices are nearly destroyed from the beginning of equilibration. However, for both the HIV IN‐LZM and the GCN4‐p1 LZM structures, there is substantial helicity being retained throughout the entire course of equilibration. Although helix propagation profiles calculated indicate that both peptides possess about the same propensity to form an α‐helix, the HIV IN‐LZM helix appears to be more stable than the GCN4‐p1 one as judged by a variety of analyses on both structures generated during the equilibration course. The fact that predicted HIV IN‐LZM can exist as an α‐helix is also supported by the results of high temperature equilibration run on the fully stretched structures generated. In this run, the RMS deviations between the backbone atoms of the structures with the lowest potential energy (PE) identified within every 2 ps and the structure with the lowest PE searched in the same course of simulation are calculated. For both the HIV IN‐LZM and the GCN4‐p1 LZM, these rms values decrease with the decrease of PE, which indicates that both structures are closer in conformations as their PEs are moved deeper into the PE well. © 1994 John Wiley & Sons, Inc.
Comparative interactions of magnesium and calcium counterions with polygalacturonic acid
Authors: Malovíková Anna , Rinaudo Marguerite , Milas Michel 
Published: December 2004

AbstractThe comparative interaction of Mg2+ and Ca2+ counterions on carboxyl groups of polygalacturonic acid is developed. Ultracentrifugation, conductimetry, potentiometry, and CD were used in this work. Evidence is provided for a simple electrostatic interaction of Mg2+ counterions; on the opposite side, cooperative interaction of Ca2+ counterions is again demonstrated, causing chain–chain association. © 1994 John Wiley & Sons, Inc.
Physical and chemical microstructure of spider dragline: A study by analytical transmission electron microscopy
Authors: Thiel Brad L. , Kunkel Dennis D. , Viney Christopher 
Published: December 2004

AbstractWe report the first direct observations of the physical and chemical microstructure of spider dragline, revealed by analytical transmission electron microscopy. Individual crystallites were imaged within the amorphous matrix. They are irregularly shaped, approximately 70–100 nm in diameter, and uniformly distributed throughout the matrix. Electron diffraction determined their space group to be P21. The corresponding orthogonal cell has lattice parameters of a = 13.31 Å (β‐sheet repeat), b = 9.44 Å (interchain repeat within β‐sheets), and c = 20.88 Å (repeat along polypeptide chain). Electron energy loss spectroscopy indicated compositional variations within the matrix, and between the crystallites and matrix. Most notably, calcium was found exclusively in the crystallites. Attempts to produce synthetic analogues of dragline, which exhibits an unparalleled combination of strength, stiffness, and toughness, cannot depend solely on duplicating the constituent proteins. The complex hierarchical microstructure of the natural material must be taken into account. © 1994 John Wiley & Sons, Inc.
Fractal‐like patterns in DNA films, B form at 0% relative humidity, and antiheteronomous DNA: An ir study
Authors: Sclavi B. , Peticolas W. L. , Powell J. W. 
Published: December 2004

AbstractThis report details the observation of (a) the intact double helix of DNA at 0% relative humidity in poly(dA) · poly(dT) and poly (dA‐dT) · poly (dA‐dT) films, (b) the fractal‐like growth of DNA crystals in films of poly (dA) · poly(dT), and (c) poly(dA) · poly(dT) with adenines in the B form and thymines in the A form. Observation (a) is based on the behavior of the middle ir signature of double‐helical base stacking, the 1714 cm−1 peak, at low water activity. This observation is modeled as a trapping of water in the polycrystalline part of these films. We interpret the glycosidic region of the middle ir spectra of the polycrystalline films of poly (dA) · poly (dT) at 0% relative humidity to indicate that at least part of the adenine strand in is the B conformation and the thymine strand is in the A form, whereas previous assignments of poly (dA) · poly (dT) films at 75% relative humidity indicated the opposite strand conformation assignment [E. Taillandier et al. (1987) Biochemistry, Vol. 26 p. 3361]. © 1994 John Wiley & Sons, Inc.
Thrombin‐bound conformation of a cyclic anticoagulant peptide using transferred nuclear Overhauser effect (NOE), distance geometry, and NOE simulations
Authors: Ning Q. , Ripoll D. R. , Szewczuk Z. , Konishi Y. , Ni F. 
Published: December 2004

AbstractA cyclic hirudin C‐terminal fragment, even truncated to eight residues, retains higher activity in binding to thrombin compared with its linear analogue of the same peptide length. In this paper, we report the results of a conformational study of a cyclic hirudin peptide 55–62 bound to the exosite of thrombin. Based on transferred NOE data and molecular modeling, conformation of the 18‐membered ring was well defined with little mobility in the loop region. The backbone conformations of residues Glu (58) to Lys (61) are very similar to those in a native 11‐residue linear peptide in the thrombin‐bound state [Ni et al. (1990) Biochemistry, vol. 29, pp. 4479–4489; Skrzypczak‐Jankun et al. (1991) Journal of Molecular Biology, vol. 221, pp. 1379–1393]. The side chain of Ile (59), the most critical residue, assumes a gauche− conformation, as observed in linear hirudin peptides. The bound conformations of residues Phe (56) and Glu (57) are defined by an iterative procedure involving the matching of computed and experimental transferred NOE intensities. The exosite of thrombin appears to be very specific to both the backbone and the side‐chain conformations of the hirudin C‐terminal peptides, especially those of residues Phe (56) and Ile (59). © 1994 John Wiley & Sons, Inc.
Observation of a sterically unfavorable side‐chain conformation in a leucyl residue: Crystal and molecular structure of L‐leucyl–L‐leucine · DMSO solvate
Authors: Mitra Shome Nath , Subramanian E. 
Published: December 2004

AbstractThe crystal structure of a dipeptide L‐leucyl–L‐leucine (C12H24N2O3) has been determined. The crystals are monoclinic, space group P21, with a = 5.434(4) Å, b = 15.712(7) Å, c = 11.275(2) Å, β = 100.41(1)°, and Z = 2. The crystals contain one molecule of dimethyl sulfoxide (DMSO) as solvent of crystallization for each dipeptide molecule. The structure has been solved by direct methods and refined to a final R index of 0.059 for 920 reflections (sinθ/λ ⩽ 0.60 Å−1) with I ⩾ 2σ (I). The trans peptide unit shows substantial degree of non‐planarity (Δω = 14°). The peptide backbone adopts an extended conformation with torsion angles of ψ1 = 138(1)°, ω1 = 166(1)°, ϕ2 = − 149.3(7)°, ψ21 = 164.2(7)°, and ψ22 = − 15(1)°. For the first leucyl residue, the side‐chain conformation is specified by the torsion angles 1χ1 = 176.7(7)°, 1χ21 = 62(1)°, 1χ22 = − 177.4(8)°; the second leucyl residue adopts a Sterically unfavorable conformation with 2χ1 = 61(1)°, 2χ21 = 97(1)°, and 2χ22 = −151(1)°. The packing involves head‐to‐tail interaction of peptide molecules and segregation of polar and nonpolar regions. The DMSO molecule is strongly hydrogen bonded to the terminal NH group. © 1994 John Wiley & Sons, Inc.
Solution structure and dynamics of a glycoinositol phospholipid (GIPL‐6) from Leishmania major
Authors: Weller C. T. , McConville M. , Homans S. W. 
Published: December 2004

AbstractBy use of a combination of 1H nuclear Overhauser effect measurements, restrained molecular dynamics simulations, and 13C spin–lattice relaxation time measurements, the solution behavior of the glycan moiety of a complex glycoinositol phospholipid termed G1PL‐6, from the protozoan parasite Leishmania major has been determined. The glycan moiety of GIPL‐6 has the following structure, which is characterized by the presence of an internal β‐galactofuranose residue:
magnified image
The glycan does not adopt a single conformation in solution, due to significant torsional variations about the two phosphodiester linkages and certain glycosidic linking in the molecule. The present of the internal galactofuranose residue results in an average solution conformation of the oligosaccharide, which resembles a “hairpin,” with the galactofuranose residue at the apex. © 1994 John Wiley & Sons, Inc.
Conformational differences between cis and trans proline isomers of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa as studied by 1H‐nmr
Authors: Mcinnes Campbell , Kay Cyril M. , Hodges Robert S. , Sykes Brian D. 
Published: December 2004

AbstractA 17‐residue disulfide‐bridged peptide (PAK 128–144) corresponding to the C‐terminus of Pseudomonas aeruginosa pilin strain K has been studied by one‐ and two‐dimensional nmr techniques. This synthetic immunogen has been found to exist as two distinct conformations in solution, which have been demonstrated to arise as a result of the isomerization of the I138‐P139 amide bond. The two isomers occur in the ratio of 3 : 1 trans to cis at 5°C. Sequential assignments for both forms have been accomplished through the use of nuclear Overhauser enhancement spectroscopy (NOESY) spectra and most side‐chain resonances have been assigned using a combination of correlated spectroscopy, total correlated spectroscopy, and NOESY spectra. The presence of the cis isomer, which is considerably more predominant in the oxidized peptide, was confirmed by the observation of the characteristic NOEs between P139 and the preceding residue. Further corroboration was given by the disappearance of the cis resonances in the spectrum of the P139A analogue of PAK 128–144. From observation of the differences in the chemical shifts and amide proton temperature coefficients of the two isomers, it is apparent that the two forms differ markedly in their solution conformation. The biological implications of the isomerization are discussed. © 1994 John Wiley & Sons, Inc.
Prediction of the conformational requirements for binding to the κ‐opioid receptor and its subtypes. I. Novel α‐helical cyclic peptides and their role in receptor selectivity
Authors: Collins Nathan , Hruby Victor J. 
Published: December 2004

AbstractA conformational search of two similar κ‐selective cyclic Dynorphin A (Dyn A) analogues is presented. Dyn A1–11‐NH2(1) and Dyn A1–11‐NH2 (2) are not only highly potent κ‐selective peptides but they also exhibit exceptional selectivity for κ receptors in the central (brain) vs. the peripheral (ileum) systems. Molecular mechanics systematic searching of the conformational preferences of the cyclic moieties of 1 and 2 produced 741 and 1003 starting ring structures, which were minimized at two dielectric constants of 2.0 and 80.0 in the AMBER force field. By rms superimposition, these low energy structures were grouped into conformational families for each ring system minimized at each dielectric. Comparison of the lowest energy structure of each of these families demonstrated that two (labeled A and B) were found as low energy ring systems for both 1 and 2 after minimization at either dielectric constant. These two structures are thus predicted to be the putative binding conformations for Dynorphin A at receptors in the brain. Interestingly, one of these putative binding structures exhibited an α‐helical conformation in the disulfide bridged ring that has not been observed for small cyclic peptides of this nature before. Molecular dynamics simulation of the helical binding structures indicated that the helical configuration in 2 is lower in energy and is more confor‐mationally stable than that of 1. We correlate this with the increased selectivity and potency of 2 for κ receptors in the brain compared to the periphery, implying that this may be due to an α‐helical conformation in the cyclized address or helical induction in the message sequence. © 1994 John Wiley & Sons, Inc.
Effect of succinylation on the membrane activity and conformation of a short cecropin A‐melittin hybrid peptide
Authors: Fernández Imma , Ubach Josep , Reig Francesca , Andreu David , Pons Miquel 
Published: December 2004

AbstractA 15‐residue hybrid peptide (KWKLFKKIGAVLKVL‐amide) incorporating partial sequences of cecropin A and melittin causes the release of carboxyfluoresceine encapsulated in phosphatidylcholine liposomes. Succinylation of the amino groups in the N‐terminus and lysine side chains inhibits the effect of this peptide on liposome permeability. Conformational analysis of the parent peptide and its succinyl derivative by CD and nmr indicates that both peptides form amphipathic α‐helices in the presence of hexafluoro‐2‐propanol, but only the unmodified peptide acquires a relevant level of α‐helical conformation in the presence of liposomes. © 1994 John Wiley & Sons, Inc.
Measurement of long‐range2 13C‐1H coupling constants of 95% uniformly 13C‐labeled polysaccharide from streptococcus mitis J22
Authors: Gitti Rossitza , Long Guixia , Bush C. Allen 
Published: December 2004

AbstractThe coaggregation of Streptococcus mitis strain J22 in the early stages of dental plaque formation has been shown to result from interaction of cell wall polysaccharides with lectins on the surface of other oral bacterial species. This bacterium was grown in a medium containing 13C as the sole carbon source. We have isolated the lectin receptor polysaccharide from this strain with full enrichment in 13C and have determined a number of two‐bond and three‐bond 13C‐1H coupling constants from measurements of the offsets in two‐dimensional homonuclear nmr spectra [exclusive correlated spectroscopy (E‐COSY) method]. A scheme for reliable extraction of these coupling constants from homonuclear Hartmann‐Hahn and nuclear Overhauser effect spectroscopy spectra is tested in model compounds. We interpret the three‐bond coupling across the glycosidic linkage in terms of dihedral angles in order to provide conformational information to supplement molecular modeling and nuclear Overhauser effect data. We show that the E‐COSY method works well even for coupling constants smaller than the nmr line width and that a number of the 3JCH across the glycosidic linkage are in the range of 1–2 Hz, which is much smaller than many previously reported values. © 1994 John Wiley & Sons, Inc.
The potential energy surface of methyl 2‐O‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside in aqueous solution: Conclusions derived from optical rotation
Authors: Stevens Eugene S. 
Published: December 2004

AbstractThe optical rotation of methyl 2‐O ‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside is calculated semiempirically as a function of the linkage dihedral angles ϕ (H1‐C1‐O1‐C2′) and ψ (C1‐O1‐C2′‐H2′). Although the rotation calculated for the global energy minimum conformation found in several rigid‐residue modeling calculations (ϕ,ψ = −40°,−20°) is in good agreement with the observed solution rotation, the observed rotation is also compatible with the limited flexibility inferred from more recent relaxed residue modeling calculations on a structurally related rhamnose disaccharide © 1994 John Wiley & Sons, Inc.