bluuebunny/crossref_metadata_2025_split huggingface dataset:
X‐Ray studies on crystalline complexes involving amino acids and peptides. XVII. Chirality and molecular aggregation: The crystal structures of DL‐arginine DL‐glutamate monohydrate and DL‐arginine DL‐aspartate
Authors: Soman Jayashree , Vijayan M. , Ramakrishnan B. , Row T. N. Guru 
Published: December 2004

AbstractDL‐Arginine DL‐glutamate monohydrate and DL‐arginine DL‐aspartate, the first DL‐DL amino acid–amino acid complexes to be prepared and x‐ray analyzed, crystallize in the space group P1 with a = 5.139(2), b = 10.620(1), c = 14.473(2) Å, α = 101.34(1)°, β = 94.08(2)°, γ = 91.38(2)° and a = 5.402(3), b = 9.933(3), c = 13.881(2) Å, α = 99.24(2)°, β = 99.73(3)°, γ = 97.28(3)°, respectively. The structures were solved using counter data and refined to R values of 0.050 and 0.077 for 1827 and 1739 observed reflections, respectively. The basic element of aggregation in both structures is an infinite chain made up of pairs of molecules. Each pair, consisting of a L‐ and a D‐isomer, is stabilized by two centrosymmetrically or nearly centrosymmetrically related hydrogen bonds involving the α‐amino and the α‐carboxylate groups. Adjacent pairs in the chain are then connected by specific guanidyl–carboxylate interactions. The infinite chains are interconnected through hydrogen bonds to form molecular sheets. The sheets are then stacked along the shortest cell translation. The interactions between sheets involve two head‐to‐tail sequences in the glutamate complex and one such sequence in the aspartate complex. However, unlike in the corresponding LL and DL complexes, head‐to‐tail sequences are not the central feature of molecular aggregation in the DL‐DL complexes. Indeed, fundamental differences exist among the aggregation patterns in the LL, the LD, and the DL‐DL complexes.
Melanin‐concentrating hormone: A structural and conformational study based on synthesis, biological activity, high‐field nmr, and molecular modeling techniques
Authors: Brown D. W. , Campbell M. M. , Kinsman R. G. , White P. D. , Moss C. A. , Osguthorpe D. J. , Paul P. K. C. , Baker B. I. 
Published: December 2004

AbstractA series of Melanin‐concentrating hormone (MCH) fragments have been synthesized and their biological activities compared with the parent peptide. The substructural units, 5‐14 linear and 5‐14 cyclic, have been used as models for MCH—
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in 1H‐nmr conformational studies. Conformational features predicted by molecular dynamics analyses find support in the nmr experiments.
Accessible conformations of melanin‐concentrating hormone: A molecular dynamics approach
Authors: Paul P. K. C. , Dauber‐Osguthorpe P. , Campbell M. M. , Brown D. W. , Kinsman R. G. , Moss C. , Osguthorpe D. J. 
Published: December 2004

AbstractMolecular dynamics simulations have been used to search for the accessible conformations of the melanin‐concentrationg hormone (MCH). The studies have been performed on native MCH and two of its peptide fragments, a cyclic MCH(5–14) fragment and a linear MCH(5–14) fragment. An analysis of the molecular dynamics trajectories of the three peptides indicates that two regions of the peptide have characteristic conformational properties that may be important for the biological activity. One is a region around Gly8, which is conformationally mobile, and the other is around Pro13, which shows unusual rigidity. The molecular dynamics simulation results are discussed in terms of backbone structural features like β turns, side‐chain interactions, and orientations of the disulfide bridge. The results of this analysis are used to suggest new analogues that will modify the conformational features of the peptide and further define the conformational requirements for activity. Finally, the results are related to nmr studies of the peptide and reveal agreements between the experimental nuclear Overhauser effect constraints and some of the accessible conformations obtained from the simulation.
Pressure‐induced reversible changes in secondary structure of poly(L‐lysine): An ir spectroscopic study
Authors: Carrier Danielle , Mantsch Henry H. , Wong Patrick T. T. 
Published: December 2004

AbstractThe effect of elevated hydrostatic pressure on the secondary structure of poly(L‐lysine) was studied using Fourier transform ir spectroscopy. According to changes observed in the amide I band, both the β‐sheet and the unordered polypeptide undergo a reversible, pressure‐induced conformational change to α‐helix. The conversion occurs at a much higher pressure from the unordered conformer (∼ 9 kbar) than from the β‐sheets (∼ 2 kbar). The structural changes were found to be slower at pH > 11, especially at the highest concentration investigated (10 wt%), reflecting the fact that extensive hydrogen‐bond networks have to reorganize. This study shows that alterations of polypeptidic conformations induced by elevated hydrostatic pressure are reversible, but that an apparent irreversibility can result from kinetic factors in the case of conformational changes involving extensive rearrangements. The present results also show that the strength of the hydrogen bonds between the backbone amide groups is not the only factor that determines the closest packing of the polypeptide molecules.
Reexamination of the polymerization of pyridoxylated hemoglobin with glutaraldehyde
Authors: Marini M. A. , Moore G. L. , Christensen S. M. , Fishman R. M. , Jessee R. G. , Medina F. , Snell S. M. , Zegna A. I. 
Published: December 2004

AbstractPyridoxylated adult human hemoglobin (HbAo) was prepared using a one molar equivalent of pyridoxal 5‐phosphate (PLP) per heme and reduced with either NaCNBH3 or NaBH4. A separate sample was pyridoxylated and passed through a mixed‐bed ion exchange column without reduction. All three preparations had a P50 of 29 ± 2 torr and a cooperativity of n = 2.4 ± 0.1. These preparations, in both the oxy and deoxy forms, were then treated with 7 equivalents of glutaraldehyde per tetramer at pH 6.8 at 4°C and at room temperature. The polymerization invariably reduced the P50 to 18 ± 2 torr with Hill coefficients of less than 2. These solutions, with or without further reduction using NaCNBH3, all retained the PLP in differing amounts (2–3 moles/tetramer). Methemoglobin concentrations were increased during the polymerization reaction. The normal pyridoxylation procedure, using sodium borohydride reduction, resulted in a number of different molecular species. Polymerization with glutaraldehyde caused a further proliferation of molecular species that could not be separated by anion exchange chromatography or by isoelectric focusing. The extent of polymerization, estimated by gel exclusion chromatography and SDS polyacrylamide gel electrophoresis, was from 40 to 50%. Analysis of the reverse phase chromatograms, which separate the heme and the α‐ and β‐chains, showed extensive polymerization and distribution of the radioactively labeled PLP on the protein for all preparations. All of the polymerized and pyridoxylated samples were unstable, and showed different chromatographic patterns after storage at 4°C for 1 month. Attempts to stabilize these preparations by further reduction with NaCNBH3 gave products with a lower P50 and lower cooperativity. When the reactions were conducted with a purified HbAo, heterogeneity was somewhat decreased compared to the normally used stroma‐free hemoglobin, but a large number of molecular species were still formed.
Computer simulation of hydrodynamic properties of semiflexible macromolecules: Randomly broken chains, wormlike chains, and analysis of properties of DNA
Authors: Molina J. J. García , Martínez M. C. López , De La Torre J. García 
Published: December 2004

AbstractThe translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormilike chains have been obtained by Monte Carlo simulation in the context of the rigid‐body treatment. Both approximate and rigorous rigid‐body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormilike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 103 base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model‐independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too high.
Disaccharide conformational flexibility. I. An adiabatic potential energy map for sucrose
Authors: Tran V. H. , 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 sucrose. The inclusion of molecular flexibility in the conformational energy analysis of this disaccharide was found to have a significant effect upon the allowed conformational space of the molecule. Three low‐energy regions were identified on the adiabatic energy surface, and two of these regions were found to contain two related local minimum‐energy conformations, with similar energies, differing only in the directionality of the intra–residue hydrogen bonds of the glucose portion of the molecule. The known crystal structures of seven molecules containing the sucrose moiety all fall within the region of the primary allowed minimum and are consistent with the relaxed energy map, while these crystal conformations could not be rationalized using energy maps for rigid residue geometries. The greater flexibility of the furanoid ring relative to that of the pyranoid ring contributed significantly to the enlargement of the low‐energy region on the adiabatic map. However, in spite of the importance of limited flexibility in understanding the conformation and fluctuations of sucrose, this molecule was found to be considerably more rigid that some other disaccharides, such as maltose and cellobiose, in accord with experimental studies.
Structure of benzyloxycarbonyl‐L‐alanyl‐α‐aminoisobutyl‐α‐aminoisobutylic acid
Authors: Taga Tooru , Itoh Masato , Machida Katsunosuke , Fujita Tetsuro , Ichihara Terumi 
Published: December 2004

AbstractThe x‐ray diffraction study of the C‐terminally unprotected tripeptide benzyloxycarbonyl‐L‐alanyl‐α‐aminoisobutyl‐α‐aminoisobutylic acid (Z‐L‐Ala‐Aib‐Aib‐OH) has shown that the molecule adopts a consecutive type III β‐turn, which characterizes a right‐handed 310 helix. A very weak 4 → 1 intramolecular hydrogen bond with the long NO distance of 3.32 Å, and a unique “oxy analogue” of the 4 → 1 hydrogen bond with the OO distance of 2.77 Å, were observed. The stability of the observed conformation with the asymmetric Aib residues was theoretically evaluated by a conformation‐energy calculation. The stereochemical characteristics of Aib and Ala residues were made clear by a comparison of the conformations of the short peptides containing both Aib and Ala residues.
Analysis of parameter resolution from derivatives of binding isotherms
Authors: Doyle Michael L. , Simmons Joe H. , Gill Stanley J. 
Published: December 2004

AbstractExamination of binding information in the form of derivative (or finite difference) measurements is explored (1) experimentally by a thin‐layer optical procedure (Dolman, D. & Gill, S. J. (1978) Anal. Biochem. 87, 127–134) and (2) theoretically by simulation in order to determine the influence of the number of data points and their standard error upon the resolvability of binding parameters in cooperative and non‐cooperative systems. The data is described by the difference in optical absorbance divided by the change in the logarithm of the ligand activity and each data point is assumed to be influenced by a random error with a given variance. It is found that increasing the number of data points, which in turn effectively reduces the magnitude of the observed absorbance changes, results in an increase in the uncertainty of the resolved parameters of the system. The effect is verified by both experimental and simulation studies. Thus one is led to suggest that fewer measurements for the change of absorbance with larger magnitudes produces the most favorable situation for parameter resolution when the data is in the form of finite difference measurements.
Excimer fluorescence of (+)‐anti‐benzo (a)pyrene diol epoxide covalently bound to poly (dG‐dC): Structural implications
Authors: Eriksson Magdalena , Eriksson Svante , Nordén Bengt , Jernström Bengt , Gräslund Astrid 
Published: December 2004

AbstractFluorescence of (+)‐anti‐benzo (a) pyrene diol epoxide [(+)‐anti‐BPDE] covalently bound to poly (dG‐dC) has been studied with steady‐state and time‐resolved techniques. Extensive formation of excimers is found, even at small (0.008) BPDE/nucleotide ratios. This indicates favored covalent binding to bases close to already modified guanines. Both fluorescence excitation spectra and lifetime measurements reveal two populations of (+)‐anti‐BPDE adducts: one that can form excimers and one that cannot. Three excimer lifetimes (4.5, 29, and 83 ns) are observed. Differently shifted monomer and excimer excitation spectra are discussed in terms of pyrene‐pyrene exciton interactions, consistent with a distance shorter than 7 Å between the excimer‐forming BPDE chromophores.
Conformational studies of nikkomycin X in aqueous solution
Authors: Krainer Eduardo , Naider Fred , Becker Jeffrey M. 
Published: December 2004

AbstractNikkomycin X is a peptidyl‐nucleoside antibiotic that inhibits chitin synthesis in fungi. Information on its conformation in aqueous solution was obtained from pH titration studies in which the nmr shifts of exchangeable and nonexchangeable protons were monitored. These studies and nuclear Overhauser effects support an unfolded or conformationally flexible structure for the antibiotic, and the syn and anti conformations of the nucleoside moiety were found to coexist. The conformation of the ribose ring was determined using a two‐state model; a slight shift from type N to type S conformers occurred as the pH was raised from 1 to 6.
The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations
Authors: Havel Timothy F. 
Published: December 2004

AbstractIn this paper we study the statistical geometry of ensembles of poly(L‐alanine) conformations computed by several different distance geometry algorithms. Since basic theory only permits us to predict the statistical properties of such ensembles a priori when the distance constraints have a very simple form, the only constraints used for these calculations are those necessary to obtain reasonable bond lengths and angles, together with a lack of short‐ and long‐range atomic overlaps. The geometric properties studied include the squared end‐to‐end distance and radius of gyration of the computed conformations, in addition to the usual rms coordinate and ϕ / ψ angle deviations among these conformations. The distance geometry algorithms evaluated include several variations of the well‐known embed algorithm, together with optimizations of the torsion angles using the ellipsoid and variable target function algorithms.The conclusions may be summarized as follows: First, the distribution with which the trail distances are chosen in most implementations of the embed algorithm is not appropriate when no long‐range upper bounds on the distances are present, because it leads to unjustifiable expanded conformations. Second, chosing the trail distances independently of one another leads to a lack of variation in the degree of expansion, which in turn produces a relatively low rms square coordinate difference among the members of the ensemble. Third, when short‐range steric constraints are present, torsion angle optimizations that start from conformations obtained by choosing their ϕ / ψ angles randomly with a uniform distribution between − 180° and + 180° do not converge to conformations whose angles are uniformly distributed over the sterically allowed regions of the ϕ / ψ plane.Finally, in an appendix we show how the sampling obtained with the embed algorithm can be substantially improved upon by the proper application of existing methodology.
Analysis of fructofuranose conformations by molecular mechanics
Authors: French Alfred D. , Tran Vinh 
Published: December 2004

AbstractEnergies for various envelope and twist conformers of α‐ and β‐D‐fructofuranose (FF) have been calculated with MMP2 (85). Values of low energy are found near T conformations, and, secondarily, to ranges near T shapes. α‐D‐FF has a path through the 0E form for transitions between forms, as found by other workers for β‐D‐ribose, while the slightly preferred transition for β‐D‐FF is through the 0E conformer. The majority of conformations of β‐D‐FF that have been determined by single‐crystal diffraction studies are in a fairly deep well, with energy values less than 0.5 kcal / mol above the minimum.
Depsipeptide analogues of elastin repeating sequences: Synthesis
Authors: Arad O. , Goodman M. 
Published: December 2004

AbstractDepsipeptide analogues of peptide sequences can help in elucidating the role of specific hydrogen bonds in determining the conformation in peptides. The repeating pentapeptide and hexapeptide sequences of elastin have been suggested to contain a type II β‐turn with a 4 → 1 hydrogen bond. Depsipeptide analogues of the repeating sequences of elastin in which this 4 → 1 hydrogen bond cannot exist were synthesized. A fragment condensation approach was employed in which the depsipeptide ester bond was introduced early in the synthesis. This approach proved to be effective, although the increased lability of the depsipeptide ester bond resulted in side products and low yields in some reactions.
Analysis of side‐chain conformational distributions in neutrophil peptide‐5 nmr structures
Authors: Kominos Dorothea , Bassolino Donna A. , Levy Ronald M. , Pardi Arthur 
Published: December 2004

AbstractThe side‐chain conformations have been analyzed in the antimicrobial peptide, Neutrophil Peptide‐5(NP‐5), whose structure was independently generated from nmr‐derived distance constraints using a distance geometry algorithm. The side‐chain and peptide dihedral angle distributions in the nmr structures were compared with those constructed from a data base of high‐resolution protein crystal structures. The side‐chain conformational preferences for NP‐5 in solution are significantly different from those observed in the crystal structure data base. These results indicate that the side‐chain conformations are quite disordered for many of the residues of NP‐5. The absence of a correlation between the width of the conformational distribution and surface accessibility suggests that the disorder may be due to limitations in the structural information extracted from the nmr data rather than to molecular motion. However, it is also observed that the degree of conformational disorder is only weakly correlated with the number of nuclear Overhauser enhancements to a given side chain. Possible reasons for this are discussed. Molecular mechanics refinement of these structures did not significantly change the side‐chain populations. Anomolously wide distributions are observed for rotations about the peptide bonds and the disulfide bonds in the NP‐5 distance geometry structures, which are improved by the refinement. The very high degree of order observed for the central dihedral angle of the disulfide bond in the high‐resolution crystal data base suggests that the rotation about this bond in proteins is determined by the local potential.
Cyclic β‐alanyl‐β‐alanine containing peptides: A new molecular tool for β‐turned peptides
Authors: Pavone V. , Lombardi A. , Yang X. , Redone C. , Di Blasio B. 
Published: December 2004

AbstractIn the present paper we describe the synthesis, purification, and single‐crystal x‐ray analysis of the cyclic tetrapeptide cyclo‐(L‐Pro‐L‐Phe‐β‐Ala‐β‐Ala). This compound contains the β‐alanyl‐β‐alanine dipeptide as putative cyclization arm to force the remaining dipeptide‐L‐Pro‐L‐Phe‐ in a β‐turned conformation. Thepeptide was synthesized by classical methods and cyclization of the free linear tetrapeptide was accomplished in reasonable yields in diluted methylene chloride solution. The compound crystallizes in space group P21 from hot water with two independent tetrapeptide molecules and seven solvent molecules in the unit cell. This compound shows in the solid state an intramolecular hydrogen bond between the CO group of the β‐Ala4 and the NH group of the β‐Ala3 residues stabilizing a type I β‐turn conformation in which Pro1 and Phe2 occupy the relative position 2 and 3 of the turn, respectively. A rather complex network of 18 hydrogen bonds involving all the remaining CO and NH groups and the water molecules is present in the crystal.
Stereochemical behavior of acyclic peptide‐cation complexes
Authors: Grimaldi Maria , Rossi Filomena , Saviano Michele , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo 
Published: December 2004

AbstractThe role of the β‐turns in the peptide interaction with several cations was investigated. In this work we report the solution studies of four linear peptides: Z‐Aib‐Aib‐Aib‐L‐Val‐OMe, Boc‐D‐alle‐L‐Ile‐D‐alle‐L‐Ile‐OMe, Boc‐L‐Leu‐L‐Leu‐L‐Leu‐L‐Leu‐OMe, and Boc‐L‐Phe‐B‐Phe‐L‐Phe‐D‐Phe‐OMe.CD and 1H‐nmr spectra reveal the presence of multiple ion‐bounding equilibria. The stoichiometry and binding constant of the four peptide in the presence of Ca2+ ions in acetonitrile solution has been determined.Variable‐temperature nmr spectra in the absence and in thepresence of a large excess of cation have shown that the complexation process is not critically dependent on the conformation of the peptide.
Theory of acoustic mode vibrations of DNA fibers
Authors: Sokoloff J. B. 
Published: December 2004

AbstractA previous model for acoustic mode vibrations of a DNA molecule in water is extended to the case of an array of many DNA molecules, as occurs in the fibers studied in most experimental work on DNA. The acoustic modes of this system are found to consist of coupled modes of water sound vibrations and DNA acoustic modes. This model is used to study the electrostatic coupling of acoustic vibrations to the relaxational modes of the orientational degrees of freedom of the water molecules. It is found that the long‐range or macroscopic electric field generated by the acoustic mode vibrations of the water‐DNA system gives too small a damping and frequency shift of the acoustic modes to account for the observations on DNA fibers. Therefore, the observed damping and frequency shifts are most likely due to either friction between the surrounding water and the vibrating DNA, or coupling to the water orientation degrees of freedom resulting from the short range (i.e., screened) Coulomb interaction. The latter explanation (which is most likely the correct one) implies that the relaxation time of the hydration shell water is longer than the observed relaxation time by a factor of the static dielectric constant of the hydration water.