bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depsipeptide analogues of elastin repeating sequences: Conformational analysis
Authors: Arad O. , Goodman M. 
Published: December 2004

AbstractIn this work the effect of elimination of a specific hydrogen bond on the conformation of the repeating peptides of elastin was studied. These repeating sequences are the pentapeptide Val‐Pro‐Gly‐Val‐Gly and the hexapeptide Val‐Ala‐Pro‐Gly‐Val‐Gly. These sequences have been proposed to occur in a β‐turn conformation with a hydrogen bond involving the amide NH of the internal valine residue and the carbonyl oxygen of the residue preceding proline. In the depsipeptide analogues studied in this work, this 4–1 β‐turn hydrogen bond cannot occur. We studied the depsipeptide sequences Val‐Pro‐Gly‐Hiv‐Gly and Val‐Ala‐Pro‐Gly‐Hiv‐Gly (Hiv denotes S‐α‐hydroxyisovaleric acid, the hydroxy acid analogue of valine), as well as the peptide sequences Val‐Pro‐Gly‐Val‐Gly and Val‐Ala‐Pro‐Gly‐Val‐Gly. Compunds studied included sequences with the Boc and benzyl ester protecting groups, derivatives with the acetyl and N‐methylamide end groups and polymers of the above sequences. Our conclusions are based on a comparison of depsipeptides with analogous peptides. Conformational analysis was carried out by nmr, CD, and ir spectroscopy. We propose that in the repeating sequences of elastin an equilibrium exists between a γ‐turn structure and a β‐turn structure in the Pro‐Gly segment resulting in a structure that combines flexibility with strong conformational preferences. The C7 involves the amide NH of the internal glycine and the carbonyl oxygen of the residue preceding proline. In the N‐methylamide derivatives a similar equilibrium exists in the Gly‐Val‐Gly segment. In the depsipeptides the β‐turn cannot occur and only the γ‐turn is seen. In the polydepsipeptides the major conformational feature is a type I β‐turn involving Gly5 NH and Pro CO.
Statistical descriptors for the size and shape of globular proteins
Authors: Abad‐Zapatero C. , Lin C. Thomas 
Published: December 2004

AbstractThe atomic structures of proteins epitomize the ideas of complexity and irregularity in three‐dimensional objects. For such objects, size and shape are difficult to quantify, and therefore the development of unbiased parameters for these properties could facilitate their description. Statistical analysis of the frequency distribution of interatomic distances in protein structures of different classes has revealed two numerical descriptors that correlate with physicochemical properties of these macromolecules. The median (μ) of the distribution correlates (r> .98,n= 45) with variables indicative of size (e.g., molecular weight and radius of gyration). The exponent of the Box–Cox transformation λ, used for converting this distribution into a symmetrical one, correlated (r= .75,n= 43) with a general dimensionless shape parameter defined as the combination of the shape‐related accessible surface (A), molecular volume (V), and radius of gyration (Rg) in the forms= (ARg/V). It is suggested that for globular proteins λ is a function of both the shape parametersand the fractal dimensionDof the protein surface. These objective descriptors of size and shape could be useful to describe other complex objects.
Structural effects of hydration: Studies of lysozyme by 13C solids nmr
Authors: Kennedy Scott D. , Bryant Robert G. 
Published: December 2004

Abstract13C‐nmr spectra of lysozyme obtained at 50.3 MHz using both static and magic‐angle‐spinning‐cross‐polarization methods are reported at several water contents. The line widths and consequent resolution in the hydrated material is substantially improved over that in the lyophilized protein. The line narrowing is not commensurate with loss of a proton–carbon dipole–dipole coupling or dramatic changes in the relaxation parameters characterizing magnetization transfer from protons to carbon in the Hartmann–Hahn cross‐polarization experiment. We interpret these data in terms of the water inducing a decrease in the conformational reorientations required to account for the data are not necessarily large nor do they imply a major unfolding of the protein on dehydration.
Gel electrophoresis of micron‐sized particles: A problem and a solution
Authors: Griess Gary A. , Serwer Philip 
Published: December 2004

AbstractThe gel electrophoresis of spherical particles with a radius above 0.2 μm has not been reported yet. In the present study, video phase‐contrast light microscopy is used to observe the motion of individual latex spheres, 0.52 μm in radius, during electrophoresis in 0.1% agarose gels. At 2V/cm, the spheres initially migrate in the direction of the electrical field. However, each sphere eventually undergoes a cessation of all motion. Brownian motion is restored when the electrical potential gradient is reduced to zero. Arrest can be prevented by periodically inverting the direction of the electrical field. These observations are explained by electrical field‐ induced steric trapping of the spheres by gel fibers. Inversion of the electrical field should assist the application of agarose gel electrophoresis to micron sized cellular organelles and cells.
Solvent effect on the stability of isomaltose conformers
Authors: Tvaroska Igor , Imberty Anne , Pérez Serge 
Published: December 2004

AbstractThe conformational equilibria of the low‐energy conformers of isomaltose have been studied in different solvents. The structure of each individual conformer was refined from the 18 distinct low‐energy regions determined from potential energy function. Molecular geometry optimization was carried out using the quantum chemical method of perturbative configuration interaction with localized orbitals or PCILO and yielded to 15 distinct minima. Carbon‐proton vicinal coupling constants 3JC‐H have been calculated based on the finite perturbation theory formulation with the intermediate neglect of differential overlap for these minima. For evaluation of the influence of the environment on the conformational structure of isomaltose, the population of the low‐energy conformers was estimated in four solvents by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. The calculated abundances of conformers depend strongly on the solvents. Based on the determined abundance of conformers, thermodynamically averaged torsion angles and coupling constants 3JC‐H describing the “average” conformation about glycosidic linkage have been calculated. Results obtained are compared with available experimental data from solution and solid state.
On the physicochemical properties of gellan gum
Authors: Milas M. , Shi X. , Rinaudo M. 
Published: December 2004

AbstractThis paper concerns the behavior in dilute and semidilute solutions of deacetylated gellan. The conformational transition, controlled by temperature and ionic strength, is investigated. It corresponds to a double‐helix single‐chain transition. Large ionic selectivity is observed in the helical conformation that controls the degree of aggregation upon gelation. Potentiometry and conductivity measurements are interpreted in terms of the Manning poly‐electrolyte theory in the sol state.
Conditions for the stability of the alternative structures of duplex poly(dA‐dT)
Authors: Loprete D. M. , Hartman K. A. 
Published: December 2004

AbstractThe alternative structures of the lithium, sodium, potassium, and rubidium salts of poly(dA‐dT) were studied using ir spectra of hydrated, nonoriented gels. Poly (dA‐dT) · Na existed as the B structure at high hydration and as the A structure at moderate hydration. A disordered state occurred at low hydration. No hint of the C, D, or other structures was observed at any hydration for nonoriented gels containing NaCl up to 0.56 moles NaCl/mole of nucleotide residue. Poly (dA‐dT) · Li existed as the B structure at high hydration, made a gradual transition to the C structure at moderate hydration, and became disordered at low hydration. Poly (dA‐dT) · K and poly (dA‐dT) · Rb existed as the B structure at high hydration and as the presumptive D structure at lower hydration. The addition of Zn(II) to poly (dA‐dT) · Na produced a gradual transition from the B to the C structure upon dehydration. The addition of NaNO3 to poly (dA‐dT) · Na gave only the A and B structures, and not the C or Z structures that are promoted by NO3 in other base sequences. The DNA secondary structure stabilized by a given ion is determined by a specific base sequence and not simply by the properties of the ion.
Thermodynamic cycle‐perturbation study of the binding of trifluoroacetyl dipeptide anilide inhibitors with porcine pancreatic elastase
Authors: Lesyng Bogdan , Meyer Edgar F. 
Published: December 2004

AbstractThe variety of results of crystallographic studies of the serine proteases complexed with isocoumnrin inhibitors presents a challenging problem to modeling methods and molecular energetics. Therefore, the thermodynamic cycle‐perturbation technique has been used to study a model system of elastase and two peptidic inhibitors. Using the program AMBER, the technique correctly predicts changes of the binding constants for the trifluoroacetyl dipeptide inhibitors in comparison with available experimental (kinetic and crystallographic) data. However, the absolute values obtained are shown to be sensitive to the specific electrostatic interaction potential parameters used in the simulations. The reader and user are cautioned that thermodynamic cyle‐perturbation results may be too optimistic by underestimating the accuracy of free energy values. This is especially a matter of concern for those cases where a direct comparison with experimental values is not possible, viz., (1) the simulation of binding of novel compounds, (2) structurally uncertain binding sites, or (3) structurally different binding modes. With our best 4‐31G* ESP (electrostatic potential) charges we were able to reproduce experimentally determined free energy differences (ΔΔA) with an accuracy of about 1.5 kcal/mol. Dynamically induced structural changes in the binding site of elastase, and particularly changes in hydrogen‐bond patterns of the binding site, are also reported.
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. II. Homopolymers and copolymers
Authors: Zagari Adriana , Némethy George , Heraga Harold A. 
Published: December 2004

AbstractThe alteration of polymer conformational properties caused by the replacement of L‐proline by L‐azetidine‐2‐carboxylic acid (Aze) has been studied by means of conformational energy computations. In addition to poly (Aze), two sequential copolymers, poly (Pro‐Aze) and poly(Aze3‐Pro3), have been investigated. All polymers containing Aze are more flexible than poly(Pro). This is a consequence of an increased number of permitted conformational states for the Aze residue, as compared to Pro, when they are incorporated into a polypeptide, as well as of a lessened cooperativity of the trans‐cis transition. The results of the computation can be used to interpret the observed physical properties of poly (Aze) and of its copolymers.
Multiple helix–coil transitions
Authors: Dupré Donald B. 
Published: December 2004

AbstractConditions for the occurrence of one, two, and even three helix–coil transitions are summarized and further delineated in terms of thermodynamic parameters in simple modifications of a 2 × 2 matrix of statistical weights for amino acid residues in the coiled and helical conformations. Solvent interaction with segments in both the exposed, coiled and compact, helical conformations is worked into the model. Theoretical expressions for the temperature dependence of helical fractions, maximum attained degrees of helicity, and the compositional dependence of transition temperatures are compared with experimental data for two synthetic polypeptides that exhibit multiple helix–coil transitions.
Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in α‐, β‐, and random coil conformations
Authors: Venyaminov S. Yu. , Kalnin N. N. 
Published: December 2004

AbstractInfrared spectra of poly(D,L‐alanine), poly(L‐glutamic acid), poly(L‐lysine), silk fibroin, and tropomyosin have been registered for various conformations of the polypeptide chain. Assuming additivity of the main‐ and side‐chain absorption, spectral parameters of amide I and II absorption bands corresponding to α‐, β‐, and random coil conformations have been derived. The amide I band parameters for H2O and D2O have been compared.
Prediction of the rotational diffusion behavior of biopolymers on the basis of their solution or crystal structure
Authors: Müller Jürgen J. 
Published: December 2004

AbstractTwo low structure‐resolution methods are proposed for prediction of rotational diffusion parameters. The indirect procedure is based on the structure of a molecule in solution or in crystal, and uses the structure parameters of radius of gyration, and low‐resolution molecular surface and volume, determined from measured or theoretically calculated small‐angle x‐ray scattering intensities, to estimate a frictional equivalent ellipsoid of revolution. The direct method starts mainly from the crystallographic structure of a molecule and calculates the triaxial inertia equivalent ellipsoid, experimentally calibrated by translation diffusion data, to simulate the frictional behavior. The predicted harmonic mean of the rotational correlation times of compact globular macromolecules with molar masses of 14,000–65,000 g/mol agree with experimental results within the error limits. The prediction method is recommended for expert systems in structure research and for detection of internal protein flexibility or marker mobility by nmr and electron paramagnetic resonance experiments.
A vibrational spectroscopic study of the self‐association of 5′‐GMP in aqueous solution
Authors: Audet Pierre , Simard Christine , Savoie Rodrigue 
Published: December 2004

AbstractThe Raman spectra of highly concentrated solutions of 5′‐GMP at neutral and acid pH were recorded in order to better characterize the structure of the self‐aggregates formed in these solutions and their melting behavior. Vibrational coupling of the CO stretching vibrations in tetrameric units at neutral pH is shown to yield a characteristic pattern of two Raman bands at ca. 1730 and 1680 cm−1 (1708 and 1664 cm−1 in D2O), and an iractive mode at 1678 cm−1 in D2O. From the intensity of the 1730‐cm−1 band, proportional to tetramer concentration, and that at 1485 cm−1, which reflects the stacking of the bases, the thermal stability of the self‐associates formed at neutral pH is shown to be higher for stacked tetramers. At acid pH, the melting of the helical aggregates responsible for the formation of a gel is preceded by the freeing of the hydrogen‐bonded phosphate groups, accompanied by a change of conformation from C3′‐endo to C2′‐endo in some of the associated ribose units. Previous spectroscopic results suggesting the formation of tetramers as an intermediate step in the melting of the gel were not reproduced in this study.
Effect of basic oligopeptides on the B‐Z transition of poly(dG‐dC)·poly(dG‐dC) in water–methanol solutions
Authors: Votavová H. , Pírková J. , Gut V. , Šponar J. , Bláha K. 
Published: December 2004

AbstractThe effect of basic oligopeptides (Lys‐Ala‐Ala)n (n = 1–5, 10) and (Lys‐Leu‐Ala)n (n = 1–4) on the B‐Z transition of poly (dG‐dC)·poly (dG‐dC) in water–methanol solutions was investigated using CD and uv spectroscopy: In the absence of peptides, the concentration of methanol at the midpoint of the B‐Z transition is 64% at 25°C. The transition is temperature dependent and the B conformation is preferred at higher temperatures.All peptides tested shift the midpoint of the B‐Z transition to lower concentrations of methanol. For shorter peptides this effect increases with an increasing number of monomeric units, showing the importance of the number of positive charges in the peptide molecule. At conditions of low methanol content, the trimer and tetramer of the (Lys‐Leu‐Ala)n series have a greater effect on the B‐Z transition than the corresponding oligomers of the (Lys‐Ala‐Ala)n series. This indicates an important influence of the presence of hydrophobic groups in the peptide side chains on the binding.In the presence of peptides, the B‐Z transition is also temperature dependent and the B conformation is preferred at higher temperatures. The addition of peptides results in an increase of the transition midpoint and of the transition width. These parameters were used for the calculation of the transition enthalpy ΔHB‐Z in 65% methanol, which is −1.15 ± 0.25 kcal/base pair. Since the van't Hoff enthalpy ΔHVH calculated from the temperature dependence of the B‐Z transition in the absence of peptides is −130 kcal/mol, the length of the cooperative unit is about 110 base pairs. The results suggest that the mechanism of Z‐DNA induction is similar but not identical with that involved in the action of metal cations in aqueous solution.
1H‐ and 31P‐nmr studies of ditercalinium binding to a d(GCGC)2 and d(CCTATAGG)2 minihelices: A sequence specificity study
Authors: Delepierre Muriel , Milhe Catherine , Namane Abdelkader , Dinh Tam Huynh , Roques Bernard P. 
Published: December 2004

AbstractThe structures of the complexes formed in aqueous solution between ditercalinium, a bisintercalating drug, and both the self‐complementary tetranucleotide d(GCGC)2 and octanucleotided(CCTATAGG)2, have been investigated by 400‐MHz 1H‐nmr and 162‐MHz 31P‐nmr. All the nonexchangeable protons, as well as the exchangeable imino protons and the phosphorus signals, have been assigned. Both oligonucleotides have been shown to adopt a right‐handed B‐DNA type structure. The addition of ditercalinium to the oligo‐nucleotides lead to the formation of complexes in slow exchange at the nmr time scale with the free helices. At all drug‐to‐helix ratios studied, the ditercalinium was found in the bound form, whereas free and complexed oligonucleotides were in slow exchange, allowing resonance assignments through two‐dimensional chemical exchange experiments.For d(GCGC)2 the strong upfield shifts induced on all aromatic protons of both the bases and the drug by complexation with ditercalinium suggest an interaction by intercalation of the two rings. However, the loss of twofold symmetry upon binding, as well as the chemical shift variation of the drug proton signals of one of the chromophores with temperature and concentration, favor a model in which the drug–nucleotide complexes have one ring of the drug intercalated and the other stacked on top of the external base pair. The intermolecular contacts between drug protons and nucleotide protons give a defined geometry for complexation that is consistent with the proposed model.In contrast, with d(CCTATAGG)2 several drug–nucleotide complexes were formed and a large increase in line broadening was observed at high drug‐to‐DNA ratios, precluding a detailed analysis of these complexes. However, the large upfield shift in the imino proton resonances together with the shielding of the ditercalinium ring protons favor a model with bis‐intercalation of ditercalinium. This model is supported by the downfield shift of at least 4 out of 14 phosphorus signals. The results are compared with those obtained on ditercalinium binding to the homologous sequences d(CGCG)2 and d(TTCGCGAA)2, and discussed in terms of sequence specificity.
A sequence preference for nucleation of α‐helix—crystal structure of Gly‐L‐Ala‐L‐Val and Gly‐L‐Ala‐L‐Leu: Some comments on the geometry of leucine zippers
Authors: Chaturvedi Sanjeev , Go Kuantee , Parthasarathy R. 
Published: December 2004

AbstractThe synthetic peptide Gly‐L‐Ala‐L‐Val (C10H19N3O4·3H2O; GAV) crystallizes in the monoclinic space group P21, with a = 8.052(2), b = 6.032(2), c = 15.779(7) Å, β = 98.520(1)°, V = 757.8 Å3, Dx = 1.312 g cm−3, and Z = 2. The peptide Gly‐L‐Ala‐L‐Leu (C11H21N3O4·3H2O; GAL) crystallizes in the orthorhombic space group P212121, with a = 6.024(1), b = 8.171(1), c = 32.791(1) Å, V = 1614 Å3, Dx = 1.289 g cm−3, and Z = 4. Their crystal structures were solved by direct methods using the program SHELXS‐86, and refined to an R index of 0.05 for 1489 reflections for GAV and to an R index of 0.05 for 1563 reflections for GAL. The tripeptides exist as a zwitterion in the crystal and assume a near α‐helical backbone conformation with the following torsion angles: ψ1 = −150.7°; ϕ2, ψ2 = −68.7°, −38.1°; ϕ3, ψ31, ψ32, = −74.8°, −44.9°, 135.9° for GAV; ψ1 = −150.3°; ϕ2, ψ2 = −67.7°, −38.9°; ϕ3, ψ31, ψ32 = −72.2°, −45.3°, 137.5°, for GAL. Both the peptide units in both of the tripeptides show significant deviation from planarity [ω1 = −171.3(6)° and ω2 = −172.0(6)° for GAV; ω1 = −171.9(5)° and ω2 = −173.2(6)° for GAL]. The sidechain conformational angles χ21 and χ22 are −61.7(5)° and 175.7(5)°, respectively, for valine, and the side‐chain conformations χ12 and χ23's are −68.5(5)° and (−78.4(6)°, 159.1(5)°) respectively, for leucine. Each of the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH and COO− groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an α‐helix.
The structure of [D‐Hyi2, L‐Hyi4]meso‐valinomycin revealed by X‐Ray analysis
Authors: Pletnev V. Z. , Mikhailova I. Yu. , Ivanova V. T. , Langs D. A. , Grochulski P. , Duax W. L. 
Published: December 2004

AbstractDirect x‐ray analysis has been used to determine the crystal structure of [D‐Hyi2, L‐Hyi4]meso‐valinomycin {cyclo[‐D‐Val‐D‐Hyi‐L‐Val‐L‐Hyi‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐], C60H102N6O18}, which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cell Z = 3, cell parameters a = b = 15.2085 (8) Å, c = 29.3250 (9) Å, γ = 120°. The standard (R)and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six NH …︁ OC 4 → 1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast to meso‐valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residues D‐Val1 and L‐Val3 are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion‐binding center, it is inaccessible because the hydrophobic isopropyl groups of the D‐Hyi2 and L‐Hyi4 residues screen the molecular cavity on both sides.