bluuebunny/crossref_metadata_2025_split huggingface dataset:
Azobenzene‐Containing polypeptides: Photoregulation of conformation in solution
Authors: Ciardelli Francesco , Pieroni Osvaldo , Fissi Adriano , Houben Julien L. 
Published: December 2004

AbstractPhotochromic polypeptides, with 16 to 56% azobenzene groups in the side chains, have been prepared by reaction of poly(L‐glutamic acid) with p‐aminozaobenzene, both in the presence of dicyclohexyl carbodiimide/N‐hydroxybenzotriazole and of pivaloyl chloride. Analogous modification reactions carried out on poly(L‐aspartic acid) were unsuccessful owing to the formation of N‐succinimide rings. In trimethylphosphate, all the azopolypeptides exhibit the α‐helix CD pattern. Irradiation produces the trans‐to‐cis isomerization of the azo side chains, but does not induce any variations of the backbone conformation. In water, the CD spectra indicate the presence of appreciable amounts of α helix in 16 and 21% mol azo‐containing poly‐(Lglutamates), while a β structure is present in a 36% mol azopolypeptide. Light produces conformational changes of the polypeptide conformation which are completely reversed in the dark. The extent and kind of photobehavior depend on the azo content and the pH value at which irradiation is carried out. The light‐induced effects are discussed on the basis of the pH‐induced order‐disorder conformational transitions. In fact, the pK values and the transition curves of the dark‐adapted samples were found to be different from those of the irradiated ones.
Polypeptide matrices as active catalytic supports for stereoselective electron‐transfer reactions
Authors: Pispisa B. , Farinella M. 
Published: December 2004

AbstractThe oxidation of L‐adrenaline (epinephrine) in the presence of [Fe(tetpy)(OH)2]+ ions bound to poly(L‐glutamate) or to poly(D‐glutamate) has been studied at pH 7 (tetpy = 2,2′:6′,2″:6″,2‴‐tetrapyridyl). Electron transfer from the substrate to the central metal ion, which is rate‐determining, proceeds stereoselectively only when extensive and possibly specific interactions between adrenaline and the peptidic residues of the ordered polymer in the close environment of the active sites occur. This ensures different steric constraints for the two diastereomeric precursor complexes, which are thought to affect the separation and orientation of the redox centers differently, leading to the observed phenomena. Some data on the catalytic oxidation of L‐dopa(3,4‐dihydroxyphenylalanine) are also presented, showing stereoselective effects similar to those observed with L‐adrenaline, despite the diverse distance of the chiral center from the reacting OH groups. A mechanistic interpretation of the results is discussed in the light of a few general considerations concerning the structural features of the catalytic systems. Possible explanations for the finding that stereoselectivity occurs at the expense of the efficiency of catalysis are also considered.
Structural dynamics of melanin investigated by Rayleigh scattering of Mössbauer radiation
Authors: Albanese G. , Bridelli M. G. , Deriu A. 
Published: December 2004

AbstractMeasurements of Rayleigh scattering of Mössbauer radiation (RSMR) have been performed on synthetic L‐Dopa melanin as a function of the scattering vector, Q, and temperature, T, and are compared with the results of X‐ray diffraction analyses. The data obtained allow us to derive a radial distribution function for the atomic positions not affected by the dynamic disorder and determined only by the distribution of equilibrium interatomic distances. The mean‐square atomic displacements, <u2>, derived from the RSMR measurements, evidence a strong anisotropy of the atomic vibrations: even at room temperature, <u2> reaches fairly high values for off‐plane displacements, as compared with those for motions within the planes of the structure. A connection is suggested between the observed dynamics and the biological screening action of melanins.
A consistent empirical potential for water–protein interactions
Authors: Hermans Jan , Berendsen Herman J. C. , Van Gunsteren Wilfred F. , Postma Johan P. M. 
Published: December 2004

AbstractA simple point‐charge potential, developed earlier for the calculation of intermolecular forces in molecular‐dynamics simulations of liquid water, has been extended to include interactions between water molecules and polar groups of proteins. A complete potential for use in the simulation of protein dynamics in water is reported.
Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results
Authors: Sen A. C. , Keiderling T. A. 
Published: December 2004

AbstractVibrational CD (VCD) of amide I and II vibrations of several α‐helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21, 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right‐handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low‐energy) component. However, left‐handed α helices formed from L‐amino acids gave positive amide II bands at higher frequencies than found for the right‐handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide‐I VCD spectra of some deuterated right‐handed α‐helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide‐II and amide‐A VCD of a few deuterated polypeptides imply retention of the secondary‐structure‐dependent characteristics seen in the hydrogenated VCD.
DNA gelation in concentrated solutions
Authors: Fried Michael G. , Bloomfield Victor A. 
Published: December 2004

AbstractSonicated calf‐thymus DNA (200 ± 30 base pairs) spontaneously forms viscoelastic gels over a wide range of concentration, temperature, and buffer conditions. Quasielastic light scattering (QLS) can be used to monitor this process, because the ratio of dynamic‐to‐static scattering intensity decreases dramatically as gelation occurs. Using QLS, we have explored the effects of DNA concentration and mono‐ and divalent cations on the thermal stability of DNA gels. We found that the gel–sol transition temperature (Tgel) varies linearly with [DNA] from 7.5 to 17 mg/mL. Both Na+ and Mg2+ strongly stabilize the gel state. The sharpness of the transition increases with increasing ionic and DNA concentrations. Analysis of the Na+‐dependent gelation indicates that the process requires the association of one Na+ per 118 base pairs. Mg2+ effectively stabilizes the gel at concentrations 10‐fold below those required for Na+. The unexpectedly large effect of Mg2+ suggests that ion‐specific interactions may play an important role in determining gel stability.
Conformation of control and acetylated HeLa stripped chromatin after reassociation with H1
Authors: Hüvös Piroskae , Sasi Ramakrishnan , Fasman Gerald D. 
Published: December 2004

AbstractThe effect of histone H1 on the conformation and stability of control and acetylated HeLa high‐molecular‐weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
Catalytic influence of heparin on auramine O hydrolysis: A basis for differentiating heparin from other glycosaminoglycans based on its properties as a polyelectrolyte
Authors: Band Philip , Lukton Aaron 
Published: December 2004

AbstractThe basis for heparin's ability to accelerate the conversion of auramine O (AuO) to Michlers ketone [P. Band & A. Lukton (1982) Anal. Biochem. 120, 19–24] is here explained in terms of well‐known polyelectrolyte phenomena. Acceleration of this acidcatalyzed hydrolysis appears to be due to colocalization of the cationic dye and hydronium ion within the microenvironment of heparin's electrostatic domain. The dependence of reaction rate on polymer, dye, and hydronium ion concentration, ionic strength, and various ratios of these parameters is consistent with what others have observed for polyelectrolyte catalysts. Dextran sulfate, polyvinyl sulfate, and polyanethole sulfonate likewise accelerate this reaction, thus precluding any explanation of the catalysis in terms of a specific catalytic site. A striking aspect about the polyanion–AuO system is the inability of all other natural glycosaminoglycans tested to catalyze this reaction, despite their analogous polyanionic nature. Manning's limiting laws describing counterion condensation in polyelectrolyte solutions provide a simple context within which to interpret these results. Calculation of the structural linear charge density parameter, ξ, based on analytically determined sulfate‐to‐hexosamine ratios, reveals that heparin is unique among the glycosaminoglycans in possessing an ξ value greater than unity under the conditions described. Thus, heparin's differential ability to catalyze AuO hydrolysis is a reflection of the fact that only heparin is sulfated to an extent great enough to maintain ξ > 1, even when the negative charge of carboxylate groups is neutralized. It is proposed that this distinction may be important to the unique biochemical attributes of heparin and that such considerations may prove useful in establishing structure–function relationships when comparing different glycosaminoglycan classes.
Synthesis and β‐conformation of sequential polypeptides containing arginine, histidine, and leucine
Authors: Barbier Bernard , Caille Anita , Brack André 
Published: December 2004

AbstractAlternating poly(Arg‐Leu) and copolypeptides with Arg‐Leu and His‐Leu sequences were prepared by condensation of the corresponding p‐nitrophenyl dipeptide esters in the presence of 1‐hydroxybenzotriazole. Arginine was used without any protection and histidine side chains were protected using π‐benzyloxymethyl group recently introduced in peptide chemistry. The ability of these polypeptides with alternating hydrophilic and hydrophobic residues to form water‐soluble β‐sheets was investigated by CD.
Conformational effects on peptide aggregation in organic solvents: Spectroscopic studies of two chemotactic tripeptide analogs
Authors: Raj P. Antony , Balaram P. 
Published: December 2004

AbstractThe aggregation behavior of the chemotactic peptide analogs, Formyl‐Met‐Leu‐Phe‐OMe (1) and Formyl‐Met‐Aib‐Phe‐OMe (2), has been studied in chloroform and dimethylsulfoxide over the concentration range of 0.2–110 mM by 1H‐nmr spectroscopy. Both peptides associate in CDCl3 at concentrations ≥ 2 mM, while there is no evidence for aggregation in (CD3)2SO. Analog 1 adopts an extended conformation in both solvents favoring association to form β‐sheet structures. A folded, γ‐turn conformation involving a 3 → 1 hydrogen bond between Met CO and Phe NH is supported by 1H‐, 13C‐nmr, and ir studies of analog 2. The influence of backbone conformation on the ease of peptide aggregation is demonstrated by ir studies in CHCl3 and CD studies in dioxane.
Quantum‐mechanical theory of CD for infinite helical polymers
Authors: Pamuk H. Onder , Dougherty Anne M. , Johnson W. Curtis 
Published: December 2004

AbstractQuantum‐mechanical equations are derived that are particularly well suited to actual computations of the CD for helical polymers. They make use of cyclic boundary conditions and helical symmetry, so that only two matrices with a size equal to the number of transitions considered need be diagonalized. The final equations are expressed directly in terms of monomer properties and helical parameters to invite the same input as earlier calculations, and are given as a rotational strength times a shape function for ease of comparison with the earlier work. The shape of the helix term is expressed as a derivative with respect to ω and depends on the distance between monomers along the helix axis. Other terms involving two electric transition dipoles depend on the distance from the helix axis to the transition center. These equations are directly comparable to the classical equations derived for cyclic boundary conditions and helical symmetry. We present an outline of the derivation and enough intermediate steps to clarify how the equations arise.
Random‐phase calculation of the low‐energy circular dichroism in glucans
Authors: Sathyanarayana B. K. , Stevens E. S. , Texter J. 
Published: December 2004

AbstractThe CD of the long‐wavelength electronic transition in the α‐(1 → 4)‐linked glucan dimer (maltose) and polymer (amylose), and in the β‐(1 → 6)‐linked dimer (gentiobiose) and polymer (pustulan), are calculated in the random‐phase approximation using time‐dependent Hartree theory. This long‐wavelength transition (180–190 nm) is assumed to be localized on the linkage oxygen atom and to be of a σ*/3 s ← n character. The zerothorder σ*/3s ← n magnetic‐dipole transition moment is coupled to the CC, CO, and CH bond density of states via a polarizability approximation. We assume this coupling is dominated energetically by the electric‐dipole, electric‐dipole interaction terms in the context of Schellman's μe‐μm coupling mechanism of rotatory power. The CD is calculated as a function of rotation about the two single bonds of the linkage oxygen atom and also as a function of rotation about the C(5)‐C(6) bond. For maltose, four rotational isomers are considered, resulting from combinations of the gg and gt C(6)H2OH group rotational isomers. The calculated CD values were then Boltzmann‐averaged over an empirical potential, and the resulting CD was found to compare satisfactorily with experiment. In the case of the polymers, only structures having periodicity (helicity) were examined.
Type I collagen segment long spacing banding patterns: Improved correlation with models using a variable h‐spacing
Authors: Bender Edward , Silver Frederick H. 
Published: December 2004

AbstractFive models of collagen molecular structure incorporating a variable h‐spacing were evaluated by comparing theoretical densitometric scans of segment long spacing (SLS) banding patterns with experimental densitometric scans. The five models tested assumed a shift in the h‐spacing of different residues: (1) proline only, (2) hydroxyproline only, (3) proline and hydroxyproline (in the same direction), (4) proline and hydroxyproline (in opposite directions), and (5) all residues shifted depending on their relative hydrophobicity. The best correlation coefficients were obtained when, in the theoretical models, the proline residues were expanded axially and/or the hydroxyproline residues were contracted. Using the hydrophobic model, the results showed that in general the more hydrophobic a residue is, the larger its h‐spacing. Theorectical models with the α2‐chain in the A position of the triple helix (α2,α1,α1) correlated best with the experimental data. In conclusion, these studies suggest that variation exists in the h‐spacing of the amino acid residues proline and hydroxyproline in SLS prepared for electron microscopy and stained with phosphotungstic acid and uranyl acetate. Some of this variation may be due to drying and may not be present in hydrated molecules.
Two‐dimensional 1H‐nmr studies on the lac repressor DNA binding domain: Further resonance assignments and identification of nuclear overhauser enhancements
Authors: Zuiderweg E. R. P. , Scheek R. M. , Kaptein R. 
Published: December 2004

AbstractThe assignments of several 1H lines in the spectrum of the lac repressor DNA‐binding domain (or “headpiece”) are documented. These new assignments complement those obtained in a previous study [E.R.P. Zuiderweg, R. Kaptein, and K. Wüthrich (1983) Eur. J. Biochem. 137, 279] and were made from pure absorption phase two‐dimensional nuclear Overhauser enhancement (2D NOE) spectra and 1H 2D double‐quantum spectra of this protein. Based on the complete set of resonance assignments, a large number of interresidue NOEs are identified; these are documented and their relation with distance constraints is discussed. The identification of these NOEs is a prerequiste for the determination of the spatial structure of this protein, for which no crystallographic data are available.
Cross‐polarization/magic‐angle spinning 13C‐nmr of (1 → 6)‐β‐D‐glucan (pustulan): Mechanism of gelation
Authors: Stipanovic Arthur J. , Giammatteo Paul J. , Robie Stephen B. 
Published: December 2004

Abstract13C‐nmr has been employed to probe the molecular conformation and crystal structure of (1 → 6)‐β‐D‐glucan (pustulan) in the solution, gel, and solid states. CP/MAS 13C‐nmr spectra recorded for partially crystalline solid pustulan display a resonance near 82 ppm that is absent in solution spectra. The intensity and peak width of this resonance were found to depend on relative crystallinity as determined by x‐ray diffraction. CP/MAS spectra of aqueous pustulan gels also exhibit the 82‐ppm resonance, suggesting that the gelation mechanism may involve microcrystalline junction zones. Since the 82‐ppm resonance is absent in the CP/MAS spectrum of the (1 → 6)‐β‐linked dimer gentiobiose, we tentatively conclude the crystal structure of this dimer does not adequately model the yet undetermined structure of pustulan.
Proton magnetic resonance studies on conformation and association of oligo‐γ‐benzyl‐L‐glutamates in solution
Authors: Imae Toyoko , Ikeda Shoichi , Kobayashi Yuji , Kyogoku Yoshimasa 
Published: December 2004

AbstractThe proton magnetic resonance spectra of o‐nitrophenylthio‐tetra‐ and hexa‐γ‐benzyl‐L‐glutamate ethylamides have been measured at different concentrations in CDCl3 and CD22C1. The NH and α‐CH resonances of the tetrapeptide show downfield shifts with increasing concentration, accompanying disappearance of their fine structure and line broadening. The apparent feature of chemical shifts against concentration is sigmoidal, and it can be interpreted by assuming the presence of a step or more of association–dissociation equilibria of tetrapeptide. With increasing concentration, small aggregates are formed by intermolecular hydrogen bonding, the size of which is not sufficiently large to exhibit critical micelle concentrations. In contrast to the tetrapeptide, the hexapeptide has constant chemical shifts of the NH and α‐CH resonances, independent of concentration, which implies that only the unassociated molecules show observable sharp resonances. In the hexapeptide, the phenyl CH and benzyl CH2 groups of the side chains exhibit new resonances above certain critical concentrations, indicating the restriction of rotational freedom of the side chains in the aggregated states.
Conformational analyses of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in a helix‐supporting environment, trifluoroethanol
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray 
Published: December 2004

AbstractA detailed conformational analysis of C‐terminal polyoxyethylene‐bound homo‐oligo‐L‐glutamates (dimer, penta‐heptamer) with N‐terminal blocking groups, X = Boc, Ac, or pGlu, was carried out in the helix‐supporting environment, trifluorethanol, using 1H‐nmr spectroscopy to observe backbone NH resonances. The nmr structural investigations for the three glutamate POE series were based on the assignment of individual amide NH resonances through deuteration, analyses of vicinal coupling constants (3JNH‐α‐CH), measurements of the temperature‐dependence of NH chemical shifts, saturation‐transfer experiments, stable free radical titration studies, and titration experiments using a denaturing solvent (DMSO). From these investigations, a detailed picture was derived for the possible conformations of these POE‐peptides.
Hydrogen‐bonding preferences in 2,6‐diaminopurine: uracil (thymine) and 8‐methyl adenine:uracil (thymine) complexes
Authors: Rao Shashidhar N. , Kollman Peter A. 
Published: December 2004

AbstractWe present molecular mechanical calculations on 2,6‐diaminopurine (2,6‐DAP):uracil (thymine) and 8‐methyladenine (8‐methyl A): uracil (thymine) hydrogen‐bonded complexes of various geometries, namely, Watson‐Crick (normal and reverse), Hoogsteen (normal and reverse), and purine N3 type. In contrast to earlier calculations [Ornstein, R. L. & Fresco, J. R. (1983) Proc. Natl. Acad. Sci. USA 80, 5171–5175], the 2,6‐DAP:uracil (thymine) complexes are predicted to be Watson‐Crick and the 8‐methyladenine:uracil (thymine) to be Hoogsteen. The results presented here are more consistent with the observed crystallographic preferences.
Examination of the secondary structure of proteins by deconvolved FTIR spectra
Authors: Byler D. Michael , Susi Heino 
Published: December 2004

AbstractFourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm−1 resolution from 1600 to 1700 cm−1 in deuterium oxide solution. Fourier self‐deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well‐defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm−1. The observed components are assigned to helical segments, extended beta‐segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta‐structure band can vary within a range of approximately 15 cm−1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss–Newton, iterative curve‐fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta‐structure for each of 21 globular proteins. The results are in good general agreement with values derived from x‐ray data by Levitt and Greer. The RMS deviation between 22 values (alpha‐ and beta‐content of 11 beta‐rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.
Macroscopic polarity of connective tissue is due to discrete polar structures
Authors: Freund Isaac , Deutsch Moshe 
Published: December 2004

AbstractApplying scanning optical harmonic microscopy to biological tissue for the first time, we have discovered that the macroscopic polarity of rat‐tail tendon is due to a coherent network of discrete polar structures. This finding permits isolation of these structures for further detailed analysis, which should lead to their complete characterization and thus to a solution of the twenty‐year‐old mystery of connective tissue polarity.