bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of α‐amanitin in dimethylsulfoxide solution
Authors: Tonelli Alan E. , Patel Dinshaw J. , Wieland Th. , Faulstich H. 
Published: December 2004

AbstractThe backbone and side‐chain conformations of the bicyclic octapeptide α‐amanitin indimethylsulfoxide (DMSO) solution have ben deduced from analysis of the nmr spectrl parameters and conformational energy calculations. Several ambiguities in the nmr spectral assignments were resolved following a comparison with the recently published conformation of β‐amanitin in the crystalline state. The peptide proton exchange and temperature coefficient data demonstrate strong intramolecular hyfrogen bonds for the GLY5 and Cys8 peptide protons. The vicinal proton coupling constants are consistent with the cyclic octapeptide udergoing chain reversl at the Ile6‐Gly7 abd the Hyp2‐Hyi3 dipeptide segments. The upfield shifts of the glycine and isoleucine protons demonstrate the folding of the indole ring of the Trp4‐Cys8 brifge towards the Gly5‐Ile6‐Gly7 half of the Ile‐amanitin molecule. The structure af α‐amanitin in DMSO is defined by the (ϕψ) backbone rotation angles Trp4(−90, −60), Gly5 (+120, −120), Ile6(−6, +120), Gly7 (+45, +60), Cys8(−120, −60), Asn1 (+175, −175), Hyp2 (−160, −45), and Hyi3 (−90, −60). The study demonstrates that the structure of α‐amanitin in solution is similar to the structure f β‐amanitin in the crystalline state.
Study of DNA sequence supraorganization by intramolecular renaturation
Authors: Vizard Douglas L. 
Published: December 2004

AbstractThe method of DNA partial denaturation and intramolecular renaturation (in the absence of biomolecular reassociation) is developed analytically and presented as a means by which the supraorganization of the DNA sequences within large complex genomes may be studied. This analysis provides for the comparison of the actual borganization of DNA sequences with a random arrangement of the same sequences. The sequence organization of the E. coli genome does not appear to be very different from DNA sequences arranged along the genome without preference to sequence stabilities, whereas an orderly physical arrangement of DNA sequences is implicated for the human genoma.
Conformational features of oligocellulose acetates in the solid state and their implications for the structures of cellulose triacetate
Authors: Pérez S. , Brisse F. 
Published: December 2004

AbstractThe crystal data on cellobiose octaacetate and cellotriose undecaacetate are compared in an effort to analyze what information available from crystal structures of oligosaccharides can be used to arrive at the three‐dimensional structure of the related polysaccharides. This comparison points out the remarkable behavior of the reducing end of both molecules. The glycosidic torsion angles (ϕ,ψ) around the reducing and the middle residues in the disaccharide and in the trisaccharide have values around 45° and 14°, while the conformational angles about the nonreducing residues in cellotriose acetate are 24° and −20°. The conformations of the primary acetate groups on the two nonreducing residues are similar, but they differ from those observed for the acetate groups belonging to the reducing residues. The possibility of a 21 symmetry axis between contiguous triacetate residues within the oligosaccharide is examined, along with a comparison of the molecular packing found in the oligomer structures. Conformational energy calculations have been performed on two dimeric entities derived from cellotriose acetate. The isoenergy maps show the drastic influence of the relative orientations of the primary acetate groups. It is proposed that the nonreducing dimer, as found in the crystal structure of cellotriose acetate, most nearly expresses the “polymer averaged” interactions for contiguous residues in cellulose triacetate.
Theoretical studies on peptidoglycans. I. Effect of L‐alanyl, D‐butyl, or D‐valyl residuces at the positions 4 or 5 of the pentapeptide moiety of peptidoglycan on the cross‐linking reaction
Authors: Virudachalam R. , Rao V. S. R. 
Published: December 2004

AbstractPossible conformations of X‐D‐alanyl4‐D‐alanine5 and its analogs X‐L‐analyl4‐D‐alanine5 X‐D‐alanyl4‐L‐alanine5, X‐D‐butyl4‐D‐alanine5, X‐D‐alanyl4‐D‐butyric acid5, X‐D‐valyl4‐D‐alanine5, and X‐D‐alanyl4‐D‐valine5 have been analyzed by theoretical methods. These studies suggest that L‐alanine and D‐valine at the 4 or 5 postion of the pentapeptide moiety of peptidoglycan will drastically reduce the cross‐linking in peptidoglycan biosynthesis, whereas the effect of D‐ butyric acid will be marked at the 4 postition and modeate at the 5 position. This is in good agreement with experimental results. The cross‐linking enzyme transpeptidase requires a specific confroamation for the 4th and 5th residues for optimal binding.
Rotating frame spin‐lattice relaxation experiments and the problem of intramolecular motions of peptides in solution
Authors: Bleich Hermann E. , Glasel Jay A. 
Published: December 2004

AbstractThe application of rotating frame spin‐lattice relaxtion to the determination of the intramolecular motions in peptides is discussed, and results are presented on the application of 13C T1p to peptide microdynamics in solution. The effective molecular rotational reorientation times at the amide and amino nitrogens may be derived from appropriate data onT1p of the carbons adjacent to them. We also show by theoretical caculations that 1H and 13C T1p experiments of suitable 2H and 15N substituted peptides will allow intramolecular main‐ and sidechain motions, characterized by times in the range 10−1–10−6 sec, to be investigated.
Conformational properties of the N‐terminal residues of S‐peptide. I. The ribonuclease S′ system
Authors: Filippi Bruno , Borin Gianfranco , Anselmi Ugo , Marchiori Fernando 
Published: December 2004

AbstractThe contribution of the 1–6 N‐terminal sequence to the conformational properties of the S‐peptide (the 1–20 sequence of ribonuclease A) was assessed by determining in the ribonuclease S′ system the helical content and the binding capability of synthetic [Orn10]‐S‐peptide analogs, in which lysine1, glutamic2 and threonine3 were progressively deleted, alanine4 and alanine5were alternatively replaced by serine, and alanine6 was substituted by serine or proline. Both the deletion of the three N‐terminal residues and the alanine6/proline replacement produces the loss of the helical structure up to lysine7. No or minor effects are found in all other cases. From the comparison of the binding data, the energy for the conformational stabilization of the N‐terminal region was calculated to amount to 1.4 kcal/mol. The results are discussed in comparison with the known x‐ray data of the enzyme, with some predictive rules of secondary structure which were applied to this region and with the known phylogenetic variance of the residues in this region.
Studies of the thyrotropin‐releasing factor. II. Conformations of TRF and some analogs
Authors: Flurry R. L. , Abdulnur S. F. , Bopp J. M. 
Published: December 2004

AbstractThe conformation of the thyrotropin‐releasing factor (TRF) and four analogs have been studied by the CNDO/2 molecular orbital method. The Nδ‐protonated tautomer of TRF is predicted to be the more stable of the two tautomeric forms; however, it is postulated that the Nε‐tautomer possesses the most active minimum‐energy conformation. The peptide backbone for the five compounds remains nearly constant. The conformations predicted from model fragments are very near to those found for the full compound.
13C‐NMR spectroscopic investigation of α‐ and β‐1,4‐D‐glucose homooligomers
Authors: Heyraud Alain , Rinaudo Marguerite , Vignon Michel , Vincendon Marc 
Published: December 2004

AbstractA complete, unambiguous assignment of all the 13C signals of cellobiose and maltose has been achieved using methods such as selective proton decoupling, 13C selective spin labeling, and isotopic chemical shift induced by deuterium. The chemical‐shift variation of the 13C signals with the degree of polymerization in each α or β (1 → 4) series is discussed. The chemical‐shift dependence on temperature and solvent in these two series is shown and interpreted in terms of modifications of the solvation and of the conformation.
Interactions between bovine plasma albumin and sodium dodecyl sulfate studied by means of 13C‐nmr spectra
Authors: Inoue Yoshio , Sase Shigeru , Chûjô Riichiro , Nagaoka Shunji , Sogami Masaru 
Published: December 2004

AbstractThe interactions between the protein, bovine plasma albumin, and surfactant, sodium dodecyl sulfate, have been studied by 13C‐nmr spectroscopy at pH 5.4–6.8 in D2O solution. The 13C chemical shifts and the 13C spin‐lattice relaxation time of the individual carbons of the surfactant were measured as a function of the molar ratio of the surfactant to albumin in order to analyze the surfactant‐protein interaction and the molecular motion of the surfactant. It was found that in the region of initial binding of the surfactant to the high‐affinity sites on the protein, both the surfactant head group and alkyl chain interact with the protein. With an excess of high‐affinity sites at the beginning of the reaction, surfactant molecules are in a micellelike environment in which the surfactant's alkyl chains are associated with nonpolar groups of the protein. Even after the denaturation by many surfactant bindings, much of the secondary and higher structure seems to remain intact.
Thermodynamics and kinetics of the interaction of copper (II) ions with native DNA
Authors: Förster W. , Bauer E. , Schütz H. , Berg H. , Akimenko N. M. , Minchenkova L. E. , Evdokimov Yu. M. , Varshavsky Ya. M. 
Published: December 2004

AbstractBased on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ ions with atoms N(7) of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7) and O of C(6) of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequence dGpC. CD spectra of the resulting nondenatured complex (DNA–Cu2+)nat may be interpreted in terms of a conformational change of DNA from the B‐form to a C‐like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA–Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ ions to atoms N(3) of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ ions between atoms N(7) and O of C(6) of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence‐specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ ions with DNA.In temperature‐jump experiments with the nondenatured complex (DNA–Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex formation) may proceed.
On the blue color of triiodide ions in starch and starch fractions. I. Characterization and assignment of absorption and circular dichroism spectra of triiodide ions in amylose
Authors: Handa Takashi , Yajima Hirofumi 
Published: December 2004

AbstractFour fundamental Raman lines were observed at 159, 111, 55 and 27 cm‐1 corresponding to the I bound (I) in amyloses with DP from 20 to 100, regardless of the degree of polymerization of I and the excitation wavelength. The spectral resolution was based on the molar extinction coefficient and molar ellipticity spectra of I. Eight bands, named, S1, S2, ⃛, S8 from long to short wavelength, were isolated. These were found regardless of the DP. By a resonance excitation Raman study, the characteristics of S3 and S4, comprising the shoulder around 480 nm, were found to be different from those of S1 and S2, comprising the blue band. The assignment of the spectra was based on the electronic states of the monomeric I in the exciton‐coupled dimeric unit. It was concluded that the blue band (S1,S2) belonged to the long‐axis transitions and the shoulder band (S3,S4) to the short‐axis ones on the monmeric coordinate system.
Single crystals and oriented crystallization of ivory nut mannan
Authors: Chanzy Henri , Dube Michel , Marchessault R. H. , Revol J. F. 
Published: December 2004

AbstractThe preparation of lamellar single crystals of mannan[poly((1 → 4)‐β‐D‐mannose)] is described. Electron diffractograms clearly identify the perpendicular orientation of the chain axis with respect to the lamellar surface. Since the degree of polymerization is 40 or less, no conclusion is made as to chain folding. The unit cell corresponds to the mannan I structure derived from x‐ray fiber data on oriented algal mannan. The baseplane dimensions found were a = 7.22 Å and b = 8.92 Å, and the systematic absences observed confirm the proposed P212121 group. It was found that cellulose microfibrils from Valonia ventricosa and bacterial cellulose could serve as extended chain nuclei for inducing oriented crystallization of mannan on cellulose. This produces a shish‐kebab type of morphology.
Theoretical investigation of semiconductive properties in proteins. II. The possibility of charge transfer between proteins and different acceptor molecules
Authors: Suhai Sáandor , Collins Thomas C. , Ladik János 
Published: December 2004

AbstractThe results of theoretical investigations are reported concerning the possibility of impurity‐type charge carrier production in proteins. The energy band structures of the periodic protein model polyglycine calculated with the aid of the ab initio Hartree‐Fock crystal orbital method and corrected afterwards for long‐range correlation effects are compared with the empty levels of glyoxal, methyl‐glyoxal, acrolein, and croton‐aldehyde, suggested recently by Albert Szent‐Györgyi as possible acceptors against proteins. The comparison with previous supermolecule calculations shows that appreciable charge transfer can be expected to glyoxal, methyl‐glyoxal, and acrolein from the polypeptides, while croton‐aldehyde is probably less efficient in this relation.
Hydroxyproline content and location in relation to collagen thermal stability
Authors: Burjanadze Tengiz V. 
Published: December 2004

AbstractA new analysis has been made on studies of the influence of imino acid content on the changes of collagen thermal stability (tm). It is shown that, for the interstitial vertebrate collagens, there is a strict regularity in the changes of tm depending on hydroxyproline content. No correlation is observed between tm and proline content. Also, no correlation between tm and hydroxyproline content is observed for invertebrate and basement membrane collagens. On the basis of the reported data, the dependence of tm on hydroxyproline content is considered to be not a correlation between tm and the total content of hydroxyproline, but only as the correlation between tm and the content of hydroxyproline occurring at the third position in the sequence (Gly‐R2‐R3)n. The results agree with the idea that the influence exerted by proline and hydroxyproline on the stabilization of the triple helix of collagen is different.
Salt‐induced conformational change of random copolymers (Lys50Tyr50)n and (Lys50Phe50)n studied by 1H‐ and 13C‐nuclear magnetic resonances. Aggregation behavior of helical segments
Authors: Saitô Hazime , Ohki Toyokazu , Kodama Masahiko , Nagata Chikayoshi 
Published: December 2004

Abstract1H‐ and 13C‐nmr studies of conformational transitions of random amino acid copolymers containing aromatic residues (Lys50Tyr50)n and (Lys50Phe50)n in the presence of neutral salts were performed to serve as models of the aggregation behavior of polypeptides of biological significance. The 1H and 13C signal intensities of Tyr and Phe residues decreased preferentially with increasing concentration of neutral salts such as NaCl and NaClO4. This behavior contrasts with that of (Lys)n in the presence of similar neutral salts, where the displacement of the 13C signal is clearly seen on transition from the random‐coil to the helical conformation. On the basis of the previous conformational studies, the loss of the peak areas is ascribed to the presence of immobilized helical segments by hydrophobic interaction between aromatic side chains. The remaining resonances are due to the residual random‐coil regions, since the values of nuclear Overhauser enhancements and chemical shifts are unchanged in the presence and absence of the neutral salts.
Transport properties of particles with segmental flexibility. I. Hydrodynamic resistance and diffusion coefficients of a freely hinged particle
Authors: Harvey Stephen C. 
Published: December 2004

AbstractExpressions are derived for the hydrodynamic resistance tensor and the diffusion tensor of a particle consisting of two rigid subunits connected by a free hinge. No restrictions are placed on the shapes of the subunits. The resistance tensor is obtained by using two independent approaches: first, from the Rayleigh dissipation function and, second, from an examination of the generalized forces for the appropriate seven‐dimensional coordinate system. For the derivation of the generalized Einstein equation connecting the diffusion and resistance tensors, the Brownian motion is treated as a stochastic process. That derivation is based on the assumption that the restoring force for bending is negligible, and the Einstein relation holds instantaneously only if that assumption is true. The relationship between these tensors and the macroscopically observable parameters is discussed, and it is shown that the separate measurement of resistance and diffusion coefficients can be used to detect macromolecular flexibility. One example is treated, the diffusion of a particle composed of two long rods joined at a free hinge. Those calculations are carried out with the first‐order assumption of negligible hydrodynamic interactions between the subunits. For the hinged rod, the bending degree of freedom produces a 34% increase in the translational diffusion coefficient over that of a stiff rod of the same total length, while the rotational diffusion coefficient about the axis perpendicular to the plane of bending is increased by 125%.
Adsorption of polypeptides on solid surfaces. I. Effect of chain stiffness
Authors: Birshtein T. M. , Zhulina E. B. , Skvortsov A. M. 
Published: December 2004

AbstractThe general method of obtaining the partition function and thermodynamic characteristics of polymer chains near an adsorbing surface, simulated by random walks on a lattice, is developed. The method takes into account the effect of short‐range interactions in polymer chains, in particular, the chain stiffness and secondary structure. The theory of adsorption of chains of different stiffness is developed, and the process of adsorption which occurs when the external conditions change is shown to be always a second‐order phase transition. The critical adsorption energy decreases and the sharpness of transition grows when the chain stiffness increases. A simple model of a chain with “virtual” steps is proposed which simplifies the treatment; the results obtained are in good agreement with exact theories. A general scheme of analysis of adsorption of chains with a given secondary structure is set forth and the analogy between the stiffness of a noncooperative chain and the presence of helical segments in a polypeptide chain is discussed.
Lysozyme film hydration events: An IR and gravimetric study
Authors: Careri G. , Giansanti A. , Gratton E. , Snamprogetti  
Published: December 2004

AbstractBy a combined gravimetric and ir technique, spectra of protein films are recorded during sorption isotherms at constant water content h (mg D2O/mg dry protein) in the range 0 les; h ⩽ 0.35 at 27 and 38°C. Computer‐aided differential analysis shows the effect of progressive hydration on some significant sites of the protein such as the ionizable acidic side chains and the backbone amide carbonyls, as well as the spectrum of the adsorbed water itself. In order to derive thermodynamic properties of these sites, the measured sorption isotherm is decomposed in terms of a model which postulates the existence of two classes of primary sorption sites only, and these two contributions are independently checked by the ir data. The free energy of binding of the strong and weak binding sites is found to be 2.0 ± 0.2 and 0.40 ± 0.1 kcal/mol, respectively. A water‐induced transition region is clearly detected in all the observed properties at 0.06 < h < 0.10 at 38°C and is shown to be due to changes involving both the structure of the absorbed water and the coverage of the absorption sites. A detailed picture of the hydration events is offered, and the relevance of these findings to protein dynamics is discussed.
The flexible DNA double helix. II. Superhelix formation
Authors: Olson Wilma K. 
Published: December 2004

AbstractA simple super or s‐virtual bond scheme has been developed for the treatment of tertiary or superhelical structure in polynucleotide chains. The various spatial configurations accessible to the flexible double helix are rendered more readily intelligible by the introduction of these hypothetical bonds to replace real sequences of regular secondary structure. The scheme is utilized to examine the enormous variety of tertiary structure that can be generated by regularly bending a B‐DNA reference helix at the phosphodiester linkages. Of particular interest from the study are the large families of bends that generate superhelices of identical macroscopic dimensions. Various modes of folding the B‐type helix into superhelices that fit the experimentally measured dimensions of chromatin nucleosomes are illustrated.