bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular organization of DNA in chromosomes
Authors: Basu Samarendra 
Published: May 2005

AbstractMetaphase chromosomes of Chinese hamster and lampbrush chromosomes of Triturus viridescens were studied for DNA arrangement by polarized fluorescence microscopy and by linear dichroic ratio measurements. Intact chromosomes showed a small but negative polarization (−8%) of fluorescence, while the dichroic ratio was negative and quite appreciable (0.85). On treatment with trypsin or RNase the polarization value increased to about −34% with no change in the polarization direction. The dichroic ratio on the other hand remained unchanged on such enzyme treatments. These results, along with the data of form dichroism and the change in fluorescence color following any enzyme action, suggest that basically the preexisting DNA arrangement was revealed by these enzymes. The fully enzyme‐treated chromosome–dye complexes showed cross‐bands. Quantitatively, the highest degree of DNA orientation across the above two chromosomes was in the range of 15–34%. This orientation fits well with a coiled coil‐DNA, which is mostly longitudinal in these chromosomes. It is suggested that this longitudinal coil may have occasional defects in DNA structure. Alternatively, this coil may terminate into regions of random DNA and unsupercoiled DNA showing lateral projections, such as loops. This alternating feature of the DNA arrangement would tandemly repeat in either metaphase and lampbrush chromosomes.
Protein conformational changes induced in human stratum corneum by organic sulfoxides: An infrared spectroscopic investigation
Authors: Oertel Richard P. 
Published: May 2005

AbstractFormation of the antiparallel‐chain β‐sheet protein conformation is induced in in vitro human stratum corneum by three homologous organic sulfoxides known to enhance skin permeability: dimethylsulfoxide (Me2SO), hexylmethylsulfoxide (HxMeSO), and decylmethylsulfoxide (DecMeSO). Me2SO and HxMeSO apparently function by displacing water molecules bound to polar protein side‐chains, whereas DecMeSO probably interacts hydrophobically with the protein. The conformational transition does not result from lipid removal. The β‐sheet protein, most likely formed in normally α‐helical portions of the intracellular keratin filaments, is reconverted to α‐helix upon rehydration of the tissue. Though neat Me2SO produces the most β‐sheet of all treatments examined, the sequence of ability to promote β‐sheet formation at the 1M level is HxMeSO > DecMeSO > Me2SO. Spectroscopic evidence is presented regarding the dependence of β‐sheet formation on sulfoxide concentration, treatment duration, pH, and tissue hydration. The relationship of this conformational change to the enhancement of skin permeability is briefly discussed. The result of sulfoxide treatment is different from results of sodium dodecylsulfate and heat treatments of stratum corneum.
Proton transfer and polarizability of hydrogen bonds in proteins coupled with conformational changes. I. Infrared investigation of poly(glutamic acid) with various N Bases
Authors: Lindemann Rainald , Zundel Georg 
Published: May 2005

AbstractThe nature of hydrogen bonds formed between carboxylic acid residues and histidine residues in proteins is studied by ir spectroscopy. Poly(glutamic acid) [(Glu)n] is investigated with various monomer N bases. The position of the proton transfer equilibrium OH…︁N ⇌ O−…︁H+N is determined considering the bands of the carboxylic group.It is shown that largely symmetrical double minimum energy surfaces are present in the OH…︁N ⇌ O−…︁H+N bonds when the pKa of the protonated N base is two values larger than that of the carboxylic groups of (Glu)n. Hence OH…︁N ⇌ O−…︁H+N bonds between glutamic and aspartic acid residues and histidine residues in proteins may be easily polarizable proton transfer hydrogen bonds. The polarizability of these bonds is one to two orders of magnitude larger than usual electron polarizabilities; therefore, these bonds strongly interact with their environment.It is demonstrated that water molecules shift these proton transfer equilibria in favor of the polar proton boundary structure. The access of water molecules to such bonds in proteins and therefore the position of this proton transfer equilibrium is dependent on conformation.The amide bands show that (Glu)n is α‐helical with all systems. The only exception is the (Glu)n‐n‐propylamine system. When this system is hydrated (Glu)n is α‐helical, too. When it is dried, however, (Glu)n forms antiparallel β‐structure. This conformational transition, dependent on degree of hydration, is reversible. An excess of n‐propylamine has the same effect on conformation as hydration.
13C and 1H NMR studies of helix‐coil transition of poly(β‐benzyl‐L‐aspartate) and poly(γ‐benzyl‐L‐glutamate): Behavior in nonprotonating solvent mixtures, and origin of solvent‐induced chemical shift
Authors: Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô 
Published: May 2005

AbstractFrom the results of 13C‐nmr measurement of poly(β‐benzyl‐L‐aspartate) and its model compounds in dimethyl sulphoxide/deuterated chloroform mixtures, it was found that the side chain of poly(β‐benzyl‐L‐aspartate) is solvated by dimethyl sulphoxide in the region more than dimethyl sulphoxide 20% (v/v), where the backbone maintains the α‐helix. The chemical shift differences in the benzyl group carbons of poly(γ‐benzyl‐L‐glutamate) (trifluoroacetic acid/deuterated chloroform) accompanied by the helix‐coil transition, originate from the interaction between the ester group of the side chain and trifluoroacetic acid. The chemical shift difference in the ester carbon is similar. On the other hand, the chemical shift differences of the side‐chain carbons in the alkyl portion (Cβ, Cγ) originate not only from the interaction between the ester group of the side chain and trifluoroacetic acid, but also from some other unknown factors. The chemical shift differences of the side‐chain carbons of poly(β‐benzyl‐L‐aspartate) originate from the interaction between the ester group of the side chain and trifluoroacetic acid.
Helix–coil stability constants for amino acids in nonaqueous solvents. Studies of random poly(γ‐benzyl‐L‐glutamate‐co‐L‐alanine) and poly(γ‐benzyl‐L‐glutamate‐co‐L‐leucine) in a mixed solvent
Authors: Sridhara S. , Ananthanarayanan V. S. , Fredrickson R. A. , Zweifel B. O. , Taylor G. T. , Scheraga H. A. 
Published: May 2005

AbstractThe host–guest technique has been applied to the determination of the helix–coil stability constants of two naturally occurring amino acids, L‐alanine and L‐leucine, in a nonaqueous solvent system. Random copolymers containing L‐alanine and L‐leucine, respectively, as guest residues and γ‐benzyl‐L‐glutamate as the host residue were synthesized. The polymers were fractionated and characterized for their amino acid content, molecular weight, and helix–coil transition behavior in a dichloroacetic acid (DCA)–1,2‐dichloroethane (DCE) mixture. Two types of helix–coil transitions were carried out on the copolymers: solvent‐induced transitions in DCA–DCE mixtures at 25°C and thermally induced transitions in a 82:18 (wt %) DCA–DCE mixture. The thermally induced transitions were analyzed by statistical mechanical methods to determine the Zimm‐Bragg parameters, σ and s, of the guest residues. The experimental data indicate that, in the nonaqueous solvent, the L‐alanine residue stabilizes the α‐helical conformation more than the L‐leucine residue does. This is in contrast to their behavior in aqueous solution, where the reverse is true. The implications of this finding for the analysis of helical structures in globular proteins are discussed.
An equilibrium folding intermediate detected in the thermal unfolding transition of ribonuclease S by circular dichroism
Authors: Labhardt A. M. 
Published: May 2005

AbstractThe thermal‐denaturation transition of ribonuclease S (RNAase S) is measured by circular dichroism at 225 nm. Only conformational transitions involving the S‐peptide–S‐protein complex are detected at this wavelength. Different pathways of thermal unfolding at high and low concentrations are apparent: at low concentrations the temperature of half‐completion of denaturation (Tm) varies with concentration. Above a total enzyme concentration of 50 μM, Tm remains constant. The observed data can be explained on the basis of a model where the association–dissociation step occurs between S‐peptide and thermally (at least partly) unfolded S‐protein. The complex as a whole undergoes a major folding–unfolding transition in the course of which the S‐peptide μ‐helix appears to be formed. The unfolded complex is well populated in the unfolding transition region for enzyme concentrations of 100 μM or more. The model succeeds in deducing thermodynamic parameters from the thermal denaturation curves in various different ways. The values thus obtained are fully self‐consistent and, moreover, consistent with the values for the apparent association constant and apparent association enthalpy as measured in enzyme‐dilution experiments and by batch calorimetry.
Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains
Authors: Hagerman Paul J. , Zimm Bruno H. 
Published: May 2005

AbstractA Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field‐free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio > 20; 0.1 < L/P < 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
Isodichroic point and the β–random coil transition of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine) in the absence of added salt
Authors: Maeda Hiroshi , Ooi Kenta 
Published: May 2005

AbstractThe β‐coil transition of poly(S‐carboxymethyl‐L‐cysteine) (poly[Cys(CH2CO2H)]) and poly(S‐carboxyethyl‐L‐cysteine) (poly[Cys((CH2)2CO2H)]) was followed by CD, potentiometric titration, and viscosity in the absence of added salt. These different properties give consistent results for poly[Cys((CH2)2CO2H)]. The CD spectra of poly[Cys(CH2CO2H)] change considerably with the degree of neutralization α even for a low‐molecular‐weight sample incapable of forming the β‐structure. Because of the superposition of this additional effect, the dependence of CD on α is inconsistent with titration data for the case of poly[Cys(CH2CO2H)], particularly when the nπ transition is used to follow the β‐coil transition. The change of CD inherent to the β‐coil transition is characterized by an isodichroic point: 215 nm for poly[Cys((CH2)2CO2H)] and 218 nm for poly[Cys(CH2CO2H)]. A criterion supporting the stacking of the pleated sheet is suggested based on the isodichroic point.
Influence of interatomic interactions on the structure and stability of polypeptides and proteins
Authors: Scheraga Harold A. 
Published: May 2005

AbstractSeveral examples are cited to demonstrate how conformational‐energy calculations provide information about the manner in which interatomic interactions influence the structure and stability of polypeptides and proteins, and of intermolecular complexes involving these same species. These include the screw senses of α‐helical polyamino acids, helix–coil transition parameters, properties of β‐bends, and the structures of gramicidin S and of synthetic poly‐(tripeptide) models of collagen. In all of these calculations, the multiple‐minimum problem has been surmounted. A description is provided as to how the multiple‐minimum problem is being approached in calculations on globular proteins. These computational methods have also been applied to protein structure refinement and to the calculation of structures of homologous proteins and of enzyme–substrate complexes.
Conformer equilibria of triostin A and its conformer‐specific interaction with nucleic acid bases
Authors: Kyogoku Yoshimasa , Higuchi Naoki , Watanabe Mayumi , Kawano Keiichi 
Published: May 2005

AbstractA quinoxaline antibiotic triostin A has a bicyclic octadepsipeptide structure. Proton and carbon‐13 nmr spectra showed the presence of two symmetrical conformations favoring polar and nonpolar solvents, respectively. They interconvert slowly on the nmr time scale, and this slow interconversion is due to the cooperative effects of the presence of the quinoxaline ring and the N‐methyl peptide bonds. Reversal of the chirality of the disulfide bond as the origin of the slow exchange was excluded by the presence of two conformers for S‐benzyltriostin A. Conformer 2, which favors the polar solvent, can form hydrogen‐bonded complexes with purine nucleoside derivatives in organic solvents, but conformer 1 does not. The binding sites were elucidated and a mode of interaction with DNA proposed.
Design of protease inhibitors
Authors: Ondetti M. A. , Cushman D. W. 
Published: May 2005

AbstractThere is a general parallelism in the strategy followed in the design of hormonal peptide analogs and protease inhibitors. However, in the latter, one more dimension has been added with the development of mechanism‐based inhibitors, a dimension that is not yet available for hormonal peptides because of the lack of knowledge about receptor mechanisms. The recently advanced concepts of transition state and bi‐product analogs have made possible the development of highly potent active‐site directed reversible protease inhibitors of great therapeutic potential.
Application of the two‐dimensional nmr techniques on a des(Ala,Gly)‐somatostatin analog
Authors: Kobayashi Yuji , Kyogoku Yoshimasa , Emura Junji , Sakakibara Shumpei 
Published: May 2005

AbstractTwo‐dimensional nmr techniques have been carried out for the peak assignment of the spectrum of a somatostatin analog. Two‐dimensional J‐resolved spectroscopy simplified the rather broad and complicated spectrum to show the center of chemical shifts of each resonance and gave information on the coupling profiles. Another technique, two‐dimensional spin‐echo correlated spectroscopy, revealed the connectivities between protons which are correlated by weak spin–spin couplings. The combination of the results of these two complementary techniques made it possible for us to assign almost all peaks of the spectrum of the 11‐residue somatostatin analog.
Raman spectra of imino acids and poly‐L‐hydroxyproline
Authors: Deveney M. J. , Walton A. G. , Koenig J. L. 
Published: May 2005

AbstractThe Raman spectra of poly‐L‐hydroxyproline in the solid state and aqueous solution have been obtained. From the spectra, the conformations of the polypeptide in the solid and aqueous solution are found to be the same. Major differences in the spectra between the solid and solution are traced to environmental influences of the pyrrolidine group as indicated by studies of the monomers. The Raman spectra of the imino acids, proline and hydroxyproline, as the dipolar ions, the hydrochlorides, and the sodium salts are also reported.
Conformation of gramicidin S
Authors: De Santis P. , Liquori A. M. 
Published: May 2005

AbstractA molecular conformation of Gramicidin S was derived on the basis of conformational calculations taking into account the available experimental data.The conformation is characterized by a dyad axis which relates the two chemically equivalent halves of the molecule and contains four hydrogen bonds; other structural features agree with experimental results. X Ray Crystallographic evidences for the relative position of the Ornithine residues is also reported which supports an important feature of the structure of Gramicidin S.
A cooperative transition between two helical conformations in a linear system: poly‐L‐proline I ⇌ II. II. Kinetic studies
Authors: Winklmair D. , Engel J. , Ganser V. 
Published: May 2005

AbstractThe conformational transition between the two helical forms I and II of poly‐L‐proline serves as an experimental model for the study of the kinetic, behavior of cooperative systems. The slow I ⇌ II conversion after a sudden perturbation of the solvent composition was followed polarimetrically. The dependence of the mean relaxation times on chain length and the degree of conversion was compared with Schwarz's theory. In addition, a description of the entire relaxation curves was possible in three special cases: all‐or‐nothing, small perturbations of the I ⇌ II equilibrium in long chains, and conversions which start off with molecules completely in one or the other conformational state. The mathematical model on which the theory is based contains only one more adjustable parameter than the equilibrium model, but it adapts to the experimental results surprisingly well. The present kinetic results and equilibrium measurements on this system are described by the same values of those parameters which are common to both models. The found value of the rate constant of the propagation step, i.e. the cis ⇌ trans isomerization of a peptide bond at an existing I–II junction, agrees with the rate of isomerization in N,N‐dimethylacetamide reported in the literature. The rate of nucleation is up to 105 times smaller than the rate of propagation.
Model of the orientation symmetry of water molecules in biopolymers (by NMR Spectra)
Authors: Khanagov A. A. 
Published: May 2005

AbstractSpectra of proton and deuteron magnetic resonance of water molecules in oriented biopolymer samples (collagen, DNA, cellulose) are interpreted on the basis of a model of molecular Schottki‐type diffusion. The presence of narrow splittings are shown to be the result of slight distortions of “ideal” symmetry of orientations of p‐p and O‐D vectors, corresponding to the point symmetry group of a tetrahedron, one of whose C3‐axes is oriented along the fiber axis.
Molecular beams of macroions. III. Zein and polyvinylpyrrolidone
Authors: Clegg G. A. , Dole M. 
Published: May 2005

AbstractA 95% ethanol solution of the prolamin zein and of the synthetic polymer polyvinyl‐pyrrolidone (PVP) can be successfully electrosprayed and a molecular beam, containing ions of these substances in nitrogen carrier gas, formed. Similarly to polystyrene in benzene–acetone solvent, negative beams of zein and PVP have more substructure than beams containing positive ions. The results indicate considerable aggregation in the beam, possibly of six molecular units per aggregate, in addition to the singly charged single molecules.
Conformation of carboxymethyl amylose in aqueous solutions
Authors: Patel J. R. , Patel R. D. 
Published: May 2005

AbstractIntrinsic viscosity and specific optical rotation measurements have been carried out for Carboxymethyl amylose (CMA) solutions in 0.15M sodium chloride at various pH values. Potentiometric titrations of CMA have been performed at various polymer concentrations as well as in presence of different divalent cations. The amount of divalent cation (Ni+2) bound to CMA has been determined by using a new method af analysis based on polyelectrolyte theory. Finally from the results it is shown that CMA may exist as a random coil in solution.
Relative effects of primary and tertiary structure on helix formation in myoglobin and α‐lactalbumin
Authors: Hermans Jan , Puett David 
Published: May 2005

AbstractWe have determined the ultraviolet optical rotatory properties of the cyanogen bromide peptides of myoglobin and reduced, S‐carboxymethylated α‐lactalbumin in both aqueous and aqueous alcohol solutions. Similar measurements were also made on the tryptic digests of apomyoglobin. In aqueous solutions the α‐helicity of the various peptides was between 5 and 15%, while in concentrated ethanol solutions the helicity could be increased significantly, but never to more than about 55%. The maximum helicity attained by the various peptides at high ethanol concentrations, as well as the cooperativity of the coil‐to‐helix transition (reflected in the slope at the steep portion of the helicity‐alcohol concentration curves), does not depend on the number of residues in the peptide in the manner expected. We have used a model which treats proline residues as absolute helix breakers, thus introducing the concept of effective chain length. By applying available theories of helix–coil transitions of short‐chain polypeptides to this model, one can satisfactorily describe most of the data on the myoglobin peptides. Significantly, it was possible to predict the helicity of acid‐denatured apomyoglobin from the behavior of the shorter fragments. By using the model, the peptides were found to have an equal intrinsic helix‐forming tendency which, with only two exceptions, was not raised by the formation of tertiary structure. The exceptions were apomyoglobin and peptide 56–131, which show, respectively, a considerable and a very small helicity attributable to tertiary structure formation in water at neutral pH. These results agree with the demonstrated absence of stable intermediates in protein unfolding equilibria. The results offer a further correlation between helical structure in the native molecule and the tendency to helix formation in isolated peptides. The results do not support the hypothesis that small folded regions are responsible for initiating the folding of the molecule, and an alternate description is proposed which envisages approximately half‐folded structures at the rate limiting step in the folding reaction. Helix formation in the 33‐residue C‐terminal peptide of α‐lactalbumin was found to be as easy as in the myoglobin peptides. If the proposed structural analogy between lysozyme and α‐lactalbumin is correct, then this is a case where helix formation occurs in a peptide which is not helical in the native protein. On the other hand, an α‐lactalbumin peptide corresponding to a region which has β‐structure in lysozyme did not lend to form α‐helices.
Interaction of magnesium ions with poly A and poly U
Authors: Willemsen A. M. , Van Os G. A. J. 
Published: May 2005

AbstractThe binding of Mg++ to poly A and poly U has been measured quantitatively by using the metallochromic indicator calmagite. The method is described in detail. It is shown that there is electrostatic interaction between the binding sites, viz., the phosphate groups, and the intrinsic association constant, for the specific binding can be determined. After extrapolation to zero ionic strength we find that, for the binding of Mg++ to poly A, kint = 4 × 104 and for that, to poly U, kint = 3 × 104. The intrinsic enthalpy of association is negative. The effect of Mg++ on the secondary structure of poly A and poly U has been studied by measuring the ultraviolet absorbance, optical rotatory dispersion and viscosity as a function of the amount of added Mg++ ions. It was found that Mg++ promotes the formation of a more ordered secondary structure by neutralizing or screening the negative charges. It is concluded from the absorbance measurements that for poly A at pH ⩾ 7 and for poly U at pH >xs 9 this ordering involves stacking of the bases. Likewise, in solutions of UDP with a pH around 10, base stacking occurs on addition of Mg++.