bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of alcohols with proteins
Authors: Bull Henry B. , Breese Keith 
Published: December 2004

AbstractThe kinetics of denaturation of egg albumin have been determined for methanol, ethanol, propanol, and butanol. The reactions are first order in respect to protein but between 11th and 18th order for the alcohols. The denaturation reaction is characterized by a large temperature coefficient with little or no dependence on pH. There is a marked change of pH when proteins are denatured. A series of eight proteins has been studied. There is surprisingly little difference in susceptibility to alcohol denaturation between the various proteins. Methanol, ethanol, propanol, and butanol are strongly bound to egg albumin—butanol being the most strongly bound. The binding of alcohol is probably accompanied by protein dehydration. The polyhydric alcohols' behavior is much different. These alcohols do not denature proteins and the protein is hydrated. Sucrose produces the greatest degree of hydration.
The effect of homologous amino acid replacement on the conformation of oligopeptides. II. Synthesis of co‐oligopeptides containing methionine and glycine
Authors: Champi Jim , Steinfeld Alvin S. , Naider Fred , Becker Jeffrey M. 
Published: December 2004

AbstractThe synthess of 18 co‐oligopeptides of L‐methionine and glycine is reported. A series of oligomers, Boc‐Gly‐Metn‐OMe (n = 1–6), and six hexamers‐containing five methionyl and one glycyl residue were synthesized using the mixed anhydride procedure. Polarimetric studies give evidence that oligomers in the Boc‐Gly‐Metn‐Ome series are essentially disordered in hexafluoroacetone sesquihydrate but begin forming secondry structures at n > 4 in trifluorethanol. Difference in the molar rotation values found for the six hexamers in hexafluoroacetone sesquihydrate may indicate that these compounds, while primirily disordered, are present in slightly different conformations.
The effect of homologos amini acid replacement on the conformation of oligopeptides. III. CD studies on co‐oligopeptides of methionine and valine or methionine and glycine in organic solution
Authors: Naider F. , Becker J. M. , Ribeiro A. , Goodman M. 
Published: December 2004

AbstractA conformational analyis of co‐ologopeptides containing methionine and valine or methionine and glycine was carried out using circular dichrosim. The oligopeptides containing valine and methionine (dimer to hexamer) are disorder in hexafluoropropane diol·0.5 H2O and trimethyl phospate but become helical in trifluoroethanol at the heptamer. The CD spectra for hesamers and heptamers containing methionine or methionine and one valine give evidience that one valyl residue can be inserted into these peptides wothout affecting their secondry structure. Co‐oligomethionines. The effect of a glycyl residue are generally less ordered than the analogous homo‐oligomethionines. The effect of a glycl residue on the structure of the longer oligopeptides depends on its position in the chain. When inserted in the center of a hexamer or heptamer, the single glycyl residue destabilizes the ordered secondry structures in solution. Finally, evidence is presented that the CD patterns observed for various pentamers and hexamers are consistent with some order at these chain lenghts.
A model for the interrelationship between asymmetric interbase hydrogen bonding and base–base stacking in hemiprotonated polyribocytidylic acid: Crystal structure of 1‐methylcytosine hemihydroiodide hemihydrate
Authors: Kistemacher Thomas J. , Rossi Miriam , Marzilli Luigi G. 
Published: December 2004

AbstractAn x‐ray structural study of the 1‐methylcytosine H+ complex reveals asymmetrically hydrogen‐bonded dimers which are further stacked such that the molecular overlaps are between charged and neutral bases. This study supports the assignment of the asymmetry in the interbase hydrogen bonding in the cytidine–cytidine H+ hydrogen‐bonded complex. Furthermore, it is suggested that hemiprotonated, helical polyribocytidylic acid has as its translational repeat unit a set of highly stacked pairs of asymmetrically hydrogenbonded bases. The asymmetry in the interbase hydrogen bonding is stimulated, at least in part, by base‐stacking considerations.
The Raman spectra of Bence‐Jones proteins. Disulfide stretching frequencies and dependence of Raman intensity of tryptophan residues on their environments
Authors: Kitagawa T. , Azuma T. , Hamaguchi K. 
Published: December 2004

AbstractThe Raman spectra of Bence‐Jones proteins (BJP) were measured for their native and denatured states. All of the native BJPs investigated gave amide I at 1670–1675 cm−1 and amide III at 1242–1246 cm−1. Although the amide I was shifted to 1667 cm−1 upon the LiBr, acid, and thermal denaturation, as expected, the amide III frequency was unaltered, indicating that the antiparallel β‐ and disordered structures of BJP provide amide III at almost the same frequencies. The intensity of the 880‐cm−1 line of native BJP was relatively intense compared with that of amino acid mixed solution in which the mole ratios of Trp, Phe, and Tyr were adjusted to reproduce the corresponding ratios of BJP. However, the intensity was evidently reduced upon LiBr, acid, and thermal denaturation, approaching that of the amino acid mixture. Thus, the intensity of the 880‐cm−1 line is proposed as a practical probe for the environment of Trp residues. The pH dependence of the intensity of the 880‐cm−1 line suggests that one of two buried Trp residues is exposed between pH 4 and 3.2 and the other between pH 3.2 and 1.4. The variable fragment (VL) of BJP (Tod) exhibited a SS stretching Raman line at 525 cm−1. Provided that the crystallographic data of the VL of BJP is applicable to VL of BJP (Tod), the 525 cm−1 of the SS stretching frequency should be assigned to a TGG conformation of linkage, but not to the AGT or AGG conformation. This supports Sugeta's model rather than Scheraga's model.
1H‐ and 13C‐NMR studies of N‐acetyl‐L‐alanine methylester and N‐acetyl‐L‐alanine methylamide. I. Self‐association
Authors: Asakura Tetsuo , Kamio Masaru , Nishioka Atsuo 
Published: December 2004

AbstractThe 1H‐ and 13C‐NMR spectra of N‐acetyl‐L‐alanine methylester and N‐acetyl‐L‐alanine methylamide were measured to examine the modes of self‐association of these molecules in solution. The different dilution shifts between these molecules seem to correspond to the difference in the associated state for each molecule. Consequently, for the former molecule, a dimer model forming the intermolecular hydrogen bond through Ala NH hydrogen atom in one molecule to Ala CO oxygen atom in another molecule was proposed. Another dimer model, which coincides with that proposed recently by Neel and coworkers, was proposed for the latter molecule. This second dimer model forms an intermolecular hydrogen bond through the NH of the N‐methylamide group in one molecule to the acetyl CO in another molecule.
Association studies of N‐acetyl‐amino acid N,N‐dimethylamides in carbon tetrachloride
Authors: Mizuno Kazuko , Nishio Shigenori , Shindo Yohji 
Published: December 2004

AbstractThe self‐association of N‐acetylglycine N,N‐dimethylamide, N‐acetyl‐L‐valine N,N‐dimethylamide, and N‐acetyl‐L‐phenylalanine N,N‐dimethylamide in carbon tetrachloride was investigated by using ir and 1H‐nmr methods. It was concluded from ir measurements that the associated species is the dimer formed as a result of the simultaneous formation of two intermolecular hydrogen bonds. This is supported by the results of 1H‐nmr measurements. Thermodynamic quantities for the association were determined from the temperature and concentration dependence of the NH proton chemical shifts of the sample solutions. Compared with the Gly derivative, L‐Val and L‐Phe derivatives have larger values of −ΔH for association, which shows good correlation with ΔvNH values, the difference between the maxima of the monomer and dimer bands, obtained from ir spectra. This is due to the less stable monomer conformation and to the stronger intermolecular hydrogen bonding of the dimers in L‐Val and L‐Phe derivatives. The line shapes of both methyl proton resonances of L‐Val residue and methylene proton resonances of L‐Phe residue were found to vary with concentration and temperature of the sample solutions. These data indicate that the rotation about the Cα—Cβ bond is restricted by the steric hindrance present in the associated dimers. All these experimental results can be related to the fact that L‐Val and L‐Phe derivatives have a warped framework because of the bulky side chains, whereas the Gly derivative has a planar framework.
Salt‐concentration dependence of melting profiles of lambda phage DNAs: evidence for long‐range interactions and pronounced end effects
Authors: Gotoh Osamu , Wada Akiyoshi , Yabuki Sadato 
Published: December 2004

AbstractMelting profiles of DNAs from wild‐type λ phage and a deletion mutant phage λb2 were examined in a wide range of salt concentration. The fine structure of the melting profiles changed sharply with salt concentration, especially in the range [Na+] ⩽ 10 mM. A comparison of the melting profiles between the wild‐type and the deletion mutant DNAs provided good evidence for extremely high melting cooperativity under low salt conditions, which is clearly manifested as the long‐range interactions and the pronounced end effects; a large melting peak appeared as a result of the b2 deletion without any inserted sequence in the salt range [Na+] ⩽ 2.8 mM. It was also suggested that in the further reduced salt range [Na+] ⩽ 2.0 mM, melting of a λ DNA molecule starts from its right end rather than the most (A + T)‐rich central region. The molecular basis of the high melting cooperativity at low salt concentrations can be explained in terms of the increased free energy associated with loop formation in the double‐helical structure of DNA.
The role of water in the crystal structure of N‐acetyl‐L‐4‐hydroxyproline
Authors: Hospital M. , Courseille C. , Leroy F. , Roques B. P. 
Published: December 2004

AbstractThe crystal structure of N‐acetyl‐L‐4‐hydroxyproline (Hyp) was determined by direct methods. (The crystal is orthorhombic with the space group P212121.) The acetyl group is in the trans conformation and the pyrrolidine ring puckers at Cγ (CsCγ envelope), as in most Hyp residues. According to the rotation angle ψ = −30°, the N‐acetyl‐L‐4Hyp has the same conformation as an α‐helix of prolyl residues. The crystal packing is stabilized by hydrogen bonds between three different molecules and the same molecule of water. One of the water bridges involves the carbonyl of the N‐acetyl group of one molecule and the hydrogen atom of the 4‐OH group of another. Such an arrangement has been proposed to explain the high stability of (Gly‐L‐Pro‐L‐4Hyp)n. A second bridge involves the two hydrogens of the water molecule and the carbonyl groups of two neighbouring molecules, as already proposed in a dihydrated model of collagen. These experimental features, which are discussed in relation to the different models of collagen, allow us to propose an hypothetical arrangement for the water molecule which is strongly retained in the triple helix of (Gly‐L‐Pro‐L‐4Hyp)n.
Energetics of intercalation specificity. I. Backbone unwinding
Authors: Ornstein Rick L. , Rein Robert 
Published: December 2004

AbstractAn empirical partitioned‐potential function with optimized parameters was employed to investigate the basis of intercalation specificity recently observed by experimental techniques. The nature of this specificity is discussed in terms of component interactions for all non‐truncated complementary dinucleoside triphosphate mini‐ (or miniature) helices. Our calculations agree with available evidence indicating the preference of Pyr(3′‐5′)Pur sequences over Pur(3′‐5′)Pyr sequences to change from the B‐DNA to the intercalated conformation. Base–base (stacking) and base–phosphate interactions control the specificity. The extent of net electrostatic charge on the phosphate groups play an important but limited role in establishing the observed specificity. These results should apply for the class of aromatic agents involved in nonspecific intercalation with nucleic acids but not necessarily for aromatic agents involved in specific reactions with a particular nucleotide base.
Influence of hydration on the conformational stability and formation of bends in terminally blocked dipeptides
Authors: Hodes Zachary I. , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe conformations of 23 terminally blocked dipeptide sequences were examined by conformational energy calculations that included the effects of the aqueous solvent. Starting structures were derived from combinations of minimum‐energy conformations of hydrated single residues. Their conformational energies were then minimized using the ECEPP potential (Empirical Conformational Energy Program for Peptides) with hydration included. Short‐range interactions dominate in stabilizing the conformations of the hydrated dipeptides. Differences between conformational stabilities of hydrated and unhydrated dipeptides in many cases are due to the competition of solute–water and intramolecular hydrogen bonds. In other cases, perturbation of the hydration shell of the solute by close approach of solute atoms alters conformational preferences. Probabilities of formation of bends were calculated and compared to the corresponding quantities for unhydrated dipeptides and to those calculated from x‐ray structures. For bends in dipeptides containing two nonpolar amino acids, computations omitting hydration yield better results. However, better agreement with experimental (x‐ray) bend probabilities for dipeptides containing glycine or polar amino acids is obtained only in some sequences when hydration is included. The results are rationalized by the observation that, in proteins, bends containing nonpolar sequences occur on the inside, shielded from the solvent. Bends containing glycine or polar amino acids occur frequently on the surface of the protein, but they are not completely hydrated.
Effect of inhibitor complex formation on the hydration properties of α‐chymotrypsin. Changes induced in protein hydration by tosylation of the native enzyme
Authors: Lüscher Madeleine , Schindler Paul , Rüegg Max , Rottenberg Max 
Published: December 2004

AbstractThe effect of enzyme‐inhibitor complex formation on the hydration properties of the macromolecular moiety was investigated on the model system of α‐chymotrypsin and its Ser‐195 tosyl derivative. The primary (A‐shell) hydration of the native and modified enzyme was compared by sorption measurements. The secondary (B‐shell) hydration water was investigated by differential scanning calorimetry. Tosylation is known to induce pronounced conformational changes in the chymotrypsin molecule. These structural modifications have the following effects on the hydration of the native enzyme.The water binding capacity of the protein surface is significantly increased, as shown by both the calorimetric and the sorption results. The amount of unfreezable water of primary hydration is increased by 50 mol H2O/mol chymotrypsin.The heats (ΔH) and entropies (ΔS) of the interaction of water with chymotrypsin are strongly reduced in the modified enzyme. This effect is interpretable by a reduction of the H bonding potential of the protein surface. Parallel to this decrease in δH, the heats of fusion of the secondary hydration water (Qfus) are significantly increased by tosylation (Qfus = 256.2 ± 7.8 and 294.2 ± 4.8 J g−1 H2O for the native and the tosylated enzyme, respectively). This increase in Qfus reflects an increase in the extent of H bonding in the B‐shell hydration sphere.These changes in the hydration of the native enzyme, associated with the reaction: native chymotrypsin → tosylchymotrypsin, are interpreted by cooperative phase transitions of water molecules in the primary and secondary hydration water. One of these transitions was found to exhibit a significant, linear enthalpy–entropy compensation effect. The compensation temperature \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} is 290.7 ± 2.8°K. This \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} value agrees well with compensation temperatures reported in the literature for a series of biochemical reactions in aqueous solution (250–320° K). This agreement in \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} may point to a common source of both compensation phenomena.
Electric field effect on the helix–coil transition of poly(L‐α,γ‐diaminobutyric acid hydrochloride) in methanol/water mixtures
Authors: Fujimori Mitsuo , Kikuchi Kazuo , Yoshioka Koshiro , Kubota Shigeo 
Published: December 2004

AbstractTransient electric birefringence of poly(L‐α,γ‐diaminobutyric acid hydrochloride) in methanol/water mixtures has been measured over a wide range of field strengths and solvent compositions and at different polymer concentrations and temperatures. The molar ellipticity at 222 nm and the specific Kerr constant underwent an abrupt change between 75 and 80 vol % methanol at 25°C, accompanied by a solvent‐induced helix–coil transition. Anomalous birefringence transients were observed between 78 and 80 vol% methanol above threshold field strengths. The double logarithmic plots of the steady‐state specific birefringence versus the square of field strength for different solvent compositions and polymer concentrations could be superimposed by shifting them horizontally along the abscissa and vertically along the ordinate except for the range where anomalous transients were observed. The threshold field strength could be estimated from the point at which a downward deviation occurred. It increased with increasing polymer concentration and with increasing methanol content on the verge of the transition region. The results were interpreted as indicating that a conformational change from the charged helix to the charged coil is induced by high fields in this system, as in the case of poly(L‐lysine hydrobromide) in methanol/water mixtures.
Circular dichroism of complexes of NADH with self‐associating bovine liver glutamate dehydrogenase
Authors: Zeiri Leila , Reisler Emil 
Published: December 2004

AbstractThe CD of GDH–NADH complexes was measured in order to reexamine the binding of coenzyme to GDH. The existence of two distinct Cotton effects associated with two separate NADH binding sites/subunit was confirmed with native, polymerizing and crosslinked, unpolymerizing enzyme. CD titration of the high‐affinity NADH sites revealed significant dependence of the optical activity of the bound coenzyme on the state of protein association. Molar ellipticity of bound NADH decreased with the increasing degree of polymerization of GDH. It is suggested that the high‐affinity NADH sites are loacted at or near the association interface. Binding of NADH to the low‐affinity sites, in the presence of GTP, leads to an inversion of the CD spectrum of GDH–NADH complexes. This inversion is not related to the polymerization of GDH. However, for proper analysis of the CD of NADH bound to the low‐affinity sites, a correction for the effect of polymerization on the optical activity of NADH bound to the high‐affinity sites is required.
Nematic polymers: Excluded‐volume effects
Authors: Kim Y. H. , Pincus P. 
Published: December 2004

AbstractWe present a theoretical model which describes a cooperative helix–coil liquid‐crystal phase transition. We show that this model predicts a first‐order phase transition where certain types of chainlike macromolecules in solution make a transition from a nearly coiled to a nearly rigid conformation accompanied by a simultaneous development of long‐range nematic‐type liquid crystalline orientational order. From this model, the phase boundaries between nematic and isotropic phases are obtained as functions of concentration of macromolecules and of other physical parameters.
Dielectric relaxation of DNA solutions. III. Effects of DNA concentration, protein contamination, and mixed solvents
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku 
Published: December 2004

AbstractAs a continuation of previous papers [Biopolymers (1976) 15, 879; (1978) 17, 1508], the low‐frequency dielectric relaxation of DNA solutions was studied with a four‐electrode cell and the simultaneous two‐frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration Cp, and the dielectric increment is proportional to Cp. The critical concentration is approximately 0.02% of DNA for molecular weight Mr 2 × 106 and 0.2% for Mr 4.5 × 105 in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi‐permanent dipole due to counterion fluctuation.
Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA
Authors: Wilson W. David , Lopp Irene G. 
Published: December 2004

AbstractThe interaction of quinacrine with calf thymus DNA was monitored at several different ionic strengths using spectrophotometric and equilibrium dialysis techniques. The binding results can be explained, assuming each base pair is a potential binding site, using a model containing two negative cooperative effects: (1) ligand exclusion at binding sites adjacent to a filled binding site and (2) ligand–ligand negative cooperativity at adjacent filled binding sites. The logarithm of the observed equilibrium constant (Kobs) determined by this model varies linearily with log[Na+], as predicted by the ion condensation theory for polyelectrolytes. When the log Kobs plot is correlated for sodium release by DNA in the intercalation conformational change, the predicted number of ion pairs between the ligand and DNA is approximately two, as expected for the quinacrine dication. Even though Kobs depends strongly on ionic strength, the ligand negative cooperativity parameter ω was found to be indpendent of ionic strength within experimental error. This finding is also in agreement with the ion condensation theory, which predicts a relatively constant amount of condensed counterion on the DNA double helix over this ionic strength range. Drugs would, therefore, experience a relatively constant ionic environment when complexed to DNA even though the ionic conditions of the solvent could change considerably.