bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics of ferrocytochrome c: Time dependence of the atomic displacements
Authors: Morgan John D. , Andrew McCammon J. , Northrup Scott H. 
Published: May 2005

AbstractThe thermal motions of the atoms in a dynamical simulation of ferrocytochrome c are geometrically decomposed into local and highly collective components, and the contributions of these components to the net motion are determined for different intervals of time. It is found that the atomic displacement magnitudes and anisotropies are governed by local motions for times <10−12s, but that the highly collective motions tend to be dominant at longer times. Variations in this behavior are noted among different groups of atoms. Orientational correlations between the preferred directions of atomic displacement and elements of the protein structure are analyzed as a function of time scale. Finally, several sinificant implications of these results with respect to protein structure and function are considered.
Effects of calcium and manganese ions on the helix–coil transition of DNA
Authors: Blagoi Yu. P. , Sorokin V. A. , Valeev V. A. , Gladchenko G. O. 
Published: May 2005

AbstractThe thermal denaturation method was employed to study the effect of Ca2+ and Mn2+ ions on the DNA helix–coil transition parameters at Na+ concentrations of 10−3–10−1M. At low ion concentrations, thermal stability increases, the melting range passes through a maximum, and the denaturation curves become asymmetric. These changes are quantitatively similar for Mn2+ and Ca2+ ions. With a further increase in the concentration of bivalent ions, the conformational transition temperatures pass through a maximum, and the melting range first tends to saturation and then rapidly decreases to 1–2°C. The Mn2+ concentrations, at which the above effects occur, are an order of magnitude lower than the Ca2+ concentrations. Comparison of experimental results and calculation in terms of the ligand theory permitted estimation of binding constants characterizing association between Mn2+ and Ca2+ ions and bases of native and denatured DNA. We show that, unlike the interaction with phosphates, bivalent ion–DNA base binding is weakly dependent on monovalent ion concentration in the solution.
Solution properties of porcine submaxillary mucin
Authors: Shogren R. , Jamieson A. M. , Blackwell J. , Cheng P. W. , Dearborn D. G. , Boat T. F. 
Published: May 2005

AbstractPorcine submaxillary mucin (PSM) is a glycoprotein composed of a protein core and frequent, short oligosaccharide side chains. We report static and dynamic light scattering experiments and intrinsic viscosities for PSM in aqueous solvent systems. In 0.1M NaCl solution, the data suggest PSM exists as large, internally branched, highly hydrated, polydisperse aggregates that slowly dissociate to give a stable species of weight‐average molecular weight (Mw) 7.4 × 106. In 6M GdnHCl solution, the noncovalent bonds between PSM molecules are broken, giving a highly elongated molecule of Mw = 2.0 × 106. The irreversible nature of this dissociation suggests that the forces that stabilize the native aggregates of PSM in 0.1M NaCl are specific in nature. On reduction of PSM with mercaptoethanol, the polydispersity decreases and Mw also decreases to 9 × 105. A discrete change is observed in the solution properties of PSM in 0.1M NaCl at a concentration of 2mg/mL, manifested by a sudden decrease in the translational diffusion coefficient, an increase in viscosity number, and a decrease in slope of the osmotic compressibility. We tentatively propose that a weak and reversible secondary association process occurs at this concentration, although a purely hydrodynamic interaction cannot be ruled out.
Relaxation processes on a picosecond time scale in hemoglobin and poly(L‐alanine) observed by millimeter‐wave spectroscopy
Authors: Genzel L. , Kremer F. , Poglitsch A. , Bechtold G. 
Published: May 2005

AbstractBroadband measurements of the millimeter‐wave and far‐ir absorption (10–104 GHz) of lyophilized hemoglobin are reported. Additionally, the absorption of poly(L‐alanine) and crystalline L‐alanine at 70 GHz was measured for comparison. All measurements were extended over the temperature range from liquid helium to room temperature. For the millimeter range, this was attained by using the novel oversized‐cavity technique. It was found that the millimeter‐wave absorption of the materials increased nearly exponentially with temperature and increased as ν1.2–ν2 with frequency. The far‐ir absorption of hemoglobin showed broadbands with almost no temperature dependence. The frequency and temperature dependence of the millimeter‐wave absorption is quantitatively described as due to three distinct relaxation processes on a picosecond time scale occurring in asymmetric double‐well potentials. These processes are most probably assigned to the NH ⃛OC hydrogen bonds of the peptide backbone.
Kinetic studies of the interaction of methyl orange with poly(L‐lysine) by stopped‐flow with circular dichroism detection
Authors: Murakami Kiyofumi , Sano Takayuki , Kure Naohisa , Ishii Katsushi , Yasunaga Tatsuya 
Published: May 2005

AbstractThe interaction of methyl orange with poly(L‐lysine) was studied kinetically by the stopped‐flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer‐to‐dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped‐flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L‐lysine), the second and third process were ascribed to the intramolecular reaction of the polymer–dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer–dye complex. The origin of the stacking of methyl orange on poly(L‐lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.
Counterion binding and hydration of hyaluronate and chondroitin in solution: An 17O, 23Na, and 25Mg nuclear‐magnetic‐relaxation study
Authors: Piculell Lennart , Lindman Björn , Einarsson Roland 
Published: May 2005

AbstractNuclear magnetic relaxation rates of H217O, 23Na+, and 25Mg2+ have been measured in aqueous hyaluronate solutions. The dependence on solution pH of the relaxation rates has been investigated, as well as the competition behavior of Na+ with Ca2+ and Mg2+. H217O and 23Na+ relaxation rates in chondroitin and hyaluronate solutions have been compared in the interval, 2 ≲ pH ≲ 12.5. The ion binding of hyaluronate can be fully accounted for by Coulomb interactions, with no need to involve chemical specificity. The hydration is only slighly pH dependent, and is comparable in magnitude to hydration of synthetic polyelectrolytes and monosaccharides. Ion‐binding and hydration properties of hyaluronate and chondroitin are quite similar, except at elevated pH. At alkaline pH, an increase in charge density with pH is seen in hyaluronate and, to a much lesser degree, in chondroitin, possibly due to the titration of hydroxy groups. H217O data indicate an alkali‐induced transition in both glycosaminoglycans.
Hetero‐α‐helical, two‐chain, coiled coils: αβ hybrid tropomysin
Authors: Holtzer Marilyn Emerson , Breiner Teresa , Holtzer Alfred 
Published: May 2005

AbstractThe nature of the interhelix interaction in two‐chain, α‐helical, coiled coils is studied by experiments on the formation of hydrid molecules in which one helical chain is an α‐tropomyosin and the other a β‐tropomoysin. By means of a recently developed assay, the population of heterohelical (i.e., αβ hybrid) molecules relative to their homohelical (αα and ββ) parent species is determined under a variety of conditions, both equilibrium and nonequilibrium. It is found that mixed intact αα and ββ molecules do not form hybrid species in detectible amounts even after incubation at room temperature (or below) for periods of over one week. That the lack of αβ species in this “native‐exchange” system is a result of a kinetic barrier is evident from experiments involving a thermal denaturation–renaturation cycle in which the largely dissociated, unfolded chains at higher temperature are annealed to benign temperatures over a period of 6 h, thus assuring an equilibrium population of two‐chain species. In the resulting equilibrium state, the αβ population is one‐half the total, indicating that recombination is random. Furthermore, this same (equilibrium) state is reached if the separated, mostly unfolded chains are renatured by a rapid (∼ 40 s) quench to benign temperatures. Some implications of these results for the thermodynamics of interhelix interation, for kinetics of chain dissociation and recombination, and for in vivo genesis of two‐chain coiled coils are discussed.
Head‐to‐head dimerization of parallel β helices in a synthetic model of the linear gramicidins
Authors: Lorenzi Gian Paolo , Gerber Christoph , Jäckle Hans 
Published: May 2005

AbstractIn chloroform solution, the D,L‐alternating stereo‐co‐oligopeptide HCO‐L‐Phe‐(D‐Phe‐L‐Phe)3‐OMe (I) forms three major species, two of which are dimeric and one tetrameric. One of the two dimeric species gives a specific set of 1H‐nmr signals at 25°C; the other, together with the tetrameric species, gives another set of resonance signals. In a carbon tetrachloride or cyclohexane solution at 25°C, I forms virtually only the tetrameric species. From the nmr data, it can be shown that the dimeric and tetrameric species, that are in rapid equilibrium with each other in chloroform solutions, are a right‐handed ↑↑β5.6 helical dimer and the head‐to‐head (formyl‐ends‐to‐formyl‐ends) dimerization product of this dimer. It is suggested that the linear gramicidins may also form head‐to‐head dimers of parallel β helices, as observed for the model oligopeptide I.
Determination of peptide conformation via vibrational coupling: Application to diastereoisomeric alanyl dipeptides
Authors: Diem Max , Oboodi M. Reza , Alva Carlos 
Published: May 2005

AbstractSolution‐phase Raman spectra of diastereomeric alanyl dipeptides, D‐Ala‐L‐Ala and L‐Ala‐L‐Ala, and various mono‐ and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled‐oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.
Identification of a new electronic transition in the Z form of poly(dG‐dC)·poly(dG‐dc) by infrared absorption and resonance Raman spectroscopy
Authors: Chinsky L. , Jolles B. , Laigle A. , Turpin P. Y. , Taboury J. , Taillandier E. 
Published: May 2005

AbstractInfrared absorption and resonance Raman spectroscopy (RRS) are used to study poly(dG‐dC)·poly(dG‐dC) in two different forms: the right‐handed B form at low ionic strength and the left‐handed Z form at high ionic strength. The existence of a new electronic absorption band in the 290–300‐nm region is evidenced by uv RRS studies of the Z form at different wavelengths of excitation. Infrared absorption spectra prove that this new electronic band is polarized perpendicularly to the cytosine plane. The possibility of a nπ* character of this transition moment is discussed.
Theoretical studies on the conformation of saccharides. VIII. Solvent effect on the stability of β‐cellobiose conformers
Authors: Tvaroška Igor 
Published: May 2005

AbstractThe conformational equilibria of five β‐cellobiose conformers have been studied theoretically in 10 solvents. The stability of the conformers in dilute solution has been compared by using the method that has already been tested for 2‐methoxytetrahydropyran, β‐maltose, and D‐glucose. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from the properties of the solute calculated by the PCILO quantum‐chemical method and physicochemical properties of the solvents. The calculated abundance of conformers depends on the solvent (e.g., in dioxane C1:C2:C3:C4:C5 = 60.0:34.1:2.9:2.0:1.0; in dimethylsulfoxide, 75.5:22.1:1.8:0.5:0.2; and in water, 82.2:16.2:1.3:0.2:0.1). The results obtained indicate that the preponderant conformer in the aqueous solution is similar to the one adopted by β‐cellobiose in the crystalline form. The role of individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and nmr parameters have been calculated and compared with observable properties. The marked differences observed between solvent‐induced conformational changes for β‐cellobiose and β‐maltose have been discussed from the viewpoint of the solubility of the cellulose.
Molecular theory of the helix–coil transition in polyamino acids. V. Explanation of the different conformational behavior of valine, isoleucine, and leucine in aqueous solution
Authors: Gō Mitiko , Scheraga Harold A. 
Published: May 2005

AbstractEven though poly(L‐valine) and poly(L‐isoleucine) both contain residues that are branched at their β‐carbon atoms, they exhibit a different behavior of their Zimm‐Bragg helix‐growth parameter s in aqueous solution. This quantity increases with temperature for poly(L‐valine) but decreases for poly(L‐isoleucine). The origin of this behavioral difference was examined by computing theoretical values of s versus temperature from interatomic interaction energies, taking solvent (hydrophobic and hydrophilic) effects into account. The calculated s versus temperature curves for both homopolymers are consistent with the observed experimental behavior. The two homopolymers behave differently because of differences in the change in the number of hydration‐shell water molecules accompanying their helix–coil transitions. The larger isoleucine side chains are more crowded together in both the α‐helical and coil forms than are those of valine. Therefore, there is a smaller change in hydration of the isoleucine side chains compared to that of the valine side chains in the helix–coil transition. By analyzing the effects of hydration on the s versus temperature curves, it is possible to account also for the experimental curve for poly(L‐leucine), which exhibits an intermediate behavior between those for poly(L‐valine) and poly(L‐isoleucine).
Theoretical studies on protein–nucleic acid interactions. III. Stacking of aromatic amino acids with bases and base pairs of nucleic acids
Authors: Kumar N. Vasant , Govil Girjesh 
Published: May 2005

AbstractStacking of aromatic amino acids tryptophan (Trp), tyrosine (Tyr), phenylalanine (Phe), and histidine (His) with bases and base pairs of nucleic acids has been studied. Stacking energies of the amino acid–base (or base pair) complexes have been calculated by second‐order perturbation theory. Our results show that, in general, the predominant contribution to the total stacking energy comes from the dispersion terms. In these cases, repulsion energy is greater than the sum of electrostatic and polarization energies. In contrast to this, interaction of histidine with the bases and base pairs is largely Coulombic in nature. The complexes of guanine with aromatic amino acids are more stable than the corresponding complexes of adenine. Among pyrimidines, cytosine forms the most stable complexes with the aromatic amino acids. The G · C base pair has the highest affinity with aromatic amino acids among various sets of base pairs. Optimized geometries of the stacked complexes show that the aromatic moieties overlap only partially. The heteroatom of one residue generally overlaps with the other aromatic moiety. There is a considerable degree of configurational freedom in the stacked geometries. The role of stacking in specific recognition of base sequences by proteins is discussed.
Resonance Raman spectra of mononucleotides obtained with 266 and 213 nm ultraviolet radiation
Authors: Ziegler L. D. , Hudson B. , Strommen D. P. , Peticolas W. L. 
Published: May 2005

AbstractResonance Raman spectra of the nucleoside 5′‐monophosphates UMP, CMP, AMP, and GMP have been obtained with 266‐ and 213‐nm radiation, the fourth and fifth harmonics of a Nd:YAG laser. The 266‐nm radiation is resonant with the states giving rise to the first absorption band of the bases. The resulting spectra are in agreement with those reported previously using similar wavelength excitation but are generally of better quality. The 213‐nm radiation is resonant with those states giving rise to the second strong absorption band of the bases. The spectra obtained with this wavelength show several new features relative to the 266‐nm spectra, including strong enhancement of modes of the pyrimidines with a character similar to the e2g ν8 mode of benzene, relative enhancement of ring modes at 1580 and 729 cm−1 in AMP, and strong enhancement of the 1670‐cm−1 C = O mode of GMP. These enhancements are discussed in terms of previously reported preresonance behavior and predicted intensities based on CNDO bond‐order changes and normal‐mode calculations. The results of a preliminary study of the effect of the interaction of GMP with cis‐dichlorodiammineplatinum(II) on the 213‐nm resonance Raman spectrum is also discussed.
Transfer of peptide hormones from aqueous to membrane phases
Authors: Deber Charles M. , Behnam Basil A. 
Published: May 2005

AbstractPeptide hormones and neurotransmitters are functional amphiphilic substances that deploy their chared and nonpolar substituents as required for traversing aqueous phases en rout to their ultimate transfer into the lipid‐rich environment of their membrane‐embedded receptors. As a means of determining the role(s)that cellular membrane lipids may play in mediating these events, we describe an experimental approach, using high‐resolution 1H‐and 13C‐nmr spectroscopy, for delineation of the structures of complexes between the (neurotransmitter pentapeptide) enkephalins and micellar and vesicular phospholipid particles. Residue‐specific enkephalin interactions with lipid are identified; affinity constants for the hydrophobic component(s) of peptide/lipid association are calculated for enkephalin and several of its analogs; and comparisons with morphine are presented. Finally, based on molecular details obtained from nmr experiments, a model is proposed for the encoutner of a peptide hormone with a phospholipid membrane surface.
Peptide homologs, isosteres, and isomers: A general approach to structure–activity relationships
Authors: Goodman Murray 
Published: May 2005

AbstractA general approach to study peptide structure is presented using three areas of ongoing research in our laboratories. The first involves the molecular basis for taste of peptide derivatives. We synthesized dipeptides based on L‐aspartyl‐α‐aminocycloalkane carboxylic acid methyl ester. A homologous series of cycloalkane derivatives was studied. The cyclopropane, cyclobutane, and cyclopentane derivatives are sweet, the cyclohexane and cycloheptane peptides are bitter, and the cyclooctane homolog is tasteless. The related acyclic analog L‐aspartyl‐aminoisobutyric acid methyl ester is sweet, while the L‐aspartyl diethyl glycine carboxylic acid methyl ester is tasteless. A model is presented to explain these experimental observations. The second area involves depsipeptides as isosteric replacements of α‐hydroxy acids for amino acid residues in peptide chains. We have synthesized sequentially defined polydepsipeptides as model systems for polypeptides. A detailed analysis of the conformational order for these polydepsipeptides is presented. The third area involves partial retro–inverso peptide modifications of isomeric cyclic enkephalin analogs, which illustrate the relationship between the modification and biological activity. We are probing the intramolecular hydrogen‐bonding features for these biologically active molecules. From such findings we are relating the structural and conformational preferences deduced from spectroscopy and molecular mechanics to biological activity.
Time scale, geometrical constraints, and disulfide bond formation in the folding of small globular proteins
Authors: Gałat Andrzej 
Published: May 2005

AbstractWe hypothesize a model of protein folding based on the Poincaré recursion argument and a number of experimental results, including CD, nmr, and Raman spectra. Our model considers that protein folding in vivo proceeds through prefolded peptide segments consisting of 3 to 14 amino acid residues. Such segments may fold spontaneously into nativelike microdomains within a biologically feasible time, i.e., in the 10−6–10−1 s time scale. If, due to improper recognition and adjustment of their surfaces, these transiently formed secondary structures are not stabilized by long‐range interactions, then the protein species occur within a time‐ and number‐averaged spectrum of populations of transient conformational substates until the final, proper adjustment of the segments takes place. However, if, during protein folding, incorrect disulfide (S‐S) bonds are formed, then such unique through‐space contacts between the different parts of the polypeptide chain are usually restricted to a minimum. It is postulated that unfolding and refolding processes in vitro, and protein folding in vivo, proceed through variably populated quantized substates. The distribution of these substates depends on a number of molecular interactions between the phase and the hydration spheres surrounding the prefolded surfaces of peptide segments and long‐range interactions between these prefolded surfaces.