bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyaluronate diffusion in semidilute solutions
Authors: Wik K.‐O. , Comper W. D. 
Published: December 2004

AbstractAnalysis of the mutual diffusion coefficient of hyaluronate reveals that it rapidly increases with increasing concentration or decreasing ionic strength. The mutual diffusion coefficients analyzed by boundary relaxation in the analytical ultracentrifuge by either Raleigh interference optics or absorption optics (through the use of fluorescein‐labeled hyaluronate) yielded similar values. The theoretical treatment of the mutual diffusion coefficient has been analyzed in terms of experimentally measured intradiffusion coefficients and thermodynamic virial coefficients. Only approximate agreement between theory and experiment was found. The concept of formation of transient statistical network structures in semidilute solutions of hyaluronate was applied to evaluate a critical concentration at which network formation occurs. This has been discussed in relation to the marked decrease in the intradiffusion coefficient of hyaluronate with concentration. The formation of network structures in hyaluronate was found not to preclude the hyaluronate undergoing extremely rapid rates of mutual diffusion (with diffusion coefficients ∼30 × 10−11 m2 s1) under conditions of relatively large initial chemical potential gradients. Measurements of the unidirectional flux of hyaluronate for nonzero gradients demonstrated their marked sensitivity to the magnitude of the concentration difference across the boundary. An experimental feature of the unidrectional diffusion coefficients of hyaluronate is that they may be analyzed purely in terms of mutual and intradiffusion processes. The backflux diffusion coefficient (describing the flux against the imposed concentration gradient) appeared identical with the intradiffusion coefficient. The analysis of the various sources of errors made in this study suggests that the magnitude of the diffusion coefficients measured may be regarded only as approximate.
Kinetics of thermal denaturation of met‐hemoglobin in perturbed solvent: Relevance of bulk‐electrostatic and hydrophobic interactions
Authors: Cupane Antonio , Giacomazza Daniela , Cordone Lorenzo 
Published: December 2004

AbstractWe studied the kinetics of the heat denaturation (at 50°C) of met‐hemoglobin in the presence of various monohydric alcohols. The denaturation rate was slowed by the presence of small concentrations of methanol and ethanol; in all the other cases, i.e., at high concentrations of methanol and ethanol, and in the whole concentration range studied for iso‐ and n‐propanol, an increase in the denaturation rate was observed. Following a procedure already applied to the study of the effects of the same alcohols on the reaction of hemoglobin with oxygen, we separated the overall observed effects into contributions related to the variation of the bulk dielectric constant of the medium (bulk‐electrostatic contributions) and contributions not related to variations in this parameter (nonbulk‐electrostatic contributions). For all the alcohols, we found a unique correlation law connecting the above nonbulk‐electrostatic contributions with the analogous ones previously reported for the T → R transition of hemoglobin. This fact strongly supports the validity of the procedure used and suggests that nonbulk‐electrostatic contributions, relative to these two different processes, have a common background and are univocally determined by the extent of the “solvent perturbation” imposed by the presence of the perturbing cosolvents.
The poly(rU) coil: A minimum‐energy model that matches experimental observations
Authors: Hingerty Brian E. , Broyde Suse B. , Olson Wilma K. 
Published: December 2004

AbstractA model of the randomly coiling form of poly(rU) based on minimum‐energy conformers of UpU is described. The blend of conformers is chosen to fit the CC rotational populations derived in nmr studies of UpU and poly(rU) and to match the experimental unperturbed dimensions of the poly(rU) chain. In addition, estimates of loop closure based on the model are comparable to the sizes of loops most frequently seen in model oligonucleotides. Approximately 60% of the conformers constituting the model are characterized by stacked, extended C2′‐endo ω′ωψ = tg−g+ rotations. The remainder of the chain is described by equal numbers of C3′‐endo A (ω′ωψ = g−g−g+) and Watson‐Crick (ω′ωψ = g−tt) helical arrangements.
Steady‐state opticohydrodynamic properties of DNA: Molecular weight dependence and the internal viscosity problem
Authors: Reeg Charles F. , Harrington Rodney E. 
Published: December 2004

AbstractExtinction angles, flow birefringence, and intrinsic viscosities are compared for linear, bihelical DNAs from viral and other sources that span a range in molecular weight from ∼105 to 1.3 × 108. This range effectively spans the region over which transition from rigid‐rod to expanded‐coil hydrodynamic property behavior occurs. All DNAs are in identical, phosphate–EDTA, neutral‐pH buffers, 0.1M in NaCl. The extinction angle is a hydrodynamic property only and is thus particularly sensitive to effects of kinetic chain rigidity or internal viscosity. Our extinction angle results cannot be interpreted by any simple, single‐function theoretical expression. Rather, they must be divided into distinct high‐ and low‐molecular‐weight domains. The low‐molecular‐weight region is typical of rigid‐particle opticohydrodynamic property behaviour characterized primarily by particle orientation. The high‐molecular‐weight domain shows evidence for a finite internal viscosity effect, however, which can be interpreted as very nearly Kuhnian using Cerf's amplification of the Gaussian subchain model to include internal viscosity. It is found that the high‐molecular‐weight, monodisperse viral DNAs from T7, T5, and T2 bacteriophage show an internal viscosity contribution to the limiting extinction angle–shear rate ratio of ∼3 × 10−3 s. An effect of this magnitude may be marginally important in interpreting extinction angle and certain other hydrodynamic property data for high‐molecular‐weight DNA systems. Internal viscosity effects do not appear to be manifest in the ratio of flow birefringence to intrinsic viscosity, however, and the persistence length of the high‐molecular‐weight DNAs is found to be independent of molecular weight to within estimated experimental uncertainty.
Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H‐nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin
Authors: Iqbal M. , Balaram P. 
Published: December 2004

AbstractPeptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc‐Aib‐Pro‐Val‐Aib‐Val‐Ala‐Aib‐Ala‐Aib‐Aib‐OMe in CDCl3 (0.001–0.06M) and (CD3)2SO (0.001–0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen‐bonding pattern in the decapeptide.
Far‐infrared absorption of nucleotides and poly(I)·poly(C) RNA
Authors: Beetz C. P. , Ascarelli G. 
Published: December 2004

AbstractWe have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ∼25 to ∼500 cm−1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out‐of‐plane deformation of the bases contributes strongly to vibrations near 200 cm−1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm−1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200‐cm−1 region and sharpening of the features assigned to the low‐frequency ribose‐ring vibrations.
Examination of Haldane's first law for the partition of CO and O2 to hemoglobin A0
Authors: Wyman Jeffries , Bishop Gary , Richey Brough , Spokane Robert , Gill Stanley 
Published: December 2004

AbstractA study of the oxygen replacement reaction of carbon monoxide‐saturated hemoglobin (HbA0) was carried out using spectroscopic, calorimetric, and pH titration methods. Under fully saturated conditions the replacement reaction can be defined by a single partition constant over all ratios of bound oxygen to carbon monoxide. This indicates that under saturating conditions Haldane's first law for the ligand binding of gas mixtures holds for any CO/O2 ratio. It further shows that there is no appreciable difference in relative CO‐O2 affinity between the α‐ and β‐chains. The same partition coefficient was found to hold for different pH, buffer, and allosteric effector conditions. The lack of any pH dependence of the partition coefficient was confirmed by the absence of proton changes for the replacement reaction. The temperature dependence of the partition coefficient and calorimetric results yield a value for the enthalpy of the reaction of −3.65 ± 0.29 kcal/mol/heme.
Model for the adsorption of cytochrome c at the water–mercury interface
Authors: Serre Paule‐Andrée , Haladjian Jean , Bianco Pierre 
Published: December 2004

AbstractThe effect of cytochrome c on the redox behavior of 1,4‐benzoquinone and cystine has been investigated by differential pulse polarography. The adsorption of cytochrome c on mercury surface produces a lowering of the reduction peak of 1,4‐benzoquinone and of the cystine prepeak. When the covering of the drop is maximal, no variation in peak height is observed. By using the Koryta equation, values between 1500 and 2300 Å2 for the surface area of one adsorbed cytochrome c molecule were obtained. The capacitance dependences on concentration and time have been determined by alternating‐current polarography, and lead to the surface area values of 2800 and 2700 Å2, respectively. Results are interpreted on the basis of an unfolding of cytochrome c molecules during the adsorption process. It is likely that a rather compact covering is obtained, but about 10% of the mercury surface seems to be unoccupied and corresponds to the accessible interstices between adjacent molecules.
Theory of protein secondary structure and algorithm of its prediction
Authors: Ptitsyn O. B. , Finkelstein A. V. 
Published: December 2004

AbstractA molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long‐range interactions between different regions, incorporating all these interactions in a single Ising‐like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α‐ and β‐structures for different residues in synthetic polypeptides, while long‐range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x‐ray structural data became available.
Cis–trans peptide‐bond equilibria in cyclic hexapeptides
Authors: Kopple Kenneth D. , Zhu Peng‐Peng , Go Anita 
Published: December 2004

AbstractData are presented on the position of the equilibria of cyclo(Xxx‐Pro‐Yyy)2 backbones between forms with two cis Xxx‐Pro peptide bonds and forms with only trans peptide bonds. These data are interpreted in terms of two factors: a solvent‐independent steric interaction between the Xxx and Pro side chains, and the ability of solvent to influence the transannular electrostatic interaction between NH and CO groups of the Xxx units in the all‐trans form.
Influence of the peptide chain length on the stability of double‐stranded β‐helical species of D,L‐alternating oligovalines in chloroform solution
Authors: Lorenzi Gian Paolo , Jäuckle Hans , Tomasic Lera , Pedone Carlo 
Published: December 2004

AbstractThe type and distribution of the β‐helixes occurring in chloroform solutions of Boc‐(L‐Val‐D‐Val)6‐OMe and Boc‐(L‐Val‐D‐Val)8‐OMe have been studied by using 1H‐nmr techniques. Right‐ and left‐handed ↑↓β4.4‐helices and left‐handed β5.6‐helices occur with the dodecapeptide. β4.4‐Helices of opposite handedness occur also with the hexadecapeptide, but ↑↓β5.6‐helices could not be detected with this oligomer. At equilibrium, at 25°C, the double helix of the dodecapeptide is only moderately populated. These results indicate that increasing the chain length has a destabilizing effect on the ↑↓β5.6‐helices of D,L‐alternating oligovalines in chloroform solution.
Stabilizing effects of 2‐methylalanine residues on β‐turns and α‐helices
Authors: Jung G. , Bosch R. , Katz E. , Schmitt H. , Voges K.‐P. , Winter W. 
Published: December 2004

Abstract13C‐, 1H‐nmr, CD, and x‐ray crystallography revealed β‐turns of type III for Boc‐Gly‐L‐Ala‐Aib‐OMe, Boc‐L‐Ala‐Aib‐L‐Ala‐OMe; the 310‐helix for Boc‐Aib‐L‐Ala‐Aib‐L‐Ala‐Aib‐OMe; and antiparallel arranged α‐helices for Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe. An N‐terminal rigid α‐helical segment is found in the polypeptide antibiotics alamethicin, suzukacillin, and trichotoxin. The α‐helix dipole is essential for their voltage‐dependent pore formation in lipid bilayer membranes, which is explained by a flip‐flop gating mechanism based on dipole–dipole interactions of parallel and antiparallel arranged α‐helices within oligomeric structures.
Peptides as channel‐making ionophores: Conformational aspects
Authors: Spach Gérard , Trudelle Yves , Heitz Fréadéric 
Published: December 2004

AbstractThe β‐ and β‐helical structures do not appear consistent with the structural data and ion‐transport properties of (Ala‐Ala‐Gly) or (Leu‐Ser‐Leu‐Gly) oligomers. Oligoalanine derivatives also give rise to current fluctuations in bilayer lipid membranes. Bundles of molecules may explain the behavior of these various peptides in membranes.
β‐Galactosidase: Immune recognition of conformation and mechanism of antibody‐induced catalytic activation
Authors: Celada Franco , Strom Roberto 
Published: December 2004

AbstractActivation of mutant β‐galactosidase by antibodies can be explained by a “selection” mechanism in which the antibody binds and stabilizes those mutants in a native‐like conformation and by an “induction” mechanism where binding of the antibody itself induces a conformational change activating β‐galactosidase. The “selection” hypothesis was tested by passing β‐galactosidase through a column packed with monoclonal antibody‐derivatized Sepharose. The antibody retains the active, in preference to the inactive, proteins. The “induction” mechanism was tested by mixing antibody–Sepharose with mutant β‐galactosidase and measuring enzyme activity before mixing and that remaining in the supernatant. The activity of the antibody–Sepharose pellet exceeded the sum of the original activity plus supernatant activity. As a result of these experiments, both mechanisms are found to be operative.
13C‐ and 1H‐nmr evidence for all‐cis peptide bonds in cyclic tetrapeptide cyclo(L‐Pro‐Sar)2
Authors: Shimizu Toshimi , Tanaka Yoshio , Tsuda Keishiro 
Published: December 2004

AbstractConformations of the cyclic tetrapeptide cyclo(L‐Pro‐Sar)2 in solution were studied by 1H‐ and 13C‐nmr spectrometry and model building. The nmr data provide definite evidence that this cyclic peptide exists chiefly in two conformations, namely, a C2‐symmetric conformation and an asymmetric structure. The former was demonstrated to be predominant in polar solvents (100% in Me2SO‐d6). This structure contains all cis‐peptide bond linkages and all trans′ Pro CαCO bonds. It represents the first cyclic tetrapeptide in which all four peptide bonds have been found in the cis‐conformation. As the polarity of the solvent decreases, the population of C2‐symmetric conformers decreases (88% in CD3CN and 65% in CDCl3). At the same time, a minor asymmetric conformer, characterized by cis‐cis‐cis‐trans peptide bond sequences (two cis Sar‐Pro bonds, one cis Pro‐Sar bond, and one trans Pro‐Sar bond), is seen to increase (9% in CD3CN and 30% in CDCl3). A proposed predominant conformation in solution for cyclo(L‐Pro‐Sar)2 was compared with a crystal structure, as reported in an accompanying paper. Both structures show striking overall similarities.
Effect of ionic strength on the diffusion coefficient of chondroitin sulfate and heparin measured by quasielastic light scattering
Authors: Tivant P. , Turq P. , Drifford M. , Magdelenat H. , Menez R. 
Published: December 2004

AbstractThe normal modes for a mixture of charged macromolecules and electrolyte solution are calculated. We derive a generalized Debye relaxation time and the apparent diffusion coefficient of the macroion, which is shown to increase from its Stokes value, obtained in excess of added salt, with decreasing ionic strength. We test our result with experimental data for macromolecules with different charge densities: heparin and chondroitin sulfate. Besides, we show for this latter molecule that while the diffusion coefficient is increased, the scattered intensity is decreased but not by the same factor. Our results are compared with other theories developed in quasielastic light scattering.
Conformation of the central sequence of angiotensin II and analogs
Authors: Sakarellos Constantin , Lintner Karl , Piriou François , Fermandjian Serge 
Published: December 2004

AbstractWe describe the synthesis and the conformational analysis by ir, CD, and proton‐nmr spectroscopy of four model peptides of the type N‐Ac‐Tyr‐X‐His‐NH2 with X = Val, Leu, Ala, Gly. These peptides represent the central sequence of the hormone angiotensin II and its position‐5 analogs. We studied their conformational behavior in aqueous solution during pH titration and in organic solvents. For specific purposes of spectral analysis (ir band assignment, proton‐nmr signal assignment, heteronuclear vicinal coupling constants), we synthesized three isotopically enriched homologs of the mother sequence, i.e., N‐Ac‐(15N‐Tyr)‐Val‐His‐NH2, N‐Ac‐(13C, 2H, Tyr)‐Val‐His‐NH2, and N‐Ac‐Tyr‐(13C, 2H, Val)‐His‐NH2. Results are summarized as follows: the tyrosine and the histidine side chains influence each other through space; this mutual influence is modulated by the nature of the side chain in position X and decreases in going from XVal to XGly as a consequence of two simultaneous events, changes in the side‐chain rotamer distribution and changes in the φ and ψ angles of residue X. The decrease in the bulkiness of the side‐chain X (Val → Gly) leads to increased flexibility of the peptide backbone at this site, which is also reflected in the apparent ratio of C5, C7, and intermediate conformations present in equilibrium. The three spectroscopic techniques, in addition to the results of chymotryptic degradation experiments, show a high level of agreement, and all reflect the dynamic conformation of these peptides in a different manner.
Thermodynamics of solvation for methylproline peptides
Authors: Madison Vincent , Delaney Norma G. 
Published: December 2004

AbstractWe have determined thermodynamic parameters for transfer of N‐acetyl,N′‐methylamide derivatives of proline and methylprolines from carbon tetrachloride and from chloroform to water. The hydrophilic nature of the diamide model peptides is demonstrated by the negative free energies and enthalpies for transfer. Chloroform solvates the peptides considerably better than carbon tetrachloride. Heats of dilution in carbon tetrachloride arise from disruption of intermolecular peptide–peptide hydrogen bonds. After extrapolation to dilute solution, differences in thermodynamic parameters among the isomeric mono‐methylproline peptides are correlated with the population of the intramolecularly hydrogen‐bonded C7 conformer in the nonpolar solvent. However, the thermodynamic parameters aslo reflect differences in solvation due to the proximity of the two peptide groups and the side chain.
Comparison of analytically and numerically derived hydrogen exchange‐rate distribution functions
Authors: Gregory Roger B. 
Published: December 2004

AbstractHydrogen exchange‐rate probability density functions for lysozyme have been derived by numerical Laplace inversion with the computer program CONTIN. The resulting solution set includes a smooth bimodal solution in agreement with previous analytical results together with a smooth three‐peak solution. Numerical analysis of lysozyme hydrogen‐exchange data in glycerol/water cosolvent mixtures confirms the previous assignment of the slow‐exchange peak to an exchange mechanism involving reversible unfolding. Physicochemical constrations that can reduce the size of the solution set are described. The results are compared with those obtained from previous analytical methods and the limitations of the discrete class and analytical appraches are discussed.
An analysis of the sequence dependence of the structure and energy of A‐ and B‐DNA models using molecular mechannics
Authors: Tilton Robert F. , Weiner Paul K. , Kollman Peter A. 
Published: December 2004

AbstractMolecular‐mechanics calculations have been carried out on the base‐paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A‐ and B‐DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B‐DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A‐DNA conformation. The molecular interactions responsible for these differential stabilities include both inter‐ and intrastrand base stacking, as well as base–phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine‐3′,5′‐pyrimidine sequence over the pyrimidine‐3′,5′‐purine sequence in both the A‐ and B‐conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate–base and base–base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine‐attched sugars and only in the B‐DNA geometry. We suggest a molecular mechanism, specifically, differential base–sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.