bluuebunny/crossref_metadata_2025_split huggingface dataset:
Donnan effect as measured by sedimentation equilibrium for the protein cytochrome c
Authors: Syvanen Michael , Schachman H. K. 
Published: December 2004

AbstractThe protein turkey‐heart cytochrome c is used as a model protein to study charge effects in sedimentation equilibrium experiments in three‐component solutions. Data are given for the dependence of the apparent M (1–υρ) on ρ in solutions of KCl, RbCl, CsCl, and triethylamine hydrochloride. The results show the Donnan effect to have a significant influence on the apparent molecular weight, found by extrapolation of the data to a solution density of one. The apparent molecular weights are for protein at infinite dilution. A theoretical treatment is presented where the magnitude of this effect can be predicted accurately from the formal net charge of the protein as computed from the amino acid composition. The results are shown to be important in computing the preferential hydration of the protein in concentrated salt solutions. For such systems the Donnan effect should be subtracted from the total interaction coefficient for multicomponent system in order to obtain the preferential hydration.
Metal complexs of poly (α‐amino acids): Cu(II) chelates of acetoacetylated poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid)
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Benvegnu' C. , Peggion E. 
Published: December 2004

AbstractThe cupric complexes of poly(Nε‐acetoacetyl‐L‐lysine), [Lys(Acac)]n′ poly(Nδ‐acetoacetyl‐L‐ornithine), [Orn(Acac)]n′ and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid), [A2bu‐(Acac)]n, as well as of the model compound n‐hexyl acetoacetamide, have been investigated by means of absorption, potentiometric, equilibrium dialysis, and CD measurements. While in the complex of the model compound, one chelating group is bound to one cupric ion, in the polymeric complexes two β‐ketoamide groups are bound to Cu(II) under the same experimental conditions. The binding constant of cupric ions to the three polymers and the formation constant of the Cu(II)‐nhexylacetoacetamide complex have been evluated. Investigation on the chiroptical properties of the three polymeric complexes shows that the peptide backbone does not undergo conformational transitions, remaining α‐helical when up to 20% of the side chains are bound to Cu(II). The optical activity of the β‐ketoamide chromophores is substantially affected by complex formation and is discussed in terms of asymmetric induction from the chiral backbone.
1H and 13C nmr studies of cyclic and linear dipeptides containing threonyl, seryl, aspartyl, and histidyl residues
Authors: Ptak Marius , Heitz Annie , Dreux Michel 
Published: December 2004

AbstractThe side‐chain conformations of D‐ orL‐ Thr, D‐ or L‐Ser, L‐Asp, and L‐ His residues in cyclic and linear dipeptides in D2O or in DMSO‐d6 are deduced from vicinal (1H,1H) and (13C, 1H) coupling constants. Vicinal (13C, 13C) coupling constants strongly depend on substituents and cannot be used without a more sound analysis. In cyclic dipeptides, the Thr and Ser side chains are folded above the DKP ring, with χ1 near 60°. The L‐Asp side chain interacts more specifically with peptide bonds (χ1 near 300°). The L‐ His side chain is more flexible and its conformation depends on the proximity of a second side chain and on solute‐solvent interactions. In all cases, this side chain is not completely folded. In linear dipeptides, the conformation of a C‐terminal L‐His residue is mainly influenced by the end carboxylic group. On the other hand, a N‐terminal L‐His residue interacts more easily with a neighboring L‐Asp residue. In aqueous solution, the imidazole pKa depends on the proximity of terminal and lateral charged groups but does not reveal any specific interaction in cyclic dipeptides. A comparison between the conformations of cyclic peptides observed in solution, in the crystalline state and calculated by empirical methods, allows one to point out the discriminating role of the packing in crystals, and of solute‐solvent interactions in solution.
The solution conformation of malformin A
Authors: Tonelli Alan E. 
Published: December 2004

AbstractSolution conformations of the cyclic pentapeptide plant‐hormone malformin A, whose conformational freedom is constrained by an intramolecular disulfide bridge, are derived and presented here. The nmr and CD data of Ptak are used to place restrictions on the search for possible malformin A solution conformers of low energy. Only two distinct conformers were found to be consistent with Ptak's data. Both structures are characterized by an internally buried (solvent‐shielded) D‐Cys2 amide proton, a seven‐membered (1–3)hydrogen bond between (N–H) and (OC), and a disulfide bridge conformation with a P chirality as manifested in the nmr study by the temperature independence of the amide proton chemical shifts for the D‐Cys2 and D‐Leu4 residues and the negative sign of the long wavelength maximum in the CD spectrum, respectively. Inspection of space‐filling molecular models of both structures indicates severe steric barriers to their rapid interconversion. Thus, it appears that only one of the two conformers may be present in solution. The difference in their calculated dipole moments (4.6 and 6.9D) suggests an experimental method for distinguishing between the two proposed solution structures.
Configurational effects on conformational properties of cyclic nucleotides. I. Theoretical calculations of conformer preferences in α‐nucleoside 3′,5′ cyclic monophosphates
Authors: Tewari Ravindra , Danyluk Steven S. 
Published: December 2004

AbstractA comparative study has been made of the configurational effects on the conformational properties of α‐ and β‐anomers of purine and pyrimidine nucleoside 3′,5′,‐cyclic monophosphates and their 2′‐arabino epimers. Correlation between orientation of the base and the 2′‐hydroxyl group have been studied theoretically using the PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The effect of change in ribose puckering on the base‐hydroxyl interaction has also been studied. The result show that steric repulsions and stabilizing effects of intramolecular hydrogen bonding between the base and the 2′‐hydroxyl (OH) group are of major importance in determining configurations of α‐anomers and 2′‐arabino‐β‐epimers. For example, hydrogen bonding between the 2′‐hydroxyl group and polar centers on the base ring is clearly implicated as a determinant of syn‐anti preferences of the purine (adenine) or pyrimidine (uracil) bases in α‐nucleoside 3′,5′‐cyclic monophosphates. Moreover, barrier heights for interconversion between conformers are sensitive to ribose pucker and 2′‐OH orientations. The result clearly show that a change in ribose‐ring pucker plays an essential role in relieving repulsive interaction between the base and the 2′‐hydroxyl group. Thus a C2′‐exo‐C3′‐endo (2T3) pucker is favored for α‐anomers in contrast with the C4′‐exo‐C3′‐endo (4T3) from found in β‐compounds.
Formation of the collagen‐like triple‐helical structure in oligopeptides during elongation of the molecular chain
Authors: Lazarev Yu. A. , Lobachov V. M. , Grishkovski B. A. , Shibnev V. A. , Grechishko V. S. , Finogenova M. P. , Esipova N. G. , Rogulenkova V. N. 
Published: December 2004

AbstractOligotripeptides Z‐(Gly‐Pro‐Pro)n‐OMe (n = 1,2,…,8), Z‐Gly‐Pro_Pro‐Gly‐Pro‐Gly‐OMe, Z‐Gly‐Pro‐Pro‐Gly‐Pro‐Gly‐Gly‐Pro‐Pro‐OMe, Z‐Gly‐Pro‐Pro‐(Gly‐Pro‐Gly)2‐Gly‐Pro‐Pro‐OMe, and Z‐(Gly‐Pro‐Ala)n‐OMe (n = 1,2,…,4) were synthesized step‐by‐step and then studied by means of x‐ray diffraction, ir spectroscopy, the kinetics of hydrogen‐deuterium exchange of peptide groups, and circular dichroism,. Different stages in the formation of a triple helix in Z‐(Gly‐Pro‐Pro)n‐OMe were revealed during the chain elongation. In the solid state, at the first stage a conformation of the polyproline II‐type is formed in the tripeptide and in the second stage a triple helical complex appears in the hexapeptide. Interpeptide hydrogen bonds in this complex are still of low order. At further stages an ordered set of interpeptide hydrogen bonds is gradually formed. It is shown that the degree of order of interpeptide H bonds depends on the length of the molecular chain, the amino acid composition, and residue sequence in the triplets.
Thermodynamics of transfer ribonucleic acids: The effect of sodium on the thermal unfolding of yeast tRNAPhe
Authors: Freire Ernesto , Biltonen Rodney L. 
Published: December 2004

AbstractThe thermal unfolding of yeast phenylalanine‐specific tRNA (tRNAPhe) has been calorimetrically investigated at several salt concentrations in the absence of magnesium. Application of the deconvolution theory of macromolecular conformational transitions allows calculation of the thermodynamic parameters of unfolding. It is demonstrated that the unfolding of tRNAPhe occurs in a sequential fashion and that four separate transitions or five macromolecular thermodynamic states exist in the temperature range 8–72°C under the experimental conditions of these studies (0.067–0.52M Na+). The enthalpy and entropy changes between states and the relative population of each state as a function of temperature and salt concentration have been obtained. Sodium stabilizes the low‐temperature conformations of tRNAPhe. The increase in the melting temperatures of each transition is shown to be linearly dependent on the logarithm of sodium concentration. These results allow calculation of the “phase” diagram for the transitions as a function of salt concentration.
Laser‐excited raman spectroscopy of biomolecules. XII. Thermally induced conformational changes in poly(L‐glutamic acid)
Authors: Fasman Gerald D. , Itoh Koichi , Liu Christopher S. , Lord Richard C. 
Published: December 2004

AbstractThe α‐helical from of poly(L‐glutamic acid) [α‐poly(Glu)] gives rise to the same amide I and III lines as α‐poly(γ‐benzyl‐L‐glutamate) at 1652 and 1296 cm−1, respectively. The latter is a superposition of the amide III line near 1290 cm−1 and a line deu to vibrational made of CH2 groups of the side chain near 1300 cm−1. A line at 924 cm−1 is tentatively identified as characteristics of α‐poly(Glu). Both the β1‐ and β2‐ forms of poly(Glu) give rise to characteristic of β‐amide. III frequencies that are similar because of their similar backbone structures. Differences in the conformations of their side chains and in the environments of the backbone are reflected in the region 800–1200 cm−1 and in the amide I. A line at 1042 cm−1 and a pair at 1021 and 1059 cm−1 are tentatively assigned as characteristic of β1‐poly(Glu) and β2‐poly(Glu), respectively. The α‐β2 transition in poly(L‐Glu78L‐Val22) is shown by the appearance of all the β2‐characteristic lines in the thermally transformed sample. The same features observed in poly(L‐Glu95L‐Val5) also indicate that the α‐β2 transition of poly(Glu) is facilitated by the presence of L‐valine and that the content of L‐valine is not critical for this purpose. Investigation of the Raman spectra of the calcium, strontium, barium and sodium slats of poly(Glu) shows that these salts, under the conditions of preparation used, all the have random‐coil conformations.
Thermodynamics of the slow–fast transition in bacteriophage T2L
Authors: Welch J. B. , Bloomfield V. A. 
Published: December 2004

AbstractWe have measured the thermodynamic parameters of the slow‐fast tail‐fiber reorientation transition on T2L bateriophage. Proportions of the virus in each form were determined from peak‐height measurements in sedimention‐velocity runs and from average diffusion coefficients obtained by quasielastic laser light scattering. Computer simulation of sedimentation confirmed that there were no undetected intermediates in the transition, which was analyzed as a two‐state process. Van't Hoff‐type plots of the apparent equilibrium constant and of the pH midpoint of the transition as function of reciprocal temperature led to the following estimates of the thermodynamic parameters for the transition at pH 6.0 and 20°C: ΔH° = −139 ± 18Kcal mol−1, ΔS° = −247 ± 46 cal K−1 mol−1, and ΔG° = −66 ± 22 kcal mol−1. Per mole of protons taken up in the transition, the analogous quantities were −15.9 ± 1.7 kcal mol−1, −26.3 ± 2.2 cal K−1 mol−1, and −8.22 ± 1.8 kcal mol−1. The net number of protons taken up was about 8.5 ± 1.5. The large values of the thermodynamic functions are consistent with a highly cooperative reaction and with multiple interactions between the fibres and the remainder of the phage. The negative entropy of the transition is probably due to immobilization of the fibres.
Polypeptide models of collagen. II. Solution properties of (Pro‐Gly‐Phe)n
Authors: Brahmachari Samir K. , Ananthanarayanan V. S. , Rapaka Rao S. , Bhatnagar Rajendra S. 
Published: December 2004

AbstractThe conformation of (Pro‐Gly‐Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro‐Gly‐Phe)n can exist in a partially triple‐helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly‐R2‐R3, in collagen.
Hydrodynamic properties of aqueous solutions of galactomannans
Authors: Sharman W. R. , Richards E. L. , Malcolm G. N. 
Published: December 2004

AbstractGalactomannans were extracted from the seeds of seven different legumes to obtain samples which differed in average molecular weight, in polydispersity, and in average mannose‐to‐galactose ratio in the molecule. Measurements were made of the viscosities as a function of shear rate and of the sedimentation and diffusion coefficients of the aqueous solutions of all the galactomannans. Average molecular weights were calculated from the sedimentation and diffusion coefficients using the Svedberg equation. The Mark‐Houwink relationship between the intrinsic viscosity and the average molecular weights was found to hold for the series of galactomannans despite differences in the mannose‐to‐galactose ratios of the solutes. Estimates were made of the galactomannan polydispersities from both the sedimentation‐coeffient distributions and also from the diffusion‐coefficient ratios, Dm/DA. The two methods gave results in qualitative agreement. The hydrodynamic properties of the more homogeneous galactomannans were compared with the predictions of the Flory‐Fox hydro‐dynamic theory, with results very similar to those which were obtained for the water‐soluble synthetic cellulose derivatives, hydroxyethylcellulose and ethydroxycellulose.
An investigation of pectin and pectic acid in dilute aqueous solution
Authors: Jordan Robert C. , Brant David A. 
Published: December 2004

AbstractLight‐scattering measurements have been carried out on carefully clarified aqueous solutions of pectin and pectic acid. The strong dependence of the inverse excess scattering intensity on angle yields pectin chain dimensions that are inconsistent with the complete molecular dispersion of pectin molecules possessing the degrees of polymerization indicated by the measured osmotic molecular weights. Negligible or negative concertration dependences of the inverse scattering intensities coupled with the centrifugation, filtration, and gel permeation chromatography behavior of the samples likewise suggest nonequilibrium aggregation of the pectin molecules in solution. It is shown that the measured mean polymer chain dimensions can be rationalized in terms of the presence of a very small proportion of aggregated material.
Crystallization of chondroitin sulfate from an aqueous solution
Authors: Tanaka Ki‐Ichiro , Katsura Nobuhiko 
Published: December 2004

AbstractA new polymorph of sodium chondroitin‐4‐sulfate has been crystallized from an ethanolic aqueous solution at low pH. The crystallized spherulite specimens give considerably sharper x‐ray diffraction lines. The unit cell of the new polymorph is rectangular with dimensions (Å) a = 16.0, b = 24.1, and c = 26.0. The chondroitin‐4‐sulfate could be purified by recrystallization.
Effect of hydrophobic side chains on the pressure‐induced changes in the NMR spectra of water‐soluble biopolymers
Authors: Williams R. K. , Fyfe C. A. , Bruck D. , Van Veen L. 
Published: December 2004

AbstractMeasurements have been made of the high‐resolution nmr spectra of the polyamino acids poly[N5‐(2‐hydroxyethyl)‐L‐glutamine] and poly[N5‐(4‐hydroxybutyl)‐L‐glutamine] in mixed deuterium oxide and water solvent at varying pressures from 1.03 to 3163.7 kg/cm2. The results are compared with previously reported results for the polymer poly[N5‐(3‐hydroxypropyl)‐L‐glutamine] under similar conditions. The significance of the behaviour of the polymers is considered in terms of the effect of the presence of hydrophobic residues in their side chains.
Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B‐DNA structure and a counterclockwise helix
Authors: Miller Kenneth J. 
Published: December 2004

AbstractAn algorithm is developed that enables the routine determination of backbone conformations of nucleic acids. All atomic positions including hydrogen are specified in accord with experimental bond lengths and angles but with theoretically determined conformational angles. For two Watson‐Crick base pairs at a separation of 3.38 Å, and perpendicular to a common helical axis, minimum energy configurations are found for all 10 combinations at helical angles of α ∼ 36°–38°, corresponding to the B‐DNA structure with C(2′)‐endo sugar puckers. Backbone configurations exist only within the range 35.5° ⩽ α ⩽ 42°, which suggests the origin of the 10‐fold helix. Calculated stacking energies for the B‐DNA structure increases for each of the clustered groups of base pairs: G·C with G·C, G·C with A·T, and A·T with A·T, and they are in approximate agreement with experimental observations. The counter‐clockwise helix is examined, and physically meaningful structures are found only when the helical axes of successive base pairs are disjointed.
Dynamics of the cluster model of protein folding
Authors: Kanehisa Minoru I. , Tsong Tian Yow 
Published: December 2004

AbstractThe cluster model of protein folding [Kanehisa, M. I. & Tsong, T. Y. (1978) J. Mol. Biol. 124, 177–194] is further investigated for the thermodynamic and kinetic properties of protein folding–unfolding transitions. A cluster is a locally formed ordered region in the polypeptide chain due to cooperative interactions among residues. In the cluster model a cooperative term is assigned as proportional to the surface area of a globular cluster. This assignment is compared with that for the helix–coil transition of homopolypeptides, where the cooperative term is proportional to the two ends of a linear helical sequence. The dynamics of the cluster model exhibit a slow phase, which is well‐separated from other faster phases, because of the cooperative interaction of the macrosystem. This slow phase not only appears within the transition region, but can also persist well below the transition region if the cooperativity depends on the external condition. The amplitudes of certain kinetic phases can vary depending on the choice of physical parameters monitoring the reaction. Thus the same reaction may display different time courses. The qualitative aspects of the folding dynamics are as follows. In one case the rate‐limiting formation of a critical‐size cluster is followed by its rapid growth, while in the other the rate‐limiting step appears in a later stage, where preformed smaller clusters merge into larger ones. The former case is similar to the dynamics of the helix–coil transition, and the latter represents a stepwise mechanism of protein structure formation.
Melanostatin conformations in solution
Authors: Schwartz Robert W. , Mattice Wayne L. , Spirtes Morris A. 
Published: December 2004

AbstractThe conformations of melanostatin have been studied experimentally using CD spectroscopy and via calculations. In aqueous solution and 2,2,2‐trifluoroethanol (TFE) there is no evidence that monomers of the tripeptide exist in an ordered (β‐bend) structure. In water and TFE solutions (3–6 × 10−4M) the neutral molecules aggregate very slowly, taking about 3 days to attain equilibrium at room temperature. At equivalent concentrations in TFE, although not in water, the cationic molecules also slowly aggregate, although to a lesser extent. Calculations using rotational isomeric state theory give the most probable unperturbed end‐to‐end distance of the molecule at 9.3 ± 0.1 Å and indicate that a vast majority of the molecules exist in some extended conformation, end‐to‐end distance ≥6 Å. Only 0.4% of the molecules are calculated to have O…︁H separations compatible with a β‐bend structure. An intramolecular hydrogen bond must have an energy at least 2 kcal/mol lower than that of an intermolecular hydrogen bond to solvent if a β‐bend is to be experimentally observable.
Condensation of Co++ ions on chondroitin sulfate from transport coefficients and proton NMR measurements in aqueous solutions
Authors: Tivant P. , Turq P. , Chemla M. , Magdelenat H. , Spegt P. , Weill G. 
Published: December 2004

AbstractThe “condensed” counterions which characterize high‐charge‐density polyelectrolyte solutions can be analyzed into two subpopulations: (1) site‐bound counterions and (2) atmospherically entrapped counterions. The distinction is achieved experimentally by combining the data from self‐diffusion coefficient or electrical mobility measurements, which give the amount of “condensed” ions, and those from nmr, chemical shift measurements, which indicate the amount of site‐bound ions. In the case of a solution of chondroitin sulfate with excess Co++ counterions, it can be estimated that 20% of the structural charge of the polyion is neutralized by site‐bound, dehydrated, condensed counterions, while a further 30% is neutralized by atmospherically entrapped, hydrated counterions.