bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of the strongly held water of lysozyme by drying
Authors: Rao P. Bhaskara , Bryan William P. 
Published: December 2004

AbstractA method for the measurement of water that is strongly held by lysozyme is described. This water is slowly removed by vaccum drying of lyophilized and can be titrated with the Karl Fischer reagent. Drying curves were obtained by mechanical pumping (moderate vacuum) and diffusion pumping (high vacuum) at 20°, 10°, 0°, −10° and −20°C. About 23 water molecules per lysozyme molecule are at least moderately held by the protein. These water molecules fall into several classes. Three to four of them are quite strongly held and may correspond to the three buried water molecules observed in the x‐ray analysis of lysozyme structure. The presence of tri‐N‐acetylglycosamine in the lysozyme active cleft has no effect on drying at 0°C. The method shows promise of being generally applicable to the measurement of small amounts of water which are strongly held by biological structures.
Relaxation and electrophoretic effects in polyelectrolyte solutions. I. Salt‐free solutions
Authors: Schmitt A. , Meullenet J. P. , Varoqui R. 
Published: December 2004

AbstractRelations between relaxation and electrophoretic effects in salt‐free polyelectrolyte solutions are studied in terms of nonequilibrium thermodynamics and of binary friction coefficients. The significance and the method of determining these coefficients are explained. Consideration of experimental results and of long‐ and short‐range interactions suggests that the concept of “ion condensation” is needed to provide a consistent desciption of transport processes for linear flexible polyelectrolytes. Empirical relations previously used are shown to have only limited validity.
Helix‐coil transitions in nucleoprotein: Computer‐generated curves for independent melting of double‐stranded regions with fixed ends
Authors: Chipev C. C. , Staynov D. Z. 
Published: December 2004

AbstractHelix‐coil transitions in nucleoprotein at low salt concentrations are known to be characterized by two phases of the process: independent melting of uncomplexed “naked” regions without rearrangement of proteins, followed, at higher temperatures, by melting of complexed DNA. Blocking at the ends of these regions increases their thermal stability and three is a shift of 10–20°C in tm of the melting profiles. In this study the basic assumption is that the loop entropy effect is mainly responsible for such stabilization. Calculations are made using conventional h‐c transition theory for a system of independently melted segments with fixed ends. Segments are either homosize or have randomly distributed lengths. Calculated melting curves are used to obtain tm, and transition width‐dependence on segment length (or average length when randomly distributed) and on the nucleation parameter σ. Base‐pair heterogeneity is taken into account by averaging over different base‐pair distributions in the individual segments, using Gaussian distribution around the overall (G+C)‐content. It is shown that this causes only an additional widening of the transition but no additional tm shift. Comparison is made with similar systems in the literature. The main conclusion drawn is that the treatment proposed may be useful for analysis of the lower temperature melting phase in nucleoprotein at low counterion concentrations. It may be used as an independent method to reveal the features of nucleoprotein structure.
Structural and conformational studies of polyriboadenylic acid in neutral and acid solution
Authors: Scovell William M. 
Published: December 2004

AbstractRaman spectra of solutions of polyriboadenylic acid have been studied in the pH range of 7.2–5.2. Bands are identified which are sensitive to the characteristics of poly(rA) in the single‐and double‐stranded helical forms. Thermal melting profiles were obtained as a function of pH to monitor simultaneously the changes in (1) the phosphodiester backbone, (2) the base‐stacking interactions, (3) the perturbation of the PO unit, and (4) the degree of protonation at the N‐1 position in the adenine base. The temperature dependence of the intensity ratio of the bands at 725 and 705 cm−1 appears to be sensitive to the noncooperative and the cooperative thermal‐melting process for the single‐and double‐stranded forms of poly(rA), respectively. Concurrently, bands diagnostic of the degree of protonation reveal that the cooperative melting process for the “acid” poly(rA) clearly involves deprotonation.The progressive perturbation of the 1100 cm−1 band with an increasing degree of protonation of poly(rA) is consistent with earlier suggestions regarding a PO‐(6)‐NH2 interaction in the double‐helical form of poly(rA). The stability of the double‐helix parallels the degree of protonation over the pH range studied as reflected in the tm values, which increase linearly with decreasing pH.
Experimental study on aggregation of model dipeptide molecules. V. Stereoselective association of leucine dipeptides
Authors: Cung Manh Thong , Marraud Michel , Neel Jean , Aubry André 
Published: December 2004

AbstractInfrared spectroscopy and 1H nmr have been used to elucidate the association modes of leucine dipeptides in carbon tetrachloride solution. Two stereoselective types of aggregates have been evidenced. Homochiral molecules are associated in oligomeric aggregates and accommodate a β‐parallel‐like structure which was characterized by x‐ray diffraction. Heterochiral molecules are paired in centrosymmetrical dimers; the latter aggregation mode restricted to the dimer stage predominates in racemic solutions. A theoretical model proposed to account for this aggregation process is consistent with the experimental nmr data. Both homo‐ and heterochiral association constants are estimated from vapor pressure and nmr experiments.
A Raman and calorimetric investigation of 3′, 5′ GpG
Authors: Savoie Rodrigue , Klump Horst , Peticolas Warner L. 
Published: December 2004

AbstractThe Raman spectra of guanylyl (3′‐5′) guanosine (GpG) in solution in H2O and D2O at pH 3–7 have been recorded at various temperatures between 0 and 80°C. The results are consistent with the existence in the lower temperature range of stable aggregates formed by the stacking of GpG tetramers. The aggregates melt cooperatively near 60°C, which results in important changes in the spectra. Among these, a large increase in intensity of some of the bands assigned to the guanine residues shows that unstacking of the bases occurs at the melting. Also apparent in the spectra are changes in the intensity and frequency of band attributable to molecular groups involved in intermolecular hydrogen bonding between adjacent molecules in the complex. The melting temperature of GpG decreases by approximately 15°C upon lowering the concentration from 5 × 10−2 to 5 × 10−4M, as shown by Raman, calorimetric, CD, and uv measurements. The experimentally determined ΔH and ΔS for the melting transition are 9 Kcal/mol and 28 e.u./mol, respectively. The aggregation of GpG in 1.5 × 10−3M solutions was found to be very slow. The half‐time of the process, which roughly follows first‐order kinetics, is approximately 3 min at 10°C and 21 min at 35°C. The negative energy of activation associated with this reaction (−143 Kcal) indicated that the process involves intermediates whose concentrations decrease the temperatures raised, thus slowing down the overall process. The rate of disaggregation of GpG upon dilution to very low concentration is also extremely slow, indicating that the GpG aggregates, once formed, are very stable.
Ultraviolet photoelectron studies of 5‐halouracils
Authors: Padva A. , Peng S. , Lin J. , Shahbaz M. , Lebreton P. R. 
Published: December 2004

AbstractUltravoilet photoelectron spectroscopy has been employed to exmamin the valence electronic structure of 5‐fluorouracil, 5‐chlorouracil, 5‐bromouracil, and 5‐iodouracil. Photoelectron bands associted with the three highest π orbitals and the two oxygen atom lone‐pair orbitals were assigned by a comparison to similar bands observed in the photoelectron spectrum of uraciul. Bands arising from the halogen atom lone‐pair orbitals were assigned by comparing the present results with photoelectron spectra measured for halobenzenes, and by considering the linear dependence of halogen atom lone‐pair ionization potentials upon halogen atom electronegativities. The present spectroscopic results have been compared with results from studies of association constants of 5‐halouracil–adenine complexes. This examination in dicates that the complex association constants incresase as the ionization potentials of the highest occupied π orbital and the halogen atom lone‐pair orbitals of th halouracils decrease.
Experimental conformational study of two peptides containing α‐aminoisobutyric acid. Crystal structure of N‐acetyl‐α‐aminoisobutyric acid methylamide
Authors: Aubry A. , Protas J. , Boussard G. , Marraud M. , Neel J. 
Published: December 2004

AbstractSome theoretical studies have predicted that the conformational freedom of the α‐aminoisobutyric acid (H‐Aib‐OH) residue is restricted to the α‐helical region of the Ramachandran map. In order to obtain conformational experimental data, two model peptide derivatives, MeCO‐Aib‐NHMe 1 and ButCO‐LPro‐Aib‐NHMe 2, have been investigated. The Aib dipeptide 1 crystallizes in the monoclinic system (a = 12.71 Å, b = 10.19 Å, c = 7.29 Å, β = 110.02°, Cc space group) and its crystal structure was elucidated by x‐ray diffraction analysis. The azimuthal angles depicting the molecular conformation (ϕ = −55.5°, ψ = −39.3°) fall in the α‐helical region of the Ramachandran map and molecules are hydrogen‐bonded in a three‐dimensional network. In CCl4 solution, ir spectroscopy provides evidence for the occurrence of the so‐called 5 and C7 conformers stabilized by the intramolecular i → i and i + 2 → i hydrogen bonds, respectively. The tripeptide 2 was studied in various solvents [CCl4, CD2Cl2, CDCl3, (CD3)2SO, and D2O] by ir and pmr spectroscopies. It was shown to accommodate predominantly the βII folded state stabilized by the i + 3 → i hydrogen bond. All these experimental findings indicate that the Aib residue displays the same conformational behavior as the other natural chiral amino acid residues.
Thermal perturbation techniques in characterizing ligand–macromolecule interactions: Theory and application to the proflavin‐α‐chymotryspin system
Authors: Sturgill Thomas W. , Johnson Robert E. , Biltonen Rodney L. 
Published: December 2004

AbstractA thermal perturbation curve (TPC) is defined to be the derivative of the fractional degree of saturation, f, with respect to temperature, considered as a function of the natural logarithm of free ligand concentration, y. The theoretical framework for the use of such curves in the thermodynamic analysis of ligand binding to macromolecules is presented. The thermal perturbation curve either provides or complements the information obtained from the derivative binding isotherm ∂f/∂y. For a single set of identical and independent sites the TPC is identical to the derivative binding isotherm. Analysis of such a curve directly yield ΔH0 and ΔG0 for the binding reaction. In actual experimental work, however, the TPC can only be approximated because of “self‐buffering” effects relations between the parameter of the approximate curve and the thermodynamic quantities have been developed. This technique is applied to the proflavin‐α‐chymotryspin system to demonstrate its usefulness. The general features of thermal perturbation curves for cases of multiple sets of independent sites and cooperatively interacting sites have also been developed. The analysis of thermal perturbation curves in combination with other methods should provide a more powerful approach to the characterization of ligand‐macromolecule interactions.
Tail‐fiber attachement in bacteriophage T4D studied by quasielastic light scattering–band electrophoresis
Authors: Baran George J. , Bloomfield Victor A. 
Published: December 2004

AbstractMixtures of bacteriophage T4D particles with up to six tail fibres attached were seprated and analyzed in a quasielastic light scattering‐band electrophoresis apparatus. The electrophoretic mobilities and diffusion coefficients of the seprated bands were determined during the same experiment. Species differing in mobility by 0.05 × 10−4 cm2/V sec were resolved. Henry's electropheresis theory for spheres indicates that each tail fiber contributes about 140 effective positive charges to the phage structure. Estimate of the charge using the permanent dipole moment and the electrophorectic mobility (Bontje et. al. (1977) Biopolymers 16, 551–572) gives an effective charge of + 230 to −250 per tail fiber. The charge distribution on the fiberless particles was estimated to be −3380 on the head and −290 on the tail if the dipole moment was assumed positive and −1400 on the head and −1000 on the tail for a negative dipole. Tail‐fiber attachement does not proceed to completion in our invitro system, as substantial distributions as a function of tail‐fiber input indicates the reaction is a random, noncooperative process.
A quantitative analysis of excluded‐site effects for highly cooperative binding systems
Authors: Ramanathan Brinda , Schmitz Kenneth S. 
Published: December 2004

AbstractBinding isotherms can provide quantitive information regarding the stability of a molecular complex. Theorectical studies in recent years have been directed to systems in which a single ligand can exclude more than one polymer site (excluded‐site effect). This system has minium of thre parameters to describe the binding data: the intrinsic binding constant, B; the remote‐neighbor cooperative paramaters, σq and the number of excluded sites, q. It is suggested in the present communication that precise values for these three parameters can be obtained by utilizing the characteristics of two forms of data representation: θ vs ln m and θ/m vs θ, where θ is the degree of saturation (0⩽θ⩽1) and m is the molality of free ligand. The matrix generation method is used to obtain empirical equations relating the midpoint location and slope at the midpoint of the θ vs ln m plot to the three molecular parameters. A modified Scatchard theory is also presented for highly cooperative systems, which results in an expression relaing the maximum in the θ/m vs θ plot to the molecular parameters σq and q, thus providing the third equation for the three unknown parameters. The novel method f analysis is illustrated with the AMP‐poly(L‐arginine) and oligocytidylate–T7 DNA sstems.
The effect of homologous amino acid replacement on the conformation of oligopeptides. I. Synthesis of co‐oligopeptides containing methionine and valine
Authors: Becker Jeffrey M. , Naider Fred 
Published: December 2004

AbstractThe preparation of a series of co‐oligopeptides Boc‐Val‐Metn‐OMe(n = 1–6), as sell as Boc‐Met3‐Val‐et2‐OMe and Boc‐Met3‐Val‐Met3‐Ome, is described. The synthesis was carried out by a classic method employing the mixed anhydride procedure (isobutylchloroformate) for all coupling reactions. All oligopeptides after purification were homogenous on silica thin layers and gave correct elemental analysis. They were judged to be optically pure using molar rotation studies at the sodium D line.
Biosynthèse de cellulose bactérienne à pertir de glycérol sélectivement deutérié en position 1, 2, ou 3: Etude par résonance magnétique nucléaire
Authors: Chumpitazi‐Hermoza Bernabé F. , Gagnaire Didier , Taravel François R. 
Published: December 2004

AbstractGlycerol specifically deuterated at C‐1, C‐2, or C‐3 was prepared and used for the biosynthesis of bacterial cellulose with Acetobacter xylinum.The material obtained were converted into glucitol hexaacetate and analyzed by 250‐MHz nuclear magnetic resonance and mass spectrometry. The spectra indicated that the protons of the C‐3 position of the starting glycerol were incorporated as substituents of the C‐6 and C‐1 positions of the cellulose. Similarly, protons of the C‐2 and C‐5 positions of the cellulose came essentially from water and the protons bonded at the C‐3 and C‐4 positions of the cellulose from protons bonded to C‐1 of the starting glycerol.
Solvent accessibilities in the dimeric subunits of RNA and DNA
Authors: Ponnuswamy P. K. , Thiyagarajan P. 
Published: December 2004

AbstractTo obtain information on the solvent‐solute interactions in the dinucleoside monophosphates pertaining to the dimeric subunits of RNA and DNA, we have computed the accessibility of a water molecule to the oxygen atoms of the subunits following the method of Lee and Richards [J. Mol. Biol. 55, 379–400 (1971)]. The solute molecules (dimeric unit) is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the total surface accessible to the solvent molecule—and hence the solvent accessibility of various atoms of the solute molecule for different conformations—are computed. From the calculated atomic accessibilities, solvation maps in the (ω′,ω) space have been constructed, keeping ψ at 60°, 180°, and −60°. The C(3′)‐endo sugar system in the case of DNA subunit have been considered. The solvation maps describing the solvatability of single and groups of atoms give significant information on the backbone conformational domains that are preferred for solvent interaction, thus adding knowledge to the relative stability of the various possible conformations. The B‐DNA‐type conformer exposes three polar atoms—namely, PO1, O(3′), and O(1′)—to external solvent, whereas the A‐DNA‐ and C‐DNA‐type conformers expose only one polar atom—O(3′) and O(1′), respectively—to the solvent. The O(2′) atom of the furanose ring system in the RNA subunit could give added stability via solvent association or interunit hydrogen bonding with or without a bridging water. The superposition solvation maps describing the accessibility of a group of polar atoms help to interpret a good number of phosphodiester conformations observed in a energetically less favored conformational domains in the tRNAPhe crystal. Another intresting fact that results from this study is the prediction that the trans oriented of ω is the most favorable conformations of random‐coil polynucleotides in solution.
Conformational properties of the N‐terminal residues of S‐peptide. II. The guanidine hydrochloride–water–trifluoroethanol system
Authors: Filippi B. , Borin G. , Moretto V. , Marchiori F. 
Published: December 2004

AbstractThe Conformational properties of synthetic S‐peptide analogs, in which the residues in the N‐terminal sequence 1–6 were progressively deleted or replaced with amino acids of lower helical propensity, were studied by CD. Increasing the concentration of guanidine hydrochloride and decreasing the temperature were found to produce progressive destruction of ordered conformations, in the parallel with the increasing solubility of the peptide unit, while increasing the concentration of trifluoroethanol and decreasing the temperature produced the opposite effect. The maximum helicity determined in the these sets of experiments is found equal to or greater than that determined in the formation of the ribonuclease S′ complexes. With some peptides the maximum value of predicted helical conformation is reached, and the tendency of tertiary structure to reduce the maximum possible helicity is evident. We discuss the validity of the procedure by which conformational information, drawn from measurements in helicogenic solvents, is related to the state in native protein.
Solvent effect in the stereoselective polymerization of α‐amino acid N‐carboxyanhydride and some considerations on the mechanism of stereoregulation
Authors: Hashimoto Yutaka , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractIn the Polymerization of phenylalanine N‐carboxyanhydride (NCA) in No2Oh initiated by MeNHBzl, L‐,D‐, and DL‐NCA As were polymerized at the same rate, and no stereoselectivity was observed. When the same experiment was carried out in HCONEt2, however, L‐ and D‐NCA were both polymerized at a rate which was about twice as large as that of DL‐NCA. In this case, the polymerization is stereoselective, ascribable to a preferable reaction between the optical enantiomorphs of the terminal residue of the growing chain and the NCA of the same chirality. On the other hand, the polymerization initiated by SarNMe2 and MeNH(CH2)2CONMe2 were stereoselective in NO2Ph and HCONEt2, but they were not stereoselective in m‐(MeO)2Ph. These findings indicate that the polymerizations initiated by a strong base in highly dipolar solvents are stereoselective. Apparently, the reaction between a chiral, cyclic terminal of growing chain and a chiral, cyclic activated NCA in the activated‐NCA mechanism is highly stereoselective. In addition, from a kinetic investigation on on the copolymerization between L‐ and D‐NCAs, the penultimate chiral centers were also suggested to contribute to the stereoselection. Stereoselection by the α‐helical conformation of the growing chain and by a chiral, linear terminal amine have been considered so far, and the contribution from the present type of stereoselection must have been overlooked.
Pepsin‐catalyzed peptide synthesis
Authors: Pellegrini Antonio , Luigilusis Pier 
Published: December 2004

AbstractThe use of pepsin as a catalyst for the synthesis of peptide bonds was investigated. It is shown that the enzyme enables the preparation of several protected dipeptides and tripeptides containing two adjacent aromatic residues of the type P‐Al‐Phe‐Y, P‐PHe‐Ar‐Y, or P‐AR‐Phe‐Y where P and Y are amino and carboxyl protecting groups, AL is an aliphatic amino acid residue, and Ar is an aromatic, amino acid residue. They yields are in the rang 25–97%. The high yields, combined with the enzyme's stereospecificity, permit the isolation of optically pure enantiomers from racemic mixtures. For example, when Z‐DL‐Ph‐OH is allowed to react with an excess of H‐L‐Phe‐NH2, the stereoisomer Z‐L‐Phe‐L‐Phe‐NH2 is obtained in practically quantitative yield. At the same time, the unreacted, optically pure Z‐D‐Phe‐OH can be recovered (Z = carbobenzyloxy, Phe = phenylalanine). The advantages and disadvantages of the enzymatic coupling procedure as a possible routine method for peptide synthesis are discussed.
Thermodynamics of the partition of chondroitin sulfate–hexadecylpyridinium complexes in butanol/aqueous salt biphasic solutions
Authors: Hurst Robert E. 
Published: December 2004

AbstractThe thermodynamics of the partition of chondroitin sulfate–hexadecylpyridinium complexes wee studied in order to gain further insight into the mechanisms responsible for the sensitivity of the relative solubility of these complexes in aqueous slat and butanol phases to small changes in slat concentration. The dependence of the partition coefficient was measured as a function of temperature at three different salt concentrations. Increasing the temperature was found to favor the form of the complex which was soluble n the aqueous phase. Although the transition could be induced by temperature changes, he transition occurred over a 20°C range in temperature. The transition from the aqueous phase to the butanol phase was strongly exothermic, with ΔH = −22.3 kcal/mol polymer. The value of ΔS was found to be dependent on the salt concentration, ranging from −72.7 e.u./mol polymer in 0.05125M NaCl to −77.1 e.u./mol polymer in 0.05375M MaCl. When placed on a disaccharide basis, the corresponding values are ΔH = −402 cal/mol and ΔS = −1.31 to −1.3 e.u./mol. The sharpness of he transition was found to be due t the similarity in magnitude of ΔH and TΔS, and on the dependence of the later upon the salt concentration.