bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational analysis of peptides, polypeptides, and proteins. I. Polyglycine I
Authors: Moore W. H. , Krimm S. 
Published: May 2005

AbstractA force field has been refined for the antiparallel chain‐rippled sheet structure of polyglycine I. Transition dipole coupling and hydrogen bonding are explicitly taken into account. Amide I and amide II mode splittings are well accounted for, the latter also providing a quantitative explanation of the amide A and amide B mode frequencies and intensities. In addition to predicting other features of the vibrational spectrum of polyglycine I, this force field is completely transferable to other β polypeptides, even though these have the antiparallel chainpleated sheet structure.
The optical properties of tyrosine‐containing cyclic dipeptides
Authors: Snow Julian W. , Hooker Thomas M. , Schellman John A. 
Published: May 2005

AbstractThe chiroptical properties of the cyclic dipeptides cyclo (L‐alanyl‐L‐tyrosine) and cyclo(L‐tyrosyl‐L‐tyrosine) have been investigated as a function of molecular conformation. Theoretical optical calculations and conformational energy calculations have been carried out as a function of the side‐chain dihedral angles χ1 and χ2, and as a function of the angle of fold of the cyclic dipeptide backbone. The results of these theoretical calculations have been compared with experimental circular dichroism (CD) data. Theoretical predictions are in very good agreement with experiment for c(L‐Tyr‐L‐Tyr). Agreement was not quite as good for c(L‐Ala‐L‐Tyr), although the signs of all of the Cotton effects were apparently predicted correctly except for that associated with the lowest energy tyrosine absorption band.
Experimental and theoretical investigations on the folding modes of depsipeptide molecules
Authors: Boussard G. , Marraud M. , Neel J. , Maigret B. , Aubry A. 
Published: May 2005

AbstractThe coupling of N‐acyl‐α‐amino‐acids with α‐hydroxyacid‐methyl amides results in depsipeptide molecules containing two chiral centers and one ester function inserted between two amide functions. Their conformational features have been investigated by IR spectroscopy, proton magnetic resonance, X‐ray diffraction, and theoretical P.C.I.L.O. calculations.It is shown that most of these molecules are folded by an intramolecular 4 → 1 hydrogen bonding. Two folded conformations, similar to the well known β turn in peptides, are described, the stability of which depends on the configurational sequence in the investigated molecule.LL and LD species are folded in two different ways whereas LG sequences containing an achiral hydroxy‐acid residue accommodate both of them. The presence of a N‐terminal achiral amino acid noticeably decreases the folding ratio.The above conclusions are then compared with the conformational features of homologous tripeptide molecules.
The organization and repair of DNA in the mammalian chromosome. I. Calibration procedures and errors in the determination of the molecular weight of a native DNA
Authors: Lange Christopher S. , Liberman Daniel F. , Clark Roger W. , Ferguson Pamm 
Published: May 2005

AbstractThe semiautomated sucrose gradient system of Lange and Liberman (1974) (Anal. Biochem. 59, 129–145) has been used to determine an accurate value of the exponent k of the Burgi and Hershey equation (1963) (Biophys. J. 3, 309–321) under conditions of 1M salt. A complete analysis of the variance of k was done for data from both systems. The results lead to the conclusion that the value k = 0.401 (±0.012 for reproducibility; ±0.019 for total error) obtained here is considerably more accurate than that of Burgi and Hershey (even when corrected for DNA concentration effects and the improved size estimates of T4 DNA size). The use of the Burgi and Hershey relationship and a T4 DNA metric to determine molecular weights of mammalian DNA requires the utmost precision in the exponent if useful estimates are to be obtained. This also has implications for double‐strand breakage and repair estimates.
A study of paramyosin aggregation using transient electric birefringence techniques
Authors: Krause Sonja , DeLaney Donald E. 
Published: May 2005

AbstractThe aggregation of several forms of the molluscan muscle protein paramyosin at low concentration and at low ionic strength was studied in the pH range 6–10 using transient electric birefringence techniques. In the lower part of this pH range, the aggregates exhibit negative birefringence, but this changes to positive birefringence when the pH increases. Analysis of the field‐free birefringence decay transients of the paramyosin solutions showed that all aggregates coexisted with paramyosin monomer and allowed a determination of the rotational diffusion constant of the aggregates present at each pH. The size and shape of these aggregates were estimated from their rotational diffusion constants and were compared with the known characteristics of larger aggregates such as paracrystals. The positively birefringent aggregates appear to be staggered dimers at certain values of pH; at other pH values, these aggregates appear to be higher aggregates, probably formed by lateral aggregation of monomer or dimer onto one of these staggered dimers. The staggered dimers are formed by overlap of 200–600 Å along each cylindrical paramyosin molecule, in agreement with the 530‐Å overlap distance found in paramyosin paracrystals by Cohen et al. (1971) J. Mol. Biol. 56, 223–237. Some speculations are presented about the nature of the negatively birefringent species.
Intramolecular and overall motion of proline: The influence of viscosity on carbon‐13 spin‐lattice relaxation times
Authors: Deslauriers Roxanne , Smith Ian C. P. 
Published: May 2005

AbstractNuclear magnetic resonance of 13C is used to probe the overall and internal motions of proline. Spin‐lattice relaxation times (T1) are reported for proline monomer dissolved in water/glycerol mixtures. Rates of overall molecular motion and internal motion depend on solvent composition but to different degrees. The effective correlation times (τeff) of the various proton‐bearing carbon atoms in proline vary linearly as a function of solvent composition (%v/v) rather than of solution viscosity. The effective correlation time for molecular motion (τeff) is separated into contributions from overall molecular motion (τmol) and internal motion (τint). The γ‐carbon of proline shows the smallest dependence of τint on solvent composition. The data indicate a high degree of intramolecular motion for the γ‐carbon of proline. Inclusion of anisotropic molecular reorientation in the data analysis was found not to affect the above conclusions. The observed values of τeff indicate that the rotational diffusion model of molecular reorientations should apply to proline. The values of τeff calculated for proline using the Stokes‐Einstein relation are larger than those observed; the discrepancy is discussed in terms of solvent‐solute interactions.
1H nuclear magnetic resonance studies of N‐acetyl‐L‐proline N‐methylamide. Molecular conformations, hydrogen bondings, and thermodynamic quantities in various solvents
Authors: Higashijima Tsutomu , Tasumi Mitsuo , Miyazawa Tatsuo 
Published: May 2005

AbstractConcentration and temperature dependences of the 1H nmr spectra of N‐acetyl‐L‐proline N‐methylamide were observed in various solvents [CCl4, CDCl3, (CD3)2CO, (CD3)2SO, H2O, and D2O]. The fraction of the cis isomer (with respect to the bond between the acetyl carbonyl carbon and prolyl nitrogen atoms) depends greatly on the solvent used; the fraction of the cis isomer is higher in polar solvents than in nonpolar solvents. It depends also on concentration and temperature in nonpolar solvents but not in polar solvents. In nonpolar solvents the trans isomer mostly exists in the γ‐turn structure with an intramolecular hydrogen bond and the cis isomer tends to form molecular aggregates by intermolecular hydrogen bonds. In polar solvents both the cis and trans isomers exist in monomeric forms which interact with solvent molecules. The pH dependences of the N‐methyl proton resonances indicate that the γ‐turn structure of the trans isomer is present also in aqueous solution, though its population is difficult to determine. Apparent enthalpy and entropy changes for the conversion of the trans isomer to cis isomer are evaluated for various solvents. The results are discussed in terms of the intra‐ and intermolecular hydrogen bondings.
Cross linking of proteins in vitro by peroxidase
Authors: Stahmann M. A. , Spencer A. K. , Honold G. R. 
Published: May 2005

AbstractThe enzyme peroxidase, a substrate (hydrogen donor), and hydrogen peroxide aggregated and polymerized soluble proteins included in the reaction mixture. Gel filtration and acrylamide disk gel electrophoresis revealed newly formed dimers, trimers, and higher protein polymers. Some of the protein polymers withstood the denaturing conditions of dodecyl sulfate disk gel electrophoresis; thus the formation of some covalent cross links was indicated. It is suggested that peroxidase catalyzes the oxidation of hydrogen donors to form free radicals or quinones, which subsequently interact with, cross link, and alter the soluble proteins.
Quantum yields and fluorescence lifetimes of acridine derivatives interacting with DNA
Authors: Duortail Guy , Mauss Yves , Chambron Jacques 
Published: May 2005

AbstractInteractions of several acridine dyes with DNA from different species were studied by measuring fluorescence lifetimes in the 2–30‐nsec range, using the single‐photon counting technique, and by measuring fluorescence quantum yields in the steady state. The results confirm the existence of two principal site classes, one in which the dye fluorescence is quenched by interaction with guanine and another in which fluorescence results from the hydrophobic environment of the A·T base pairs. The emitting sites are found, in some cases, to exhibit fluorescent decay curves which can be resolved into two exponential components corresponding to a short and to a long lifetime. The deviation from one exponential component is particularly clear with rivanol, 9‐aminoacridine, and quinacrine, with which one component is two or three times longer than the other. The relative proportion of these two components depends only slightly on the DNA base composition and does not depend on the nature of the acridine derivatives. We postulate that this lifetime heterogeneity corresponds to the two discrete steps in the complex formation elucidated by kinetic studies: the first step corresponds to a semi‐intercalated, or “external,” dye with a short fluorescence lifetime and the second step corresponds to a totally intercalated dye with a long lifetime. In this model, we assumed that a transient opening of the site near a semi‐intercalated dye induces solvent diffusion which in turn is responsible for its short‐lived fluorescence.
Helical segment analysis of α‐helical regions in proteins
Authors: Rajan S. S. , Srinivasan R. 
Published: May 2005

AbstractThe methods suggested earlier for the analysis and representation of protein structural data are now extended to the helical regions in finer details. These enable better handling of characterization of bends and distortions, for which statistical parameters are also developed. Using latest myoglobin data, best experimental parameters for the α‐helix are deduced to be rN = 1.55 (0.13) Å, r = 2.28 (0.12) Å, rC′ = 1.70 (0.10) Å, r0 = 2.02 (0.12) Å, ϕ = 100.5 (2.3)°, and t = 1.495 (0.055) Å.
Helix‐coiled transition in heteropolymers. I. Ground‐state energy
Authors: Vilenkin A. 
Published: May 2005

AbstractA new technique is presented for treating the ground state of an heteropolymer with a random sequence of components. An exact system of equations is found for determining the ground state energy E which is equal to the polymer free energy f in the lowest‐order approximation in T/V (V/2 is the large “surface” energy arising at the boundaries between coiled and “helical” sections: V ≫ T, Uk; U1 and –U2 are the free energies of the components counted from the corresponding coiled state energies). These equations are essentially simplified at certain fixed values of the ratio U1/U2. For integer values of U2/U1 and U1/U2 a solution is obtained with an accuracy exp(–V/Uk). The ground‐state energy as a function of U1 and U2 is shown to be highly irregular: its derivatives have jumps at an infinite number of points. These jumps provide a fine structure of the melting curves. A smoothed over the jumps function E′ is found by way of analytic continuation from the integer values of U1/U2 and U2/U1. The accuracy of the approximation f ≈ E is estimated and the correctional term of order T/V is determined.
Extrinsic cotton effect and helix‐coil transition in a DNA‐polycation complex
Authors: Bhat G. , Roth A. C. , Day R. A. 
Published: May 2005

AbstractA strong, positive, extrinsic CD band ([θ]242.5 = ∼2 × 10−3 deg cm2/dmole) has been observed for a α‐bromo‐poly[methylene‐1,4‐phenylenecarbonyloxyethylene(dimethylamino) bromide] (I). The extrinsic Cotton effect is attributed to the ordered arrangement of the aromatic chromophores along the DNA helix.The extrinsic band had a linear dependence on the amount of polycation I added from r ≤ 0.3 to r = ∼0.5, but decreased thereafter. Addition of the polycation decreased the positive CD band of DNA at 275 nm. The transformation of B → C form in the presence of salts or other polycations caused similar changes. The decrease in [θ]275 was reversed at higher concentrations of the polycation (r > 0.4).Thermal denaturation studies indicated both stabilization of the helix conformation (Δtm = 21°C) and a high degree of cooperativity in the melting of DNA‐polycation complex as compared to native calf thymus DNA. Using the linear relationship between r (polycation residue/DNA phosphate) and F (fraction of bound base pairs), a value of 0.6 was derived for β (number of monomer residues of polycation/nucleotide).Both electrostatic and hydrophobic effects probably influence the stability of the DNA‐polycation complex, since the strength of the 242.5 nm CD band is a function of both salt and urea concentrations.
Water in keratin: Study of the depolarization thermal current peak II
Authors: Leveque J. L. , Garson J. C. , Boudouris G. 
Published: May 2005

AbstractThe depolarization thermal current method is applied to the study of the polarization phenomena in the keratin‐water system. Three depolarization thermal current peaks have been evidenced in hair keratin. This paper deals with the detailed study of peak II. For the first time, the mechanism responsible for this peak is ascribed to molecular reorientation. The effect of water upon the characteristics of peak II is also described, and an activation energy of 8.4 kcal/mol is computed. These results, in connection with other studies, lead us to interpret peak II as due to the reorientation in the bound or intermediate water molecules. The effect of copper confirms that the carboxyl groups are hydration sites.
Determination of the base‐pairing content of four specific tRNAs by infrared spectroscopy
Authors: Schernau U. , Ackermann Th. 
Published: May 2005

AbstractInfrared spectroscopy was used for the determination of the base‐pairing content of four specific tRNAs in deuterium oxide solution. Infrared spectra were obtained in the 1750–1550 cm−1 region at various temperatures ranging from about 15 to 90°C. Melting curves were constructed by plotting the molar extinction coefficient at ν = 1657 cm−1 versus temperature. These transition curves enabled us to determine the ranges of temperature which correspond to the ordered (partially double‐stranded) or randomly coiled structure of the tRNA. For a set of wavenumbers the extinction coefficients at these temperatures were used for the calculation of the base‐pairing content. The procedure employed here is based on a method described earlier by Thomas [(1969) Biopolymers 7, 325–334]. For the conditions selected for this investigation (Mg2+‐free D2O‐buffer; 0.01M tris‐DCl, 0.015M NaCl, pD 7.5) the results of this determination agree within the limits of errors with the number of base pairs predicted by the cloverleaf model.
Hydrodynamics of macromolecular complexes. III. Bacterial viruses
Authors: De La Torre Jose Garcia , Bloomfield Victor A. 
Published: May 2005

AbstractWe have calculated the translational and rotational frictional coefficients of structures related to T2 and T4 bacteriophage, using the theoretical framework developed in the preceding two papers. The structures considered were models for tail‐fiberless phage, and for whole phage with fibers in the extended and retracted portions. We also computed and compared with the experiment the changes in translational frictional coefficient produced by successive addition of 1–6 fibers to the fiberless particle. Agreement with experimental results is markedly improved over previous theoretical efforts, especially with respect to the effect of tail‐fiber extension. Some significant discrepancies remain, however, in the comparison of fiber‐retracted and fiberless phage.
Rotational isomerism of N‐acetylamino acid methylamides having serine, tyrosine, histidine, and proline residues as revealed by Raman spectroscopy
Authors: Koyama Yasushi , Uchida Hisaaki , Oyama Shigeru , Iwaki Tetsuo , Harada Kimihiko 
Published: May 2005

AbstractRotational isomerism of N‐acetylamino acid methylamides having serine, tyrosine, histidine, and proline residues was investigated by means of Raman spectroscopy. The Raman spectra of each compound for solid states (crystalline or glassy) as well as for aqueous solution were compared with each other. Different kinds of rotational isomers were found to exist in the different solid states; three such solid states for N‐acetylserine methylamide, two for N‐acetyltyrosine methylamide, and one for N‐acetylhistidine methylamide were found in the present investigation. Additional rotational isomers were found to exist in aqueous solutions. The results indicated that the inherent relative stability of the rotational isomers differs little and is very dependent on intermolecular interaction, especially that due to hydrogen bonds. The possible molecular conformations are discussed on the basis of x‐ray results now available both for the present compounds and for proteins.
Quasielastic light scattering: Effect of ionic strength on the internal dynamics of DNA
Authors: Caloin Michel , Wilhelm Bernadette , Daune Michel 
Published: May 2005

AbstractQuasielastic light scattering is used to study the effect of ionic strength on the dynamic behaviour of DNA. In a first approach the spectrum of scattered light is analyzed in terms of a single relaxation process. The large difference between the observed behaviour and that expected according to a pure diffusional process reflects the contribution associated with internal modes, which increases with decreasing ionic strength. Such behaviour is better analyzed in terms of a double relaxation process by using two relaxation times, the reciprocals of which are equal to DK2 and DK2 + τi−1 (K), respectively, where τi (K) is an average value describing the set of modes observed at a given K value. Relative intensity and relaxation times, which are the more accurate parameters, were used to interpret the results. The observed increase of the relative contribution of internal modes with decreasing ionic strength is actually a relative decrease of the diffusional contribution induced by a corresponding increase of the radius of gyration RG. On the other hand, the reciprocal τi−1 (K) of the relaxation time is a linear function of K2 in the analyzed KRG range and is insensitive to ionic strength between 10−2M and 1M. These results, when discussed according to Rouse's model, lead to define for each value of τi−1 (K) a corresponding mean‐squared equilibrium length 〈μ〉 which is found to be a linear function of K−2.
Correlation of sequence and tertiary structure in globular proteins
Authors: Crippen Gordon M. 
Published: May 2005

AbstractThe x‐ray crystal structures of 19 selected proteins are examined empirically for correlations between the amino acid sequence and long‐range, tertiary conformation. There is clear evidence for preferential associations of certain types of amino acids, particularly among the hydrophobic aliphatic, aromatic, and cysteine residues. However, the likelihoods of forming these residue‐pair contacts are all less than 12%, so packing and geometric requirements must often take precedent over energetic considerations. The prediction of long‐range contacts is not substantially improved by taking into account the sequentially previous residues. The analysis of atom–atom contacts shows a similar lack of predictive ability, but the results show that a good approximation to the interresidue energy function must include different types of interactions at two or three different sites on some amino acids. Backbone–backbone long‐range interactions are relatively rare and nonspecific, whereas some “polar” side chains form hydrogen bonds from the polar groups while occasionally forming hydrophobic contacts with the remainder of the chain.
Interaction of amylose and other α‐glucans with hydrophobic fluorescent probe (2‐p‐toluidinylnaphthalene‐6‐sulfonate)
Authors: Nakatani Hiroshi , Shibata Ken‐Ichiro , Kondo Hitoshi , Hiromi Keitaro 
Published: May 2005

AbstractFluorescence of 2‐p‐toluidinylnaphthalene‐6‐sulfonate (TNS) was enhanced in the presence of maltooligosaccharides, amylose, and other α‐glucans. The dependence of relative TNS fluorescence intensity per glucose unit on chain length of oligosaccharides was examined. The values of binding constant and thermodynamic parameters, assuming the 1:1 complex for TNS‐amylose (number‐average degree of polymerization, DPN = 17), were determined by the fluorescence titration. The values of thermodynamic parameters for 1:1 complex formation of TNS‐α‐ and β‐cyclodextrins were also determined and compared with those of TNS‐amylose (DPN = 17). The fluorescence intensity of TNS in the presence of amylose (DPN = 600) decreased by the action of glucoamylase and taka‐amylase A. The fluorescence of TNS‐amylose (DPN = 17) system increased with the increased ionic strength. In the presence of pullulan, TNS fluorescence was also enhanced and decreased by the action of pullulanase. Amylopectin enhanced TNS fluorescence rather more strongly than amylose (DPN = 17) at the same concentration. In the presence of dextran, the fluorescence of TNS was scarcely enhanced. The degree of fluorescence enhancement of TNS in the presence of α‐glucans seems to reflect the structures of α‐glucans in solution, since TNS fluorescence is enhanced in the hydrophobic environment or by the disturbance of free intramolecular rotation.
Sedimentation studies of giant DNA molecules present in unsheared whole‐cell lysates of D. melanogaster cells
Authors: Appleby David W. , Rall S. C. , Hearst John E. 
Published: May 2005

AbstractWe have used band sedimentation in shallow density gradients of CsCl in the preparative centrifuge to analyze the distribution of sedimentation coefficients present in tritium labelled DNA from D. melanogaster cells. The cells were lysed according to the method of Kavenoff and Zimm to preserve very high molecular weight DNA. Sedimentation measurements have been carried out as a function of speed of centrifugation. The resulting distribution functions have been interpreted with the aid of the Zimm‐Schumaker equation for the speed dependence of the sedimentation coefficient of very high molecular weight DNA. Low‐speed centrifugation (3000 rpm) indicates that DNA molecules from the lysate are evenly distributed over values of S20,w from 0 to 514S. This distribution is very sensitive to changes in speed of centrifugation and is transformed into a bimodal distribution at 12,080 rpm. Analysis of this transformation allows us to postulate that perhaps 55% of the DNA in the lysate may have molecular weights in excess of 40 × 109 g/mol. Some of these molecules may also possess a variety of configurations including partially replicated branched structures.