bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the helix–coil conformational changes of poly(deoxyadenylate‐deoxytymidylate) and poly(deoxyadenylate‐deoxythymidylate) induced by variations of hydrogen‐ion concentration
Authors: Hirai Toshihiro , Hamori Eugene 
Published: December 2004

AbstractDouble‐helical poly(dG‐dC) and poly(dA‐dT) are DNA analogs in which the interactions between the two strands of the helix are, respectively, either the stronger G/C type or the weaker A/T type along the entire length of macromolecules. Thus, these synthetic polynucleotides can be considered as representatives of the most stable and the least stable DNA. In the investigations presented here, potentiometric titrations and stopped‐flow kinetic experiments were carried out in order to compare the pH‐induced helix–coil conformations (10°C and 150mM [Na+]) the pH of the helix–coil transition (pHm) is 12.81 for poly(dG‐dC) and 11.76 for poly(dA‐dT). The unwinding of double‐helical poly(dG‐dC) initiated by a sudden change in pH was found to be a simple exponential process with rate constants in the range of 200–600 sec−1, depending on the final value of the pH jump. The intramolecular double‐helix formation of poly(dG‐dC) was studied by lowering the pH of the solutions from a value above pHm to that below pHm in dilute solutions (15.5 ug/ml [polymer]). Under these conditions, the observed rewinding reactions displayed a major and two exponential phases, all of which were independent of polymer concentration. From the comparison of the results of poly(dA‐dT) and poly(dG‐dT) would unwind faster than poly(dG‐dC). However, if the pH jumps are such that they present the same perturbation of these polymers relative to their pHm values, no significant differences exist between the rates of helix–coil conformation changes of poly(dA‐dT) and poly(dG‐dC).
Intensity‐fluctuation spectroscopy and tRNA conformation. II. Changes of size and shape of tRNA in the melting process
Authors: Patkowski A. , Jen S. , Chu B. 
Published: December 2004

AbstractWe have measured the translational (DT) and rotational (DR) diffusion coefficients of bulk tRNA from baker's yeast during the thermal unfolding process by means of photon‐correlation spectroscopy. It should be noted that our estimate of the rotational diffusion coefficient represented, for the first time, measurements on a small macromolecule in solution by the photoelectron time‐of‐arrival technique with a delay‐time resolution of 1 nsec. The melting curves expressed in terms of δDT vs temperature were consistent with the literature data in revealing the melting steps and their dependence on NaCl concentration. Additionally, it was possible to prove the existence of an intermediate, more compact structure during the initial steps of the thermal unfolding process. We found that the temperature ranges over which this intermediate structure appears depend strongly on salt concentration. By utilizing both translational and rotational diffusion coefficients and Perrin's equations for ellipsoids of revolution, we have computed the values of the equivalent length and width of tRNA molecules in solution at four different temperatures for NaCl concentrations of 0.2, 0.5, and 1M. The approximate model of ellipsoids of revolution also permits us to obtain an estimate of the radius of gyration, which is in very good agreement with literature data measured by means of small‐angle x‐ray scattering. Furthermore, we have measured the shape and size changes of tRNA with varying NaCl concentrations at room temperatures (25°C). The molecule becomes smaller and more spherical when NaCl concentration increases. As a result of partial melting at 70°C, the macromolecule is surprisingly elongated with an approximate axial ratio of 8:1 and has dimensions of about 180/22Å. Such information on conformational changes by a simultaneous determination of rotational and translational diffusion coefficients illustrates the potential of this approach, not available by other methods.
Transient electric birefringence of T‐even bacteriophages. IV. T2L0 and T6 with extended tail fibers
Authors: Boontje W. , Greve J. , Blok Joh. 
Published: December 2004

AbstractTransient electric birefringence measurements of the bacteriophages T2L0 and T6 were performed under such conditions that the tail fibers are extended. The data obtained are compared to previously reported data for T4B. For all T‐even phages the degree of extension of the tail fibers is a function of pH, ionic strength, and temperature. For T4B, much higher ionic strengths are needed than for T2L0 and T6 to accomplish complete tail‐fiber extension. The rotational diffusion coefficients of the phages with fully extended fibers are equal to 120 ± 3 sec−1, 132 ± 5 sec−1, 157 ± 4 sec−1 for T2L0, T4B, and T6, respectively. The respective optical anistropies are − (2.66 ± 0.05) × 10−4, and − (3.07 ± 0.15) × 10−4. The differences in the rotational diffusion coefficient and optical anisotropy arise because the conformation of the fully extended tail fibers is different for the three phages. The tail fibers of T2L0 project further into the solution (away from the head) than do those of T4B and T6. The apparent permanent dipole moments of T2L0 and T6 decrease with increasing ionic strength. This decrease is caused by the screening of the surface charges on the phage body by the counter‐ions in the solution. The biological relevance of this decrease is illustrated by the fact that the adsorption rate of T6 phages to E. coli B bacteria shows a similar dependence of ionic strength. Evidence is pressented that the tail fibers may move more or less independently of the phage body when an electric field is applied to the suspension.
Light scattering during the hysteresis effect in poly(A)·2poly(U)
Authors: Siano Donald B. 
Published: December 2004

AbstractLight‐scattering studies on buffered aqueous solutions of the triple‐stranded polyribonucleic acid poly(A)·2poly(U) were carried out at neutral pH and during titration. At pH 7.1 and 22°C, a sample of commercially available polymer in 0.005M phosphate buffer gave a Zimm plot which yielded values for the weight‐average molecular weight, Mw, of 874,000 ± 1800 g/mol, a root‐mean‐square radius, ρ of 930 ± 22 Å, and a second viral coefficient of 0.51 ± 0.05 × 10 −3 cm3g−1 mol. The light‐scattering data were also analyzed by serval linear and nonlinear least‐squares programs which were devised to determine the model (e.g., rod, coil, or zigzag) which could best describe the shape of the molecule. It was found that a rodlike model, perhaps with a few bends, was in best overall agreement with the data. The assumption that the molecule is a thin rod leads to a value for the linear density of 206 g mol−1 Å−1 and a translation of 3.3 Å per residue. These values are also in close agreement with those expected for a triple‐stranded, thin, base‐stacked molecule. During titration from neutral pH with 0.1M HCl, the observed apparent molecular weight slowly increased until at about pH 3.5 a sudden, large increase (about 30‐fold) occurred. The root‐mean‐square radius, on the other hand, after an initial small decrease (of about 25%), also exhibited a large increase (about 4‐fold). Upon back titration with 0.1M NaOH, the molecular parameters did not retrace the original path, but instead exhibited hysteresis—the Mw and ρz are both larger on the basic branch than on the acid branch at a corresponding pH. A plot of long ρz against log(Mw) during the interval in which the high‐moelcular‐weight form was present (below pH 3.5 on the acid branch, and on the basic branch) gave a straight line with a slope of ⅓. This suggests that the aggregates were composed of some tens of rather open radom coils, presumably of poly(A)·poly(A), and that the hysteresis may be caused under conditions by the metastability of the entangled coils.
The conformation of the anticodon loop of yeast tRNAPhe in solution and on ribosomes
Authors: Odom O. W. , Craig B. B. , Hardesty B. A. 
Published: December 2004

AbstractThe Y‐base of yeast tRNAPhe was replaced by the fluorophores 1‐aminoanthracene or proflavine to yield derivatives which are active in all of the reactions of peptide elongation on reticulocyte ribosomes. The relatively long lifetime, higher quantum yield, and environmental sensitivity of 1‐aminoanthracene make it a particulary useful adjunct to the Y‐base in studying conformational changes in the anticodon region. The absorption and emission spectra of 1‐aminoanthracene in tRNA in solutions in which it is active in peptide synthesis indicate that the probe is in a hydrophobic environment, apparently provided by stacking with the adjacent bases in the anticodon loop. The proflavine derivative, tRNA, was employed in iodide quenching, D2O enhancement, and fluorescence depolarization experiments. The results indicate that the fluorophore in partially but not completely protected from the solvent. Anisotropy studies indicate that in solutions approximating those which support peptide synthesis on ribosomes, the probes have significant but restricted flexibility within the anticodon loop. Considered with nmr data and Y‐base fluorescence from crystals of tRNA, the results indicate that the solution and crystal structures of tRNAPhe are very similar. In turn, fluorescene from modified tRNAPhe bound to ribosomes is similar to that observed in solution. It is of special significance for future experiments involving nonradiative energy transfer that these probles adjacent to the anticodon retain independent flexibility when bound to ribosomes with poly(U). The tRNAPhe itself appears to be held rigidly on the ribosomes. It is concluded that within the limits dictated by the position and sensitivity of the probes used in this study, the mechanism of tRNAPhe binding to ribosomes and the movement of tRNA and mRNA during the translocation steps of peptide synthesis can be interpreted in terms of the well‐defined crystal structure of tRNAPhe.
The spatial distributions of randomly coiling polynucleotides
Authors: Yevich Rosemarie , Olson Wilma K. 
Published: December 2004

AbstractStatistical mechanical averages of vectors and tensors characterizing the allowed configurations of randomly coiling polynucleotides have been calculated for chains of 20–210 repeating units. Specifically, the persistence vector p = 〈r〉 has been obtained as a function of chain length. Configurational averages of the Cartesian tensors formed from the displacement vector ρ = r–p have been computed up to and including the tensor of seventh rank. From these tensors the three‐dimensional spatial distributions of end‐to‐end vectors have been constructed to provide comprehensive pictures of the directional tendencies of the randomly coiling polynucleotide. The elements of the third and fourth moment tensors, however, give sufficient information to represent accurately the qualitative features of the spatial distributions. For long chains, more than 26 (64) repeating units, the spatial distributions assume spherically symmetric shapes that can be adequately characterized by one‐dimensional radial distribution functions. These radial distribution functions agree well with the radial distributions calculated from Monte Carlo samples containing more than 5000 chains. The constraints of fixed bond lengths, fixed bond angles, and hindered internal rotations severely distort the spatial distributions of short polynucleotide chains to mushroom‐shaped volumes. These skewed distributions provide information useful to the analysis of small, single‐stranded loops, bulges, and circles. The formation of these structures requires the termini of the polynucleotides to lie within specifically delineated volumes with respect to coordinate systems affixed to the first bonds of the chains. The extent to which these loop closure volumes overlap the three‐dimensional spatial distributions provides estimates of loop formation that are much more reliable than earlier studies based upon the radial distribution function.
Hydrophobic interactions of DNA with long‐chain amines
Authors: Chatterjee R. , Chattoraj D. K. 
Published: December 2004

AbstractThe binding ratio, Γa, for several long‐chain amines to calf‐thymus DNA was measured as function of the ligand concentration, C, using the equilibrium dialysis method. The different amines used in the binding experiments at constant temperature were dodecyl trimethyl ammonium bromide (DTAB), myristyl trimethyl ammonium bromide (MTAB), cetyl trimethyl ammonium bromide (CTAB), and cetyl pyridinium chloride (CPCL). The formation and dissociation of the saturated DNA–amine complex were reversible. The initial slope of the binding isotherm decreased sharply with the reduction of the electrostatic effect as a result of the increase of the ionic strength of the medium. A sharp inflexion region was noted in the binding isotherm where the ligands bound in significant numbers may undergo hydrophobic interactions with each other. Γa increased with C until a maximum value, Γam, was reached, beyond which binding slowly decreased with an increase of concentration. Both Γam and Γa increased significantly with the increase of the hydrocarbon chain length of a ligand. The free energy change ΔGm for each saturated DNA–amine complex was evaluated on the basis of a thermodynamic relation and the standard state for binding was defined. The average free energy change for the binding per CH2 group of the amine was found to be −1550 cal/mol. The difference between ΔGm for CTAB and CPCL was examined on the basis of the structural difference of their head groups. The binding isotherms for MTAB and CPCL were obtained from the binding data at 15, 30, and 45°C. The binding increased with increasing temperature. From the plot of ΔGm/T vs 1/T, the changes in enthalpy and entropy due to the binding were evaluated for MTAB and CPCL. The binding reactions in these two cases were driven primarily by the entropy change due to the hydrophobic interaction. Standard free energy changes ΔG0m for the unsaturated complexes were close to ΔGm for the saturated complexes. The binding isotherms also depended on the nature of the neutral salt of the medium. At a given salt concentration, the order of the binding of the inorganic salts was as follows: KCl > NaCl > LiCl > Na2SO4 > MgCl2. The effect of pH on binding was also examined. The importance of these results on the formation of the reconstituted and natural nucleohistone complexes is discussed.
Use of amide 1H‐nmr titration shifts for studies of polypeptide conformation
Authors: Bundi Arno , Wüthrich Kurt 
Published: December 2004

AbstractThis paper shows that backbone amide proton titration shifts in polypeptide chains are a very sensitive manifestation of intramolecular hydrogen bonding between carboxylate groups and backbone amide protons. The population of specific hydrogen‐bonded structures in the ensemble of species that constitutes the conformation of a flexible nonglobular linear peptide can be determined from the extent of the titration shifts. As an illustration, an investigation of the molecular conformation of the linear peptide H‐Gly‐Gly‐L‐Glu‐L‐Ala‐OH is described. The proposed use of amide proton titration shifts for investigating polypeptide conformation is based on 360‐MHz 1H‐nmr studies of selected linear oligopeptides in H2O solutions. It was found that only a very limited number of amide protons in a polypeptide chain show sizable intrinsic intration shifts arising from through‐bond interactions with ionizable groups. These are the amide proton of the C‐terminal amino acid residue, the amide protons of Asp and the residues following Asp, and possibly the amide proton of the residue next to the N‐terminus. Since the intrinsic titration shifts are upfield, the downfield titration shifts arising from conformation‐dependent through‐space interactions, in particular hydrogen bonding between the amide protons and carboxylate groups, can readily be identified.
Synthesis and conformation of a polyoxyethylene‐bound undecapeptide of the alamethicin helix and (2‐methylalanyl‐L‐alanine)1–7
Authors: Mayr W. , Oekonomopulos R. , Jung G. 
Published: December 2004

AbstractThe stepwise synthesis and conformational studies of the N‐terminal helical partial sequence of the membrane‐modifying polypeptide antibiotic alamethicin are described. The polyoxyethylen esters of the fragments N‐t‐Boc‐L‐Pro‐Aib‐Ala‐Gln‐Aib‐Val‐Aib‐Gly‐OH and N‐Ac‐Aib‐L‐Pro‐Aib‐Ala‐Aib‐Ala‐Gln‐Aib‐Val‐Aib‐Gly‐OH are synthesized using polyoxyethylene (molecular mass 10,000) as solubilizing support. CD spectra of each intermediate in ethanol show α‐helix formation of the N‐protected peptide polymers beginning with the nonapeptide and of the N‐protonated sequences beginning with the decapeptide. Compared to the helix of alamethicin, temperature‐ and solvent‐dependent CD measurements indicate analogous conformational behavior. The results suggest that in lipophilic media the alamethicin helix can extend the full length of the partial sequence between the two proline residues and that aqueous media favor an increase of random‐coil conformation.For model studies of the particular lipid interaction of alamethicin, the stepwise synthesis of peptides with the alternating (Aib‐L‐Ala)n sequence (n = 1–7) was carried out on a polyoxyethylene support (molecular mass 6000). CD and ORD studies in ethanol showed a change from the random coil to a right‐handed α‐helix with increasing peptide length. This change is observed for the N‐protected peptides at a chain length of 8 residues and for the N‐protonated peptides at a length of 9 residues. The comparison of the CD data of free and polyoxyethylene‐bound peptides revealed that the solubilizing polymeric support cannot induce conformational changes. The intensities of the CD bands of t‐Boc‐(Aib‐L‐Ala)n‐OPOE (n ≥ 6) are higher than those of alamethicin, and these model peptides show similar temperature and solvent inducible changes of their helix contents.
Quasielastic light scattering by biopolymers. III. Effect of ionic strength on internal dynamics of DNA
Authors: Schmitz Kenneth S. 
Published: December 2004

AbstractQuasielastic light‐scattering data on DNA in 0.1, 0.5, and 1.0M NaCl, neutral pH, have been obtained in the scattering angle range 15 ⩽ θ ⩽ 50. The relaxation curves have been analyzed as a single exponential with a reciprocal relaxation time of the form 2DeffK2, where K is the fluctuation vector [proportional to sin(θ/2)] and Deff is the effective diffusion coefficient. The 1/τ vs sin2(θ/2) curves exhibit two regions that are proportional to sin2(θ/2), in accordance with the Lee‐Schurr and Lin‐Schurr theories for independent segment‐mean force and Rouse‐Zimm flexible polymers, respectively. In the region KR < 1, where R is a characteristic length, Deff is simply the translational diffusion coefficient, whereas Deff in the region KR > 1 represents the diffusion coefficient for a polymer segment. The data reported here indicate that the “transition” region between the two K2 extremes is strongly dependent on the ionic strength of the solvent. This observation, along with the salt variation of the segmental diffusion coefficient, suggests the internal dynamics of DNA are dependent on the ionic strength of the solvent. The relation of the present study to those of Lin and Schurr and of Caloin et al. is discussed.
Thermodynamics of mucopolysaccharide–dye binding. III. Thermodynamic and cooperativity parameters of acridine orange–heparin system
Authors: Menter Julian M. , Hurst Robert E. , Nakamura Nobuto , West Seymour S. 
Published: December 2004

AbstractBinding isotherms for acridine orange (AO)–heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements. The evaluation of thermodynamic parameters indicates that the interactions of AO with heparins from several animal sources are similar to each other in magnitude. Binding is highly exothermic (ΔH = −6 kcal mol−1) and is stabilized by dye–polymer and dye–dye (coopertive) interactions, as well as by entropic factors (ΔS = +7 e.u.). The predominant stabilizing factor appears to be the electrostatic attraction between the AO cation and the heparin polyanion, although the other factors are important as well. At 24°C the value of the cooperative binding constants for the various heparins range from 8.8 to 11.3 × 105M−1, corresponding to a free energy of −8 kcal mol−1. The degree of cooperativity, which is a direct measure of dye–dye interaction, varies with polymer:dye ratio; the theoretical basis for this variation remains to be elucidated. Electrophoretic data indicate that each heparin sample consists of a mixture of species, each with its own charge density. This precludes definitive interpretation of observed small differences in the values of the thermodynamic parameters among the various samples until each sample can be resolved into its components.
Application of distance geometry to protein tertiary structure calculations
Authors: Kuntz I. D. , Crippen G. M. , Kollman P. A. 
Published: December 2004

AbstractA general approach to the problem of molecular conformation is advanced. We describe a formalism that permits experimental and theoretical information to be incorporated into a set of upper and lower bounds on intramolecular distances. Structures (conformations) meeting these bounds can be readily generated and compared with each other. To illustrate the use of the method, we have employed a simple “firehose” model for protein folding to predict the long‐range hydrophobic interactions in a small protein: pancreatic trypsin inhibitor. Models of this type lead to the proper hairpin turns and a reasonable set of long‐range contacts for this protein. Application of the distance geometry method then yields backbone conformations with errors of 4–8 Å compared to the native structure. We discuss both the merits and shortcomings of the firehose model and the relation between distance geometry and energy minimization techniques.
Co‐oligopeptides containing two aromatic residues spaced by glycyl residues. X. Proton magnetic resonance study of co‐oligopeptides of tryptophan and glycine
Authors: Skrabal Peter , Rizzo Vincenzo , Baici Antonio , Bangerter Felix , Luisi Pier Luigi 
Published: December 2004

AbstractThe 1H‐nmr spectra of co‐oligopeptides of tryptophan and glycine with structure H‐Gly‐Trp‐(Gly)n‐Trp‐Gly‐OH (n = 0–2) and those of several di‐ and tripeptides have been recorded at 360 MHz with CD3OD solutions containing 0.1N NaOD. The assignment of resonance signals was generally possible by comparing the spectra of structurally related peptides with each other. In order to solve the remaining ambiguities in the assignment, H‐(αL,βS)(α,β‐d2)Trp‐OH, H‐Trp‐(αL,βS)(α,β‐d2)Trp‐OH, and H‐Trp‐(δ1,ε2,ζ2,ζ3,η2‐d5)Trp‐OH have been prepared and their spectra compared with those of the undeuterated compounds. The distribution of rotamers around the χ1 and (in two cases) χ2 torsion angles of the side chains has been obtained from the vicinal coupling constants 3J and from the long‐range coupling constants 4J. These data and an analysis of the chemical shifts of the Gly‐Cα protons suggest that the orientation of the aromatic side chain is influenced by the following order of decreasing interaction with the functional groups at N‐ and C‐side: ‐NH2 > –NHCO– > –CONH–> –COO−. This rule does not hold for the second Trp residue of di‐ and tripeptides containing the ‐Trp‐Trp‐ sequence, which has tentatively been attributed to steric effects.