bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of the peptide chain length on the stability of double‐stranded β‐helical species of D,L‐alternating oligovalines in chloroform solution
Authors: Lorenzi Gian Paolo , Jäuckle Hans , Tomasic Lera , Pedone Carlo
Published: December 2004

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

13C‐, 1H‐nmr, CD, and x‐ray crystallography revealed β‐turns of type III for Boc‐Gly‐L‐Ala‐Aib‐OMe, Boc‐L‐Ala‐Aib‐L‐Ala‐OMe; the 310‐helix for Boc‐Aib‐L‐Ala‐Aib‐L‐Ala‐Aib‐OMe; and antiparallel arranged α‐helices for Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe. An N‐terminal rigid α‐helical segment is found in the polypeptide antibiotics alamethicin, suzukacillin, and trichotoxin. The α‐helix dipole is essential for their voltage‐dependent pore formation in lipid bilayer membranes, which is explained by a flip‐flop gating mechanism based on dipole–dipole interactions of parallel and antiparallel arranged α‐helices within oligomeric structures.
Peptides as channel‐making ionophores: Conformational aspects
Authors: Spach Gérard , Trudelle Yves , Heitz Fréadéric
Published: December 2004

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

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

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

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

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

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

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

Molecular‐mechanics calculations have been carried out on the base‐paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A‐ and B‐DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B‐DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A‐DNA conformation. The molecular interactions responsible for these differential stabilities include both inter‐ and intrastrand base stacking, as well as base–phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine‐3′,5′‐pyrimidine sequence over the pyrimidine‐3′,5′‐purine sequence in both the A‐ and B‐conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate–base and base–base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine‐attched sugars and only in the B‐DNA geometry. We suggest a molecular mechanism, specifically, differential base–sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
Solvent effects on the dynamics of (dG‐dC)3
Authors: Freier Susan M. , Albergo Diane Deprisco , Turner Douglas H.
Published: December 2004

The kinetics of the coil‐to‐helix transition of (dG‐dC)3 in M NaCl, 45 mM sodium cacodylate, pH 7, were measured in H2O, D2O, 10 mol % ethanol, 10 mol % urea, and 10 mol % glycerol. At 43°C in H2O the recombination rate is 1.3 ± 0.2 × 107 M−1 s−1; the dissociation rate is 68 ± 10 s−1. The destabilization of the helix in 10 mol % ethanol and 10 mol % urea relative to water is primarily due to a large increase in the helix‐dissociation rate. In 10 mol % glycerol, the destabilization of the helix is due to a decrease in the recombination rate and an increase in the dissociation rate. Above 20°C, two exponential decays longer than 1 μs are observed after a temperature jump. The slower relaxation time is 4–10 times faster than the bimolecular component and is independent of oligomer concentration. We attribute this relaxation to a rapid equilibrium between two helical states. At low temperatures and oligomer concentrations of 1 mM or greater, the helices aggregate in 1M NaCl. Experimental data are presented under conditions where aggregation is unimportant and evidence is given that the ΔH‐determined spectroscopically is unaffected by aggregation.
Translational friction of rigid assemblies of spheres: Derivation and application of new hydrodynamic interaction tensors
Authors: De Haën Christoph , Easterly Russell A. , Teller David C.
Published: December 2004

In connection with our goal of calculating by practical methods the frictional properties of biopolymers from surface shells composed of spheres, we have investigated by the method of reflections the low‐Reynolds‐number hydrodynamic interaction between two unequal‐sized spheres in translation. Previous results, in which the velocities were used as independent variables and which have the form of truncated infinite power series, were substantially extended. By inversion of the power series, new power series with better convergence properties were obtained. Equivalence of these inverted power series with those previously reported based on the method of reflections, when forces are used as independent variables, was demonstrated, and the solutions were again substantially extended. Applying the Lagrange interpolation to data generated from exact theories for the hydrodynamic inteaction between two spheres, it was demonstrated that the various forms of the method of reflections do not just give reasonable power series, but actually yield optimal ones. These findings constitute a unification of diverse approaches and show methods of interconversion of results. On the basis of the power series obtained, a set of new hydrodynamic interaction tensors for two unequal spheres were derived. While the new tensors described the case of two unequal spheres with considerably more accuracy than those previously reported, direct application of these tensors to objects composed of more than two spheres revealed some unexpected problems resulting from overcorrection in the fourth‐order term. However, when the tensors were preaveraged over all orientations of the multisphere object, a formula for the scalar translational friction coefficient was obtained that outperformed all but the most involved earlier approaches. It thus constitutes an improved and practical solution to the problem of computing translational friction coefficients of objects describable by a surface shell of many spheres, such as proteins.
Calculations of the spatial distribution of charge density in the environment of DNA
Authors: Klein Brian J. , Pack George R.
Published: December 2004

A technique for modeling the structured environmental charge distribution about isolated polyions of arbitrary geometry is presented and applied to B‐DNA. It describes the three‐dimensional variation of the continuous space charge and allows estimation of local electrostatic potentials and fields that the electrolytic environment induces at nuclei of the polyion. Calculations involve an iterative solution to the set of equations coupling electrostatic potential and average charge density in space. By dividing the region around a DNA segment into finite volume elements, sets of numerically stable atmospheric charge densities have been obtained over a range of concentrations of added monovalent salt. Results are in good agreement with those of Poisson‐Boltzmann calculations on comparable systems and are consistent with findings from Monte Carlo simulations of DNA.
Vibration of DNA polymer in viscous solvent
Authors: Dorfman B. H. , Van Zandt L. L.
Published: December 2004

The problem of viscous damping of vibrating DNA polymer in solution is solved in the low‐amplitude limit for all acoustic branches of the spectrum. The acoustic spectrum covers the microwave region of frequencies. Analytic solutions are obtained for a model describing the DNA polymer as a smooth circular cylinder. Numerical solutions are presented for a model describing the DNA polymer as a twisted cylinder of elliptical cross section. The amount of mass loading is determined for both models and the damped spectrum for the mass‐loaded oscillator is calculated. The viscous damping is found to be a strong function of frequency, singular at very low frequencies for all modes except the torsional mode of the circular cylinder. All acoustic modes are overdamped, implying that the observation of well‐defined resonances in DNA requires either highly structured water on the molecular level or very dry material.
Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains
Authors: Taylor Eric R. , Olson Wilma K.
Published: December 2004

A combined geometric and potential‐energy analysis has been carried out to identify the torsional arrangements of the nucleic acid chain that can accommodate the intercalation of small planar moieties. In contrast to previous theoretical efforts, which detail local conformations after adjacent bases are positioned in space, the likely geometries are found here on the basis of the base orientations that result from all feasible combinations of the nine torsional variables of the basic dinucleotide intercalation unit. The relatively mobile nature of the sugar‐phosphate backbone, together with the fairly long stretches of chemical bonds between adjacent units, is apparently responsible for the large number of feasible binding geometries. Some previously overlooked conformations with unusual sugar‐puckering combinations and various phosphodiester arrangements are found in the survey. A large proportion of the energetically favored intercalation states are closely related to the backbone conformations of familiar double‐helical models such as A‐, B‐, and Z‐DNA, as well as the Watson‐Crick model. Moreover, the intercalated forms are found to interconvert smoothly along a continuous conformational pathway. The intercalation structures derived from x‐ray crystallographic analyses of drug‐oligonucleotide complexes, in contrast, are stiff three‐dimensional forms essentially frozen in a single domain of conformation space. Specific ligand‐nucleic acid interactions that may be responsible for the experimental observations are not included in this study. The classical intramolecular potential energies reported here are highly approximate, providing only rough gauges of the relative importance of the many competing conformations.
A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double‐ and single‐stranded DNA
Authors: Levy George C. , Craik David J. , Kumar Anil , London Robert E.
Published: December 2004

The nature of internal and overall motions in native (double‐stranded) and denatured (single‐stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular‐dynamics modeling using 13C‐nmr spin‐relaxation data obtained over the frequency range of 37–125 MHz. The broad range of 13C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double‐stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τx = ∼10−6 s;τZ = ∼1.8 × 10−8s), which is in good agreement with values calculated from hydrodynamic theory (τx = ∼1.8 × 10−6 s; τZ = ∼2.7 × 10−8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual CH vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τw = ∼4 × 10−9 s, θcone = ∼21°) or as a bistable jump (τA = τB = ∼2 × 10−9 s, θ = ∼15°). We discuss the critical role in molecular‐dynamics modeling played by the angle (β) that individual CH vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τW = ∼0.2 × 10−9 s, θcone = ∼50°), and overall motion is affected by becoming essentially isotropic (τx = τZ = ∼5 × 10−8 s) for the single‐stranded molecules. Since 13C‐nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.
Magnetic birefringence study of the electrostatic and intrinsic persistence length of DNA
Authors: Maret G. , Weill G.
Published: December 2004

Magnetic birefringence experiments were performed on solutions of DNA of intermediate molecular weight at several concentrations (cp) over a wide range of ionic strengths (of NaCl and MgCl2). The specific Cotton‐Mouton constant (CM/cp) is found to be independent of cp when contributions from cp to the ionic strength (μeff) are taken into account according to the concept of counterion condensation. For μeff ≳ 10−2M, CM/cp is also independent of the ionic strength; the plateau value results in an acceptable value of the intrinsic persistence length, when a revised theoretical expression for the magnetic birefringence of wormlike chains is used, combined with new experimental data for the monomeric optical and magnetic anisotropy. For μeff < 10−2M, CM/cp strongly, or wealky, increases with decreasing μeff, depending on the valency of the counterion used (Na+ or Mg2+, respectively). This increase agrees quantitatively with the variation of the electrostatic persistence length as predicted by Odijk [(1977) J. Polym. Sci. Polym. Phys. Ed. 15, 477–483], Odijk and Houwaart [(1978) J. Polym. Sci. Polym. Phys. Ed. 16, 627–639], and by Skolnick and Fixman [(1977) Macromolecules 10, 944–948]. A comparison with other experimental data seems to reveal the importance of excluded‐volume effects, which are particularly pronounced in the low‐salt regime.
Interacalation of ethidium ion into DNA and RNA oligonucleotides
Authors: Nelson Jeffrey W. , Tinoco Ignacio
Published: December 2004

The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo‐oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest‐neighbor exclusion. For the ribo‐oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo‐oligonucleotide showed all sites equivalent and no cooperativity. For the ribo‐oligonucleotides the enthalpy for ethidium binding is −14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M−1 for the two strong sites (4 × 103M−1 for the weak site) or K = 2.5 × 105M−1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo‐oligonucleotide the enthalpy of binding is ‐9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M−1).
Characterization of DNA structures by laser Raman spectroscopy
Authors: Prescott B. , Steinmetz W. , Thomas G. J.
Published: December 2004

Oriented fibers drawn from aqueous gels of calf‐thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A‐DNA and B‐DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm−1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D2O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A‐ and B‐DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation‐sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700‐cm−1 interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000‐cm−1 region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A‐ and B‐DNA structures. The results are extended to Z‐DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleoproteins and viruses are considered.
Structure of hydrated Na+ ions around a region of A‐ or B‐DNA helix
Authors: Lee W. K. , Gao Y. , Prohofsky E. W.
Published: December 2004

A molecular‐dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A‐ or B‐DNA helix with one Na+ counterion per nucleotide. Four Na+ ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ ions were assumed to be Lennard‐Jones spheres that also carried charges. Stillinger four‐point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B‐DNA and 20, 32, and 46 in A‐DNA fragments. The arrangements of the Na+ ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of DNA molecules.
Variation of longitudinal acoustic velocity at gigahertz frequencies with water content in rat‐tail tendon fibers
Authors: Cusack Stephen , Lees Sidney
Published: December 2004

Brillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high‐humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799–2815] with the variations of the sonic velocity with water content.
Contributions of the PO ester and CO torsion angles of the phosphate group to 31P‐nuclear magnetic shielding constant in nucleic acids: Theoretical and experimental study of model compounds
Authors: Giessner‐Prettre Claude , Pullman Bernard , Parado Fernando Ribas , Cheng Doris M. , Iuorno Virginia , Ts'O Paul O. P.
Published: December 2004

The magnetic shielding constant of the 31P nucleus of the dimethylphosphate anion is calculated by an ab initio method for different values of the torsion angles about the PO ester bond and different orientations of the methyl groups. The results obtained tend to show that both types of conformational parameters contribute to the value of σ31P. The largest shielding is obtained when the methyl groups are staggered with respect to the PO bond; the smallest, for the eclipsed arrangement. Measurements carried out on the 16 deoxyribodinucleoside monophosphates show that in the majority of cases σ31P is shifted toward lower field for the dimers having large values of 3JPH3′ and 3JPH5′(5″). The theoretical results are discussed in relation to experimental data for polynucleotides and nucleic acids.
Ion transport through liquid membrane by cyclic octapeptides
Authors: Kimura Shunsaku , Imanishi Yukio
Published: December 2004

Cation transport through a chloroform liquid membrane by cyclic octapeptides—cyclo(Leu‐Pro)4, cyclo(Phe‐Pro)4, and cyclo[Lys(Z)‐Pro]4—was investigated. All of these cyclic octapeptides transported K+ and Ba2+, and the rate of cation transport was correlated with the ability to extract cations from the aqueous phase to the chloroform phase. Among them, cyclo (Leu‐Pro)4 was the most efficient and transported K+ and Ba2+ selectively from other alkali and alkaline earth cations, respectively. The rate of K+ transport by cyclo(Leu‐Pro)4 was about one‐third as fast as that by dicyclohexyl 18‐crown‐6. Picrate anion transport against its concentration gradient was observed by cyclo(Leu‐Pro)4, which is conjugated with the selective transport of K+. Complex formation in a liposome between cyclo(Leu‐Pro)4 and Ba2+ was observed, but the binding constant was low.
Viscometry and sedimentation equilibrium of partially hydrolyzed hyaluronate: Comparison with theoretical models of wormlike chains
Authors: Cleland Robert L.
Published: December 2004

Fractionated samples of sodium hyaluronate of low molecular weight were used to calibrate the carbazole method for glucuronyl analsis and to determine the density increment (based on dry weight) of 0.444 (±0.003) mL/g in water and 0.386 (±0.003) mL/g for samples dialyzed against 0.2M NaCl. Weight‐average molecular weights obtained by high‐speed sedimentation equilibrium were used to calibrate the limiting viscosity number [η] in 0.2M NaCl, which gave [η]/Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 105. Experimental data from this work and the literature, including viscosity and light‐ and small‐angle x‐ray scattering measurements, were compared to theoretical chain models of the Kratky‐Porod (KP) wormlike and the helical wormlike (HW) chain, as treated by Yamakawa and collaborators. Although either model could be fitted to experimental data about equally well with consistent parameters, provided those for the HW chain were of weakly helical nature, calculation of the unperturbed meansquare end‐to‐end distance as a function of chain length from a conformational model favored the KP chain alternative. The parameters that provide the best fit to experimental data for the KP wormlike model are a persistence length of 4.5–5 nm and a diameter of 1.1 nm. The latter is resonable for a hydrated hydrodynamic cylinder in view of the approximate unhydrated value of 0.7 nm estimated from the density increment.
Effects of viscous solvent on DNA polymer in a fiber
Authors: Dorfman B. H. , Van Zandt L. L.
Published: December 2004

The viscous forces acting on a DNA macromolecule in a fiber are calculated. The DNA polymer is modeled as an infinite rod of elliptical cross section with a grooved surface. The viscous solvent is hydrodynamic water. Appropriate boundary conditions for determining the viscous forces on the acoustic vibrational modes are discussed. The viscous forces acting on each mode are then calculated as functions of both frequency and amount of water in the fiber. The mass loading of the DNA due to water in the grooves is shown to reduce the longitudinal acoustic velocity, which agrees with recent experimental results. The longitudinal modes are determined to be underdamped and correspondingly sharp over a range of frequencies and humidities appropriate to experimental conditions. The torsional and transverse acoustic modes are still strongly overdamped.
Kinetics of irreversible dissociation for proteins bound cooperatively to DNA
Authors: Balazs Anna C. , Epstein Irving R.
Published: December 2004

We consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one‐dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22, 1697–1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n−2) internal positions of an n‐cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero‐order dissociation kinetics predicted by the Lohman model.
Liquid crystallinity in collagen solutions and magnetic orientation of collagen fibrils
Authors: Murthy N. S.
Published: December 2004

Studies of the optical birefringence of solutions of acid‐soluble collagen from rat‐tail tendon at 22°C in the pH range 1.0–6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt‐soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the magnetic field.
Dielectric properties of aqueous solutions of sonicated DNA above 40 MHz
Authors: de Xammar Oro Juan R. , Raul Grigera J.
Published: December 2004

The dielectric properties of sonicated calf‐thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix‐to‐coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.
Topological aspects of conformational transformations in proteins
Authors: Chiavarini S. , De Santis P. , Morosetti S. , Palleschi A.
Published: December 2004

The topological aspects of the conformational transformations in proteins are investigated using a new peptide‐ribbon representation of the tertiary structure. The topological parameters evaluated on a set of 49 proteins show striking regularities that extend beyond the secondary structures actually present and are interpreted as a manifestation of the topological invariance of conformational transformations in globular proteins.
Buried surface area, conformational entropy, and protein stability
Authors: Rashin Alexander A.
Published: December 2004

In this paper, how to calculate the loss of conformational entropy owing to protein folding from data on protein stability, the disulfide bonding pattern and the buried surface area is suggested. The average values of the initiation constant and entropy loss per residue for the helix‐coil transition, calculated according to the suggested approach, are in a good agreement with available data. It is shown that the loss of conformational entropy for proteins and protein fragments, thus calculated, can be quite accurately approximated by three straight lines, each representing the loss of conformational entropy in a given range of molecular weights. The first line corresponds to the formation of α helices, the second to proteins with molecular weights below 10,000, and the third to proteins with molecular weights above this value. The standard error varied from 1.3 kcal/mol, for the first region, to between ∼3 and 5 kcal/mol for the third. Use of these approximating linear functions is proposed for the calculation of protein stabilities from x‐ray data. Such calculations, performed for more than 20 proteins and their fragments, have led to at least qualitative agreement between the calculated stabilities and available data for more than 90% of the cases. While quantitative predictions are at the limit of the method's accuracy, predictions of the probabilities of proteins or their fragments to be stable are expected to give a correct answer in ∼95% of the cases.
Large‐amplitude bending motions in phenylalanine transfer RNA
Authors: Tung Chang‐Shung , Harvey Stephen C. , McCammon J. Andrew
Published: December 2004

Conformational energy calculations on yeast tRNAPhe reveal several likely modes of intramolecular bending, including both hingelike motions (rotations about a discrete point) and distributed flexibility (deformations that bend a double‐helical segment along a smooth curve). By combining these modes of motion, the molecule can be bent from the L‐shaped crystallographic structure to two extremes. It can be straightened into a nearly linear conformation at an energy cost of about 50 kcal/mol, and it can be doubled over to a conformation where the anticodon and the amino acid acceptor terminus are separated by about 40 Å at an energy cost of less than 100 kcal/mol. A bending range of over 100° can be covered for 50 kcal/mol, and we estimate that this value could be cut in half with a minimization algorithm that produced optimum stereochemistry. These energies are comparable to those that would be associated with changes in solvation due to changes in surface area as the molecule bends, indicating that there are no major steric barriers to tRNA flexibility and that variations in solvent conditions and interactions with other molecules may produce large changes in the overall conformation of tRNA.
A high‐resolution 13C‐nmr study of collagenlike polypeptides and collagen fibrils in solid state studied by the cross‐polarization–magic angle‐spinning method. Manifestation of conformation‐dependent 13C chemical shifts and application to conformational characterization
Authors: Saitô Hazime , Tabeta Ryoko , Shoji Akira , Ozaki Takuo , Ando Isao , Miyata Teruo
Published: December 2004

We have recorded high‐resolution 13C‐nmr spectra of collagen fibrils in the solid state by the cross‐polarization–magic‐angle‐spinning(CP–MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31‐helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (AlaGlyGly)nII], and the triple‐helical polypeptides [(ProGlyPro)n and (ProAlaGly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31‐helical (AlaGlyGly)n and triple‐helical (ProAlaGly)n are significantly displaced, compared with those of the α‐helix, β‐sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen‐like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple‐helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31‐helix, reflecting further conformational change from the 31‐helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C  O carbons of the triple‐helical polypeptides are substantially displaced upfield (4.1–5.1 ppm), with respect to those of the 31‐helical polypeptides. These displacements are interpreted by that Gly C  O of the former is not involved in NH …︁ O  C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.

On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C‐nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
Stress relaxation in fine fibrin films: Comparison of films prepared with thrombin and ancrod
Authors: Müller Michael F. , Ferry John D.
Published: December 2004

Measurements of stress relaxation in uniaxial extension have been made on fibrin film prepared from fine bovine fibrin clots (i.e., clots in which there is minimal lateral aggregation of protofibrils), both ligated and unligated, and polymerized with both thrombin and ancrod, plasticized with either aqueous buffer or glycerol. The stress 100 s after imposition of strain was approximately proportional to In λ, where λ is the stretch ratio. Ligated thrombin films showed comparatively little relaxation over a period of one day and almost complete recovery after release of stress. In unligated thrombin films, there was substantial relaxation in two stages, as previously observed for coarse films, and substantial irrecoverable deformation. The extent of relaxation and the proportion of strain that was irrecoverable increased with the magnitude of the strain. In ancrod films (unligated), there was much more relaxation (stress decaying by as much as a factor of 10) and much more irrecoverable deformation (about 70% of the initial deformation); these results did not depend on the magnitude of the strain. When an ancrod film was released after relaxation and submitted to a second stretch, the extent of the second relaxation was much less. These observations are discussed in relation to the structure of fine films and possible mechanisms for relaxation and irrecoverable deformation.
Conformational transitions and geometry differences between low‐energy conformers of N‐acetyl‐N′‐methyl alanineamide: An ab initio study at the 4‐21G level with gradient relaxed geometries
Authors: Schäfer Lothar , Klimkowski V. J. , Momany Frank A. , Chuman H. , Van Alsenoy C.
Published: December 2004

Energy pathways between the αR, β′, C, and β‐regions of the conformational energy surface of N‐acetyl‐N′‐methylalanyl amide were obtained by SCF ab initio calculations on the 4‐21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between αR and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x‐ray methods are identified. In addition to the ϕ,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β‐region is described.
Polyelectrolyte effects on site‐binding equilibria with application to the intercalation of drugs into DNA
Authors: Friedman Richard A. G. , Manning Gerald S.
Published: December 2004

A theory of polyelectrolyte effects on site‐binding equilibria is generalized to multivalent ligands, multivalent supporting salt, intercalation, and multiple‐site exclusion. The theory, which contains no adjustable parameters, except the number of sites excluded by a bound ligand, gives the dependence of the equilibrium constant on the binding fraction and the salt concentration. The theory is compared with prior experimental data for the dissociation of poly(acrylic acid), the binding of magnesium to polyphosphate, and the binding of ethidium and actionomycin D to DNA. The theory predicts the binding fraction dependence of the dissociation constant of poly(acrylic acid) well. The theory predicts the binding fraction dependence of the association constant of the binding of Mg2+ to polyphosphate well, if either one or two phosphates are bound by a magnesium ion. We conclude that polyelectrolyte effects on drug‐DNA equilibria must be substantial. It follows that an incorrect estimate of the number of sites excluded by a bound drug molecule (because of its size or some other nonpolyelectrolyte effect) can be obtained from binding data if polyelectrolyte effects are ignored. The estimate is also within the context of, and subject to the validity of, the model used to describe the nonpolyelectrolyte contribution to binding. Our results suggest that, subject to these conditions, the anticooperativity of the binding of ethidium to DNA might be explained solely in terms of polyelectrolyte effects, and without reference to multiple‐site exclusion, if sequence‐specificity effects can be safely ignored. Our results also suggest that as few as two base pairs might be excluded by an actinomycin molecule. The theory gives fairly good agreement for the salt‐concentration dependence of the association constant of all of the systems studied, including the complex of the neutral drug actinomycin with DNA.
Magnetic circular dichroism of adenine, hypoxanthine, and guanosine 5′‐diphosphate to 180 nm
Authors: Sutherland John Clark , Griffin Kathleen
Published: December 2004

The magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′‐diphosphate reveals that, for each species, the uv‐absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
On the precipitation of proteins by polymers: The hemoglobin—polyethylene glycol system
Authors: Haire Robert N. , Tisel William A. , White James G. , Rosenberg Andreas
Published: December 2004

The addition of polyethylene glycol (PEG) of MW 6000 to solutions of oxy‐ and deoxyhemoglobins results in an increase in the thermodynamic activity of these proteins. This in turn results, when PEG concentration is high enough, in phase separation into two phases; a protein‐rich, PEG‐poor phase and a PEG‐rich, protein‐poor phase. With increasing PEG concentration, the protein‐rich amorphous phase becomes metastable and is converted into a well‐defined crystalline or polymer phase. The logarithm of protein solubility is a linear function of PEG content up to a protein concentration of 150 g/L because the expression for the activity coefficient can, up to this concentration range, be approximated by a logarithmic function. Curvature appears at higher protein concentrations. Activities obtained by extrapolation from linear portions of the function, showing an unchanged, well‐defined crystalline state, yield an activity coefficient for the saturated PEG‐free protein solution in agreement with the appropriate values obtained from hard‐sphere calculations of excluded volume [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437–452]. Solutions containing two hemoglobin species showed cocrystallization of the hemoglobins with a triple point where two crystal forms can be shown to coexist.