bluuebunny/crossref_metadata_2025 huggingface dataset:
Factors affecting the kinetics of DNA reassociation in phenol–water emulsion at high DNA concentrations
Authors: Wieder Robert , Wetmur James G.
Published: December 2004

DNA reassociation kinetics using the phenol emulsion reassociation technique (PERT) [Kohne, D. E., Levison, S. A. & Byers, M. J. (1977) Biochemistry 16, 5329–5341] has been investigated at high DNA concentrations using an endonuclease S1 assay of reaction progress. Apparent second‐order rate constants fall on two intersecting straight lines when presented as a function of DNA concentrations on a log–log plot. In the low DNA concentration range, the rate constants drop about 10‐fold when concentration increases 1000‐fold. In the high DNA concentration range, the rate constants drop more than 10‐fold when concentration increases 10‐fold. The slopes of these lines are the same in different solvents and at different temperatures. The intersection between the lines occurs when the available catalytic surface is saturated. At high DNA concentrations, high‐complexity heterologous denatured DNA apparently competes 2–4 times better for the surface than homologous DNA because it does not participate in a reassociation reaction. Native and partially native DNA molecules cannot compete with single‐stranded DNA for a saturated surface. At high DNA concentrations, reactions using PERT become dependent on the single‐strand DNA length. Increasing length lowers reassociation rates.
Polydispersion in the diameter of fibers in fibrin networks: Consequences on the measurement of mass–length ratio by permeability and turbidity
Authors: Shah G. A. , Ferguson I. A. , Dhall T. Z. , Dhall D. P.
Published: December 2004

The diameters of the fibrin fibers in a clot are not uniform. Morphometric analysis of transmission electron micrographs show a bimodal distribution. The effect of polydispersity of fiber diameter on mass–length ratio calculated from the turbidity and permeability of a clot has been investigated with the aid of a two network model, the networks being called Major and Minor. The fibers in the Major network are many times thicker than those in the Minor network. In a model in which Major network fibers are 10 times thicker than fibers of the Minor network, the fibers in the Minor network make a negligible contribution to the turbidity of the clot. However, they may have a marked effect on its permeability. Experiments with clots made from human fibrinogen show that the Minor network is stabilized by α‐polymer and γ‐γ linkages and that without such linkages it is washed away during permeation. It remains relatively intact in crosslinked clots. In agreement with the theoretical model, when mass–length ratios calculated from the turbidity are compared with those calculated from the permeability, the latter were reduced in crosslinked clots with an intact Minor network.
Cu(II)–protamine interaction. II. The formation and structure of Cu(II) complexes of clupeine YII and of peptides mimicking clupeine N‐terminals
Authors: Salardi Sergio , Tosi Lucia , Garnier‐Suillerot Arlette , Toniolo Claudio , Bonora Gian Maria , Marchiori Fernando
Published: December 2004

The interaction of Cu(II) with the protamine clupeine YII (containing proline at the N‐terminal) and with four peptides (H‐Ala‐Arg‐OMe, H‐Ala‐Arg2‐OMe, H‐Pro‐Arg‐OMe, and H‐Arg4‐Tyr) has been studied by means of absorption, CD, and pH neasurements. The first two peptides mimic clupeine YI and Z N‐terminals; the third, the clupeine YII N‐terminal. At 1:1 molar ratio, clupeine YII yields two complexes: the first (I), at pH 6.6, through coordination via the N‐terminal and the contiguous peptide nitrogen forming a five‐membered chelate; the second (II), at pH 8.5, through the occupancy of the other two corners of the coordination square by amino nitrogens of the lateral chains. These complexes are strictly analogous and occur at the same pH as those formed with clupeine Z. Under the same conditions, all the peptides yield complex I in the first step, although the pH at which this complex is fully defined depends on the number of residues in the chain. It is 8.5 for dipeptides, decreases to 6.5 by the addition of a third residue to the chain, and remains constant when the number of residues is three or more. The amino nitrogens of lateral chains are unable to coordinate to the metal in a second step unless one additional peptide bond lies between the N‐terminal residue and that containing the lateral chain bound to the metal. Thus, H‐Ala‐Arg‐OMe and H‐Pro‐Arg‐OMe form hydroxyl complexes in a second step (pH 11), by deprotonation of one of the water molecules coordinated to the metal; one of the lateral chains of H‐Ala‐Arg2‐OMe is able to coordinate in a second step (pH 8.5), but it is only with H‐Arg4‐Tyr that a second complex (II) is obtained in which two amino nitrogens of lateral chains supersede the oxygens of water molecules in I, at pH 8.5.
Broadline proton magnetic resonance study of cellulose, pectin, and bean cell walls
Authors: MaCkay Alex L. , Bloom Myer , Tepfer Mark , Taylor Iain E. P.
Published: December 2004

We have used broadline proton magnetic resonance to study molecular motion in cellulose, a sodium pectate solution, a calcium pectate gel, and isolated bean cell walls. All samples were prepared in D2O to minimize the contribution of water to the observed signals. For each sample, a free induction decay was obtained, and the second moment, spin‐lattice relaxation, and dipolar relaxation were measured. Our results show that the large majority of protons in cellulose are immobile. Rigid and mobile domains were also observed in the pectate samples. We have shown that gelation induces large‐scale changes in the free induction decay, the second moment, and the relaxation behavior of the pectate. As with the other samples, rigid and more mobile domains were found in bean cell walls. The fraction in the rigid domains is much larger than the fraction of cellulose in the sample, suggesting that the noncellulosic wall components are also organized into rigid and mobile domains.
Photoselective synthesis of azobenzene‐containing cyclic oligosarcosine and its thermal cis → trans isomerization in solution
Authors: Sisido Masahiko , Ito Hiroshi , Imanishi Yukio
Published: December 2004

Oligosarcosines, which contain as azobenzene group at the center of the chain and amino groups at both ends [(Sar)nAzo(Sar)n], were prepared with the N‐carboxyanhydride method. The oligomers were coupled with an equimolar amount of succinyl chloride in the presence of triethylamine. When the condensation was carried out under photo irradiation, the azobenzene group assumed the cis configuration and the intramolecular reaction (cyclization) was facilitated. Intermolecular polycondensation occurred preferentially in the dark, in which case the azo group was trans. Cyclic oligosarcosine, which contains one azo group, was isolated by gel chromatography, and its thermal cis → trans isomerization was examined in dimethylformamide. The isomerization rate depended strongly on the number of sarcosine units n in the oligomer; for very small rings (n < 5), the rate constants were less than those for open‐chain analogs; for rings of medium size (n = 5 ∼ 10), they were larger than those for open‐chain analogs; and for longer chains, no significant difference was observed. This specific chain‐length dependence was explained by the conformational restrictions of the cyclic oligomers. The ring‐restricted isomerization was evidenced by an isomerization‐induced conformational change observed in 1H‐nmr spectroscopy.
Solution properties and chain flexibility of pullulan in aqueous solution
Authors: Kato Tadaya , Okamoto Toshihiro , Tokuya Tadashi , Takahashi Akira
Published: December 2004

Molecular characteristics for pullulan, a polysaccharide produced by a fungus Aureobasidium pullulans, were measured by light scattering, viscometry, and gel‐permeation chromatography. From the experimental data the Mark‐Houwink‐Sakurada viscosity equation in water at 25°C was determined for samples having the molecular weight M ranging from 48 × 103 to 2.18 × 106 g mol−1 as [η] = (1.91 ± 0.02) × 10−2Mw0.67±0.01 (in cm3 g−1); and as molecular weight decreased, the slope of the viscosity equation decreased, although the molecular weight values below 30 × 103 g mol−1 evaluated by gel‐permeation chromatography were somewhat unreliable. The unperturbed dimensions 〈R2〉01/2 of pullulan were estimated by determining the expansion factor αs, from the theoretical combination of theories for the interpenetration function Ψ and those for αs. The 〈R2〉0/M value estimated from this procedure in 6.7 × 10−17 cm2 mol g−1. We concluded that the polysaccharide chain that is linked by the α‐1,6‐glucosidic linkage behaves like a flexible chain in aqueous solution.
Kinetic and equilibrium studies of the interactions of silver ions with poly(A)
Authors: Yakabe Yoshikuni , Sano Takayuki , Kure Naohisa , Murakami Kiyofumi , Yasunaga Tatsuya
Published: December 2004

The interaction of silver ions with poly(A) was studied by potentiometric titration, uv spectrophotometry, and stopped‐flow spectroscopy. For 0 < rb < 0.5, where rb is moles of silver ion bound per mole of nucleotide base, there exists only one type of binding for poly(A). Using McGhee's theory, the binding parameters, such as intrinsic binding constant, number of sites per nucleotide, and cooperativity, were determined from the potentiometric titration data. Using the stopped‐flow method, one relaxation time was observed in 0 < r0 < 0.5, where r0 is the moles of silver ions added per mole of nucleotide base. The concentration dependences of the relaxation time suggest that the binding of silver ions to poly(A) proceeds through the following mechanism:

equation image

where M is free silver ions, P the free binding sites on poly(A), and C and C′ are two forms of the complex. The nature of the binding of silver ions to poly(A) is also discussed.
Ligand‐induced melting reaction of specific‐sequence DNA molecules
Authors: Tachibana Hideki , Wada Akiyoshi
Published: December 2004

An algorithm for the calculation of ligand‐induced helix–coil transitions of macromolecules of any specific sequence was derived. The probabilities of each residue to be in helix and ligand‐free, helix and ligand‐bound, coil and ligand‐free, and coil and ligand‐bound states can be calculated by extending the recursion relation formula proposed by D. Poland [(1974) Biopolymers 13, 1859–1871]. Calculations using hypothetical DNAs having block heterogeneities for melting reactions showed that cooperative binding specific to single strands weakens the effect of the heterogeneity. Fine structures in the melting profiles or cooperatively melting regions, which have so far been found in thermal melting experiments, were predicted to exist in ligand‐induced melting reactions for natural DNA fragments.
Conformation and folding in histones H1 and H5
Authors: Crane‐Robinson C. , Privalov P. L.
Published: December 2004

Denatured histones H1 and H5 can be readily refolded on salt addition. Their digestion by trypsin leads to limit peptides of about 80 residues having the same nmr and CD spectra as those of the intact parent histones. Scanning microcalorimetry shows that (1) the folded structures of H1 and H5 are located entirely in their limit peptides; (2) both have values of the specific denaturation enthalpy typical for small globular proteins; and that (3) both exhibit a classic “2‐state” transition (ΔH = ΔH). The heat‐denaturation profiles of H5 measured using intrinsic and extrinsic Cotton effect and side‐chain nmr peaks do not coincide at all. Only the intrinsic Cotton effects give a Tm and ΔH close to that from microcalorimetry. We conclude that these proteins exhibit large‐scale side‐chain motions that precede the macroscopic cooperative transition.
NMR analysis of structure and function of snake neurotoxins
Authors: Miyazawa Tatsuo , Endo Toshiya , Inagaki Fuyuhiko , Hayashi Kyozo , Tamiya Nobuo
Published: December 2004

The 270‐MHz proton‐nmr spectra of short neurotoxins (erabutoxins from Laticauda semifasciata and cobrotoxin from Naja naja atra) and long neurotoxins (toxin B from Naja naja and α‐bungarotoxin from Bungarus multicinctus) have been analyzed. The conformation of erabutoxin b in solution is largely consistent with the x‐ray crystal analysis, although the environment of His‐7 in solution is definitely different from that in the crystal. The pH‐dependent transition has been found for toxin B, indicating that the conformation in neutral solution is different from that in the crystal as grown from acidic solution. The deuterium‐exchange rates of the amide protons for the four neurotoxins have been measured. The order of structural rigidity is the same as the order of the irreversibility of neuromuscular block by neurotoxins.
1H‐NMR studies on poly(oxyethylene)‐bound oligopeptides
Authors: Bode Karsten , Mutter Manfred , Saltman Robert P. , Goodman Murray , Ribeiro Anthony A.
Published: December 2004

Conformational studies on poly(oxyethylene)‐bound homo‐, oligo‐, guest‐host, and sequential peptides synthesized according to the liquid‐phase method were carried out by means of 1H‐nmr spectroscopy. The solubilizing effect of the C‐terminal polymeric support allowed a thorough investigation of the secondary structure in solution.
Insulin's structural behavior and its relation to activity
Authors: Dodson E. J. , Dodson G. G. , Hubbard R. E. , Reynolds C. D.
Published: December 2004

This paper discusses the hypothesis that insulin undergoes a conformational change either before or during its binding to the receptor. The evidence for this is not conclusive but allows us to reconcile the following observations: (1) no chemical modification or deletion of invariant surface residues has abolished the hormone's activity—only reduced its potency. (2) Reduction in potency follows many modifications to different side chains, both variant and invariant. (3) There are insulins with perfectly preserved structure (by the criteria of aggregation, spectroscopy, and x‐ray analysis) that have markedly reduced potency. (4) Insulins with disturbed structure still exhibit real, sometimes substantial activity.
Microheterogeneity of bovine myelin basic protein studied by nuclear magnetic resonance spectroscopy
Authors: Deber Charles M. , Cheifetz Sela , Moscarello Mario A.
Published: December 2004

Myelin basic protein isolated from bovine white matter is known to consist of a mixture of three or more “charge isomers”, which can be separated by cation‐exchange chromatography. We are using 360‐MHz 1H‐nmr spectroscopy to establish the chemical and structural differences among them. Preliminary studies by difference spectroscopy between two of the isomers suggest (a) all aromatic residues, and probably their nearest‐neighbors, are unchanged; (b) the less cationic isomer lacks one (or two) of its C‐terminal Arg residues; and (c) a significant fraction of the two Met residues in the less cationic isomer is present as methionine sulfoxide.
Peptide factors as pharmaceuticals: Criteria for application
Authors: Wünsch E.
Published: December 2004

The increasing interest in the pharmaceutical use of peptide factors in human medicine presents formidable challenges for peptide chemistry. Fully reproducible multistage syntheses with a definite assessment of the degree of purity represent the crucial premise for the introduction of peptide factors as pharmaceuticals. Extensive studies of the stability of peptidic material on storage allows identification of the most suitable form of administration. Nevertheless, the high clearance rate of peptides as pharmaceuticals presents new challenges for improvement by structural modification of resistance to enzyme degradation without creating new problems related to metabolites.
Specific and nonspecific macromolecule–drug conjugates for the improvement of cancer chemotherapy
Authors: Hurwitz Ester
Published: December 2004

Antineoplastic drugs such as daunomycin, adriamycin, methotrexate, 5‐fluorouridine, cytosine arabinoside, and platinate were bound to antibodies directly or via a polymeric bridge. The drug antibody conjugates retained most of their drug and antibody activities when tested in vitro. Daunomycin–antibody conjugates were shown to penetrate tumor cells in the conjugated form. In animals, daunomycin–antibody conjugates were at least as effective chemotherapeutically as the corresponding free drugs and considerably less toxic. In some tumor systems, the daunomycin–antibody conjugates represented an improvement over the free drug. This improvement was restricted in some tumors to a particular injection route of the tumor and the treatment.
Breathing and bending fluctuations in DNA modeled by an open‐base‐pair kink coupled to axial compression
Authors: Manning Gerald S.
Published: December 2004

We develop a model designed to show that flexibility in the DNA molecule can arise from relatively improbable transient opening of base pairs. The axial direction changes at the site of an open base pair. The region between open base pairs is a double helix of hydrogen‐bonded base pairs with a slightly decreased rise per residue and a slightly increased helical winding angle. An analysis of the model yields several testable predictions. For example, we predict probability 0.026 for a base pair to be open at 25°C, a value close to that measured by hydrogen‐exchange experiments. Other predictions involve matters like the variation of persistence length with ionic strength and temperature, the variation of helical winding angle with temperature, and the kinetics of heat denaturation. An additional result of the analysis is an explanation of the high degree of local stiffness of the DNA molecule. Strong resistance to bending fluctuations is provided from two sources: increased polyelectrolyte repulsion among phosphate groups in the axially compressed stacks between open base pairs and the tendency of stacking forces to oppose opening of a base pair. Stacking forces, however, also support compression of the stacks between open base pairs, so that the net effect of stacking forces on elastic bending of DNA is small relative to the polyelectrolyte effect. If the ionic charges on the phosphate groups were absent, DNA would spontaneously fold, driven by the entropy gained when about 1% of its base pairs open.
Hydrogen bonding of the carbonyl groups of uridine nucleosides
Authors: Scheiner Steve
Published: December 2004

Molecular‐orbital calculations are used to compare the hydrogen‐bonding characteristics of the two carbonyl groups of uridine nucleosides. Various numbers of water molecules are allowed to interact with uracil. The hydrogen‐bond energies and the effects of these bonds on the electronic structure of uracil provide no evidence of a significant difference between the two carbonyls in terms of intrinsic properties. Calculations are also performed upon MMU, a derivative of the uridine nucleoside and a close analog of a system studied previously by nmr measurements. Energy minima are located on the conformational energy surface. The calculated anti‐gg global minimum is quite similar to the x‐ray structure. Electronic parameters examined in the various minima, as well as in hydrated complexes of MMU, again indicate no significant chemical differences between the two carbonyls. The theoretical data offer an explanation of the observed differences in shift of the two carbonyl 17O resonance signals when an aprotic solvent is replaced by water. Whereas the two carbonyls are found to be chemically similar, the observed difference in behaviour is attributed to steric factors. The lesser accessibility of the C2 carbonyl to solvation allows a smaller number of hydrogen bonds with water and hence a reduced shift when the solvent is changed.
Copolymerization kinetics of N‐carboxyanhydrides of some α‐amino acids: Influence of nature of amino acids
Authors: Atreyi M. , Rao M. V. R. , Kumar Satish
Published: December 2004

Studies on copolymerization kinetics of N‐carboxyanhydride (NCA) of O‐acetyl‐L‐tyrosine (T) with NCAs of L‐valine (V) and glycine (G) were carried out in dioxane at 25°C with n‐butylamine as initiator. The reactivity ratios for the VT system were found to be rV:rT:0.57:0.22; and for the GT system, rG:rT:0.26:0.42. A comparison of this data with that obtained when L‐analine was used in place of L‐valine or glycine showed that in the three systems, the reactivity ratio of the amino acid residue with a greater tendency to form ordered secondary structure was greater than that of its comonomer. Among the variable comonomers (glycine, L‐alanine, L‐valine) of O‐acetyl‐L‐tyrosine, it is again L‐alanine, whose tendency to form helical structure is very high, that has the greater reactivity ratio.
Circular dichroism of nucleic acid monomers. II. Derivation and application to polymers of a consistent set of guanine and cytosine transition parameters
Authors: Williams Arthur L. , Moore Dexter S.
Published: December 2004

An approximate semiempirical procedure has been developed in order to derive nucleic acid monomer π → π* electronic transition moment parameters. Using the approximate procedure, guanine (G) and cytosine (C) transition moment parameters have been derived from agreement found between calculated weight‐averaged and measured CD spectra of cyclic‐GMP and cyclic‐CMP. The derived base transition moment parameters have been assessed in CD spectral calculations on some G‐ and C‐containing nucleic acids for which reasonably good structural information exists. An attempt was also made at evaluating the likely CD spectral contributions of G and C electric n → π* transition moments whose magnitudes were taken to be the maximum expected. Overall, the results indicate that the derived G and C π → π* transition moment parameters are more successful in nucleic acid CD spectral calculations than those used in previous DeVoe theory CD calculations. In addition, the results indicate that electric n → π* transitions may be of importance in understanding nucleic acid monomer CD spectra but appear to be relatively unimportant in understanding nucleic acid polymer CD spectra. It is concluded that the derived G and C π → π* parameters are more useful in DeVoe theory CD calculations than parameters used previously.
Dynamic light scattering from thin rigid rods: Anisotropy of translational diffusion of tobacco mosaic virus
Authors: Wilcoxon Jess , Schurr J. Michael
Published: December 2004

An Exact theoretical expression for the apparent diffusion coefficient Dapp(K) of a thin rigid rod with arbitrary anisotropy of its translational diffusion diffusion coefficient is derived from the first cumulant of its dynamic structure factor. Dapp(K) is predicted to reach a limiting plateau value at extermely large values of KL, where K is the scattering vector and L the rod length. Howerver, that limiting plateau value is approached only very slowly along a quasi‐plateau with a very gradual slope. Dynamic light‐scattering studies have been performed on tobacco mosaic virus from K2 = (0.4–20) × 1010 cm−2 using 632‐8‐nm laser radiation. The present data yield D0 = (4.19 ± 0.10) × 10−8 cm2/s (corrected to 20,w conditions) and, with literature data to establish L = 2980 Å and the rotational diffusion coefficient DR = 318s−1, yield also Δ ≡ D∥ − D⊥ = (1.79 ± 0.38) × 10−8 cm2/s. The experimental data closely follow the curve of Dapp(K) vs K2 calcuated for these parameters. The present value of D0 substantially exceeds all previous dynamic light‐scattering values, but is in good aggreement with previous sedimentation data, which were confirmed for the presemt sample. The anisotropy ratio Δ/D0 = 0.43 ± 0.09 is in accord with theoretical predictions based on the modified Kirkwood algorithm, despite the fact the D0 lies significantly below its corresponding theoretical value. The present data largely predlude the possibility that both D0 and Δ/D0 could simultaneously match their theoretical predictions. We present a detailed comparison of the experimental data with the calculations of Tirado and Garcia de la Torre based on the modified Kirkwood algorithm and with the Broersma formulas.
Optical properties of cyclic dimers of amino acids: An experimental and theoretical study
Authors: Bowman Richard L. , Kellerman Martin , Johnson W. Curtis
Published: December 2004

CD spectra have been measured in the vacuum‐uv region to about 135 nm for cyclo(Lalanyl‐glycine), cyclo(Lalanyl‐L‐alanine), and cyclo(L‐prolyl‐L‐proline). In addition to the amide CD bands usually observed at wavelengths longer than 180 nm, a Independent systems calculations show that these intense short‐wavelenght bands can be attributed to σσ* transitions of the backbone. Transitions of the amide chromophore expected at wavelenghts shorter than 180 nm cannot account for the observed CD.
Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA
Authors: Holbrook Stephen R. , Kim Sung‐Hou
Published: December 2004

Chemical reactivities of the functional groups of yeast phenylalanine transfer RNA are compared with surface accessibilities of the groups calculated with various probe radii representing effective radii of the chemical reagents used. We observe 97% agreement with the hypothesis that the chemically modified bases are those with the greatest surface accessibility. This overall strong correlation supports the conclusion that base exposure in an important determinant of chemical modification in this polynucleotide.
Preparation of fractionated low‐molecular‐weight poly(S‐carboxymethyl‐L‐cysteine) by ion‐exchange chromatography
Authors: Maeda Hiroshi , Ito Takeshi , Suzuki Hidetoshi , Hirata Shuzo , Kako Isao , Yoshino Masachika , Ikeda Shoichi , Kobayashi Yuji
Published: December 2004

N‐Carboxyanhydride of S‐carbobenzoxymethyl‐L‐cysteine was polymerized by the addition of ethylamine as an initiator at anhydride–initiator ratios A/I = 3, 4, 6, 8, 12, and 16. Acetylation of the amino terminal was carried out with p‐nitrophenylacetate. After debenzylation, low‐molecular‐weight samples of poly(S‐carboxymethyl‐L‐cysteine) were obtained for A/I = 8, 12, and 16. These samples were fractionated by ion‐exchange chromatography (DEAE–cellulose). About six fractions of narrow molecular‐weight distributions were obtained. Their degrees of polymerization (DP) ranged from 8 to 16, as determined from proton nmr and also estimated based on their elution volumes on the ion‐exchange chromatography at constant ionic strengths. This range of DP covered the range of interest concerning the formation of the β‐structure in aqueous solutions; a fraction did not form the β‐structure, whereas another fraction did. The results of the gel filtration (Biogel P‐10) of the fractionated samples were consistent with the estimated DPs.
Influence of conformation on the fluorescence of tryptophan‐containing peptides
Authors: Anderson Janet S. , Bowitch Gary S. , Brewster Robert L.
Published: December 2004

Conformational‐energy calculations of the zwitterionic forms of Trp, Gly‐Trp, Pro‐Trp, Phe‐Trp, Trp‐Gly, Trp‐Phe, Trp‐Trp, and Trp‐Gly‐Gly were done using an empirical energy program for peptides (ECEPP). The resulting low‐energy conformations were analyzed for the presence of hydrogen bonds, the distances between carbonyl groups and the indole ring, the distances between the N‐terminal amino group and the indole ring, the dihedral angle between the planes containing carbonyl groups and the indole ring, and for dipeptides with two aromatic side chains, the dihedral angle and distance between the planes of the aromatic rings. This information was correlated with literature data from x‐ray crystallographic studies, fluorescence lifetime studies, and quantum‐yield experiments; proposed models of intramolecular quenching are discussed in light of the peptide conformations.
An affinity scale for the interaction of amino acid residues with nucleic acids
Authors: Porschke Dietmar , Ronnenberg Jorg
Published: December 2004

The affinity of amino acid residues to nucleic acids is probed by measurements of melting temperatures tm for the helix–coil transition at various concentrations of amino acid amides. The increase of tm on addition of ligand is described by the equation tm = t*m + αlog(1+Ktcλ), where t*m is the melting temperature in the absence of ligand, cλ the ligand concentration, and Kt the “tm‐onset” constant, which is analogous to an equilibrium constant. It is shown that Kt is closely related to the affinity of the ligands to the double helix, whereas the slope α mainly reflects the preference of the ligand binding to the helix versus the coil form. In the case of the amino acid amides, α is found to be virtually independent of the nature of the side chain with few exceptions, e. g., aromatic amides. The tm‐onset constant, however, strongly depends on the nature of the amino acid side chain. For simple aliphatic amino acids, the relative free energy of binding decreases with increasing hydrophobic free energy, e.g., a high affinity is found for Gly‐amide and a low affinity for Leu‐amide. This relation is modified by functional groups like OH in Ser‐amide. The helices poly[d(A‐T)], ploy[d(I‐C)]. and poly[d(A‐C)]·poly[d(G‐T)] exhibit similar affinity scales with relatively small variations. Our results demonstrate that the hydrophilic character of double helices at their surface disfavors binding of hydrophobic ligands unless special contacts can be formed. From our results we establish an affinity scale for the binding of amino acids to double helices.
Mean‐square hydrophobic moment for partially helical polypeptides
Authors: Hamed Maher M. , Mattice Wayne L.
Published: December 2004

A mean‐square helical hydrophobic moment, 〈h2〉, is defined for polypeptides in analogy to the mean‐square dipole moment, 〈μ2〉, for polymer chains. For a freely jointed polymer chain, 〈μ2〉 is given by Σm, where mi denotes the dipole moment associated with bond i. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣH, where Hi denotes the hydrophobicity of residue i. The tendency for correlations in orientations of residue hydrophobic moments in helices therefore dictates the size of 〈h2〉/〈H2〉, where 〈H2〉 denotes the average value of ΣH for all helices. The value of 〈h2〉/〈H2〉 will be greater than one in amphiphilic helices. A necessary prerequisite for this diagnostic usage of 〈h2〉/〈H2〉 is that the residue hydrophobic moment be oriented prependicular to the principal axis of the helix. Matrix‐generation schemes are formulated that permit rapid evaluation of 〈h2〉 and 〈H2〉. The behavior of 〈h2〉/〈H2〉 is illustrated by calculations performed for model sequential copolypeptides.
Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte
Authors: Bret Marc Le , Zimm Bruno H.
Published: December 2004

We report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson‐Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson‐Boltzmann equation when only the species with 1‐Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson‐Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter‐ and co‐ions, but particularly co‐ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surface of the polyion.
Distribution of counterions around a cylindrical polyelectrolyte and manning's condensation theory
Authors: Bret Marc Le , Zimm Bruno H.
Published: December 2004

The distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye‐Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear‐charge‐density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye‐Hückel theory. Therefore, we turn to the analytical solution of the Poisson‐Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we call RM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration; RM varies as κ−1/2, where κ is the Debye‐Hückel screening parameter. The Manning fraction, 1 – 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ−1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson‐Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson‐Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given polyion radius and charge density.
Interaction of poly‐5‐bromouridylic acid. I. Formation of helical complexes with various adenine and 2‐aminoadenine derivatives
Authors: Higuchi Shigesada
Published: December 2004

Complexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9‐substituted adenine and 2‐aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well‐resolved bands in the range of 210–350 nm. Other adenine derivative–poly(BU) complexes also afford similar CD spectra, while 2‐aminoadenine derivative–poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative–poly(BU) complexes are nearly identical in structure except for the ribose–phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9‐methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer–poly(U) system was found to be about 20°C in 0.4M NaCl–0.02M Na–cacodylate–5 × 10−4M EDTA (pH 7.0). Further, it was noted that the monomer–poly(BU) complexes are formed even when the Tm is lower than that of self‐folded poly(BU).
Conformational study of trinucleoside tetraphosphate d(pCpGpCp): Transition of right‐handed form to left‐handed form
Authors: Yoon Chang No , Kang Young Kee , Jhon Mu Shik
Published: December 2004

Using the semiempirical potential functions, conformational energies of the model compounds DMP−, d(pCp), d(pGp), and d(pCpGpCp) are calculated, and the B → Z transition is discussed along the pseudorotational path of the sugar ring. For dimethylmonophosphate anion, DMP−, the energy contour map is presented and the stabilities of the phosphodiester conformations discussed. For the sugar ring without the base attached, the minimum energies for each sugar‐puckering form are calculated along the pseudorotational path. The energy barrier of the interconversion between the C(3′)‐endo form and the C(2′)‐endo form is calculated to be about 2.0 kcal/mol. From the conformational energy calculations of the interconversions of mononucleoside diphosphates, d(pCp) and d(pGp), between the C(2′)‐endo conformer and the C(3′)‐endo conformer, the purine sugar segment is known to be more convertible than the pyrimidine sugar segment. The results also support the finding that the pseudorotational transition occurred with the O(1′)‐endo form more easily than with the O(1′)‐exo form. Based on the results of conformational studies of DMP−, d(pCp), and d(pGp), a topological transition of the handedness of the model compound, d(pCpGpCp), is studied. The left‐handed Z‐form is found to be less stable by about 8.5 kcal/mol than is the right‐handed B‐form. The energy barrier of the Z → B transition is calculated to be about 17.4 kcal/mol. The contributions of the electrostatic and nonbonded energies to the energy barrier are discussed in connection with the conformation changes of the model compound, d(pCpGpCp).
Proton polarizability of poly(L‐tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations
Authors: Zundel Georg , Leberle Klaus
Published: December 2004

We studied films of poly(L‐tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li+, Na+, K+) and of the degree of hydration were clarified. If Li+ ions are present, the OH ⃛−OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li+ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K+ ions are present. In dry films, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K+ ions when compared to the system with Li+ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K+ ions. Furthermore, POH ⃛−OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the ‐PO3− groupings are in a symmetrical environment, indicating that the K+ ions are removed from these groupings. If the degree of hydration increases further, hydrogen‐bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na+ ions are present, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.
Electric birefringence study of the purple membrane of Halobacterium halobium
Authors: Kahn Leo D. , Tu Shu‐I
Published: December 2004

An electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10−14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10−14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X‐100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk‐shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
Self‐association of the neuroregulatory peptide substance P and its C‐terminal sequences
Authors: Rueger Margitta , Bienert Michael , Mehlis Burkhard , Gast Klaus , Zirwer Dietrich , Behlke Joachim
Published: December 2004

Self‐association of substance P and its C‐terminal partial peptide sequences was studied by CD, quasi‐electric light scattering, and sedimentation experiments. CD spectra of these peptides are strongly influenced by self‐association. They exhibit strong characteristic negative ellipticities, suggesting the formation of a presumably B‐type ordered structure. The tendency to form multimers depends on chain length and constitution and has its maximum at the octapeptide (SP 8). The peptide multimers have a broad distribution of sizes in the range of 30‐ and 800‐nm diameter. Subdivision of this distribution into two size classes gives mean diameters of 60–100 nm (predominating)/200–800 nm for substance P and 30–50 nm/200–800 nm for SP 8 multimers.
Cation‐induced conformational changes in tRNA molecules
Authors: Mazzei F. , Onori G.
Published: December 2004

The uv absorption spectra and melting profiles of an initially ion‐free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first‐series transition‐metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4‐TU absorption region. Sharp differences have, however, been detected in the 290–305‐nm range in the presence of the various ions studied. When transition‐metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition‐metal ions are also able to bind directly to the bases.
Quasielastic light‐scattering studies on dinucleosomal‐sized DNA: Ionic‐strength dependence
Authors: Schmitz Kenneth S. , Lu Mei
Published: December 2004

Quasielastic light‐scattering (QELS) studies were performed on a monodisperse preparation of dinucleosomal‐sized DNA having an average of 375 base pairs. The QELS data were obtained at several time intervals at each angle examined over the range 30° < θ < 60° for the ionic strength solvents 500, 50, 10, and 1 mM in KCl. What results from this study is that two relaxation domains persist over the entire ionic strength range where the “splitting” between these two domains increases as the ionic strength is lowered. The ordinate intercept of Dapp vs Cp/2Cs, where Cp is the polyion concentration and Cs is the added salt concentration, is shown to give the “true” hydrodynamic value for the diffusion coefficient. The “splitting phenomenon” is interpreted in terms of two models currently in vogue: small ion–polyion coupled modes and translational–rotational coupled modes for rigid rods in congested solutions. Although neither model is in perfect agreement with the experimental results, the small ion–polyion coupled mode theory appears to provide a better quantitative description of the observations.
13C‐NMR chemical shifts and the conformations of rigid polypeptides
Authors: Tonelli Alan E.
Published: December 2004

13C‐nmr chemical shifts of backbone carbonyl and side‐chain β‐carbons in polypeptides provide structural information. Recent utilization of substituent effects on 13C‐nmr chemical shifts (principally γ‐effects) has permitted the rationalization of their sequence and conformation dependence when observed in linear, flexible polypeptides. In this report, we apply the γ‐effect method to study the 13C‐nmr chemical shifts observed in solution and in the solid state for the backbone carbonyl and side‐chain β‐carbons in conformationally rigid polypeptides, which are usually cyclic. As found previously for flexible, linear polypetides, the relative 13C‐nmr chemical shifts observed for the backbone carbonyl and side‐chain β‐carbons in conformationally rigid polypeptides are predictable from knowledge of their peptide residue sequence (primary structure) and conformation (secondary structure) via the γ‐effect method.
Solvent isotope effect on the differences in structure and stability between normal and deuterated proteins
Authors: Chen Chang‐Hwei , Tow Fred , Berns Donald S.
Published: December 2004

Differential scanning microcalorimetry was used to investigate the enthalpy (ΔHd) and the temperature (td) of thermal denaturation of normal (nondeuterated) (H‐PC) and deuterated (D‐PC) phycocyanins in D2O solvent. Values of td in D‐PC are about 5–7°C lower than those in H‐PC. The magnitudes of ΔHd in D‐PC are only 21–32% of those in H‐PC. During the protein unfolding, the heat‐capacity changes (ΔCp) in D‐PC are also lower than those in H‐PC. CD was employed to evaluate the secondary structure and the urea denaturation of these proteins in D2O solvent. These proteins have about the same α‐helix content. D‐PC is less resistant to the denaturant urea than is H‐PC. In general, the apparent free‐energy change in the process of protein unfolding at zero denaturant concentration is higher in H‐PC than in D‐PC. Comparisons of the present results for D2O solvent with those previously reported for H2O reveal that solvent isotope effect essentially does not change the α‐helix content in H‐PC and D‐PC. However, D‐PC or H‐PC has a higher random‐coil content in its secondary structure in D2O than in H2O. Substitution of H2O with D2O as the solvent increases td in both D‐PC and H‐PC, lowers ΔHd in H‐PC, and greatly lowers ΔHd in D‐PC. The deuterium solvent isotope effect does not change ΔCp in H‐PC but lowers ΔCp in D‐PC. In the urea denaturation, the magnitudes of (Cu)1/2 in H‐PC and D‐PC are not affected by such a solvent effect, whereas those of ΔG are greatly increased. These results are correlated with the structure and stability of the proteins.