bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA bis‐intercalation: Theoretical calculation of binding curves
Authors: Shafer Richard H.
Published: December 2004

A statistical mechanical calculation of the binding properties of DNA bis‐intercalators is presented, based on the sequence‐generating function method of Lifson. The effects of binding by intercalation of one or both chromophores of a bifunctional intercalating agent are examined. The secular equation for a general model that includes the effects of neighbor (nearest and non‐nearest) exclusion and/or cooperativity in the binding of both singly and doubly intercalated ligands is derived. Numerical results for binding curves are presented for a more restricted model in which each type of bound ligand rigorously excludes its nearest neighbor and the total number of sites covered by a doubly intercalated ligand is variable. At low values of free ligand concentration bis‐intercalation dominates the binding process, while at high value of free ligand concentration, intercalation of only one chromophore per ligand becomes significant due to the unavailability of contiguous free sites required for bis‐intercalation. Also, depending on the binding parameters, the free energy of the system can be lowered by a loss of doubly intercalated ligands in favor of singly intercalated ones. Corresponding to this transition in binding mode, the average number of sites occupied by a bound ligand decreases from that characteristic of bis‐intercalation to that characteristic of mono‐intercalation as free ligand concentration increases. An analysis of Scatchard plots describing bis‐intercalation is presented.
Absorption and circular dichroic spectral studies on the self‐association of daunorubicin
Authors: Martin S. R.
Published: December 2004

The self‐association of daunorubicin in aqueous solution has been examined using visible absorption, fluorescence, and CD measurements. Spectral changes in the concentration range 10−6 to 1.5 × 10−3M have been interpreted in terms of a monomer–dimer equilibrium for daunorubicin. The data have been analyzed using a nonlinear curve‐fitting technique. The results obtained in this study differ markedly from previously published results, and possible reasons for this difference are discussed. The effect of solvent, temperature, and ionic strength on the dimerization process is investigated.
Kinetics of macromolecules reacting with ligand
Authors: Phillipson Paul E. , Wyman Jeffries
Published: December 2004

In order to get an idea of the transient and stationary behavior to be looked for in a biological macromolecular system such as an enzyme or respiratory protein in the presence of its ligands, we have studied the coupled kinetic equations applicable to a simple allosteric model, based on the concerted two‐state model of Monod et al. [(1965) J. Mol. Biol. 12, 88–118]. Exact solutions of the equations are given for three special cases, and two complementary methods are developed to generate approximate solutions in the general case, always, however, with the assumption that the equations are linear due to maintenance of ligand activity at a constant level. Subject to this assumption, these approximation methods have applicability to coupled rate equations beyond those considered here. As an illustration of how the results can provide the basis for a detailed analysis of actual kinetic data on working proteins, the formalism is applied to the kinetics of binding of oxygen by hemoglobin. An important result is that although time evolution to the steady state is in principle determined by several relaxation times, the effect of cooperativity for the case considered is to establish the dominance of one of them relative to the others. This suggests that for a macromolecule with a large number of binding sites, only one, or at most a few, of the many possible relaxation times are significant for specification of cooperative kinetics. The methods developed here, which will be applied more extensively elsewhere, provide a systematics for finding these dominant relaxation times.
Dielectric changes in hyaluronate solutions at microwave frequencies as a function of concentration, system pH, and temperature
Authors: Jani S. K. , Dahiya J. N. , Roberts J. A.
Published: December 2004

The dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic‐type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6–8 and at constant ionic strength 0.1. A temperature‐dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature‐dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
Experimental support for a right‐handed vertical double helix
Authors: Mitra C. K. , Dhingra M. M. , Sarma Ramaswamy H.
Published: December 2004

The experimentally observed geometry of a miniature double helix of high anti (χCN fixed ≃ 120°) nucleic acid structure indicates substantial interstrand base stacking with little intrastrand base stacking. This geometry is consistent with the right‐handed vertical double helix in which the base planes are parallel to helical axis proposed by Olson [(1977) Proc. Natl. Acad. Sci. USA 74, 1775] from theoretical calculations. The experimental data do not agree with the left‐handed model in which the base planes are perpendicular to helical axis that has been proposed by Yathindra and Sundaralingam [(1976) Nucl. Acids Res. 3, 729]. The theoretically computed chemical shift changes for the various double‐helical configurations show that for the system examined, only the vertical model can explain the experimentally observed shift trends. The melting curve for the helix–coil transition for high anti dinucleoside monophosphate has been observed for the first time. Even though the experimental data support vertical double helices when χCN is fixed at 120°, data on naturally occurring nucleic acid structures indicate that they have no proclivity to enter into vertically stabilized double‐helical arrays.
Models for boundary effects on molecular rotation in membranes
Authors: Andersen Gregory R. , Mazo Robert M.
Published: December 2004

Rotational and wobbling diffusion coefficients for spherical and long‐chain molecules in membranes are calculated using a simple hydrodynamic model. Estimates of the contributions to the diffusion coefficients arising from hydrodynamic interactions between molecules and membrane interfaces are obtained and found to be small. For molecules containing polar head groups, we show that the presence of a membrane interface can produce a significant reduction in the wobbling diffusion coefficient over what would be obtained in an isotropic fluid.
Infrared study of the secondary structure of lac repressor and its tryptic core
Authors: Schnarr Manfred , Maurizot Jean‐Claude
Published: December 2004

The lac repressor and its tryptic core were studied by ir spectroscopy, and their β‐structure content was determined by analysis of the spectra. Using protein‐derived reference spectra, we find a β‐content for lac repressor of 18% and of 23% for its tryptic core. The higher amount of β‐conformation in the tryptic core is confirmed by another type of analysis (decomposition of the spectra in Gaussian curves). These results are discussed with respect to their implications for the structure of the N‐terminal “headpiece” of lac repressor and for the mode of interaction of lac repressor with lac operator.
Interaction of poly(α‐L‐glutamic acid) and sodium poly(α‐L‐glutamate) with solvent components in water–2‐chloroethanol mixtures
Authors: Morcellet M. , Loucheux C.
Published: December 2004

The preferential interaction of sodium poly(α‐L‐glutamate) and poly(α‐L‐glutamic acid) with the solvent components in water/2‐chloroethanol mixtures has been determined using density‐increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2‐chloroethanol and at constant chemical potential of 2‐chloroethanol. Sodium poly(α‐L‐glutamate) and poly(α‐L‐glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2‐chloroethanol‐induced coil‐to‐helix transition of sodium poly(α‐L‐glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α‐L‐glutamate) is solvated by one 2‐chloroethanol molecule. The location of water and 2‐chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
Investigation on oligo‐ and polygalacturonic acids by potentiometry and circular dichroism
Authors: Ravanat G. , Rinaudo M.
Published: December 2004

The potentiometric data concerning the dependence of the apparent pK with the degree of neutralization and the nature of counterions (Na or Ca) of galacturonic oligomers and polymers are discussed. They are characterized by an apparent charge density λapp which predicts their electrostatic behavior. The calculated osmotic coefficients from Katchalsky and Manning's theories are in good agreement with the experimental data obtained by potentiometry. The dependence of the osmotic coefficient (ϕCa) as a function of the polymer concentration is established by potentiometry and interpreted in terms of a multichain aggregation. In addition, it is proven that no Ca2+ is ever fixed in excess of stoichiometry. The dependence of CD spectra obtained under the same conditions as the pK measurements shows analogies between the two sets of results. The CD data, in agreement with 13C‐nmr measurements, suggest that in dilute solutions the polymer adopts two conformations: one (acidic form) which may be represented by threefold screw symmetry and a second (Na or Ca form) which can be related to a twofold screw symmetry. The twofold screw symmetry is known to allow the formation of cooperative “egg‐box” fixation of Ca without conformation change.
Diffusion coefficients for rigid macromolecules with irregular shapes that allow rotational‐translational coupling
Authors: Wegener William A.
Published: December 2004

We consider six‐dimensional diffusion and frictional tensors for a rigid macromolecule immersed in a viscous fluid at low Reynolds number. Our treatment allows for screwlike properties which couple rotational and translational movements. We show that the center of diffusion of a screwlike body can be distinct from its hydrodynamic center of reaction. Symmetry conditions which ensure coincidence are examined. The center of diffusion is found to be the point of a body with the slowest diffusive movements, while rotations about the center of reaction encounter the least average resistance. The macroscopic translational diffusion coefficient is evaluated from a perturbation analysis of the six‐dimensional diffusion equation. We show that methodologies which ignore translational–rotational coupling will necessarily underestimate the diffusion rate of screwlike particles. A procedural framework is presented to calculate diffusion coefficients of complicated bodies. As an example we treat a long bent rod.
Enantiomer selection in the addition reaction of optically active 3‐methyl‐5‐substituted hydantoins to N‐[(S)‐α‐methylbenzyl]glycine N‐Carboxyanhydride: Model Reaction for the Stereoselective Polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio
Published: December 2004

In order to investigate the contribution from the chiral penultimate unit to the enantiomer selection in the activated N‐carboxyanhydride (NCA) polymerizations, the addition reaction to N‐[(S)‐methylbenzyl]glycine NCA of various α‐amino acid hydantoins activated by the tertiary amines was investigated in different solvents. The reactions of activated Ala, Val, and Phe hydantoins were stereoselective and suggested the participation of the penultimate unit in the enantiomer selection of the activated NCA type of polymerization. The degree of enantiomer selection was not well correlated with the structure of hydantoins. Taking into account the dipole repulsion and the orbital overlapping between the reaction species, the transition‐state model was proposed, which gave a good explanation of the selectivity for (R)‐hydantoin in PhNO2 and CH3CN and the selectivity for (S)‐hydantoin in AcNMe2 and HCONMe2. In these two types of solvents the orientation of the methylbenzyl group with respect to the NCA ring is so different that the direction of the approach of the activated hydantoin to the NCA is different. This difference leads to the inversion of enantiomer selection in amide solvents and in others. Cationic species derived from tertiary amines and the chiral amide compound were found to affect the enantiomer selection in the model reaction. The implications of these findings with regard to enantiomer selection in the activated NCA type of polymerization are discussed.
Proton and phosphorus nmr investigation of the conformational states of acid polyadenylic double helix
Authors: Lerner Deborah B. , Kearns David R.
Published: December 2004

Proton and phosphorus nmr have been used to investigate the double‐helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH < 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71–86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half‐protonated state. Although the base‐stacking arrangement of this state is similar to that observed in the more extensively protonated low‐pH state, the phosphate backbone conformation is different from that found in either the neutral or low‐pH structures.
Vacuum‐ultraviolet circular dichroism of acetylated glucans
Authors: Stipanovic Arthur J. , Stevens E. S.
Published: December 2004

We have measured the solution and film vacuum ultraviolet circular dichroism of a series of acetylated glucans containing α‐ and β‐(1→3), (1→4), and (1→6) linkages. In addition to the 210‐nm band studied previously, we observe the entire π‐π* band near 190 nm; these bands are negative for all triacetates regardless of configuration and conformation. A band near 170 nm shows configurational sensitivity for (1→3)‐ and (1→6)‐linked polysaccharides. The band is positive for both (1→4)‐linked triacetates, but when cellulose triacetate is partially deacetylated, the 170‐nm band becomes negative, thus making the correlation complete. The positive 170‐nm band in cellulose triacetate films is more than an order of magnitude more intense than in any other case and, further, is accompanied by an equally large negative band near 153 nm, raising the possibility that the dichroism in the triacetate arises from strong excitonic interactions which are disrupted upon partial deacetylation.
Structure of cellulose II hydrate
Authors: Lee David M. , Blackwell John
Published: December 2004

A hydrate of cellulose II can be formed by swelling Fortisan fibers in hydrazine and then washing in water. The hydrate is stable at 93% relative humidity and has a monoclinic unit cell with dimensions a = 9.02 Å, b = 9.63 Å, c = 10.34 Å, and γ = 116.0°; the space group is P21. The unit cell contains disaccharide sections of two chains and approximately four water molecules. The structure was refined using the LALS method, based on 10 observed and 10 unobserved reflections. An antiparallel arrangement of adjacent chains was assumed, since this occurs in cellulose II (the starting material), and the hydrate also reverts to cellulose II on dehydration. Refinement of the positions and side‐chain conformations of the chains shows that the chains are stacked in the same way as in cellulose II, and the hydrate is formed by insertion of water molecules between the stacks. However, all efforts to arrange the water molecules in crystallographically regular positions led to unsatisfactory agreement between the observed and calculated intensities. These results suggest an irregular arrangement of the water molecules, which was modeled using water‐weighted atomic scattering factors. The analysis resulted in two refined models with relative chain staggers of ∼ +c/4 and ∼ ‐c/4, which are indistinguishable in terms of the x‐ray agreement. Our preference is for the +c/4 model, for which the stacks of chains are analogous to those in cellulose II.
Comparison of Poisson‐Boltzmann and condensation model expression for the colligative properties of cylindrical polyions
Authors: Klein Barbara Kure , Anderson Charles F. , Record M. Thomas
Published: December 2004

Closed‐form expression have been derived for the polyelectrolyte contribution to the colligative properties of solutions containing rodlike polyions in the presence of excess added salt. The derivations are based on: the conventional Poisson‐Boltzmann equation for cylindrical symmetry; the thermodynamics of the cell model developed by Marcus [J. Chem. Phys. 23, 1057–1068 (1955)]; and an equation derived from the cylindrical Poisson‐Boltzmann cell model by Anderson and Record [Biophys. Chem. 11, 353–360 (1980)]. Subject to the inherent limitations of the Poisson‐Boltzmann approximation [Fixman (1979) J. Chem. Phys. 70, 4995–5005], the resulting expressions are nevertheless applicable outside the “limit of infinite dilution.” They conform over a range of salt concentrations to the limiting laws deduced by Manning from the hypothesis of counterion condensation [J. Chem. Phys. 51, 924–933 (1969)]. This hypothesis is found to be compatible with the Poisson‐Boltzmann cell model but is not required in the derivation of the thermodynamic coefficients presented here. It is demonstrated that the magnitude of the polyion axial charge density plays a critical role in determining the low‐salt limiting forms of the colligative properties obtained from the Poisson‐Boltzmann equation, in close analogy with Manning's model.
Dielectric studies of aqueous solutions of poly(L‐glutamic acid)
Authors: Nakamura Haruki , Wada Akiyoshi
Published: December 2004

The dielectric features of poly(L‐glutamic acid) are studied by the Fourier synthesized pseudorandom noise method in a time domain combined with a four‐electrode cell. Polymer concentration dependence, the effect of the solvent viscosity, salt effects, and pH dependence are studied concomitantly with measurements of CD. A helix‐to‐coil transition occurs near pH 5.6 for a salt‐free solution; at higher pH values, the polymer has an ionized random‐coil conformation, and at lower pH, it has a deionized α‐helical conformation. When it is in the ionized random‐coil conformation, with the usual features of an electrolytic polymer, the solution shows a relaxation spectrum with a large dielectric increment at low frequencies. In the deionized α‐helical state, no distinct relaxation curves are obtained, which does not deny the existence of a permanent peptide dipole. The pH dependence of the dielectric increment does not mainly correspond to the conformational change from helix to coil, but rather corresponds to the change of chain expansion on account of a charge–charge interaction under low ionic strength, which is conceived of by a viscosity measurement.
Studies of nucleotide conformations and interactions. The relative stabilities of double‐helical B‐DNA sequence isomers
Authors: Kollman Peter A. , Weiner Paul K. , Dearing Andrew
Published: December 2004

We present the results of molecular‐mechanics studies on base‐paired dinucleoside phosphates and hexanucleoside pentaphosphates. Starting from B‐DNA‐like conformations, we have refined the nucleic acid conformations, allowing all degrees of freedom to relax. The calculated energies of different base sequences are used to investigate the basis for the different stabilities of DNA polymers of different sequences, as found by Wells et al. [J. Mol. Biol. 54, 465–497, 1970]. Our calculations appear to reproduce the relative melting temperatures of sequence isomers as well or better than any of the previous calculations which addresssed the question of nucleotide stability. We offer a detailed physical explanation of three observations, that poly(dA)·poly(dT) melts higher than poly[d(A‐T)]·poly[d(A‐T)] by 6°C, that poly(dG)·poly(dC) melts lower than poly[d(G‐C)]·poly[d(G‐C)] by 12°C, and that poly(dA‐dG)·poly(dT‐dC) melts lower than poly(dA‐dC)·poly(dT‐dG) by 6°C. The dihedral angles found after refinement are similar to those of Levitt [Proc. Natl. Acad. Sci. USA 75, 640–644, 1978] and differ by ∼20° from the B‐DNA values. We also see evidence of base tilting and twisting similar to that found by Levitt. The two main differences in the results of our calculations and Levitt's lie in the sugar puckers [we find mainly C(2′)endo] and in the tendency to stay in local “torsional” minima (we find a number of examples of C(3′)endo sugar puckering and ω′ = trans rather than gauche). Both of these results are dependent on the nature of the potential function used in our study. However, our finding of movement from local torsional minima is suggestive of the significant flexibility of double‐stranded deoxynucleotides.
Methacrylate polymerization by azoRNA: Potential usefulness for chromosomal localization of genes
Authors: Hartman Rosemarie F. , Brown Gary L. , Rose Seth D.
Published: December 2004

An azo pyrimidine nucleotide has been prepared and enzymatically attached to oligo(A) primers. The nucleotide's azo pyrimidine group has previously been shown to initiate polymerization of methacrylate esters designed to bind marker groups for visualization by microscopy. When attached to RNA molecules complementary to a chromosomal DNA segment, these nucleotides may allow localization of the DNA segment following in situ hybridization of the probe, methacrylate polymerization, and marker attachment. Since mRNA molecules of potential interest as probes bear a 3′‐poly(A) tail, the modified nucleotides were added to oligo(A) primers as models. First, N4‐ureidocytosine nucleotides were enzymatically added to ApApA, (Ap)9A, or [5′‐32P]‐(pA)10, using the modified cytidine 5′‐diphosphate and “primer‐dependent” polynucleotide phosphorylase (M. luteus). In the case of the ApApA‐primed reaction, the N4‐ureidocytosine nucleotides in the product polynucleotide were converted into azo nucleotides by oxidation with N‐bromosuccinimide. The other two primers were employed to study the time course of polynucleotide formation and to verify that primer was indeed being utilized by the enzyme. The suitability of the modified nucleotide for in situ hybridization studies was examined. Poly(N4‐ureidocytidylic acid) was prepared from poly(C) and semicarbazide by the bisulfite‐catalyzed transamination reaction. It was found that 95% of the N4‐ureidocytosine nucleotides in this polynucleotide survive the elevated temperatures typically required for DNA:DNA denaturation and RNA:DNA annealing. When poly(N4‐ureidocytidylic acid) was mixed with poly(I) in buffered aqueous salt solutions, no evidence for hybridization was found, so binding of the probe RNA to the denatured chromosomal DNA molecule via the modified nucleotides is not expected. Upon oxidation of poly(N4‐ureidocytidylic acid) with N‐bromosuccinimide, the azo nucleotides were formed, as judged by the appearance of a characteristic peak at approximately 350 nm in the uv‐absorption spectrum of the yellow‐orange product, azoRNA. The azo nucleotides in azoRNA exhibited the expected acid lability, which is known to be accompanied by 1‐glyceryl methacrylate polymerization in the case of the simple azo pyrimidine. Because 1‐glyceryl metharcylate bears substituent glycol groups for attaching heavy atoms or fluorescent markers, it is possible that probe RNA molecules bearing azo nucleotides may be useful for localizing low‐multiplicity genes along eukaryotic chromosomes.
Simplified theory of the helix–coil transition in DNA based on a grand partition function
Authors: Lifson Shneior , Zimm Bruno H.
Published: December 2004

The statistical mechanics of the helix–coil transition in DNA is treated by means of a grand partition function. This method is simpler than methods used previously, although it is suitable only in the limit of great chain lengths. Expressions for the number of base pairs bonded are obtained and shown to be identical to those obtained by other methods in the limit of great chain lengths. The physical meaning of the grand partition function is also discussed.
The presence in collagen of γ‐glutamyl peptide linkages
Authors: Franzblau Carl , Gallop Paul M. , Seifter Sam
Published: December 2004

A method is described for formation of hydroxamic acids by direct coupling, in aqueous medium, of hydroxylamine hydrochloride and the sodium salt of a carboxylic acid. The reaction is mediated by a water‐soluble carbodiimide, 1‐cyclohexyl‐3‐[2‐morpholinyl‐(4)‐ethyl]‐carbodiimide metho‐p‐toluene sulfonate. Using model compounds, the production of α‐, β‐ and γ‐acyl hydroxamic acids was studied. Hydroxamic acid derivatives of α‐polyglutamic and γ‐polyglutamic acids were also prepared. Dinitro‐phenylhydroxamate derivatives were prepared and subjected to Lossen rearrangement, and the reaction mixtures hydrolyzed. Analysis showed that α‐polyglutamic acid yielded as many molecules of α,γ‐diaminobutyric acid as there had been glutamic acid residues in the form of the dinitrophenylhydroxamate, and gave rise to no ammonia and succinic semialdehyde. In contrast, γ‐polyglutamic acid yielded exactly twice the molar quantity of ammonia as there had been glutamic acid residues in the form of dinitrophenylhydroxamate, and also gave rise to significant quantity of succinic semi‐aldehyde but no α,γ‐diaminobutyric acid. Since production of the latter is characteristic of α‐glutamyl hydroxamates and production of the former is associated with γ‐glutamyl hydroxamates, the results indicated that the side‐chain carboxyl groups of either polymer retained their identities during formation of the hydroxamic acid derivative, and no interchange had occurred between α‐ and γ‐carboxyl groups. These methods were then used to establish that gelatin of ichthyocol contains (per 1000 total residues) at least 20 residues of glutamic acid in γ‐peptide linkage. Due to the incomplete dinitrophenylation of the hydroxamic acid derivative of the protein, gelatin of calf skin collagen gave a lower figure of 10 such linkages per 1000 total amino acid residues–a value which must be considered a minimum value. These results show that γ‐glutamyl peptide bonds exist in collagen.
Theory of helix–coil transitions involving complementary poly‐ and oligo‐nucleotides. I. The complete binding case
Authors: Magee William S. , Gibbs Julian H. , Zimm Bruno H.
Published: December 2004

A statistical thermodynamic treatment of thermally induced helix–coil transitions is formulated with the matrix method for an (ensemble) of system(s) in which one strand of a double helix consists of a homopolymeric polynucleotide and the other strand comprises a number of complementary oligonucleotides. Each oligonucleotide is considered to be completely bound to the longer chain when in the helical configuration and completely free from it when in the randomly coiled configuration. The case of partial binding; i.e., “dangling,” is treated in a later paper. Taken into account in both cases are intrachain “stacking” interactions between nearest neighbor residues and interchain hydrogen bonding.

An approximate treatment of the characteristic equation of the formulation indicates that the reciprocal of the transition temperature (1/T0) is a linear function of the reciprocal of the degree of polymerization (D.P.) of the oligonucleotides. In the same approximation, 1/T0 is also a linear function of the negative logarithm of the absolute activity of the oligonucleotides. Transition curves obtained by exact calculation on a computer are presented for various degrees of polymerization of both the oligo‐ and polynucleotides. These curves show a sharpening of the transition with increasing D.P. of the long chain and the aforementioned reciprocal D.P. dependence of 1/T0.
Reaction of formaldehyde with soluble ribonucleic acid
Authors: Penniston John T. , Doty Paul
Published: December 2004

The reaction of soluble RNA with formaldehyde was measured as a function of time. The rate of this reaction can be treated as a combination of simple first‐order rates, such as those observed for the reaction of mononucleotides with formaldehyde. The equilibrium position of the reaction of formaldehyde with soluble RNA in the absence of Mg++ is consistent with the equilibrium constants observed for mononucleotides. There is no evidence for the occurrence of crosslinking under the conditions used. All the nucleotides of sRNA are available for reaction with formaldehyde in the absence of Mg++, even though a considerable amount of secondary structure remains under these conditions. The presence of Mg++ stabilizes the secondary structure considerably, protecting about two‐thirds of the nucleotides from reaction. The rate of reaction of formaldehyde with sRNA is six times slower than that for mononucleotides. This slowing down of the reaction is interpreted as being due to the weak involvement of the reactive groups in secondary structure, while strong involvement in secondary structure, as in the presence of Mg++, prevents reaction completely.
The inactivation of soluble ribonucleic acid by formaldehyde
Authors: Penniston John T. , Doty Paul
Published: December 2004

The inactivation of sRNA by reaction with formaldehyde has been reported as it occurs under various conditions giving differing amounts of secondary structure. The theory of inactivation of an active macromolecule by a chemical reaction is developed. Results obtained with a partially melted out secondary structure show that formaldehyde inactivates sRNA by a single reaction at any one of about ten sites, while reaction at other sites does not affect the activity of the sRNA. In the presence of Mg++ at neutral pH, a large proportion of the active molecules are completely protected against inactivation. From the correlation between the amount of secondary structure and the difficulty of inactivation, it is shown that at least a portion of the secondary structure of sRNA is essential to its amino acid acceptor ability. A comparison of results of various workers shows that formaldehyde does not alter RNA as drastically as other reagents and thus enables more discrimination between sites of reaction which are essential and those which are not essential to biochemical activity.
Optical properties of chromophore‐macromolecule complexes: Absorption and fluorescence of acridine dyes bound to polyphosphates and DNA
Authors: Weill G. , Calvin M.
Published: December 2004

Dye–macromolecule complexes provide good models for the study of the effects of coupling between chromophores. In addition to modifications of the visible and UV absorption spectra of the dyes at small interchromophore distances, very efficient energy transfer has been demonstrated at longer distances. The probability of nonradiative transition increases with the number of excitation transfers so that an array of oscillators close to one another becomes nonfluorescent. The insertion of a dye molecule, acting as a trap for the excitation energy, in the highly ordered system of chromophores constituted by the purine and pyrimidine bases of native DNA has given results supporting the intercalation model of Lerman and providing an experimental approach to the problem of the path length of energy migration in the DNA molecule. The average excitation path length seems to be of the order of only ten base pairs, a result which can explain the lack of fluorescence of the DNA.
Interactions of DNA with divalent metal ions. II. Proton relaxation enhancement studies
Authors: Granot Joseph , Kearns David R.
Published: December 2004

The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA–bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron‐nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2–3‐fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order‐of‐magnitude increase in their rotational correlation time are attributed to hydrogen‐bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
Anomalous temperature dependence of frictional coefficients: Diffusion and sedimentation measurement of low‐density lipoproteins, albumin, and polystyrene latex
Authors: Crossley J. M. , Spraggs S. P. , Creeth J. M. , Noble N. , Slack J.
Published: December 2004

Using quasielastic light scattering, we have determined the diffusion coefficients of low‐density lipoprotein (LDL) and polystyrene latex spheres over the temperature range of 293–318 K. The results show that after correction for thermal changes in the solvent, there remains a residual negative temperature coefficient in the diffusion amounting to about −0.6%/K that is independent of the chemical type of complex. Confirmation of these results was obtained for LDL through sedimentation studies over a similar range of temperatures. The residual temperature coefficient was similar to that reported for oxyhemoglobin [W. B. Veldkamp and R. Votano (1980) Biopolymers 19, 111–124] and greater than that found for bovine serum albumin by these and earlier workers. These observations show that the residual dependence on temperature is not an isolated phenomenon and could in part be explained by increased aggregation of particles, although this is not the primary cause of the effect.
Equilibrium swelling of pigment gallstones: Evidence for network polymer structure
Authors: Black Brian E. , Carr Stephen H. , Ohkubo Hideki , Ostrow J. Donald
Published: December 2004

A major component of pigment gallstones (PS) is a black, insoluble substance. It has been suggested that this pigment material might be a highly crosslinked polymer, and if such were the case, it should imbibe solvent (swell) to the maximum permitted by the crosslinks of its macromolecular network. We measured the equilibrium amount, qeq, by which pulverized, desiccated PS swells in different liquids, including isotonic aqueous buffers at pH values from 1.5–11.5. For ionic strengths ≥ 0.15, the dependence of qeq on pH exhibits a broad titration curve with a midpoint near pH 7. qeq was < 1.2 in methanol, dimethylformamide, dimethylsulfoxide, and chloroform. The ir absorbance from vinyl groups in the black pigment was only one‐eighth that of unconjugated bilirubin, the primary chemical building block of PS; this implicates vinyl groups in the formation of a polymer network. The rise in qeq with increasing pH suggests that the carboxyl groups are free to ionize and are therefore not involved in the covalent bonds that make the crosslinked polymer. A network polymer structure would account for the inability to dissolve PS in those solvents in which unconjugated bilirubin is soluble.
Synthesis of sequential polypeptides containing L‐β‐3,4‐dihydroxyphenyl‐α‐alanine (DOPA) and L‐lysine
Authors: Yamamoto Hiroyuki , Hayakawa Tadao
Published: December 2004

Six different sequential polypeptides with the repeating units L‐lysyl‐L‐DOPA, L‐DOPA‐L‐lysine, L‐lysyl‐L‐lysyl‐L‐DOPA, L‐DOPA‐L‐DOPA‐L‐lysine, L‐lysyl‐L‐lysyl‐L‐lysyl‐L‐DOPA, and L‐DOPA‐L‐DOPA‐L‐DOPA‐L‐lysine have been synthesized by solution polymerization of the p‐nitrophyenyl esters of the corresponding di‐, tri‐, and tetrapeptides. The O,O′‐dimethyl and N‐ε‐2‐chlorobenzyloxycarbonyl groups were used to protect side chains of L‐DOPA and L‐lysine. The monomers for the polytripeptides and polytetrapeptides were prepared by stepwise elongation, using the dicyclohexylcarbodiimide coupling method. Moderately high molecular weight sequential polypeptides were obtained. The addition of 1‐hydroxybenzotriazole increased their molecular weights, but not so effectively. The protected groups of the side chains were removed simultaneously by use of boron tribromide in chloroform. Water‐soluble sequential polypeptides containing L‐DOPA were obtained.
CD and nmr studies on the interaction of lithium ion with valinomycin and gramicidin‐S
Authors: Sankaram M. B. , Easwaran K. R. K.
Published: December 2004

The conformation of the valinomycin–lithium complex has been studied using CD and nmr techniques. The lithium ion induced significant changes in the chemical shifts of the NH and CαH protons, as well as in the CD spectra of valinomycin. From the analysis of the lithium ion titration data, it is concluded that valinomycin forms a 1:1 type weak complex with lithium, having a stability constant of 48 L mol−1 at 25°C. This conformation is different from the familiar valinomycin–potassium complex. The nature of the interaction at low and high concentrations of lithium ions with valinomycin (ionophore) and gramicidin‐S (nonionophore) has been compared. At high salt concentrations, there was a further change in the CD and nmr spectra of valinomycin, giving a second plateau region at > 3M of the salt. In the case of gramicidin‐S, no significant changes in the nmr or CD spectra were observed in the lower concentration range corresponding to where changes were observed in the case of valinomycin. However, the addition of lithium salt at concentrations greater than 3M induced changes in both the CD and nmr spectra of gramicidin‐S, and the titration graph of molar ellipticity versus concentration of lithium perchlorate gave a plateau region at concentrations greater than this. These results indicate that the effects of lithium at low and high concentrations are independent of each other. The conformational transitions at very high salt concentrations (denaturation) are more likely due to solvent structural perturbations rather than to the consequences of ion binding.
Dependence of thermal stability on the number of hydrogen bonds in water‐bridged collagen structure
Authors: Burjanadze T. V. , Kisiriya E. L.
Published: December 2004

The probable number of hydrogen bonds has been calculated as a function of the imino acid content for water‐bridged collagen structures. With increasing imino acid content in collagen, the number of hydrogen bonds stabilizing triple‐helical structures become saturation. This might explain the asymptotic character of the empirical relation between thermostability and hydroxyproline content for collagen.
Polynucleotide conformation from flow dichroism studies
Authors: Causley Gary C. , Johnson W. Curtis
Published: December 2004

We demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218‐nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
Equilibrium folding–unfolding pathways of model proteins: Effect of myoglobin–heme contacts
Authors: Jernigan Robert L. , Miyazawa Sanzo
Published: December 2004

The equilibrium of protein folding–unfolding has been investigated with a simple two‐state, native and random‐coil, model; we have termed this the globule–coil model. Energies are calculated by favoring native long‐range contact pairs. Most‐probable native domains are obtained at all stages of the transition; plausible folding pathways are constructed by connecting these domains by assuming simple growth. Even though native heme–protein contacts represent less than 6% of the total number of native contact pairs, their inclusion appears to change the folding pathway of apomyoglobin from the growth and merging of two native domains to the growth of a single domain. This indicates that pathways derived with this method may be critically sensitive to the details of the contact map and physical constraints during the folding process.
Conformational and functional properties of hemoglobin in water–organic cosolvent mixtures: Effect of ethylene glycol and glycerol on oxygen affinity
Authors: Bulone Donatella , Cupane Antonio , Cordone Lorenzo
Published: December 2004

We report on the effects that the presence of ethylene glycol or glycerol has on the oxygen affinity of hemoglobin. We attribute these effects to an altered equilibrium between T and R quaternary conformations of hemoglobin and separate them into bulk‐electrostatic and non‐bulk‐electrostatic contributions to the standard free‐energy difference between the R and T states.
Genetic and biochemical analysis of in vivo protein folding and subunit assembly
Authors: Goldenberg David P. , Smith Donna H. , King Jonathan
Published: December 2004

The in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature‐sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature‐sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
Conformational comparison of cyclic peptide and pseudopeptide structures with intramolecular hydrogen bonding
Authors: Spatola Arno F. , Gierasch Lila M. , Rockwell Arlene L.
Published: December 2004

An nmr spectral comparison of a model cyclic pentapeptide cyclo(Gly‐Pro‐Gly‐D‐Phe‐Pro) with an analogous pseudopeptide has been made. The pseudopeptide contains a ψ[CH2S] amide bond replacement at the only amide linkage that, in the model, is not involved in an intramolecular hydrogen bond. Both proton and carbon‐13 nmr spectral evidence confirms the retention of β‐ and γ‐turns in the pseudopeptide in chloroform. Characteristic chemical shifts, temperature dependence, and glycine α‐resonances support this interpretation. However, evidence of a more flexible conformation involving cis–trans proline isomerism is seen on addition of dimethylsulfoxide.
A simple model for the optical properties of chiral amides
Authors: Woody Robert W.
Published: December 2004

The intramolecular charge‐transfer model for the electronic structure of amides has been extended to include the effects of torsion about the peptide bond (Δω = ω – 180) and pyramidalization at the peptide nitrogen (θN). The model is used to calculate the absorption and CD spectra of nonplanar amides as a function of the angles Δω and θN. For cis‐amides, the rotational strengths of the nπ* and ππ* transitions are much more sensitive to θN for a given value of Δω than is the case for trans‐amides. The results from the model are compared with available experimental and previous theoretical treatments of such systems. The contributions of nonplanarity in amides to the CD of various polypeptide conformations is discussed. The effects should be negligible for α‐helixes but may be quite significant in β‐sheets and β‐turns. The CD spectrum of unordered peptides would be readily explained if there were a significant bias toward negative Δω values in polypeptides of L‐amino acids. However, the evidence currently available does not indicate such a bias.
Conformational preferences of side‐chain protected amino acid residues and their impact in peptide synthesis
Authors: Maser F. , Klein B. , Mutter M. , Toniolo C. , Bonora G. M.
Published: December 2004

Using the host‐guest technique, tentative scales for the helix‐inducing power and the β‐structure‐forming potential of various side‐chain protected amino acid residues in trifluoro‐ethanol are established mainly by CD measurements. The generally lower tendency for β‐structure formation of the host–guest peptides compared to that of the host peptide is discussed. The influence of these conformational features on the solubility of the peptides is also pointed out.
Structural aspects of the interaction of bee venom peptide melittin with phospholipids
Authors: Strom Roberto , Podo Franca , Crifo Carlo , Berthet Carmen , Zulauf Martin , Zaccai Giuseppe
Published: December 2004

In aqueous solution, melittin structure, investigated by CD and 1H‐nmr, depends on pH and ionic composition, which also regulate the aggregation state of the peptide. When interacting with phospholipids, however, melittin exhibits a right‐handed helical conformation without any evidence of oligomeric association. The overall bilayer structure of phospholipid aqueous dispersions is also maintained in the presence of melittin, although the permeability to aqueous solutes is considerably increased. Small‐angle neutron‐diffraction analysis of oriented multilayers confirms the existence of a lamellar profile, despite the presence of the peptide throughout each bilayer and exchangeable protons almost reaching the center of the hydrophobic alkyl chains region.
Design, synthesis, and conformation of ion carriers
Authors: Shanzer Abraham , Felder Clifford E. , Lifson Shneior
Published: December 2004

Macrocyclic molecules can serve as ion carriers when their polar groups form an inner cage to capture ions while their hydrophobic groups form an outer layer to dissolve the molecule in lipid membranes. A “template method” has been developed for high‐yield synthesis of a whole variety of macrocyclic esters, amides, and other families which may show ionophoric properties. In order to select the more promising compounds for synthesis, energetic and conformational characteristics of such molecules have been calculated from empirical energy functions. Calculations are examined using known structures and are employed to predict the properties of molecules not yet synthesized.