bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of salt on the stability of the pH 4.2 rA8 double helix in a series of organic/aqueous mixed solvents: A test of oligoelectrolyte theory
Authors: Breslauer Kenneth J. , Bodnar Catherine M.
Published: December 2004

Temperature‐dependent uv absorption spectroscopy has been used to investigate the salt dependence of the order–disorder transition for the pH 4.2 rA8 double helix in 100% aqueous buffer and in a series of organic/aqueous mixed solvents. Melting temperature, Tm, data were obtained for the transitions in the different solvents by analysis of the uv melting curves. For the pure aqueous buffer solvent, the melting temperature was found to exhibit a reduced salt dependence (∂tm/∂ log Na+) when compared to the corresponding polymer. This reduction is explained in terms of end effects and is shown to be consistent with the theoretical treatments of oligoelectrolyte transitions developed by Record and Lohman [Biopolymers, 17, 159–166 (1978)]. In the mixed solvents, the salt dependence of the melting temperature (∂tm/∂ log Na+) is shown to exhibit a linear dependence on the bulk dielectric constant of the medium for all of the hydroxyl‐containing solvents studied. Significantly, N,N‐dimethylformamide demonstrated different behavior.
Study by circular dichroism of soluble fragments of elastin from porcine and normal and pathological human aortas
Authors: Davril Monique , Han Kia‐Ki , Loucheux‐Lefebvre Marie‐H.
Published: December 2004

A CD study was carried out on elastin peptide samples obtained from porcine and normal and pathological human aortas. Different solubilization procedures were used: (1) an ethanolic‐KOH hydrolysis to obtain porcine κ‐elastins; (2) oxalic acid hydrolysis to obtain porcine α‐ and β‐elastins; and (3) enzymatic digestions and a partial acid hydrolysis to obtain porcine and human crosslinked peptides. The comparison of the results obtained from the dichroic study of porcine and normal human aorta peptides does not reveal any differences. On the contrary, the dichroic spectra obtained for the human pathological aorta peptides at different stages of atheromateous lesions exhibit some differences which are attributed to some variations of the conformation around the bridging zones.
Nuclear magnetic resonance investigation of lysine–oligopeptides and a complex with d(pA)3pGpC(pT)3
Authors: Davanloo Pari , Crothers Donald M.
Published: December 2004

We report proton magnetic resonance studies of a series of lysine oligopeptides in H2O solution. At pH 5 the protonated ε‐amino groups are seen as broad resonances; the peptide NH proton resonances are split by spin–spin coupling with the Cα‐H proton, and appear at positions which depend on position in the chain and on chain length. Assignments were made by the europium shift method, and we observed the expected effect of catalysis by the terminal —NH3+ of exchange of the adjacent peptide NH. Coupling constants and the temperature coefficient of chemical shift values were consistent with a non‐hydrogen‐bonded structure for the oligolysines. The rate and mechanism of NH hydrogen exchange were investigated by line‐broadening measurements of the peptide protons as a function of pH. Exchange was found to be OH− catalyzed, with large differences in the rate depending on position in the chain. Preliminary studies of the complex between double‐helical d(pA)3pGpC(pT)3 and tetra(L‐lysine) were performed using 1H‐ and 31P‐nmr techniques. Pmr spectra of the complex at pH values ranging from 3.98 to 8.15 showed very complicated patterns. Downfield shifts and reduction in exchange rates were observed for several tetra(L‐lysine) protons. 31P‐nmr spectra of the complex reveal an upfield shift of 1 ppm for 3′‐5′ phosphate diester resonances on complexation. 31P T1 relaxation times change little on complex formation at low temperature but are altered at higher temperature.
Effect of Centrifuge Speed on the Sedimentation of High‐Molecular‐Weight Bacteriophage G DNA
Authors: Krasin Frank
Published: December 2004

Large molecular weight bacteriophage G DNA, about five times larger than T2 DNA, was used to test Zimm's theory [(1974) Biophys. Chem. 1, 279–291] for the effect of rotor speed on the sedimentation of large linear monodisperse DNA. Sedimentation profiles from neutral sucrose gradinets at low and high rotor speeds show G DNA sedimenting from 1.8 to 0.7 times as fast as T2 DNA. Experimental measurements indicate that the sedimentation coefficient of G DNA decreases with increasing rotor speed about as fast as predicted by theory.
Incorporation of lone pairs into the electrostatic term in the empirical intra‐ and intermolecular energy calculations
Authors: Tvaroška Igor , Bleha Tomáš
Published: December 2004

The method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum‐chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra‐ and intermolecular energy.
Composite predictions of secondary structures of lac repressor
Authors: Bourgeois Suzanne , Jernigan Robert L. , Szu Shousun C. , Kabat Elvin A. , Wu Tai Te
Published: December 2004

The secondary structure of the lac repressor protein proposed by Chou et al. has been modified to include the recent revisions in sequence. In addition to the Chou and Fasman method, five other methods were used; they include those of (1) Lim, (2) Ptitsyn and Finkelstein, (3) Burgess et al., (4) Bunting et al., and (5) Wu and Kabat. Any two individual methods gave results differing sharply from one another. Three or more methods were in agreement for 91, 39, and 126 residues in helix, in β, and in combined coil plus turn conformations, respectively; there were such agreements for a total of 256 of the 360 residues. Agreements in the amino‐terminal third of the molecule were found for 68% of the residues, whereas in the remainder of the molecule only 53% of the residues showed such agreements. Only two helix‐breaking and two β‐breaking tripeptides were inconsistent with the composite predictions by three or more methods. The large number of disagreements among the results for different methods indicates that only very limited information is provided by each method and that the basis on which they operate is not clear. There is no a priori reason for a composite prediction to be more reliable than any individual prediction, and such a procedure does not permit the determination of an unambiguous secondary structure. Since these methods were applied to lac repressor before any three‐dimensional crystallographic structure was known, the methods may ultimately be evaluated should such a structure become available.
Statistical‐mechanical treatment of violations of the double helix in supercoiled DNA
Authors: Anshelevich V. V. , Vologodskii A. V. , Lukashin A. V. , Frank‐Kamenetskii M. D.
Published: December 2004

We consider the problem of making allowance for superhelicity in the statistical‐mechanical calculations of fluctuational violations of the DNA double helix. A simple model is discussed, making it possible in the calculations to use an approach based on the theory of helix–coil transition in DNA. The proposed algorithms allow calculating the effect of superhelicity on the base‐pair fluctuational opening for any given sequence of nucleotides. An algorithm is also proposed allowing for the hairpin and cruciform structures in the palindromic regions of a sequence, as well as the open and helical states. The theory is used to calculate the melting curve for superhelical DNA at temperatures well below the melting point of the linear or nicked forms. The maps of opening probability are calculated for SV40 and ϕX174 DNA using their recently published complete nucleotide sequences. The data explain well the experimental results of probing the secondary structure of these DNA by single strand‐specific endonucleases.
Transient electric birefringence of T7 viral DNA
Authors: Rau Donald C. , Bloomfield Victor A.
Published: December 2004

The electric birefringence properties of intact bacteriophage T7 DNA are investigated as a function of field strength and ionic environment. At low field strengths, E < 40 V/cm, Kerr behavior is observed. The birefringence decay kinetics are consistent with a Gaussian chain viscoelastic treatment for an induced dipole model of orientation. The observed relaxation time for the longest mode is 37 msec, in 0.5 mM Na+ at 15°C, and is in agreement with flow experiments. In order to account for the observed differences in rise and decay kinetics, a field‐induced, anharmonic restoring force is postulated. The magnitude of the apparent induced dipole moment is found to be inversely proportional to the Debye‐Hückel shielding parameter κ for a series of Na+ concentrations. The magnitude of the induced dipole moment is found to be very sensitive to the addition of Mg2+. When analyzed in terms of the counterion condensation theory of Manning, it appears that the induced dipole moment is proportional to the square of the reduced effective DNA charge density.
Moments of the distribution of the amino acid residues in tertiary structures of globular proteins
Authors: De Santis P. , Morosetti S. , Palleschi A.
Published: December 2004

Moments of the distributions of the Cα and “side‐chain atoms” and associated properties were examined in 22 globular proteins, considered as statistical aggregates of atoms. Although the distributions are generally anisotropic, the densities of the evaluated distributions are highly uniform in the interior of a single protein, as well as among the proteins investigated. The tertiary structure of proteins is characterized by a compact and uniform distribution of amino acids, independent of their molecular weight and hydrophobic character, and by an isotropic distribution of the virtual bond directions in the polypeptide folding. While the general uniformity of the density of distributions in the bulk of proteins can be justified by the architectural requirements of high thermodynamic stability, significant differences in the distribution of the Cα with respect to the “side‐chain atoms” suggest a plausible explanation of the general anisotropic morphology of the proteins. The invariance of the density of distributions allows easy recognition of proteinlike domains in more complex proteins and suggests a practical way to predict the following path in single proteins.
Role of the amino‐terminal extrahelical region of type I collagen in directing the 4D overlap in fibrillogenesis
Authors: Helseth Donald L. , Lechner Joseph H. , Veis Arthur
Published: December 2004

The amino‐terminal telopeptide of the collagen α1(I) chain has a highly conserved sequence. This sequence was analyzed by the Chou‐Fasman criteria, and a folded β‐sheet conformation, including a β‐turn, was predicted. This folded “hairpin” region favors both ionic and hydrophobic intermolecular interactions with α1(I) chain residues 930–938 on a neighboring, end‐overlapped molecule. An end‐overlap interaction of this nature could direct the initial step in fibril formation. The predicted structure also places the potential crosslink‐forming lysyl residue, 9N, in a unique site at the β‐turn end of the telopeptide.
DNA sequencing and helix–coil transition. I. Theory of DNA Melting
Authors: Azbel M. Ya.
Published: December 2004

An explicit analytic formula accurately describing the melting of a natural DNA is derived. For phage ϕX‐174 and virus SV‐40, the nucleotide sequences of which are known, the formula fits experimental data for the differential melting curve almost within the experimental accuracy.
DNA sequencing and helix–coil transition. II. Loop entropy and DNA melting
Authors: Azbel M. Ya.
Published: December 2004

An explicit analytical theory of DNA melting is constructed. It accounts for the loop entropy and the elasticity of DNA strands. Explicit analytical formulas are presented for the melting curves of natural DNA and periodic polymers. The nature of the DNA helix–coil transition is investigated, and it is found to crucially depend on the nucleotide sequence.
Preferred phosphodiester conformations in nucleic acids. A virtual bond torsion potential to estimate lone‐pair interactions in a phosphodiester
Authors: Srinivasan A. R. , Yathindra N. , Rao V. S. R. , Prakash S.
Published: December 2004

The lone‐pair orbital interactions arising in a phosphodiester are incorporated into semiempirical conformational energy calculations using a unifold “torsional potential” around the virtual bond linking the ester oxygen atoms. The results explain the observed experimental data better than other methods.
Contribution of electrodiffusion to the dynamics of electrically stimulated changes in mechanical properties of collagen membranes
Authors: Shoenfeld Norman A. , Grodzinsky Alan J.
Published: December 2004

We have studied the kinetics of oscillatory tensile forces in collagen membranes. These forces were generated by sinusoidal electric fields applied across the membrane. Both the magnitude and phase of the measured force changed with frequency over a three‐decade range. The membrane‐separated electrolyte baths had different ionic strength but identical non‐isoelectric pH. Changes in intramembrane ionic strength due to the electric field were calculated over the same frequency range via an electrodiffusion model that was generalized to include convection and electrokinetic coupling. A comparison of the experimental and theoretical phases and amplitudes versus frequency suggests that electrodiffusion is the dominant rate‐limiting process in this electromechanochemical transduction. These results are relevant to electrostatic interactions in connective tissues and to membrane‐based filtration devices in which membrane permeability may be actively varied and controlled by an applied electric field.
Heat capacity changes and partial molal heat capacities of some di‐ and tripeptides in water
Authors: Prasad K. P. , Ahluwalia J. C.
Published: December 2004

Integral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔC at 30°C. Limiting partial molal heat capacities ΔC have been determined by combining ΔC with Cp2 (heat capacity of pure solid peptides). Using the data on ω‐amino acids and these peptides, the partial molal heat capacity of a peptide group CONH was semiquantitatively estimated.
Polyelectrolyte theory. I. Counterion accumulation, site‐binding, and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations
Authors: Guéron M. , Weisbuch G.
Published: December 2004

We have computed the Poisson‐Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations. The polyelectrolytes considered here are highly charged in the sense that ξ > 1, ξ being the linear charge density parameter for cylinders, which is generalized by us to other shapes.

Contrary to the situation at zero salt concentration, the counterion distribution is not strongly shape dependent, being similar for cylinders or spheres which have the same superficial charge density and radius of curvature Rc. The distribution resembles that in the neighborhood of a plane with the same charge density.

Three regions are distinguished. (1) In the “inner region” which extends up to a distance Rc/2ξ from the surface, the counterion distribution is essentially salt independent. The counterion concentration in the immediate vicinity of the polyelectrolyte surface (CIV) is quite high, typically 1–10M, and proportional to the square of the surface charge density, which is its main determinant. (2) An intermediate region extends out to a distance where the electrostatic potential is equal to κT/e. This distance is comparable to λ for plane and cylinder, and smaller for the sphere. (3) In the outer region, the distribution is hardly influenced by the details of the inner region, on which it cannot, therefore, give much information. Colligative properties are dependent on the distribution in the outer region and are fairly well predicted even by a rudimentary theory.

The large value of the CIV implies that site binding must often be significant. It can be computed by applying the mass‐action law to site‐bound counterions in equilibrium with the counterions in the neighborhood, whose concentration is the CIV, the relevant equilibrium constant being that for the binding of counterions to isolated monomer sites. Because the CIV is insensitive to salt concentration, this will also be the case for site binding. With the graphs provided, one can compute the extent of sitebinding within the Poisson‐Boltzmann framework.

The “condensation radius,” i.e., the radius encompassing a counterionic charge 1 − ξ−1 around a cylinder, is found to be large. It varies with salt concentration and tends to infinity as the salt is diluted. Neither this radius nor the charge fraction 1 − ξ−1 of condensation theory plays any special role in the counterion distribution.

The “finite‐salt” results apply to salt concentrations, typically as low as 1–10 mM. This encompasses, among others, all experiments on biological polyelectrolytes.
Time‐dependent phosphorescence anisotropy measurements of the slow rotational motions of proteins in viscous solution
Authors: Strambini Giovanni B. , Galley William C.
Published: December 2004

A method of monitoring slow rotational motions of proteins from the decay of the intrinsic phosphorescence is described. The phosphorescence is excited with a 10‐μsec pulse of vertically polarized light from an air gap lamp, and the anisotropy was computed as a function of time from the simultaneously detected vertically and horizontally polarized components of the emission. The approach is illustrated with time‐dependent measurements of the anisotropy of the tryptophan phosphorescence of Staphylococcus aureus nuclease, bovine carbonic anhydrase, and liver alcohol dehydrogenase in glycerol‐phosphate buffer between −90 and −70°C. The temperature‐ and molecular‐weight dependence of the exponential decays in the anisotropy indicate that overall rotation of the proteins is at the origin of the depolarization. The potential of the approach as a probe of the slow rotational motions of proteins in membranes and other macromolecular complexes is stressed.
Nearest‐neighbor and next‐nearest‐neighbor effects in the proton NMR spectra of the oligoribonucleotides ApGpX and CpApX
Authors: Everett Jeremy R. , Hughes Donald W. , Bell Russell A. , Alkema Dirk , Neilson Thomas , Romaniuk Paul J.
Published: December 2004

The variable‐temperature proton nmr spectra of the oligoribonucleotides in the series CpApX and the series ApGpX, X = A, G, C, U, together with the parent dimers CpA and ApG have been measured. A complete analysis of all the nonexchangeable base proton resonances and ribose H‐1′ proton resonances was made. The presence of trends in the shielding abilities of the various bases at both the nearest‐neighbor and next‐nearest‐neighbor positions were identified. The observed shieldings could be used to predict the chemical shifts of protons in related systems. Based on the empirical results from ribodinucleoside monophosphates, the temperature‐dependent behavior of the J1′2′ coupling constants of the triribonucleotides suggested that the compounds in the CpApX series stacked from the 5′‐end to the 3′‐end, while those in the ApGpX series stacked from the 3′‐end to the 5′‐end.
On the blue color of triiodide ions in starch and starch fractions. II. Characterization of the changes in absorption and circular dichroism spectra of triiodide ions in amylose with the DP
Authors: Handa Takashi , Yajima Hirofumi
Published: December 2004

Three steps appeared in the color change of triiodide ions in amylose with the degree of polymerization (DP), associated with the change in the CD spectra. First, the shoulder around 480 nm developed strikingly from the achromic point of DP 10 to DP 30. Second, the blue color developed critically from DP 30 and deepened on going to DP 100, where the consistent increase in the intensities of the absorption and mutually split CD bands (+,−) was observed. Third, the deep bluing associated with the shallowing of the dual CD band was observed above DP 100. This change depended strongly on the mixing rate of I2 with amylose in the presence of excess KI. In particular, the signs of the dual CD band changed from (+,−) to (+,+) for high‐DP amyloses at high I2 in the rapid‐mixing system. The first and second phenomena are explained in terms of the enhancements in the short‐ and long‐axis transitions dipoles of the ions in the dimeric unit, respectively, being associated with the change in their spatial configuration due to the augmented shear from the stepwise promotion in the types and number of hydrogen bonds in the complex with the DP. The third phenomenon was attributed to the interactions of the skewed ions located in the knot portions and in the associated helices of the aggregate.
Transport properties of particles with segmental flexibility. II. Decay of fluorescence polarization anisotropy from hinged macromolecules
Authors: Harvey Stephen C. , Cheung Herbert C.
Published: December 2004

An algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single‐ and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two‐exponential approximation used by some investigators in the past.
13C‐nmr spectroscopy of red algal galactans
Authors: Usov Anatoly I. , Yarotsky Sergey V. , Shashkov Alexandr S.
Published: December 2004

13C‐nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C‐nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C‐nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6‐anhydrogalactose), and the positions of the sulfate and O‐methyl groups in a polysaccharide molecule.
Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra
Authors: Moore Dexter S.
Published: December 2004

A combination of the DeVoe and Kirkwood polarizability concepts is developed to calculate CD spectra of nucleic acid monomers. The method is perfectly general and applies to any system where the constituents have absorption properties which are widely separated in terms of frequency. The theory is applied to calculate the CD spectra of adenosine and 2′‐deoxyadenosine conformers. Bond polarizabilities are evaluated for the ribosyl moiety of adenosine, as a function of glycosidic rotational angles and polarizability anisotropies. It is found that a wide range of C‐C and C‐O bond polarizabilities give similar CD results. Isotropic atom polarizabilities are also evaluated. It is found that the CD results using these polarizabilities do not differ significantly from those obtained with bond polarizabilities. The CD spectra of adenosine and 2′‐deoxyadenosine are calculated for three x‐ray diffraction determined geometries: A‐form RNA, B‐form DNA, and C‐form DNA. The results indicate that the monomer CD spectra are strongly dependent on the precise geometry and appear to be of importance in understanding the spectra of oligomers and polymers. The deoxyadenosine conformers are found to have calculated CD spectra which are less intense than those of the ribosyl conformers. These results indicate that the measured differences between the CD magnitudes of ribo‐ and deoxyriboadenosine are due to the presence or absence of the 2′‐hydroxyl. Weighted averaged adenosine CD spectra are calculated with the aid of probability distributions from conformational energy calculations. The results suggest a new method for obtaining empirical monomer parameters for use in optical calculations. The calculations in this paper indicate for the first time that DeVoe theory, in combination with the Kirkwood theory, provides a useful method for the calculation of the CD spectra of nonpolymeric molecules.
Fluorescence quenching of methyl‐2‐aminobenzoate in the presence of beta‐cyclodextrin: A model for the dynamic quenching of chromophores in hydrophobic regions of biopolymers
Authors: De Korte Aart , Langlois Richard , Cantor Charles R.
Published: December 2004

The binding constant of methyl‐2‐aminobenzoate to beta‐cyclodextrin was determined by fluorescence titration to be 92.1M−1 at 25°C in pH 7 buffer. Beta‐cyclodextrin dramatically protects methyl‐2‐aminobenzoate against quenching by iodate and protects, though much less efficiently, against the smaller quencher, iodide. The observed decrease in fluorescence lifetime of the methyl‐2‐aminobenzoate‐beta‐cyclodextrin complex on addition of quencher indicates that the quenching mechanism is collisional (dynamic). The dependence of quenching rate on solvent viscosity is less than expected from simple theoretical considerations. However, the extent of beta‐cyclodextrin protection is essentially viscosity‐independent. These model studies show the usefulness of iodate as a quencher and encourage further attempts at quantitative interpretation of quenching studies on chromophores attached to biopolymers.
DNA sequencing and helix–coil transition. IV. Very long DNAs
Authors: Azbel M. Ya.
Published: December 2004

Helix–coil transition in very long DNA (containing hundreds of thousands of nucleotides or more) is considered. Certain statistical information about DNA nucleotide sequence is obtained.
Variation in the degree of branching of the glycogens and an approximate relationship between average exterior chain length and iodine staining
Authors: Fales Frank W.
Published: December 2004

Precise evaluation of the branching characteristics of glycogen complex from a variety of sources was made by replicate determinations of end groups by a reproducible periodate oxidation method and by replicate determinations of the percentage degradation by exhaustive β‐amylase activity. Also, the iodine staining characteristics of these samples were studied. The following observations were made. During the synthesis of glycogen by baker's yeast, there was a significant increase in the average chain length of the glycogen, and the maximal optical absorbance AM of the glycogen–iodine complex doubled. The AM decreased linearly with increasing temperature, and increases in iodine concentration caused increases in both the AM and the wavelength of maximal absorbance. There was a general increase in the AM of the glycogen with increasing exterior chain length, but there were minor deviations due to some dependence on the source of the glycogen. Unlike the linear relationship between the AM per chain and the average chain length of the amyloses, the AM per chain was exponentially related to the average exterior chain length of the glycogens.
Axial ranking of residues in collagen in relation to edge association and fibril formation
Authors: Kumar Narinder G. , Cunningham Leon W.
Published: December 2004

In our earlier analysis of intermolecular interactions between collagen molecules, a major concern with the program employed is that it compared numbers of interactions between residues located on edges of defined, identical width and thus would not necessarily compare the same number of residues in each edge. This would be particularly true of some values of θ where well‐defined vertical ranking of residues occurs. We have examined ranking of residues in relation to intermolecular edge association between bovine skin [α1(I)]3 model collagen molecules by utilizing two different methods of counting intermolecular interactions between residues. The interaction peaks at θ = 27.69° and 36.00° are absent or relatively less intense in the plots obtained by utilizing radial distances between interacting residues instead of vertical bands of defined width. These studies suggest caution in accepting recently reported analyses of superhelix coiling of the collagen molecule which point to values of 27.69° or 36.00° for the twist of the superhelix. Although intramolecular interactions clearly point to interaction of collagen molecules at D intervals, they are insufficiently restricted in distribution to provide a reliable estimate of the superhelix angle by procedures so far employed.
Solid‐state conformation of copolymers of β‐benzyl‐L‐aspartate with L‐alanine, L‐leucine, L‐valine, γ‐benzyl‐L‐glutamate, or ϵ‐carbobenzoxy‐L‐lysine
Authors: Sederel Willem L. , Bantjes Adriaan , Feijen Jan , Anderson James M.
Published: December 2004

The solid‐state conformation of copolymers of β‐benzyl‐L‐aspartate [L‐Asp(OBzl)] with L‐leucine (L‐Leu), L‐alanine (L‐Ala), L‐valine (L‐Val), γ‐benzyl‐L‐glutamate [L‐Glu(OBzl)], or ϵ‐carbobenzoxy‐L‐lysine (Cbz‐L‐Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700–250 cm−1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L‐Asp(OBzl)] induces a change from the left‐handed into the right‐handed α‐helix. This conformational change for the poly[L‐Asp(OBzl)] copolymers was observed in the following composition ranges: L‐Leu, 0–15 mol %; L‐Ala, 0–32 mol %; L‐Val, 0–8 mol %; L‐Glu(OBzl), 3–10 mol %; and Cbz‐L‐Lys, 0–9 mol %.
Local hydrophobicity stabilizes secondary structures in proteins
Authors: Kanehisa Minoru I. , Tsong Tian Yow
Published: December 2004

The probability of occurrence of helix and β‐sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki‐Tanford transfer free energies at two nearest‐neighbors on both sides of the amino acid sequence. In general, hydrophilic amino acids favor neither helix nor β‐sheet formations when neighbor residues are also hydrophilic but favor helix formation at higher local hydrophobicity. On the other hand, some hydrophobic amino acids such as Met, Leu, and Ile favor helix formation when neighbor residues are hydrophilic. None of the hydrophobic amino acids favor β‐sheet formation with hydrophilic neighbors, but most of them strongly favor β‐sheet formation at high local hydrophobicity. When the average of 20 amino acids is taken, both helix and β‐sheet residue probabilities are higher at higher local hydrophobicity, although the increase is steeper for β‐sheets. Therefore, β‐sheet formation is more influenced by local hydrophobicity than helix formation. Generally, helices are nearer the surface and tend to have hydrophilic and hydrophobic faces at opposite sides. The tendency of alternating regions of hydrophilic and hydrophobic residues in a helical sequence was revealed by calculating the correlation of the Nozaki‐Tanford values. Such amphipathic helices may be important in protein–protein and protein–lipid interactions and in forming hydrophilic channels in the membrane. The choice of 30 nonhomologous proteins as the data set did not alter the above results.
1H‐ and 13C‐nmr studies on caffeine and its interaction with nucleic acids
Authors: Kan Lou‐sing , Borer Philip N. , Cheng Doris M. , Ts'o Paul O. P.
Published: December 2004

The relative orientation of caffeine in stacks formed by self‐association in aqueous solution has been evaluated by both 1H‐ and 13C‐nmr spectroscopy. The data, which were interpreted through the calculation of ring‐current and atomic diamagnetic anisotropic effects of the caffeine molecule, suggest two caffeine bases may stack in a nearly orthogonal manner. The interactions between caffeine and adenylyl‐3′,5′‐adenosine, polyadenylic acid, and ribo‐(A‐A‐G‐C‐U‐U)2 helix were also studied by nmr at different caffeine/base ratios and at varying temperatures. The results show that caffeine tends to stack on the top of the terminal purine bases or to insert (the single‐stranded) or to intercalate (the double‐stranded) between purine bases.
On the blue color of triiodide ions in starch and starch fractions. III. Resonance Raman spectra of bluing species in amylose
Authors: Handa Takashi , Yajima Hirofumi , Kajiura Teruo
Published: December 2004

In order to clarify the characteristics of the basic units responsible for the blue coloring of iodine/iodide in amylose, we made a resonance Raman spectroscopic study at several KI concentrations using excitation by Ar+, He‐Ne, and Kr+ lasers and amyloses with the degrees of polymerization (DP) of 30, 100, 300, and 1000. Similar Raman spectra were observed, regardless of the KI and I2 concentrations, DP, and excitation wavelengths. Four Raman lines appearing at 159, 111, 55, and 27 cm−1 were obviously fundamental tones, with a degree of depolarization ρ of ca. 1/3 for every spectrum. However, the internal ratios of the intensities of the 159, 55, and 27 cm−1 lines to that of the 111‐cm−1 line decreased with increasing KI concentration. Based on the value of ρ, the assignment of the fundamental lines was made by taking a schematic model of the true motions as a projection in separately analyzing the modes of stretching and bending vibrations for a pseudolinear polyiodide chain, which we found to be perturbed by the external forces of the amylose lattice. In accordance with the variation of the force constants from the assignment of the spectra associated with the change in the composition of the bound species, it was concluded that the basic unit changed from I to I through I with decreasing KI concentration.
Solution properties of sodium alginate
Authors: Mackie W. , Noy R. , Sellen D. B.
Published: December 2004

Sodium alginate fractions derived from three different sources—Laminaria hyperboria (75% guluronate), Fucus vesicularus (95% mannuronate), and Azotobacter vinelandii (85% mannuronate)—were investigated in aqueous solution over a wide range of ionic strength and pH using the techniques of light scattering, viscometry, and osmometry. Light‐scattering data extrapolated to infinite ionic strength yielded b0 = 4.7 ± 0.3 and 3.0 ± 0.2 nm for the unperturbed effective bond lengths of the guluronate‐ and mannuronate‐rich samples, respectively. These values are in the same ratio as predicted by conformational analysis, although lower by a factor of 0.7, probably due, in part at least, to the fact that measurements cannot be made on pure homopolymers. A comparison of the light‐scattering and the viscosity data indicated that Φ in the Flory‐Fox equation is lower than for more flexible polymers and increases with molecular weight, probably due to decreasing hydrodynamic permeability. Mark‐Houwink exponents obtained from data extrapolated to infinite ionic strength were found to be considerably greater than 0.5, and we attribute this entirely to a variation in Φ. Comparison of the results obtained for the two mannuronate‐rich samples indicated that the value of Φ and its variation with molecular weight can, in the case of alginates, differ markedly for chains, which, although having chemical differences, have similar chain statistics.
Helix–coil transitions in a simple polypeptide model
Authors: McCammon J. A. , Northrup S. H. , Karplus M. , Levy R. M.
Published: December 2004

A simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix–coil transition. The equilibrium properties examined include helix–coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix–coil transition rates.
Kinetics of reactions involving DNA containing stress‐induced single‐stranded regions
Authors: Benham Craig J.
Published: December 2004

The theoretical kinetics are analyzed for reactions between torsionally stressed DNA and another compound which reacts at different rates with portions of the substrate molecule which are in different conformational states. These reactions are assumed to obey Michaelis‐Menten kinetics, so no cooperative effects occur. The DNA is regarded as being susceptible to a stress‐induced local conformational transition as described recently by Benham. Briefly, alterations in torsional stress consequent on superhelicity effectively change the relative concentrations of the two conformational states of the substrate, thereby influencing the course of the reaction. This theory is developed for transition between the B‐form helix and the single‐stranded, random‐coil states. To illustrate the influence of posited stress‐induced melting on kinetics, calculations are made on simple models of two biochemical phenomena. First, the variations in initial nicking rates of single‐strand‐specific endonucleases with substrate superhelicity are interpreted as arising from changes in the concentration of (stress‐induced) single‐stranded binding sites. Second, the observed dependence of the transcription rate of RNA polymerase core enzyme on substrate superhelicity is interpreted in terms of a model in which the rate‐limiting step in the initiation event is the formation of a complex between the enzyme and a single‐stranded region. Related experimental results are shown to be qualitatively consistent with the suggestion that sufficiently supercoiled DNA contains locally melted regions.
Effect of some organic cosolvents on the reaction of hemoglobin with oxygen
Authors: Cordone Lorenzo , Cupane Antonio , San Biagio Pier L. , Vitrano Eugenio
Published: December 2004

We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod‐Wyman‐Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
Temperature dependence of the effects of some monohydric alcohols on the oxygen affinity of hemoglobin: Determination and analysis of thermodynamic parameters
Authors: Cordone Lorenzo , Cupane Antonio , San Biagio Pier L. , Vitrano Eugenio
Published: December 2004

We studied the effects of methanol, ethanol, iso‐propanol, and n‐propanol on the reaction of hemoglobin with oxygen at various temperatures. The analysis of the results in terms of the Monod‐Wyman‐Changeux model allowed determination of the overall contribution of the alcohols to the standard enthalpy and entropy differences between the T and R states of hemoglobin. A phenomenological approach allowed us to obtain separately the contributions related to the variations of the bulk dielectric constant of the solvent (bulk electrostatic contributions) and the contributions related to other effects (non‐bulk‐electrostatic contributions). The values of non‐bulk‐electrostatic contributions to ΔΔH and ΔΔS supported the suggestion that these contributions are mainly related to protein‐solvent hydrophobic interactions.
Conformation and dynamic structure of poly(inosinic acid) in neutral aqueous solution by 1H‐, 2H‐, 13C‐, and 31P‐NMR spectroscopy
Authors: Neumann J. M. , Tran‐Dinh S.
Published: December 2004

The conformation and dynamic structure of single‐stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies: 1H (90 and 250 MHz), 2H (13.8 MHz), 13C (75.4 MHz), and 31P (36.4 and 111.6 MHz). Measurements of the proton‐proton coupling constants and of the 1H and 13C chemical shifts versus temperature show that the ribose is flexible and that base‐base stacking is not very significant for concentrations varying from 0.04 to 0.10M in the monomer unit. On the other hand, the proton T1 ratios between the sugar protons, T1 (H1′)/T1 (H3′), indicate a predominance of the anti orientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation time T2. For a given temperature between 22 and 62°C, the 13C‐{1H} NOE value is practically the same for seven protonated carbons (C2, C8, C1′, C2′, C3′, C4′, C5′). This is also true for the T1 ratio of the corresponding protons. Thus, the motion of the ribose–base unit can be considered as isotropic and characterized by a single correlation time, τc, for all protons and carbons. The τc values determined from either the 13C‐{1H} NOE or proton T1 ratios, T1(90 MHz)/T1(250 MHz), and/or deuterium transverse relaxation time T2 agree well. The molecular motion of the sugar‐phosphate backbone (O‐P‐O) and the chemical‐shift anisotropy (CSA) were deduced from T1 (31P) and 31P‐{1H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ − σ⟂). Activation energies of 2–6 kcal/mol for the motion of the ribose–base unit and the sugarphosphate backbone were evaluated from the proton and phosphorus relaxation data.
Dynamic light‐scattering studies of internal motions in DNA. III. Evidence for titratable joints associated with bound polycations
Authors: Lin S. C. , Thomas J. C. , Allison S. A. , Schurr J. M.
Published: December 2004

Dynamic light‐scattering techniques are employed to study the internal Brownian motions of a commercial calf thymus DNA, clean and contaminated ϕ29 DNAs, and a clean ϕ29 DNA with bound spermidine as a function of pH. The Rouse‐Zimm model parameters of both calf thymus and contaminated ϕ29 DNAs differ substantially from those of clean ϕ29 DNA in the neutral‐pH region. However, this difference is largely removed by adding 0.01M EDTA (which has no effect on clean ϕ29 DNA) to the calf thymus DNA sample. These findings imply the existence in that preparation of polycation contaminants, presumably basic proteins, that can substantially alter the local mechanical properties of the DNA near their binding sites. The internal motion parameters kBT/f and b of both calf thymus and contaminated ϕ29 DNAs are found to exhibit pronounced characteristic variations between pH 8.5 and 10.5, over which range there is essentially no detectable titration to a resolution of about 1% of the base pairs. These variations, which are not observed for clean ϕ29 DNA, are qualitatively similar to those previously reported for a ϕ29 DNA with 21 single‐strand breaks per chain. This indicates the formation of titratable joints associated with bound polycation contaminants. These basic ligands presumably facilitate local denaturation by stabilizing the titration of one or more protons on base‐ring nitrogens near their binding sites. Spermidine binding up to 85–87% of neutralization of the total DNA charge has only a relatively minor effect on the internal motion parameters at neutral pH in 0.01M NaCl. However on raising the pH to 10.2, the internal motion parameter kBT/f undergoes a marked decrease similar to that observed for both calf thymus and contaminated ϕ29 DNAs and also ϕ29 DNA with single‐strand breaks. This indicates that spermidine, too, is capable of inducing titratable joints. Evidence is presented that the titratable joints associated with bound polycations on the calf thymus DNA may serve primarily as torsion joints, as was found previously for the titratable joints associated with single‐strand breaks.
Theoretical π‐π* circular dichroic spectra of helical poly(glycine) and poly(L‐alanine) as functions of backbone torsion angles
Authors: Applequist Jon
Published: December 2004

Circular dichroic spectra and oscillator strengths of the π‐π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (ϕ,ψ) over the range ‐180° ≤ ϕ ≤ ‐60°, −60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (ϕ,ψ) angles corresponding to the α‐helix, the poly(Pro) II helix, a collagen single helix, a poly‐(MeAla) helix, and single β‐helices are found to agree well with most of the available experimental data.