bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational analysis of polynucleotide chains. Double‐stranded structures
Authors: Calascibetta F. G. , Dentini M. , De Santis P. , Morosetti S.
Published: December 2004

Conformational analysis of double‐stranded helical polynucleotides was carried out in terms of internal and external parameters, using semiempirical energy potential functions. The results obtained show that the structures proposed on the basis of the X‐ray analysis for A‐DNA and RNA's are almost identical to those corresponding to the conformational energy minima, whereas that proposed for B‐DNA still appears to suffer from conformational strains. On the other hand, the B‐DNA structure theoretically predicted is stabilized by both van der Waals energy and possible specific interactions with water molecules and counterions. This may explain the stability of the B form with respect to the A form at high relative humidity and ion strength. A possible role of the A + T fraction in stabilizing the B‐type DNA emerges in connection with its preferential ability to bind ions. This agrees with the results on the crystalline structures of GpC and ApU. For RNA's, the occurrence of only A‐type structures is explained as being due to the C(3′)‐endo puckering of ribose in a double helix.
Poly(L‐valine). Conformational dependence on the degree of polymerization: Infrared studies
Authors: Itoh Koichi , Fasman Gerald D.
Published: December 2004

The infrared spectra of poly(L‐valine)'s with varying degrees of polymerization have been investigated, as well as copolymers of L‐alanine and L‐valine. The spectra of nujol mulls of various molecular‐weight poly(L‐valine)'s, isolated directly from the polymerization media, as well as spectra of these same samples after treatment with strong acid, are recorded. In the 700–250‐cm−1 region, bands at 543 and 414 cm−1 are found to increase with increasing degree of polymerization in the nujol mulls, but are missing in the acid‐treated samples. These bands are assigned to the L‐valine residues with an β‐helixlike local conformation. It is inferred that the polymerization proceeds initially in the β form, and after a critical degree of polymerization the chains adopt an appreciable amount of an α‐helixlike local conformation.
Reversible structural changes in a hydrophobic protein, elastin, as indicated by fluorescence probe analysis
Authors: Gosline John M. , Yew Foch F. , Weis‐Fogh Torkel
Published: December 2004

Fluorescent probe analysis of purified elastin using 1‐anilinonaphthalene‐8‐sulfonate has been used to investigate reversible structural changes that accompany stretching of this rubberlike protein. There is a specific binding of 1‐anilinonaphthalene‐8‐sulfonate to elastin with a single dye molecule attached per 74,000 molecular‐weight protein subunit. When labeled elastin is stretched, the intensity of the 1‐anilinonaphthalene‐8‐sulfonate fluorescence decreases reversibly, and this decrease appears to be linked to an increase in the environmental polarity in the immediate vicinity of the bound dye molecule. The results of experiments carried out in H2O and D2O indicate that this polarity change is due to an increase in the exposure of the 1‐anilinonaphthalene‐8‐sulfonate to water as the hydrophobic interior of the protein subunit is unfolded during stretching. The data are consistent with the proposal that the elastin network is a two‐phase system of hydrophobic protein globules surrounded by free solvent spaces.
Conformation of histidine model peptides. III. Chiroptical properties of cyclo‐L‐alanyl‐L‐histidine and cyclo‐L‐histidinyl‐L‐histidine
Authors: Grebow Peter E. , Hooker Thomas M.
Published: December 2004

The chiroptical properties of the cyclic dipeptides cyclo‐L‐alanyl‐L‐histidine and cyclo‐L‐histidinyl‐L‐histidine have been investigated as a function of molecular conformation. The rotatory strengths of the n‐π* transitions of the peptide chromophores and the lowest energy π‐π* transitions of the imidazole chromophores have been calculated as a function of the angle of fold of the cyclic dipeptide group and the dihedral angles χ1 and χ2 of the amino acid side chains. The results of this investigation are consistent with the preferred position of the dihedral angle χ1 occurring near 60° in the free base form of cyclo‐L‐alanyl‐L‐histidine, and near 180° when the imidazole side chain is protonated. Furthermore, in the case of the free base form of the imidazole group, it is possible that the tautomeric isomer in which Nε is protonated may be more prevalent than the isomer in which Nδ is protonated.
Infrared and Raman spectroscopy of carbohydrates. Part VI: Normal coordinate analysis of V‐amylose
Authors: Cael John J. , Koenig Jack L. , Blackwell John
Published: December 2004

A normal coordinate analysis of V‐amylose has been performed for an isolated 61 helical chain. Negligible splitting from interactions of vibrations of successive residues is expected between A and E vibrational species due to the large size of the monomer unit. As a result, calculation of only the totally symmetric A modes represents an adequate approximation to the vibrational spectrum of helical polysaccharides. Using this method together with a valence force field we have obtained good agreement between the observed and calculated frequencies. In addition, the computed potential energy distribution and Cartesian displacement coordinates match previous experimental assignments, based on deuterium exchange. The analysis also supports the proposed mechanism for conversion of V‐amylose to the more extended B‐form. This conversion results in an observed frequency shift for the Raman line at 946 cm−1 which is predicted by the calculations.
Ordered forms of 5′‐8‐aminoguanylic acid
Authors: Hattori Masao , Frazier Joe , Miles H. Todd
Published: December 2004

5′‐8NH2GMP forms an ordered structure in moderately acid (pD 4.7) solution. We propose for this ordered form a novel hemiprotonated G·G structure with a twofold rotation axis and three hydrogen bonds between each pair of guanine residues. Gel formation does not occur with this nucleotide in either neutral or acid solution. In neutral solution 5′‐8NH2GMP also forms a regular, ordered structure, quite different from the acid form and similar to that formed by 5′‐GMP under the same neutral conditions. We suggest that this ordered structure consists of a regularly stacked array of planar tetramers, similar to that proposed for 3′‐GMP at pH 5.2
Backbone conformations in deoxyribonucleic acids. Conformational role of the 2′‐hydroxyl group on the internucleotide phosphodiester conformations
Authors: Yathindra N. , Sundaralingam M.
Published: December 2004

The conformations accessible to the internucleotide phosphodiester group in deoxydinucleoside monophosphates, deoxydinucleoside triphosphates, and deoxypolynucleotides have been explored in detail by potential energy calculations. The two most predominant conformations for the nucleotide moiety (3E and 2E) and their possible combinations (3E−3E, 3E−2E, 2E−2E, 2E−3E) have been employed, similar to our earlier studies on polyribonucleotides. The internucleotide P‐O bond torsions are very sensitive to the sugar pucker (3E and 2E) and sugar type (ribose and 2′‐deoxyribose) on the 3′‐residue of dinucleoside phosphates. The preferred phosphodiester conformations found for the deoxydinucleoside monophosphates and triphosphates, in general, follow the same pattern as those obtained for ribose sugars when the sugar on the 3′‐side of the molecule has the 3E sugar‐ring conformation. The internucleotide P‐O bonds show a greater degree of conformational freedom when the 3′‐sugar has the 2E pucker. The double gauche g−g− conformation for the phosphodiester, which leads to the overlap of the adjacent bases, is shown to be one of the energetically most favored conformations for all the sequence of sugar puckers. It is found that the 2E−2E sequence of sugar puckers shows a greater energetic preference for the stacked helical conformation (g−g−) than the (3E−3E) and the mixed sugar‐pucker combinations. This effect becomes more pronounced in going from a dinucleoside monophosphate to a dinucleoside triphosphate suggesting that the 2′‐deoxy sugars favor the 2E sugar pucker in di‐, oligo‐, and polydeoxyribonucleotide structures. In addition to g−g−, the conformations g+g−, tg−, g−t, tg+, and g+t are also found to be possible for the phosphodiester in a polydeoxyribonucleotide and their populations depend to some extent on the sugar‐pucker sequence. It is shown that the short‐range intramolecular interactions involving the sugar and the phosphate groups dictate to a large extent the backbone conformations of nucleic acids and polynucleotides.
Influence of Mn2+ ion coordination on tRNAVal1 macrostructure and determination of some coordination sites of Mn2+ ions in tRNAVal1
Authors: Vocel S. V. , Slepneva I. A. , Backer J. M.
Published: December 2004

Electron paramagnetic resonance spectroscopy has been used to study the coupling of Mn2+ ions with the tRNAVal1 modified with a spin label at four pseudouridylic residues and with the valyl‐tRNAVal1 modified with a spin label at the α‐amine group of the valyl residue. A sharp increase of spin‐label mobility has been found in these samples, due to the conformational transition induced by the first and second Mn2+ ions. Analysis of dipole–dipole couplings of spin labels with the coordinated ions revealed a definite order in the occupation of ion coordination sites in the tRNA. For some valyl‐tRNAVal1 molecules, the second Mn2+ ions were shown to coordinate on the α‐amine group of the valyl residue at a distance of 15–25 Å from a spin label. As a result of the conformational transition, a coordination site appeared in the tRNA at one of the pseudouridylic residues, its distance from the spin label being less than 10 Å. It has been suggested that the conformational transition induced by ions excluded some bases from the system of hydrogen bonds at the level of the tRNA tertiary structure. As a result, these bases acquired sufficient sterical freedom to participate in the Mn2+ ion coordination.
Levans. III. A light‐scattering study of Streptococcus salivarius levan in dimethyl sulfoxide
Authors: Bahary W. S. , Stivala S. S. , Newbrun E. , Ehrlich J.
Published: December 2004

A light‐scattering study of unfractionated and five fractions of Streptococcus salivarius levan was performed in dimethyl sulfoxide. The weight‐average molecular weights M̄r in dimethyl sulfoxide, after adequate dissolution, agree with those obtained in water within a mean difference of 7%. The intrinsic viscosities [η] and root‐mean‐square z‐average radii of gyration (Rg2)z1/2 are significantly higher in dimethyl sulfoxide than in water, reflecting the higher hydrodynamic volume in the former. The M̄r, [η], and (Rg2)z1/2 of the fractions suggest that levan has a low polydispersity. The exponent of 0.12 of the Mark‐Houwink plot and model analysis confirm the branched and compact structure of levan.
Polarized fluorescence in an electric field. A model calculation with application to the geometry of the 2‐hydroxy‐4,4′‐diamidinostilbene–DNA complex
Authors: Weill G. , Sturm J.
Published: December 2004

Theoretical expressions are derived for the change in the polarized components of the fluorescence, resulting from the orientation of a rigid molecule bearing a chromophore with arbitrary angles for the absorption and transition moments \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document} with respect to the molecular axis. The break in the symmetry relation HV = VH is related to the tilt angle between \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document}. The theory is applied to a sonicated DNA–2‐hydroxy‐4,4′‐diamidinostilbene complex, in the blue and red emission bands of this peculiar dye. Simultaneous measurements of linear dichroism and fluorescence lead to the determination of an angle of 47° between a fluorescent bound dye and the DNA axis, with no difference for the blue‐ and red‐emitting species, but confirm the presence of nonfluorescent bound dye in a more perpendicular arrangement.
Irreversible thermodynamic analysis of electrophoretic light scattering experiments
Authors: Friedhoff L. , Berne B. J.
Published: December 2004

A fluctuation theory for electrolyte solutions is developed based on the coupling between the equations of nonequilibrium thermodynamics and the Poisson equation. The resulting fluctuation theory is applied to the analysis of electrophoretic light scattering. It is shown that in a binary electrolyte solution (two ionic species), the Doppler shift is not determined by the electrical mobility of either ion, but depends instead on the rate of change of transference number with salt concentration. In addition the ionic relaxation time is shown to be proportional to the conductivity of the solution.
Application of the nearest‐neighbor ising model to the helix–coil transition of polypeptides in mixed organic solvents
Authors: Cabani S. , Paci A. , Rizzo V.
Published: December 2004

Using the formalism of nearest‐neighbor Ising model and assuming that the allowed states for a monomeric unity of a polypeptide chain in solutions containing strong acids are E (helix), C (coil), and CS (solvent‐bonded coil), the partition function of the system was deduced analytically. Equations were obtained which permitted the prediction of the characteristic thermodynamic behavior of the helix–coil transition under these conditions. These equations were used to examine critically the possible correlations between experimental data obtained using different techniques. Particular attention was devoted to quantities called “transition enthalpies,” obtained from the slope of the transition curves at the point where the helix fraction is one‐half (ΔH), or for measurements of the heat of solution of the polymer over the total range of solvent composition (ΔH), or from heat capacity measurements taken at various temperatures (ΔH). Literature data of ΔH(j = opt, sol, cal) for the system poly‐γ‐benzyl‐L‐glutamate in mixtures of dichloroacetic acid and 1,2‐dichloroethane were carefully analyzed.
High‐resolution thermal denaturation of DNA. I. Theoretical and practical considerations for the resolution of thermal subtransitions
Authors: Ansevin Allen T. , Vizard Douglas L. , Brown Barry W. , McConathy Judy
Published: December 2004

The fidelity achieved in first derivative profiles of DNA thermal denaturation is shown to depend on a number of factors including the thermal increment of data gathering, the precision of absorbance readings, and the manner in which data are smoothed prior to calculating the derivative of hyperchromicity. The closeness with which thermal denaturation data can be fitted by a cubic polynomial is carefully considered, and a derivation is presented for the estimated error in calculated values of the derivative of hyperchromicity with respect to temperature. After reviewing both theoretical and experimental evidence for the expected minimum width of a thermal transition in DNA, we conclude that thermal increments of 0.05°C or less are required for an adequate representation of transitions in naturally occurring DNA's.

Data gathered under conditions meeting the requirements suggested here for quantitative recording of thermal denaturation profiles (Vizard and Ansevin, submitted for publication) show that virtually all of the high‐resolution thermal denaturation profile of a simple, naturally occuring DNA may consist of small subtransitions, which we call thermalites. The finding of substransitions is consistent with current theories of DNA melting. A particularly well‐resolved thermalite of λ bacteriophage DNA has a breadth of only 0.30°C (2σ width), and thus is narrower than previously reported thermal transitions for DNA. For this thermalite, the combination of width, shape, and position in the profile suggests that the substransitions observed in accurately recorded DNA thermal denaturation profiles are not described satisfactorily by existing theories.

Knowledge of the requirements for the quantitative recording of thermal denaturation profiles should greatly favor the usefulness of denaturation experiments for physical genomic analysis.
Comparison of four proteoglycans in terms of their interactions with poly(L‐arginine)
Authors: Schodt K. P. , Blackwell J.
Published: December 2004

Connective tissue proteoglycans undergo interaction with poly(L‐arginine) when mixed in dilute neutral aqueous solution. Circular dichroism spectroscopy indicates that the polypeptide adopts the α‐helical conformation rather than the extended coil form normally observed at neutral pH. The interactions of a series of proteoglycans with different protein and glycosaminoglycan contents have been compared. The arginine/disaccharide residue ratio at maximum interaction appears to be constant with varying protein content of the proteoglycans that contain chondroitin 4‐sulfate. The thermal stability of the proteoglycan interaction is the same as for the component polysaccharide. Thus in terms of the strength of interaction with homopolypeptides, the properties of proteoglycan and the component glycosaminoglycans are the same, and this is likely also to be the case for collagen–proteoglycan systems.

The interactions of keratan sulfate‐2 have also been investigated. These are similar but have much lower thermal stability than corneal keratan sulfate‐1. The results are consistent with the weak interaction of the keratan sulfate‐2 component of bovine nasal septum proteoglycan.
Infrared spectra and resonance interaction of amide‐I vibration of the antiparallel‐chain pleated sheet
Authors: Chirgadze Yu. N. , Nevskaya N. A.
Published: December 2004

Theoretical treatment of resonance interaction of amide‐I vibration has been done in a dipole–dipole approximation on the basis of perturbation theory. A single infinite antiparallel‐chain pleated sheet as well as different kinds of its finite fragments have been considered. A good agreement has been obtained between calculated spectral parameters of amide I of the infinite sheet and observed ones in infrared and Raman spectra of synthetic polypeptides and fibrous proteins. A theoretical dependence of the resonance frequency shift of the main component and frequency splitting of two components active in the infrared spectra on the number of polypeptide chains in the finite sheet has been found.
Peptide synthesis using o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydrides. Sequential oligopeptides having alternate γ‐methyl L‐glutamyl and L‐phenylalanyl residues
Authors: Katakai Ryoichi , Nakayama Yohko
Published: December 2004

A series of sequential oligopeptides having the sequence alternating γ‐methyl L‐glutamyl and L‐phenylalanyl residues have been successfully prepared by a rapid method involving the reaction of o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydrides with amino acid and peptide esters. The sequential oligopeptides, which are interesting from a conformational aspect, were obtained in optical pure forms above 74% yields. This result demonstrates that the o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydride method is especially useful for easy synthesis of protected oligopeptides with o‐nitrophenylsulfenyl group.
Ultrasonic absorption in aqueous solution of lysozyme
Authors: Kanda Hiroshi , Ookubo Norio , Nakajima Haruhiko , Suzuki Yasuko , Minato Michio , Ihara Takuro , Wada Yasaku
Published: December 2004

The titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74, 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton‐transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm3/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH‐independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′p − iβ″p of lysozyme molecule is evaluated as β′p = 7.2 × 10−12 cm2/dyne and β″P = 4.3 × 10−14 cm2/dyne from the increments over solvent in absorption as well as in sound velocity.
Conformational studies in aqueous solution on random copolymers of L‐glutamic acid and ortho‐nitrobenzyl‐L‐glutamate. Circular dichroism and potentiometric titration studies
Authors: Estevez Jacky , Loucheux‐Lefebvre Marie H.
Published: December 2004

Random copolymers of L‐glutamic acid and ortho‐nitrobenzyl‐L‐glutamate were synthesized with different percentages of nitrobenzyl‐L‐glutamate, from 3 to 22%. These copolymers were studied by circular dichroism (CD) and potentiometric titrations in aqueous solutions in order to determine the variation of the stability of the secondary structure when the concentration of nitrobenzylglutamate varies in the copolymer. We observed that the stability increases with the concentration of glutamate. Such a stabilization could be due to either side‐chain interactions or interactions between the aromatic side chain with the backbone. An intermolecular aggregation was observed when the percentage of nitrobenzylglutamate was sufficently important, but such an aggregation may be avoided if a dioxane/water mixture is used as a solvent.
A potentiometric and CD investigation on the conformational properties of poly (L‐p‐aminophenylalanine) in aqueous solution
Authors: Peggion E. , Cosani A. , Palumbo M. , Terbojevich M. , Goodman M.
Published: December 2004

The conformational properties of poly(L‐p‐aminophenylalanine) have been investigated by potentiometric and circular dichroism (CD) techniques. It has been found that the polymer in the charge‐free state can assume two ordered conformations, depending upon temperature conditions. At room temperature the polymer assumes the right‐handed helical form by described Goodman and Peggion.1 At temperatures higher than 40°C a new ordered conformation has been found, whose slow rate of formation and ir absorption properties are typical of the β‐structure. The thermodynamic parameters relative to the coil‐β transition, determined by potentiometric titration techniques, revealed that the thermodynamic stability of the β‐structure is mainly due to enthalpic factors. The formation of this structure is unfavored on a kinetic basis.
Ferric complexes of acetoacetyl derivatives of poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid). II. Conformational properties in solution. Evidence for a stereospecific complex formation
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Peggion E.
Published: December 2004

The conformational properties of ferric complexes of poly(Nε‐acetoacetyl‐L‐lysine), poly(Nδ‐acetoacetyl‐L‐ornithine), and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid) were investigated in 1:1 water/dioxane by CD techniques. Optical activity was found in the visible and in the uv absorption region of the polymeric complexes. The conformation of the peptide backbone was always that of a right‐handed α‐helix, and was found independent of the degree of complexation, at least up to a degree of binding of 20%. In the absorption region of the side‐chain chromophores the optical activity is substantially affected by complex formation. In all three cases a splitting of the ligand π → π* transition centered at 257 nm is observed. These data suggest a stereospecific complex formation. From the signs of the splitting it also appears that the chirality of the poly(Nδ‐acetoacetyl‐L‐ornithine) complex is opposite that of the other two polymers.
Interaction of sodium decyl sulfate with poly(L‐ornithine) and poly(L‐lysine) in aqueous solution
Authors: Satake Iwao , Yang Jen Tsi
Published: December 2004

The binding isotherms of sodium decyl sulfate to poly(L‐ornithine), poly(D,L‐ornithine), and poly(L‐lysine) at neutral pH were determined potentiometrically. The nature of a highly cooperative binding in all three cases suggests a micelle‐like clustering of the surfactant ions onto the polypeptide side groups. The hydrophobic interaction between the nonpolar groups overshadows the coulombic interaction between the charged groups. The titration curves can be interpreted well by the Zimm–Bragg theory. The average cluster size of bound surfactant ions is sufficiently large to promote the β‐structure of (L‐Lys)n even at a very low binding ratio of surfactant to polypeptide residue, whereas the onset of the helical structure for (L‐Orn)n begins after about 7 surfactant ions are bound to two turns of the helix. The CD results are consistent with this explanation.
Interaction of water with native collagen
Authors: Nomura S. , Hiltner A. , Lando J. B. , Baer E.
Published: December 2004

The interaction of water with collagenous tissue was investigated using dynamic mechanical spectroscopy and cryogenic X‐ray techniques. The loss spectrum was found to be very sensitive to water which is highly associated with the macromolecule. Two water‐sensitive loss peaks were observed below 0°C: the β2 or “water dispersion” at 150°K and the β1 at 200°K which is attributed to motion of polar side chains. Changes in peak temperature and intensity were not continuous with water content, but exhibited regimes in behavior which were associated with two types of nonfreezable water, structural and bound water. In cryogenic X‐ray experiments, specimens which contained some freezable water exhibited reflections identified with the cubic form of ice. These ice crystals underwent an irreversible transition to the more common hexagonal form when warmed above 200°K. On the basis of these experiments, a model for the hydration of native collagenous tissue was proposed.
Intensity fluctuation spectroscopy of deoxyribonucleic acid (DNA). II. Temperature profile of bacteriophage ϕ29‐DNA
Authors: Schmidt R. L. , Whitehorn M. A. , Mayo John A.
Published: December 2004

Intensity‐fluctuation laser‐scattering spectroscopy measurements have been reported for the DNA isolated from bacteriophage ϕ29. The cumulant method of data analysis gives well‐defined weighted average decay frequencies. Available theoretical models are shown to yield good values for the diffusion coefficient and longest intramolecular relaxation time for low‐molecular‐weight DNA's but not for higher molecular weight species. The temperature dependence of the apparent diffusion coefficient exhibits drastic oscillations in the helix–coil transition region. The number of these oscillations is consistent with independent measurements of uv hyperchromicity measurements and suggests that ϕ29‐DNA is composed of at least three regions of differing G + C content.
Spectral analysis on the melting fine structure of λ DNA and T2 DNA
Authors: Akiyama Chuji , Gotoh Osamu , Wada Akiyoshi
Published: December 2004

The fine structure of the thermal denaturation of viral DNA's was analyzed with the spectral method established by Felsenfeld and Hirschman, and Fresco et al. A fully automated system measuring melting curves at four wavelengths at the same time was developed for this purpose. With this device, (G + C)‐contents of melting components of λ DNA's were determined. The correlation between the (G + C)‐content and the melting temperature of each melting component is found to be well described by the linear relationship given by Marmur and Doty. The denaturation of each component is regarded as cooperative. The Marmur–Doty relation also stands for the local denaturation of T2 DNA, which has a narrow melting range.
Interpretation of energy‐transfer experiments by theoretical studies of model compounds using semiempirical potential functions. II. Monte Carlo calculations on oligopeptides
Authors: Leclerc Marc , Premilat Samuel , Guillard Roger , Renneboog‐Squilbin Claire , Englert Anne
Published: December 2004

The properties relevant to nonradiative energy transfer have been computed in the unperturbed chain model for oligopeptides composed of from 4 to 21 residues of the formula Tyr‐(Ala)n‐Tyr and Trp‐(X)n‐Tyr, X being either Ala or Gly. A Monte Carlo method has been used for the generation of the chains.

The relation between the distribution functions of the distances between the luminophores and the various properties in energy transfer has been examined for chains of different lengths and compositions.

The averge of the orientation factor κ2 has been computed as a functions of chain length both for molecules in a randomly coiled state and for molecules with backbones in a well‐defined three‐dimensional structure.

The various averaging regimes of energy‐transfer efficiency and of fluorescence decay are compared. Theoretical curves relating experimental efficiencies to the mean distance between the luminophores are proposed.
Translational diffusion coefficient of α‐chymotrypsinogen A by laser‐light‐scattering spectroscopy
Authors: Raj T. , Flygare W. H.
Published: December 2004

The translational diffusion coefficient of a pure sample of α‐chymotrypsinogen A is measured by laser light scattering to give a value of D20,w0 = (8.40 ± 0.15) × 10−7 cm2/sec.
Transient electric birefringence of the bacteriophages T3 and T7
Authors: De Groot G. , Greve J. , Block Joh.
Published: December 2004

Electric birefringence measurements of suspensions of T3 and T7 bacteriophages in 10−2 M phosphate buffer, pH 6.9, show that there is a difference in their rotational diffusion coefficient. The values corrected to 25°C and water viscosity are D25,w = 4630 ± 130 sec−1 and D25,w = 5290 ± 260 sec−1 for T3 and T7, respectively. The value obtained from shell model calculations (according to Filson and Bloomfield) is D25,w = 4500 ± 600 sec−1. The apparent permanent dipole moments are 4.5 × 10−26 C·m and 1.7 × 10−26 C·m for T3 and T7, respectively. For both phage particles the intrinsic optical anisotropy is +7.2 × 10−3. It is shown that this anisotropy is mainly due to the DNA molecule inside the head of the phage. Its positive value means that there exists an excess orientation of the DNA helix perpendicular to the symmetry axis of the particle. For T7 an unexpectedly large increase of Δns and Ksp occurs at a glycerol concentration of about 30% (v/v). This increase is interpreted as being caused by a change of the shape of the particle and/or a change in the secondary structure of the DNA inside the head of the bacteriophage.
Thermodynamics of mucopolysaccharide–dye binding. II. Binding constant and cooperativity parameters of acridine orange–dermatan sulfate system
Authors: Menter Julian M. , Hurst Robert E. , West Seymour S.
Published: December 2004

In the acridine orange–dermatan sulfate system, free and bound dye can be distinguished from each other spectroscopically. This permits the use of fluorometric methods to study the binding of acridine orange to the acid mucopolysaccharide dermatan sulfate. Experiments were conducted at 24°C in 10−3 M citrate/phosphate buffer at pH = 7.0. The binding of the dye is highly cooperative, as evidenced by considerable interaction between adjacent bound dye molecules. Analysis of the data indicates that dermatan sulfate binds 2.3 ± 0.3 mol of acridine orange per dermatan sulfate uronic acid residue with a cooperative binding constant, Kq ranging from 4.9 to 6.0 × 105 M−1 which corresponds to a free energy of 7.74 ⩽ ΔG° ⩽ 7.86. The cooperativity parameter q apparently increases with increasing polymer‐to‐dye ratio.
Kinetic analysis of the reversible folding reactions of small proteins: Application to the folding of lysozyme and cytochrome c
Authors: Hagerman Paul J.
Published: December 2004

A general kinetic analysis for unimolecular three‐species models is presented. Criteria are established for each model in order to allow selection among alternative models on the basis of their amplitude behavior. These criteria are applied to the previously reported kinetic data for the folding transitions of lysozyme and cytochrome c in guanidine hydrochloride. The degree of success in applying these criteria is found to depend on the extent to which the apparent rate constants, λ1 and λ2, approach each other in certain conditions. Ikai and Tanford have presented a similar kinetic analysis, although these authors considered only the case where no intermediate kinetic species was populated initially. For one protein system, namely, ribonuclease A (RNase A), at least one stable intermediate exists after unfolding outside of the equilibrium transition zone. The criteria developed by Ikai and Tanford cannot be applied to RNase A kinetics and, therefore, a more general analysis is presented. Previously published studies of the reversible folding kinetics of lysozyme and cytochrome c are reexamined using the current amplitude analysis, and it is found that both of these folding transitions can be described by the three‐species model,

used previously to describe the folding kinetics of RNase A (U1 and U2 are two forms of unfolded enzyme and N is the native species). These results suggest that this three‐species model may provide a fairly general description of the reversible folding kinetics of small proteins. As an outgrowth of the current analysis, several suggestions for experimental design in studying protein folding will be presented and discussed.
Investigation of molecular motion in collagen using the spin‐probe technique
Authors: Nagamura T. , Woodward A. E.
Published: December 2004

The spin‐probe technique was employed to study molecular motion in collagen and modified collagen samples in the −160° to +200°C region. The effect of water content in the 0–30‐wt. % range, relative to vacuum dried samples, on the electron spin resonance spectrum of the probe was also investigated. The spectra at the lowest temperatures consisted of a broad asymmetric triplet. Narrowing of this triplet above −40° to −70°C and the appearance of additional lines in the spectrum, interpreted as due to a narrow triplet, at a temperature dependent on the water content were observed. For samples with low water contents [(0–0.4)%] the broad triplet was that expected for a glassy system up to 150–190°C; for these samples the narrow triplet appears at a temperature above 50°C, its intensity increasing with increasing temperature up to 70–100°C, then decreasing with a further temperature increase. For samples with water contents near 30%, the narrow triplet first completely appears at about 0°C, and reaches relative intensities of 35% at 30°C. The motion taking place in collagen and related samples is discussed in terms of these results.
A study of the growth of normal and iodinated collagen fibrils in vitro using electron microscope autoradiography
Authors: Haworth R. A. , Chapman J. A.
Published: December 2004

Electron microscopic autoradiographic observations on collagen fibrils grown in vitro allow growth rates in the N‐ and C‐terminal directions to be measured on individual fibrils. Such observations, made on normal and iodinated collagen, show that normal fibrils grow at both ends (although rather more rapidly at the N‐terminal end), whereas fully‐iodinated collagen fibrils grow only at the N‐terminal end.

Measurements of growth rates at different temperatures provide estimates of the activation enthalpy (ΔH≠) and entropy (ΔS≠) of precipitation for the two types of collagen. Solubility measurements have also yielded values for the thermodynamic enthalpy (ΔH) and entropy (ΔS) of precipitation. Results show that the activated (rate‐limiting) state is characterized by a large positive ΔH≠ and ΔS≠ similar in magnitude to the ΔH and ΔS of transition from solution to fibril. It is also concluded that the different rates of precipitation of normal and iodinated collagen cannot be explained in terms of fibril formation requiring ionization of the tyrosine residues.
Hydrodynamic properties of a rigid molecule: Rotational and linear diffusion and fluorescence anisotropy
Authors: Small Enoch W. , Isenberg Irvin
Published: December 2004

The fluorescence anisotropy of a general rigid body is formally the sum of five exponentials. We show that, to a high degree of approximation, there are relationships between the five time constants. As we define the time constants here, τ1 ≅ τ5, τ2 ≅ τ3, and τ1−1 + 3τ4−1 ≅ 4τ2−1. In practical cases, at most only three exponentials will be observed, and, of these, only two are independent.

Using a numerical integration procedure, Perrin's equations for the rotational and translational diffusion of a general ellipsoid are solved. Rotational friction coefficients, frictional ratio, rotational relaxation times, and the five exponential terms in the fluorescence anisotropy are tabulated as functions of the axial ratios of the ellipsoid.

In principle, the three axes of a general ellipsoid may be determined by a simultaneous measurement of the anisotropy and the linear diffusion constant. We examine, and illustrate, the effect of experimental error on such a determination.
Theoretical conformational analysis of Asn1, Val5 angiotensin II
Authors: De Coen Jean‐Louis , Ralston Evelyn
Published: December 2004

A theoretical analysis of the conformation of the octapeptide hormone Asn1, Val5 angiotensin II has been carried out by semiempirical potential energy calculations. A preliminary study of the Ala6‐Pro‐Ala molecule, which mimics the angiotensin backbone, provided us with likely backbone structures on which the effect of the full side chains of the hormone could be assessed. For angiotensin II, the calculations show that only a small number of folded, compact conformations have a high probability of existence. This is the consequence of favorable packing and of the presence of proline in position 7. These results are consistent with various experimental data, both structural and biological. This method is readily applicable to the study of analogs of the hormone or to other peptides of comparable size.
Conformational energy calculations for dinucleotide molecules: A study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+)
Authors: Thornton Janet M. , Bayley Peter M.
Published: December 2004

A study of the conformational states of the dinucleotide coenzyme NAD+ has been made using semiempirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The lowest energy states are stacked structures, with interactions between the adenine and nicotinamide rings. Some structures show stabilization gained from electrostatic attractions between the positively charged nicotinamide and negatively charged phosphate oxygens. These predictions correlate well with the available experimental data.
Effect of charge density of cationic polyelectrolytes on complex formation with DNA
Authors: Mita Kazuei , Zama Mitsuo , Ichimura Sachiko
Published: December 2004

The interaction between DNA and ionen polymers, ‐[N+(CH3)2(CH2)mN+(CH3)2(CH2)n], with m‐n of 3–3, 6–6, and 6–10 were examined in order to know how the binding behavior of cationic polymers with DNA depends on the charge density of polycation. The ionen polymer has no bulky side chain and the binding forces with DNA would be attributed mainly to electrostatic interaction. When 3–3 ionen polymers were added to DNA solution, precipitable complexes with the ratio of cationic residue to DNA phosphate (+/−) of 1/1 and the free DNA molecules were segregated, while 6–6 and 6–10 ionen polymers formed soluble complexes with DNA molecules up to (+/−) = 0.5. This suggests that 3–3 ionen polymers bind cooperatively with DNA while 6–6 and 6–10 ionen polymers bind noncooperatively. The cooperative binding of 3–3 ionen polymer and the noncooperative binding of 6–6 ionen polymer were also supported by the thermal melting and recooling profiles from the midpoint between first and second meltings. It was concluded that the charge density of DNA phosphate is a critical value determining whether the ionen polymers bind to DNA by a cooperative or by a noncooperative binding, since the distance between successive cationic charges of 3–3 ionen polymer is shorter than that between successive phosphate charges on DNA double helix and those of 6–6 and 6–10 ionen polymers are longer.
Flexibility of the pyrrolidine ring in proline peptides
Authors: Madison Vincent
Published: December 2004

A survey of over 50 crystal structures indicates that both imino acid and peptide derivatives of proline populate ring conformers consistent with the torsional potentials about single bonds. In both cases, lower barriers for rotation about CN bonds relative to those about CC bonds favor smaller values for dihedral angles about the former bonds. In peptides a minimum in the torsional potential about CN bonds occurs at zero dihedral angle, further favoring small angles. The pyrrolidine‐ring dihedral angles of the proline compounds in the solid state obey a cyclopentane‐type pseudorotation function. Thus the puckering of the five‐membered ring can be quantitatively described by two parameters. Consistent with small dihedral angles about CN bonds, Cβ and/or Cγ are puckered out of the mean plane of the ring in nearly all of the nonstrained compounds.

Utilizing the consistent force‐field method of Lifson and coworkers [see A. Warshel, M. Levitt, and S. Lifson (1970) J. Mol. Spectrosc. 33, 84] the intramolecular energy of five proline peptides was minimized with respect to all internal coordinates. In addition, the energy surface near minima was explored by constraining a particular dihedral angle and reminimizing the energy with respect to all remaining variables. In linear peptides two types of pyrrolidine‐ring conformers have identical predicted energies. In the cyclic dipeptide cyclo (Pro‐Gly) one of the ring conformers is favored by about 3 kcal/mol, while the cyclic tripeptide cyclo(Pro‐Gly‐Gly) favors the other conformer by a comparable margin. In agreement with observations in the solid state and in solution, Cβ and/or Cγ are puckered in the predicted conformers. A correlation between proline Φ and the details of the puckered conformation was predicted and found to match precisely conformers observed in crystals.

For the diamides N‐acetyl‐L‐proline‐N′‐methyl‐amide and N‐acetyl‐L‐proline‐N′,N′‐dimethylamide (AcProMe2A) 30% and 60% cis acetyl peptide bonds were predicted in good agreement with observations in nonpolar solvents for the respective compounds. The conformational distributions with respect to proline Ψ are also in accord with experimental observations. For AcProMe2A, a model for a ‐Pro‐Pro‐sequence in a peptide chain, this study is the first to predict stable conformers for proline Ψ either ca. −50° or 140° for both cis and trans peptides.
The application of infinite‐order perturbation theory to biological polymers
Authors: Groskreutz Harvey , Wu Shi‐Yu , Schwartz Manuel
Published: December 2004

Quantum mechanical perturbation theory of infinite order is applied to an infinitely long biological polymeric chain. The resulting ensemble‐averaged density of electronic states is approximately calculated by truncation according to a method introduced by S. Y. Wu [(1974) J. Math. Phys. 15, 947–949]. The results are found to require reasonable computational facilities and the method may be applied to a study of mutagenicity.
Conformational studies on polynucleotide chains. III. Intramolecular energy maps and comparison with experiments
Authors: Tosi Camillo , Clementi Enrico , Matsuoka Osamu
Published: December 2004

Conformational energy maps for the four combinations of two consecutive torsional angles of the backbone structure of polydeoxyribonucleotides are presented. Both the C(2′)‐endo and the C(3′)‐endo conformation of sugar rings were considered. The energies were evaluated with an analytical expression representing the best fit to ab initio energies computed in the Hartree‐Fock approximation, and consisting of a contribution from nonbonded interactions of the Lennard‐Jones 6‐12 type and an intrinsic torsional potential. It is shown that the minima of these maps are in excellent agreement with the most stable conformations as obtained from x‐ray crystallographic analysis of nucleic acids and polynucleotides.
Conformational studies of the copolymer poly(L‐lysine, L‐tyrosine) 1:1 in aqueous solution
Authors: Garnier Arlette , Tosi Lucia
Published: December 2004

The absorption and circular dichroism spectra of the 1:1 copolymer (L‐Lys, L‐Tyr)n have been investigated in aqueous solutions at pH ranging from 3 to 13. The spectral patterns indicate that the fully charged polympholyte assumes a nonperiodic conformation on the acid and basic sides of the isoelectric point. At pH ranging from 9.2 to 11.6, the polymer is largely ordered and takes mostly an antiparallel β‐structure as is shown by the infrared spectra in D2O solutions. Moreover, the rotational strength of the La transition of tyrosyl is independent of the polymer conformation, whereas that of the Lb transition is strongly sensitive to it.
Statistical mechanical deconvolution of thermal transitions in macromolecules. I. Theory and application to homogeneous systems
Authors: Freire Ernesto , Biltonen Rodney L.
Published: December 2004

The theoretical basis for the statistical mechanical deconvolution of a thermally induced macromolecular melting profile is presented. It is demonstrated that all the thermodynamic quantities characterizing a multistate macromolecular transition can be obtained from the average excess enthalpy function, 〈ΔH〉, of the system, without any assumption of the particular model or mechanism of the reaction.

Experimentally, 〈ΔH〉 is obtained from scanning calorimetric data by direct integration of the excess apparent molar heat capacity function, ΦCp. Once 〈ΔH〉 is known as a continuous function of the temperature, the partition function, Q, of the system can be calculated by means of the equation

From the partition function all the thermodynamic quantities of the system can be obtained. It is shown that the number of discrete macroscopic energy states, the enthalpy and entropy changes between them, and the relative population of each state as a function of temperature can be calculated in a recursive form.
Compressibility studies of three proteins in CsCI solutions in the analytical ultracentrifuge
Authors: Sharp Dan S. , Fujita Norman , Kinzie Kathleen , Ifft James B.
Published: December 2004

The compositional buoyant densities, ρ;, of human γ‐immunoglobulin, bovine serum mercaptalbumin, and egg albumin have been measured in CsCl solutions in the analytical ultracentrifuge as a function or pressure. Standard pressure coefficients, ψ0, and standard partial specific volumes of the solvated proteins, υ,0, have been computed from these data. The ψ0 values obtained are strikingly different from each other and from the only other pressure coefficients which have been measured, those values obtained for nucleic acids and nucleoproteins. The ψ value for γ‐immunoglobulin is negative, the first nonpositive value obtained, and suggests an unusual internal structure for this protein. The pressure coefficient of mercaptalbumin is not constant. A second‐order relation is derived and utilized to interpret these data. The slope of the ρ(P) plot for egg albumin was constant and negative and yielded values of ψ0 which are about 20% as large as those reported for DNA. Evaluation of published isopiestic data for egg albumin in CsCl solutions provided the dependence of preferential hydration on water activity. This quantity, (dΓ′/da) as well as α, were found to be negative. The values of ψ0 and α were used to compute the effective density gradient from which the correct molecular weight of egg albumin was obtained. The apparent specific volume of egg albumin in a buoyant CsCl solution was measured using the Mettler‐Paar densimeter.