bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnesium ion effect on the helix‐coil transition of DNA
Authors: Blagoi Yu. P. , Sorokin V. A. , Valeyev V. A. , Khomenko S. A. , Gladchenko G. O.
Published: December 2004

The effect of magnesium ions on the parameters of the DNA helix‐coil transition has been studied for the concentration range 10−6–10−1M at the ionic strengths of 10−3M Na+. Special attention has been given to the region of low ion concentrations and to the effect of polyvalent metallic impurities present in DNA. It has been shown that binding with Mg++ increases the DNA stability, the effect being observed mainly in the concentration range 10−6–10−4M. At[Mg++]>10−2M the thermal stability of DNA starts to decrease. The melting range extends to concentrations ∼10−5M and then decreases to 7–8°C at the ion content of 10−3M. Asymmetry of the melting curves is observed at low ionic strengths ([Na+] = 10−3M) and [Mg++] ⩽ 10−5M. The results, analyzed in terms of the statistical thermodynamic theory of double‐stranded homopolymers melting in the presence of ligands, suggest that the effects observed might be due to the ion redistribution from denatured to native DNA. An experimental DNA–Mg++ phase diagram has been obtained which is in good agreement with the theory. It has been shown that thermal denaturation of the system may be an efficient method for determining the ion‐binding constants for both native and denatured DNA.
Base stacking in A fluorescent dinucleoside monophosphate: εApεA
Authors: Baker B. M. , Vanderkool J. , Kallenbach N. R.
Published: December 2004

The optical properties of the 1,N6 ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo4>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.
Aromatic side‐chain contributions to the far ultraviolet circular dichroism of peptides and proteins
Authors: Woody Robert W.
Published: December 2004

The rotational strength of the La transition in phenylalanine and tyrosine side chains has been calculated for dipeptides with various backbone and side‐chain conformations. Similar calculations have also been performed for tripeptides in the β‐turn conformation with aromatic residues at the corners of the turn. The interaction of the aromatic ring with neighboring peptides generates rotational strengths in the La transition of the order of 0.1 Debye‐Bohr magneton. When the preferred backbone and side‐chain conformations are considered, it is found that the most probable conformations have positive La bonds. This result accounts for the observation that the N‐acyl amino acid amides of L‐Tyr and LPhe have positive La bands. It also suggests that, although other interactions may affect the numerical value and even the sign, there will be a significant positive contribution to the rotational strength of aromatic residues in globular proteins from nearest‐neighbor interactions. Calculations on proteins of known conformation at the nearest‐neighbor level confirm the tendency toward positive La contributions for Phe and Tyr residues. This contribution can be of the order of 10% of the observed CD even in proteins with rather strong amide contributions. In some proteins, such as the gene 5 protein from bacteriophage fd and many snake‐venom toxins, side‐chain contributions from Tyr and Trp residues manifest themselves as positive CD bands in the 225–250‐nm region. The magnitude of the nearest‐neighbor contributions and the trend toward positive contributions are consistent with the observation of such CD bands in globular proteins. No special stacking interaction among aromatic side chains needs to be invoked.
Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT
Authors: Broyde S. , Wartell R. M. , Stellman S. D. , Hingerty B.
Published: December 2004

Minimum energy conformations have been calculated for the deoxydinucleoside phosphates dGpdC, dApdA, dCpdC, dGpdG, and dTpdT. In these potential energy calculations the eight diheldral angles and the sugar pucker were flexible parameters. A substantial survey of conformation space was made in which all staggred combination ofthe dihedral angles ω′,ω, and ψ, in conjuction with C(2′)‐endo puker, were used as starting conformers for the energy minimization. The most important conformations in the C(3′)‐endo‐puckering domain have ψ = g+; ω′,ω = g−,g−(A‐form),g+, g+, and g−,t. With C(2′)‐endo‐type puker the most important conformations have ψ = g+; ω′,ω =g_,g_(B‐form) and g+,t; and ψ =t; ω′,ω =g_,t(Watson‐Crick from) and t,g+ (skewed). Stacked bases are a persistent feature of the low‐energy conformations, the g+ conformer being an exception. Freeing the suger puker allowed this conformation to become low energy, with C(3′)‐exo puker. It also caused other low‐energy forms, such and the Waston‐Crick conformation, to become more favourable. Conformation flexibility in the sugar puker and in ψ, as well as the ω′,ω angle pair, is indicated for the dimeric subunits of DNA.
Dielectric relaxation of DNA solutions. II
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku
Published: December 2004

Real and imaganiry parts of complex dielectric constant of dilute solutions of DNA in 10−3M NaCl with molecular weight ranging from 0.4 × 106 to 4 × 106 were measured at frequencies from 0.2 Hz to 30 kHz. Dielectric increments Δε were obtained from Cole‐Cole plots and relaxation times τD from the loss maximum frequency. The τD of all samples agrees well with twice of the maximum viscoelastic relexation time in the Zimm theory, indicating that the low‐frequency dielectric relaxiation should be ascribed to be the rotation of DNA. The rms dipole moment, which was obtained from Δε, agree well with that calculated from the counterion fluctuation theory. The dielectric increment was found to be greatly depressed in MgCl2, which is resonably interpreted in terms of a strong binding of Mg++ ions with DNA.
Linear dichroism and radial flow birefringence of stream‐oriented hyaluronate solutions as a function of system pH
Authors: Barrett T. W.
Published: December 2004

The linear dischroism in the radial direction of solution flow over a velocity gradient of approximately 10–850 sec−1 has been obtained for human umbilical cord hyaluronic acid at concentrations of 0.1, 0.0666, and 0.0333%, and pHs 6.0, 6.5, 7.0, 7.5, 8.0, and 8.5, at constant ionic strength 0.1. The redial flow briefingenece has also been obtained for these solutions by a Kroing‐Kramers transformation. The data indicate a change in linear dichroism and optical anisotrophy as a function of pH, with most of the transition across the physiological range: 7.0–7.5. Previously reported axial flow birefringence and extinction angles indicating a similar pH‐dependent structural change in hyaluronate solutions across the same pH range are thus confirmed with other instrumentation. The radial birefringence measurements reported here, together with the axial measurements previously reported, permit a complete description of the refractive index tensor for each of the six solutions. The interpretation of these tensors in terms of the Peterlin modification of the Rouse‐Zimm Gaussian subchain theory results in a description of entropy production induced by changes in system pH.
Electric dichroism of poly(riboadenylic acid)
Authors: Charney Elliot , Milstien Julie B.
Published: December 2004

Electric dichroism measurements on poly(A) in low‐ionic‐strength solution demonstrate that below a molecular weight of 130,000 the double‐stranded polymer is hydrodynamically rigid and above that molecular weight becomes increasingly flexible. At 500,000 it is considerably more flexible than DNA of the same molecular weight, with a mean end‐to‐end distance of about 1150 Å compared to approximately 1600 Å for DNA. The fully extended length for both DNA and poly(A) of this molecular weight is about 2750 Å. It is further shown that the orientation of these polyelectrolytes in an electric field is consistent with theoretical treatments of the counter‐ion distribution and a preliminary model based on the additivity of classical valence charge anisotropy and counter‐ion polarization is postulated for the orientation mechanism. Single‐stranded pol (A) is shown not only to retain its base stacking in the presence of the electric field but to extend the persistent regions of stacked bases so that it attains a rodlike structure very similar to the one in the double‐stranded polymer is found to be less than that expected from consideration of the x‐ray structure. An explanation for this result is sought in the electric asymmetry of the helical polymer.
Measurement of the strongly held water of myoglobin by drying
Authors: Rao P. Bhaskara , Bryan William P.
Published: December 2004

The karl Fischer reagent method has been used to study the drying of whale skeletal muscle myoglobin. Drying curves for metmyglobin were obtained by mechanical pumping (moderate vacuum) and diffusion pumping (high vacum) at 20, 10, 0, −10, and −20°C. Strongly held water is present in about the same amounts as were previously observed with lysozyme. Nearly all of this strongly held water is still present during the drying of acid denatured metmyoglobin. This suggest that a core structure containing strongly held water is still present at pH 4.0. Comparison of the drying of metmyoglobin, deoxymyoglobin, and oxymyoglobin indicates that the iron‐coordinated water of methyoglobin is the second most strongly held water of the molocule.
Carbon‐13 NMR chemical shifts of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐ X‐L‐ Ala‐OH
Authors: Richarz René , Wüthrich Kurt
Published: December 2004

The 13C nmr chemical shifts of the common amino acid residues were measured in D2O solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH. For Asp, Glu, Lys, Tyr and His, the titration shifts arising from the ionization of te amino acid side chains were also obtained. These data are compared with the corresponding 13C chemical shifts in the protected tetrapeptides CF3CO‐Gly‐Gly‐X‐L‐Ala‐OCH3, the linear pentapeptides H‐Gly‐Gly‐X‐Gly‐Gly‐OH, and the free amino acids. On this basism the selection of suitable “random coil” 13C chemical shifts for conformational studies of polypeptides chain is discussed.
A general method for the evaluation of diffusion constants, dilute‐solution viscoelasticity, and the complex dielectric constant of a rigid macromolecule with an arbitrary configuration. II
Authors: Nokajima Haruhiko , Wada Yasaku
Published: December 2004

As a continuation of a previous paper [Biopolymers 16, (1977)], in which we described a general method for the evaluation of the diffusion constants of a rigid macromolecule with an arbitrary configuration, this paper presents a theory for evaluating the relaxational behavior of the molecule in solution. The diffusion equation of a molecule subjected to hydrodynamic or electric forces is solved and both a complex viscosity and a complex dielectric constant are obtained by assuming that the molecule is composed of Tokes spheres and, in the dielectric property, the molecule possesses a fixed charge distribution. The viscoelasticity of a rigid rod is calculated and compared with the analytical results.
Nonradiative energy transfer in oligopeptide chains generated by a monte‐cralo mehod including long‐range interactions
Authors: Leclerc Marc , Prémilat Samuel , Englert Anne
Published: December 2004

A Monte‐Carlo method including long‐range interactions is used to oligopeptide chains in random‐coil state. The chains are composed of 4, 9, or 14 repeating units and are labeled with the luminopheres tyrosine or tryptophan. Interactions with a solvent (water) are taken into account in the calculations through modifications of the semiempirical potential‐energy functions. The chains represent oligopeptides composed of hydrophobic or hydrophilic amino acid residues. Various properties relavent to the interpretaiton of nonradiative enrgy‐transfer experiments, such as the average value of the orientation factor for dipole‐dipole interaction of the luminophores, 〈k2〉, the distribution function of the distances between the luminophores f(rl), the efficiences of energy transfer in the static and dyamic averaging regimes, 〈T〉s amnd 〈T〉d, as well as the fluorescence decay I(t) of the donor luminophore in various averaging conditions, are computed. It is shown that, for all chains considered, 〈k2〉 is not vary far form 0.67 and that 〈T〉s and 〈T〉d have completely different values. Due to the small extent of correlation between the distances rl and the mutual orientations of the lumninophores, the decay kinetics 〈I(t)s corresponding to a static averaging regime can be expressed in terms of distribution functions f(rl). These results are in agrrement with those obtained previously for the unperturbed chain model.
A Monte Carlo study of the amylosic chain conformation
Authors: Jordan Robert C. , Brant David A , Cesàro Attilio
Published: December 2004

Monte Carlo studies of the unperturbed amylosic chain conformation have been carried out in the approximation of separable chain configuration energies. Sample chains of arbitrary chain length have been generated so as to be distributed consistent with refined estimates of the configuration energy and thus suitable for evaluation of averages of the desired configuration‐dependent properties. Perspective drawings of representative chains from the Monte Carlo sample have been made for comparison with standard idealizations of amylosic chain conformation. He molecular model employed generates a randomly coiling chain possessing perceptible regions of left‐handed pseudohelical backbone trajectory. Distribution functions for the end‐to‐end distance of short amylosic chains disclose some propensity for the chain to suffer self‐intersections at sort range in the chain sequence, which may vitiate the usual amylosic chain models based on the assumed independence of sets of glycosidic linkage torsion angles. The amylosic persistence vector and persistence length have been calculated as a function of chain length for the chain model employed.
1H‐15N Spin–spin couplings in alumichrome
Authors: Demarco Antonio , LlináS Miguell , Wuthrich Kurt
Published: December 2004

We report the determination of two‐ and three‐bond 1H‐15N spin–spin couplings in the nmr spectra of a polypeptide. The 1H‐ and 15N‐nmr spectra of 99.2% 15N‐enriched alumichrome have been studied at 360 MHz and 10.1 MHz, repectively. While some 2J and 3J coupling are of the order of 5 Hz, most splitting resulting from the heteronuclear interaction are ≲2 Hz, which introduces strigent requirements of spectral resolution. In the 1H spectra these requirements were met by digital deconvolution with a sine bell routine combined with positive exponential filtering. Although the 15N spectra clearly exhibit features of fine structure, mainly because of the intrinsic higher nmir sensitivity of protons, observation of 1H‐15N spin–spin couplings was found to be more practical in the 1H than in the 15N spectra. We find that the alumichrome data do not satisfy a simple cyclic relationship linking the heteronuclear couplings to the crystallographic ψ dihedral angles. It is suggested that a formal treatment of the ψ‐related interresidue 1H‐15N coupling might have to take into account a more complex dependence of the intervening 3J on the overall local electronic structure, which is dependent on ϕ,ψ, and ω simultaneoulsy. In contrast, our analysis indicates that χ1 can be readily determined from the measurement of the corresponding heteronuclear 3J coupling in the 1Hβ or in the amide 15N resonances. Karplus relationships are proposed that relate this heteronuclear 3J to the corresponding dihedral angle θ and which, on average, yield
Conformation of poly(L‐arginine). I. Effects of anions
Authors: Ichimura Sachiko , Mita Kazuei , Zama Mitsuo
Published: December 2004

The conformational transition of poly(L‐agrignine) by binding with various mono‐, di‐, and polyvalent anions, especially with SO, was studied by CD measurements. The intramolecular random coil‐to‐α‐helix conformational transition and the subsequent transition to the β‐turn‐like structure was caused by binding with SO. The binding data obtained from equilibrium dialysis experiments showed that the α‐helical conformation of poly(L‐arginine) is stabilized at a 1:3 stoichiometric ratio of bound SO to arginine residue; at higher free SO concentrations, the α‐helix converts to the β‐turn‐like structure accompanied by a decrease in amount of bound SO. The same conformaitonal transition of poly(L‐arginine) also occurred in the solutions of other divalent anions (SO, CO, and HPO) and polyvalent anions (P2O, P3O). Among the monovalent anions examined, CIO and dodecyl sulfate were effective in including α‐helical conformation, while the other monovalent anions (OH−, Cl−, F−, H2PO, HCO and CIO) failed to induce poly(L‐arginine) to assume the α‐helical conformation. Thus, we noticed that, except for dodecyl sufate, the terahedral structure is common to the α‐helix‐forming anions. A well‐defined model to the α‐helical poly(L‐arginine)/anion complex was proposed, in which both the binding stoichiometry of anions to the arginine residue and the tetrahedral structure of anions were taken into consideration. Based on these results, it was concluded that the tetrahedral‐type anions stabilize the α‐helical conformation of poly(L‐arginine) by crosslinking between two guanidinium groups of nearby side chains on the same α‐helix through the ringed structures stabilized by hydrogen bonds as well as by electrostatic interaction. Throughout the study it was noticed that the structural behavior of poly(L‐arginine) toward anions is distinct from that of poly(L‐lysine).
Mathematical method for determining the distribution of substituted DNA zone lengths with reference to equilibrium density profiles
Authors: Delcroix C. , Cantraine F. R. L. , Hardt N.
Published: December 2004

A method of calculation to determine the profile in density‐gradient sedimentation of bromodeoxyuridine‐substituted DNA lengths prior to sonication is developed. The method may be summarized as follows: (1) A description of a formulation of random cleavage of a substituted zone i in fragments of length m; (2) generalization and application of this formulation to all substituted zone lenghts simultaneously present in a given DNA extract, such generalization being performed by means of a matrix calculation; (3) adjustment of this formulation for the limits of the experimental method, i.e., number of gradient fractions which can be recovered, and for the evolution of the DNA fragment lengths which drop in the course of successive sonications; (4) simulation of the radioactive profiles. By this method it is possible to obtain certain indications concerning the types of initial (i.e., presonication) distributions that are compatible with observed profiles and to test the validity of assumptions relating to the initial distribution. This method has been applied in analyzing DNA synthesis in lymphocytes stimulated by Concanavalin and allowed us to determine the significance of the discontinuties appearing in the elongation with a suboptimal stimulating dose. The proposed method could also be applied to the analysis of all random populations of mixed sequences.
The molecular details of collagen hydration
Authors: Grigera J. Raul , Berendsen Herman J. C.
Published: December 2004

Nuclear magnetic resonance and dielectric data on hydrated collagen are interpreted in terms of Ramachandran's hydration model. It is found that all data are compatible with this model, indicating two specific binding sites per three amino acids in the threefold collagen helix. Sorption data have been interpreted according to the multilayer theory of Guggenheim and used to derive the fraction of bound water in the primary sites. From magnetic resonance anisotropies structural details of the position of the water molecules can be derived under the assumption that both sites are equally occupied. The residence time of a water molecule in one of these sites in moderately hydrated collagen (45 g H2O/100 g collagen) is 1.2 × 10−6 sec. The remainder of the water is weakly bound and consists of rapidly exchanging species with rotational correlation time shorter than 10−10 sec. The sites are 50% occupied at a water content of 10 g/100 g collagen and may contribute significantly to the stability of the collagen threefold helix.
1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH
Authors: Bundi Arno , Wüthrich Kurt
Published: December 2004

The 1H‐nmr chemical shifts and the spin–spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH in D2O and H2O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pKa values obtained in D2O, with the use of pH‐meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pKa values in H2O. This suggests that the present data are suitable “random‐coil” 1H‐nmr parameters for conformational studies of polypeptide chains in D2O and H2O solutions.
Spectroscopic origin of conformation‐sensitive contributions to polysaccharide optical activity: Vacuum‐ultraviolet circular dichroism of agarose
Authors: Liang J. N. , Stevens E. S. , Morris E. R. , Rees D. A.
Published: December 2004

The vacuum‐uv CD of agarose solid films has been measured to 145 nm and shows a positive band near 180 nm and a larger negative band at around 152 nm. The positive band remains accessible in aqueous solution and has been used to characterize changes in molecular conformation and interaction during the sol–gel transition. The temperature profile of vacuum‐uv CD shows sharp, discontinuous changes around the melting and setting points of the gel, which are interpreted in terms of cooperative intermolecular association through double helices, and pronounced hysteresis, which is discussed in terms of helix–helix aggregation.
Conformational energy calculations with averaged potential functions: Application to the repeat peptides of elastin
Authors: Ralston Evelyn , Somorjai R. L.
Published: December 2004

We present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues (n‐peptide) to the complexity of a computation for (Gly)n. This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone CαHα and CαH2α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space‐averaged effective center‐center and center‐atom potentials, respectively. This averaged‐interaction method is tested on the repeat tetra‐, penta‐, and hexapeptides of elastin, Val‐Pro‐Gly‐Gly (VPGG), Val‐Pro‐Gly‐Val‐Gly (VPGVP), and Ala‐Pro‐Gly‐Val‐Gly‐Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom‐atom calculations and extensive nmr data, coupled with the order‐of‐magnitude reduction in computer time, augurs well for the potential usefulness of the method.
Far‐infrared spectrum of crystalline lysozyme
Authors: Ataka Mitsuo , Tanaka Shoji
Published: December 2004

The far‐ir absorption spectrum of lysozyme was measured at room and liquid‐nitrogen temperatures. Dried layers of single crystals of tetragonal lysozyme chloride with a diameter of 100–300 μm were grown on a silicon plate. Such single‐crystalline samples were considered to have the following advantages in obtaining far‐ir spectra: (1) surface scattering is reduced, (2) the protein molecules are closely packed, and (3) air‐drying of the crystals reduces the number of water molecules without considerably changing the original configuration. The spectrum obtained consisted of a strong background absorption and a number of absorption peaks that were not clearly observed with the sample in the form of lyophilized powder. The peaks were ascribed to various delocalized vibrations of the main and side chains in the molecule. The peaks were also compared with the positions of Raman lines. The uniform background was assigned to the water molecules remaining in the crystals.
Steric effects of cis‐trans isomerism on neighboring residues in proline oligopeptides: A 13C‐nmr study of conformational heterogeneity in linear tripeptides
Authors: Deslauriers R. , Becker J. M. , Steinfeld A. S. , Naider F.
Published: December 2004

A series of proline‐containing linear oligopeptides (4 dipeptides and 15 tripeptides) were synthesized and examined in aqueous and nonaqueous solutions using 13C‐nmr spectroscopy. Spectra of linear tripeptides showing cis‐trans isomerism about the X‐Pro bond (X = Pro, Gly, and Ala) also show neighboring effects on the chemical shifts of residues both preceding and following the prolyl moiety. The extent of cis‐trans isomerism observed about the X‐Pro peptide bond correlates not only with the nature of X, but also depends on the size of the residue following proline; the larger substituents favor an increase in cis content about the X‐Pro bond.
An elastic model of the large‐scale structure of duplex DNA
Authors: Benham Craig J.
Published: December 2004

A general model for the large‐scale, time‐independent structure of duplex DNA is developed based on elastic considerations. The general conditions of elastic equilibrium are given. These equations are solved for the equilibrium shape of stressed duplex DNA, based on the assumption that the double helix behaves mechanically as a symmetric, linearly elastic rod. It is shown that, in general, two orders of superhelicity will arise at equilibrium. Several possible applications of this approach to the supercoiling of closed circular DNA are described.
Examen par la méthode des orbitales moléculaires des préférences conformationnelles intrinsèques du squelette des acides nucléiques
Authors: Broch Henri , Vasilescu Dane
Published: December 2004

This paper reports a systematic PCILO study of the conformation of the nucleic acid backbone. The authors principally studied the ω′ and ω phosphodiester torsion angles of the disugar triphosphate model as a simultaneous function of (1) the sugar nature, ribose or deoxyribose, (2) the different combinations of the sugar ring puckers C(2′)‐endo‐C(2′)‐endo, C(3′)‐endo‐C(3′)‐endo, C(3′)‐endo‐C(2′)‐endo, and C(2′)‐endo‐C(3′)‐endo, and (3) the different conformations around the ψ(C4′–C5′) exocyclic bond. The dependence of the (ω′,ω) conformational energy maps upon these different factors, is discussed. The results are in very good agreement with the observed structures of ribonucleic (RNA10, RNA11, A′‐RNA12, tRNAPhe) and deoxyribonucleic acids (D‐DNA, C‐DNA 9.3, B‐DNA 10, A‐DNA 11). Thus the validity of this model, the disugar triphosphate unit, is ensured.

The main conclusions that can be drawn from this systematic study are the following:

The torsion around P‐05′ (angle ω) is, as a general rule, more flexible than the torsion around P‐03′ (angle ω′).

There is no notable difference between the ribose–triphosphate units and the deoxyribose–triphosphate units for the C(3′)‐endo–C(3′)‐endo and C(3′)‐endo–C(2′)‐endo sugar puckers.

The deoxyribose–triphosphate units with C(2′)‐endo–C(2′)‐endo and C(2′)‐endo–C(3′)‐endo sugar puckers show much more ω′ flexibility than the ribose–triphosphate units with the same sugar puckers and cis position for the 2′hydroxyl group.

The preferred values of ω′ are independent of the sugar nature (ribose or deoxyribose) and of ψ values; they are correlated with the sugar pucker of the first sugar‐phosphate unit:

C(3′)‐endo‐C(3′)‐endo and C(3′)‐endo‐C(2′)‐endo puckers ⟹ ω′ ≃ 240° (g− region)

C(2′)‐endo‐C(2′)‐endo and C(2′)‐endo‐C(3′)‐endo puckers ⟹ ω′ 180° (t region)

The preferred values of ω are independent of the nature and the puckering of the sugars; they are correlated with the rotational state of the torsion angle ψ(C4′–C5′): ψ ≃ 60° (gg) ⟹ ω ≃ 300° (g−), ψ ≃ 180° (gt) or 300° (tg) ⟹ ω ≃ 60° (g+)
The conformation and aggregation of bovine β‐casein A. I. Molecular aspects of thermal aggregation
Authors: Andrews A. L. , Atkinson D. , Evans M. T. A. , Finer E. G. , Green J. P. , Phillips M. C. , Robertson R. N.
Published: December 2004

The conformation of β‐casein A in the monomeric and thermally aggregated states has been investigated by a range of techniques. β‐Casein exists as a monomer in solution at 4°C and at concentrations up to at least 3 g/dl. The molecule is flexible and exhibits a lot of segmental motion, but its secondary structure is not wholly random coil; about one‐third of the polypeptide chain is ordered and the likely locations of these regions are discussed. The radius of gyration, representing the time‐average distribution of the flexible chain, is 46 Å. Increasing temperature leads to aggregation of the β‐casein molecules. The degree of association is very sensitive to experimental conditions, and under our conditions a 14‐mer exists at 20°C. The aggregate is spherical with a radius of about 100 Å. The interior of the aggregate is relatively disordered, and the β‐casein molecules remain in a largely flexible, hydrated conformation. The volume restriction of the protein molecules which occurs on association leads to some immobilization of the hydrophobic C‐terminal region, which is packed toward the center of the aggregate.
Experimental studies of molecular interactions between nitrogen bases of nucleic acids
Authors: Yanson I. K. , Teplitsky A. B. , Sukhodub L. F.
Published: December 2004

New experimental results concerning molecular interactions between the nitrogen bases of nucleic acids in the crystalline phase and in vacuo are reported. The temperature dependence of the evaporation rate is measured for solid species. The sensitivity of conventional methods of sublimation heat measurements was improved essentially using a quartz resonator serving as a precise sensor of evaporation rate. Sublimation heats were found for both canonical bases and a number of their derivatives. The in vacuo formation of base associates interacting through hydrogen bonds was observed with a field mass spectrometer. The dimer formation enthalpies, which are indicative of a stronger attraction in complementary pairs compared with noncomplementary ones, were derived from the temperature dependence of ionic currents. Hydrogen‐bound complexes of more intricate associates (base trimers and aqueous molecules associates) were studied. The energy gain in the formation of trimers of identical molecules was shown to be larger (per base molecule) than that for dimers.
Diffusion–collision model for protein folding
Authors: Karplus Martin , Weaver David L.
Published: December 2004

The basic equations for the elementary step in the diffusion–collision–coalescence model of protein folding are derived for the case of two radially diffusing spherical microdomains. Refinements and biological implications of the mechanism are considered; included are detailed discussions of the parameters of the model, the possibilities of rotational diffusion and surface diffusion in one or two dimensions, the nature of the microdomains, and the application of the model to protein unfolding.
Inelastic light‐scattering study of polyadenilic acid
Authors: Mathiez P. , Weisbuch G. , Mouttet C.
Published: December 2004

We report a systematic study of inelastic light scattering for semidilute solutions of poly(adenilic acid). The results are analyzed in terms of a fast and a slow relaxation time. From their dependence on the wave vector and the polymer concentration, we are able to interpret the results in terms of a collective mode for the fast relaxation time at low wave vector, an individual chain motion for the fast time at large wave vector, and structural relaxation for the slow relaxation time.
Crystal and molecular structure of benzyloxycarbonyl‐α‐aminoisobutyryl‐L‐prolyl methylamide: The observation of an X2‐Pro3 Type III β‐Turn
Authors: Prasad B. V. Venkataram , Shamala N. , Nagaraj R. , Chandrasekaran R. , Balaram P.
Published: December 2004

The crystal and molecular structure of N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐L‐prolyl methylamide, the amino terminal dipeptide fragment of alamethicin, has been determined using direct methods. The compound crystallizes in the orthorhombic system with the space group P212121. Cell dimensions are a = 7.705 Å, b = 11.365 Å, and c = 21.904 Å. The structure has been refined using conventional procedures to a final R factor of 0.054. The molecular structure possesses a 4 → 1 intramolecular N‐H—O hydrogen bond formed between the CO group of the urethane moiety and the NH group of the methylamide function. The peptide backbone adopts the type III β‐turn conformation, with ϕ2 = −51.0°, ψ2 = −39.7°, ϕ3 = −65.0°, ψ3 = −25.4°. An unusual feature is the occurrence of the proline residue at position 3 of the β‐turn. The observed structure supports the view that Aib residues initiate the formation of type III β‐turn conformations. The pyrrolidine ring is puckered in Cγ‐exo fashion.
Thermometric titration studies of the interaction of block polypeptides with surfactants
Authors: Kale K. M. , Vitello L. , Kresheck G. C. , Vanderkooi G. , Albers R. J.
Published: December 2004

The interactions between surfactants and block polypeptides were investigated by titration calorimetry and CD. The polypeptides exhibited signs of an interaction only with surfactants bearing a charge opposite to the charge on the polymer. The stoichiometry of the resulting complex was determined to be approximately equal to the polymer net charge. In general, a decrease in helical content accompanied the interaction between the block polypeptides and the surfactants. Both positive and negative enthalpy changes were noted, depending on the heat of micelle formation. None of the thermal effects noted were preceded by polymer unfolding, as is characteristic of the interaction between surfactants and typical globular proteins.
Effect of some monohydric alcohols on the oxygen affinity of hemoglobin: Relevance of solvent dielectric constant and hydrophobicity
Authors: Cordone Lorenzo , Cupane Antonio , Biagio Pier L. San , Vitrano Eugenio
Published: December 2004

We studied the effect of methanol, ethanol, iso‐propanol, and n‐propanol on the reaction of hemoglobin with oxygen. The oxygen affinity was found to decrease with increasing alcohol concentration and alkyl group size; no detectable effect on Hill's constant was found. Difference spectroscopy indicated KR not to be affected by the presence of alcohols; the lowered affinity was then attributed to an altered equilibrium between T and R conformations of hemoglobin. The results have been analyzed in such a way as to allow separation of electrostatic contributions to free energy difference between the T and R states from nonelectrostatic ones. The nonelectrostatic term has been attributed to protein–solvent hydrophobic interactions. Values of hydrophobic free energy are in good agreement with analogous data estimated by correlating different results previously reported in the literature.
Dynamic mechanical properties of elastin
Authors: Gosline John M. , French Christopher J.
Published: December 2004

The dynamic mechanical properties of water‐swollen elastin under physiological conditions have been investigated. When elastin is tested as a colsed, fixed‐volume system, mechanical data could be temperature shifted to produce master curves. Master curves for elastin hydrated at 36°C (water content, 0.46 g water/g protein) and 55°C (water content, 0.41 g/g) were constructed, and in both cases elastin goes through a glass transition, with the glass transition temperatures of ‐46 and ‐21°C, respectively. Temperature shift data used to construct the master curves follow the WLF equation, and the glass transition appears to be characteristic of an amorphous, random‐polymer network. For elastin tested as an open, variable‐volume system free to change its swollen volume as temperature is changed, dynamic mechanical properties appear to be virtually independent of temperature. No glass transition is observed because elastin swelling increases with decreased temperature, and the increase in water content shifts elastin away from its glass transition. It is suggested that the hydrophobic character of elastin, which gives rise to the unusual swelling properties of elastin, evolved to provide a temperature‐independent elastomer for the cold‐blooded, lower vertebrates.
Viscosometric investigation of the ordinary–extraordinary phase transition in dilute polylysine solutions
Authors: Martin Nicholaus B. , Tripp John B. , Shibata John H. , Schurr J. Michael
Published: December 2004

Low shear viscosities have been determined for a 1 mg/ml poly(L‐lysine) solution as a function of added salt concentration in the region of the previously reported ordinary–extraordinary phase transition. The measured viscosities indicate that the polyions are far from completely extended at the transition. Estimates of the longest internal relaxation time for an equivalent free‐draining Rouse‐Zimm chain give τ ≃ 10−5 sec, similar to that of the rapid, angle‐independent component previously observed in the dynamic light‐scattering correlation function at the transition. An unusual peak and valley are observed in the curve of [η]0 versus [NaBr] in the transition region. Possible interpretations of these features, and their bearing on the nature of the extraordinary phase, are discussed.
Differentiation between the α‐helical and coillike conformations of poly(L‐glutamic acid) in aqueous solution through binding of pinacyanol
Authors: Pal M. K. , Mandel M.
Published: December 2004

Pinacyanol in the presence of an excess of poly(L‐glutamic acid) [polymer/dye ratio (P/D) > 10] exhibits different absorption spectra in the visible region when bound to the slightly charged polypeptide in the α‐helical conformation or to the nearly completely dissociated polypeptide in the coillike conformation. These spectra reveal aggregation of the dye bound to the macromolecular chain in both conformations, although in the coillike one different kinds of aggregates may be present. Dye binding is accompanied by the appearance of CD bands in the visible region which are also different for the α‐helical and the coillike conformations. The aggregates formed in the presence of the latter change slowly in time and seem to induce some conformational changes in the polypeptide chain. Furthermore, they have been found to be, at least partially, stable with respect to a subsequent reversal to the α‐helical conformation. All results could be qualitatively interpreted assuming that in the coillike conformation, ordered regions exist along the chain as proposed by Krimm and Tiffany.
Study of thermal and acid denaturation of DNA by means of voltammetry at graphite electrodes
Authors: Brabec Viktor
Published: December 2004

Conformational changes in guanine–cytosine (G·C) and adenine–thymine (A·T) pairs in DNA were investigated by means of differential pulse voltammetry at a pyrolytic graphite electrode (PGE). As a monitor of these conformational changes, two separated voltammetric peaks, G and A, which correspond to electrochemical oxidation at the PGE of guanine and adenine residues, respectively, were used. It was found that peak A was first increased in the course of thermal denaturation of DNA. This indicates that, on heating a native DNA sample, regions rich in A·T pairs melt first. In the course of acid denaturation of a native DNA sample, the height of peak A was changed just before the denaturation. It is suggested that protonation of adenine residues in DNA regions rich in A·T pairs was responsible for these changes.
Molecular and crystal structure of an intercalation complex: Proflavine–cytidylyl‐(3′,5′)‐guanosine
Authors: Berman Helen M. , Stallings W. , Carrell H. L. , Glusker J. P. , Neidle S. , Taylor G. , Achari A.
Published: December 2004

The high‐resolution crystal and molecular structure of a 3:2 complex of proflavine and cytidylyl‐(3′,5′)‐guanosine is described. The complex exhibits more than one mode of dye binding to the dinucleoside phosphate. One proflavine cation is symmetrically intercalated between the base pairs. The other proflavine cations and ones related by symmetry stack above and below the base pairs and also hydrogen bond externally to the duplex. The conformation of the CpG is most similar to A‐RNA with all C(3′)‐endo sugar puckering. To allow the base pairs to stretch from the normal 3.4‐Å separation to a 6.8‐Å separation, the torsion angles ϕ and χ of the guanosine are increased by about 60° from the values found in RNA. The crystal structure itself contains disordered sulfate anions and is highly solvated, with all but one water molecule involved in a continuous water–sulfate channel.
Type I Collagen Fibrillogenesis: Initiation via Reversible Linear and Lateral Growth Steps
Authors: Silver F. H. , Langley K. H. , Trelstad R. L.
Published: December 2004

Type I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes‐Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.
Conformational difference in cation complexes of tetranactin in solution
Authors: Ueno Masaharu , Kyogoku Yoshimasa
Published: December 2004

The conformational changes and binding behavior of tetranactin on complexation with sodium, potassium, rubidium, cesium, and ammonium ions were investigated by the measurements of proton magnetic resonance, ir, and Raman spectra. It has been clearly shown that alkali cations coordinate to the oxygen atoms of both the carbonyl group and the tetra‐hydrofuran ring, but the ammonium ion coordinates only to the oxygen atom of the tetrahydrofuran. Among the alkali cations the potassium ion most strongly coordinates to the tetrahydrofuran oxygen atoms. The complexation with larger cations induces an expansion of the cavity of the macrocyclic ring of tetranactin and smaller cations contract the cavity. The evidence is revealed by the coupling constants of the methylene protons and the frequency separation between the carbonyl stretching vibrations of the ir‐ and Raman‐active modes. The conformations of the cation complexes in the solid are maintained in solution but that of the cation free form is not.
Characterization of meningococcal polysaccharides by light‐scattering spectroscopy. IV. Molecular weight distribution of group B meningococcal polysaccharide in buffer solution
Authors: Gulari Esin , Chu B. , Liu T. Y.
Published: December 2004

We report the first characterization of group B meningococcal polysaccharide at 28°C in 0.4M KCl and 0.05M sodium acetate at pH 5.61 and in pure water by means of light‐scattering spectroscopy. In buffer solution, the weight‐average molecular weight Mr = 1.46 × 105 g/mol, the Z‐average radius of gyration 〈rg2〉z1/2 = 26.3 nm, the second virial coefficient A2 = (2.12 ± 0.17) × 10−4 cm3 mol/g2, and the second virial coefficient of the diffusion expansion kD ≈ 79 g/g. By using a histogram approximation on the correlation function profile analysis, we observed size fractions of two sizes with rhL/rhS = 298 Å/50 Å and AL/AS = 82/18, where rh and A are the respective effective hydrodynamic radius and the integrated intensity and the subscripts L and S denote the large and small size fractions. In pure water, rhL/rhS = 402 Å/29 Å with AL/AS = 84/16. The linewidth results are consistent with the measurements on the angular distribution of scattered intensity. Furthermore, if we take the large fraction to behave more like solid spheres, we are able to determine a molecular weight distribution of B‐polysaccharide in buffer solution in a bimodal size distribution function.
Density gradient proportionality constants, density distributions, and pressure effects for three salt solutions
Authors: Sharp Dan S. , Ifft James B.
Published: December 2004

Earlier determinations of density gradient proportionality constants β0, density distributions ρ(r), and the effect of pressure on density gradients in the analytical ultracentrifuge have been of limited precision and usefulness in the study of proteins and polypeptides. Reasons for these difficulties are that numerous intermediate relationships were required in the calculations, and the density ranges studied were generally above 1.2 g/ml. Relations are derived in the present paper to directly compute β0(ρ) values and β0′(ρ) values from the original data without any intermediate expansions or approximations. Data are presented for CsCl, CsBr, and Cs2SO4 and compared with literature values. Density distributions are computed for all three salts under a wide variety of experimental conditions of density, column length, and angular velocity. These values of ρ(r) and re are obtained by a numerical iterative technique. Values obtained by this new method are compared with values obtained using closed‐form expressions. The effects of pressure on the composition density gradient for the three salts given above are calculated and found to be significant for Cs2SO4 solutions.
Vibrational analysis of peptides, polypeptides, and proteins. VI. Assignment of β‐turn modes in insulin and other proteins
Authors: Bandekar Jagdeesh , Krimm S.
Published: December 2004

The normal modes have been calculated for structures having the dihedral angles of the four β‐turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α‐helix band at 1658 cm−1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303‐cm−1 band in insulin and similar bands in other globular proteins.