bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of thin film dialysis to the determination of equilibrium constants
Authors: Russo Salvatore F. , Engel Randall G.
Published: December 2004

A theoretical basis for thin‐film dialysis involving binding between a ligand and nondialyzing species is presented. A general differential equation that applies to the case of equivalent, noninteracting sites is derived relating [A]F, [A]T, [P]T, and K. Numerical solutions to this equation are used to develop a series of escape curves corresponding to specific values of the parameters [P]T, [A]i, K, and k0. A general method for determining an equilibrium binding constant from thin‐film dialysis data is given. A comparison of thin‐film dialysis results predicted by this theory with literature data shows essential agreement.
Conformation of amino acid residue contiguous to helical polypeptide
Authors: Nakata Yoshiro , Akaike Toshihiro , Inoue Shohei
Published: December 2004

The calculation of the conformational energy of the terminal D‐ or L‐alanine residue contiguous to an α‐helical polypeptide, polyalanine, was made. Both L‐and D‐residues contiguous to the carboxyl terminal of α‐helical poly(L‐alanine) are considered to prefer the α‐helical conformation due to the effect of the α‐helical structure of the polymer. The residue at the amino terminal is found to be less affected by the α‐helical structure of the polymer.
Donnan effect as measured by sedimentation equilibrium for the protein cytochrome c
Authors: Syvanen Michael , Schachman H. K.
Published: December 2004

The protein turkey‐heart cytochrome c is used as a model protein to study charge effects in sedimentation equilibrium experiments in three‐component solutions. Data are given for the dependence of the apparent M (1–υρ) on ρ in solutions of KCl, RbCl, CsCl, and triethylamine hydrochloride. The results show the Donnan effect to have a significant influence on the apparent molecular weight, found by extrapolation of the data to a solution density of one. The apparent molecular weights are for protein at infinite dilution. A theoretical treatment is presented where the magnitude of this effect can be predicted accurately from the formal net charge of the protein as computed from the amino acid composition. The results are shown to be important in computing the preferential hydration of the protein in concentrated salt solutions. For such systems the Donnan effect should be subtracted from the total interaction coefficient for multicomponent system in order to obtain the preferential hydration.
Metal complexs of poly (α‐amino acids): Cu(II) chelates of acetoacetylated poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid)
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Benvegnu' C. , Peggion E.
Published: December 2004

The cupric complexes of poly(Nε‐acetoacetyl‐L‐lysine), [Lys(Acac)]n′ poly(Nδ‐acetoacetyl‐L‐ornithine), [Orn(Acac)]n′ and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid), [A2bu‐(Acac)]n, as well as of the model compound n‐hexyl acetoacetamide, have been investigated by means of absorption, potentiometric, equilibrium dialysis, and CD measurements. While in the complex of the model compound, one chelating group is bound to one cupric ion, in the polymeric complexes two β‐ketoamide groups are bound to Cu(II) under the same experimental conditions. The binding constant of cupric ions to the three polymers and the formation constant of the Cu(II)‐nhexylacetoacetamide complex have been evluated. Investigation on the chiroptical properties of the three polymeric complexes shows that the peptide backbone does not undergo conformational transitions, remaining α‐helical when up to 20% of the side chains are bound to Cu(II). The optical activity of the β‐ketoamide chromophores is substantially affected by complex formation and is discussed in terms of asymmetric induction from the chiral backbone.
1H and 13C nmr studies of cyclic and linear dipeptides containing threonyl, seryl, aspartyl, and histidyl residues
Authors: Ptak Marius , Heitz Annie , Dreux Michel
Published: December 2004

The side‐chain conformations of D‐ orL‐ Thr, D‐ or L‐Ser, L‐Asp, and L‐ His residues in cyclic and linear dipeptides in D2O or in DMSO‐d6 are deduced from vicinal (1H,1H) and (13C, 1H) coupling constants. Vicinal (13C, 13C) coupling constants strongly depend on substituents and cannot be used without a more sound analysis. In cyclic dipeptides, the Thr and Ser side chains are folded above the DKP ring, with χ1 near 60°. The L‐Asp side chain interacts more specifically with peptide bonds (χ1 near 300°). The L‐ His side chain is more flexible and its conformation depends on the proximity of a second side chain and on solute‐solvent interactions. In all cases, this side chain is not completely folded. In linear dipeptides, the conformation of a C‐terminal L‐His residue is mainly influenced by the end carboxylic group. On the other hand, a N‐terminal L‐His residue interacts more easily with a neighboring L‐Asp residue. In aqueous solution, the imidazole pKa depends on the proximity of terminal and lateral charged groups but does not reveal any specific interaction in cyclic dipeptides. A comparison between the conformations of cyclic peptides observed in solution, in the crystalline state and calculated by empirical methods, allows one to point out the discriminating role of the packing in crystals, and of solute‐solvent interactions in solution.
The solution conformation of malformin A
Authors: Tonelli Alan E.
Published: December 2004

Solution conformations of the cyclic pentapeptide plant‐hormone malformin A, whose conformational freedom is constrained by an intramolecular disulfide bridge, are derived and presented here. The nmr and CD data of Ptak are used to place restrictions on the search for possible malformin A solution conformers of low energy. Only two distinct conformers were found to be consistent with Ptak's data. Both structures are characterized by an internally buried (solvent‐shielded) D‐Cys2 amide proton, a seven‐membered (1–3)hydrogen bond between (N–H) and (OC), and a disulfide bridge conformation with a P chirality as manifested in the nmr study by the temperature independence of the amide proton chemical shifts for the D‐Cys2 and D‐Leu4 residues and the negative sign of the long wavelength maximum in the CD spectrum, respectively. Inspection of space‐filling molecular models of both structures indicates severe steric barriers to their rapid interconversion. Thus, it appears that only one of the two conformers may be present in solution. The difference in their calculated dipole moments (4.6 and 6.9D) suggests an experimental method for distinguishing between the two proposed solution structures.
Configurational effects on conformational properties of cyclic nucleotides. I. Theoretical calculations of conformer preferences in α‐nucleoside 3′,5′ cyclic monophosphates
Authors: Tewari Ravindra , Danyluk Steven S.
Published: December 2004

A comparative study has been made of the configurational effects on the conformational properties of α‐ and β‐anomers of purine and pyrimidine nucleoside 3′,5′,‐cyclic monophosphates and their 2′‐arabino epimers. Correlation between orientation of the base and the 2′‐hydroxyl group have been studied theoretically using the PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The effect of change in ribose puckering on the base‐hydroxyl interaction has also been studied. The result show that steric repulsions and stabilizing effects of intramolecular hydrogen bonding between the base and the 2′‐hydroxyl (OH) group are of major importance in determining configurations of α‐anomers and 2′‐arabino‐β‐epimers. For example, hydrogen bonding between the 2′‐hydroxyl group and polar centers on the base ring is clearly implicated as a determinant of syn‐anti preferences of the purine (adenine) or pyrimidine (uracil) bases in α‐nucleoside 3′,5′‐cyclic monophosphates. Moreover, barrier heights for interconversion between conformers are sensitive to ribose pucker and 2′‐OH orientations. The result clearly show that a change in ribose‐ring pucker plays an essential role in relieving repulsive interaction between the base and the 2′‐hydroxyl group. Thus a C2′‐exo‐C3′‐endo (2T3) pucker is favored for α‐anomers in contrast with the C4′‐exo‐C3′‐endo (4T3) from found in β‐compounds.
Formation of the collagen‐like triple‐helical structure in oligopeptides during elongation of the molecular chain
Authors: Lazarev Yu. A. , Lobachov V. M. , Grishkovski B. A. , Shibnev V. A. , Grechishko V. S. , Finogenova M. P. , Esipova N. G. , Rogulenkova V. N.
Published: December 2004

Oligotripeptides Z‐(Gly‐Pro‐Pro)n‐OMe (n = 1,2,…,8), Z‐Gly‐Pro_Pro‐Gly‐Pro‐Gly‐OMe, Z‐Gly‐Pro‐Pro‐Gly‐Pro‐Gly‐Gly‐Pro‐Pro‐OMe, Z‐Gly‐Pro‐Pro‐(Gly‐Pro‐Gly)2‐Gly‐Pro‐Pro‐OMe, and Z‐(Gly‐Pro‐Ala)n‐OMe (n = 1,2,…,4) were synthesized step‐by‐step and then studied by means of x‐ray diffraction, ir spectroscopy, the kinetics of hydrogen‐deuterium exchange of peptide groups, and circular dichroism,. Different stages in the formation of a triple helix in Z‐(Gly‐Pro‐Pro)n‐OMe were revealed during the chain elongation. In the solid state, at the first stage a conformation of the polyproline II‐type is formed in the tripeptide and in the second stage a triple helical complex appears in the hexapeptide. Interpeptide hydrogen bonds in this complex are still of low order. At further stages an ordered set of interpeptide hydrogen bonds is gradually formed. It is shown that the degree of order of interpeptide H bonds depends on the length of the molecular chain, the amino acid composition, and residue sequence in the triplets.
Thermodynamics of transfer ribonucleic acids: The effect of sodium on the thermal unfolding of yeast tRNAPhe
Authors: Freire Ernesto , Biltonen Rodney L.
Published: December 2004

The thermal unfolding of yeast phenylalanine‐specific tRNA (tRNAPhe) has been calorimetrically investigated at several salt concentrations in the absence of magnesium. Application of the deconvolution theory of macromolecular conformational transitions allows calculation of the thermodynamic parameters of unfolding. It is demonstrated that the unfolding of tRNAPhe occurs in a sequential fashion and that four separate transitions or five macromolecular thermodynamic states exist in the temperature range 8–72°C under the experimental conditions of these studies (0.067–0.52M Na+). The enthalpy and entropy changes between states and the relative population of each state as a function of temperature and salt concentration have been obtained. Sodium stabilizes the low‐temperature conformations of tRNAPhe. The increase in the melting temperatures of each transition is shown to be linearly dependent on the logarithm of sodium concentration. These results allow calculation of the “phase” diagram for the transitions as a function of salt concentration.
Laser‐excited raman spectroscopy of biomolecules. XII. Thermally induced conformational changes in poly(L‐glutamic acid)
Authors: Fasman Gerald D. , Itoh Koichi , Liu Christopher S. , Lord Richard C.
Published: December 2004

The α‐helical from of poly(L‐glutamic acid) [α‐poly(Glu)] gives rise to the same amide I and III lines as α‐poly(γ‐benzyl‐L‐glutamate) at 1652 and 1296 cm−1, respectively. The latter is a superposition of the amide III line near 1290 cm−1 and a line deu to vibrational made of CH2 groups of the side chain near 1300 cm−1. A line at 924 cm−1 is tentatively identified as characteristics of α‐poly(Glu). Both the β1‐ and β2‐ forms of poly(Glu) give rise to characteristic of β‐amide. III frequencies that are similar because of their similar backbone structures. Differences in the conformations of their side chains and in the environments of the backbone are reflected in the region 800–1200 cm−1 and in the amide I. A line at 1042 cm−1 and a pair at 1021 and 1059 cm−1 are tentatively assigned as characteristic of β1‐poly(Glu) and β2‐poly(Glu), respectively. The α‐β2 transition in poly(L‐Glu78L‐Val22) is shown by the appearance of all the β2‐characteristic lines in the thermally transformed sample. The same features observed in poly(L‐Glu95L‐Val5) also indicate that the α‐β2 transition of poly(Glu) is facilitated by the presence of L‐valine and that the content of L‐valine is not critical for this purpose. Investigation of the Raman spectra of the calcium, strontium, barium and sodium slats of poly(Glu) shows that these salts, under the conditions of preparation used, all the have random‐coil conformations.
Thermodynamics of the slow–fast transition in bacteriophage T2L
Authors: Welch J. B. , Bloomfield V. A.
Published: December 2004

We have measured the thermodynamic parameters of the slow‐fast tail‐fiber reorientation transition on T2L bateriophage. Proportions of the virus in each form were determined from peak‐height measurements in sedimention‐velocity runs and from average diffusion coefficients obtained by quasielastic laser light scattering. Computer simulation of sedimentation confirmed that there were no undetected intermediates in the transition, which was analyzed as a two‐state process. Van't Hoff‐type plots of the apparent equilibrium constant and of the pH midpoint of the transition as function of reciprocal temperature led to the following estimates of the thermodynamic parameters for the transition at pH 6.0 and 20°C: ΔH° = −139 ± 18Kcal mol−1, ΔS° = −247 ± 46 cal K−1 mol−1, and ΔG° = −66 ± 22 kcal mol−1. Per mole of protons taken up in the transition, the analogous quantities were −15.9 ± 1.7 kcal mol−1, −26.3 ± 2.2 cal K−1 mol−1, and −8.22 ± 1.8 kcal mol−1. The net number of protons taken up was about 8.5 ± 1.5. The large values of the thermodynamic functions are consistent with a highly cooperative reaction and with multiple interactions between the fibres and the remainder of the phage. The negative entropy of the transition is probably due to immobilization of the fibres.
Polypeptide models of collagen. II. Solution properties of (Pro‐Gly‐Phe)n
Authors: Brahmachari Samir K. , Ananthanarayanan V. S. , Rapaka Rao S. , Bhatnagar Rajendra S.
Published: December 2004

The conformation of (Pro‐Gly‐Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro‐Gly‐Phe)n can exist in a partially triple‐helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly‐R2‐R3, in collagen.
Hydrodynamic properties of aqueous solutions of galactomannans
Authors: Sharman W. R. , Richards E. L. , Malcolm G. N.
Published: December 2004

Galactomannans were extracted from the seeds of seven different legumes to obtain samples which differed in average molecular weight, in polydispersity, and in average mannose‐to‐galactose ratio in the molecule. Measurements were made of the viscosities as a function of shear rate and of the sedimentation and diffusion coefficients of the aqueous solutions of all the galactomannans. Average molecular weights were calculated from the sedimentation and diffusion coefficients using the Svedberg equation. The Mark‐Houwink relationship between the intrinsic viscosity and the average molecular weights was found to hold for the series of galactomannans despite differences in the mannose‐to‐galactose ratios of the solutes. Estimates were made of the galactomannan polydispersities from both the sedimentation‐coeffient distributions and also from the diffusion‐coefficient ratios, Dm/DA. The two methods gave results in qualitative agreement. The hydrodynamic properties of the more homogeneous galactomannans were compared with the predictions of the Flory‐Fox hydro‐dynamic theory, with results very similar to those which were obtained for the water‐soluble synthetic cellulose derivatives, hydroxyethylcellulose and ethydroxycellulose.
An investigation of pectin and pectic acid in dilute aqueous solution
Authors: Jordan Robert C. , Brant David A.
Published: December 2004

Light‐scattering measurements have been carried out on carefully clarified aqueous solutions of pectin and pectic acid. The strong dependence of the inverse excess scattering intensity on angle yields pectin chain dimensions that are inconsistent with the complete molecular dispersion of pectin molecules possessing the degrees of polymerization indicated by the measured osmotic molecular weights. Negligible or negative concertration dependences of the inverse scattering intensities coupled with the centrifugation, filtration, and gel permeation chromatography behavior of the samples likewise suggest nonequilibrium aggregation of the pectin molecules in solution. It is shown that the measured mean polymer chain dimensions can be rationalized in terms of the presence of a very small proportion of aggregated material.
Crystallization of chondroitin sulfate from an aqueous solution
Authors: Tanaka Ki‐Ichiro , Katsura Nobuhiko
Published: December 2004

A new polymorph of sodium chondroitin‐4‐sulfate has been crystallized from an ethanolic aqueous solution at low pH. The crystallized spherulite specimens give considerably sharper x‐ray diffraction lines. The unit cell of the new polymorph is rectangular with dimensions (Å) a = 16.0, b = 24.1, and c = 26.0. The chondroitin‐4‐sulfate could be purified by recrystallization.
Effect of hydrophobic side chains on the pressure‐induced changes in the NMR spectra of water‐soluble biopolymers
Authors: Williams R. K. , Fyfe C. A. , Bruck D. , Van Veen L.
Published: December 2004

Measurements have been made of the high‐resolution nmr spectra of the polyamino acids poly[N5‐(2‐hydroxyethyl)‐L‐glutamine] and poly[N5‐(4‐hydroxybutyl)‐L‐glutamine] in mixed deuterium oxide and water solvent at varying pressures from 1.03 to 3163.7 kg/cm2. The results are compared with previously reported results for the polymer poly[N5‐(3‐hydroxypropyl)‐L‐glutamine] under similar conditions. The significance of the behaviour of the polymers is considered in terms of the effect of the presence of hydrophobic residues in their side chains.
Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B‐DNA structure and a counterclockwise helix
Authors: Miller Kenneth J.
Published: December 2004

An algorithm is developed that enables the routine determination of backbone conformations of nucleic acids. All atomic positions including hydrogen are specified in accord with experimental bond lengths and angles but with theoretically determined conformational angles. For two Watson‐Crick base pairs at a separation of 3.38 Å, and perpendicular to a common helical axis, minimum energy configurations are found for all 10 combinations at helical angles of α ∼ 36°–38°, corresponding to the B‐DNA structure with C(2′)‐endo sugar puckers. Backbone configurations exist only within the range 35.5° ⩽ α ⩽ 42°, which suggests the origin of the 10‐fold helix. Calculated stacking energies for the B‐DNA structure increases for each of the clustered groups of base pairs: G·C with G·C, G·C with A·T, and A·T with A·T, and they are in approximate agreement with experimental observations. The counter‐clockwise helix is examined, and physically meaningful structures are found only when the helical axes of successive base pairs are disjointed.
Dynamics of the cluster model of protein folding
Authors: Kanehisa Minoru I. , Tsong Tian Yow
Published: December 2004

The cluster model of protein folding [Kanehisa, M. I. & Tsong, T. Y. (1978) J. Mol. Biol. 124, 177–194] is further investigated for the thermodynamic and kinetic properties of protein folding–unfolding transitions. A cluster is a locally formed ordered region in the polypeptide chain due to cooperative interactions among residues. In the cluster model a cooperative term is assigned as proportional to the surface area of a globular cluster. This assignment is compared with that for the helix–coil transition of homopolypeptides, where the cooperative term is proportional to the two ends of a linear helical sequence. The dynamics of the cluster model exhibit a slow phase, which is well‐separated from other faster phases, because of the cooperative interaction of the macrosystem. This slow phase not only appears within the transition region, but can also persist well below the transition region if the cooperativity depends on the external condition. The amplitudes of certain kinetic phases can vary depending on the choice of physical parameters monitoring the reaction. Thus the same reaction may display different time courses. The qualitative aspects of the folding dynamics are as follows. In one case the rate‐limiting formation of a critical‐size cluster is followed by its rapid growth, while in the other the rate‐limiting step appears in a later stage, where preformed smaller clusters merge into larger ones. The former case is similar to the dynamics of the helix–coil transition, and the latter represents a stepwise mechanism of protein structure formation.
Melanostatin conformations in solution
Authors: Schwartz Robert W. , Mattice Wayne L. , Spirtes Morris A.
Published: December 2004

The conformations of melanostatin have been studied experimentally using CD spectroscopy and via calculations. In aqueous solution and 2,2,2‐trifluoroethanol (TFE) there is no evidence that monomers of the tripeptide exist in an ordered (β‐bend) structure. In water and TFE solutions (3–6 × 10−4M) the neutral molecules aggregate very slowly, taking about 3 days to attain equilibrium at room temperature. At equivalent concentrations in TFE, although not in water, the cationic molecules also slowly aggregate, although to a lesser extent. Calculations using rotational isomeric state theory give the most probable unperturbed end‐to‐end distance of the molecule at 9.3 ± 0.1 Å and indicate that a vast majority of the molecules exist in some extended conformation, end‐to‐end distance ≥6 Å. Only 0.4% of the molecules are calculated to have O…︁H separations compatible with a β‐bend structure. An intramolecular hydrogen bond must have an energy at least 2 kcal/mol lower than that of an intermolecular hydrogen bond to solvent if a β‐bend is to be experimentally observable.
Condensation of Co++ ions on chondroitin sulfate from transport coefficients and proton NMR measurements in aqueous solutions
Authors: Tivant P. , Turq P. , Chemla M. , Magdelenat H. , Spegt P. , Weill G.
Published: December 2004

The “condensed” counterions which characterize high‐charge‐density polyelectrolyte solutions can be analyzed into two subpopulations: (1) site‐bound counterions and (2) atmospherically entrapped counterions. The distinction is achieved experimentally by combining the data from self‐diffusion coefficient or electrical mobility measurements, which give the amount of “condensed” ions, and those from nmr, chemical shift measurements, which indicate the amount of site‐bound ions. In the case of a solution of chondroitin sulfate with excess Co++ counterions, it can be estimated that 20% of the structural charge of the polyion is neutralized by site‐bound, dehydrated, condensed counterions, while a further 30% is neutralized by atmospherically entrapped, hydrated counterions.
Interaction of molecules with nucleic acids. II. Two pairs of families of intercalation sites, unwinding angles, and the neighbor‐exclusion principle
Authors: Miller Kenneth J. , Pycior Joseph F.
Published: December 2004

Intercalation‐site geometries are generated for a tetramer duplex extracted from B‐DNA. Glycosidic angles and puckers of the deoxyribose sugar groups bonded to base pairs BP1 and BP4, namely, those at either end of the tetramer duplex, are assumed to be those of B‐DNA to insure continuity. All possible geometrical conformations for combinations of C(2′)‐endo, C(3′)‐endo, C(2′)‐exo, and C(3′)‐exo sugar puckers are determined for the tetranucleotide backbone. Those with minimum energy are selected as candidates for intercalation sites. Calculations reveal two pairs of physically meaningful families of intercalation sites which occur in two distinct regions, I and II, of helical angles which orient BP2 relative to BP3 and with the helical axis disjointed between these base pairs. For each site I and II within BP2 and BP3, there are two distinct backbone conformations, A and B, connecting BP3 to BP4 or BP1 to BP2 which do not disrupt backbone conformations connecting BP2 to BP3. Hence two pairs, IA and IB, and IIA and IIB, of intercalation sites exist in which the sugar puckers along the backbone of the tetramer alternate from C(2′)‐endo to C(3′)‐endo on the backbone (5′p3′) connecting BP2 to BP3. The glycosidic angles of the C(3′)‐endo sugar χ3γ are, coincidentally, 80° ± 2° for both conformations γ = A and B connecting BP3 to BP4 along the phosphate backbone (5′p3′). Consistent with the theoretical results, the experimental unwinding angles can be grouped into two categories with absolute values of 18° and 26°. The theoretical unwinding angles for sites IA and IB of 16° and for sites IIA and IIB of 20° occur for a displacement of ‐0.8 Å in the helical axes of BP2 and BP3 and for a 100% G·C composition, with a decrease depending on the amount of A·T base pairs present. Ratios of theoretical unwinding angles of sites I and II, which range from 0.75 to 0.84 for the two principal sites, compare well with the experimental value of 0.71. The theoretical results, in agreement with experimental observation, provide a new interpretation of the nature and conformation of the possible binding sites. Conformations obtained from these studies of intercalation sites in a tetramer duplex are used to rationalize the well‐known neighbor‐exclusion principle. The possibility of violation of this principle is demonstrated by the existence of two families of physically meaningful conformations. Conformations of unconstrained dimer duplexes are also obtained, one of which corresponds to the experimental crystal structure of ethidium–dinucleoside complexes, but these cannot be joined to the B‐DNA structure. Backbone conformations of the tetramer duplex can be constructed until the base‐pair separation reaches 8.25 Å, which may limit the molecules that can intercalate.
Absorption and circular dichroism spectra of methylene blue bound to alginate
Authors: Seely G. R. , Hart R. L.
Published: December 2004

The addition of methylene blue to certain samples of Na alginate produces a complex succession of spectrally distinguishable aggregated (metachromatic) dye species. Three of these species are active in CD; they are interpreted as aggregates of dye, but probably dimers, bound in orientations characteristic of the constituent copolymer blocks of alginate to which they are tentatively assigned. The aggregates compete with divalent metal ions and hydrogen ion for the binding sites of the polymer. Other samples of alginate give a modified succession of aggregated spectral species, which are almost devoid of CD activity. Mild treatment with acid, insufficient for hydrolysis, converts forms of alginate with CD activity into modified forms without it, the absorption spectra of which resemble those of samples originally devoid of activity. It is implied, subject to confirmation, that the chiral properties of the binding sites of the native polysaccharide are diminished or lost by acid treatment during commercial preparation.
Effect of sodium ion on the high‐resolution melting of lambda DNA
Authors: Blake R. D. , Haydock Paul V.
Published: December 2004

A series of high‐resolution melting curves were obtained by the continuous direct‐derivative method [Blake, R. D. & Lefoley, S. G. (1978) Biochim. Biophys. Acta 518, 233–246] on lambda DNA (cI857S7 strain) under varying conditions of [Na+]. Examination of the denaturation patterns at close intervals of [Na+] indicates that frequent changes in mechanism occur below 0.04M Na+, while almost none occurs above 0.1M Na+. Changes at low [Na+] generally occur in an abrupt fashion, in most cases within a 3 mM change in [Na+], and in at least one case within 0.6 mM, indicating the balance between alternative mechanisms is frequently quite delicate. These changes involve segments of between 900 and 1500 or more base pairs in length and are therefore not insignificant. Changes at low [Na+] reflect a perturbation of the energetic balance between competing mechanisms by weakly screened long‐range electrostatic forces. Some perturbation probably also arises from variations in the linear charge density of the double helix induced by the proximity of premelted loop segments; however, this contribution cannot be evaluated without a detailed denaturation map.

At high [Na+] the mechanism of melting is more conserved, permitting the dependence of subtrasitional melting temperature tm(i) on [Na+] to be examined for almost all 34 ± 2 subtransitions. The G + C composition of segments responsible for each subtransition was determined by a quantitative spectral method. Analysis according to the Manning‐Record expression [Manning, G. (1972) Biopolymers 11, 937–949; Record, M. T., Jr., Anderson, C. F. & Lohman, T. M. (1978) Q. Rev. Biophysics 11, 103–178] relating ΔHm and dtm(i)/d log[Na+] to the fraction of Na+ released during melting, appears to indicate almost 40% more Na+ is bound to the single‐stranded G and/or C residues than to A and T residues. This is consistent with a much shorter mean axial spacing and higher charge density in the former, particularly single‐stranded G residues, which have an extraordinary tendency to stack.
Thermodynamic stability theory for DNA doughnut shapes induced by charge neutralization
Authors: Manning Gerald S.
Published: December 2004

A thermodynamic analysis of the bending free energy of DNA, initiated previously, is extended. It was demonstrated that the ionic‐strength dependence of the persistence length of DNA in aqueous NaCl can be understood by postulating (1) a rigid‐rod 60 base‐pair unit and (2) a negative contribution from nonelectrostatic sources to the bending free energy of this unit. On electrostatic neutralization of the phosphate charge, the latter term alone survives, and bending becomes a spontaneous process. In this paper it is demonstrated from a theoretical analysis of the ionic‐strength dependence of the rate of denaturation of DNA that the above statements are restricted in their validity to radii of curvature greater than 170 Å; beyond this limit, the steeply rising repulsive energy of tightly packed atoms dominates the bending free energy. Therefore, spontaneous bending on charge neutralization proceeds up to, but not beyond, this barrier to curvature. It is noted that doughnut forms of DNA induced by binding of cationic spermidine, or mixtures of Mg2+ and polyamines are observed to possess maximum curvatures, corresponding to the radius of the “hole in the middle,” in the range 1/150–1/200 Å.
13C‐1H magnetic double‐resonance study of fetal enamel matrix proteins
Authors: Termine J. D. , Torchia D. A.
Published: December 2004

Recently developed 13C‐1H nuclear magnetic double‐resonance techniques have been used to study proteins in the intact fetal enamel matrix. Enamel protein chains undergoing rapid, almost isotropic motion were detected in scalar decoupled 13C‐nmr spectra, while motionally restricted enamel protein chains were principally observed in proton‐enhanced spectra. The latter spectra were obtained using a matched Hartmann‐Hahn contact to transfer polarization from protons to carbons (cross‐polarization). Both mobile and motionally restricted enamel protein chains were observed in dipolar decoupled 13C‐nmr spectra. A comparison of integrated intensities obtained from the scalar decoupled and dipolar decoupled spectra showed that 70% of the fetal enamel protein chains exhibit rapid, nearly isotropic molecular motion (τ ≲ 10−6 sec), while the remaining 30% are rigid or undergo only anisotropic molecular motion.
Influence of double scattering in determination of rotational diffusion coefficients by depolarized dynamic light scattering: Application to the bacteriophages T7 and T4B
Authors: Hopman P. C. , Koopmans G. , Greve J.
Published: December 2004

Dynamic light scattering experiments were performed on solutions of the bacteriophages T7 and T4B in order to obtain the rotational diffusion coefficients of these phages. Correlation functions were determined from the depolarized intensity scattered in the forward direction. The apparatus used in this study is described in detail. Particular attention is paid to the minimalization of the depolarized intensity due to double scattering. If double scattering cannot be neglected, the correlation function of the depolarized field is the sum of the correlation functions resulting from single and double scattering. It is shown that by correcting for double scattering, it is then possible to obtain the rotational diffusion coefficient of the macromolecules. Although the optical anisotropy of both T4B (retracted fibers) and T7 is very small, the experimental conditions could be chosen in such a way that no depolarized scattering due to double scattering was observed. The measured rotational diffusion coefficients for T4B and T7 are D = 258 ± 12 and 4528 ± 100 sec−1, respectively. These values compare very well with those obtained by electric birefringence experiments.
Physical aging of dry elastin
Authors: Struik L. C. E. , Pezzin G.
Published: December 2004

Dry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from −20 to +180°C. At each temperature, the small‐strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
Preferred conformations of protected homo‐oligo‐L‐glutamate peptides in CDCl3 and CDCl3/TFA mixtures
Authors: Ribeiro Anthony , Saltman Robert P. , Goodman Murray
Published: December 2004

A conformational analysis of protected glutamate homo‐oligopeptides Z‐[Glu(OEt)]n‐OEt (n = 2–7) was carried out in chloroform solution using high‐resolution 1H‐nmr spectroscopy. At dilute peptide concentrations, the backbone NH and α‐CH resonances are well resolved and can be assigned by combining extensive homonuclear decoupling experiments with data for co‐oligopeptide derivatives. The structure of these peptides in solution was then assessed using information from chemical shifts, coupling constants, temperature coefficients, and titration of each oligomer with trifluoroacetic acid (TFA). The di‐ and tripeptides are found to be in disordered forms in deuterochloroform (CDCl3) and CDCl3/TFA mixtures. The tetrapeptide exhibits a folded structure with intramolecular hydrogen bonding at Glu2 in CDCl3 and undergoes a transition to increasingly disordered forms as TFA is added. The pentamer to heptamer show a folded structure with a strong intramolecular hydrogen bond at Glu2 and a weaker hydrogen bond at Glu3, which are disrupted as these peptides go to random coils at high TFA/CDCl3 ratios. In addition, the N‐terminal portions of these glutamate peptides appear to be involved in side chain–main chain interactions. The results support the hypothesis that protected linear homo‐oligopeptides may possess two or more segments of conformation with intramolecular folding preferred near the N‐terminal portion.
Role of aldehydes in collagen fibrillogenesis in vitro
Authors: Brennan Maureen , Davison Peter F.
Published: December 2004

The process of in vitro fibrillogenesis of type I collagen from bovine tendon has been studied with particular attention to the events occurring in the lag phase. From the conditions under which those events can be reversed or stabilized and from the effects of reduction on the length of the lag phase, we conclude that one event is the reaction of aldehydes on the molecules. However, we have been unable to detect the products of these reactions or any physical changes in the solution, so the change most probably involves the inter‐ or intramolecular reaction of a very small fraction of the molecules. In particular, the viscosity appears unchanged in solutions in which nucleation‐promoting structures have been stabilized, and so measurable numbers of polymers are not formed in this process.
Modification of the apparent radius of gyration of cytochrome c by the distribution of counterions in solution
Authors: Borso C. S. , Stamatoff J. B.
Published: December 2004

Small changes in the apparent radius of gyration of native cytochrome c were measured as a function of pH in solutions of 0 and 50 mM ruthenium hexicyanide. The forward scattering was also measured as a function of pH under the same conditions to ascertain the contribution of the Ru ion shell to the forward scattering and concomitantly to the radius of gyration. The forward scattering and small alterations in the radius of gyration were then measured as a function of Ru counterion concentration. These results are then interpreted in terms of the mechanisms which influence the measured apparent radius of gyration. It is shown that the Debye‐Hückel theory of counterion distributions can be used to describe the data in situations where scattering from the bound Ru ions contributes less significantly than scattering from the ion cloud.
Differential equation systems for heat‐loss corrections of isoperibolic microcalorimeters: A computer‐modeling approach
Authors: Martin C. J. , Sreenathan B. R. , Marini M. A.
Published: December 2004

The problem of adequately correcting thermal titration curves for heat losses in isoperibolic microcalorimeters during rapid reactions in small volumes has been examined. With a data‐acquisition system for the simultaneous encoding of changes in heat, pH, and time linked directly to a DEC‐20 computer, various possible mechanisms for heat‐loss corrections were tested using computer‐modeling techniques. Models expressed by series exponential terms, as commonly used in linear pharmacokinetics to describe the time‐course concentration of a drug, proved to be inadequate to reconstruct the “adiabatic” thermal curve, since its apparent magnitude increased with the time taken for its generation. However, models based on mechanisms incorporating at least two heat sinks, one of which can be equated to the surroundings, have proved successful. The differential equations descriptive of the various models examined have rate constants characteristic of the reaction cell and its inserts, the reaction volume, and the calorimeter used. These can be evaluated by a curve‐fitting algorithm (MLAB) using standard thermal‐titration data (the neutralization of HCL with KOH). Once the rate constants are known, the differential equation solver of MLAB is then used to deconvolute any time: heat‐change matrix to that which would obtain in the absence of heat loss (the “adiabatic” state). With an appropriate differential equation model, the magnitude of the corrected heat change is independent of the time taken for its production and so‐called best model(s) have been judged on the basis of Akaike's information criterion. The application of the heat‐loss correction procedure to the thermal titration of chymotrypsinogen is illustrated.
Electric dichroism and birefringence of poly(ribocytidylic acid). I. Optical properties and stability
Authors: Chen Holly Ho , Charney Elliot
Published: December 2004

Measurements of the uv absorption and melting profiles of poly(rC) at low‐salt conditions confirm the existence of a double‐stranded complex at low pH and imply, but do not prove, the structure proposed by Akinrimisi et al. (1963) Biochemistry 2, 340–343. Electric dichroism and birefringence provide additional supporting evidence and indicate that the complex is one in which the bases are tilted considerably from the major molecular axis. The base‐stacking tendency of single‐stranded poly(rC), unlike poly(rA), is found to be insufficient to maintain a rodlike structure; the persistence length of stacked bases in poly(rC) must be very small. The existence of an out‐of‐plane transition in poly(rC) in the vicinity of 300 nm is conclusively demonstrated by both dichroism and birefringence measurements.
Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes
Authors: Poltev V. I. , Milova L. A. , Zhorov B. S. , Govyrin V. A.
Published: December 2004

Using classical potential functions, we carried out potential‐energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum‐energy conformations of the complexes are close to DNA A‐ and B‐family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low‐energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.
XII. Conformational studies of histidine‐containing peptides in solution
Authors: Jäckle Hans , Luisi Pier Luigi
Published: December 2004

The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200–320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first‐approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
Kinetics of nucleosome unfolding at low ionic strength
Authors: Dieterich Ann E. , Cantor Charles R.
Published: December 2004

The kinetics of a conformational change which occurs in nucleosome core particles at about 1 mM ionic strength have been studied by observing changes in the fluorescence of labeled histone H3. The unfolding reaction is intramolecular since no concentration dependence is observed. However, the kinetics are unexpectedly complicated and reveal evidence of at least three relaxation times. It is possible to fit the kinetics observed under several conditions to a consistent four‐state cyclic mechanism in which folded and unfolded forms can inter‐convert by two parallel pathways, each involving a distinct intermediate. While the data are not sufficient to establish this mechanism as a unique choice, they exclude many simpler possibilities. The cyclic mechanism is quite reasonable in view of what is currently known about the structures of the folded and unfolded forms.
Evidence for the binding states of copper(II)–serum albumin complexes as revealed by transient electric dichroism measurements
Authors: Yamagishi Akihiko
Published: December 2004

Transient electric dichroism has been measured for a Cu(II)–bovine serum albumin (BSA)–2‐(2‐pyridylazo)‐1‐naphthol (αPAN) complex at pH 5.5–12. From the magnitude of the reduced linear dichroism and the disorientation rate of the oriented chromophore, at least three kinds of binding states of Cu(αPAN)+ complex exist. They are present predominantly at pH 5.5–10, 7.5–10, and 10–12, with the αPAN plane approximately parallel, vertical, and parallel with respect to the oriented axis of a BSA molecule.
Quantum‐mechanical study of model molecules in relation to collagen structure. II. (Gly‐Phe‐Pro) and (Gly‐Pro‐Phe) repeating units
Authors: Cabrol Daniel , Broch Henri , Vasilescu Dane
Published: December 2004

A conformational quantum‐mechanical study of (Gly‐Phe‐Pro) and (Gly‐Pro‐Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple‐helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly‐Pro‐Pro and Gly‐Phe‐Pro indicates that phenylalanyl in the second position favors the triple‐helix formation.
Conformational aspects of gastrin‐related peptides: A circular dichroism study
Authors: Peggion E. , Jaeger E. , Knof S. , Moroder L. , Wuensch E.
Published: December 2004

The conformational properties of a series of gastrin‐related peptides in aqueous solution and in 2,2,2‐trifluoroethanol (TFE) have been investigated by CD measurements. In aqueous solution the peptides Leu32‐HG‐34 (human big gastrin), Nle15‐HG‐17 (human little gastrin), and Nle11‐HG‐13 assume a random‐coil structure in the pH range 3–7. In TFE the three hormones fold into partially ordered structures, consisting of mixtures of α‐helix, β‐form and random coil. Comparison with the CD properties of the shorter gastrin peptides HG‐4 (tetragastrin), Nα‐Boc‐HG‐5 (pentagastrin), and HG‐7 (heptagastrin) indicates that the biologically important C‐terminal sequence Trp‐Met‐Asp‐Phe‐NH2 in TFE does not maintain the same geometry upon elongation of the chain at the N‐terminus from 4 to 34 residues. Thus, the various conformations in solution of the gastrin peptides examined do not provide a structural explanation for their very similar biological activity. Therefore, we hypothesize that the C‐terminal tetrapeptide amide folds into an “active” structure only upon interaction with the receptor.