bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐resolution study of the helix–coil transition of poly(L‐glutamic acid): Spectroscopic data correlation and the discovery of a new transition
Authors: Hayashi Hidechika , Wada Akiyoshi
Published: December 2004

This article reports on both (1) the precision and capability of a computerized multidimensional spectrophotometric system recently developed in our laboratory and (2) the high‐resolution study of the helix–coil transition of poly(L‐glutamic acid)[poly(Glu)], especially with regard to the discovery of an overlooked transition which is attributable to order–disorder rearrangement of the poly(Glu) side chain in the α‐helical conformation. This study was made possible by the high performance of the system used. The simultaneous and continuous measurement of the circular dichroism, the absorbance and light‐scattering intensity, and the pH titration curve of poly(Glu) in aqueous salt solution was carried out under continuous scanning of pH ranging from 8 to 2. Besides the well‐known random coil to α‐helix transition that occurs at about pH 5.5, a highly cooperative transition, which is indicated as a small but definite step in several spectral dimensions, is observed for the first time at pH 4.3. The transition is ascribed to an order–disorder conversion of the side chain on the α‐helix backbone.
Binding of ligands to a one‐dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach
Authors: Sturm Jean
Published: December 2004

A Monte Carlo method is presented to calculate equilibria for the binding of ligands to one‐dimensional heteropolymers. Equivalency with other methods suitable for particular cases was verified (i.e., matrix and combinatorial methods). The principal interest of this Monte Carlo method is in its facility for adaptation to any physically conceivable binding model and that it gives access to the parameters accounting for partial binding to each different type of site. General properties of binding isotherms with excluded‐site effects and relations between partial binding ratios and partial free site ratios are discussed. An effective calculation is presented for illustration of the method.
Binding of ligands to a one‐dimensional heterogeneous lattice. II. Intercalation of tilorone with DNA and polynucleotides
Authors: Sturm Jean , Schreiber Lisbeth , Daune Michel
Published: December 2004

The interaction of tilorone with DNA and five synthetic polydeoxyribonucleotides [(I): poly[d(A‐T)]·poly[d(A‐T)]; (II): poly[d(A‐C)]·poly[d(G‐T)]; (III): poly[d(G‐C)]·poly[d(G‐C)]; (IV): poly(dG)·poly(dC); and (V): poly(dA)·poly(dT)] has been investigated. Binding isotherms for the homopolymers were obtained by microdialysis equilibria using 14C‐labeled tilorone and interpreted with different models: exclusion effect, associated or not associated with cooperativity, or variable exclusion. Affinity appears to be related more to local structure than to base composition and decreases in the following order: (I) > (II) > (III) > (IV) > (V). Intercalation in circular DNA was demonstrated by electrophoresis migration and electron microscopy, which yielded an average unwinding angle of 7° per bound dye. The behavior observed in CD and UV spectroscopy shows a sequence similar to the affinities. Tilorone seems to be less intercalated in (IV) and not at all in (V). The experimental binding isotherm of tilorone to DNA was well fitted on the basis of a model where DNA acts as a heterogeneous lattice built with the six different possible couples of adjacent base pairs, each potential site behaving as if it were in the corresponding homopolymer. The results are discussed in terms of specificity of alternating Pyr‐Pur sequences and related to theoretical calculations on intercalation energies of DNA.
Gel filtration studies of methylene blue–heparin interactions in aqueous solution
Authors: Kadokura Satoru , Miyamoto Takeaki , Inagaki Hiroshi
Published: December 2004

The gel filtration method was applied to the study of the interaction of the metachromatic cationic dye methylene blue (MB) with heparin in aqueous solution. This method requires the determination of the total MB concentration in the effluent. It was found that (i) MB in aqueous solution can be extracted quantitatively with benzyl alcohol (BzlOH), (ii) the metachromatic effect of MB is not observed in BzlOH, and (iii) the presence of heparin in aqueous solution does not interfere in the BzlOH extraction of MB. Accurate determination of MB concentration in the effluent can be made by extraction of MB with BzlOH, followed by the usual absorption spectroscopy. In addition, the use of the spectrophotometric method with this procedure entailed no serious problem relating to adsorption of MB on the glass walls. Gel filtration binding experiments were successfully carried out on a Sephadex LH‐20 column using 0.005M acetate buffer as effluent. The binding data obtained were analyzed in terms of the cooperativity parameter according to the method of Schwarz. The thermodynamic parameters for the binding process of MB were also evaluated. It is shown that the binding of MB to heparin is highly cooperative, exothermic, and stabilized by entropic factors.
Optical anisotropies of amides and peptides in dioxane
Authors: Khanarian G. , Mack P. , Moore W. J.
Published: December 2004

The molar Kerr constants mK, molar refractions mR, and dipole moments μ are reported for the N‐methylacetamides CX3CONHCH3 (X = H, CH3, F. CI, Br) and acetamides CX3CONH2 (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N‐methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N‐methylacetamide were used to calculate mK, μ, and γ2 (anisotropy squared) of N‐acetyl‐N′‐methylglycine amide and N‐acetyl‐N′‐methyl‐alanine amide as functions of the torsional angles (ϕ,Ψ). The statistical mechanical averages of mK, μ, and γ2 were calculated from conformational energies obtained by the methods of Scheraga.
Electrostatic interactions in ionic homopolypeptides in solutions of moderate ionic strength
Authors: Santiago German , Maroun Rachid C. , Hawkins Erin R. , Mattice Wayne L.
Published: December 2004

At sufficiently high ionic strength, long‐range electrostatic interactions in a polyelectrolyte such as poly(L‐glutamic acid) might be adequately approximated in matrix calculations by use of statistical weights representing second‐order interactions. The validity of this assumption has been investigated making use of experimental observations (CD spectra and titration curves) for poly(L‐glutamic acid) as a function of temperature in 0.1–0.5M sodium chloride. Theoretical analysis, using a statistical weight matrix proposed by Warashina and Ikegami, is based on the Zimm‐Rice theory. Implementation differs from that of Warashina and Ikegami in one respect. Refinement of the initial estimates is achieved using a form of the configuration partition function which does not assume diagonalization of the statistical weight matrix. This difference is of no consequence for the values of σ and s, but it does produce somewhat different values for the statistical weights used to represent the electrostatic interactions. The method used to treat electrostatic interactions in poly(L‐glutamic acid) in 0.1M sodium chloride can be viewed as successful in that it properly reproduces the helix–coil transition and titration curves in this solvent and the molecular‐weight dependence of the titration curves yields values for s in harmony with those obtained using a treatment which is independent of model, and gives a reasonable ionic‐strength dependence for the electrostatic parameters. Furthermore, the model can account for measured helix–coil transitions and titration curves in homopolypeptides in which the side chain is —(CH2)xNHCO(CH2)yCOOH. The model, however, is not exact. It does not properly account for the molecular‐weight dependence of the helical content for polymers of low degree of polymerization.
Analysis of the ionization constants and heats of ionization of reduced and oxidized horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Berger R. L. , Forlani L.
Published: December 2004

Simultaneous curve fitting for the ionization parameters of oxidized and reduced horse heart cytochrome c in 0.15M KCl and 20°C yields values for the ionization constants (as pK′) and the heats of ionization (ΔHi) which can reconstruct either the potentiometric or thermal titration curves. Reduced cytochrome c requires 8 sets of groups, whereas oxidized cytochrome c requires 10 sets of groups. The additional groups in the oxidized preparation appear to involve the ferriheme (pK′, 9.25; ΔHi, 13.7 kcal/mol) and a tyrosine (pK′ ≃ 10.24) that is not present in the reduced form. The potentiometric and thermal difference curves (reduced – oxidized) involve the appearance of 17 kcal/mol centered at pH 9.7 and 5.8 kcal/mol centered at pH 4.9. The carboxyl groups in both species appear to be normal for the hydrogen‐bonded form. Only one histidine has normal ionization properties (pK′, 6.7; ΔHi, 7.5 kcal/mol), as do 17 of the lysine residues (pK′, 10.8; ΔHi, 11.5 kcal/mol).
Induced circular dichroism and mode of binding of acridine orange adsorbed on β‐form poly(S‐carboxyethyl‐L‐cysteine) in aqueous solutions
Authors: Ikeda Shoichi , Yoshida Tomohiko , Imae Toyoko
Published: December 2004

The absorption spectra and circular dichroism (CD) have been measured for aqueous solutions of acridine orange of a constant concentration, [D] = 5 × 10−5M, mixed with poly(S‐carboxyethyl‐L‐cysteine) in various mixing ratios, [P]/[D], ranging from 330 to 11, at different pH. The absorption spectra of the dye–polymer solutions are hypochromic, and the main band is located at 470 nm, accompanying a shoulder at 500 nm. At alkaline pH, no CD is induced in the visible region. At neutral and acidic pH, where the polymer is in the β‐conformation, CD is induced in the visible and near‐uv regions. A pair of CD bands is located at the region around 450 nm, when the pH is around the neutrality, while it appears at the region around 500 nm at acidic pH. Thus, the optically active species of bound dye changes from dimer to monomer on lowering the pH. These species form dissymmetric arrays along a polypeptide chain. The fraction of bound dye forming dissymmetric sequences is not high, but most of bound dye is adsorbed randomly on the ionized carboxyl groups of polypeptide chain and gives rise to hypochromism only. A dissymmetric structure of dye–polymer complexes is presented, in which the polymer has the β‐conformation and the dye cations, either dimeric or monomeric, bind to its side chains, in such a way that the longer axes of molecular planes of bound dye form a two‐fold, right‐handed helix along the extended polypeptide chain. A zeroth‐order calculation of CD based on the coupled oscillator model leads to the result that each dissymmetric array of dye consists, on the average, of two dimeric or monomeric cations. This low number of bound cations in a dissymmetric array and the large fraction of randomly adsorbed dye suggest that the hydrophobic interaction of dye with the polymer is strong, so that dye cations are adsorbed sparsely on both sides of the extended polypeptide chain.
Modification of the reactivity of a small molecule by reversible association with a synthetic polymer. Inhibition of the hydrolysis of cationic esters by polyanions
Authors: Morawetz Herbert , Shafer Jules A.
Published: December 2004

The base‐catalyzed hydrolysis rate of the cationic esters obtained by quaternization of N,N,N′,N′‐tetramethylethylenediamine with phenylbromoacetate was studied in buffers and in solutions of partially neutralized polymeric acids. The polyanions were found to be powerful inhibitors of the reaction. This effect was interpreted as due to the association of the ester with the polyanion, from which the catalytically active hydroxyl groups are repelled. It is shown that kinetic data may be interpreted by a procedure similar to the Lineweaver‐Burk plot to yield the reactivity of the bound ester and the dissociation constant of the polymer–ester complex.
Polyelectrolyte behavior of charged polyamino acids in aqueous solutions
Authors: Ascoli F. , Botré C.
Published: December 2004

The conductivity and activity coefficient of counterions of sodium salts of some charged polyamino acids, as poly‐L‐glutamic acid, poly‐L‐aspartic acid, and poly‐L‐cysteic acid, were measured in aqueous solution. The results show that the degree of binding of small counterions to the charged macroions shows a characteristic dependence on dilution and temperature which is not common for other simple polyelectrolytes. Such behavior is very likely related to conformational changes induced by the above factors.
Raman scattering of some synthetic polypeptides: Poly(γ‐benzyl L‐glutamate), poly‐L‐leucine, poly‐L‐valine, and poly‐L‐serine
Authors: Koenig J. L. , Sutton P. L.
Published: December 2004

The Raman spectra of poly‐γ‐benzyl‐L‐glutamate, poly‐L‐leucine, poly‐L‐valine, and poly‐L‐serine are reported. For the α‐helical polymers, the conformationally sensitive amide I, II, and III modes are observed in the Raman as, well as the infrared. For the β form, the Raman effect, supplies the infrared inactive inphase motion which is useful for the determination of a parallel or antiparallel chain alignment. Modes characteristic of the specific polypeptide are also observed which are insensitive to conformation.
The lattice energetics of some polypeptide chains
Authors: Hopfinger A. J.
Published: December 2004

The interchain energetics of alpha, beta, and PGII conformations of polyglycine, the PPII and left‐handed 3.30 fold helical conformations of trans poly‐L‐proline, and the Yonath and Traub triple helix and left‐handed three fold helices of poly(gly‐pro‐pro) were investigated. Intra‐ and inter‐chain stabilization energies appear to be inversely related, and the interchain stabilization energy can be as large its the intrachain energy. The minimization of the interchain energy can be described by the simultaneous optimization of interchain hydrogen bonding and intermolecular‐sidechain digitation. The stability of the poly(gly‐pro‐pro) triple helix can be readily explained in terms of these two factors. In all cases the experimentally observed lattice packing is predicted, although the calculated lattice constants are slightly larger than those observed. The small differences between observed and predicted lattice constants probably reflect small errors in present conformational potential functions. Homopolymers are probably the best systems to use in the refinement of conformational potential functions because solvent effects arc minimized and the experimentally observed lattice constants provide a check on the configurational calculations.
Dielectric disperison of linear polyelectrolytes
Authors: Michael Schurr J.
Published: December 2004

A three‐dimensional (gaussian) model is formulated that permits evaluation of the one‐dimensional fourier cosine transform of the counterion‐counterion coulombic interaction energy ϕk. It is shown that ϕkis much larger for small k than was assumed by Oosawa; consequently, the magnitude of his dielectric increment, and also his relaxation time, must be drastically revised to smaller values. Evidently, the self‐field of the fluctuation is large enough to seriously depress the amplitude of the spontaneous fluctuations, and to force Ohmic conduction of the ions at a rate far in excess of the rate of translational diffusion. Finally, it is noted that in highly conducting bulk solvents, where both positive and negative counterfoils coexist in the ion‐atmosphere, one might expect to observe a low‐frequency component of the dielectric relaxation arising from unequal rates of diffusion of the positive and negative species, in analogy with the situation for spherical colloidal particles. In such a circumstance, the basic counterfoil fluctuation mechanism proposed by Oosawa would acquire a new validity.
Theory of the influence of oligonucleotide chain conformation on double helix stability
Authors: Delisi C. , Crothers D. M.
Published: December 2004

We consider theoretical aspects of reactions that form base pairs in a double helix. The equilibrium constant for such reactions depends on the probability of finding the two bases in the correct orientation for pairing. This probability can be expressed in terms of the spatial and angular distribution of one micleotide around the other. In this paper we use Monte‐Carlo techniques to calculate the distribution of distances between chosen phosphates in nonhclical oligonucleotide backbones, using crystallographic data for bond lengths and angles, and a screened Coulomb potential for phosphate–phosphate interactions. The model chosen is one that predicts correctly the observed dimensions of an unperturbed polynucleotide chain. Knowledge of distance distribution functions permits calculation of the dependence on loop size of the probability of closing a single backbone strand into a hairpin helix. Our results agree roughly, although not exactly, with the semiempirical ring‐weighting functions determined by Schefller. Elson, and Baldwin. Further results are a comparison of intramolecular and bimolecular helix nucleation equilibrium constants and a calculation of the stacking free energy in a double helix.
Circular dichroism calculation for random‐coil polypeptide chains
Authors: Zubkov V. A. , Birshtein T. M. , Milevskaya I. S. , Volkenstein M. V.
Published: December 2004

A method of calculation of the circular dichroism (CD) of random‐coil polypeptides has been developed by means of a Monte‐Carlo approach to the treatment of statistical systems and exciton theory of optical activity of polymers. The contribution of π–π* and n–π* amide transitions to the CD has been taken into account. The π–π* transition gives rise to two CD bands: a negative short‐wavelength band and a weak positive long‐wavelength one. The n–π* transition gives rise to one negative CD band.
Thermodynamic parameters of helix–coil transition in polypeptide chains. II. Poly‐L‐lysine
Authors: Barskaya T. V. , Ptitsyn O. B.
Published: December 2004

The helix–coil transitions for poly‐L‐lysine (PL) were investigated by the methods of spectropolarimetry, viscometry and potentiometric titration in 0.2M NaCl at different temperatures as well as in 0.2MNaBr, 1MKCl, and in mixtures of 0.2MNaCl or NaBr with methanol at room temperature. The enthalpy and entropy differences between the helical and coillike states of uncharged PL molecules in 0.2.M NaCl were determined from the potentiometric titration curves. The cooperativity parameters σ for PL in different solvents were determined by two methods (from the sharpness of the transition and from the dependence of the intrinsic viscosity on the helical content in the transition region). In 0.2MNaCl σ has a value of (2.3 ± 0.5) × 10−4 and does not depend on temperature, i.e., the cooperativity of the helix‐coil transition, as for PGA, is mainly of an entropy origin (the initiating of the helical region is accompanied by the entropy decrease ΔSi = −12 eu/mole of helical regions). A comparison of the obtained results for PGA and PL with the molecular theories of the helix‐coil transitions shows that the role of dipole‐dipole interactions of nonneighboring peptide groups is greatly overestimated in these theories, leading to a considerable enthalpy contribution to the free energy of initiating helical regions which is not observed in the experiment.
Stepwise synthesis of oligopeptides with N‐carboxy α‐amino acid anhydrides. II. Oligopeptides with some polar side chains
Authors: Katakai Ryoichi , Oya Masanao , Uno Keikichi , Iwakura Yoshio
Published: December 2004

The reaction of NCA's with some amino acids having a nucleophilic functional group on the side chain was studied in a heterogeneous reaction medium (acetonitrile‐water). Glutamic acid and aspartic acid, having a free carboxyl group on the side chain, were successfully used to synthesize oligopeptides without interactions of the γ‐ and β‐carboxyl group with NCA's. Two products were obtained by the reaction of NCA with L‐lysine, which contains a free amino group on the side chain. ε‐Protected lysine was used to prepare α‐peptides as a nucleophile in the reaction. No racemization was observed in the synthesis of peptides by the NCA method in the heterogeneous solvent system. Oligopeptides with some polar side chains were synthesized by the NCA method.
Simplified force field calculations of the low‐frequency motions of the α‐helix
Authors: Fanconi Bruno , Peticolas W. L.
Published: December 2004

Using valence force field constants and a highly simplified model of the α‐helix consisting of only two masses per repeat unit we have been able to very nearly reproduce the low frequency phonon dispersion curves which we had obtained earlier with the use of a seven mass model and a Urey‐Bradley force field. Since the frequencies obtained from this latter model agree well with the observed Raman frequencies it appears that the low frequency chain motions of polypeptide chains may be calculated from a very simple model involving the amino acid residues as essentially a single mass. Such techniques appear to offer the possibility of making normal mode calculations for the chain dynamics of polypeptide chains of low symmetry such as proteins.
Electrostatic contributions to oligonucleotide transitions
Authors: Delisi Charles , Crothers Donald M.
Published: December 2004

In a previous paper we employed Monte Carlo techniques to calculate distribution functions for distances between charged phosphates of randomly coiled oligonucleotides in solution. The average energy of the random coil, as well as the loop weighting function and bimolecular nucleation parameter, was obtained as a function of chain length and salt concentration. In the present paper we apply the results to a consideration of the electrostatic dependence of the helix–coil transition in oligonucleotides. By considering the equilibrium among three species: hairpin, dimer, and random coil, we have calculated (1) the variation in melting temperature of dimer, hairpin, and the dimer‐hairpin mixture with salt concentration and chain length, (2) the variation in the equilibrium between dimer and hairpin as a function of salt concentration, temperature, and length, (3) the variation in the transition breadth with salt concentration and chain length.
Conformational energy calculations on glycosylated turns in glycoproteins
Authors: Bush C. Allen
Published: December 2004

Analysis of the amino acid sequence of glycoproteins has suggested the β‐turn as a likely site of glycosylation in glycoproteins. According to this model, the peptide chain traverses the interior of a globular protein, reversing its direction at the protein surface, a likely point for the attachment of hydrophilic carbohydrate residues. In order to search for plausible conformations of glycosylated β‐turns in asparagine‐linked glycoproteins, we have adapted the conformational energy calculation method of Scheraga and coworkers for use in carbohydrates. The parameters for nonbonded and hydrogen‐bonded interactions have been published, and electrostatic parameters are derived from a CNDO calculation on a model glycopeptide. Our results indicate that the orientation of the glycosyl amide bond having the amide proton nearly trans to the anomeric proton of the sugar has the lowest energy. Although CD and nmr experiments in our laboratory have consistently found this conformation, our calculations show the conformation having these two protons in a cis relationship to lie very close in energy. Calculations on the glycopeptide linkage model, α‐N‐acetyl, δ‐N(2‐acetamido‐1,2‐dideoxy‐β‐D‐glucopyranosyl)‐N′‐methyl‐L‐asparaginyl amide show that several distinct geometries are allowed for glycosylated β‐turns. For a type I β‐turn, three conformations of the glycosylated side chain are found within 4 kcal of the minimum, while two conformations of the glycosylated side chain are allowed for a type II turn. The hydrogen‐bonded C7 conformation is also allowed. Stereoviews of the low‐energy conformations reveal no major hydrogen‐bonding interaction between the peptide and sugar.
Lipid‐induced conformational changes in glucagon, secretin, and vasoactive intestinal peptide
Authors: Robinson Randall M. , Blakeney Ernest W. , Mattice Wayne L.
Published: December 2004

The CD of glucagon, secretin, and vasoactive intestinal peptide has been studied as a function of temperature in water and in aqueous solutions of dodecyl sulfate, phosphatidyl glycerol, and L‐α‐phosphatidic acid (dipalmitoyl). The anionic detergent and lipids induce helix formation in all three peptides, with the amount of induced helical content increasing in the order glucagon < secretin < vasoactive intestinal peptide. These observations are subject to quantitative rationalization using a matrix formulation for the configuration partition function. In this formulation the major conformational consequences of the interaction with anionic lipids or detergents is an increase in the probability for helix formation by arginyl, histidyl, and lysyl residues. The region in which helix formation is maximal is found to be at amino acid residues 13–20 in all three peptides. Other studies have implicated this portion of the polypeptide chain in receptor binding. Thus, the helical segment induced by interaction with anionic lipids may play an important physiological role.
Type II β‐turn conformation of pivaloyl‐L‐prolyl‐α‐aminoisobutyryl‐N‐methylamide: Theoretical, spectroscopic, and X‐ray studies
Authors: Prasad B. V. Venkataram , Balaram Hemalatha , Balaram P.
Published: December 2004

Pivaloyl‐L‐Pro‐Aib‐N‐methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H‐nmr methods, suggesting the existence of β‐turns, with Pro‐Aib as the corner residues. Theoretical conformational analysis suggests that Type II β‐turn conformations are about 2 kcal mol−1 more stable than Type III structures. A crystallographic study has established the Type II β‐turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β‐turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ϕPro = −57.8°, ψPro = 139.3°, ϕAib = 61.4°, and ψAib = 25.1°. The Type II β‐turn conformation for Pro‐Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.
Ionization behavior of proteins. I. Spectral titration of the tyrosyl groups of chymotrypsinogen and nitrated‐chymotrypsinogen
Authors: Martin Charles J. , Marini Mario A.
Published: December 2004

The ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated‐chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time‐dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′1 9.75 ± 0.07, pK′2 11.55 ± 0.05, pK′3 13.30 ± 0.05. In nitrated‐chymotrypsinogen, the two nitrated tyrosyl residues have pK′1 6.44 and pK′2 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer‐assisted curve‐fitting analysis.
Theoretical studies on the conformation of saccharides. IV. Solvent effect on the stability of β‐maltose conformers
Authors: Tvaroška Igor
Published: December 2004

The conformational equilibria of four β‐maltose conformers have been studied theoretically in 12 solvents. The stability of the conformers in dilute solution has been compared by using the continuum reaction field method. The solvation energy consists of electrostatic, dispersion, and cavity terms, which have been determined from the calculated properties of β‐maltose and physicochemical properties of solvents. The calculated population of four conformers significantly depends on the solvent (e.g., in dioxane, M1:M2:M3:M4 = 53.3: 20.3:17.7:8.7; in dimethyl sulfoxide, 40.1:21.8:22.8:15.3; and in water, 25.7:17.5:26.3:30.5) and was found to correlate with experimentally observed data. The results obtained indicate that the conformation adopted by β‐maltose in the crystalline form is not the one preferred in solution. The roles of the individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and vicinal carbon–proton coupling constants have been calculated and discussed from the point of view of the solution behavior of β‐maltose.
Recent progress in the theoretical treatment of protein folding
Authors: Scheraga Harold A.
Published: December 2004

The multiple‐minima problem encountered in computations of the conformational energy of a globular protein can be approached by extending, in part, the methodology used heretofore to treat small oligopeptides and fibrous proteins, and by incorporating procedures to treat short‐, medium, and long‐range interactions. The latter consist primarily of energy minimization and application of distance constraints. Initial tests with the 20‐residue membrane‐bound portion of melittin and with the 58‐residue bovine pancreatic trypsin inhibitor are sufficiently encouraging to suggest that the potential functions and computational algorithms are reasonable and extendable to globular proteins containing as many as 200 amino acid residues.
An empirical approach to protein conformation stability and flexibility
Authors: Creighton Thomas E.
Published: December 2004

Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
Folding of protein fragments: Conformational and biological studies on thioredoxin and its fragments
Authors: Reutimann Herbert , Luisi Pier Luigi , Holmgren Arne
Published: December 2004

Thioredoxin can be cleaved enzymatically into the two fragments (1–73) and (74–108) and chemically into two different ones (1–37) and (38–108). In this paper, the conformational properties of the short fragment (1–37) are reported and compared with those of the larger fragment (1–73). Using mainly circular dichroism (CD), it is shown that the (1–37) fragment, which contains the active disulfide unit center, is present as an unordered structure in the neutral pH range, but assumes a rigid folding at pH values below 6. The form of the CD spectrum is very similar to that of the complete native protein, and to that of the folded (1–73) fragment. The possible mechanisms for refolding of the short fragment are discussed.
Vibrational analysis of conformation in peptides, polypeptides, and proteins
Authors: Krimm S.
Published: December 2004

A vibrational force field for the polypeptide chain has been developed for normal‐mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm−1. We review the application of this technique to conformational problems in peptides (β‐turns and their model compounds), polypeptides [the αII‐helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).
Spectroscopic studies of a hydrophobic peptide in membranelike environments
Authors: Gierasch Lila M. , Lacy Jeffrey E. , Anderle Gloria , Lalancette Roger , Mendelsohn Richard
Published: December 2004

A hydrophobic linear peptide has been synthesized and studied over a range of environments using several complementary spectroscopic approaches, including nmr, CD, and vibrational spectroscopies. The sequence of this model peptide, carbobenzoxy‐L‐Pro‐D‐Phe‐D‐Ala‐L‐Pro‐NHCH3, was designed such that a small number of “folded” conformations, stabilized by intramolecular hydrogen bonding, would be accessible to it. Additionally, the extremely hydrophobic character of the peptide favors its interactions with hydrophobic regions of a membrane. The conformational impact of the membrane environment on the peptide, and the effect of the peptide on lipid organization have been explored both in micellar media and in vesicles. To facilitate nmr analysis, the peptide has been synthesized with one of the prolines perdeuterated. Results of these studies reveal that the peptide experiences a microenvironment of moderate polarity in micellar media and causes changes in lipid structure in a vesicle that are indicative of a hydrophobic peptide–lipid interaction.
Exploitation and exploration of ceruletide and eledoisin, two peptides of nonmammalian origin
Authors: De Castiglione R.
Published: December 2004

Eledoisin and ceruletide, two nonmammalian hormonelike peptides, have been explored for possible pharmaceutical application. At present, only a few of the potentialities of the two drugs have been exploited. Eledoisin is used in ophthalmology as a lachrymal secretagogue; ceruletide is applied in the radiological diagnosis of gallbladder, biliary system, and digestive tract disorders, in the study of exocrine pancreatic function, and in the treatment of postoperative paralytic ileus and intestinal hypotony and atony. Possible analgesic and antipsychotic applications of ceruletide are under study. Developments of synthetic and analytical methods for both peptides are briefly reviewed. Technical devices or alternative routes of administration are envisaged in order to enlarge both the present market and the field of application.
Salt‐ and sequence‐dependence of the secondary structure of DNA in Solution by 31P‐nmr spectroscopy
Authors: Chen Chi‐wan , Cohen Jack S.
Published: December 2004

We examined three sonicated, specific‐seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P‐nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P‐nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche−‐gauche− conformation and shifts upfield in all four monovalent salts used, relative to a single‐stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans‐gauche− conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly‐(dAdT) from a presumed right‐handed dinucleotide‐repeat B‐form to another conformation with a dinucleotide‐repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans‐gauche− conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly‐(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right‐handed regular B‐form to a left‐handed Z‐form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B‐form with a gauche−‐gauche− phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
Structure of amphotericin B aggregates based on calculations of optical spectra
Authors: Hemenger R. P. , Kaplan Theodore , Gray L. J.
Published: December 2004

The Degenerate ground state approximation was used to calculate the optical absorption and CD spectra for helical polymer models of amphotericin B aggregates in aqueous solution. Comparisons with experimental spectra indicate that a two‐molecule/unit cell helical polymer model is a possible structure for aggregates of amphotericin B.
Temperature‐jump kinetics of the dC‐G‐T‐G‐A‐A‐T‐T‐C‐G‐C‐G double helix containing a G·T base pair and the dC‐G‐C‐A‐G‐A‐A‐T‐T‐C‐G‐C‐G double helix containing an extra adenine
Authors: Chu Y. Gloria , Tinoco Ignacio
Published: December 2004

The kinetics of helix formation were investigated using the temperature‐jump technique for the following two molecules: dC‐G‐T‐G‐A‐A‐T‐T‐C‐G‐C‐G, which forms a double helix containing a G·T base pair(the G·T 12‐mer), and dC‐G‐C‐A‐G‐A‐A‐T‐T‐C‐G‐C‐G, which forms a double helix containing an extra adenine (the 13‐mer). When data were analyzed in an all‐or‐none model, the activation energy for the helix association process was 22 ± 4 kcal/mol for the G·T 12‐mer and 16 ± 7 kcal/mol for the 13‐mer. The activation energy for the helix‐dissociation process was 68 ± 2 kcal/mol for the G·T 12‐mer and 74 ± 3 kcal/mol for the 13‐mer. Rate constants for recombination were near 105s−1M−1 in the temperature range from 32 to 47°C; for the dissociation process, the rate constants varied from 1s−1 near 32°C to 130s−1 near 47°C. Possible effects of hairpin loops and fraying ends on the above data are discussed.
Boundaries of the universal K3 region and plateau region of the dynamic structure factor for DNA
Authors: Schurr J. Michael
Published: December 2004

A sufficiently long semiflexible filamentous macromolecule is theroretically expected to exhibit three different domains of behavior of its apparent diffusion coefficient Dapp(K) as a function of scattering vector K: (1) the small wave vector limit, where Dapp(K) = D0 is the translational diffusion coefficient of the center‐of‐mass; (2) the universal K3 region, where Dapp(K) = (kBT/6πη)K is a universal function of K independent of any property of the molecule itself; (c) the plateau region at large K2, where Dapp(K) approaches either a plateau, or gradually sloping quasiplateau, characteristic of local (elastic) rigid‐body motions of the filament. The existence of each of these different domains has now been established experimentally for at least some polymers. The boundaries of the universal K3 region and the plateau region are determined theoretically here using precise quantitative criteria for universal or plateau behavior of Dapp(K) for a Rouse‐Zimm model containing N + 1 subchains with rms subchain extension b. Allowing a maximum of 13% nonuniversal behavior, the domain of the universal K3 region is given by K2R2G = K2Nb2/6 ≥ 7 and K2b2 ⩽ 0.54. Allowing as much as 10% nonplateau behavior, the boundary for onset of plateau behavior is K2b2 = 18.3. Dapp(K) is at least 50% nonuniversal when K2b2/6 = 6 ln 3. Extension of these results to DNA is examined theoretically, and good agreement of the pertinent predictions with published experimental data is demonstrated.

It is concluded that no truly universal K3 region exists for DNA with Mr ⩽ 107 and persistence length a ≥ 450 Å, although marginally (⩽17% nonuniversal) universal behavior, is exhibited in a very narrow domain 0.64 × 1010 ⩽ K2 ⩽ 0.84 × 1010 cm−2 for ϕ29 DNA (Mr = 11.5 × 106). More than 50% of Dapp(K) is governed by local (elastic) rigid‐body motions when K2 = 5.23 × 1010 cm−2. The existence of a very wide region of nonuniversal apparent K3 behavior extending up to very large K2, far into the plateau region, is demonstrated in a plot of Dapp(K)/K vs K2 for the Rouse‐Zimm model. This is shown to stem in part from visual artifacts of plotting Dapp(K)/K vs K2, even for rigid species.
Conformation of sequential polypeptides of (Lysi‐Leuj), (Lysi‐Serj), and (Lys‐Gly) in sodium dodecyl sulfate solution
Authors: Kubota Shigeo , Ikeda Kiyoshi , Yang Jen Tsi
Published: December 2004

A series of sequential polypeptides (LysiRj)n (R is Leu, Ser, or Gly) and random copolypeptides, (Lysx, Leuy)n, were synthesized. Their conformation in NaDodSO4 solution was determined by CD. Only (Lys‐Leu)n, (Lys‐Ser)n, and (Lys3‐Ser)n adopt a stable β‐form in the surfactant solution; (Lys‐Ser2)n, (Lys‐Ser3)n, (Lys2‐Ser2)n, and (Lys2‐Ser)n have an unstable β‐form, which reverts to an unordered form in high NaDodSO4 concentrations, even though both Ser and DodSO‐bound Lys+ are β‐formers. In contrast, (Lys‐Gly)n remains unordered in NaDodSO4 solution. On the other hand, Lys‐rich (Lys2‐Leu)n forms an unstable helix and (Lys2‐Leu2)n a stable helix in NaDodSO4 solution. In 25 mM NaDodSO4 (Lysx, Leuy)n also forms a helix up to x = 75 and reverts to the β‐form at x = 90. This compares with the helical conformation of (Lysx, Alay)n up to x = 65 and its β‐form at x = 90, suggesting that Leu is an even stronger helix‐former than Ala. Our results may provide a plausible explanation for the increase in helicity and disruption of the β‐form for many proteins in NaDodSO4 solution, that is, the polypeptide chain of a protein usually favors a helical conformation over a β‐form in the presence of excess surfactant.
Cooperative ligand binding on multidimensional lattices: Bethe approximation
Authors: Miyazawa Sanzo
Published: December 2004

A binding isotherm for ligands on multidimensional lattices has been calculated in the Bethe approximation. In this lattice model, a single bound ligand is assumed to occupy a contiguous sequence of lattice sites in all possible configurations; interactions between neighboring bound ligands are included. This lattice model is equivalent to one used for treating polymer solutions; a configurational entropy of athermal polymer solutions has been utilized directly to represent bound ligands. Binding isotherms are examined for their dependences on lattice coordination numbers and the number of sites occupied by a single bound ligand. Critical conditions for phase transitions in single‐ligand‐species systems are also presented. The binding isotherm reported here can be applied to a wide variety of binding phenomena; it is exact for one‐dimensional cases, i.e., it reduces to the binding isotherm of McGhee and von Hippel [(1974) J. Mol. Biol. 86, 469–489] and should serve as a good approximation for higher‐dimensional binding phenomena.
Extended retro‐inverso analogs of somatostatin
Authors: Pallai Peter , Struthers Scott , Goodman Murray , Rivier Jean , Vale Wylie
Published: December 2004

An extended retro‐inverso modification was introduced at the central six residues of the somatostatin molecule, the region of internal enzymatic degradations. The synthesis of the analog [Ala4,g‐Phe6‐r‐D‐Phe7‐r‐D‐Trp8‐r‐D‐Lys9‐r‐D‐Thr10‐m‐R,S‐Phe11]‐somatostatin required a unique strategy accommodating the unusual structure. Side‐chain protection based on the t‐butyl group in combination with Fmoc and Nps α‐amino protection was employed. The key component containing the gem‐diaminoalkyl residue was generated by an iodobenzene bistrifluoroacetate‐mediated reaction. The separation of diastereomers of the cyclic tetradecapeptide in highly pure form was accomplished by high‐performance liguid chromatography on a semipreparative scale. The analogs exhibited very low potency in the growth hormone inhibition test in vitro. This is interpreted as the consequence of the complex structural changes created by the extended retro‐inverso modification.
The C‐terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro: Effects of Ethylurea
Authors: Capaldi Michael J. , Chapman John A.
Published: December 2004

Ethylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in vitro. Intact and enzyme‐digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme‐digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin‐digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C‐terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C‐terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and growth in vitro.
Formation of ψ(+) and ψ(−) DNA
Authors: Shin Y. A. , Eichhorn G. L.
Published: December 2004

DNA molecules can be organized into ordered aggregates of opposite handedness by complexation with polylysine and other polypeptides; we have investigated the conditions under which ψ(+) and ψ(−) structures are produced with double‐helical synthetic polynucleotides. Both poly(dGdC)·poly(dGdC) and poly(dAdT)·poly(dAdT) readily form ψ(−) structures with polylysine, although the method of preparation can alter the CD spectra. The GC copolymer, which is more susceptible to conversion into A or Z conformers, forms ψ(+) structures with lysine–alanine copolypeptides more readily than the AT copolymer. Nucleotide base modifications that favor the Z structure, such as bromination and methylation, also favor ψ(+) formation, and the Co(NH3)6Cl3 reagent that readily induces the Z structure also leads to ψ(+). Thus, the production of the ψ(+) structure seems to be frequently correlated with susceptibility to A or Z formation, although there are some cases in which the B conformer also leads to ψ(+). Polyethylene glycol generally produces a ψ(−) structure; the differentiation between ψ(+) and ψ(−) structures seems to require electrically charged polymers.
Studies of collagen fold formation in aqueous solutions of α‐gelatin III
Authors: Thorn I. , Eagland D.
Published: December 2004

Optical rotation, viscosity, and density studies are reported on solutions of α‐gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
Conformation study on heparin by intermediate‐angle X‐ray scattering
Authors: Yamaguchi Saburo , Hayashi Hisao , Hamada Fumiyuki , Nakajima Akio
Published: December 2004

The conformation of heparin in water was investigated by intermediate‐angle x‐ray scattering (IAXS). The theoretical scattering function for the coil conformation was calculated by the Monte Carlo method using the approximation of separable conformation energies and the conformation energies computed for two disaccharide pairs in heparin. From x‐ray scattering in a relatively small‐angle region, the conformation of heparin is not the ordered 21 helix conformation but the coil conformation obtained by the Monte Carlo calculation. It is expected, from x‐ray scattering in a relatively wide‐angel region, that the sulfate groups of heparin maintain about 7 Å between them.