bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformations of a monodisperse homohexapeptide, Nps‐[Glu(OBzl)]6‐NHEt, and its critical concentration of β‐form formation in solution
Authors: Okahashi Kenji , Ikeda Shoichi
Published: December 2004

Nps‐[Glu(OBzl)]6‐NHEt has been prepared by coupling Nps‐[Glu(OBzl)]2‐OH with HCl,H‐[Glu(OBzl)]4‐NHEt by means of dicyclohexylcarbodiimide. The ir spectra of its nujol mull show that the hexapeptide has the β‐structure of antiparallel chains. When it is dissolved in dioxane or ethylene dichloride, the hexapeptide consists of a mixture of the β‐form and the solvated σ‐form, but the β‐form can exist only above a certain critical concentration. The critical concentration is about 0.4g dl−1 in dioxane and 0.08g dl−1 in ethylene dichloride, and the content of β‐form increases with increasing concentration above it. The CD of the dioxane and ethylene dichloride solutions shows concentration dependence in visible and uv regions.
Vibrational approach to the dynamics of an α‐helix
Authors: Levy Ronald M. , Karplus Martin
Published: December 2004

The dynamics of a finite α‐helix have been studied in the harmonic approximation by a vibrational analysis of the atomic motions about their equilibrium positions. The system were represented by an empirical potential energy function, and all degrees of freedom (bond lengths, bond angles, and torsional angles) were allowed to vary. The complete results were compared with a more restrictive model in which the peptide dihedral angle was kept rigid; also, a model potential excluding hydrogen bonds was examined. Thermal fluctuations in the backbone dihedral angles ϕ and ψ are 12° to 15°. The fluctuations of adjacent dihedral angles are highly correlated, and the correlation pattern is affected by the flexibility of the peptide dihedral angle. Time‐dependent autocorrelations in the motion of ϕ and ψ appear to decay due to dephasing in less than 1 psec, while the motions of the carbonyl oxygen and amide hydrogens out of the peptide plane are more harmonic. Length fluctuations have been evaluated and exhibit a strong end effect; the calculated elastic modulus is in agreement with other values. Rigid and adiabatic total energy surfaces corresponding to dihedral angle rotations in the middle of the helix have been obtained and compared with the quadratic approximation to those surfaces. The magnitudes and correlations between the fluctuations obtained by averaging over the adiabatic energy surface most closely resemble the vibrational results. Of particular interest is the fact that hydrogen bonds play a relatively small role in the local dihedral angle fluctuations, though the hydrogen bonds are important in the energy of overall length changes.
Infrared spectra of the N‐acetyl‐N′‐methylamides of glycine, L‐alanine, and L‐leucine in dilute solutions of chloroform and carbon tetrachloride
Authors: Maxfield F. R. , Leach S. J. , Stimson E. R. , Powers S. P. , Scheraga H. A.
Published: December 2004

We have examined the NH stretching frequencies of N‐acetyl‐N′‐methyl‐L‐alanineamide (blocked Ala), N‐acetyl‐N′‐methylglycineamide (block Gly), and N‐acetyl‐N′‐methyl‐L‐leucineamide (blocked Leu) in chloroform using irspectroscopy. Their spectrum of blocked Leu in carbon tetrachloride was also obtained. A major absorption band at 3450 cm−1 is attributed to the unperturbed NH stretching frequency. Another major band at 3437 cm−1 (for Ala) or 3432 cm−1 (for Leu) is attributed to conformations in which the NH stretching frequency is perturbed by the spatial proximity of the Cβ atom. An absorption band between 3300 and 3370 cm−1, which has in the past been assigned to the intramolecular hydrogen‐bonded NH in the C conformation, was found to be concentration dependent and could not be observed below 5 × 10−4M in chloroform; thus we find no evidence for a strongly hydrogen‐bonded NH in the C conformation in chloroform. An absorption band at 3416 cm−1 was observed in chloroform solutions of blocked Gly, and a similar absorption appeared as a shoulder on the 3437‐ and 3432‐cm−1 bands of blocked Ala and blocked Leu, respectively, in the same solvent. These bands, occurring near 3416 cm−1, may be assigned to extended (C5) conformations [Avignon et al., Biopolymers 8, 69 (1969)]. In CCl4 the spectrum of blocked Leu remained concentration dependent below 2.8 × 10−4M, with the 3300–3370‐cm−1 band progressively weakening and shifting to higher frequencies on dilution from higher concentrations. Analysis of the spectra indicates that there is considerable flexibility in the blocked single residues, in agreement with the results of conformational energy calculations.
Origin of multipeak behavior in the NMR spectra of poly(L‐glutamic acid)
Authors: Lader H. J. , Mandelkern L.
Published: December 2004

The previous report that poly(L‐glutamic acid) exhibits doubled resonances in the helix–coil transition region by either proton or carbon‐13 nmr resolves the question of whether or not this behavior is limited to uncharged polypeptides in organic solvents, as had been previously thought. In the present work, we show that the underlying principle causing this anomalous double‐peak behavior is due to molecular‐weight polydispersity of the sample. The molecular‐weight range in which this phenomenon is observed is largely dependent on the values of σ, the nucleation or cooperativity factor. The principles developed are shown to encompass all classes of polypeptides in a very natural way and to explain the key experimental data in the literature.
Ionic strength‐dependent conformational transitions of chromatin. Circular dichroism and thermal denaturation studies
Authors: Fulmer Andrew W. , Fasman Gerald D.
Published: December 2004

High‐molecular‐weight chicken erythrocyte chromatin was prepared by mild digestion of nuclei with micrococcal nuclease. Samples of chromatin containing both core (H3, H4, H2A, H2B) and lysine‐rich (H1, H5) histone proteins (whole chromatin) or only core histone proteins (core chromatin) were examined by CD and thermal denaturation as a function of ionic strength between 0.75 and 7.0 × 10−3M Na+. CD studies at 21°C revealed a conformational transition over this range of ionic strengths in core chromatin, which indicated a partial unfolding of a segment of the core particle DNA at the lowest ionic strength studied. This transition is prevented by the presence of the lysine‐rich histones in whole chromatin. Thermal‐denaturation profiles of both whole and core chromatins, recorded by hyperchromicity at 260 nm, reproducibly and systematically varied with the ionic strength of the medium. Both materials displayed three resolvable thermal transitions, which represented the total DNA hyperchromicity on denaturation. The fractions of the total DNA which melted in each of these transitions were extremely sensitive to ionic strength. These effects are considered to result from intra‐ and/or internucleosomal electrostatic repulsions in chromatin studied at very low ionic strengths. Comparison of the whole and core chromatin melting profiles indicated substantial stabilization of the core‐particle DNA by binding sites between the H1/H5 histones and the 140‐base‐pair core particle.
Poly(ε‐L‐lysine): Synthesis and conformation
Authors: Kushwaha D. R. S. , Mathur K. B. , Balasubramanian D.
Published: December 2004

The synthesis of poly(ε‐L‐lysine) is described. This is a poly(ε‐amino acid) in which the ε‐amino group of lysine is condensed with the α‐carboxyl group to produce a chain backbone that is a variant of the usual one seen in proteins and the side chain is the α‐amino group. Conformational studies of poly(ε‐L‐lysine) and its t‐butyloxycarbonyl derivative suggest the likelihood of a chain order that is formally similar to the antiparallel pleated‐sheet conformation of proteins.
Dynamic light scattering in a flow—a new method of particle anisotropy investigation
Authors: Lomakin A. V. , Noskin V. A.
Published: December 2004

This paper deals with the light scattering from particles rotating in a flow with a transverse velocity gradient. It is theoretically substantiated and experimentally proved that the scattered light spectrum contains reliable information of the particle configuration and dimensions. The proposed technique may prove also very promising for the analysis of particle polydispersion.
Monte carlo simulation of the solvent structure in crystals of a hydrated cyclic peptide
Authors: Hagler A. T. , Moult J. , Osguthorpe D. J.
Published: December 2004

The Monte Carlo simulation of the structure of the 16 ordered and disordered waters in the unit cell of crystals of the cyclic peptide cyclo(‐L‐Ala‐L‐Pro‐D‐Phe)2 is reported. The water structure has been characterized in terms of the statistically averaged positions of the individual molecules, their root‐mean‐square movements about these positions, the probability of finding a water in a given spatial position in the crystal (probability maps), and examination of individual configurations of the system. In this way a picture is obtained of the water structure, including water orientations (hydrogen positions), the hydrogen‐bonding network, and fluctuations in these structural features, to a degree hitherto unavailable either from experimental or theoretical studies. In addition, the variation in water structure in various peptide environments was studied and correlated with the energetics of the individual water molecules. Variations in the crystalline environment of different water molecules lead to energy differences of as much as 4–5 kcal/mol in their average energies. Similarly, differences are observed in the water–peptide and water–water components of the energy. Two different water potentials were tested. The results were compared with experimental data in terms of mean positions, root‐mean‐square movements, and the Fourier transform of the simulated water structure. The agreement factor (R factor) calculated from the theoretical water probability distribution was 18.8% compared to the x‐ray value of 14.5%, and the value of 28% when the water is omitted.
31P‐NMR studies of DNA in nucleosome core particles
Authors: Shindo Heisaburo , McGhee James D. , Cohen Jack S.
Published: December 2004

31P Nmr parameters (δ, T1, W1/2, and NOE) were measured for the DNA in nucleosome core particles at three frequencies and compared with similar data for the histone‐free DNA. An essentially linear relationship was found between the frequency of observation and line‐width for the single broad envelope of 31P resonances of the DNA in the nucleosome cores. We attributed this largely to chemical shift dispersion, with smaller contributions from chemical shift anisotropy and dipolar broadening. These results suggest the presence of different environments for phosphorus atoms in the core particles. However, within the accuracy of the method, no asymmetry in the resonance could be detected, which would tend to rule out any significant degree of DNA “kinking.” To investigate the interactions of the DNA and histones within the core particles we also studied transitions induced by urea and by temperature. Urea caused two stepwise increases in linewidth, which we attributed to conformational changes. A biphasic transition was also observed in the temperature profile, consistent with previous optical studies [Weischet et. al. (1978) Nucleic Acids Res. 5, 139]. Various models with different types of local mobility were examined by the relaxation theory. A model of isotropic motion having a broad distribution of correlation times gave a fairly good fit to the 31P‐nmr data.
Reversion of the B to A transition of DNA induced by specific interaction with the oligopeptide distamycin A
Authors: Minchenkova L. , Zimmer Ch.
Published: December 2004

The effect of the DNA‐binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.

The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B‐conformation.
Enzymatic depolymerization of lamellar single crystals of nigeran
Authors: Marchessault R. H. , Revol J.‐F. , Bobbitt T. F. , Nordin J. H.
Published: December 2004

Lamellar single crystals of the α‐glucan: nigeran have been subjected to controlled enzymic degradation as an approach to understanding polysaccharide organization in these crystals. Analysis of both reactant and products by various methods argues that a situation exists where the crystals are inaccessible at 20°C but become increasingly accessible as the temperature approaches that of solution for the crystals in water. One has to conclude that chain folds are inaccessible to enzymes at 20°C and become increasingly accessible as one approaches the “melting temperature.” This could be due to increased mobility of the surface chains as temperature is raised, which produces large dynamic loops and makes enzyme degradation possible. The general conclusion is that nigeran single‐crystal surfaces are disordered and increasingly mobile close to their dissolution temperature in water.
Transformation of the ϕ‐ψ plot for proteins to a new representation with local helicity and peptide torsional angles as variables
Authors: Peticolas Warner L. , Kurtz Beth
Published: December 2004

A new representation of protein structure is obtained by the angular coordinate transformations ηi = (ϕi+1−ψi)/2 and ξi = ϕi+1+ψi with careful mathematical attention to the cyclical boundary conditions of all of the variables involved. From published ϕ‐ψ data it is possible to obtain a new η‐ξ plot. As the angle ξi is varied from – 180° through 0° to + 180° in this plot, the local helicity of the polypeptide chain changes continuously and contiguously without sudden reversals in handedness. The variable, ηi, gives the torsional position of the ith peptide group. Some peptide groups in proteins, such as the second peptide residue in a type II β‐turn, are nonhydrogen‐bonded and can undergo considerable torsional oscillation. In such cases the η angle should be represented by a line whose length reflects the allowed dynamical variations in the peptide torsional position. Certain peptide residues in proteins may be able to undergo a complete torsional rotation of 360°. Such residues would be represented on the η‐ξ plot as a straight line across the plot parallel to the abscissa. Other examples of the possible usefulness of this plot are also given.
Syn–anti equilibrium of purine bases in dinucleoside monophosphates as studied by proton longitudinal relaxation
Authors: Chachaty Claude , Perly Bruno , Forchioni Alain , Langlet Gérard
Published: December 2004

The preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10−2M neutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ϒ of the standard deviation between the isotropic reorientation correlation times τR derived from the relaxation rates of these protons. The average H(1′) – H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τR governing the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ⇄ S interconversion of the ribose ring. For 10−10 < τR < 2 × 10−10 sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 109 sec−1.

The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60° < ϒ < 80° (syn) and 180° < ϒ < 210° (anti). For ribose S conformer, it is observed that this orientation is mainly syn with 5° < ϒ < 90°. The average H(1′) – H(8) distance provides semiquantitative information on the overall syn or anti orientations of the base in each nucleoside moiety. At 298 K the population of the anti conformer is found to increase in the order A‐ pG < Ap‐G ∼ Gp‐A < Ap‐A < A‐pA < G‐pA. A more detailed analysis of relaxation data shows that the maximum possible fraction of the stacked form of dinucleotides, due to the occurrence of N‐anti conformers in both nucleoside moieties, is in the order ApG < GpA < ApA, in agreement with previous works, with however smaller values.

Lastly the deuteron linewidth in position 8 of the bases indicates a syn–anti transition rate of the order of 109 sec−1 at room temperature, without noticeable effects therefore on the proton relaxation.
Rigidity of fibrin gels as measured by quasielastic light scattering
Authors: Gelman R. A. , Gladner J. A. , Nossal R.
Published: December 2004

The strength of fibrin gels has been investigated by a recently developed laser light scattering technique for determining the shear modulus of soft gels. By this method, changes in the modulus were monitored as a function of time without perturbing the material. Fibrin gels were crosslinked with blood coagulation factor XIII. Rigidity measurements and SDS–polyacrylamide gel electrophoresis were used to correlate gel strength with the number of covalently bonded subunit chains. The modulus was found to vary linearly with the number of crosslinks until maximum rigidity was achieved.
Physicochemical investigation of k‐carrageenan in the random state
Authors: Vreeman H. J. , Snoeren T. H. M. , Payens T. A. J.
Published: December 2004

Light‐scattering, viscosity, and sedimentation experiments on aqueous solutions of k‐carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long‐range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer‐Fixman analysis, giving a value for the Mark‐Houwink coefficient under theta‐conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark‐Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light‐scattering radius. The relations between molecular parameters are corrected for the poly‐dispersity of the sample.
Crystal and molecular structure of isoleucinomycin, cyclo[‐(D‐Ile‐Lac‐Ile‐D‐Hyi)3‐](C60H102N6O18)
Authors: Pletnev V. Z. , Galitskii N. M. , Smith G. D. , Weeks C. M. , Duax W. L.
Published: December 2004

The crystal structure of a synthetic analog of valinomycin, cyclo[‐(D‐Ile‐Lac‐Ile‐D‐Hyi)3‐] (C60H102N6O18), has been determined by x‐ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds NH…︁OC, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso‐valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L‐Lac residues, the less crowded face.
Structurally symmetrical, easily polarizable hydrogen bonds between side chains in proteins and proton‐conducting mechanisms. III
Authors: Kristof Wolfgang , Zundel Georg
Published: December 2004

(L‐Cys)n, (L‐Lys)n, and (L‐Glu)n were studied by ir spectroscopy in terms of their degree of deprotonation or protonation. It is shown that structurally symmetrical, easily polarizable SH ⃛S− ⇌ −S ⃛HS, N+H ⃛N ⇌ N ⃛H+N, and OH ⃛O− ⇌ −O ⃛HO hydrogen bonds are formed between the side chains. The different wave number distributions of the ir continua caused by these hydrogen bonds show that the barrier in the double‐minimum proton potential decreases in the series of these hydrogen bonds. The stability of these hydrogen bonds against hydration increases in this series. The OH ⃛O− ⇌ −O ⃛HO bonds are not broken by small amounts of water. With (L‐Cys)n the formation of easily polarizable hydrogen bonds and a β‐structure–coil transition are strongly interdependent. As a result of this coupling effect, the β‐structure–coil transition becomes cooperative. With (L‐Glu)n, the formation of the polarizable hydrogen bonds and the observed conformational change are independent processes. The (L‐Glu)n conformation changes from α‐helix to coil only if more than 80% of the residues are deprotonated. Finally, on the basis of the various types of easily polarizable hydrogen bonds, charge shifts in active centers of enzymes and the proton‐conducting mechanism through hydrophobic regions of biological membranes are discussed.
Use of natural‐abundance 15N‐nmr spectroscopy to investigate the secondary structure of peptides: Gramicidin S
Authors: Hawkes Geoffrey E. , Randall Edward W. , Hull William E. , Convert Odile
Published: December 2004

The natural‐abundance 15N‐nuclear magnetic resonance (nmr) spectrum of the cyclic decapeptide gramicidin S has been measured and assigned in the solvents dimethyl sulfoxide, methanol, and 2,2,2‐trifluoroethanol. Three methods have been investigated to distinguish between peptide groups which are exposed to or shielded from the solvent. The solvent dependence of the 15N chemical shift is correlated with the two types of peptide group in gramicidin Sthose with the carbonyl group exposed or shielded from the solvent. The second method monitors the lability of the NH proton (via the collapse of the reduced 15N‐1H coupling) in the presence of added base used to promote intermolecular exchange—peptide protons shielded from the solvent exchange more slowly. The third method looks at the temperature dependence of the 15N chemical shifts in dimethyl sulfoxide. Here the data are not so distinctive as to allow the differentiation between solvent‐exposed or shielded NH bonds at all peptide groups.
Transport properties of oligomeric subunit structures
Authors: Bernal José M. García , De La Torre José García
Published: December 2004

The translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well‐known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulated.
Physical properties of type i collagen in solution: Structure of α‐Chains and β‐ and γ‐components and two‐component mixtures
Authors: Silver F. H. , Trelstad R. L.
Published: December 2004

The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α‐chains and β‐ and γ‐components are 1.550 ± 0.08 × 10−7, 1.000 ± 0.05 × 10−7, and 0.835 ± 0.04 × 10−7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α‐chain), 21.5 nm (β‐component), and 25.7 nm (γ‐component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α‐chains and β‐and γ‐components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
Spectroscopic investigations of peptide 401 from bee venom
Authors: Walde P. , Jäckle H. , Luisi P. L. , Dempsey C. J. , Banks B. E. C.
Published: December 2004

The circular dichroism (CD) and 1H‐nmr properties of peptide 401, a bee venom component with 22 amino acid residues and two disulfide bridges, have been studied under a variety of conditions and compared with those of the structurally related octadecapeptide apamin. The major component of the relatively intense CD signal in the 200–230‐nm region in both cases probably arises from the rigid asymmetric ring structures of the disulfide bridges. CD spectra are practically unaffected by pH (in the region 1–7), solvent (water, trifluoroethanol, dioxane/water mixtures), concentration of peptide, or additions of salt (guanidinium chloride, KCl). Temperature changes (in the range 20–59°C) have only a modest influence. For both apamin and peptide 401, reduction of the two disulfide bridges results in a dramatic change of the CD spectrum, which acquires the characteristic form of a random coil. Preliminary 1H‐nmr data are presented for both the reduced and the oxidized form. Several resonance peaks could be assigned on the basis of the theoretical random‐coil spectrum. In the oxidized forms, six slowly exchangeable amide protons could be found in a spectrum taken at low pH, which are ascribed to intramolecular hydrogen bonds. Each of the four protons of the two histidine residues of peptide 401 appears as two distinct resonance peaks in the oxidized form but not in the reduced form. This is interpreted as arising from conformational heterogeneity of peptide 401.
Simulations of the solvent structure for macromolecules. I. Solvation of B‐DNA double helix at T = 300 K
Authors: Corongiu Giorgina , Clementi Enrico
Published: December 2004

Monte Carlo simulations are reported for a system of 447 water molecules enclosing a B‐DNA double‐helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen‐bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption–desorption experiments on related systems. The expected main features for the structure of water molecules solvating B‐DNA with Na+ counterions are briefly discussed at the end of the paper.
Physicochemical parameters of partially hydrolyzed S. salivarius levan fractions
Authors: Stivala S. S. , Zweig J. E.
Published: December 2004

The fractions obtained from the partially hydrolyzed branched Streptococcus salivarius levan were examined in solution. Sedimentation coefficients, S0, intrinsic viscosities, [η], weight‐average molecular weights, Mw, and radii of gyration were obtained from sedimentation velocity, viscosity, and light‐scattering measurements. Double logarithmic plots of [η] vs Mw and S0 vs Mw each yielded two linear segments intersecting at Mw ≈ 105. Hydrodynamic data suggest that fractions of Mw > 105 behave as compact spheres, whereas for Mw < 105, the particles are best characterized as linear random coils. Calculations based on theories of random coils and spheres support the above observations.
Stability and geometry of hydrogen‐bonded complexes of peptides
Authors: Madison Vincent , Lasky Jerry , Currie Bruce
Published: December 2004

Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2‐pyridone and 2,6‐dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L‐Pro‐X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the ‐CONH‐ of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m−1 for the secondary amide and 50m−1 for the tertiary amide. For pyridone the binding constant is about 45m−1 for either the secondary or tertiary amide. For comparison self‐dimerization constants determined by vapor‐pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m−1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L‐Pro‐Gly), respectively.
Theoretical studies on β‐lactam antibiotics. IV. Conformational analysis of novel β‐lactam antibiotics and the binding specificities of crosslinking enzyme(s) and β‐lactamases
Authors: Vasudevan T. K. , Rao V. S. R.
Published: December 2004

Conformational‐energy calculations were carried out on the new family of β‐lactam antibiotics (viz., thienamycin, PS‐5, 1‐oxa‐ and 1‐thiapenems, and their close analogs); these exhibit broad‐spectrum antibacterial activity and stability towards β‐lactamase‐producing strains. The bicyclic ring system in all the compounds studied was found to be highly rigid and to favor only one conformation. This is in contrast to findings in penicillins, where the five‐membered ring assumes two puckered conformations. The relative orientations of the bicyclic ring system and the nature and configuration of the substituent at C‐5 position, besides nonplanarity of the lactam peptide bond, are shown to be important for biological activity. The present study, in agreement with x‐ray studies, predicts that the lactam peptide bond in 1‐carbapenem is more nonplanar than in 1‐thiapenem. These studies also suggest that the conformational requirement of bicyclic ring system to bind to crosslinking enzyme(s) and β‐lactamases is very similar.
Mechanism of DNA denaturation in the presence of manganese ions
Authors: Yurgaitis A. P. , Lazurkin Yu. S.
Published: December 2004

The unwinding of DNA strands in the presence of small concentrations of Mn2+ ions (2 × 10−4−4 × 10−4M) has been studied. The process of unwinding is nonequilibrium; the DNA strands are gradually unwound at a constant temperature corresponding to the beginning of the melting curve. There is no true renaturation in the partially melted DNA. It is shown in the paper that these effects are due to the aggregation of the unwound DNA regions. The Mn2+ ions are responsible for the binding of the unwound strands. The aggregation precludes renaturation, shifts the equilibrium towards the melted state, and causes slow unwinding at a constant temperature. The binding of denaturated regions seems to occur through the guanines.
Polarized luminescence and mobility of tryptophan residues in polypeptide chains
Authors: Semisotnov G. V. , Zikherman K. Kh. , Kasatkin S. B. , Ptitsyn O. B. , Anufrieva E. V.
Published: December 2004

Polarized luminescence was used to study the mobility of tryptophan residues in polypeptide chains of different chemical composition and structural organization. It has been shown that the luminescence depolarization of tryptophan residues in coillike, helical, and β‐structural polypeptide chains is mainly caused by “fast” torsional vibrations and “slow” rotational isomerization of indole groups of tryptophan side chains. The characteristics of these types of motions are practically the same for tryptophan residues included in coillike chains of different chemical structure. Helix–coil transitions in copolymers of glutamic acid and lysine with tryptophan (Glu, Trp) and (Lys, Trp) (where side groups of tryptophan residues weakly interact with the surrounding side groups) do not appreciably change the amplitude of torsional vibrations or rotational isomerization. At the same time, in the helical state of glutamic acid–leucine–tryptophan copolymers (Glu, Leu, Trp) and in the β‐structural state of (Lys, Trp) copolymers (where direct interactions of Trp side groups with other side groups are possible), the amplitudes of the torsional vibrations are smaller and the rotational isomerization times larger than in the coil. The transition of (Glu, Leu, Trp) polypeptide chains into a compact state is accompanied by a marked decrease of both “fast” and “slow” intra‐molecular mobility and by an increase of the contribution made by the rotation of the macromolecule as a whole, as shown by the decrease of the luminescence polarization.
Binding of multivalent ligands to mobile receptors in membranes
Authors: Dwyer John D. , Bloomfield Victor A.
Published: December 2004

We present a model to describe the equilibrium binding properties for the attachment of multivalent ligands to mobile receptors in membranes. The interaction is assumed to be governed by two inherently different association constants. The first of these controls the initial attachment of a ligand to its first receptor, by adsorption from bulk solution, while the second governs subsequent receptor attachments to this initially bound ligand by rearrangement of membrane‐bound species. Simple statistical mechanical expressions are used to estimate contributions to these association constants that are attributable to losses of translational and rotational degrees of freedom occurring upon binding. Suitable combinatorial expressions are combined with these association constants to derive the concentrations of bound species and the binding isotherms. Examination of these expressions leads to the conclusion that once initially bound, most multivalent ligands will be completely saturated by receptors and that partially bound species will be essentially nonexistent. This behavior is attributable to the generally high overall affinities of these ligands and to the mobility of the membrane‐bound species. Some specific comments are made, in light of this theory, about the binding of cholera toxin to its membrane receptor, the ganglioside GM1.
Transient electric birefringence study of the length and stiffness of short DNA restriction fragments
Authors: Elias John G. , Eden Don
Published: December 2004

Transient electric birefringence measurements of the rotational diffusion constant of five short restriction fragments of the plasmid pBR322 show that the hydrodynamic length is independent of sodium ion concentration in the range of 0.2 to 2.5 mM. The fragments are too stiff to be modeled as wormlike molecules. The rotational relaxation times of the fragments, which range from 64 to 124 base pairs, have been used to calculate the rise per base pair using six different theoretical expressions for the length dependence of the rotational diffusion coefficient of straight cylinder. The best estimate for the rise per base pair of Na‐DNA in solution is 3.3 ± 0.1 Å.
Simulations of the solvent structure for macromolecules. II. Structure of water solvating Na+‐B‐DNA at 300 K and a model for conformational transitions induced by solvent variations
Authors: Corongiu Giorgina , Clementi Enrico
Published: December 2004

The structure of water and its interaction energy with a fragment of B‐DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen‐bonded filaments of water are reported and discussed. The stabilization of the B‐conformation induced by the solvent with counterion (“ion‐induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x‐ray and neutron beam) data on DNA insolution.
Dependence of laser light scattering of DNA on NaCl concentration
Authors: Kam Zvi , Borochov Nina , Eisenberg H.
Published: December 2004

We show that the persistence length a of DNA, derived from total intensity laser light scattering of linear Col E1 DNA and corrected for excluded‐volume effects, varies from about 68 nm in 0.005M NaCl to about 40 nm in 0.2M NaCl, leveling off to a constant value (about 27 nm) at high NaCl (1–4M) concentration. These observations do not agree with current views on the effect of electrostatic charge and ionic conditions on DNA dimensions. The apparent diffusion constant Dapp, determined from laser light scattering autocorrelation as a function of scattering vector q, at NaCl concentrations 0.005–4M, correctly yields the translational diffusion coefficient Dt at low values of q and scales with molecular dimensions rather than segment length at high values of q; thus, Dapp/Dt yields a universal curve when plotted against q2R, where Rg is the radius of the gyration. The sedimentation coefficients s at 0.1 and 0.2M NaCl concentration closely agree with the well‐tested empirical relations, and a combination of s, Dt, and the appropriate density increments yield correct molar masses over the whole salt concentration range. Approximate constancy of DtRg indicates limited draining in translational flow. We present some observations and thoughts on the regimes in which a dependence of the correlation decay times on q3 rather than q2 applies. We conclude that quasielastic laser light scattering discloses little information about dynamics of internal motion of DNA chains.
Investigation of structural aspects and classification of plant sulfated polysaccharides on the basis of the optical properties of their complexes with metachromatic dyes
Authors: Stone Audrey Larack , Childers Lillian G. , Bradley Dan F.
Published: December 2004

Optical properties of complexes of plant sulfated polysaccharides with basic dyes have been examined. Spectral shifts in the dye have been used as the basis for quantitative analysis of anionic sites in these compounds. The κ‐ and λ‐carrageenans have been shown to give characteristically different titration curves. Other, similar, plant extractives have been shown to fall into one or the other of these two classes. Cotton effects in the region of the absorption spectrum of the dye have been discovered, indicating the presence of long range order and asymmetry in the λ‐C2 carrageenan. The relation of the optical effects to each other and to the structure of the polymer is discussed briefly in terms of recent developments in the theory of metachromasy.
Characterization of a second helical amylose modification
Authors: Zaslow B.
Published: December 2004

From x‐ray diffraction data, a pseudohexagonal unit cell with a = b = 14.94 A. and c = 7.93 A. has been obtained for partially dried precipitate of amylose and tertiary butyl alcohol. Geometrical considerations establish a helical amylose configuration which has seven glucose residues per helix turn.
Conformational aspects of polypeptides. XI. The nitroaromatic effect
Authors: Goodman Murray , Felix Arthur M. , Deber Charles M. , Brause Allan R. , Schwartz Gerald
Published: December 2004

β‐ρ‐Nitrobenzyl‐L‐aspartate and γ‐p‐nitrobenzyl‐L‐glutamate were synthesized, and copolymers were prepared respectively with β‐benzyl‐D‐(and ‐L‐) aspartate and γ‐benzyl‐L‐glutamate. In chloroform there is a reversal in helical sense of poly‐β‐benzyl‐L‐aspartate to the right‐handed sense of poly‐β‐p‐nitrobenzyl‐L‐aspartate when 26–32 mole‐% of the latter is present in the copolymer. A new conformationally dependent Cotton effect was found for these copolymers at 370 mμ. In dimethylformamide there is a transition from the random conformation of poly‐β‐benzyl‐D‐(or ‐L‐) aspartate to the right‐handed helical sense of poly‐β‐p‐nitrobenzyl‐L‐aspartate. The formation of a side chain helix is proposed to explain the enhanced rotatory properties for the nitrated aspartates. In the glutamate series no helix reversal or unusual rotatory properties were observed in DMF or chloroform.
Conformational dependence of the Raman scattering intensities from polynucleotides. III. Order‐disorder changes in helical structures
Authors: Small Exoch W. , Peticolas Warner L.
Published: December 2004

Raman spectra are presented on ordered and presumably helical structures of DNA and RNA as well as the poly A·poly U helical complex, polydAT, and the helical aggregates of 5′‐GMP and 3′‐GMP. The changes in the frequency and the intensity of the Raman bands as these structures undergo order‐disorder transitions have been measured. In general the changes we have found can be placed into three categories: (1) A reduction in the intensities of certain ring vibrations of the polynucleotide bases is observed when stacking or ordering occurs (Raman hypochromism). Since the ring vibrational frequencies are different for each type of base, we have been able to obtain some estimate of average amount of order of each type of base in partially ordered helical systems. (2) A very large increase in the intensity of a sharp, strongly polarized band at about 815 cm−1 is observed when polyriboA and polyriboU are formed into a helical complex. Although this band is not present in the separated chains at high temperature, a broad diffuse band at about 800 cm−1 is present. The 815 cm−1 band undoubtedly arises from the vibrations of the phosphate‐sugar portions of the molecule and provides a sensitive handle to the back‐bone conformation of the polymer. This band also appears upon ordering of RNA, formation of the helical aggregate of 5′‐riboGMP, and to some extent in the selfstacking of the polyribonucleotides polyA, polyU in the presence of Mg++, PolyC, and polyG. No such intense, polarized band is found, however, in ordered DNA, polydAT, or the 3′‐riboGMP aggregate, although there is a conformationally independent band at about 795 cm−1 in DNA and polydAT. (3) Numerous frequency changes occur during Conformational changes. In particular the 1600–1700 cm−1 region in D2O shows significant conformationally dependent changes in the CO stretching region analogous to the changes in this region which have been observed in these substances in the infrared. Thus, Raman scattering appears to provide a technique for simultaneously observing the effects of base stacking, backbone conformation and carbonyl hydrogen bonding in nucleic acids in moderately dilute (10–25 mg/ml) aqueous solutions.
Melting experiment concerning the topological structure of closed circular double‐stranded DNA
Authors: Giacomoni Paolo U.
Published: December 2004

A melting experiment was performed on the whole set of populations of the replicative form of ϕX174 DNA, which can be obtained treating this DNA with rat liver nicking‐closing enzyme in the presence of ethidium bromide. Gel electrophoresis performed by loading the DNA samples at neutral and alkaline pH allows separation of these populations in discrete sets of bands, which can then be compared. The outcome of the experiments indicates that in the range of electrophoretic mobilities which can be explored, no band is formed exclusively by circular complementary strands which can be separated by alkaline denaturation. These results are compared with what would be expected if double‐stranded closed circular DNA had structures other than the canonical double helix. Under nonrestrictive hypotheses, the experiments reported allow one to obtain a minimum estimate of the absolute value of the linking number of a closed circular double‐stranded DNA: for native ϕX174 RF DNA, the linking number appears to be greater than 12 (in absolute value). Some data on the electrophoretic mobility of denatured closed circular duplexes are reported, which still wait for a physicochemical interpretation.
A stereospecific complex of poly(I) with ammonium ion
Authors: Howard Frank B. , Miles H. Todd
Published: December 2004

We describe conditions which lead to complete helix formation of poly(I) in the presence of NH. Binding of NH is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH–poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH. A stereospecific model is proposed for the NH–poly(I) helix in which the N of NH is located on the axis of the four‐stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
Conformations of cyclic peptide/calcium complexes in solution
Authors: Hughes Donald W. , Deber Charles M.
Published: December 2004

Synthetic cyclic octapeptides of general structure cyclo[Glu(γOBzl)‐Sar‐Gly‐(N‐R)Gly]2 (R = n‐hexyl and cyclohexyl) transport calcium ions selectively across organic phases and phospholipid membranes. We have now used proton nmr spectroscopy (360 MHz) to study the solution conformation(s) of their calcium complexes. When Ca(ClO4)2 was added to solutions of these peptides in CDCl3, nmr spectra of the resulting calcium complexes were characteristic of a single C2‐symmetric conformer. From a Karplus‐Bystrov analysis of vicinal coupling constants in both the peptide backbone and Glu side chain (treated as an ABCC′MX spin system), in conjuction with model‐building studies, a structure was proposed in which the calcium ion is bound in an octahedral‐type complex by the four (coplanar) carbonyl groups of the (all‐trans) Glu‐Sar and Gly‐(N‐R)Gly peptide bonds. Occurrence of preferred rotamers about Glu side chain Cα–Cβ bonds indicated that restricted rotation in peptide side chains arises upon calcium binding.