bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions of mono‐ and divalent counterions with alkali‐ and enzyme‐deesterified pectins in salt‐free solutions
Authors: Thibault J. F. , Rinaudo M.
Published: May 2005

The free fractions of monovalent and divalent counterions were determined on salt‐free solutions of pectins. The effects of charge density, distribution of the carboxyl groups, polymer concentration, and the nature of the counterion were investigated by determinating the calcium and sodium activity coefficients (with specific electrodes) and by measuring the transport parameters (by conductimetry). Poor agreement for calcium ions was found with the Manning theory. The strong binding of these ions to highly charged polymers, which is ascribed to a dimerization process was demonstrated in very dilute solutions.
Diffusion coefficients of segmentally flexible macromolecules with two sphrical subunits
Authors: de la Torre Joseacute; García , Mellado Pelayo , Rodes Vicente
Published: May 2005

The translational and rotational diffusion coefficients have been calculated for a simple, segmentally flexible model: the hinged dumbbell (HD). In the HD, two spherical subunits are attached to an universal joint by means of frictionless connectors. In addition to the case in which hydrodynamic interactions are neglected (NI), we have also considered two more cases, including hydrodynamic interaction by means of the Kirkwood‐Riseman approximate treatment (KR) and using accurate procedure based in the series expansions for the two‐sphere diffusion tensor (SE). Expressions for the friction coefficients of the HD are given for the three cases, and the diffusion coefficients are evaluted inverting the 9 × 9 resistance matrix, for two HDs with different dimensions. The KR treatment, which includes a contribution from the finite volume of the subunits, is shown to be an excellent approximation to the more rigorous procedure. In the NI case for rotation, the various coefficients present different deviations with respect to the SE results. A rough estimate of the errors of the NI relaxation times indicates that they may be smaller than 15% for a HD with identical beads. However, the influence of hydrodynamic interaction should be more important for the rotational diffusivity of a small sphere attached to a larger one. The error of the NI result for the translational diffusion coefficient is of about 25% for the two HDs.
Basis for large differences in the cooperativity of the formation of antiparallel β‐sheets and clusters of interacting α‐helices in isolated chains
Authors: Mattice Wayne L. , Tilstra Luanne
Published: May 2005

Configuration partition functions that describe the intramolecular formation of antiparallel β‐sheets and clusters of antiparallel interacting α‐helices are very nearly of the same form. They can be interconverted by a simple change in notation and the addition of one weighting factor for each cluster of interacting α‐helices. This extra weighting factor is the Zimm–Bragg σ which must be less than one. When it is assigned a reasonable numerical value, it plays an important role in the determination of the nature of the transition from the disordered chain to the ordered structure. It causes the formation of clusters of interacting α‐helices to be more cooperative than the formation of antiparallel β‐sheets in isolated chains.
Equilibrium theory for the binding of bivalent antibodies to regularly spaced sites on a DNA molecule
Authors: Wiegel Frederik W. , Goldstein Byron
Published: May 2005

In the autoimmune disease, Systemic Lupus Erythematosus, an individual produces antibodies that bind to his or her own DNA. In this paper we consider a single, long DNA‐like molecule in a solution containing bivalent antibodies that can bind to the DNA molecule at regularly spaced sites. The antibody can be attached to DNA by either one or two binding sites. We assume that, when an antibody molecule binds through both its sites, it spans a fixed number of free sites that remain accessible to antibody binding. In this model, antibody molecules can interdigitate along the DNA molecule. We allow steric hindrance within such interdigitating clusters of bound antibodies. We derive analytical expressions for the average number of free, monovalently bound and bivalently bound antibodies, and see how this distribution is influenced by steric hindrance and by the relative binding strengths of the singly and doubly bound antibody.
DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality
Authors: Joanicot Mathieu , Revet Bernard
Published: May 2005

Plots of end‐to‐end distance (R0) vs contour length (S) measured from electron micrographs of double‐stranded DNA molecules reveal typical power laws (R0 ∼ S3/5 and S3/4) and confirm the evident qualitative differences of structure observed when using various spreading techniques. We propose to relate these power laws to the structure dimensionality of DNA as a function of the conditions of spreading. To pursue this idea, our experimental results are compared with models of polymer conformation that incorporate the excluded volume effect.
Double‐stranded helix of xanthan: Rigidity in 0.01M aqueous sodium chloride containing 0.01 N hydrochloric acid
Authors: Zhang Lina , Liu Wei , Norisuye Takashi , Fujita Hiroshi
Published: May 2005

Six samples of Na xanthan in 0.01M aqueous NaCl containing 0.01 N HCl (pH = 2) were studied by light scattering and viscosity. This study was motivated by the finding that the intrinsic viscosity [η] fairly sharply decreased when the pH of the solvent was lowered from about 6 to 2 by adding HCl to 0.01M aqueous NaCl in which Na xanthan dissolves as rigid dimers having a double‐helical structure. The data for weight‐average molecular weight, radius of gyration, and [η] showed that Na xanthan at pH = 2 remains a dimer behaving as a semiflexible chain. Data analysis in terms of known theories for unperturbed wormlike chains yielded 0.47 ± 0.02, 2.0 ± 0.6, and 68 ± 7 nm for the contour length h per main‐chain residue, diameter d, and persistence length q of the dimer, respectively. these h and d values agreed with the pitch per main‐chain residue and the diameter of the double helix of Na xanthan in 0.01 or 0.1M aqueous NaCl. However, the q value, which was close to the intrinsic persistence length q0 ( = q in the absence of electrostatic interaction) of Na xanthan at pH = 2, was much smaller than the q0 (106 nm) of this helix. We concluded that the xanthan dimer at pH = 2 assumes a double‐helical structure, which is geometrically the same as, but is more flexible than, that at neutral pH.
Correlation between computed conformational properties of cytochrome c peptides and their antigenicity in a T‐lymphocyte proliferation assay
Authors: Vasquez Max , Pincus Matthew R. , Scheraga Harold A.
Published: May 2005

By means of conformational energy calculations, we previously showed that the antigenic strength of a series of oligopeptides (derived from the carboxyl terminal sequence of cytochrome c) in a T‐lymphocyte proliferation assay depends on their ability to adopt the α‐helix conformation. Using experimentally determined statistical weights (within the framework of the Zimm–Bragg theory for the helix–coil transition), here we present a simple free energy analysis of the ability of these peptides to adopt the α‐helix conformation in water. The experimental statistical weights have been modified to include the effect of long‐range charge–dipole interactions on helix stability. We find that there is a close correlation between the tendency of a peptide to adopt the α‐helix conformation and its ability to stimulate antigen‐primed T cells. The shortest peptide with a tendency to adopt the α‐helix conformation is also the shortest one that exhibits antigenic activity. The rapid and simple method presented here can thus be used to predict relative antigenicities for different peptides derived from cytochrome c.
Molecular mechanical studies on left‐ and right‐handed B‐DNA
Authors: Pattabiraman N. , Rao Shashidhar N. , Scott Kevin , Langridge Robert , Kollman Peter A.
Published: May 2005

Molecular mechanical simulations on base‐paired deoxyhexanucleoside phosphates, (dAdT)3 · (dAdT)3, (dTdA)3 · (dTdA)3, (dGdC)3 · (dGdC)3, and (dCdG)3 · (dCdG)3, have been carried out to assess their energetic stabilities in left‐ and right‐handed forms. These hexamers have also been simulated with alternating sugar‐puckering profiles with the combinations (purine : C2′‐endo–pyrimidine : C3′‐endo) and (purine : C3′‐endo–pyrimidine C2′‐endo). The right‐handed models have been found to be the energetically most stable structures and the left‐handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar‐phosphate backbone on the other.
Sedimentation equilibrium in macromolecular solutions of arbitrary concentration. I. Self‐associating proteins
Authors: Chatelier Ronald C. , Minton Allen P.
Published: May 2005

Relations describing sedimentation equilibrium in solutions of self‐associating macromolecules at arbitrary concentration are presented. These relations are obtained by using scaled‐particle theory to calculate the thermodynamic activity of each species present at a given radial distance. The results are expected to be valid for solutions of globular proteins under conditions such that interactions between individual solute molecules may be approximated by a hard‐particle potential. Sedimentation equilibria in solutions containing either a nonassociating solute or a solute that self‐associates according to several different schemes are simulated using the derived relations. The results of these simulations are presented in terms of the dependence of apparent weight‐average molecular weight upon solute concentration. Simple empirical relations are presented for estimating the true weight‐average molecular weight from the apparent weight‐average molecular weight, without reference to any particular self‐association scheme. The weight‐average molecular weight estimated in this fashion is within a few percent of the true weight‐average molecular weight at all experimentally realizable solute concentrations ( < 400 g/L).
Small‐angle x‐ray scattering of bovine nasal cartilage proteoglycan in solution
Authors: Stivala S. S. , Patel A. , Khorramian B. , Gregory J. D. , Damle S.
Published: May 2005

The proteoglycan subunit (PGS) from bovine nasal cartilage was examined in water and in 0.15 N LiCl by small‐angle x‐ray scattering (SAXS). The molecular weight of 2.5 × 106 and the radius of gyration, Rg = 493 Å, in 0.15 N LiCl, obtained by SAXS, are in good agreement with values reported by others for similar preparations. Values of the radius of gyration of the cross section, mass per unit length, and persistence length of the PGS are also reported. The low value of intrinsic viscosity ([η]) found in 0.15 N LiCl, and a comparison of the experimental distance distribution function to that of the theoretical distance distribution function for sphere, suggest that the PGS in salt solution approaches spherical symmetry. The much higher value of [η] in water suggests a prolate ellipsoid of low axial ratio.
Reversing‐pulse electric birefringence of poly(γ‐benzyl‐L‐glutamate). III. The temperature dependence of the transient and steady‐state behavior in cyclohexanone
Authors: Yamaoka Kiwamu , Yamamoto Shinobu , Ueda Kazuyoshi
Published: May 2005

The reversing‐pulse electric birefringence (RPEB) technique was applied to the study of the temperature effect on the electrooptical and hydrodynamic properties of a fractionated [Glu(OBzl)]n sample, which is molecularly dissolved in cyclohexanone. The aim was to develop a standard analytical method for thermal denaturation and temperature‐induced conformational transitions. The field‐on reverse and steady‐state signal, and the field‐off decay signal, were measured at 535 nm and at a constant low field strength (ca. 3 kV/cm) over a wide temperature range (5–90°C). The steady‐state birefringence and the relaxation time in the decay process were also measured at two constant temperatures (5 and 70°C) over a wide field strength range (E ≤ 20 kV/cm). By the combination of these two different sets of RPEB measurements, the unwanted effect of the high pulse field on polymer conformation at elevated temperatures could be minimized. Together with the density and viscosity of cyclohexanone measured between 5 and 95°C, the following quantities could be evaluated: the weight‐average permanent dipole moment and polarizability anisotropy, the reduced optical anisotropy factor (Δg/n), the weight‐average length, and the degree of polydispersity. All these quantities, except for Δg/n, were found to be almost independent of temperature (5–90°C) and concentration (1.54–4.27 mM).
A theoretical study of the effects of driven motion on rotational correlations of biological systems
Authors: Scalettar Bethe A. , Klein Melvin P. , Hearst John E.
Published: May 2005

We have mathematically analyzed the angular correlation of molecules subject to coupled Brownian torques and driven rotational motion. In our approach a stochastic rotation operator is used to generate the time‐dependent orientation of a Brownian particle. All required expectation values can then be computed from just a knowledge of the average of the rotation operator. In particular, the angular correlation function of molecules moving under the influence of both Brownian and driving torques can be shown to exhibit an exponential decay modulated by a periodic term arising from the nonrandom force. The associated power spectrum exhibits a resonance at a frequency characteristic of the driving torque. We discuss DNA/RNA polymerase, muscle, and flagellar systems to which our analysis is applicable.
Induced CD of DNA intercalators: Electric dipole allowed transitions
Authors: Lyng Reidar , Härd Torleif , Norden Bengt
Published: May 2005

The induced CD of an electric dipole allowed transition of a DNA intercalator has been calculated using the “matrix method” and a set of DNA ππ* transitions recently adopted for calculating the CD of DNA by Rizzo and Schellman [(1984) Biopolymers 23, 435–470]. The induced CD is strongly dependent on the angular orientation of the intercalator and only moderately dependent on its location within the intercalation pocket. The dependence of the CD on the orientation and location of the intercalator was studied for some representative conformations of di‐ and tetranucleotide duplexes of (dGdC) and (dAdT). The effect of alternative DNA transition moment directions was also tested. The orientation dependence compares well with the previously predicted 1‐2 cos2 γ dependence [B. Nordén and F. Tjerneld (1982) Biopolymers 21, 1713–1734]. Measured induced CD spectra of methylene blue (MB) intercalated in double‐stranded poly(dAdT), poly(dGdC), and calf‐thymus DNA are discussed on the basis of the results of the calculations. Major differences between the induced CD spectra are likely to reflect different modes of intercalation for the different nucleotide sequences. In particular, the concluded geometry in solution for MB intercalated in poly(dAdT) differs significantly from the corresponding geometry found in dinucleotide–intercalator crystals.
Tryptophan fluorescence studies of plasma fibronectin: Effects of environmental factors
Authors: Lai Ching‐San , Homandberg Gene , Miziorko Henry , Wolff Carl
Published: May 2005

Steady state fluorescence measurements have been used to study tryptophan fluorescence of plasma fibronectin. The native protein has an emission maximum at 337 nm with a quantum yield of 0.03. A red shift of emission maximum was observed in 3–5M urea and a further red shift in 7–8M urea. The emission maximum shifted from 337 to 345 nm when the temperature was changed from 30 to 80°C, with a midpoint of thermal denaturation at 58°C. Similarly, the emission maximum shifted from 337 to 345 nm when the solution pH was increased from 9 to 12, with a midpoint of pH transition at 10.6. The results obtained from difference absorption spectroscopy studies suggest that the unfolding of fibronectin at alkaline pH is related at least in part to ionization of tyrosine residues. Since most of the tryptophan residues are in invariant positions in homology sequences, it is suggested here that tryptophan residues are useful intrinsic probes for elucidating fibronectin structure in solution.
Changes in CD of hyaluronates and chondroitins upon periodate oxidation
Authors: Ueno Norio , Chakrabarti Bireswar
Published: May 2005

Changes in conformation of hyaluronate and chondroitin sulfates following periodate oxidation were studied by CD. We monitored the progressive oxidation of these polymers by periodic acid at 4°C in pH 5.6 buffer. The negative CD band of hyaluronate at 208 nm decreased in intensity upon oxidation and changed its sign after 16 h of oxidation. In contrast, the 208‐nm CD band of chondroitin sulfates decreased, but showed no change in sign even after 48 h of oxidation. A specific difference in solution conformation between hyaluronate and chondroitins may be responsible for the difference in oxidation‐induced dichroic behavior. The results are discussed in terms of available x‐ray diffraction analyses of these polymers.
Hydration structure and dynamics of B‐ and Z‐DNA in the presence of counterions via molecular dynamics simulations
Authors: Swamy Kandadai N. , Clement Enrico
Published: May 2005

Following our previous attempts at understanding the structural and dynamical properties of water and counterions hydrating nucleic acids, we have performed molecular dynamics simulations for B‐ and Z‐DNA. In these simulations, the nucleic acids were held rigid. In the case of B‐DNA, one turn of B‐DNA double helix was considered in the presence of 1500 water molecules and 20 counterions (K+). The simulations were performed for 4.0 ps after equilibrating the system. For Z‐DNA, we considered one turn of the double helix in the presence of 1851 water molecules and 24 counterions (K+). The simulations were carried out for 3.5 ps after equilibration. The average temperature of these simulations was ∼ 360 K for Z‐DNA and ∼ 345 K for B‐DNA. In these simulations the hydrogen atoms were explicitly taken into account. For both simulations, a fifth‐order predictor‐corrector was used for solving the translational equations of motion. The rotational motion of the water molecules was represented in terms of quaternion algebra and the rotational equations of motion were solved with a second‐order quaternion method using a sixth‐order predictor‐corrector method. A time step of 0.5 · 10−15 s was used in these simulations. The structural and the dynamical properties of water solvating the counterions, and the phosphate groups of the DNA, were computed to understand the hydration structure. Diffusion coefficients and velocity correlation functions were calculated for both ions and the water molecules. The velocity correlation functions for the ions exhibit a caged behavior. The dipole correlation functions for the water molecules indicate that the water molecules close to the helix retain the memory of their initial orientations for longer periods of time than those away from the helix. During the time period of our simulation (3–4 ps) the ion probability distributions show a well‐defined pattern and suggest limited mobility for the ions, being close to the helix.
Does DNA absorb microwave energy?
Authors: Maleev V. Ya. , Kashpur V. A. , Glibitsky G. M. , Krasnitskaya A. A. , Veretelnik Ye. V.
Published: May 2005

The microwave absorption of chicken erythrocytes and E. coli DNA aqueous solutions was studied in the 9–12‐GHz frequency range by the method of variable thickness. At the same frequencies, fragments of sonicated erythrocyte DNA (average size about 500 base pairs) and of E. coli DNA treated with DNase (most of which were 800–2800 base pairs) were investigated. In neither case was any effect of enhanced microwave absorption by DNA observed. It was shown that an excess absorption of DNA solution falls within the 1% experimental error range, provided the conductivity contribution of 1% MgCl2, required for DNase action, to the microwave absorption is taken into account.
Photoresponsive polymers: Azobenzene‐containing poly(L‐lysine)
Authors: Fissi Adriano , Pieroni Osvaldo , Ciardelli Francesco
Published: May 2005

Poly(L‐lysine) was reacted with various azo‐reagents, including p‐phenylazobenzoic acid, p‐phenylazobenzoyl chloride, and p‐phenylazobenzoic N‐hydroxy‐succinimide ester, to give polypeptides containing 5–44 mol % azobenzene units in the side chains. The conformation of the azo‐modified polypeptides was investigated in connection with their photochromic behavior caused by the trans ⇌ cis photoisomerization of the azo groups present in the side chains. In methanol/water solvent mixture, the 20% azo‐poly(L‐lysine) adopts the α‐helix conformation. The helix stability was found to be higher when the azo side chains are in cis than when they are in trans configuration. So irradiation at 340 nm (trans‐to‐cis isomerization), and alternately at 450 nm (cis‐to‐trans isomerization), produced reversible variations of the α‐helix content. In hexafluoro‐2‐propanol/water/sodium dodecyl sulfate mixture, the 43% azo‐poly(L‐lysine) adopts a β‐structure, as indicated by CD spectra. Irradiation at 340 nm caused the disruption of the β‐structure and promoted the α‐helix conformation. The effect was reversed upon irradiation at 450 nm. The photoinduced β ⇌ helix change was explained on the basis of the different geometry and hydrophobic character of the trans and the cis azobenzene units.
Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
Authors: Shenkin Peter S. , Yarmush David L. , Fine Richard M. , Wang Huajun , Levinthal Cyrus
Published: May 2005

One approach to finding the conformation of minimum energy for a complicated molecule is to perform energy minimization, perhaps coupled to more exhaustive search procedures such as dynamics or Monte Carlo sampling, from many starting conformation. Where there are geometric constraints on the conformations, as in a ring molecule, or a variable loop starting and ending in known constant regions of one of a series of homologous proteins, rapidly generating many such starting conformations, all satisfying the constraints, has been a problem in the past. We have devised an algorithm, which we call random tweak, which performs this task in the context of a torsional description of a molecule, and have used it to model the backbones of the six CDRs (complementarity determining regions) of the immunoglobulin MCPC603. These range in size from 5 to 19 residues, and have from 8 to 36 variable dihedral angles. Ensembles of 100 properly closed backbone structures for each CDR were generated under several conditions of van der Waals screening internally and against the rest of the molecule, and ensembles of 1000 were generated for selected CDRs. These structure “libraries” reveal how the geometry at the base of a CDR and the topography of the surrounding protein surface restrict the region of space that a given CDR can occupy. In accord with simple notions of chain molecule statistics, the more highly extended a CDR at its base, the more similar the possible structures and the fewer that are necessary to span the conformational space. Energy minimization and molecular dynamics studies (reported elsewhere) using these libraries to furnish starting conformations show that, as the number of residues in a CDR goes from five to nine, the number of randomly generated structures necessary to ensure that low‐lying energetic minima, such as the native conformation, will be found several times goes from a few tens to a few hundred. Some of the spatial features of an ensemble of random conformations are implicit in the histogram of the rms atomic displacements calculated for all the pairs in the ensemble. The random tweak method is carried out by setting each dihederal angle on the main chain of the variable fragment to a random value, then using an iterated linearized Lagrange multiplier technique to enforce the geometric constraints with the minimal conformational perturbation. The time required for the algorithm is linear in fragment length, and the resulting ability of the method to handle large loops makes it especially applicable to the modeling of homologous proteins. In most cases, hundreds of acceptable structures could be generated in a few hours on a VAX 11/780. Where van der Waals screening against fixed atoms need not be performed, as for isolated ring molecules, generation times go down by an order of magnitude or more.
Characterization of the interactions of an amino‐terminal fibronectin fragment with the native molecule: Implications for polymerization of fibronectin
Authors: Homandberg Gene A.
Published: May 2005

Plasma fibronectin is a 450‐kD glycoprotein composed of two similar subunits connected by interchain disulfide bridges that may fold over in solution, allowing the amino terminus of each chain to bind the carboxyl terminus of the same subunit or a different subunit, thereby allowing polymerization. In order to study the characteristics of the fold‐over interaction, the interaction between the amino terminal 29‐kD fragment of fibronectin with native fibronectin has been studied in detail. One 29‐kD molecule bound per fibronectin subunit, the apparent equilibrium dissociation constant was 40 nM, and the half‐times for association and dissociation at 22°C were, respectively, 16 h and 23 days. Complexation could be inhibited by high concentrations of salt, but not by 8M urea. Amino terminal 20‐kD and carboxyl terminal 8‐kD subfragments of the 29‐kD fragment also bound fibronectin and the activity was dependent on the integrity of the type 1 loop structures. The kinetics of the interaction of 29‐kD fragment with fibronectin were unaffected by the presence of ligands, but were affected by detergents such as sodium dodecyl sulfate or deoxycholate, which enhanced the rate of interaction over 100‐fold or 6‐fold, respectively. Therefore, the interaction of fibronectin with ionic cell membrane components such as deoxycholate in vivo may trigger polymerization.
Parameters of helix–coil transition theory for alanine‐based peptides of varying chain lengths in water
Authors: Scholtz J. Martin , Qian Hong , York Eunice J. , Stewart John M. , Baldwin Robert L.
Published: May 2005

Thermal unfolding curves have been measured for a series of short alanine‐based peptides that contain repeating sequences and varying chain lengths. Standard helix–coil theory successfully fits the observed transition curves, even for these short peptides. The results provide values for σ, the helix nucleation constant, ΔH°, the enthalpy change on helix formation, and for s(0°C), the average helix propagation parameter at 0°C. The enthalpy change agrees with the value determined calorimetrically. The success of helix–coil theory in describing the unfolding transitions of short peptides in water indicates that helical propensities, or s values, can be determined from substitution experiments in short alanine‐based peptides.
Conformational energy studies of β‐sheets of model silk fibroin peptides. I. Sheets of poly(Ala‐Gly) chains
Authors: Fossey Stephen A. , Némethy George , Gibson Kenneth D. , Scheraga Harold A.
Published: May 2005

A new model structure is proposed for the silk I form of the crystalline domains of Bombyx mori silk fibroin and the corresponding crystal form of poly(L‐Ala‐Gly). It was deduced from conformational energy computations on stacked sheet structures of poly(L‐Ala‐Gly). The novel sheet structure contains interstrand hydrogen bonds but is composed of antiparallel polypeptide chains whose conformation differs from that of the antiparallel β‐sheets that constitute the silk II structure. The strands of the new sheet have a two‐residue repeat, in which the Ala residues adopt a right‐handed and the Gly residues a left‐handed sheet‐like conformation. The computed unit cell is orthorhombic, with cell dimensions a = 8.94 Å, b = 6.46 Å, and c = 11.26 Å. The model accounts for most spacings in the observed fiber x‐ray diffraction patterns of silk I and of the silk‐I‐like form of poly(L‐Ala‐Gly), and it is consistent with nmr and ir spectroscopic data. As a test of the computations, the well‐established β‐sheet structure of silk II and the corresponding form of poly(L‐Ala‐Gly) have been reproduced. The computed energies for the two forms of poly(L‐Ala‐Gly) indicate that the silk‐II‐like form is more stable, by about 1.0 kcal/mol per residue. The main difference between the two structures is the orientation of the Ala side chains of neighboring strands in each sheet. In the Pauling–Corey β‐sheet and in the silk II form, referred to as an “in‐register” structure, the Ala side chains of every strand point to the same side of a sheet. In the silk I structure, referred to as “out‐of‐register,” the side chains of Ala residues in adjacent strands point to opposite sides of the sheet.
A probabilistic model for genetic recombination of nonreplicating λ–phage DNA, stimulated by “mismatch repair” of UV photoproducts
Authors: Hays John B. , Hays Judith G.
Published: May 2005

Genetic recombination of nonreplicating phage λ‐DNA, during infection of homoimmune lysogenic bacteria, was previously observed to be dramatically stimulated by prior uv irradiation of the phages, even when the Escherichia coli hosts lacked the major uv‐photo‐product excision‐repair system (UvrABC). UvrABC‐independent recombination of circular phage molecules depends on host MutHLS functions and on undermethylation of adenines at GATC sites in the phage DNA, and thus appears to be the result of “mismatch repair” of uv photoproducts. Recombinant frequencies pass through a relatively sharp maximum at 20 J/m2 and decrease at higher doses, whereas most plausible models for the process predict monotonic increases with dose, or a plateau at high uv doses. A uv‐dose‐dependent loss of biological activity (restriction) of all intracellular phage DNA was also observed previously. In order to provide a framework for testing possible explanations for the unusual recombinant‐frequency vs uv‐dose curve, a statistical model was constructed. This model includes probability terms for all possible one‐exchange and two‐exchange recombination processes, and incorporates the assumption that dimer recombinants are more susceptible to restriction than monomer parents (or recombinants), because of their larger target size. By adjustment of model parameters, particularly ϵ, the efficiency per photoproduct of initiation of a recombinational exchange, a theoretical dose–response curve that agreed well with experiment was obtained. The best fit corresponded to ϵ = 0.035, close to the previously observed restriction efficiency of 0.053. In the calculations, the value for h0, the average length of heteroduplex DNA, was taken to be 0.5 λ units, i.e., about 25 kilobase pairs. This estimate for h0 was obtained here by analysis of the density distributions of the progeny of crosses between nonreplicating density‐labeled λ‐phage chromosomes, published by others [M. S. Fox, C. S. Dudney and E. J. Sodergren (1979) Cold Spring Harbor Symposium on Quantitative Biology, Vol. 43, pp. 999–1007].
Comparison of the conformational dynamics of the (1 → 4)‐ and (1 → 6)‐linked α‐D‐glucans using 13C‐NMR relaxation
Authors: Kadkhodaei Mehran , Wu Helen , Brant David A.
Published: May 2005

The conformational dynamics of α‐ (1 → 4)‐ and α‐ (1 → 6)‐glucan homooligomers in the nanosecond time domain have been compared by measuring the 13C‐nmr longitudinal relaxation times T1 for carbons of the terminal and interior sugar residues. Measurements are reported on monomeric glucose and on oligomers containing up to ten glucose residues at room temperature in aqueous solution at concentrations of 3 and 20 g/dL. The carbons of terminal residues display longer relaxation times than do those of interior residues, presumably as a consequence of a greater degree of conformational mobility of the chain ends. The T1s of the reducing terminal residues of all oligomers are significantly longer than those of the corresponding nonreducing termini, a phenomenon that we associate tentatively with the anomeric equilibrium at the reducing end. Carbons of the reducing terminal residues in the β‐anomeric form relax more slowly than their α‐anomeric counterparts. At 20 g/dL the mean T1s for carbons of the terminal and interior residues attain asymptotic behavior with increasing chain length at a chain length of about six residues, and carbons of the α‐ (1 → 4)‐linked maltooligomers relax significantly more slowly than those of the corresponding α‐(1 → 6)‐linked isomaltooligomers. The T1s of both glucan series increase with decreasing concentration. This concentration dependence disappears below 3 g/dL, where the T1s of the two series of homoligomers are no longer distinguishable. This suggests that in dilute aqueous solution at room temperature viscous damping effects predominate over contributions to the T1‐sensitive conformational dynamics from structural differences in the glycosidic linkage region. At 3 g/dL the approach to long chain‐length asymptotic behavior is more protracted than at 20 g/dL, and the T1s of carbons of interior oligomeric residues appear to match the corresponding high‐polymer behavior at a chain length of eight and greater.
Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
Authors: Olmsted Martha C. , Anderson Charles F. , Record M. Thomas
Published: May 2005

Effects of salt concentration on the stabilities of oligonucleotide helices are analyzed directly in terms of ΔΓN→yN ≡ Γ − ΓNnat, the difference in the salt–nucleotide phosphate preferential interaction coefficients for the denatured state, having yN phosphate charges, and for the native state, having N phosphate charges (y = 1 for hairpin denaturation and y = 0.5 for dimer denaturation). Previous experimental studies of the denaturation of hairpin oligo‐nucleotides (having 18 < N < 44) indicate significant differences between ΔΓN→N and ΔΓ∞, the value determined for the denaturation of the corresponding polynucleotide. These differences are thermodynamic manifestations of the oligoelectrolyte end effect. In contrast, the available data on the denaturation of oligonucleotide dimer helices (N ⩽ 22) imply that differences between ΔΓ∞ and ΔΓN→0.5N, and hence oligoelectrolyte end effects, are small or negligible. To determine the origin of these apparently conflicting implications concerning the importance of oligoelectrolyte end effects, we have calculated the N dependence of ΓN from grand canonical Monte Carlo simulations for an idealized model of the structure and charge distribution of each oligomer conformation. Our calculations are in quantitative agreement with the experimental finding for d(TA) hairpin oligomers that − ΔΓN→N decreases linearly as N−1 increases, and with the extant experimental determinations of ΔΓN→0.5N. These results provide an illustration of how the large electrostatic end effects exhibited by the hairpin denaturation data are masked when ΔΓ∞ is compared with values of ΔΓN→0.5N for short dimer helices (N ⩽ 22). For 0.5N > 24, − ΔΓN→0.5N is predicted to be a linear function of N−1 whose slope has the opposite sign from, and is more salt‐concentration dependent than, the corresponding slope of − ΔΓN→N as a function of N−1. Our calculations also yield predictions about the N dependences of the individual values of ΓN that can be tested by determining Donnan coefficients from membrane dialysis equilibrium experiments. For long enough hairpin and dimer oligonucleotides (yN ⩾ 24), in either native or denatured forms, we predict that the (positive) difference Γ∞ − ΓN increases linearly with increasing N−1. For smaller values of N the difference Γ∞ − ΓN continues to increase with increasing N−1.
The three states of globular proteins: Acid denaturation
Authors: Alonso Darwin O. V. , Dill Ken A. , Stigter Dirk
Published: May 2005

We describe statistical mechanical theory that aims to predict protein stabilities as a function of temperature, pH, and salt concentration, from the physical properties of the constituent amino acids: (1) the number of nonpolar groups, (2) the chain length, (3) the temperature‐dependent free energy of transfer, (4) the pKa's (including those in the native state) and their temperature dependencies. We calculate here the phase diagrams for apomyoglobin and hypothetical variant proteins. The theory captures essential features of protein stability including myoglobin's Tm vs pH as measured by P. L. Privalov [(1979) Advances in Protein Chemistry, Vol. 33, pp. 167–241] and its ionic strength vs pH phase diagram as measured by Y. Goto and A. L. Fink [(1990) Journal of Molecular Biology, Vol. 214, pp. 803–805].

The main predictions here are the following: (1) There are three stable states, corresponding to native (N), compact denatured (C), and highly unfolded (U), with transitions between them. (2) In agreement with experiments, the compact denatured state is predicted to have enthalpy closer to U than N because even though there is considerable hydrophobic “clustering” in C, this nevertheless represents a major loss of hydrophobic contacts relative to configurations (N) that have a hydrophobic “core.” (3) C becomes more prominent in the phase diagram with increasing nonpolar content or decreasing chain length, perhaps thus accounting for (a) why lysozyme and α‐lactalbumin differ in their denatured states, and (b) why shortened Staph nuclease molecules are compact. (4) Of major importance for protein calorimetry is Privalov's observation that the enthalpy of folding, ΔH (T, pH) is independent of pH. The theory accounts for this through the prediction that the main electrostatic contribution to stability is not enthalpic; the main contribution is the entropy, mainly due to the different distributions of protons and small ions in the native and denatured states.
Crystal state conformation of three model monomer units for the β‐bend ribbon structure
Authors: Valle G. , Bardi R. , Piazzesi A. M. , Crisma M. , Toniolo C. , Cavicchioni G. , Uma K. , Balaram P.
Published: May 2005

The molecular and crystal structures of three compounds, representing the repeating units of the β‐bend ribbon (an approximate 310‐helix, with an intramolecular hydrogen‐bonding donor every two residues), have been determined by x‐ray diffraction. They are Boc‐Aib‐Hib‐NHBzl, Z‐Aib‐Hib‐NHBzl, and Z‐L‐Hyp‐Aib‐NHMe (Aib, α‐aminoisobutyric acid; Bzl, benzyl; Boc, t‐butyloxycarbonyl; Hyp, hydroxyproline Hib, α‐hydroxyisobutyric acid; Z, benzyloxycarbonyl). The two former compounds are folded in a β‐bend conformation: type III (III′) for Boc‐Aib‐Hib‐NHBzl, while type II (II′) for the Z analogue. Conversely, the structure of Z‐L‐Hyp‐Aib‐NHMe, although not far from a type II β‐bend, is partially open.
On the flexibility of myosin in solution
Authors: Curry James F. , Krause Sonja
Published: May 2005

Rabbit skeletal muscle myosin from the same rabbit was prepared by two different methods, and then purified by either Sephadex or hydroxylapatite chromatography. The resulting myosin samples were analyzed in 2–10 mM sodium pyrophosphate solutions at pH 9 using transient electric birefringence. The birefringence decay signals were fitted using a Fortran program called DISCRETE and two relaxation times, 49.7 ± 5.6 and 11.2 ± 2.5 μs, were determined. These relaxation times were independent of the method of myosin preparation, the method of myosin purification, the concentration of sodium pyrophosphate between 2 and 10 mM, the concentration of myosin between 0.08 and 1.59 mg/mL, and the temperature between 4.0 and 20.0°C, after correction to 20.0°C. The longer relaxation time is consistent with a rigid, linear myosin molecule. The shorter relaxation time is consistent with myosin that has a completely flexible hinge region in the myosin tail. Both relaxation times are inconsistent with the previously reported single relaxation time of myosin obtained by fitting the birefringence decay data to only 90% of the decay signal. By forcing some of the birefringence decay data in the present work to fit 90% of the decay signal with a single relaxation time, approximately the same relaxation time as previously reported was obtained.
Heterogeneous molecular aggregation and fractal structure in chitosan/acetic acid systems
Authors: Matsumoto Takayoshi , Kawai Masahiro , Masuda Toshiro
Published: May 2005

The influence of deacetylation degree on heterogeneous molecular aggregation has been investigated for chitosan solution in 2 wt % acetic acid aqueous solution using rheological and small‐angle x‐ray scattering (SAXS) methods. Three samples of chitosan, which were designated CS62, CS79, and CS96, were used, and the deacetylation degrees of these samples were 0.62, 0.79 and 0.96, respectively.

Rheological properties show that the systems of CS62 and CS96 are homogeneous, and the system of CS79 has a certain heterogeneous structure with a long‐time relaxation mechanism. According to the SAXS measurement, the heterogeneous system has a fractal structure and the fractal dimension is about 1.3.
Molecular dynamics simulation of Lewis blood groups and related oligosaccharides
Authors: Mukhopadhyay Chaitali , Bush C. Allen
Published: May 2005

Molecular dynamics simulations without explicit inclusion of solvent molecules have been performed to study the motions of Lewisa and Lewisb blood group oligosaccharides, and two blood group A tetrasaccharides having type I and type II core chains. The blood group H trisaccharide has also been studied and compared with the blood group A type II core chain. The potential energy surface developed by Rasmussen and co‐workers was used with the molecular mechanics code CHARMM. The lowest energy minima of the component disaccharide fragments were obtained from conformational energy mapping. The lowest energy minima of these disaccharide fragments were used to build the tri‐ and tetrasaccharides that were further minimized before the actual heating/equilibration and dynamics simulations. The trajectories of the disaccharide fragments, e.g., Fuc α‐(1 → 4) GlcNAc, Gal β‐(1 → 4) GlcNAc, etc., show transitions among various minima. However, the oligosaccharides were found to be dynamically stable and no transitions to other minimum energy conformations were observed in the time series of the glycosidic dihedral angles even during trajectories as long as 300 ps. The stable conformations of the glycosidic linkages in the oligosaccharides are not necessarily the same as the minimum energy conformation of the corresponding isolated disaccharides. The average fluctuations of the glycosidic angles in the oligosaccharides were well within the range of ±15°. The results of these trajectory calculations were consistent with the relatively rigid single‐conformation models derived for these oligosaccharides from 1H‐nmr data.
Reassessment of the random coil conformation: Vibrational CD study of proline oligopeptides and related polypeptides
Authors: Dukor Rina K. , Keiderling Timothy A.
Published: May 2005

The “random coil” conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly (L‐proline). VCD, ir and uv CD spectra of blocked L‐proline oligopeptides [(Pro)n, n = 2–12] in different solvents are reported and compared to the spectra of poly (L‐proline) II, poly (L‐glutamic acid), and unblocked proline oligomers. Based on the chain‐length dependence of the VCD and electronic CD (BCD) spectra of proline oligomers, it is established that VCD spectra are dominated by short‐range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly (L‐proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the “random coil” conformation has a large fraction of helical regions, conformationally similar to the left‐handed, 31 polyproline II helix, as was previously suggested by Krimm and co‐workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5–75°C), and pH on the VCD spectra of L‐proline oligomers, poly (L‐proline) II, and poly (L‐glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly (L‐glutamic acid) are more flexible than are polyproline or even L‐proline oligomers.
A vibrational spectroscopic study of the self‐association of polyinosinic acid and polyguanylic acid in aqueous solution
Authors: Simard Christine , Savoie Rodrigue
Published: May 2005

We have studied by Raman and ir spectroscopy the structure of self‐associated polyinosinic acid and polyguanylic acid in aqueous solution. The results are consistent with the formation of a four‐stranded complex, which melts cooperatively near 60°C in the case of poly (I) in the presence of K+ ions. The conformation of the ribose in both systems is mixed C2′‐endo/C3′‐endo, giving a structure that is intermediate between the extremes proposed previously from x‐ray diffraction studies. Characteristic Raman bands for the C2′‐endo ribose conformation in polyribonucleotides are identified. The four‐stranded structure of poly (I) appears to be very flexible, with ≈15% of the tetrameric segments being disrupted and ≈30% of the ribose units adopting a disordered conformation prior to melting. This disordering process increases to ≈75% above the melting transition, with the remaining ≈25% of the ribose units keeping an ordered C2′‐endo or C3′‐endo conformation. © 1994 John Wiley & Sons, Inc.