bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractBy 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

AbstractMolecular 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

AbstractRelations 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

AbstractThe 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

AbstractThe 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

AbstractWe 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

AbstractThe 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

AbstractSteady 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

AbstractChanges 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

AbstractFollowing 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

AbstractThe 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

AbstractPoly(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

AbstractOne 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

AbstractPlasma 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

AbstractThermal 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

AbstractA 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.