bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational analysis of peptides, polypeptides, and proteins. XXXII. α‐Poly(L‐glutamic acid)
Authors: Sengupta Pradeep K. , Krimm S. 
Published: May 2005

AbstractThe Raman and ir spectra of α‐helical poly(L‐glutamic acid) have been assigned on the basis of a normal mode calculation for this structure. The force field was based on our previously refined main‐chain force constants for α‐poly(L‐alanine) and side‐chain force constants for β‐calcium–poly(L‐glutamate). Despite the identical backbone α‐helical structures, significantly different frequencies are calculated, and observed, in the amide III and backbone stretch regions of α‐poly(L‐glutamic acid), as compared with α‐poly(L‐alanine). This clearly demonstrates the influence of side‐chain structure on mainchain vibrational modes.
Binding of CC‐1065 to poly‐ and oligonucleotides
Authors: Krueger W. C. , Li L. H. , Moscowitz A. , Prairie M. D. , Petzold G. , Swenson D. H. 
Published: May 2005

AbstractThe binding of the antitumor agent CC‐1065 to a variety of poly‐ and oligonucleotides was studied by electronic absorption, CD, and resistance to removal by Sephadex column chromatography. Competitive binding experiments between CC‐1065 and netropsin were carried out with calf‐thymus DNA, poly(dI‐dC) · poly(dI‐dC), poly(dI) · poly(dC), poly(rA) · poly(dT), poly(dA‐ dC) · poly(dG‐dT), and poly(dA) · 2poly(dT). CC‐1065 binds to polynucleotides by three mechanisms. In the first, CC‐1065 binds only weakly, as judged by the induction of zero or very weak CD spectra and low resistance to extraction of drug from the polynucleotide by Sephadex chromatography. In the second and third mechanisms, CC‐1065 binds strongly, as judged by the induction of two distinct, intense CD spectra and high resistance to extraction of drug from the polynucleotide, by Sephadex chromatography in both cases. The species bound by the second mechanism converts to that bound by the third mechanism with varying kinetics, which depend both on the base‐pair sequence and composition of the polynucleotide. Competitive binding experiments with netropsin show that CC‐1065 binds strongly in the minor groove of DNA by the second and third mechanisms of binding. Netropsin can displace CC‐1065 that is bound by the second mechanism but not that bound by the third mechanism. CC‐1065 binds preferentially to B‐form duplex DNA and weakly (by the first binding mechanism) or not at all to RNA, DNA, and RNA–DNA polynucleotides which adopt the A‐form conformation or to single‐strand DNA. This correlation of strong binding of CC‐1065 to B‐form duplex DNA is consistent with x‐ray data, which suggest an anomalous structure for poly(dI) · poly(rC), as compared with poly(rI) · poly(dC) (A‐form) and poly(dI) · poly(dC) (B‐form). The binding data indicate that poly(rA) · poly(dU) takes the B‐form secondary structure like poly(rA) · poly(dT). Triple‐stranded poly(dA) · 2poly(dT) and poly(dA) · 2poly(dU), which are considered to adopt the A‐form conformation, bind CC‐1065 strongly. Netropsin, which also shows a binding preference for B‐form polynucleotides, also binds to poly(dA) · 2poly(dT) and occupies the same binding site as CC‐1065. These binding studies are consistent with results of x‐ray studies, which suggest that A‐form triplex DNA retains some structural features of B‐form DNA that are not present in A‐form duplex DNA; i.e., the axial rise per nucleotide and the base tilt. Triple‐stranded poly(dA) · 2poly(rU) does not bind CC‐1065 strongly but has nearly the same conformation as poly(dA) · 2poly(dT) based on x‐ray analysis. This suggests that the 2′‐OH group of the poly(rU) strands interferes with CC‐1065 binding to this polynucleotide. The same type of interference may occur for other RNA and DNA–RNA polynucleotides that bind CC‐1065 weakly.
Expressions for the interpretation of circular intensity differential scattering of chiral aggregates
Authors: Bustamante Carlos , Maestre Marcos F. , Keller David 
Published: May 2005

AbstractThe derivation of compact expressions of the circular intensity differential scattering (CIDS) of chiral molecules is presented in the first Born approximation of the fields. The expressions derived are valid for a suspension of scattering chiral particles free to adopt any orientation in solution. The connection is established between the preferential scattering cross section for right‐ vs left‐circularly polarized light for a given scattering angle and the geometrical parameters of the molecule. As observed experimentally, the equations predict that the circular differential scattering patterns must show as a function of the scattering angle a series of lobes of alternating sign. In between these lobes, zeros in the differential scattering cross section occur. For the case of two dipole moments arranged in chiral fashion, an expression is derived that shows how the relative arrangement of the dipoles and their separation relative to the wavelength of light control the number and the position of the zeros. A compact expression predicting the CIDS of a sample for very small angles of scattering is derived for a system of helices whose dimensions are small compared with the wavelength of light. Finally, the presence of CIDS in a sample is related to the appearance of anomalous signals in the CD spectrum of chiral systems. Expressions and computations of the magnitudes and sign of the anomalies are presented. The expressions obtained confirm the main features of the experimental CIDS patterns of chiral molecules previously published.
Temperature‐dependent optical rotatory dispersion properties of helical muscle proteins and homopolymers
Authors: Hvidt Søren , Rodgers Michael E. , Harrington William F. 
Published: May 2005

AbstractThermally induced helix–coil transitions of myosin rod, light meromyosin, and tropomyosin were studied by optical rotatory dispersion (ORD). Fractional helicity was calculated from both the Moffitt‐Yang parameter, b0, and the corrected mean residue rotation [m′] at 231.4 nm. Between 3 and 30°C, [m′] increases linearly with a slope of 59/°C, whereas b0 is virtually constant, indicating apparently different thermal melting behavior. Poly(L‐lysine) and poly(L‐glutamic acid) in their helical forms and myoglobin also show a nearly linear temperature dependence of [m′]231.4. Muscle proteins in 6M guanidine hydrochloride and the random‐coil forms of the homopolymers exhibit temperature‐dependent values of [m′]231.4 and b0. We conclude from these observations that ORD properties of both α‐helices and random‐coil polypeptides have significant intrinsic temperature dependencies. A new method of estimating fractional helicity as a function of temperature is proposed.
Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity
Authors: Liebman Michael N. , Venanzi Carol A. , Weinstein Harel 
Published: May 2005

AbstractA combination of novel methods of macrostructural analysis and theoretical chemistry were applied to study the metalloenzyme carboxypeptidase A and its complexes with two inhibitors—glycyl‐L‐tyrosine and a protein inhibitor isolated from potatoes. The methods of macrostructural analysis applied to the study of the crystal structures of these molecules include structural superposition, distance matrix analysis, and linear distance plot analysis, and the approach is complemented by the examination of computed physicochemical properties, including electrostatic potential surfaces, bulk hydrophobicity, and complementarity of van der Waals surfaces. The structural analysis identified folding domains in carboxypeptidase A that relate to such domains in carboxypeptidase B and are involved in the conformational changes following complexation with the inhibitors. The nature of these conformational changes and their relation to the physicochemical properties suggest their role in determining recognition and reactivity characteristics of the enzyme. The analysis also revealed a distinction between conformational changes in the secondary and tertiary structure of the protein that provides insight into the structure–function relationship in carboxypeptidase. Notably, some inhibitor‐induced changes in structure occur in regions in which the interacting molecules are not in contact, while some of the contact regions, such as the active site, incur only minor perturbation. The analysis reveals the interrelation between the enzyme–ligand interaction and the structural perturbation outside the active site, thus illuminating one aspect of the link between the structural organization of the protein and its function.
Low‐temperature glass transition in proteins
Authors: Morozov V. N. , Gevorkian S. G. 
Published: May 2005

AbstractThe viscoelastic properties of solid samples (crystals, amorphous films) of hen egg white lysozyme, bovine serum albumin, and sperm whale myoglobin were studied in the temperature range of 100–300 K at different hydration levels. Decreasing the temperature was shown to cause a steplike increase in the Young's modulus of highly hydrated protein samples (with water content exceeding 0.3 g/g dry weight of protein) in the temperature range of 237–251 K, followed by a large increase in the modulus in the broad temperature interval of 240–130 K, which we refer to as a mechanical glass transition.Soaking the samples in 50% glycerol solution completely removed the steplike transition without significantly affecting the glass transition. The apparent activation energy determined from the frequency dependence of the glass‐transition temperature was found to be 18 kcal/mol for wet lysozyme crystals. Lowering the humidity causes both the change of the Young's modulus in response to the transition and the activation energy to decrease. The thermal expansion coefficient of amorphous protein films also indicates the glass transition at 150–170 K. The data presented suggest that the glass transition in hydrated samples is located in the surface layer of proteins and related to the immobilization of the protein groups and strongly bound water.
Poly(Pro‐Nle‐Gly): Can an amorphus polypeptide take up a supramolecular elastinlike structure?
Authors: Tamburro A. M. , Gordini D. Daga 
Published: May 2005

AbstractPoly(Pro‐Nle‐Gly) was found to have a CD spectrum characteristic of a random polypeptide and an x‐ray powder pattern that does not reveal any regular secondary structure. In its electron micrograph, however, filaments and fibers were seen. This is a random polymer with supramolecular structure. It suggests that the supramolecular structure seen in electron micrographs of elastin preparations and related polypeptides does not necessarily imply an ordered structure at the molecular level.
Mechanism of intercalation: Ion effects on the equilibrium and kinetic constants for the interaction of propidium and ethidium with DNA
Authors: Wilson W. David , Krishnamoorthy C. R. , Wang Yueh‐Hwa , Smith J. C. 
Published: May 2005

AbstractThe effects of sodium ion concentration on the binding isotherms and association and dissociation reaction rates for the interaction of the closely related intercalating dication, propidium, and the monocation, ethidium, with DNA have been determined by spectrophotometric binding and stopped‐flow kinetics methods. The binding of propidium to DNA is best described by a neighbor‐exclusion binding isotherm (two base pairs per binding site) with negative ligand cooperatively on binding. The cooperativity parameter is fairly independent of salt concentration, while the log of the observed equilibrium binding constant varies with −log [Na+], with a slope of two for the propidium–DNA interaction. These effects of the sodium ion on the equilibrium binding of propidium with DNA are similar to those previously described for the dication, quinacrine [Wilson, W.D. & Lopp, I.G. (1979) Biopolymers, 18, 3025–3041]. Ethidium behaves, as a function of salt, as a monocation binding to DNA with neighbor exclusion and without ligand cooperativity. Equations are derived for two limiting kinetics models for intercalation involving binding of the intercalator to a preequilibrium, open state of DNA (model I) or binding form a preequilibrium externally associated state of the intercalator with DNA (model II). Model II gives the best fit to all of the kinetic results if it is assumed that the initial external interaction of the intercalator with DNA is similar to the exchange of free and condensed simple counterions. Intercalation then occurs from this state following an opening transition of the base pairs of the double helix. This model predicts a larger effect of salt concentration on the association than on the dissociation reaction, and that is what is experimentally observed. The intercalation conformational change makes a significant contribution to the ionic effects for both the equilibrium binding and the kinetic constants. The dissociation results and the association reaction results under pseudo‐first‐order conditions could be fit with single exponential curves under the conditions of our experiments.
Imino 1H‐ and 31P‐nmr analysis of the interaction of propidium and ethidium with DNA
Authors: Chandrasekaran Subramanian , Jones Robert L. , Wilson W. David 
Published: May 2005

AbstractAt low temperature and low salt concentration, both imino proton and 31p‐nmr spectra of DNA complexes with the intercalators ethidium and propidium are in the slow‐exchange region. Increasing temperature and/or increasing salt concentration results in an increase in the site exchange rate. Ring‐current effects from the intercalated phenanthridinium ring of ethidium and propidium cause upfield shifts of the imino protons of A · T and G · C base pairs, which are quite similar for the two intercalators. The limiting induced chemical shifts for propidium and ethidium at saturation of DNA binding sites are approximately 0.9 ppm for A · T and 1.1 ppm for G · C base pairs. The similarity of the shifts for ethidium and propidium, in both the slow‐ and fast‐exchange regions over the entire titration of DNA, shows that a binding model for propidium with neighbor‐exclusion binding and negative ligand cooperativity is correct. The fact that a unique chemical shift is obtained for imino protons at intercalated sites over the entire titration and that no unshifted imino proton peaks remain at saturation binding of ethidium and propidium supports a neighbor‐exclusion binding model with intercalators bound at alternating sites rather than in clusters on the double helix. Addition of ethidium and propidium to DNA results in downfield shifts in 31P‐nmr spectra. At saturation ratios of intercalator to DNA base pairs in the titration, a downfield shoulder (approximately −2.7 ppm) is apparent, which accounts for approximately 15% of the spectral area. The main peak is at −3.9 to −4.0 ppm relative to −4.35 in uncomplexed DNA. The simplest neighbor‐binding model predicts a downfield peak with approximately 50% of the spectral area and an upfield peak, near the chemical shift for uncomplexed DNA, with 50% of the area. This is definitely not the case with these intercalators. The observed chemical shifts and areas for the DNA complexes can be explained by models, for example, that involve spreading the intercalation‐induced unwinding of the double helix over several base pairs and/or a DNA sequence‐ and conformation‐dependent heterogeneity in intercalation‐induced chemical shifts and resulting exchange rates.
Short electric‐field pulses convert DNA from “condensed” to “free” conformation
Authors: Porschke Dietmar 
Published: May 2005

AbstractElectric‐field pulses of e.g. 20 kV/cm and 100 μs induce a strong decrease in the scattered light intensity of DNA condensed by spermine. Analysis of this effect demonstrates that the decrease of the scattered light intensity results from decondensation of DNA. The decondensation reaction requires an electric‐field strength exceeding a threshold value. Complete decondensation can be achieved at field strength that are only slightly higher than the threshold value. The decondensation process is strongly accelerated at high electric‐field strengths. At 30 kV/cm, the decondensation time constant is ∼8 μs, corresponding to an acceleation factor of 105 relative to the field‐free decondensation reaction. The dependence of the time constants on the electric‐field strength suggests that the field‐induced decondensation is due to a dissociation field effect. The condensation process observed after electric‐field pulses at low concentrations of DNA and spermine shows a characteristic induction period, which strongly depends on the spermine concentration. This induction period reflects the time required for the binding of spermine to DNA, until the degree of binding is sufficiently high for the condensation reaction. The fast dissociation of condensed DNA by electric‐field pulses together with a relatively long lifetime of the free DNA results in a reaction cycle resembling a hysteresis loop.
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

AbstractThe 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

AbstractThe 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

AbstractConfiguration 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

AbstractIn 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

AbstractPlots 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

AbstractSix 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.