bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electric dichroism studies on ferriheme– and ferroheme–poly(L‐lysine) complexes at pH 9–12
Authors: Yamagishi Akihiko , Watanabe Fumiyuki 
Published: December 2004

AbstractTransient electric dichroism has been measured for the ferriheme–poly(L‐lysine)[(Lys)n], ferroheme–(Lys)n, and ferroheme–(Lys)n–carbon monoxide (CO) solutions at pH 9–12. The Soret absorption maximum in electronic spectrum (λ), the reduced linear dichroism (ρ∞) at complete orientation and the calculated angle (ϕ) between the porphyrin plane of a bound heme and the oriented polymer axis are determined for the following complexes: a ferriheme–(Lys)n complex at pH 9.5–10.5 (λ = 420 nm, ρ∞ = 0.50, and ϕ = 19°), a ferroheme–(Lys)n complex at pH 9.5–10.2 (λ = 432 nm, ρ∞ = 0.77, and ϕ = 0°), and a ferroheme–(Lys)n–CO complex at pH 9.25 (λ = 430 nm, ρ∞ = 0.38, and ϕ = 24°). Based on the above data, the validity of the structures of heme–(Lys)n complexes proposed by other investigators is discussed.
The δ‐function counterion condensate around a line charge derived from the Fuoss, Katchalsky, and Lifson polyelectrolyte theory
Authors: Lampert Murray A. 
Published: December 2004

AbstractIt has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson‐Boltzmann theory, is an encapsulating δ‐function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson‐Boltzmann equation.
Interactions of DNA with divalent metal ions. III. Extent of metal binding: Experiment and theory
Authors: Granot Joseph , Kearns David R. 
Published: December 2004

AbstractDNA with Mn2+ as the only counterion has been prepared, and the extent of the Mn2+ binding was determined under a variety of conditions through measurements of the proton relaxation enhancement of water. The total extent of Mn2+ binding per DNA phosphate is found to be 0.43 ± 0.04, independent of the metal ion concentration in the experimental range of 2.8 × 10−5 to 2.1 × 10−3M. The predictions of Manning's condensation theory and those obtained from solution of the generalized Poisson‐Boltzmann equation regarding the extent of divalent ion binding to polyelectrolytes, in the presence and absence of monovalent counterions, are compared with one another and with the experimental results. Good agreement between the two theoretical approaches is found, with less than 14% variance in the predicted extent of binding over a large range of mono‐ and divalent ion concentrations. While the predictions of both theoretical approaches generally agree with the experimental results, some discrepancies are noted and their possible origins discussed.
Conformational study of poly(α‐L‐aspartic acid)
Authors: Saudek V. , Štokrová Š. , Schmidt P. 
Published: December 2004

AbstractThe conformation of poly(α‐L‐aspartic acid) was investigated on a sample in which β‐bonds were not detected. CD and ir spectroscopy showed that poly(α‐L‐aspartic acid) passes through a conformational change induced by changes of the degree of ionization that is accompanied by precipitation; the precipitate is probably highly helical. The change was also detected by potentiometric titration.
Binding of ligands to a one‐dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides
Authors: Sturm Jean 
Published: December 2004

AbstractA temperature‐jump relaxation study of the interaction of tilorone with different polynucleotides and DNA has been performed. A single relaxation time, attributed to the intercalation step, has been observed in the case of poly[d(A‐T)]·poly[d(A‐T)], poly[d(A‐C)]·poly[d(G‐T)], poly[d(G‐C)]·poly[d(G‐C)], and poly(dG)·poly(dC). No intercalation into poly(dA)·poly(dT) occurs, and the interaction with poly(dG)·poly(dC) is different from what is observed with the other intercalating homopolymers. Refinement of the binding model is suggested from the analysis of the kinetic data. The relaxation curves obtained with DNA are well simulated based on a binding mechanism where DNA is considered a heterogeneous lattice and each type of site behaves as if it were located in the corresponding homopolymer. Poly(dA)·poly(dT) shows a unique behavior: studies of the effects of concentration and temperature indicate that tilorone acts as a probe of a process involving the polynucleotide alone. This process appears to be related to the dynamic structure of the nucleic acid and is detectable only when the bound dye is not intercalated.
Equilibrium folding and unfolding pathways for a model protein
Authors: Miyazawa S. , Jernigan R. L. 
Published: December 2004

AbstractThe folding–unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only Cα and Cβ atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (ϕ,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding–unfolding transition for this idealized model is an “all‐or‐none” type; this is attributable to the specific long‐range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding–unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium‐range contacts at a β‐turn and at the α‐helix. (2) These grow to include the native pair of interacting β‐strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long‐range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.
Quasielastic light scattering by biopolymers. V. Interparticle interactions between polynucleosomes
Authors: Schmitz Kenneth S. , Parthasarathy Nambi , Kent Jacqueline C. , Gauntt Jennifer 
Published: December 2004

AbstractQuasielastic light scattering and electrophoretic light scattering experiments were performed on chicken erythrocyte polynucleosome solutions at various temperatures and ionic strengths. The apparent diffusion coefficient, Dapp, was found to depend on the scattering vector K. In general, Dapp can be described as a damped oscillatory function of K in the ionic strength range of 10 to 60 mM and over the temperature range of 10 to 40°C. Electrophoretic light scattering studies on total digest chromatin samples indicate the apparent charge on the polynucleosomes increases as the ionic strength is lowered from 10 to 1 mM. These data are interpreted in terms of fluctuations in the surface charge distribution of the polyion and subsequent inducement of an asymmetric distribution of small ions about the polyion. These fluctuation components lead to the formation of “clusters” of polyions.
Dissociation of bovine and bacterial catalases by sodium n‐dodecyl sulfate
Authors: Jones M. N. , Manley P. , Midgley P. J. W. , Wilkinson A. E. 
Published: December 2004

AbstractThe dissociation of beef liver and bacterial (Micrococcus lysodeikticus) catalases by the action of sodium n‐dodecyl sulfate (SDS) has been investigated as a function of SDS concetration and time by ultracentrifugation. The rate of dissociation of beef liver catalase is found to be much faster than that for bacterial catalase in 25 mM SDS at pH 7.0. Beef liver catalase is dissociated into its four subunits after 24 h, whereas bacterial catalase is not completely dissociated after 36 days of incubation. The binding of SDS to beef liver catalase obeys a Hill equation with a cooperativity exponent of 2.0 and a binding constant of 440. The initial interaction of SDS with beef liver catalase can be detected by microcalorimetry, whereas the mixing of SDS with bacterial catalase is athermal. Bacterial catalase retains enzymic activity in the presence of SDS, whereas beef liver catalase is completely deactivated at SDS concentrations above 5 mM. Beef liver catalase is more sensitive to acid denaturation than bacterial catalase, and the rate of dissociation for both catalases is sixth‐order in proton concentration. Comparison of the amino acid analysis of the two catalases shows that bacterial catalase has a smaller number of lysyl residues and a larger number of glutamyl residues than beef liver catalase. Taken together these structural differences could lead to a reduced affinity of bacterial catalase for the binding of SDS as observed.
Light‐scattering spectroscopic study of polysaccharide protein conjugate
Authors: Patkowski A. , Bujalowski W. , Chu B. , Schneerson R. , Robbins J. B. 
Published: December 2004

AbstractBy combining gel permeation chromatography (GPC) and light‐scattering spectroscopy, including photon correlation and angular distribution of absolute scattered intensity, we were able to characterize immunologically active Haemophilus influenzae type b polysaccharide (HIB Ps) bovine serum albumin (BSA) conjugates in terms of equivalent hydrodynamic radius rh ∼ (6.2 ± 0.6) × 102 Å, apparent radius of gyration rg ∼ (5.4 ± 0.3) × 102 Å, apparent molecular weight Mw ∼ (3.5 ± 0.4) × 106 g/mol, and a second virial coefficient A2 ∼ (1.9 ± 0.3) × 10−4 cm3 mol/g2. We could study the effects of each of the processes in the conjugate formation according to the following procedure: BSA (dialysis, modification, fractionation) + HIB Ps → HIB Ps/BSA conjugate (conjugate formation, fractionation). Narrow distributions of HIB Ps BSA conjugate formation can be achieved using fractionated BSA.
Cooperative effects in α‐helices: An ab initio molecular‐orbital study
Authors: Van Duijnen P. T. , Thole B. T. 
Published: December 2004

AbstractSome properties of α‐helices of polyclycine and polyalanine, up to the decapeptide, were investigated by ab initio molecular‐orbital calculations. These helices were found to be unstable relative to the corresponding “fully extended chain” conformation. The electric field of helices of 8–10 residues is about 20% stronger than that of models built from noninteracting monomers, for example. This is a result of cooperativity, which is essentially governed by the intramolecular hydrogen bonds. The cooperativity is manifest in all properties of the helices: relative stability, dipole moment, proton affinity, electrical potential. The electric potential of helices of three and four residues is such that their instability can be compensated for by a single charged group acting as an “initiator.” The computed proton affinity of the (Ala)8 α‐helix is about 45 kcal/mol larger than that of formamide, which confirms that long helices may be protonated at the carboxyl end in solution.
Theoretical study of the fraction of a long‐chain DNA that can be incorporated in a recombinant DNA partial‐digest library
Authors: Seed Brian 
Published: December 2004

AbstractExperimental evidence indicates that the cleavage sites for site‐specific DNA cleavage enzymes are randomly distributed throughout the DNA polymer [Botchan et al. (1973) Cold Spring Harbor Symp. Quantum Biol. 38, 383–395; Hamer and Thomas (1973) Chromosoma 49, 243–267]. Using this information we derive equations for the probability that a DNA base pair chosen at random can be found within the population of enzymatically generated partial cleavage products whose lengths fall between L + 1 and L + r base pairs. The results describe the fraction of a long‐chain DNA that can be incorporated in a recombinant DNA partial digest library. The weight‐fraction distribution of Kuhn (1930) is a special case of the distribution derived here.
Study of agarose gels by electron microscopy of freeze‐fractured surfaces
Authors: Waki Seichi , Harvey J. D. , Bellamy A. R. 
Published: December 2004

AbstractThe distribution of fibers in agarose gels has been studied by electron‐microscopic examination of replicas formed from freeze‐fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10–30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze‐fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non‐Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.
Monte carlo simulations of peptide solvation
Authors: Madison Vincent , Osguthorpe David J. , Dauber Pnina , Hagler Arnold T. 
Published: December 2004

AbstractTo increase our understanding of peptide–water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x‐ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
Coupling between the helix–coil transition and nematic–isotropic transitions in polypeptide solutions
Authors: Matheson Robert R. 
Published: December 2004

AbstractThe lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix–coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix–coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.
Domain characteristics of the carboxyl‐terminal fragment 206–316 of thermolysin
Authors: Fontana Angelo , Vita Claudio , Chaiken Irwin M. 
Published: December 2004

AbstractThe existence, location, and characteristics of protein domains have been investigated by studying the structural properties of the carboxyl‐terminal cyanogen bromide fragment 206–316 of thermolysin. As judged by far‐uv CD measurements in aqueous solution under neutral conditions, the fragment attains a substantial degree of α‐helical structure comparable to that exhibited by the corresponding region in native thermolysin. By radioimmunoassay techniques, a considerable degree of nativeness of fragment conformation has been deduced from comparison of the relative affinities of thermolysin and fragment 206–316 for antibodies specific for the 206–316 region in the intact protein. The fragment shows noteworthy stability to protein denaturants. The overall spectroscopic and immunochemical data suggest that fragment 206–316 is able to refold into a stable, nativelike structure independently from the rest of the molecule, thus providing support for the view that this fragment may contain a substantial part, if not all, of a protein domain structure.
The unfolding mechanism of thermolysin
Authors: Corbett R. J. T. , Roche Rodney S. 
Published: December 2004

AbstractThe ligand‐modulated kinetics of the autoproteolysis of thermolysin and the high‐molecular‐weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
The optical activity of polypeptides
Authors: Schellman John A. , Becktel Wayne J. 
Published: December 2004

AbstractThe present status of the theory of the optical properties of polypeptides is discussed in a general way. Arguments are presented that indicate that the interaction of exciton bands in helices will occur in a tensorial way with the parallel polarized bands normally having stronger interactions than the perpendicular polarized bands, with only small cross‐interactions. The net result is an anisotropy of the hyperchromism of the ππ* band and an imbalance of the rotatory strengths of the parallel and perpendicular components. According to the evidence of Mandel and Holzwarth [(1973) Biopolymers 13, 655–674], this is, in fact, the origin of the strongly nonconservative CD bands of polyproline II and related structures. The implications of anisotropic hyperchromicity on the interpretation of the linear dichroism of crystals is discussed.
1H‐NMR studies on substance P hexapeptide analogs
Authors: Ribeiro Anthony , Jardetzky Oleg , Gilon Chaim , Teitelbaum Dina , Chorev Michael 
Published: December 2004

Abstract1H‐nmr studies of [pGlu6]SP6–11, [gpGlu6,mPhe7]SP6–11, and [pGlu6,N‐CH3Phe7]SP6–11 in DMSO‐d6 reveal characteristic chemical shifts, 3JNH‐αCH, temperature dependence, as well as deuterium exchange half‐times. Marked similarities are revealed for the two first analogs, whereas the N‐methylated analog is clearly different. Possible conformations are considered.
Sequential hydration of a dry globular protein
Authors: Poole P. L. , Finney J. L. 
Published: December 2004

AbstractUsing direct difference ir and laser Raman spectroscopy, the sequential hydration of hen egg‐white lysozyme was monitored. The ir data allowed us to identify some specific molecular hydration events that occur as water is added, whereas the Raman is interpreted in terms of conformational changes. The largest of these solvent‐induced changes occurs below the hydration level at which activity commences.
Functional significance of flexibility in proteins
Authors: Huber Robert , Bennett William S. 
Published: December 2004

AbstractThe structural basis and the functional implications of large‐scale flexibility are discussed for three systems: trypsin–trypsinogen, immunoglobulins, and citrate synthase. The trypsin–trypsinogen system provides an example in which an order–disorder transition is used as a means to regulate enzymatic activity. Immunoglobulins demonstrate how flexibly linked domains may be used to allow the binding of ligands with diverse arrangements. In citrate synthase, domain motion forms an active site that is shielded from solvent. Analogous large‐scale flexibility has been observed in a number of other systems.
Conformational flexibility in a small globular hormone: X‐ray analysis of avian pancreatic polypeptide at 0.98‐Å resolution
Authors: Glover Ian , Haneef Illyas , Pitts Jim , Wood Steve , Moss David , Tickle Ian , Blundell Tom 
Published: December 2004

AbstractThe 36‐amino acid avian pancreatic polypeptide has been studied by x‐ray analysis at 0.98‐Å resolution and refined using a restrained least‐squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline–like helix (residues 2–8) and an α‐helix (residues 14–32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high‐resolution analysis defines sequence‐dependent distortions in the α‐helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C‐terminal residues. For the first time, six‐parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
Multiple intermediates in the reaction of bovine β‐trypsin with bovine pancreatic trypsin inhibitor (kunitz)
Authors: Antonini Eraldo , Ascenzi Paolo , Menegatti Enea , Guarneri Mario 
Published: December 2004

AbstractThe kinetics of the formation of the complex between bovine β‐trypsin and the bovine basic pancreatic trypsin inhibitor (BPTI) was investigated using three different signals: the displacement of proflavine, the optical density changes in the UV region, and the loss of the enzymatic activity. For the three different signals, with inhibitor in excess over bovine β‐trypsin ([BPTI] ≥ 5 × [bovine β‐trypsin]), the time course of the reaction corresponds to a pseudo‐first‐order process. The concentration dependence of the rate is second order at low BPTI concentrations and tends to first order at high inhibitor concentrations. This behavior may be explained by relatively rapid preequilibria followed by limiting first‐order processes according to

The values of Ki, k+i, and k(on)i ( = k+i/Ki) have been determined for the different reactions at three pH values: 6.80, 4.80, and 3.50. The kinetic parameters differ widely for the processes reflected by the various signals; the difference increases upon lowering pH. The results indicate that the formation of the bovine β‐trypsin–BPTI complex is not an all‐or‐nothing process, but involves several intermediates corresponding to discrete reaction steps, which are differently affected by ionization processes.
How antigenic are antigenic peptides?
Authors: Leach S. J. 
Published: December 2004

AbstractMost of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody‐combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid‐phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross‐reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72–89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25–55) is also antigenic.