bluuebunny/crossref_metadata_2025_split huggingface dataset:
Excluded volume as a determinant of macromolecular structure and reactivity
Authors: Minton Allen P. 
Published: December 2004

AbstractThe effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard‐particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi‐spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self‐ and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi‐spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme‐catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self‐association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self‐association of larger macromolecules.
Effects of some organic cosolvents on the functional properties of hemoglobin: Kinetics of O2 displacement by CO
Authors: Cordone Lorenzo , Cupane Antonio 
Published: December 2004

AbstractWe studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso‐propanol, n‐propanol, formamide, acetamide, N‐methyl‐formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
Interaction of calcium ions with α‐elastin: An equilibrium dialysis, circular dichroism, and microcalorimetric study
Authors: Terbojevich M. , Palumbo M. , Cosani A. , Peggion E. , Gotte L. , Garbisa S. 
Published: December 2004

AbstractThe interaction of calcium ions with α‐elastin has been investigated by equilibrium dialysis, CD, and microcalorimetric techniques. Consistent with literature data, it was found that the interaction in water is very poor. In trifluoroethanol (TFE), equilibrium dialysis experiments showed that calcium ions bind to ∼‐elastin with an association constant of ∼250 L × mol−1. Such a figure is not consistent with highly specific, highly selective binding. It was also found that the CD response is not directly proportional to the amount of bound calcium but depends on the protein concentration. From microcalorimetric experiments it was found that the heat effect relative to the binding process is of the order of 1.9 kcal/g ion. From this figure and from the binding constant, a positive ΔS value of about 17 e.u. was evaluated, leading to the conclusion that the binding process is entropy driven. From microcalorimetric measurements a ΔH of 1.5 kcal/residue was found for the calcium‐induced conformational transition of the protein.
Quasielastic light‐scattering study of polyadenylic acid solutions. II
Authors: Mathiez P. , Mouttet C. , Weisbuch G. 
Published: December 2004

AbstractQuasielastic light scattering is used to study saline solutions of polyadenylic acid with varying polymer concentrations and molecular masses. These experiments clearly show the existence of two relaxation times. For dilute solutions, when the chains are mutually independent, the fast mode is due to the free diffusion of the polymer chains. For concentrations above the overlap concentration C*, the fast mode is due to the propagation of collective excitations of the pseudolattice of polymer chains. The slow modes are observed when the polymer concentration is in the vicinity of the overlap concentration C*. A series of experiments shows that both their relaxation time and amplitude depend only on the polymer concentration and not on the polymer molecular mass. This result rules out any previous explanation based on individual chain motion. Furthermore, since the amplitudes depend on the time elapsed from the preparation of the solution, the slow modes are due to the diffusion of concentration inhomogeneities in the pseudolattice.
Determination of molecular weight by neutron scattering
Authors: Jacrot Bernard , Zaccai Giuseppe 
Published: December 2004

AbstractTheoretical and practical advantages of neutron scattering for the determination of molecular weights of particles in solution are discussed. The method presented does not use known particles for calibration and is applicable to a wide molecular weight range (104–109); it is not sensitive to assumptions about the partial specific volume of the particles, and the experiments are performed quite easily in standard spectrophotometer cells using 100–500 μg of material. The method is nondestructive and the sample can be recovered totally. The use of D2O in solvents has particular advantages especially for multicomponent particles, for which the in situ molecular weight of each component can be determined separately.
Condensed states of nucleic acids. III. Ψ(+) and Ψ(−) Conformational transitions of DNA induced by ethanol and salt
Authors: Huey Ruth , Mohr Scott C. 
Published: December 2004

AbstractThe conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro‐molecule with unusually large positive ellipticity in the 250–300‐nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples—via a series of intermediate forms with CD spectra resembling those of A‐DNA, then B‐DNA—into Ψ(−) states having anomalously large negative ellipticity similar to the well‐known Ψ(−) forms produced by above‐critical concentrations of poly‐(ethylene oxide) and salt. These ethanol/salt‐induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B‐form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(−) interconversion has been reported. A “skein‐of‐yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
DEPBT as an efficient coupling reagent for amide bond formation with remarkable resistance to racemization
Authors: Ye Yun‐hua , Li Haitao , Jiang Xiaohui 
Published: December 2004

Abstract3‐(Diethoxyphosphoryloxy)‐1, 2, 3‐benzotriazin‐4(3H)‐one (DEPBT) is an effective coupling reagent for synthesis of linear and cyclic peptides by both solution and solid‐phase peptide synthesis. DEPBT mediates amide bond formation with remarkable resistance to racemization. When DEPBT is used as a coupling reagent, it is not necessary to protect the hydroxy group of the amino component (such as tyrosine, serine, and threonine) and the imidazole group in the case of histidine. The high efficiency of DEPBT and its utility have been demonstrated in the syntheses of complex natural products such as ramoplanin A2, ramoplanose aglycon, ustiloxin, and teicoplanin aglycon. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Theory of the helix–coil transition in DNA considered as a copolymer
Authors: Lifson Shneior 
Published: December 2004

AbstractThe grand‐partition‐function theory of the preceding paper is used to derive expressions for the number of base pairs bonded in DNA with explicit consideration of the copolymeric nature of the DNA. The following features of the DNA molecule are taken into account: (1) the DNA's from different sources have different ratios of a–t and g–c pairs; (2) the a–t pair is weaker than the g–c pair; (3) the nearest‐neighbor frequencies of the two kinds of base pairs are nonrandom; (4) the stacking energies (nearest‐neighbor energies) of the various combinations of pairs may be different. An ensemble is constructed in which the features (1) through (4) are introduced by means of statistical weights on the various pairs and combinations of pairs, and an expression for the corresponding partition function is written. Expressions are derived for the number of bonded base pairs and the number of helical sequences.
Absorption and rotation of light by helical oligomers: The nearest neighbor approximation
Authors: Bradley D. F. , Tinoco I. , Woody R. W. 
Published: December 2004

AbstractExplicit expressions for the DK and RK associated with the excitation of regular oligomers from their ground states to the Kth exciton state as functions of N, P, μ, μ∥, μt, and μr have been derived on the assumption that the only perturbation Vij to the N singly excited states results from exciton transfer between adjacent residues, V12. The DK relation predicts the occurrence of a perpendicularly polarized absorption band arising from μ⟂ and a parallel polarized band from μ∥ with maxima at K = [2(N + 1)/P] and 1, which are shifted from the monomer band by 2V12 cos(2π/P) and 2V12cos[π/(N + 1)], respectively. Overlapping of the bands, which may occur in oligomers, decreases rapidly with N, leaving two perfectly polarized bands in the polymer. Within each band which includes only a few levels near the maxima, the most probable transition may be associated with all of the intensity for very short chains but only 40.2–50% (⟂) and 80.9% (∥) as N → ∞ (polymer case). A relation was derived by which V12 may be simply calculated from μ, μr, μt, μ∥, a, and z. The nearest neighbor theory was compared with experiment by calculating a reasonable set of the relevant parameters which exactly account for known spectral shifts.
Polynucleotides. VI. Molecular properties and conformation of polyribouridylic acid
Authors: Richards Edward G. , Flessel C. Peter , Fresco Jacques R. 
Published: December 2004

AbstractOptical, hydrodynamic, and titration properties of polyribouridylic acid (poly U) were investigated in 0.2M Na+, pH 6. Above 15°C., poly U was shown to be a randomly coiled single chain, devoid of secondary structure. There is no shear rate dependence of viscosity; molecular weight is independent of ionic strength; there is virtually no conformationally dependent hypochromicity; no anomalous optical rotatory dispersion; and no anomalous titration behavior. The dependence of the sedimentation constant and intrinsic viscosity on molecular weight was determined. Poly U was shown to be the most highly expanded of all synthetic and naturally occurring randomly coiled polynucleotides.
Studies of the conformation of amylose in solution
Authors: Rao V. S. R. , Foster Joseph F. 
Published: December 2004

AbstractIt has been suggested previously that water is a nearly indifferent solvent for amylose on the basis that the exponent a of the Mark‐Houwink equation is very nearly 0.50 and the second virial coefficient A2 is extremely small. It is shown that such solutions do not show the expected precipitation on cooling and the temperature coefficient of the intrinsic viscosity is small and negative. It is suggested that water is both an indifferent and a nearly athermal solvent for this polymer. Various lines of evidence suggest the polymer to exist as a very stiff coil in this and in other solvents. Variations in the intrinsic viscosity and radius of gyration in various solvents show the importance of skeletal effects in addition to the usual osmotic effects. Application of the Porod‐Kratky wormlike coil model leads to unreasonably short persistence lengths if the contour length is based on a fully extended conformation but large and reasonable values of the order 40–70 A. if it is assumed that the basic conformation is the helical one observed in various amylose complexes in the crystalline state. As was previously known, the specific optical rotation decreases sharply in aqueous solutions above approximately pH 12. Accompanying this change in rotation there is first a decrease, then an increase in intrinsic viscosity. This later behavior is strikingly reminiscent of the known behavior of polyglutamic acid in the pH‐dependent transition from helix to coil. It is concluded that the conformation is that of a stiff coil with essentially helical backbone contour in neutral solution, and the decrease in rotation and in intrinsic viscosity at high pH results from a partial breakdown of the helical structure with a concomitant increase in backbone flexibility. The increase in viscosity and radius of gyration in extreme alkaline solution is probably due to a polyelectrolyte expansion of the polymer coil. Some other miscellaneous observations which are in accord with this model are also pointed out.
Phonon dispersion curves and normal coordinate analysis of α‐poly‐L‐alanine
Authors: Fanconi Bruno , Small Enoch W. , Peticolas W. L. 
Published: December 2004

AbstractThe vibrational frequencies of α‐helical poly‐L‐alanine and its N‐deuterated analog have been assigned by normal coordinate analyses. The phonon dispersion curves and frequency distribution of α‐poly‐L‐alanine have been calculated by using a model which includes hydrogen bonding. The frequency distribution was used to interpret the inelastic neutron scattering data and to calculate the heat capacity. The low‐frequency chain modes involving accordian‐like motions of the whole helix have been calculated and their dispersion investigated by means of a simplified model.
Time dependent model for hemoglobin and allosteric enzymes. II.
Authors: Bush Robert Ter , Thompson Colin J. 
Published: December 2004

AbstractThe time‐dependent theory developed in Part I is specialized to treat tetrameric hemoglobin, and the results of the theory for dimeric‐and tetrameric hemoglobin are compared with data on the kinetics of the reactions of hemoglobin with carbon monoxide and oxygen at various salt concentrations for the case of large concentration of ligand relative to that of hemoglobin. The fit of the theoretical results to the data suggests that hemoglobin at a 2 M salt concentration is predominantly dimeric and that the tetramer should be taken as the functional unit to explain the kinetics of the reactions of normal hemoglobin. A relationship is established between the time‐dependent theory arid Adair's Intermediate Compound Hypothesis (I.C.H.) for hemoglobin, as brought to its present state by Gibson and Roughton. A generalization (G.I.C.H.) of the I.C.H. is presented and is shown to be equivalent to the time‐dependent theory in the limit of infinite ligand concentration. The I.C.H. is shown to be an excellent approximation to the centralized theory (G.I.C.H.) in this limit.
Proton transfer and polarizability of hydrogen bonds formed between cysteine and lysine residues
Authors: Kristof Wolfgang , Zundel Georg 
Published: December 2004

Abstract(L‐Cys)n + N‐base systems and (L‐Cys)n + (L‐Lys)n systems were studied by ir spectroscopy. It is shown that in the water‐free systems, SH ⃛N ⇌ S− ⃛H+N hydrogen bonds are formed. With the (L‐Cys)n + N‐base systems, both proton‐limiting structures in the SH ⃛N ⇌ S− ⃛H+N bonds have equal weight when the pKa of the protonated N‐base is 2 pKa units larger than that of (L‐Cys)n. The same is true with the water‐free (L‐Cys)n + (L‐Lys)n system. Thus, with regard to the type of proton potentials present, these hydrogen bonds are proton‐transfer hydrogen bonds showing very large proton polarizabilities. This is confirmed by the occurrence of continua in the ir spectra. Small amounts of water open these hydrogen bonds and increase the transfer of the proton to (L‐Lys)n. In the (L‐Lys)n + N‐base systems, with increasing proton transfer the backbone of (L‐Cys)n changes from antiparallel β‐structure to coil. In (L‐Cys)n + (L‐Lys)n, the conformation is determined by the (L‐Lys)n conformation and changes depending on the chain length of (L‐Lys)n. Finally, the reactivity increase in the active center of fatty acid synthetase, which should be caused by the shift of a proton, is discussed on the basis of the great proton polarizability of the cysteine–lysine hydrogen bonds.
Intramolecular low‐frequency vibrations in lysozyme by neutron time‐of‐flight spectroscopy
Authors: Bartunik H. D. , Jollès P. , Berthou J. , Dianoux A. J. 
Published: December 2004

AbstractHigh‐resolution neutron time‐of‐flight (TOF) spectra were measured for partly deuterated hen egg‐white lysozyme in solution with and without N‐acetyl‐glucosamine inhibitor bound to the cleft, and in polycrystalline form. Weak but reproducible bands occur at frequencies between 25 and 375 cm−1. The bands were tentatively assigned on the basis of previous results for homopolypeptides. At very small energy transfers (between about 1 cm−1 and 40 cm−1), the TOF spectra show a dependence both on inhibitor binding and crystalline environment. This is interpreted in terms of conformational flexibility.
Influence of ionic strength on the dichroism properties of polynucleosomal fibers
Authors: Lee Keun Su , Crothers Donald M. 
Published: December 2004

AbstractWe report electric‐dichroism and electron‐microscopic studies of chromatin fibers fixed by protein–protein crosslinking at salt concentrations ranging from 10 to 100 mM. The results confirm a progressive disorganization of the fiber as the salt concentration is lowered. The positive dichroism and large polarizability anisotropy characteristic of the 300‐Å diameter fiber found in 100 mM salt are replaced by negative dichroism and smaller effective polarizability anisotropy or dipole moment for samples fixed at lower salt concentration. We interpret the results in terms of segmental, field‐induced orientation of the disorganized structure which is present in low salt concentrations. We also observed a field‐induced absorbance decrease in chromatin fibers fixed at salt concentration at and below 100 mM. All three optical effects, namely overall orientation of the high‐salt fixed fiber, segmental orientation of the low‐salt fixed fiber, and field‐induced absorbance decrease, occur on roughly the same time scale, 20–100 μs for 50 nucleosome polynucleosomes. The polarizability anisotropy of fibers fixed in 100 mM salt was found to be proportional to the length of the fragment and to the reciprocal square root of the conductivity of the solution used for electric‐dichroism measurements. Addition of Mg2+ to the measurement buffer affected the dichroism amplitude of samples fixed below 100 mM salt but not those fixed at 100 mM salt. The results reinforce the need for caution in interpreting electric‐dichroism measurements on chromatin fibers because of possible field‐induced distortion effects.
Structure of the deoxytetranucleotide d‐pApTpApT and a sequence‐dependent model for poly(dA‐dT)
Authors: Viswamitra M. A. , Shakked Zippora , Jones P. G. , Sheldrick G. M. , Salisbury S. A. , Kennard Olga 
Published: December 2004

AbstractThe x‐ray structure of the hydrated ammonium salt of the deoxytetranucleotide d‐pApTpApT was determined by Patterson and direct methods at a resolution of 1 Å. The crystal structure contains right‐handed double‐helical segments formed by complementary Watson‐Crick‐type hydrogen bonding between the adenine and thymine bases of neighboring molecules. The minihelix contains two base pairs. The chains are antiparallel. The A‐T and T‐A sequences have different phosphodiester conformations. The deoxyribose‐pucker and the sugar–base orientation alternate along the chain depending on the nature of the base (3′‐endo for purine and 2′‐endo for pyrimidine). The extended structure is stabilized by base–base, base–sugar, and hydrogen‐bond interactions. The minihelix of two base pairs provides starting coordinates for model‐building studies of the dA‐dT polymer. A B‐DNA‐type polymer structure is described, which has sequence‐dependent alternations of both the deoxyribose pucker and the phosphate diester bridge conformation. Such sequence‐dependent DNA structures, if present locally in regions such as operator sequences, could facilitate sequence‐specific interactions. The crystal study also suggests possible geometrical parameters for the replication fork.
The chiroptical properties of proteins. III. Adenylate kinase
Authors: Snyder Robert W. , Hooker Thomas M. 
Published: December 2004

AbstractThe CD spectrum of the enzyme adenylate kinase has been investigated. Theoretical calculations, based on the x‐ray crystal structure, have been carried out by means of an origin independent matrix formalism. The entire molecule was included in the calculations in the sense that essentially all electronic transitions that occur at wavelengths longer than 185 nm were included in the basis set. A linear dielectric function was utilized to evaluate the intertransition coupling potentials. The results of the theoretical calculations were in reasonable agreement with experimental CD spectra of the molecule.
Dynamics of folding and unfolding transition in a globular protein studied by time correlation functions from computer simulation
Authors: Kanô Fumiaki , Gō Nobuhuro 
Published: December 2004

AbstractA method of calculating time correlation functions from records of computer simulated equilibrium conformational fluctuations in a globular protein is discussed. Use of the calculated time correlation function for discussions of dynamics of folding and unfolding transition in the two‐dimensional lattice model of proteins. The time correlation functions can be approximated in general by a sum of two simple exponential terms. The relaxation time of the slower mode does not depend on the nature of the physical quantity with respect to which the time correlation function is calculated. This time characterizes the overall folding and unfolding transition. The relaxation time of the faster mode depends on the nature of the physical quantity and characterizes conformational fluctuations within each of the native and denatured states. The mechanism of a previously observed phenomenon of the acceleration of the folding and unfolding transition by short‐range interactions is discussed.