bluuebunny/crossref_metadata_2025_split huggingface dataset:
A ligand binding model of counterion condensation to finite length polyelectrolytes
Authors: Dewey T. G. 
Published: December 2004

AbstractA ligand binding model of counterion association in finite length polyelectrolytes is presented. This model introduces counterion condensation features into a binding formalism. It agrees well with the predictions of other finite length models and is consistent with experimental data on helix–coil melting transitions for short nucleic acid oligomers. This model uses a discrete charge distribution for the polyelectrolyte. An expression for the electrostatic self‐energy of finite length polyelectrolytes is derived using the Euler–Maclaurin sum formula. This sum is shown to be accurate over a wide range of salt concentrations. This electrostatic term is used in an energy minimization analysis. The energy minimization is solved analytically using a Lagrange inversion formula. This general procedure gives a rapidly convergent series and requires no assumptions with regard to “limiting law” behavior. However, when used in the Manning minimization formalism [(1977) Biophysical Chemistry, 24, 2086], the volume of the condensed phase becomes unrealistically large at low ionic strength. The ligand binding model does not have a condensed phase volume as a parameter. It provides a single expression that agrees both with Manning's theory and with the theory of Ramanathan and Woodbury [(1982) Journal of Chemical Physics 77, 4133] under the respective conditions of these theories.
Solvent effects on the cooperative order–disorder transition of aqueous solutions of schizophyllan, a triple‐helical polysaccharide
Authors: Hirao Takayuki , Sato Takahiro , Teramoto Akio , Matsuo Takasuke , Suga Hiroshi 
Published: December 2004

AbstractA triple‐helical polysaccharide schizophyllan in aqueous solution exhibited a highly cooperative transition between ordered and disordered states associated with the conformation of its side chains and nearby water molecules. The transition was followed by optical rotation and containing additives such as NaOH and DMSO as solvents. The ordered state was stabilized or destabilized or depending on the kind and amount of the additive employed; in particular, the addition of DMSO had a remarkable stabilizing effect. This effect was analyzed by means of a statistical mechanical theory of linear cooperative transitions, where DMSO was assumed to interact favorably with the ordered side chains. A small amount of NaOH in a solvent mixture stabilized the ordered state and made the transition curve very gradual. No molecular mechanism was elucidated to account for the role of NaOH.
Helix‐coil stability constants for the naturally occurring amino acids in water. XXIV. Half‐cystine parameters from random poly(hydroxybutylglutamine‐CO‐S‐methylthio‐L‐cysteine)
Authors: Wójcik J. , Altmann K.‐H. , Scheraga H. A. 
Published: December 2004

AbstractWater‐soluble, random copolymers containing N5‐(4‐hydroxybutyl)‐L‐glutamine (host) and S‐methylthio‐L‐cysteine (guest) have been prepared, fractionated, and characterized, with S‐methylthio‐L‐cysteine serving as a model for cystine residues in proteins. From the thermally induced helix‐coil transition curves of these copolymers in water at neutral pH, the Zimm‐Bragg parameters σ and s for the helix‐coil transition of “poly(L‐cystine)” were deduced. The results show that the cystine model acts as a weak helix‐breaker over the entire temperature range from 0 to 60°C. The implications of this finding are evaluated in the context of a general discussion of the Zimm‐Bragg parameters for all the 20 naturally occurring amino acids.
Monte carlo method applied in the search for low‐energy conformations of βαβαβ structures
Authors: Carlacci Louis , Chou Kuo‐Chen 
Published: December 2004

AbstractA Monte Carlo approach was used to find low‐energy conformations of sequentially linked βαβαβ structures to be used as initial conformations in energy minimizations. Only L‐type amino acids were used in the study. The composition of the linked polypeptide chain was H(Val)6(R)4(Ala)14(R)4(Val)6(R)4(Ala)14(R)4(Val)6OH. A loop region was represented by (R)4, where R was either Gly or Ala. Two types of connections were considered: connections between nearest neighbor strands in the β‐sheet, and connections between β‐strands separated by one intervening β‐strand. The loop energy and the total energy of the α‐helical and β‐strand segments in the energy‐minimized structures were analyzed. The orientations of the secondary structural elements were characterized. In agreement with the handedness observed by experiment, all right‐handed crossover conformations were computed to have lower conformational energies than the corresponding left‐handed crossover conformations. The energy gaps between the corresponding loop energies also favored right‐handed conformations. Furthermore, the packing angles between the α‐helix axis and the β‐sheet axis are also in good agreement with experimental observations. Therefore the right‐handedness of the observed βαβαβ structure can be understood from the viewpoint of energetics.
Polarized electronic spectra of Z‐DNA single crystals
Authors: Ho Pui S. , Zhou Guangwen , Clark Leigh B. 
Published: December 2004

AbstractPolarized electronic absorption spectra of the (100) face of single crystals of the Z‐form double helical duplex of d(m5CGUAm5CG) have been obtained from Kramers‐Kronig analysis of reflection data. The c crystallographic axis is parallel to the helix axis and shows but weak absorption. The b axis is perpendicular to the helix axis and shows a structureless absorption band centered at 270 nm with an oscillator strength of 0.26. Calculations of the crystal spectra utilizing available transition moment data for the individual chromophores are carried through using the oriented gas model (no interbase interactions) and, again, employing all base‐base interactions (point dipole) in the duplex. The calculated hypochromism of the 270 nm band is much less than the experimental value obtained from the crystal data. The crystal spectra appear to be representative of Z‐form double helices of essentially infinite length and not of a collection of twelve base duplexes. No evidence for nπ* transitions polarized parallel to the helix axis is found.
Studies on the conformation of and metal ion binding by teichoic acid of Staphylococcus aureus
Authors: Pal Medini Kanta , Ghosh Tapash Chandra , Ghosh Jimut Kanti 
Published: December 2004

AbstractTeichoic acid (TA) isolated from the gram‐positive bacteria S. aureus binds cationic dyes like pinacyanol (PCYN), 1,9‐dimethyl methylene blue, acridine orange, etc., depicting blue‐shifted metachromasia, and they bind the cationic dye carbocyanine depicting the red‐shifted J band. TAs do not show any uv absorption band, and exhibition of tailing CD in the short uv region hints at its chiral conformation. Chiral conformation of TA has been confirmed from the induction of strong biphasic CD in the TA–carbocyanine system.Relative affinities for Ca2+, Mg2+, and Na+ have been probed from the disruption of metachromasia of the TA–dye system by these ions. Results show Ca2+ and Mg2+ to be almost equally effective in destroying the metachromasia of the TA–PCYN system, thus not supporting the hypothesis of special affinity for Mg2+ ion.
Theoretical analysis of deoxycytidine‐5′‐phosphate protonation
Authors: Starikov E. B. , Pedash Yu. F. 
Published: December 2004

AbstractThe electron density distribution in deoxycytidine‐5′‐monophosphate (5′‐dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim13 shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X‐ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy‐cytidine‐5′‐monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum‐chemical CNDO/2 technique is applicable to the mono‐nucleotide studies.
Temporary network formation of hyaluronate under a physiological condition. 1. Molecular‐weight dependence
Authors: Yanaki Toshio , Yamaguchi Toshijiro 
Published: December 2004

AbstractThe dynamic shear moduli at various frequencies and stress growth after the sudden start of steady shear were measured for 1% HA (hyaluronic acid) solutions with different molecular weights. From the results of the zero shear viscosity, η0, the steady shear compliance, J and Δη defined as Δη = η0 − ηa (∞), where ηa(∞) is the apparent viscosity at the steady state, it was shown that the molecular mechanism of flow of 1% HA solutions was classified into four regions with respect to molecular weight: (I) the viscosity‐average molecular weight Mv < 35 × 104 HA chains are dispersed molecularly in solution; (II) 35 × 104 < Mv < 100 × 104, the polymer chains form a weak entanglement network observed only through η0 (HI) 100 × 104 < Mv < 160 × 104, the network is strengthened with increasing molecular weight and becomes detectable through both η0 and J and also through the overshoot phenomenon; and (IV) 160 × 104 < Mv, the network is “saturated” or “completed” dynamically. This is the conjecture presented for the first time by the present work.
Nmr conformational analysis of cyclopeptidic substrates of serine proteases, containing an ortho or meta aminobenzoic acid residue
Authors: Convert Odile , Mazaleyrat Jean‐Paul , Wakselman Michel , Morize Isabelle , Reboud‐Ravaux Michèle 
Published: December 2004

AbstractCyclopeptides I and II containing an ortho‐ or meta‐aminobenzoic acid residue are comparatively analysed by 1H‐ and 13C‐nmr. The 1H‐nmr results, i.e., the temperature coefficients ΔδNH/ΔT, the exchange rates of the amide protons, and nuclear Overhauser effects, suggest a predominant conformation for cyclopeptides I. The meta analogues II present a greater conformational mobility. This observation is related to the greater reactivity of peptides II toward enzymatic hydrolysis, compared to their ortho analogues I.
Condensation of DNA by trivalent cations. 2. Effects of cation structure
Authors: Plum G. Eric , Arscott Patricia G. , Bloomfield Victor A. 
Published: December 2004

AbstractElectron microscopy is employed to examine DNA aggregates produced by three tripositively charged condensing agents. Spermidine, hexammine cobalt (III), and me8spermidine (in which the amine groups of spermidine are exhaustively methylated) all produce condensates. The predominant form of condensate observed is toroidal; however, me8spermidine produces a large fraction of rodlike condensates. Distributions of toroidal radii and estimated volumes suggest that the size of condensates depends on the condensing agent employed, its concentration, and the time elapsed after addition of condensing agent. While ligand charge seems to be the major factor in predicting condensing power, ligand structure influences the morphology and dimensions of the particles produced. The ability to form hydrogen bonds is not required to promote condensation, since me8spermidine has no NHs. There may be a kinetic barrier to condensation at low me8spermidine concentrations. The relative proportions of toroids and rods may depend on the energetic compensation between bending and binding in cyclic structures, or on rate‐limiting formation of sharply bent or kinked regions in rods.
Dynamics of F‐actin and F‐actin/filamin networks as studied by photon correlation spectroscopy
Authors: Seils J. , Jockusch B. M. , Dorfmuller Th. 
Published: December 2004

AbstractPhoton correlation spectroscopy was used to study both F‐actin and F‐actin/filamin networks in solution. The measured autocorrelation functions were analyzed with the inverse Laplace transform CONTIN. The resulting frequency distributions consist of maximal five relatively narrow peaks. This rather unexpected finding disagrees with the frequency spectra calculated for an entangled rigid rod model. For this model, we expect spectra consisting of a single broad peak. Factors like flexibility, deviation from an experimental length distribution, interference with chemical reactions, and translation rotation coupling that would influence the profile of the frequency distribution could be excluded by comparison of the data with model calculations or qualitative estimates. We conclude that our data for F‐actin are consistent with the dynamics of an infinite network stable on the time scale of the observed modes. Further support for this interpretation is provided by a comparison with frequency spectra of actin/filamin networks. These appear to be very similar in shape. The main peak of these spectra that corresponds to the slow motions shifts to lower frequencies with increasing cross‐link density. It appears that higher frequency modes of the gel are more efficiently damped with progressive cross‐link density, resulting in a predominance of the slow motions in the spectra. This behavior has been already found in other systems and seems to be a general feature of cross‐linked systems.
Hydration effects on dynamics of polyglycine and sodium poly(L‐glutamate)
Authors: Kennedy Scott D. , Bryant Robert G. 
Published: December 2004

AbstractSolid state nmr methods were applied to the study of the motions and structural heterogeneity in polyglycine, sodium poly (L‐glutamate), and poly(L‐alanine). The response of both the main‐chain and side‐chain resonances to the addition of water was studied using static and magic‐angle sample‐spinning line shapes as well as the carbon spin‐lattice relaxation times, the proton spin‐lattice relaxation time in the rotating frame, and the proton‐carbon cross‐polarization time. The polyglycine motions are not drastically affected by the addition of water when the polymer is in the 31‐helix or the β‐sheet structure. The sodium poly(L‐glutamate), however, responds to increased hydration with little motion in the main‐chain carbon atoms, but considerable flexibility of the side‐chain atoms. The greatest motions are reported for the C5 carbon with rotational amplitudes about the C47‐C5 bond of about of 50°. In addition, motions somewhat less than half this size are required closer to the main chain.
Dynamic properties of the first enzymatic reaction steps of porcine pancreatic elastase. How rigid is the active site of the native enzyme? Molecular dynamics simulation
Authors: Geller Maciej , Carlson‐Golab Gail , Lesyng Bogdan , Swanson Stanley M. , Meyer Edgar F. 
Published: December 2004

AbstractTwo molecular dynamics simulations (100 and 50 ps) of native porcine pancreatic elastase i.e., without bound substrate and with the active site hydrated by a dome of water (630 molecules) have been performed. Dynamical properties of the catalytic tetrad have been examined. While relative conformations of the Asp 102, His 57, and Ser 214 are rather stable in time, the side chain of Ser 195 undergoes several conformational changes. No preferences are observed for the formation of a hydrogen bond between the OγH group (Ser 195) and nitrogen Nϵ (His 57). A cluster of ordered water molecules effectively competes with the HOγ group (Ser 195) and thereby prevents the formation of this H bond, which is generally agreed to be crucial for catalysis.
Saturation photodimerization of thymines in DNA
Authors: Texter John 
Published: December 2004

AbstractAcetophenone sensitizes the uv photodimerization of adjacent thymines in nucleic acids and under steady state irradiation induces irreversible saturation dimerization. Monte Carlo and analytical techniques are used to calculate the saturation dimerization limits for various nucleic acids, under the assumption that acetophenone‐sensitized dimerization occurs by a random irreversible process. A comparison of these calculated results with experimental values indicates that sensitized dimerization occurs by an effectively random process only in single‐stranded DNA or in native DNA of very high A·T content. In general, nucleation phenomena operate in native DNA that serve to stereochemically restrict saturation dimerization limits below those expected for random dimerization.
Experimental evidence for predicted transmembrane peptide topography: Incorporation of hydrophobic peptide α‐helical rods with an N‐terminal positive charge having a length comparable to the thickness of lipid bilayers into the membranes
Authors: Katakai Ryoichi , Wanikawa Kunihiko , Saga Katsuyuki 
Published: December 2004

AbstractLiposomes consisting of egg yolk phosphatidylcholine and hydrophobic peptides Nps‐ and Cl−·+H2−(Met‐Met‐Leu)n‐OEt (n = 6–10) with various polypeptide chain lengths were prepared by the sonication method. The conformation of the peptides incorporated into the liposomes was examined by CD spectroscopy. All the peptides incorporated assumed α‐helical conformation. Quantitative analyses of the peptides and lipids in the membranes showed that the concentration of the peptides with a positive charge at the N‐terminus in the liposomes decreased markedly as the peptide chain length increased, reaching zero for the peptides over n = 8. The peptides without a positive charge were hardly incorporated into the liposomes. Infrared attenuated reflection spectroscopy of multilayered membranes containing the peptides suggests that the axis of the α‐helical peptide rods is oriented in parallel with the molecular axis of lipids in the membranes. These results suggest that the hydrophobic peptides can be incorporated into the lipid bilayers of the liposomes in the α‐helical conformation, the rods of which have a length comparable to the thickness of the lipid bilayers, and the N‐terminal positive charge of the peptides is essential for the stable peptide incorporated into the membranes.
Ab initio self‐consistent field and potential‐dependent partial equalization of orbital electronegativity calculations of hydration properties of N‐acetyl‐N′‐methyl‐alanineamide
Authors: Grant J. A. , Williams R. L. , Scheraga H. A. 
Published: December 2004

AbstractUsing a recently developed parallel computation algorithm, ab initio self‐consistent field (SCF) calculations were carried out to estimate the relative hydration energies for 12 low‐energy conformations of N‐acetyl‐N′‐methyl‐alanineamide. The requisite SCF calculations were carried out using 6‐31G and 6‐31G* basis sets, both in the absence and presence of a perturbing potential arising from a model solvent. The αR, αL, polyproline II (PII), and π helical conformations were preferentially stabilized by the solvent potential, whereas conformations with intramolecular hydrogen‐bonding C5 and C7 were preferred in the gas phase. Average vicinal nmr coupling constants (J), calculated using the total energies of the various solvated conformations, were consistent with observed coupling constants for this peptide in aqueous solution. Substantial alteration of the solute charge density occurred upon equilibration with the reaction field, as was exemplified in changes both in the molecular dipole moments and in atom‐centered multipoles, when the molecule was transferred from a medium of low dielectric constant to one of high dielectric constant. In order to model these changes in charge density with an empirical scheme, we have implemented a novel monopolar representation of the solute charge density based on a potential‐dependent form of partial equalization of orbital electronegativities (PDPEOE). In the atom‐centered point charge PDPEOE representation, charge Hows from one region of the solute to another in response to external fields. Hydration energies calculated using the PDPEOE representation are similar to those calculated by the SCF procedure. Also, the PDPEOE calculations yielded changes in molecular dipole moments upon solvation that agreed closely with the changes in the calculated ab initio SCF dipole moments.
The effects of ligands on the conformation of phosphoglycerate kinase: Fluorescence anisotropy decay and theoretical interpretation
Authors: Mouawad Liliane , Desmadril Michel , Perahia David , Yon Jeannine M. , Brochon Jean‐Claude 
Published: December 2004

AbstractHorse muscle phosphoglycerate kinase (PGK) is a monomer folded into two widely distant domains. In the glycolytic pathway, this enzyme catalyzes the first reaction that produces ATP. It was suggested, by analogy with yeast hexokinase, that a hinge‐bending motion may be induced by the binding of specific substrates to the protein. To analyze such a motion, or any structural changes induced by ligand binding, fluorescence anisotropy decay of tryptophan residues in free and liganded PGK was studied. At 293 K, for the free protein and the binary complex with 3‐phosphoglycerate, a single correlation time of 26 ns was observed, corresponding to the rotation of the overall protein, whereas upon addition of MgADP, this correlation time decreased to 10 ns. Such a decrease cannot be merely due to a change of the protein's shape and volume. To explain this, it was suggested that the fluorescence anisotropy decay of the PGK–MgADP complex corresponded to the rotation of the only buried tryptophan (Trp 335). The rotational paths of this tryptophan, in the presence and absence of the nucleotide, were established by potential energy minimization calculations. The results indicated that MgADP induces a displacement of helix α‐13 that decreases the rotational energy barrier of Trp 335 from 16 kcal/mol in the free protein to 8 kcal/mol in the complex.
A fourier transform IR study of the gelation of amylose and amylopectin
Authors: Goodfellow B. J. , Wilson R. H. 
Published: December 2004

AbstractFourier transform ir spectroscopy has been used to study the gelation and retrogradation of amylose and amylopectin. Results indicate that two processes occur: a fast change complete within 0.5 h shown by both samples and a much slower change that continues up to 400 h seen only for amylopectin. These processes are related to changes in molecular conformation, and are explained in terms of existing models for gelation and retrogradation in amylose and amylopectin.