bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of solvent composition on the mechanical properties of arterial elastin
Authors: Winlove C. P. , Parker K. H. 
Published: December 2004

AbstractWe have investigated the effects of changes in solution composition on the mechanical properties of rings of arterial elastin. The time course of force equilibration at constant strain following a change in the composition of the bathing solution was measured. Both the force developed during slow extension and force relaxation following rapid straining were also measured in each of the test solutions. The results are difficult to summarize because all of the primitive quantities measured—sample dimension, slope of the force‐extension curve, force overshoot and time of relaxation—as well as the derived quantities such as elastic modulus changed in different and apparently uncorrelated ways. Changes in pH and ionic composition of the bathing solution had small effects consistent with the low fixed charge density of elastin. Solutions of glucose, sucrose, and ethylene glycol had larger effects consistent with changes in hydrophobic interactions. The viscosity of the solution that penetrated the intrafibrillar space of the elastin appeared to be a major determinant of the dynamic response.
A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: Comparison with crystallographic ordered water sites
Authors: Subramanian P. S. , Pitchumani S. , Beveridge D. L. , Berman Helen M. 
Published: December 2004

AbstractMonte Carlo computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water–water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar–phosphate backbone were examined, and the probabilities of occurrence for one‐ and two‐water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x‐ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and ammonium salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation to compete unfavorably with the adjacent donor site at guanine N2. There is, however, a significant probability of finding a one‐water G‐N3–W–G‐N2 bridge indicated in the simulation. An explanation for the guanine N3 discrepancy in terms of electrostatic potentials is also offered. The calculated one‐and two‐water bridges in the rGpC hydration complex coincide in a number of cases to those observed in the ordered water structure of the sodium rGpC crystal hydrate.
Solvent effect on binding thermodynamics of biopolymers
Authors: Ben‐Naim A. , Ting K. L. , Jernigan R. L. 
Published: December 2004

AbstractThe indirect solvent‐induced effect on the free energy of binding of biopolymers is examined within the framework of classical statistical mechanics. We focus specifically on the role of the solute–solvent hydrogen bonding. In particular, we have estimated the first order solvent effedt on the indirect interaction between two biopolymers. We find that the solvent‐induced interactios between two hydrophilic groups through water‐bridged hydrogen bonds could significantly enhance the binding free energy. Some preliminary estimates indicate that this effect is significant and perhaps could be crucial in molecular recognition processes. Furthermore, we have calculated, from crystal structure data, the distance distribution between all the oxygens and nitrogens on the surface of some proteins that do not belong to the binding domain. In most cases we found an enhanced peak in the range of 4–5 Å, which is where we expect to find strong solvent‐induced interactions.
The relative contribution of electrostatic interactions to stabilization of collagen fibrils
Authors: Wallace Donald G. 
Published: December 2004

AbstractElectrostatic energies of interaction between type I collagen molecules were calculated, using models developed by Timasheff and Hill. These energies, along with a contribution from hydrophobic forces, were then incorporated into an equation due to Flory that described phase equilibria of rod‐like polymers. The Flory formalism in turn permitted a calculation of the overall free energy of fibril formation (ΔFf), and an assessment of the relative contribution of electrostatic and hydrophobic forces to ΔFf. Lastly, ΔFf Lastly, ΔFf was used in a nucleation‐growth model relating halftimes of fibril formation (t1/2) to ionic strength (I) and temperature. Because the theory provided no basis for setting absolute levels of the energetic contributions, five parameters in the model had to be derived from experimental data. Based on the fit of theory to experimental results both for intact and pepsinized collagen, it was found that very low electrostatic energies (about −1 kcal/mole per collagen molecule) were sufficient to explain experimental t1/2 vs I relationships. This energy is equivalent to 1 close charge‐pair interaction per molecule and appears to be lower than the energy assignable to hydrophobic interactions.
Analysis of the charge distribution in the C‐terminal region of histone H1 as related to its interaction with DNA
Authors: Subirana Juan A. 
Published: December 2004

AbstractWe have studied the net positive charge distribution in the C‐terminal region of histone H1. We find that it is not random, but rather uniform. In most histone H1 sequences, 4 ± 1 positive charges are found in this region of the molecule in over 95% of all possible segments that are 10 amino acids long. Neither alternating sequences (basic–;nonbasic) nor more complex repeating sequences are ever found. Clusters of three or more basic amino acids are seldom observed in somatic H1s, yet their presence increases in sperm histones and even more so in protamines. It is concluded that the C‐terminal region of histone H1 has a remarkably uniform distribution of charge, in spite of its apparent variactions in sequence in different proteins and within individual molecules. The functional significance of these findings is discussed, suggesting a purely electrostatic role for the C‐terminal region of histone H1, which may be evenly wrapped around individual segments of DNA molecules, thus decreasin its net charge. A likely candidate for a long α‐helical region in the C‐terminal region of histone H1 from sea urchin spermatozoa also has been located. This region may contribute to the aggregating properties of this histone in sperm chromatin.
Block‐units method for conformational calculations of large nucleic acid chains. I. Block‐units approximation of atomic structure and conformational energy of polynucleotides
Authors: Vorobjev Yu. N. 
Published: December 2004

AbstractA new block‐units method for rapid conformational calculation of large nucleic acid fragments has been developed. Atomic structure of polynucleotides has been approximated by the block‐units structure. Each monomer of the polynucleotide consists of three one‐center block units: phosphate, ribose, and nucleic base. Full conformational energy of the polynucleotide is separated into two parts. The first part is the energy of the short‐range interactions between adjacent block units and is calculated on the basis of the potential energy surface model of the dinucleotide fragment pXp (where × = A, G, T, U, C). The second part is the energy of the middle‐ and long‐range interactions between separated block units, and is calculated as a sum of the effective interaction energies between centers of the block units. The present block‐units method is in agreement within the range of ±0.5 kcal/mol with the method of the atom‐atom potentials, but the former is 30–100‐fold faster. The block‐units method is recommended for screening of the probable conformations of the large polynucleotide systems.
Thermodynamics of solvation of proteins in guanidine hydrochloride
Authors: Ahmad Faizan , Bigelow Charles C. 
Published: December 2004

AbstractThe interpretation of the thermodynamic quantities of solvation, that is, Gibbs free energy, enthalpy, and entropy changes for the transfer of proteins from water to 6M guanidine hydrochloride, in terms of the thermodynamic transfer parameters of the groups that make up the protein molecule, is unsatisfactory. We believe this is because the latter are assumed to be identical to the transfer parameters of similar groups attached to smaller model compounds (amino acids and dipeptides). We have empirically determined relationships between transfer quantities for individual protein components and similar groups in model compounds. Comparison of calculated values, based on the modified theory, with the experimental values, reveals very good agreement.
The effect of linear anisotropies on the CD spectrum: Is it true that the oriented polyvinyalcohol film has a magic chiral domain inducing optical activity in achiral molecules?
Authors: Shindo Yohji , Nishio Motohide 
Published: December 2004

AbstractRecent publication of the induced CD studies by Ritcey and Gray [(1988) Biopolymers 27, 1363–1374] states that the Congo red dye bound to regenerated cellulose in highly swollen gel films formed shows induced optical activity, reflecting the chiral molecular arrangement of the cholesteric structure. In this paper, we show that this conclusion is erroneous owing to a misinterpretation of the experimental results. We point out in detail where the errors were committed, and present our experimental data to prove that the average CD signal obtained with using the method of Tunis‐Schneider and Maestre [(1970) J. Mol. Biol. 52, 521–541] can never be regarded as the true induced CD signal. We further present the result of analyzing our data with the Mueller matrix approach to confirm our conclusion. We repeat the conclusion of our previous paper [(1985) J. Am. Chem. Soc. 107, 91–97] that the CD spectra observed in cholesteric liquid structure cannot provide us with the proof showing the optical activity induced in achiral molecules.
Phase transitions of concentrated DNA solutions in low concentrations of 1 : 1 supporting electrolyte
Authors: Strzelecka Teresa E. , Rill Randolph L. 
Published: December 2004

AbstractTransitions between isotropic and liquid crystalline phases of concentrated solutions of DNA with an average contour length (500 Å) near the persistence length were examined in 0.01 M supporting 1 : 1 electrolyte (predominantly NaCl). A quantitative phase diagram describing the transitions occurring over a DNA concentration range from 100 to 290 mg/mL and temperatures from 20 to 60°C was constructed from solid‐state31P‐nmr data and examination of the morphologies of the mesophases by polarized light microscopy. Three anisotropic phases were observed in solutions with DNA concentrations of 160–290 mg/mL: an unidentified, weakly birefringent phase termed “precholesteric” a true cholesteric phase with pitch ≈ 2 μm, and a third, presumably more highly ordered phase. Comparison with previous studies showed that the critical concentration for anisotropic phase formation and the nature of the phases formed by these DNA molecules are not strongly affected by decreasing the supporting electrolyte concentration from ∼ 0.2 M to 10 mM. There are, however, profound effects of decreasing the supporting electrolyte concentration on the width of the transition from isotropic to totally anisotropic solutions, and the nature of the transitions between phases. Decreasing the supporting electrolyte concentration significantly increases the concentration range of persistence of the isotrophic phase, and results in the formation of triphasic solutions (isotropic and two liquid crystalline phases).Values of the critical DNA concentrations for anisotropic phase formation calculated from the theory of A. Stroobants et al. [(1986) Macromolecules 19, 2232 to 2238] were found to be significantly lower than the observed values for any reasonable estimate of the effective radius, probably because of the relatively short lengths of DNA fragments examined in the present study. Comparison of the experimentally determined DNA concentrations required for anisotropic phase formation with the values predicted from Flory's lattice statistics theory, which explicitly considers the rod length, permitted estimation of the effective DNA radius. The estimated radius was inconsistent with effective radii calculated from Poisson‐Boltzmann (P‐B) theory based on a supporting electrolyte concentration of 10 mM, but was in fair agreement with P‐B theory assuming that Na+ DNA contributes approximately 0.24 Na+ counterions/nucleotide to the effective free sodium ion concentration.
The solution conformations of ferrichrome and deferriferrichrome determined by 1H‐nmr spectroscopy and computational modeling
Authors: Constantine K. L. , De Marco A. , Madrid M. , Brooks C. L. , Llinás M. 
Published: December 2004

AbstractWe have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x‐ray crystallographic structure [D. van der Helm et al. (1980) J. Am. Chem. Soc. 102, 4224–4231]. The Al3+ and Ga3+ diamagnetic analogues, alumichrome and gallichrome, dissolved in d6‐dimethylsulfoxide (d6‐DMSO), were investigated via one‐ and two‐dimensional 1H‐nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984) Bull. Math. Biol. 46, 673–691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983) J. Comp. Chem. 4, 187–217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the14N‐1H dipolar interaction, demonstrate that the x‐ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6‐DMSO at 23°C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CHα multiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH‐CHα and NH‐NH Overhauser connectivities, which reflects the 〈r−6〉 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the “true” structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straightforward approach can be misleading since the nmr parameters are averaged over substantially different conformational states.
Size, shape parameters, and Ca2+‐induced conformational change of the gelsolin molecule: A dynamic light scattering study
Authors: Patkowski A. , Seils J. , Dorfmüller Th. , Hinssen H. 
Published: December 2004

AbstractWe have investigated the size and shape of gelsolin, a calcium‐dependent actin‐binding protein, by means of combined photon correlation spectroscopy and depolarized dynamic light scattering. From the measured rotational and translational diffusion coefficients, a hydrodynamically equivalent ellipsoid of revolution with an axial ratio of 0.23 is obtained in the presence of EGTA. Such a distinctly elongated shape is suggested also by the depolarization ratio of 1.6 × 10−3. In the presence of Ca2+, when gelsolin has two Ca ions bound, a significant decrease in the translational diffusion coefficient and a smaller decrease in the rotational diffusion coefficient are observed. Both effects can be assigned to a change of shape from the elongated toward a more spherical form with an axial ratio of 0.37 and a hydrodynamic volume more than twice as large as in the absence of Ca2+. The apparent molecular mass as measured by static light scattering remains unchanged, indicating that the volume increase is not due to aggregation of gelsolin. The relatively large conformational changes observed upon binding of Ca2+, are probably related to an alteration of the surface charge of the molecule. As a result of these conformational changes, actin binding sites may become exposed and the molecule gains a high affinity for two actin molecules.
Excluded volume effects on the partition of macromolecules between two liquid phases
Authors: Zimmerman Steven B. , Trach Stefan O. 
Published: December 2004

AbstractPartition parameters of several proteins and other macromolecules are measured in an aqueous two‐phase liquid system containing polyethylene glycol and phosphate buffer. Distribution of macromolecules is a function of the relative volume excluded to the macromolecules in the two phases. A simple model with no adjustable parameters yields covolumes of the macromolecules with the polyethylene glycol. Covolumes are used to estimate effective molecular volumes and the magnitudes of excluded volume effects. The same approach is applied to mixtures of macromolecules.
Counterion effects on the physical properties and the A to B transition of calf‐thymus DNA films
Authors: Lavalle N. , Lee S. A. , Rupprecht A. 
Published: December 2004

AbstractWe report measurements of the water content and swelling of wet‐spun films of Na‐, K‐, Rb‐, and Cs‐DNA as a function of relative humidity (rh). The water contents (number of water molecules per base pair of DNA) of these films are found to be quite similar, indicating that the identity of the counterion species is unimportant for the water content. Since the A to B transition for these DNAs occurs at different rhs, the corresponding water contents of the A to B transition are found to be quite different. These films swell as a function of rh in a very similar manner, implying that the changes in the intermolecular bonds in the different DNAs are similar. Dramatic changes are observed in the dimensions of the films above 84% rh for all types of DNA. Combining the water content and swelling measurements yields the dependence of the volume per base pair on water content. The volume per base pair is observed to be a nonlinear function of water content, indicating nonideal mixing of the water with the DNA.
Crystal and molecular structure of Boc‐D‐Ala‐ΔPhe‐Gly‐ΔPhe‐D‐Ala‐OMe: A 310‐helical dehydropeptide
Authors: Ciajolo M. Rosaria , Tuzi Angela , Pratesi Claudio R. , Fissi Adriano , Pieroni Osvaldo 
Published: December 2004

AbstractThe crystal and molecular structure of the pentapeptide Boc‐D‐Ala‐ΔPhe‐Gly‐ΔPhe‐D‐Ala‐OMe, containing two dehydrophenylalanine residues, was determined by x‐ray diffraction. The molecule crystallizes in the orthorombic P212121 space group, with a = 10.439(3), b = 15.319(3) and c = 21.099(4) Å.In the solid state, the conformation of the pentapeptide is characterized by the presence of two type III′ β‐turns. Thus the peptide assumes a left‐handed 310‐helical conformation, the left sense being due to the D configuration of the alanine residues. The two unsaturated residues are located in the (i + 1) position of the first β‐turn and in the (i + 2) position of the second β‐turn, respectively.In the crystal, the helical molecules are linked head to tail by hydrogen bonds. Lateral hydrogen bonds are also formed between molecules related by a twofold screw symmetry. This gives rise to a typical mode of packing characterized by infinite helical “chains,” smiliar to the packing found in other oligopeptides that adopt a 310‐helical structure.
Conformational search in enkephalin analogues containing a disulfide bond
Authors: Froimowitz Mark 
Published: December 2004

AbstractA systematic Conformational search has been performed for the 14‐membered ring in model compounds for disulfide‐containing enkephalin analogues. The model compounds examined are , and the corresponding compounds with L‐amino acids at the C‐terminus. About 100 starting conformations were generated for each compound with the RNGCFM program and energy minimized with the AMBER program. Between 21 and 38 conformers within 3 kcal/mole of the apparent global minimum were found for each compound. There appeared to be fewer possible conformations of the disulfide‐containing side chain than of the main chain. , whose parent compound is selective for opioid δ receptors, was found to prefer conformers with a positive dihedral angle of the disulfide bond, which is consistent with the previous proposal that δ‐receptor selectivity may be associated with this conformational preference. Additional calculations were performed on the complete structure of (DPDPE) with various possible conformations of the tyrosine and phenylalanine side chains. Conformational free energies and entropies were computed for these conformers from the molecular vibrations obtained from a normal mode analysis. As was found previously, conformers with low energies tended to have lower entropies, which resulted in a narrowing of the free energy differences between conformers. A conformer is identified that has the lowest energy hitherto found for DPDPE. It is suggested that DPDPE may be a useful compound for evaluating conformational search strategies because of its relatively small size and the number of conformers that have already been identified. Conformational energy calculations are also reported for naltrindole using the MM2(87) program. Naltrindole, which incorporates two aromatic 6‐membered rings in a rigid structure, is a highly selective and potent opioid δ‐receptor antagonist and may be an important clue regarding the biologically active conformer of DPDPE. Various conformers of DPDPE have been superimposed quantitatively onto the structure of naltrindole using the SUPER program and those conformers of DPDPE that are the best fit to naltrindole are reported.