bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competitive reactions in solutions of DNA and water‐soluble interpolyelectrolyte complexes
Authors: Izumrudov V. A. , Kargov S. I. , Zhiryakova M. V. , Zezin A. B. , Kabanov V. A. 
Published: December 2004

AbstractThe reaction of competitive binding of two polyanions—DNA and synthetic fluorescence‐tagged poly(methacrylate) (PMA*)—with the polycation‐quencher poly(N‐ethyl‐4‐vinyl‐pyridinium) (PEVP) was studied by fluorescence quenching technique. It was found that ability of DNA to displace PMA *from the water‐soluble nonstoichiometric interpolyelectrolyte complex (NPEC) formed by PMA* and PEVP—NPEC(PMA*‐PEVP)—and to form water‐soluble NPEC(DNA‐PEVP)

can be determined by the parameter Ψ = PPMA*/PPEVP where PPMA* and PPEVP are the degrees of polymerization of PMA* and PEVP, respectively. In the case of Ψ < 1 the decrease of Ψ leads to the shift of the reaction equilibrium to the right, which can be explained by the gain of entropy due to the increase of the total number of polymeric particles in the solution. Introduction of alkali metal cations into the reaction mixture results in the shift of the reaction equilibrium, and according to their ability to shift the equilibrium to the right the cations can be arranged in the series Na+ > K+ > Li+. The substitution of native DNA by denatured DNA practically does not affect the reaction equilibrium in solutions of NaCl and KCl but considerably shifts it to the right in solutions of LiCl. The data obtained are in accordance with the differences in the selectivity of alkali cations binding with competitive polyanions. © 1995 John Wiley & Sons, Inc.
Sequence and temperature dependence of the interbase hydrogen‐bond breathing modes in B‐DNA polymers: Comparison with low‐frequency Raman peaks and their role in helix melting
Authors: Chen Y. Z. , Prohofsky E. W. 
Published: December 2004

AbstractWe carry out temperature‐dependent lattice dynamics calculations to determine the vibrational normal modes associated with the interbase H‐bond breathing motion in several B‐DNA copolymers at temperatures from room temperature to the melting temperatures. We take into consideration Raman selection rules and incorporate a simple empirical model of Raman susceptibility in the interbase H bonds in our calculation and compare them to Raman measurements. Our calculations are carried out using empirical force constants that are not further refined to low‐frequency spectra. Our calculations show the existence of strong interbase H‐bond breathing modes at frequencies and with relative oscillator strengths close to the observed Raman peaks in the range of 60–140 cm−1 for the DNA sequences considered except for one helix. The correlation between the calculated and observed frequencies and oscillator strengths indicates that the observed Raman peaks in the frequency range are likely interbase H‐bond breathing modes. We find that these modes exhibit sizable temperature as well as sequence dependence. We show the softening of these modes on approaching thermal denaturation that is also in agreement with the observed behavior in Raman and melting measurements. The sensitivity of the calculation on the empirical model of Raman susceptibility and the possible reasons for the discrepancy between a few calculated values and observations are discussed. © 1995 John Wiley & Sons, Inc.
Observation of unfreezable water in aqueous solution of globule protein by microwave dielectric measurement
Authors: Miura Nobuhiro , Hayashi Yoshihito , Shinyashiki Naoki , Mashimo Satoru 
Published: December 2004

AbstractA freezing process analyzed by the dielectric method on aqueous solution of albumin has revealed water structure around protein molecule. A relaxation peak due to bound water attached on the protein surface around 100 MHz at room temperature was found. It could be seen commonly in globule proteins. Another peak due to a different kind of unfreezable water was found around 1 GHz at −6°C. The amount of this water is estimated as 0.36 g water/g protein and in good agreement with that obtained by differential scanning calorimetry and nmr measurements. The water molecules form a shell layer around the protein molecule. © 1995 John Wiley & Sons, Inc.
Searching for foldable protein structures using optimized energy functions
Authors: Govindarajan Sridhar , Goldstein Richard A. 
Published: December 2004

AbstractDuring evolution, the effective interactions between residues in a protein can be adjusted through mutations to allow the protein to fold to its native structure on an adequate time scale. We seek to address the question: Are there some structures that can be better optimized than others? Using exhaustive enumeration of the compact conformations of short proteins confined to simple lattices, we find that the best structures are those that contain contacts rare in random structures, indicating the importance of nonlocal contacts for assisting the folding process. Certain structural motifs such as long β‐hairpins, Greek‐key motifs, and jelly rolls, commonly found in proteins of known structure, have a high degree of optimizability. Contrary to what might be expected, positive correlations between the various interactions reduce optimizability. The optimization procedure produces a correlated energy landscape, which might assist folding. © 1995 John Wiley & Sons, Inc.
A reexamination of the double‐helix model for agarose gels using optical rotation
Authors: Schafer Steven E. , Stevens Eugene S. 
Published: December 2004

AbstractThe diffuse x‐ray diffraction patterns of agarose gels are compatible with both the “chicken‐wire” gel model consisting of associated double‐helix chain conformations and a network of more extended, but unentwined helices. Preference f or the double‐helix model has largely rested on an early interpretation of optical rotation data. Applying a recent, less empirical, chiroptical model of saccharide rotation, we confirm the earlier analysis by concluding that the rotation observed in the gel can be satisfactorily accounted for in terms of wide‐diameter agarose helices, capable of intertwining. In addition, we have found that the extended helices found in dried sols do not yield the observed gel rotations. © 1995 John Wiley & Sons, Inc.
Docking of congo red to the surface of crystalline cellulose using molecular mechanics
Authors: Woodcock Steve , Henrissat Bernard , Sugiyama Junji 
Published: December 2004

AbstractA method for the docking of ligands to crystalline surfaces using molecular mechanics was developed and applied to study the molecular features of the adsorption of Congo Red to cellulose crystals. The docking procedure was based on a grid search exploring the surface repeat unit of the cellulose crystals using several orientations of Congo Red at each grid point. Results suggest a preferential adsorption of Congo Red onto certain faces of the cellulose crystals and that the lower energy conformers have a similar positioning and orientation with respect to the cellulose chains at the surface repeat unit. © 1995 John Wiley & Sons, Inc.
Polyelectrolyte electrostatics: Salt dependence, entropic, and enthalpic contributions to free energy in the nonlinear Poisson–Boltzmann model
Authors: Sharp Kim A. 
Published: December 2004

AbstractUsing the nonlinear Poisson–Boltzmann (PB) equation, expressions for the nonspecific salt dependence of the free energy, and the entropic and enthalpic contributions to the electrostatic free energy of a polyelectrolyte are derived. The results are generalized for any number and valence of mobile ions, and now permit a more rigorous treatment of the salt dependence of polyelectrolyte–ligand binding using the PB equation. The salt dependence of the electrostatic free energy depends on an “osmotic pressure like” term identified previously [K. Sharp and B. Honig (1990), Journal of Physical Chemistry, Vol. 94, pp. 7684–7692], which in turn depends on the integrated excess/deficit of all mobile ion species around the polyelectrolyte. For the simple salt case (two ions only) this expression is equivalent to that derived previously [H. Eisenberg (1976), Biological Macromolecules and Polyelectrolytes in Solution, Clarendon. Oxford] in terms of Donnan, or preferential interaction coefficients. Moreover, since all ions enter into the PB expression for the salt dependence of the free energy in an identical way, it is equally applicable to polyelectrolytes with charge of one sign (e.g., nucleic acids), with oppositely charged groups (such as proteins), and even polyelectrolytes that have no net charge, for which the Donnan coefficient is ill‐defined. The distribution of counterions around three simple polyelectrolyte geometries—spherical, cylindrical, and planar—was examined. In each case the excess number of counterions associated with the polyelectrolyte is not constant, but increases with decreasing salt. Although a limiting value is reached at low salt for a cylinder, in agreement with the limiting law condensation models, for the spherical geometry the number of associated counterions decreases to zero, while for the planar case it increases to 100%. For the cylindrical case Donnan coefficients agree closely with those computed previously by Monte Carlo simulations [M. C. Olmstead, C. F. Anderson, and M. T. Record (1991) Biopolymers, Vol. 31, pp. 1593–1604]. An all atom B‐DNA model shows about 5% less accumulation of counterions than a cylinder, due to the helical charge arrangement and groove structure. The entropic and enthalpic contributions to the salt‐dependent free energy of a cylinder were examined in the PB model. In addition to the well known ion cratic (redistribution) entropy, there are significant contributions from electrostatic enthalpy, and from dielectric entropy (water re‐orientation due to the electrostatic field from polyelectrolyte charges and salt ions). The latter entropy contribution has not previously been taken into account in salt‐dependent polyelectrolyte phenomena, but at higher salt concentrations (> 0.01M), this can be as large as the cratic entropy contribution. © 1995 John Wiley & Sons, Inc.
Comparison of base inclination in ribo‐AU and deoxyribo‐AT polymers
Authors: Jin Xiaokui , Johnson W. Curtis 
Published: December 2004

AbstractThe inclination angle between the base normal and the helix axis is measured for ribo‐AU polymers by using flow linear dichroism (LD), and compared to measurements for deoxyribo‐AT polymers under dehydrating conditions. The CD of the DNA polymers under the dehydrating conditions is not the same as the corresponding RNA polymers, which are presumed to be in the A form. However, the LD indicates that poly(dAdT)‐poly(dAdT) can assume the A form in 80% 2,2,2‐trifluoroethanol, although poly(dA)‐poly(dT) retains B form structure in this dehydrating solvent. The inclination angles are similar for B form poly(dAdT)‐poly(dAdT) and poly(dA)‐poly(dT), and these parameters are also similar for A form poly(rArU) ‐poly(rArU) and poly(rA) ‐poly(rU). All the inclination axes are similar. © 1995 John Wiley & Sons, Inc.
Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs
Authors: Schurr J. Michael , Babcock Hazen P , Gebe John A 
Published: December 2004

AbstractIn principle, the supercoiling free energy of a small circular DNA will be enhanced by increasing the anisotropy of its bending potential at constant persistence length. The magnitude of this effect is investigated by Monte Carlo simulation using an extension of a previously proposed algorithm. The supercoiling free energy at 298 K is simulated for circular DNAs containing N = 100 bp with torsion constant α = 5.8 × 10−12 dyne cm. persistence lengths P = 500 Å and 10,000 Å and a range of anisotropies of the bending potential from p = 1.0 to 16.0. The apparent torsion constants, reckoned from these supercoiling free energies by assuming an isotropic bending potential, are found to increase by less than 3% as the input anisotropy increases from 1.0 to 16.0. When P = 500 Å, the apparent torsion constant never rises significantly above the input value over the entire range of input anisotropies. When P = 10,000 Å, the apparent torsion constant rises only about 3% above the input value for anisotropies ρ = 8.0 and 16.0. Evidently, anisotropy of the bending potential cannot account for the fact that the torsion constants reported for small circular DNAs exceed those reported for longlinear DNAs by a factor of 1.6 or more. © 1995 John Wiley & Sons, Inc.
A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and organic solvents
Authors: Langlet J , Gresh N , Giessner‐Prettre C 
Published: December 2004

AbstractAn integrated procedure that computes in a consistent way both the intermolecular interaction energies and the solvation energies is reported. It interfaces the Sum of Interactions Between Fragments Ab initio computed molecular mechanics and the Langlei–Claverie continuum reaction field procedures. These two methodologies formulate the interaction energy as a sum of separate electrostatic, polarization, dispersion, and repulsion terms; the first two are computed with the help of distributed charges, dipoles, and quadrupoles derived from the ab initio SCF or MP2 molecular wave fundctions of individual solutes. This computational procedure will be used to estimate the solvent contribution to the interaction energy between polar amino acids side chains. We will consider, on the one hand, the terminal fragments of the side chains of aspartate and glutamate—namely the acetate anion and its protonated counterpart, acetic acid—and on the other hand, the terminal fragments of the cationic residues lysine, histidinium, and arginine, as represented by methylammonium, imidazolium, and methylguanidinium cations, respectively. The deprotonated counterpart of imidazolium, imidazole, is also investigated. With water as a solvent, and for each of the three anion‐cation complexes investigated, the total energy value DE (intermolecular + solvation) of the associated ion pair is only slightly larger (≈ 5 kcal/mol out of ≈ 170) than that of the fully dissociated arrangement and has a virtually flat dependence as a function of intermolecular separation. The associated complex has an enhanced stability in DMSO, a trend accented in chloroform and carbon tetrachloride. In water, the acetic acid–imidazole complex is less than 1 kcal/mol more stable than the dissociated pair. Energy balances, taking into account the experimental values of protonation energies of acetate and imidazole, indicate that the acetate‐imidazolium complex is more stable than its nonzwitterionic counterpart, acetic acid‐imidazole in water. In carbon tetrachloride, by contrast, the two complexes are of similar stabilities in terms of internal energies. When we consider free instead of internal energies of solvation, the three organic solvents stabilize the complex between the neutral molecules. The investigation of the interaction of two methylguanidiniums in the polar solvents suggests that the solvation energy of a complex, larger than that of the two isolated entities, could be able to overcome their electrostatic repulsion. This results in a small preference in favor of the complex. Implications of the findings of this study, and future prospects of applications to molecular recognition and conformational studies of oligopeptides and possibly proteins, are discussed. © 1995 John Wiley & Sons, Inc.
Interaction of mastoparan‐B from venom of a hornet in taiwan with phospholipid bilayers and its antimicrobial activity
Authors: Park Nam Gyu , Yamato Yuhji , Lee Sannamu , Sugihara Gohsuke 
Published: December 2004

AbstractMastoparan B (MP‐B), an amphiphiphilic α‐helical peptide newly isolated from the hornet Vespa basalis, was studied in comparison with mastoparan (MP), in terms of interaction with the phospholipid bilayer and of hemolytic and antimicrobial activity. The amphiphiphilic structure of MP‐B has more hydrophilic amino acid residues in the hydrophilic surface than that of MP. Although each peptide had a considerably different effect on the interaction with lipid bilayers (e. g., their conformation in the presence of acidic and of neutral lipids and dye‐release ability from the encapsulated liposomes), on the whole the interaction mode was similar. MP‐B caused a change in the shape of erythrocytes from normal discoid to a crenated form (named echinocytes). MP exhibited strong activity against gram‐positive bacteria but not against gram‐negative ones. Contrary to this, MP‐B showed both strong activity against gram‐positive bacteria and potent activity against gram‐negative bacteria. Whereas both peptides have almost the same residues on the hydrophobic side, the difference in the hydrophilic surface area on the molecules seems to lead to the subtle change in its interaction with membranes, resulting in the alteration of biological activity. © 1995 John Wiley & Sons, Inc.
Dielectric study of the cooperative order–disorder transition in aqueous solutions of schizophyllan, a triple‐helical polysaccharide
Authors: Teramoto Akio , Gu Hong , Miyazaki Yuji , Sorai Michio , Mashimo Satoru 
Published: December 2004

AbstractSchizophyllan exists in aqueous solution as a triple helix, which is intact at room temperature. Its aqueous solution forms some ordered structure at low temperatures but undergoes a sharp transition to a disordered structure as the temperature is raised. The transition temperature Tc is about 7 and 18°C for H2O and D2O solutions, respectively. This transition was followed by time‐domain reflectometry to investigate dynamic aspects of the transition. In addition to a major peak around 10 GHz, the dielectric dispersion curve of a 20 wt % schizophyllan in D2O exhibited a small peak around 100 MHz below Tc and around 10 MHz above Tc. The major peak is due to bulk water, whereas the 100 MHz peak is assigned to “bound” or “structured” water, and that around 10 MHz to side‐chain glucose residues. However, unlike usual bound water reported for biopolymer solutions, this “structured” water disappears abruptly when the temperature becomes close to Tc without accompanying a conformational transition of the main chain. The above assignment is consistent with the structure of the ordered phase derived from previous static data that it consists of side‐chain glucose residues along with nearby water molecules surrounding the helix core that are interacting with each other loosely through hydrogen bonds, and spreads radially only a layer of one or two water molecules but a long distance along the helix axis. © 1995 John Wiley & Sons, Inc.
Design and development of a vasoactive intestinal peptide analog as a novel therapeutic for bronchial asthma
Authors: Bolin David R. , Michalewsky Joseph , Wasserman Martin A. , O'Donnell Margaret 
Published: December 2004

AbstractAnalogs of vasoactive intestinal peptide (VIP) were synthesized and screened as bronchodilators with the ultimate goal of enhancing the potency and extending the duration of action of the native peptide. Several design approaches were applied to the problem. First, the amino acid residues required for receptor binding and activation were identified. A model of the active pharmacophore was developed. With knowledge of the secondary structure (NMR) of the peptide, various analogs were synthesized to stabilize α‐helical conformations. Having achieved a level of enhanced bronchodilator potency, our approach then concentrated on identification of the sites of proteolytic degradation and synthesis of metabolically‐stable analogs. Two primary cleavage sites on the VIP molecule were identified as the amide bonds between Ser25‐Ile26 and Thr7‐Asp8. This information was used to synthesize cyclic peptides which incorporated disulfide and lactam ring structures. Analog work combined the best multiple‐substitution sites with potent cyclic compounds which resulted in identification of a cyclic lead peptides. This compound, Ro 25‐1553, exhibited exceptionally high potency, metabolic stability, and a long duration of action and may be an effective therapeutic for the treatment of bronchospastic diseases. © 1994 John Wiley & Sons, Inc.
One‐bead–one‐structure combinatorial libraries
Authors: Lebl Michal , Krchňák Viktor , Sepetov Nikolai F. , Seligmann Bruce , Štrop Peter , Felder Stephen , Lam Kit S. 
Published: December 2004

AbstractCombinatorial libraries employing the one‐bead–one‐compound technique are reviewed. Two distinguishing features characterize this technique. First, each compound is identified with a unique solid support, enabling facile segregation of active compounds. Second, the identity of a compound on a positively reacting bead is elucidated only after its biological relevance is established. Direct methods of structure identification (Edman degradation and mass spectroscopy) as well as indirect “coding” methods facilitating the synthesis and screening of nonpeptide libraries are discussed. Nonpeptide and “scaffold” libraries, together with a new approach for the discovery of a pentide binding motif using a “library of libraries,” are also discussed. In addition, the ability to use combinatorial libraries to optimize initially discovered leads is illustrated with examples using peptide libraries. © 1994 John Wiley & Sons, Inc.
Mechanisms for the modulation of membrane bilayer properties by amphipathic helical peptides
Authors: Epand Richard M. , Shai Yechiel , Segrest Jere P. , Anantharamiah G. M. 
Published: December 2004

AbstractThe amphipathic helix, in which hydrophobia and hydrophilic residues are grouped on opposing faces, is a structural mot if found in many peptides and proteins that bind to membranes. One of the physical properties of membranes that can be altered by the binding of amphipathic helices is membrane monolayer curvature strain. Class A amphipathic helices, which are present in exchangeable plasma lipoproteins, can stabilize membranes by reducing negative monolayer curvature strain; proline‐punctuated class A amphipathic helical segments are particularly effective in this regard. This property is suggested to be associated with some of the beneficial biological effects of this protein. On the other hand, lytic amphipathic helical peptides can act by increasing negative curvature strain or by forming pores composed of helical clusters. Thus, different amphipathic helical peptides can be membrane stabilizing or be lytic to membranes, depending on the structural motif of the helix, which in turn determines the nature of its association with membranes. Features of these peptides that are responsible for their specific properties are discussed. © 1994 John Wiley & Sons, Inc.