bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pressure dependence of the helix–coil transition temperature of poly[d(G‐C)]
Authors: Wu John Q. , Macgregor Robert B. 
Published: December 2004

AbstractThe Pressure Dependence of the Helix‐Coil Transition Temperature (Tm) of Poly[d(G‐C)] was studied as a function of sodium ion concentration in phosphate buffer. The molar volume change of the transition (ΔV) was calculated using the Clapeyron equation and calorimetrically determined enthalpies. The ΔV of the transition increased from +4.80 (±0.56) to +6.03 (±0.76) mL mol−1 as the sodium ion concentration changed from 0.052 to 1.0M. The van't Hoff enthalpy of the transition calculated from the half‐width of the differentiated transition displayed negligible pressure dependence: however, the value of this parameter decreased with increasing sodium ion concentration, indicating a decrease in the size of the cooperative unit. The volume change of the transition exhibits the largest magnitude of any double‐stranded DNA polymer measured using this technique. For poly[d(G‐C)] the magnitude of the change in ΔV with sodium ion concentration (0.94 ± 0.05 mL mol−1) is approximately one‐half that observed for either poly[d(A‐T)] or poly (dA)·poly(dT). The ΔV values are interpreted as arising from changes in the hydration of the polymer due to the release of counterions and changes in the stacking of the bases of the coil form. As a consequence of solvent electrostriction, the release of counterions makes a net negative contribution to the total ΔV, implying that disruption of the slacking interactions contributes a positive volume change to the total ΔV. The larger magnitude of the ΔV compared with that of other double‐stranded polymers may be due in part to the high helix‐coil transition temperature of poly[d(G‐C)], which will attenuate the contribution of electrostriction to the total volume change. The data in addition show that in the absence of other cellular components, the covalent structure of DNA is stabile under conditions of temperature and pressure more extreme than those experienced by any known organism. © 1995 John Wiley & Sons, Inc.
A dynamic laser light‐scattering study of chitosan in aqueous solution
Authors: Wu Chi , Zhou Shuiqin , Wang Wei 
Published: December 2004

AbstractThe solution behavior of four chitosans (91% deacetylated chitin) with different molecular weights in 0.2M CH3COOH/0.1M CH3COONa aqueous solution was investigated at 25°C by dynamic laser light scattering (LLS). The Laplace inversion of the precisely measured intensity‐intensity lime correlation function leads us to an estimate of the line‐width distribution G(Γ), which could be further reduced too translational diffusion coefficient distributions G(D). By using a combination of static and dynamic LLS results, i.e., Mw and G (D), we were able to establish a calibration of D = kDM with kD = (3.14 ± 0.20) × 10−4 and αD = 0.655 ± 0.015. By using this calibration, we successfully converted G(D) into a molecular weight distribution fw(M). The larger αD value confirms that the chitosan chain is slightly extended in aqueous solution even in the presence of salts. This is mainly due to its backbone and polyelectrolytes nature. As a very sensitive technique, our dynamic LLS results also revealed that even in dilute solution chitosan still forms a small amount of larger sized aggregates that have been overlooked in previous studies. The calibration obtained in this study will provide another way to characterize the molecular weight distribution of chitosan in aqueous solution at room temperature. © 1995 John Wiley & Sons, Inc.
Fluctuations in molecular size, entanglement complexity, and anisometry along molecular dynamics trajectories of short α‐helices
Authors: Arteca Gustavo A. 
Published: December 2004

AbstractWe present a detailed study of the intrinsic shape stability of short flexible polypeptide chains by using a number of distinct descriptors. Some large‐scale structural features found in macromolecular folding—unfolding dynamics can be monitored in terms of molecular size and compactness. Similarly, one could employ descriptors of anisometry to that purpose. In addition, we have recently proposed a new family of global, absolute shape descriptors to quantify the complexity of the self‐entanglements in a polymer, or, loosely, its “degree of folding.” This latter aspect of the molecular shape is characterized by combining simple geometrical and topological properties of the α‐carbon backbone. The resulting descriptor, the probability of observing a rigid backbone as a projected curve exhibiting N overcrossings, has been employed already for the analysis of molecular dynamics of linear hydrocarbons and aliphatic carboxylic acids. In this work, three distinct properties of a molecular chain are monitored simultaneously, for the first lime, along computer‐simulated dynamic trajectories: size, anisotropy, and entanglements. The systems studied are a series of 3 polypeptide helices: 10‐polyalanine, 10‐polyvaline, and 10‐polyglycine. Constant temperature trajectories have been computed for these helices, at thermal equilibrium with a simulated external bath, with temperatures ranging from 300 to 700 K. The differential structural stability of the helices is assessed from the various viewpoints. Even though the systems are simple, they contain some of the essential features expected in polypeptides of relevance to structural biology. The results show that the, descriptors of anisometry and entanglements are rather independent. For instance, it is found that, contrary to intuition the unfolding of helices may involve nonhelical “coil” configurations that are both self‐entangled and prolate. The simultaneous study of independent shape descriptors provides a new picture of the nature of conformations found during dynamics trajectories. The resulting description characterizes a polymer conformation in a absolute terms, and not relative to an ad hoc reference structure. The proposed approach gives some insights into the stability of secondary structural motifs in proteins and the mechanisms involved into their formation or unfolding. © 1995 John Wiley & Sons, Inc.
The interaction of methylene blue, azure B, and thionine with DNA: Formation of complexes with polynucleotides and mononucleotides as model systems
Authors: Tuite Eimer , Kelly John M. 
Published: December 2004

AbstractThe interactions of methylene blue, azure B, and thionine with calf thymus DNA, [poly (dG‐dC)]2, [poly(dA‐dT)]2, and the constituent mononucleotides 2′‐deoxyguanosine‐5′‐monophosphate(dGMP), 2′‐deoxyadenosine‐5′‐monophosphate(dAMP), 2′‐deoxycytidine‐5′‐monophosphate(dCMP), and thymidine‐5′‐monophosphate(dTMP) have been studied by steady‐state absorption spectroscopy and with equilibrium dialysis. Scatchard plots for binding of the dyes to the nucleic acid polymers were convex downward at low binding ratios, characteristic of intercalation, and binding constants for this mode were calculated under conditions of varying ionic strength. For each of the dyes, binding constants with [poly(dG‐dC)]2 and [poly(dA‐dT)]2 were of the same order of magnitude, so that previously reported (G‐C) preferentially is not very marked. At high binding ratios, the Scatchard plots did not return to the abscissa but curved upward, indicative of a weaker cooperative binding mode, occurring under conditions where the dye is in excess, which is suggested to be external stacking of the dye molecules promoted by the polyanion. The dependence of the absorption spectra on added salt demonstrated a shift in the strong binding mode for the three dyes with [poly(dA‐dT)]2 with increasing ionic strength, while with [poly(dG‐dC)]2 this does not occur. The dyes were found to bind to purine but not pyrimidine mononucleotides with dGMP and dAMP, 1:1 complexes were formed initially and also 1:2 dye/nucleotide complexes with increasing nucleotide concentrations. Under low salt conditions, binding to dAMP was slightly stronger than to dGMP for the three dyes studied, while at high ionic strength, when the binding constants are significantly lower, all binding constants become very similar. Binding to mononucleotides is suggested to be primarily stabilised by π‐π stacking interactions between the planar dyes and the nucleobases: for thionine and azure B there also appears to be H‐bonds between the exocyclic amines and the sugar–phosphates conferring extra stability. Neither increasing the number of phosphate groups on the nucleotides nor changing from deoxyribose to ribose sugars had any significant effect on the binding constants. © 1995 John Wiley & Sons, Inc.
Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal
Authors: Alexov E. , Atanasov B. , Ueki T. 
Published: December 2004

AbstractA numerical simulation of the Young's modulus pH dependence in a triclinic crystal of hen egg white lysozyme is performed. On the basis of calculation of electrostatic interactions between the molecules in the crystal at different pH values, we obtain the Young's modulus quantity as a function of pH. The analysis is carried out along the main crystal axes as well as along the [011] direction. In the last case, a good agreement between our calculations of Young's modulus pH dependence and the experimental data [V. N. Morosov and T. Ya. Morozova (1981) Biopolymers, Vol. 20, pp. 451–467] is obtained.The calculations show a strong anisotropy of both the absolute value of the electrostatic part of Young's modulus and its pH dependence along different directions. A detailed analysis of the electrostatic potential inside the crystal, as well as the charged group distribution in the contact areas, permit us to find the reason for the anisotropy. It is caused by a nonuniform distribution of the charged residues in the lysozyme molecule and especially by the titration behavior of certain acidic groups. It is also shown that Young's modulus depends on the ionic strength, being anisotropic. The reason is that the cavities are not uniformly distributed within the crystal. They are located predominantly along the c axis. © 1995 John Wiley & Sons, Inc.
Design of B‐DNA cross‐linking and sequence‐reading molecules
Authors: Walker Wynn L. , Kopka Mary L. , Filipowsky Mark E. , Dickerson Richard E. , Goodsell David S. 
Published: December 2004

AbstractWe report the design of hybrid molecules to bind in the minor groove of B‐DNA, which combine DNA alkylating and cross‐linking ability for increased chemotherapeutic efficacy, with sequence specificity, to minimize side effects. Optimal linkage geometries have been determined for the synthesis of bis‐anthramycin and anthramycin‐netropsin hybrid molecules. Earlier studies on linked drugs have typically been based on molecular mechanics calculations. This work, in contrast, uses the observed crystal structures of a netropsin/DNA complex and a new anthramycin/DNA complex to determine the exact spacing between two individual drugs when bound in the minor groove of B‐DNA. Molecular linkers then are designed and tested between these two experimental positions, to form a chimeric or bis‐linked compound molecule. A linked anthramycin‐netropsin molecule has been designed specifically to target the polypurine tract second‐strand primer site of the reverse transcriptase of HIV‐1. © 1995 John Wiley & Sons, Inc.
Predictions of protein backbone bond distances and angles from first principles
Authors: Scháfer Lothar , Cao Ming , Meadows Mary Jane 
Published: December 2004

AbstractA procedure is described, based on a spline‐function representation of ab initio peptide conformational geometry maps, that allows one to predict backbone bond distances and angles of proteins as functions of the peptide ϕ(N‐Cα)/Ψ(Cα‐C′) torsions with an accuracy comparable to that of high‐resolution protein crystallography. For example, for the more than 40 residues of crambin, the rms deviation between predicted and crystallographic values of N‐Cα‐C′ is 1.9° for the 1.5 Å resolution structure and 1.9° for the 0.83 Å resolution structure, compared with angle variations of < 10°. Accurate information on protein backbone geometries is important for establishing dictionaries of flexible geometry functions for use in empirical peptide and protein modeling. © 1995 John Wiley & Sons, Inc.
Atypical gly‐X‐Y sequences surround interruptions in the repeating tripeptide pattern of basement membrane collagen
Authors: Long Cynthia Gwynne , Thomas Michael , Brodsky Barbara 
Published: December 2004

AbstractThe triple‐helical domains of type IV collagen chains have more than 20 sites at which the repeating (Gly‐X‐Y)n pattern is interrupted. Analysis of α1 (IV) and α2 (IV) chains indicates the residues in the three Gly‐X‐Y triplets preceding or following interruptions differ statistically from the rest of the chain. Unusually high frequencies of charged residues are seen at a number of X and Y sites, with the charge density being particularly high C‐terminal to the interruption site. Analyses were carried out on individual categories of interruptions, classified as insertions or deletions in the Y position. All of the residues in the X and Y positions of the triplets flanking insertion sites are atypical, with a high concentration of charged residues. Triplets flanking sites where there has been a deletion in the Y position show unusually high frequencies of charged residues at some sites, hydrophobic residues at other sites, and an invariant imino acid N‐terminal to the interruption. The presence of atypical sequences surrounding interruptions could be important at a molecular level, related to triple‐helix stability, or at a supramolecular level, related to the association of molecules to form networks in basement membranes. © 1995 John Wiley & Sons, Inc.
Synthesis and interfacial behavior of poly(Lys‐Tyr‐Tyr‐Lys)
Authors: Maget‐Dana Régine , Bolbach Gérard , Trudelle Yves 
Published: December 2004

AbstractPoly(Lys‐Tyr‐Tyr‐Lys) was synthesized by polycondensation of the tetrapeptide unit using paranitrophenyl esters. The conformation of poly (Lys‐Tyr‐Tyr‐Lys) is very dependent on its environment. CD spectra in bulk are difficult to interpret owing to the contribution of Tyr residues, but from ir spectra it seems that poly(Lys‐Tyr‐Tyr‐Lys) adopts preferentially an unordered conformation in water. Addition of salts induces a partial transition to a β structure. The behavior is different at interfaces. When poly(Lys‐Tyr‐Tyr‐Lys) is spread as a film on a water subphase, the shape of the compression isotherm curves is compatible with a stacking of two β‐sheets. On a KCl subphase, the polymer film is more expanded and more compressible, and the isotherm curve resembles that of a polymer in a random conformation. The analysis by CD and ir spectroscopy of transferred monolayers using the Langmuir–Blodgett technique allowed us to confirm and make these data more precise: on a water subphase the spectra are those of an antiparallel β structure. At the interface of a saline solution the spectra are compatible with a mixture of random coil (largely) and a small content of β structures. © 1995 John Wiley & Sons, Inc.
Energetics of protein–DNA interactions: An exact calculation for binding of ligands to a lattice of overlapping sites
Authors: Saroff Harry A. 
Published: December 2004

AbstractExact equal ions are developed for analyzing the binding of ligands to a linear lattice of overlapping sites in which occupied–unoccupied as well as occupied–occupied interactions are included for the analysis of the binding isotherms. We demonstrate that positive cooperativity on the binding of ligands to multiple sites may derive from either occupied–unoccupied or occupied–occupied interactions. When the binding of proteins to linear polynucleotides and DNA has exhibited positive cooperativity protein–protein (occupied–occupied), interactions have heretofore been invoked as the sole energetic source in determining the cooperative effect. Models and equations developed previously for the analysis of these binding isotherms have included only the protein–protein interactions (usually characterized with the symbol ω). The exact equations of this paper are capable of analyzing binding data in a manner to evaluate the relative importance of both occupied–unoccupied and occupied–occupied interactionsRelations derived here are employed to analyze some existing data, and the resulting parameter values are compared to those developed with equations employing only the protein–protein (occupied–occupied) interactions. The resulting parameter values are qualitatively different. Values of the binding constants differ by about three orders of magnitude. When only protein–protein interactions are taken into account, the resulting free energy of interaction is negative, indicating attractive forces between bound protein molecules; when both occupied–unoccupied and occupied–occupied interactions are applied, the resulting free energies of interaction are positive, indicating destabilizing forces acting primarily on the polynucleotide lattice. © 1995 John Wiley & Sons, Inc.
Conformational states governing the rates of spontaneous transition mutations
Authors: Mitra Rahul , Pettitt B. Montgomery , Blake R. D. 
Published: December 2004

AbstractWe report the results of a theoretical study, combining the results of sequence analysis and integral equation structural methods for nucleic acids in aqueous solutions, on the effects of nearest neighbors on the (T.G) mispair in solution, for 12 nearest neighbor contexts. Attempts have been made to classify the structural and energetic effects of the 5′ and 3′ neighbors with respect to the observed spontaneous mutation rates in vertebrates. It is found that 5′ nearest neighbor is probably the most critical structural factor in facilitating or discouraging mutations. Local conformational states correlate with discrimination of bases to be excised in mispairs. Our study confirms the role of the flexibility of the DNA molecule in governing the rates of spontaneous mutations. © 1995 John Wiley & Sons, Inc.
Symmetry and structure of RNA and DNA triple helices
Authors: Raghunathan G. , Miles H. Todd , Sasisekharan V. 
Published: December 2004

AbstractDespite wide interest in nucleic acid triple helices, there has beenno stereochemically satisfactory structure of an RNA triple helixin atomic detail. An RNA triplex structure has previously been proposed based on fiber diffraction and molecular modeling [S. Arnott and P. J. Bond (1973) Nature New Biology, Vol. 244. pp. 99–101; S. Arnott. P. J. Bond. E. Seising, and P. J. C. Smith (1976) Nucleic Acids Research, Vol. 3. pp.2459–2470], but it has nonallowed close contacts at every triplet and is therefore not stereochemically acceptable. We propose here a new modelfor an RNA triple helix in which the three chains have identical backbone conformations and are symmetry related. There are no short contacts. The modeling employs a novel geometrical approach using the linked atom least squares [P. J. C. Smith and S. Arnott (1978) Acta Crystallographica, Vol. A34, pp. 3–11] program and is not based on energy minimization. In general, the method leads to a range of possible structures rather than a unique structure. In the present case, however, the constraints resulting from theintroduction of a third strand limit the possible structures to a very small range of conformation space. This method was used previously to obtain a model for DNA triple helices [G. Raghunathan, H. T. Miles, and V. Sasisekharan (1993) Biochemistry, Vol. 32, pp. 455–462], subsequently confirmed by fiber‐type x‐ray diffraction of oligomeric crystals [K. Liu. H. T. Miles. K. D. Parris, and V. Sasisekharan (1994) Nature Structural Biology, Vol. 1. pp. 11–12]. The above triple helices have Watson–Crick–Hoogsteen [K. Hoogsteen (1963) Acta Crystallographica, Vol. 16. pp. 907–916] pairing of the three bases.The same modeling method was used to investigate the feasibility of three‐dimensional structures based on the three possible alternative hydrogen‐bonding schemes: Watson–Crick–reverse Hoogsteen, Donogue [J. Donohue (1953) Proceeding of the national Academy of Science USA, Vol. 39, pp. 470–475] (reverse Watson–Crick)–Hoogsteen, and Donohue–reverse Hoogsteen. We found that none of these can occur in either RNA or DNA helices because they give rise only to structures with prohibitively short contacts between backbone and base atoms in the same chain. © 1995 John Wiley & Sons, Inc.
Structural properties and thermal stability of human liver and heart fatty acid binding proteins: A fourier transform IR spectroscopy study
Authors: Tanfani Fabio , Kochan Zdzislaw , Swierezynski Julian , Zydwo Mariusz M , Bertoli Enrico 
Published: December 2004

AbstractThe secondary structure and the thermal stability of human liver (L‐FARP) and heart (77‐FAUP) fatty acid‐binding proteins were analyzed, in the absence and in the presence of oleic acid, by Fourier transform ir spectroscopv. The study was done in order to gain information on the secondary us well three‐dimensional structure of L.‐FARP and to check the possible H‐FABP self‐association that has been found to occur in rat and pig H‐FABP. Comparison of human L‐FABP and H‐FABP ir spectra reveals that, in spite of the low sequencehomology, the two proteins have similar secondary and probably tertiary structures. The air data indicates that a larger amount of β‐strands are exposed to the solvent in H‐FABP as compared to L‐FABP, suggesting mi nordifferences in the three‐dimensional structures of these proteins. The binding of oleic acid to L‐FABP and H‐FABP stabilizes their structures and does not modify their secondary structure. Their spectra neither confirm nor exclude self‐association of human H‐FABP. © 1995 John Wiley & Sons, Inc.
Effect of locust bean gum and konjac glucomannan oh the conformation and rheology of agarose and κ‐carrageenan
Authors: Goycoolea F. M. , Richardson R. K. , Morris E. R. , Gidley M. J. 
Published: December 2004

AbstractMixing with locust bean gum (LBG) induces obvious gel‐like character in very dilute solutions of K+κ‐carrageenan (< 0.01% w/w in 100 mM KCl). At higher concentration (0.085%), addition of LBG (0.036%) gives a shoulder on the high‐temperature side of the DSC (differential scanning calorimetry) exotherm associated with the carrageenan disorder‐order transition, with an accompanying increase in gelation temperature and enhancement in gel strength (storage modulus, G′). On substitution of LBG by konjac glucomannan (KM) the shoulder in DSC cornverts to a discernable peak. Van't Hoff analysis of optical rotation data indicates that the high‐temperature thermal processes could arise from association of LBG or KM chains to the carrageenan double helix as it forms, with the main transition at lower temperature corresponding to ordering of surplus carrageenan. WithK‐carrageenan in the nongelling tetra‐methylaminonium salt form, addition of LBG causes no delectable change in DSC; rheological enhancement at high concentration (1% w/w) is limited to development of a very tenuous network, and in dilute solution a decrease in viscosity is observed. Agarose shows only a very slight increase in the disorder‐order transition temperature on addition of KM, and it shows no detectable change with LBG. These observations are interpreted as showing that efficient binding of mannan or glucomannan chains requires some aggregation of the algal polysaccharide helices, but that extensive aggregation restricts synergistic interaction by competition with heterotypic association. © 1995 John Wiley & Sons, Inc.