摘要:

AbstractThe double‐stranded helical complexes of poly(dG‐dC) and of poly(dG‐m5dC) are shown to convert from B‐ to Z‐DNA‐type conformations at moderate or low ionic strengths, lower for the 5‐methyl than for the non‐methyl species, in a highly cooperative temperature‐dependent equilibrium. In the presence of low concentrations of divalent ion, e.g., Mg2+, the temperature at which the B → Z transition occurs is virtually independent of the salt concentration and the B‐conformation is favored at lower temperature, while the Z‐conformation is favored at higher temperature. Since the Debye‐Hückel screening parameter changes rapidly with ionic strength in this region, electrostatic interaction with the free ions appears to be only a small factor in the forces that promote the transition; the temperature dependence must derive principally from effects on the solvent. The temperature dependence at high salt conce

ISSN:0006-3525    

DOI:10.1002/bip.360240202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractExchange‐rate probability‐density functions (pdf) have been calculated for lysozyme hydrogen‐exchange data by numerical Laplace inversion over the temperature range 5–45°C. The smoothest numerical solutions show three broad overlapping peaks. Analysis of the temperature dependence of the cumulative exchange‐rate distributions provides the model‐independent probability‐density function for the activation energies. For the most rapidly exchanging protons, the activation energies are low, consistent with hydroxyl‐ion catalysis in the protein–water interface. The second peak of the exchange‐rate pdf's contains those protons located in regions of lower motility we call “matrices,” for which exchange rates are limited by gated‐diffusion of the hydroxyl‐ion catalyst. The most slowly exchanging protons are located on groups forming strong, dense “knot” structures, identified by neutron‐diffraction and nmr data as clustered segments of β‐sheet with well‐organized hydrogen bonding and sections of the internal faces of α‐helices. Exchange from knot structures occurs through local disordering with little loss of strength or stability to expose one or more protons at a time for exchange. Knots appear to be responsible for the two‐state character of thermal unfolding that occurs by cooperative disruption of the dominant structures of this type. Below about 55°C, all protons exchange from folded states. Contributions to exchange from unfolding processes occur only at temperatures above 55°C.There is a qualitative difference between the two types of structures indicated by the appearance of two and only two enthalpy–entropy compensation patterns. The compensation temperature,Tc, for the matrices is about 470 K; that for the knots, about 360 K. The preservation of rank‐order with temperature change is shown to be a consequence of the fact that all exchange rates in the slow and very slow peaks of the pdf lie on one or the other of the two compensation lines. Although the same electrostatic factors are present in all parts of the protein, we have been forced to conclude that given certain necessary geometric possibilities, these factors cooperate to produce the knots. The knots appear to be the most significant structural element in globular proteins responsible for the structural form of the matrix regions and the dynamic behavior of the protein interior. The knots have high density and low permeability to water, hydroxyl ion, etc., and are probably the explanation for the very low compressibilities, the matrices being nearly mechanically transparent. The knots must make some contribution to folded stability, but it is not clear that this contribution is large. Their major thermodynamic function is to establish kinetic stability; that is, to make the activation free energy for unfolding high. The most important factor in the existence of knots appears to be the ease with which hydrogen bonds adapt in length, angle, and strength to local electrostatic conditions. In proteins, as in water, adaptation is cooperative in local groups of hydrogen bonds, and as in water, this cooperation is enha

ISSN:0006-3525    

DOI:10.1002/bip.360240203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractThe firstexperimentallyderived set of partial charges for a nucleotide has been determined. A high‐resolution x‐ray data set (5122 independent observed reflections to sin(θ)/λ = 0.995 Å−1) has been collected atT= −150°C for 2′‐deoxycytidine‐5′‐monophosphate monohydrate in the zwitterionic form. Radial refinement was carried out on the data, a refinement method that allows variation of atomic valence sphere radii and populations and hence directly yields the partial charges of atoms in a structure [Coppens, P., Guru Row, T. N., Leung, P., Stevens, E. D., Becker, P. J.&Yang, Y. W. (1979)Acta Crystallogr., Sect. A35, 63–72]. The atomic partial charges thus determined are in general qualitative agreement with theoretical values, but significant differences exist, indicating a reassessment of the applicability of the theoretical sets currently in use is necessary. Theab initiocharges determined by Nuss and Kollman [(1979)J. Med. Chem.22, 1517–1524] are closest to experiment in the sugar and base regions, while the Del Re charges of Renugopalakrishnan et al. [(1971)Biopolymers10, 1159–1167] match best in the phosphate region. The presence of an additional hydrogen on N3 appears to have a small effect on the charge densities of all base atoms, rather than a large localized effect on adjacent atoms. Inspection of deformation density maps for the hydrogen bonds in this crystal suggests possible differences between those bonds that include a nitrogen atom as part of the

ISSN:0006-3525    

DOI:10.1002/bip.360240204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractDifferential melting curves (DMCs) of DNAs pA03 and pBR322 in solutions of different ionic strength (0.02 and 0.2MNa+) were obtained. A previously developed procedure of glyxal fixation of partially denatured DNA molecules at temperatures within the melting range was used to construct electron‐microscopic melting maps for pBR322 and pAO3 plasmid DNA and for the replicative form of bacteriophage ϕX174 DNA, allowing the melting of these DNA molecules to be followed in solutions of low (0.1 × SSC) and high (1 × SSC) ionic strength. In spite of the fact that the melting was at nonequilibrium at the low ionic strength, the melting maps for the two kinds of solutions practically coincided. Experimental data are compared with theoretical calculations based on the Fixman‐Freire algorithm. The conclusion is that the melting pattern of these DNAs is, on the whole, correctly described by the theory, although there are appreciable differences between the theoretical and experimental differential melting curves. We have also determined the relation between the melting temperature of a region and its GC content, with allowances made for the boundary conditions of melting in 0.1 × SSC and 1 × SSC solutions, and have analyzed the theoretical shape of peaks of

ISSN:0006-3525    

DOI:10.1002/bip.360240205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractThe diffusion coefficientDof bovine serum albumin through various solutions (pH 7.0, 0.5MNaCl) of polythylene oxide (Mw∼ 1 × 105, 3 × 105) was studied with quasielastic light scattering. In solutions of the 1 × 105polymer solution at polymer concentrations above 0.5 g/L,Dis considerably greater than would have been expected from the viscosity of water:polymer mixtures, the deviations being larger at low protein concentration that at high protein concentration. With either polymer,Dfalls with increasing protein concentra

ISSN:0006-3525    

DOI:10.1002/bip.360240206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractSeveral theories describing the physical properties of solutions containing rod‐shaped molecules are reviewed. The results of the various theories are presented in a convenient form for implementation on a calculator or microcomputer. Expressions are derived for light scattering from thin rods using rational approximations for the sine and cosine integrals. These expressions apply to turbidity, Rayleigh, and dynamic light‐scattering measurements. Accurate approximating equations are given for the various diffusional motions involved in dynamic light scattering. For shear‐dependent viscosity and flow birefringence, empirically derived interpolation formulas are given. These provide values of the Simha factor, extinction angle and orientation function for a wide range of axial ratios and velocity gradients with relative errors less than 1%. We demonstrate how these equations can be applied to predict or model the properties of a solution containing thin rods of various le

ISSN:0006-3525    

DOI:10.1002/bip.360240207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

摘要:

AbstractFluorescence and absorbance methods were used to study the interaction of daunomycin with calf‐thymus DNA over a wide range of temperatures and NaCl concentrations. van't Hoff analysis provided estimates for the enthalpy of the binding reaction over the NaCl range of 0.05–1.0M. Daunomycin binding is exothermic over this entire range, and the favorable binding free energy arises primarily from the large, negative enthalpy. Both the enthalpy change and entropy change are strong functions of ionic strength. Possible molecular contributions to the enthalpy and entropy are discussed, leading to the tentative conclusion that hydrogen‐bonding interactions at the interacalation site are the primary contributors to the observed thermodynamic parameters. The dependence of the enthalpy on the ionic strength is well beyond the predictions of current polyelectrolyte theory and cannot be fully accounted for. The enthalpy and entropy changes observed compensate one another to produce relatively small free‐energy changes over the range of solution conditions

ISSN:0006-3525    

DOI:10.1002/bip.360240208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.360240209

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.360240201

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1985

数据来源: WILEY