摘要:

AbstractPoly(O‐benzyl‐L‐serine) of degree. polymerization 90 in oriented film cast from dichloroacetic acid (DCA) solution yielded the x‐ray patterns of the intramolecular cross‐β form, in which the extended segments stand upward and downward to the surfaces of a thin film. These x‐ray photographs further suggest that residual solvent molecules are bound to the polymer, and it may provide an important clue in understanding the nature of the cross‐β conformation in a dilut

ISSN:0006-3525    

DOI:10.1002/bip.360290802

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

年代:1990

数据来源: WILEY

摘要:

AbstractExamination of binding information in the form of derivative (or finite difference) measurements is explored (1) experimentally by a thin‐layer optical procedure (Dolman, D.&Gill, S. J. (1978) Anal. Biochem.87, 127–134) and (2) theoretically by simulation in order to determine the influence of the number of data points and their standard error upon the resolvability of binding parameters in cooperative and non‐cooperative systems. The data is described by the difference in optical absorbance divided by the change in the logarithm of the ligand activity and each data point is assumed to be influenced by a random error with a given variance. It is found that increasing the number of data points, which in turn effectively reduces the magnitude of the observed absorbance changes, results in an increase in the uncertainty of the resolved parameters of the system. The effect is verified by both experimental and simulation studies. Thus one is led to suggest that fewer measurements for the change of absorbance with larger magnitudes produces the most favorable situation for parameter resolution when the data is in the form of finite difference measure

ISSN:0006-3525    

DOI:10.1002/bip.360290803

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

年代:1990

数据来源: WILEY

摘要:

AbstractDespite its antiparallel symmetry, DNA often appears to possess a permanent electric dipole moment in transient electro‐optical experiments. We propose that this may be due to the asymmetric binding of charged ligands to the DNA. We have used the fluctuating dipole theory of Kirkwood and Shumaker to calculate the contribution of asymmetric ligand binding to the electro‐optic orientation function, and Monte Carlo computer simulation to calculate the reversing pulse behavior, as a function of ligand binding density. The results indicate that the effect should be observable even against the background of the sizable induced dipole moment produced by polarization of the counterion atmosph

ISSN:0006-3525    

DOI:10.1002/bip.360290804

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe dynamic mechanical properties of elastin have been quantified over a temperature and hydration range appropriate for a biological polymer. Composite curves of the tensile properties at constant water contents between 28.1 and 44.6% (g water/100 g protein) were typical of an amorphous polymer going through its glass transition. Water content had no effect on the shape of the curves, but shifted them a distanceaCalong the frequency axis. The combined effects of hydration and temperature are given in a series of isoshift curves where elastin's properties are constant along any one curve. A 1% change in hydration has the same effect as a 1°–2° change in temperature, depending on the initial water content and temperature. Theoretical isoshift curves that matched the experimental data were predicted using the WLF equation and coefficients determined from the data. These data form a basis to predict the role of elastin in arterial disease based on changes in its chemical and physical environm

ISSN:0006-3525    

DOI:10.1002/bip.360290805

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

年代:1990

数据来源: WILEY

摘要:

AbstractA simple theory is developed for the extension of a uniformly charged linear polyion attached at one end in an electric field. For a polyion consisting of a very large number (N) of Kuhn lengths (b), the mean extension in the direction of the electric field (E) is given accurately byRz= (b/A) In (sinh (NA)/NA), whereA=EQb/kBTandQis the effective charge associated with each Kuhn length. For any value ofE, no matter how small, a polyion of sufficient length, such thatNA≫ 1.0, will be essentially fully extended. WhenA≪ 1.0, as is the case for DNA in weak electric fields, the head end of the chain is only weakly oriented, even though the stem and tail may be completely aligned. In the linear regime,NA<1.0,Rzis proportional toE, Q, andN2. The linear density of chain elements is calculated for a chain in the linear regime. This theory provides a basis to determine the productQbfrom direct microscopic measurements ofRzvs.Efor fluorescent‐labeled circular DNAs that are topologically snared near voids or surfaces of gels. Experimental realization of this suggestion is described in the following

ISSN:0006-3525    

DOI:10.1002/bip.360290806

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

年代:1990

数据来源: WILEY

摘要:

AbstractIndividual ethidium‐stained DNA molecules, embedded in an agarose gel made with electrophoresis buffer (0.05 molar salt), are observed using a fluorescence microscope. In the first experiment, open circular 66 kilobase pair (kbp) plasmids, immobilized by agarose fibers threaded through their centers, display entropic “rubber” elasticity. The charged molecules extend in an electric field of several volts per centimeter and contract to a compact random coil when the field is removed. The extension of the plasmids as a function of field strength is consistent with the freely jointed chain model when the effective electrophoretic charge density is set at 15 e−per persistence length. In a second experiment, stained linear 48.5 kbp DNA molecules are observed as random coils immobilized in agarose. A measure of their size, here named the “maximal‐X‐extent,” is taken for 100 molecules and found to average 1.47 μ. A Monte Carlo computer simulation of random coils (freely jointed chain model) gives the same maximal‐X‐extent value when the persistence len

ISSN:0006-3525    

DOI:10.1002/bip.360290807

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe temperature dependence of hydrogen isotope exchange rates for lysozyme in 5 molal aqueous glycerol and for poly (D,L‐alanine) in a range of glycerol concentrations from 0 molal to 8 molal have been determined. The activation enthalpy of base‐catalyzed exchange for poly (D,L‐alanine) in water is 4 kcal/mol and passes through a minimum at about 2 molal glycerol before returning to a value of 4 kcal/mol at 4 molal glycerol. Exchange rates for lysozyme have been analyzed with transition state and Kramers's theories. The activation parameters for exchange of protons in lysozyme in the presence of 5 molal glycerol show a similar qualitative behavior to those determined for exchange in the absence of glycerol [R. B. Gregory et al. (1982)Biochemistry24, 6523–6530]. The activation enthalpies and entropies for the fast‐exchanging protons show a gentle increase asH(t), the number of hydrogens remaining unexchanged, decreases. By contrast, the activation parameters for the slowest exchanging protons [H(t)<20] increase dramatically asH(t)decreases. As in water, the activation parameters for exchange of the fast‐ and slow‐exchanging protons in glycerol solution are characterized by two distinct compensation temperatures (510 ± 100 K for the fast protons and 340 ± 40K for the slow protons). These values are not significantly different from those determined for exchange in water.The activation parameters, ΔH‡, andTΔS‡, are both several kcal/ mol lower for exchange in glycerol solutions compared with water. Enthalpy and entropy changes for the thermal unfolding of lysozyme in glycerol solutions [results of K. Gekko (1982)J. Biochem.19, 1197–1204] are larger than those determined for unfolding in water. This suggests that exchange does not involve local unfolding of segments of the protein. There is evidence for a contribution from thermal unfolding for exchange of the slowest protons in glycerol solutions which is not observed in water.Analysis of exchange rates for the fast protons as a function of temperature and viscosity with Kramers' equation provides values of the viscosity exponent. This is found to increase with decreasing values ofH(t). These results are not easily rationalized with Gavish's model [(1980)Phys. Rev. Lett.44, 1160] of a “position‐dependent, internal protein viscosity” and suggest that the Gavish model of the friction coefficient is incorrect. A dissection of the effect of glycerol on exchange of the fast protons into viscosity and thermodynamic contributions is not possible with the present data. Both factors are suggested to influence

ISSN:0006-3525    

DOI:10.1002/bip.360290808

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

年代:1990

数据来源: WILEY

摘要:

AbstractTwo dielectric relaxation peaks were found in moist collagen by the time domain reflectometry. The low‐frequency peak around 100 MHz moves little as the water content is varied. Its relaxation strength depends on the content and vanishes for completely dried collagen. This process is concluded to be due to water molecules strongly bound to the tropocollagen. Amount of the bound water is estimated as 0.12 g water/g collagen. Twenty‐one water molecules are bound to one repeat of the triple helix. The existence of stringlike water chains is suggested. If the water content is less than 0.5 g water/g collagen, the high frequency peak locates between those of bound and bulk water. Water among the tropocollagen is weakly bound to the collagen. In the higher region it does not change much with the content, being close to that of bulk water. The bulk water appears in this reg

ISSN:0006-3525    

DOI:10.1002/bip.360290809

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

年代:1990

数据来源: WILEY

摘要:

AbstractWe have examined the free energy effects of 5‐methylation of cytosine on the B ⟷ Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems aretotalfree energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B ⟷ Z transitions observed under real(physiological) conditions. We calculate that in solution, methylation makes the B → Z transition more favorable by about −0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about −0.3 kcal/ mole‐bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA

ISSN:0006-3525    

DOI:10.1002/bip.360290810

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

年代:1990

数据来源: WILEY

摘要:

AbstractA theory is developed for dynamic light scattering (DLS) from rigid double spirals by treating an invisible rigid cylinder with two helical scattering stripes on opposite sides of its cylindrical surface. The exact initial, or first cumulant, diffusion coefficientDapp(K) is obtained in terms of the translational diffusion coefficients (D∥andD⟂) parallel and perpendicular to the symmetry axis, the rotational diffusion coefficients (D R∥andD R⟂) around the symmetry and transverse axes, the length(L)and radius(b)of the cylindrical surface bearing the stripes, and the pitch(p). Interference effects, namely geometrical antiresonances, between strands, produce deep minima in the static structure factorS(K)and corresponding prominent peaks inDapp(K). These peaks inDapp(K)depend sensitively on the rotational dynamics around the symmetry axis, and nearly vanish whenD R∥= 0. Some results for single spirals are also presented. A simpler model in which scattering points are attached at opposite ends of an otherwise invisible thin rigid rod is also treated, and shown to exhibit modest minima inS(K)and corresponding maxima inDapp(K). Confining this rod to a plane containingKenhances the amplitudes of the oscillations inS(K)andDapp(K), as expected.Rigid double spirals are employed as crude models for interwound supercoiled DNAs in order to assess the possible occurrence of interference effects. Although native supercoiled DNAs exhibit a cylinder diameter that is much too small to exhibit geometrical antiresonances in the presently accessible range ofK2, nearly relaxed supercoiled DNAs are predicted to exhibit their first maximum inDapp(K)just inside this range. Previously reported data for the effect ofEscherichia colisingle‐strand binding (ssb) protein on the DLS of supercoiled pBR322 DNA cannot be mimicked by a gradual homogeneous reduction of superhelix density with increasing ssb, but instead can be mimicked by inhomogeneous all‐or‐none binding in which uncomplexed native DNAs and nearly relaxed saturated ssb/DNA complexes coexist in varying proportions. ExperimentalDapp(K)andS(K)data for a sample of relaxed pUC8 dimers display, respectively, a broad maximum and a corresponding minimum, in qualitative agreement with rough th

ISSN:0006-3525    

DOI:10.1002/bip.360290811

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

年代:1990

数据来源: WILEY