摘要:

AbstractWe have recorded high‐resolution13C‐NMR spectra of linear (curdlan) and branched (lentinan, HA‐β‐glucan and its polyol and aldehyde derivatives) (1 → 3)‐β‐D‐glucans in hydrate and gel states, in order to gain insight into their gelation mechanism. Network structure of curdlan turned out to be highly heterogeneous from its motional state, from liquid‐like, through intermediate, to solid‐like domains. They are studied by a variety of experiments, conventional high‐resolution NMR by broad‐band decoupling, high‐power decoupling with magic angle spinning (MAS), and cross‐polarization‐magic‐angle‐spinning (CP‐MAS). Nevertheless, we found that conformations of these distinct liquid‐like and solid‐like do‐ mains exhibit an identical single helix conformation with a small proportion of a triple helix form, supporting our previous view as to the gelation mechanism. In contrast, the network structure of branched (1 → 3)‐β‐D‐glucans in the gel state arises mainly from the triple helix conformation. This means that gelation of branched (1 → 3)‐β‐D‐glucan proceeds from partial association of the triple helical chains, previously proposed for gelation of a linear glucan. Furthermore, we found that conversion from the single chain to the single helix was not achieved readily by hydration of over 8h at 96% R. H. for branched glucan but the triple helix form is o

ISSN:0006-3525    

DOI:10.1002/bip.360291402

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

年代:1990

数据来源: WILEY

摘要:

AbstractDifferential scanning calorimetry studies have been carried out on the sequential polypeptide of elastin, (L‐Val1–L‐Pro2–Gly3–L‐Val4–Gly5)n,abrreviated as PPP, and its more hydrophobic analogues (L‐Val1–L‐Pro2–Gly3–L‐Val4–Gly5)n, referred to as Leu1‐PPP, and (L‐Ile1–L‐Pro2–Gly3–L‐Val4–Gly5)n, referred to as Ile1‐PPP. Consistent with inverse temperature transitions, the temperatures of the transitions for which maximum heat absorption occurs are inversely proportional to the hydrophobicities of the polypentapeptides (31°C for PPP, 16°C for Leu1‐PPP, and 12°C for Ile1‐PPP), and the endothermic heats of the transitions are small and increase with increasing hydrophobicity, i.e.,1.2,2.9, and3.0kcal/mol pentamer for PPP, Leu1‐PPP, and Ile1‐PPP, respectively. Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order, as the temperature is raised above that of the transition, has been repeatedly observed using different physical characterizations. Furthermore, the studies demonstrated indentical conformations for PPP and Ile1‐PPP above and below the transition. Both heats and temperature of the transitions v

ISSN:0006-3525    

DOI:10.1002/bip.360291403

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe influence of added salts on the dynamic viscoelastic properties are investigated for aqueous solutions of alginates that have various molecular weights and mannuronate/guluronate (M/G) ratios. The dynamic moduli of the systems increase with increasing concentration of the added salt in the low‐frequency region. The effect is notable in the order of KCl

ISSN:0006-3525    

DOI:10.1002/bip.360291404

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

年代:1990

数据来源: WILEY

摘要:

AbstractOptical melting transitions of the short DNA hairpins formed from the self‐complementary DNA oligomers d[GGATACX4GTATCC] where X = A, T, G, or C measured in 100 mMNaCl are presented. A significant dependence of the melting transitions on loop sequence is observed and transition temperatures,tm, of the hairpins vary from 58.3°C for the T4loop hairpin to 55.3°C for the A4loop. A nearest‐neighbor sequence‐dependent theoretical algorithm for calculating melting curves of DNA hairpins is presented and employed to analyze the experimental melting transitions. Experimental melting curves were fit by adjustment of a single theoretical parameter,Fend(n), the weighting function for a hairpin loop comprised ofnsingle‐strand bases. Empirically determined values ofFend(n) provide an evaluation of the free‐energy of hairpin loop formation and stability. Effects of heterogeneous nearest‐neighbor sequence interactions in the duplex stem on hairpin loop for mation were investigated by evaluatingFend(n) in individual fitting procedures using two of the published sets of nearest‐neighbor stacking interactions in DNA evaluated in 100 mMNaCl and given by Wartell and Benight, 1985. In all cases, evaluated values ofFend(n) were obtained that provided exact theoretical predictions of the experimental transitions.Results of the evaluations indicate: (1) Evaluated free‐energies of hairpin loop formation are only slightly dependent on loop sequences examined. At the transition temperature,Tm, the free‐energy of forming a loop of four bases is approximately equal for T4, G4, or C4loops and varies from 3.9 to 4.8 kcal/mole depending on the set of nearest‐neighbor interactions employed in the evaluations. This result suggests, in light of the observed differences in stability between the T4, G4, and C4loop hairpins, that sequence‐dependent interactions between base residues of the loop are most likely not the source of the enhanced stability of a T4loop. In contrast, the evaluated free‐energy of forming an A4loop is approximately 400 cal/mole higher for each nearest‐neighbor set indicating unfavorable interactions between A bases in a loop‐affect loop formation and overall hairpin stability, (2) The absolute value for the free‐energy of loop formation at theTmof each hairpin varies by about 1 kcal/mole depending on the set of nearest‐neighbor interactions employed and the relative hierarchy of stability for each loop is conserved for different nearest neighbor sets, (3) The melting process of each hairpin deviates from strict two‐state behavior in the order according to loop sequence of T>A>G>C, (4) Results of our analysis are compared with the early work of Scheffler et al., 1970 on the hairpins formed from the copolymer sequences d(T – A)qwhereq= 9–21. Comparisons with the more recent works a DNA dumbbell (Benight et al., 1988) and the very similar DNA hairpins studi

ISSN:0006-3525    

DOI:10.1002/bip.360291405

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

年代:1990

数据来源: WILEY

摘要:

AbstractA flow linear dichroism technique is utilized to study the unwinding of supercoiled DNA induced by the binding of ethidium bromide (EB) and proflavine (PF) at different ratiosr(drug added/DNA base). In the case of either EB or PF bound to linear calf thymus DNA, the reduced linear dichroism signals LD/A (LD: linear dichroism; A: absorbance, both measured at the same wavelength), determined at 258, and 520 or 462 nm (corresponding to contributions predominantly from the partially oriented DNA bases, intercalated EB, or PF, respectively) are nearly independent of drug concentration. In the case of supercoiled DNA, the magnitude of LD/A at 258 nm first increases to a maximum value nearr= 0.04–0.05, and then decreases asris increased further, mimicking the behavior of the sedimentation coefficients, viscosities, and gel electroporphoresis patterns measured by other workers at similar values ofr. However, LD/A at 520 nm, which is due to DNA‐bound EB molecules, is constant within the range ofrvalues of 0.02–0.06 in which the magnitude of LD/A determined at 258 nm due to the DNA bases exhibits a pronounced maximum. In contrast, in the case of PF, the magnitudes of LD/A determined at 258 or 462 nm are characterized by similar dependencies onr, both exhibiting pronounced maxima atr= 0.05; this parallel behavior is expected according to a simple interacalation model in which the DNA bases and drug molecules are stacked on top of one another, and in which both are oriented to similar extents in the flow gradient. The unexpected differences in the dependencies of (LD/A)258and (LD/A)520onrin the case of EB bound to supercoiled DNA, are attributed to differences in the net overall alignment of the EB molecules and DNA bases in the flow gradient. The magnitude of the LD signal at 258 nm reflects the overall degree of orientation of the supercoiled DNA molecules that, in turn, depends on their hydrodynamic shapes and sizes; the LD signals characterizing the bound EB molecules may reflect this orientation also, as well as the partial alignment of individual DNA segments containing bound EB molecules. The differences in the LD characteristics of the bound PF and EB molecules may be due to subtle differences in the mechanisms of binding, perhaps reflecting differences in the torsional dynamics and local rigidities in superhelical DNA [Wu et al. (1988)Biochemistry27, 8128–8144] induced by these two different in tercalating

ISSN:0006-3525    

DOI:10.1002/bip.360291406

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe atomic structures of proteins epitomize the ideas of complexity and irregularity in three‐dimensional objects. For such objects, size and shape are difficult to quantify, and therefore the development of unbiased parameters for these properties could facilitate their description. Statistical analysis of the frequency distribution of interatomic distances in protein structures of different classes has revealed two numerical descriptors that correlate with physicochemical properties of these macromolecules. The median (μ) of the distribution correlates (r>.98,n= 45) with variables indicative of size (e.g., molecular weight and radius of gyration). The exponent of the Box–Cox transformation λ, used for converting this distribution into a symmetrical one, correlated (r= .75,n= 43) with a general dimensionless shape parameter defined as the combination of the shape‐related accessible surface (A s0), molecular volume (V), and radius of gyration (Rg) in the forms= (A s0Rg/V). It is suggested that for globular proteins λ is a function of both the shape parametersand the fractal dimensionDof the protein surface. These objective descriptors of size and shape could be useful to describe other com

ISSN:0006-3525    

DOI:10.1002/bip.360291407

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

年代:1990

数据来源: WILEY

摘要:

AbstractA combinatorial optimization approach is used for solving the multiple‐minima problem when determining the low‐energy conformations of short polypeptides. Each residue is represented by a finite number of discrete states corresponding to single residue local minima of the energy function. These precomputed values constitute a search table and define the conformational space for discrete minimization by a generalized dynamic programming algorithm that significantly limits the number of intermediate conformations to be generated during the search. Since dynamic programming involves stagewise decisions, it results in buildup‐type procedures implemented in two different forms. The first procedure predicts a number of conformations by a completely discrete search and these are subsequently refined by local minimization. The second involves limited continuous local minimization within the combinatorial algorithm, generally restricted to two dihedral angles in a buildup step. Both procedures are tested on 17 short peptides previously studied by other global minimization methods but involving the same potential energy function. The discrete method is extremely fast, but proves to be successful only in 14 of the 17 test problems. The version with limited local minimization finds, however, conformations in all the 17 examples that are close to the ones previously presented in the literature or have lower energies. In addition, resutls are almost independent of the cutoff energy, the most important parameter governing the search. Although the limited local minimization increases the number of energy evaluations, the method still offers substantial advantages in

ISSN:0006-3525    

DOI:10.1002/bip.360291408

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

年代:1990

数据来源: WILEY

摘要:

AbstractA normal mode theory is developed for the Brownian dynamics of weakly bending rods with preset hydrodynamic interactions. The rod is replaced by a chain of contiguous spheres whose radius is chosen to yield the appropriate uniform translational and rotational diffusion coefficients. Despite the inclusion of preset hydrodynamic interactions in the dynamical operator, its normal modes are not coupled by the potential energy, so their amplitudes remain pairwise “orthogonal” under equilibrium averaging. The uniform translational and rotational diffusion coefficients obtained from Langevin theory are shown to be identical to those obtained from the Kirkwood algorithm, despite their rather different appearance. An expression is given for the mean squared angular displacement 〈Δxm(t)2〉 of themth bond vector around the instantaneousxaxis (perpendicular to the end‐to‐end vectorz). Necessary algorithms are presented for the numerical evaluation of all quantities. The normal mode theory is compared with Brownian dynamics simulations for the same model by examining 3〈Δxm(t)2〉 for the central bond vector of rods comprising 10 and 30 subunits with various persistence lengths. The normal mode theory works very well for all times forL/P≲ 0.6, whereP= κ/kBTis the persistence length and κ is the bending rigidity. With increasing flexibility, the domain of validity of the normal mode theory is restricted to shorter times, where violations of the weak bending approximation are less severe. However, increasing the length of the rod from 10 to 30 subunits yields improved agreement with the simulations for the same and even longer times. This latter effect is tentatively attributed to the greater fluctuating tension in the longer chains, which acts to retard the rotational relaxation in the simulations, but is not taken into account in the prese

ISSN:0006-3525    

DOI:10.1002/bip.360291409

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

年代:1990

数据来源: WILEY

摘要:

AbstractA ligand binding model of counterion association in finite length polyelectrolytes is presented. This model introduces counterion condensation features into a binding formalism. It agrees well with the predictions of other finite length models and is consistent with experimental data on helix–coil melting transitions for short nucleic acid oligomers. This model uses a discrete charge distribution for the polyelectrolyte. An expression for the electrostatic self‐energy of finite length polyelectrolytes is derived using the Euler–Maclaurin sum formula. This sum is shown to be accurate over a wide range of salt concentrations. This electrostatic term is used in an energy minimization analysis. The energy minimization is solved analytically using a Lagrange inversion formula. This general procedure gives a rapidly convergent series and requires no assumptions with regard to “limiting law” behavior. However, when used in the Manning minimization formalism [(1977)Biophysical Chemistry,24, 2086], the volume of the condensed phase becomes unrealistically large at low ionic strength. The ligand binding model does not have a condensed phase volume as a parameter. It provides a single expression that agrees both with Manning's theory and with the theory of Ramanathan and Woodbury [(1982)Journal of Chemical Physics77, 4133] under the respective conditions of these

ISSN:0006-3525    

DOI:10.1002/bip.360291410

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

年代:1990

数据来源: WILEY

摘要:

Abstract13C‐nmr spectra of lysozyme obtained at 50.3 MHz using both static and magic‐angle‐spinning‐cross‐polarization methods are reported at several water contents. The line widths and consequent resolution in the hydrated material is substantially improved over that in the lyophilized protein. The line narrowing is not commensurate with loss of a proton–carbon dipole–dipole coupling or dramatic changes in the relaxation parameters characterizing magnetization transfer from protons to carbon in the Hartmann–Hahn cross‐polarization experiment. We interpret these data in terms of the water inducing a decrease in the conformational reorientations required to account for the data are not necessarily large nor do they imply a major unfolding of the prote

ISSN:0006-3525    

DOI:10.1002/bip.360291411

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

年代:1990

数据来源: WILEY