摘要:

AbstractHorse muscle phosphoglycerate kinase (PGK) is a monomer folded into two widely distant domains. In the glycolytic pathway, this enzyme catalyzes the first reaction that produces ATP. It was suggested, by analogy with yeast hexokinase, that a hinge‐bending motion may be induced by the binding of specific substrates to the protein. To analyze such a motion, or any structural changes induced by ligand binding, fluorescence anisotropy decay of tryptophan residues in free and liganded PGK was studied. At 293 K, for the free protein and the binary complex with 3‐phosphoglycerate, a single correlation time of 26 ns was observed, corresponding to the rotation of the overall protein, whereas upon addition of MgADP, this correlation time decreased to 10 ns. Such a decrease cannot be merely due to a change of the protein's shape and volume. To explain this, it was suggested that the fluorescence anisotropy decay of the PGK–MgADP complex corresponded to the rotation of the only buried tryptophan (Trp 335). The rotational paths of this tryptophan, in the presence and absence of the nucleotide, were established by potential energy minimization calculations. The results indicated that MgADP induces a displacement of helix α‐13 that decreases the rotational energy barrier of Trp 335 from 16 kcal/mol in the free protein to 8 kcal/mol in the

ISSN:0006-3525    

DOI:10.1002/bip.360301302

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

年代:1990

数据来源: WILEY

摘要:

AbstractElectron micrographs of alginate, xylinan, xanthan, and scleroglucan were prepared by vacuum‐drying aqueous glycerol‐containing solutions, and then heavy‐metal, low‐angle rotary replicated. Quantitative methods for excluding streamlining effects and deformation artifacts were developed and applied to the digitized polymer contours prior to analysis of stiffness. The apparent macromolecular dimensionalities were not obtainable on the basis of the change in the scaling coefficient a relating the rms end‐to‐end distance and the contour length, 〈r2〉1/2∼Lα, for chains subject to the excluded volume effect in two and three dimensions. Using a two‐dimensional model, the persistence length of these molecules was estimated to be (9 ± 1) nm (alginate), (25 ± 4) nm (xylinan), (30 ± 4) nm (single‐stranded xanthan), (68 ± 7) nm (double‐stranded xanthan), and (80 ± 10) nm (scleroglucan). Monte Carlo calculations for wormlike chains close to an interacting surface or confined to the region between two surfaces showed that (1) strongly adsorbed molecules are essentially two‐dimensional and (2) molecules restricted to the space between two surfaces separated by a distance less than 20% of the persistence length are two‐dimensional in their directional correlation. The somewhat low estimates of the persistence lengths obtained from the electron micrographs compared with those reported from solution measurements can be accounted for by the adoption of a strictly two‐dimensional model in the analysis, whereas the adsorbed polymers are most likely intermediate between the two‐and three‐dimensional cases. The model calculations and the analysis of the electron micrographs suggest that stiffness parameters are obtainable from the electron micrographs when the proper theoretic

ISSN:0006-3525    

DOI:10.1002/bip.360301303

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

年代:1990

数据来源: WILEY

摘要:

AbstractFourier transform ir spectroscopy has been used to study the gelation and retrogradation of amylose and amylopectin. Results indicate that two processes occur: a fast change complete within 0.5 h shown by both samples and a much slower change that continues up to 400 h seen only for amylopectin. These processes are related to changes in molecular conformation, and are explained in terms of existing models for gelation and retrogradation in amylose and amylopectin.

ISSN:0006-3525    

DOI:10.1002/bip.360301304

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

年代:1990

数据来源: WILEY

摘要:

AbstractAccording to counterion condensation theory, one of the contributions to the polyelectrolyte free energy is a pairwise sum of Debye–Hückel potentials between polymer charges that are reduced by condensed counterions. When the polyion model is taken as an infinitely long and uniformly spaced line of charges, a simple closed expression for the summation, combined with entropy‐derived mixing contributions, leads to the central result of the theory, a condensed fraction of counterions dependent only on the linear charge density of the polyion and the valence of the counterion, stable against increases of salt up to concentrations in excess of 0.1M. Here we evaluate the sum numerically for B‐DNA models other than the infinite line of B‐DNA charges. For a finite‐length line there are end effects at low salt. The condensation limit is reached as a flat plateau by increasing the salt concentration. At a fixed salt concentration the condensation limit is reached by increasing the length of the line. At moderate salt even very short B‐DNA line‐model oligomers have condensed fractions not far from the infinite polymer limit. For a long double‐helical array with charge coordinates at the phosphates of B‐DNA, the limiting condensed fraction appears to be approached at low salt. In contrast to the results for the line of charges, however, the computed condensed fraction varies strongly with salt in the range of experimentally typical concentrations. Salt invariance is restored, in agreement with both the line model and experimental data, when dielectric saturation is considered by means of a distance‐dependent dielectric function. For sufficiently long B‐DNA line and helical models, at typical salt concentrations, the counterion binding fraction approaches the polymer limit as a linear function of 1/P, wherePis the number of pho

ISSN:0006-3525    

DOI:10.1002/bip.360301305

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

年代:1990

数据来源: WILEY

摘要:

AbstractWe examine the salt dependence of the B‐Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference ΔGis computed for both the ZIand ZIIconformations over broad ranges of NaCl and MgCl2concentrations and polymer lengths. For the solvent we employ both a constant‐dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance‐dependent dielectric constant). Where comparison can be made, the results for the constant‐dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low‐salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZIand ZIIare qualitatively similar throughout the entire salt range for the constant‐dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic ΔG, in the presence of dielectric saturation, bears comparison with the high‐salt trend of the measured total ΔGif “Z‐DNA” is predominantly ZI, but not if i

ISSN:0006-3525    

DOI:10.1002/bip.360301306

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe kinetics of oligomer binding to a polymer are treated in the approximation that the internal states of the oligomer–polymer complex equilibrate rapidly compared with the rate of binding. In that case one can use equilibrium statistical mechanics to give the density of appropriate binding sites required in the kinetic equation. In this manner one can obtain a general differential equation in one variable (the net density of oligomer bound) for the case of cooperative binding. Several simple, but accurate, approximate solutions to the binding kinetics are presente

ISSN:0006-3525    

DOI:10.1002/bip.360301307

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

年代:1990

数据来源: WILEY

摘要:

AbstractTwo extant models of thermal folding/unfolding equilibria in two‐chain, α‐helical coiled coils are tested by comparison with experimental results on excised, isolated subsequences of rabbit αα‐tropomyosin (Tm). These substances are designatediTmjwhereiandjare, respectively, the residue numbers (in the 284‐residue parent chain) of the N‐ and C‐terminal residues of the subsequence. One model postulates that a coiled coil consists of segments, each denaturing in an all‐or‐none manner, like small globular proteins. Thus this model yields a small number of populated molecular species. In an extant calorimetry study of11Tm127and of190Tm284, each required only two all‐or‐none‐segments, and their enthalpies and transition temperatures were assigned. These assignments are shown here to yield the concentration of all molecular species, and therefore the helix content, as a function of temperature. Such calculations for190Tm284are in tolerable agreement with CD experiments, but those for11Tm127are in gross disagreement. Thus, either the model itself or the calorimetric assignment is faulty. In the second model, all conformational states are counted and weighted, as in the Zimm–Bragg theory for single‐chain polypeptides. This theory has been extended (by Skolnick) to two‐chain coiled coils and is here used to fit CD data for11Tm127,142Tm281, and190Tm284. The fit is tolerable for11Tm127, good for142Tm281, and quantitative for190Tm284. Thus this comparison does not falsify this second model. The helix–helix interaction free energy, obtainable from the fit, shows nonadditivity when isolated subsequences are compared with the parent. This suggests that removal of a region from a long coiled coil allows energetically substantial adjustments in side‐chain packing in the helix–helix interface. Thus, the helix–helix interaction in long coiled coils is characteristic of a global free energy minimum and not just of the

ISSN:0006-3525    

DOI:10.1002/bip.360301308

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

年代:1990

数据来源: WILEY

摘要:

AbstractInfrared spectra of the amino acid residues in H2O solution have been obtained in the 1800–1400‐cm−1region. It has been established that amino acid residues of arginine, asparagine, glutamine, aspartic and glutamic acids, lysine, tyrosine, histidine, and phenylalanine have intensive absorption in this spectral region. Infrared spectra for a set of model compounds have been measured. On the basis of these data, spectral parameters of amino acid residue absorption bands have been deter

ISSN:0006-3525    

DOI:10.1002/bip.360301309

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

年代:1990

数据来源: WILEY

摘要:

AbstractInfrared spectra of poly(D,L‐alanine), poly(L‐glutamic acid), poly(L‐lysine), silk fibroin, and tropomyosin have been registered for various conformations of the polypeptide chain. Assuming additivity of the main‐ and side‐chain absorption, spectral parameters of amide I and II absorption bands corresponding to α‐, β‐, and random coil conformations have been derived. The amide I band parameters for H2O and D2O hav

ISSN:0006-3525    

DOI:10.1002/bip.360301310

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

年代:1990

数据来源: WILEY

摘要:

AbstractInfrared spectra of 13 globular proteins have been obtained in the 1800–1480‐cm−1region for H2O solutions. A method for estimating protein secondary structure from the ir spectrum has been developed. The method can also be used for estimating polypeptide and fibrous protein conformation. For the globular and fibrous proteins and polypeptides analyzed, the correlation coefficients between the ir and x‐ray estimates of ordered helix, disordered helix, ordered β‐structure, disordered β‐structure, turns, and remainder were 0.98, 0.80, 0.99, 0.87, 0.90, and 0.92

ISSN:0006-3525    

DOI:10.1002/bip.360301311

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

年代:1990

数据来源: WILEY