摘要:

AbstractPoly(Pro‐Nle‐Gly) was found to have a CD spectrum characteristic of a random polypeptide and an x‐ray powder pattern that does not reveal any regular secondary structure. In its electron micrograph, however, filaments and fibers were seen. This is a random polymer with supramolecular structure. It suggests that the supramolecular structure seen in electron micrographs of elastin preparations and related polypeptides does not necessarily imply an ordered structure at the molecular

ISSN:0006-3525    

DOI:10.1002/bip.360241002

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

年代:1985

数据来源: WILEY

摘要:

AbstractMolecular mechanical calculations were done on complexes of ethidium cation with various base‐paired deoxydinucleoside monophosphates [(ApT)2, (TpA)2, (A2· T2), (GpC)2, (CpG)2, and (G2· C2)] and deoxyhexanucleoside pentaphosphates [(ATATAT)2, (TATATA)2, (A6· T6), (GCGCGC)2, (CGCGCG)2, and G6· C6]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all‐atom force field) gave results in good agreement with previous calculations and experimental work. Less‐sophisticated models did not perfor

ISSN:0006-3525    

DOI:10.1002/bip.360241003

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe configurational properties of an isotropically bendable wormlike chain have been investigated using a Monte Carlo approach. In particular, radial distributions for end‐to‐end separation, ring closure probabilities, and the angular correlation of the two ends of the chain have all been determined as a function of the contour length of the chain. The results of this analysis, when applied to the data of Shore et al. [(1981)Proc. Natl. Acad. Sci. USA78, 4833–4837] for the length dependence of ring closure for doublehelical DNA, yields a value for the persistence length of DNA in remarkable agreement with earlier hydrodynamic st

ISSN:0006-3525    

DOI:10.1002/bip.360241004

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

年代:1985

数据来源: WILEY

摘要:

AbstractHeat denaturation of native globular proteins is a cooperative process usually connected with the melting of the main part of their regular secondary structure. In this paper, a noncooperative temperature‐induced melting of the regular secondary structure in the carbonic anhydrase B at pH 2.6 in heavy water is observed by ir spectroscopy. The molecules of carbonic anhydrase B in an acid medium, unlike the native ones, do not have a specific tertiary structure. Nevertheless, the β‐structure content is about the same in both of these states. A temperature‐induced noncooperative melting process takes place from 10 to 67°C with a decrease of the antiparallel β‐form content by about one third. The remaining part of the β‐form melts with a more intensive heat absorption, with a maximum at 87°C. The whole melting process is practically reversible. We assume that the observed noncooperative process displays a general property of a new type of structural state of the globular protein—the “mol

ISSN:0006-3525    

DOI:10.1002/bip.360241005

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

年代:1985

数据来源: WILEY

摘要:

AbstractOptical anisotropy data spanning a very wide time range are analyzed using a recently developed theory for filamentous macromolecules that can bend, twist, and also admit overdamped local libration (or wobble) of the chromophore. A rapid relaxation in the fluorescence polarization anisotropy (FPA) near 10−10s is fitted well by superimposing isotropic wobble of the chromophore (7° rms polar and azimuthal amplitude) on the long‐wavelength twisting and bending motions that characterize the relaxation at longer times but not by the latter alone. Moreover, the decay of the FPA from 0.5 to 150 ns cannot be satisfactorily fitted by chromophore wobble in an otherwise rigid DNA and must be assigned primarily to twisting, as noted previously.Data from 26 ns to 20 μs for 600 base‐pair DNA are accurately fitted with only a single adjustable scaling factor when the tumbling correlation function is taken to be the empirical electric birefringence decay function of Elias and Eden. The Barkley‐Zimm (BZ) tumbling correlation for very long filaments appears to decay too rapidly and results in significant overestimation of the depolarization fort≤ 300 ns. In the range of the FPA experiments (t≥ 150 ns), equally good fits with equally uniform torsion constants are obtained for long DNAs, whether one assumes the BZ tumbling correlation function or neglects tumbling entirely, but the best‐fit torsion constant (actually the product of the torsion constant and friction factor) is increased by the factor 1.9 when the BZ result is used with a persistence length ofa= 500 Å. The BZ bending theory is compared with other experimental data, and also with a simulation at very short times with mixed results. Present uncertainties regarding the tumbling dynamics and the friction factor for azimuthal rotation allow the torsion constant to be as much as 3.8 times larger than the initial estimate of Thomas et al. Apparent torsion constants obtained from relative ligase kinetics measurements are also b

ISSN:0006-3525    

DOI:10.1002/bip.360241006

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

年代:1985

数据来源: WILEY

摘要:

AbstractTransient photodichroism (TPD) data of Wang, Hogan and Austin [(1982)Proc. Natl. Acad. Sci. USA79, 5896–5900] for methylene blue intercalated in nucleosomal DNA are reanalyzed using correct expressions for the twisting correlation functions of short DNAs. The data are found to rule out several models, including one in which the helix axis is constrained to girdle the equator of the sphere (representing a core particle) but the DNA iseverywhereable to undergo twisting deformations and/or spinning around its local helix axis. However, when the ends of the DNA are rigidly clamped (against twisting/spinning) to the sphere, the same model gives an excellent fit to the data with suitable choices of parameters. From these and other observations, it is concluded that nucleosomal DNA must be rigidly clamped to the core particle at one or more points, although it is free to twist at most sites of binding of the dye. Moreover, if the dye is actually bound between two clamped points, then the torsional rigidity of DNA in the nucleosome is at least 2.5 times smaller than that of an ordinary linear DN

ISSN:0006-3525    

DOI:10.1002/bip.360241007

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe effects of sodium ion concentration on the binding isotherms and association and dissociation reaction rates for the interaction of the closely related intercalating dication, propidium, and the monocation, ethidium, with DNA have been determined by spectrophotometric binding and stopped‐flow kinetics methods. The binding of propidium to DNA is best described by a neighbor‐exclusion binding isotherm (two base pairs per binding site) with negative ligand cooperatively on binding. The cooperativity parameter is fairly independent of salt concentration, while the log of the observed equilibrium binding constant varies with −log [Na+], with a slope of two for the propidium–DNA interaction. These effects of the sodium ion on the equilibrium binding of propidium with DNA are similar to those previously described for the dication, quinacrine [Wilson, W.D.&Lopp, I.G. (1979)Biopolymers,18, 3025–3041]. Ethidium behaves, as a function of salt, as a monocation binding to DNA with neighbor exclusion and without ligand cooperativity. Equations are derived for two limiting kinetics models for intercalation involving binding of the intercalator to a preequilibrium, open state of DNA (model I) or binding form a preequilibrium externally associated state of the intercalator with DNA (model II). Model II gives the best fit to all of the kinetic results if it is assumed that the initial external interaction of the intercalator with DNA is similar to the exchange of free and condensed simple counterions. Intercalation then occurs from this state following an opening transition of the base pairs of the double helix. This model predicts a larger effect of salt concentration on the association than on the dissociation reaction, and that is what is experimentally observed. The intercalation conformational change makes a significant contribution to the ionic effects for both the equilibrium binding and the kinetic constants. The dissociation results and the association reaction results under pseudo‐first‐order conditions could be fit with single exponential curves under the conditions of ou

ISSN:0006-3525    

DOI:10.1002/bip.360241008

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

年代:1985

数据来源: WILEY

摘要:

AbstractAt low temperature and low salt concentration, both imino proton and31p‐nmr spectra of DNA complexes with the intercalators ethidium and propidium are in the slow‐exchange region. Increasing temperature and/or increasing salt concentration results in an increase in the site exchange rate. Ring‐current effects from the intercalated phenanthridinium ring of ethidium and propidium cause upfield shifts of the imino protons of A · T and G · C base pairs, which are quite similar for the two intercalators. The limiting induced chemical shifts for propidium and ethidium at saturation of DNA binding sites are approximately 0.9 ppm for A · T and 1.1 ppm for G · C base pairs. The similarity of the shifts for ethidium and propidium, in both the slow‐ and fast‐exchange regions over the entire titration of DNA, shows that a binding model for propidium with neighbor‐exclusion binding and negative ligand cooperativity is correct. The fact that a unique chemical shift is obtained for imino protons at intercalated sites over the entire titration and that no unshifted imino proton peaks remain at saturation binding of ethidium and propidium supports a neighbor‐exclusion binding model with intercalators bound at alternating sites rather than in clusters on the double helix. Addition of ethidium and propidium to DNA results in downfield shifts in31P‐nmr spectra. At saturation ratios of intercalator to DNA base pairs in the titration, a downfield shoulder (approximately −2.7 ppm) is apparent, which accounts for approximately 15% of the spectral area. The main peak is at −3.9 to −4.0 ppm relative to −4.35 in uncomplexed DNA. The simplest neighbor‐binding model predicts a downfield peak with approximately 50% of the spectral area and an upfield peak, near the chemical shift for uncomplexed DNA, with 50% of the area. This is definitely not the case with these intercalators. The observed chemical shifts and areas for the DNA complexes can be explained by models, for example, that involve spreading the intercalation‐induced unwinding of the double helix over several base pairs and/or a DNA sequence‐ and conformation‐dependent heterogeneity in intercalation‐induced chemica

ISSN:0006-3525    

DOI:10.1002/bip.360241009

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

年代:1985

数据来源: WILEY

摘要:

AbstractElectric‐field pulses of e.g. 20 kV/cm and 100 μs induce a strong decrease in the scattered light intensity of DNA condensed by spermine. Analysis of this effect demonstrates that the decrease of the scattered light intensity results from decondensation of DNA. The decondensation reaction requires an electric‐field strength exceeding a threshold value. Complete decondensation can be achieved at field strength that are only slightly higher than the threshold value. The decondensation process is strongly accelerated at high electric‐field strengths. At 30 kV/cm, the decondensation time constant is ∼8 μs, corresponding to an acceleation factor of 105relative to the field‐free decondensation reaction. The dependence of the time constants on the electric‐field strength suggests that the field‐induced decondensation is due to a dissociation field effect. The condensation process observed after electric‐field pulses at low concentrations of DNA and spermine shows a characteristic induction period, which strongly depends on the spermine concentration. This induction period reflects the time required for the binding of spermine to DNA, until the degree of binding is sufficiently high for the condensation reaction. The fast dissociation of condensed DNA by electric‐field pulses together with a relatively long lifetime of the free DNA results in a reaction cycle resemblin

ISSN:0006-3525    

DOI:10.1002/bip.360241010

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

年代:1985

数据来源: WILEY

摘要:

AbstractWe examine the correlation between the sequence and tertiary structure for 212 domains from globular proteins and polypeptides. The sequence of each domain is described as a set of 25 features: the mole percent of 20 amino acids, the number of residues in the domain, and the abundance of four simple patterns in the hydrophobicity profile of the sequence. Each domain, then, is described as a location in 25‐dimensional sequence‐feature space. We use pattern‐recognition methods to find the two axes through the 25‐dimensional sequence‐feature space that best discriminate, respectively, predominantly α‐helix domains from predominantly β‐strand domains (the “secondary structure vector,”SV) and parallel α/β domains from other domains (the “parallel vector,”PV). When we divide the domains into two categories based on whether the cysteine content is above (CYS‐RICH) or below (NORMAL) 4.5%, we find the secondary structure vector for the subset ofCYS‐RICHdomains points in a significantly different direction than the equivalent vector for theNORMALdomains. Thus,CYS‐RICHandNORMAL, domains are best treated separately. The secondary structure vector and the parallel vector forNORMALdomains describes statistically meaningful information, but the secondary structure vector forCYS‐RICHdomains may not be as reliable. We show how the secondary structure content of aNORMALdomain can be predicted by projecting the domain in the feature space onto the secondary structure vector. We subdivide the domains into five structural classes based on whether there is a parallel or mixed β‐sheet in the domain and whether there are more helix or strand residues:NORMAL ALPHA,NORMAL BETA,NORMAL PARALLEL,CYS‐RICH ALPHA, andCYS‐RICH BETA. When we project theNORMALdomains onto the plane containing the origin of the feature space andSVandPV, we see thatALPHA,BETA, andPARALLEL, domains cluster in the plane, with theBETAcluster partially overlapping thePARALLELcluster. The separations between the clusters are such that, by looking at the location of any givenNORMALdomain in the plane, we can correctly predict its structural class with 83% accuracy.CYS‐RICH ALPHAandBETAdomains cluster when projected onto theCYS‐RICHSVvector, and the classes can be preducted with 83% accuracy, but this accuracy forCYS‐R

ISSN:0006-3525    

DOI:10.1002/bip.360241011

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

年代:1985

数据来源: WILEY