ISSN:0006-3525    

DOI:10.1002/bip.360241202

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

年代:1985

数据来源: WILEY

摘要:

AbstractPoly(dA‐dT) · poly(dA‐dT) undergoes a reversible conformational transition in the presence of Co(NH3) 63+or spermidine in low salt (10 mMNaCl + 1 mMNa cacodylate). This transition is similar, as judged by changes in the CD spectrum, to the B‐to‐X transition of the polymer provoked by alcohol and Cs+[Vorlickova et al. (1983)J. Mol. Biol.166, 85–92; (1982)Nucleic Acids Res.10, 6969–6979] and by meso‐substituted porphyrin ligands [Carvlin et al. (1983)Nucleic Acids Res.11, 6141–6154]. Under the salt conditions indicated, the CD transition begins with Co(NH3) 63+at about 70 μMand is complete by 150 μM; with spermidine, it begins at about 300 μMand is complete by 600 μM. Total intensity light scattering shows a marked increase at trivalent cation concentrations somewhat below those at which the CD transition begins. Quasielastic laser light scattering (QLS) measurement of the translational diffusion coefficient,DT, shows that, in the presence of Co(NH3) 63+, the hydrodynamic radius,Rh, increases from 260 to 1450 Å over the concentration range of 25 to 200 μM. With spermidine,Rhis 550±50 Å up to 200 μM, then increases rapidly. Values ofRhin this range are generally found for toroidal or other compact condensed forms of DNA. Such forms—toroidal, spheroidal, and rodlike structures—are observed in electron micrographs of poly(dA‐dT) · poly(dA‐dT) when the trivalent cation concentration is in the transition range. Above that range, extensive aggregation of the polymer chains is seen. Taken together, these results suggest a sequenc of related secondary and tertiary structure changes as trivalent cations are added to a low‐salt solution of poly(dA‐dT) · poly(dA‐dT). At very low Co(NH3) 63+or spermidine, condensation of the polymer takes place while it is still in the B‐form. Further additions of trivalent cation provoke a transition from B‐ to X‐form, finally resulting in extensively aggregated polymer. These results are different from those generally observed with native DNA, where condensation with polyamines or Co(NH3) 63+in aqueous solution is not accompanied by secondary structural change. They are also different from those we have seen with poly(dG‐me5dC) · poly(dG‐me5dC), where condensation and the B–Z transition occur at the same ionic conditions. These distinctions are another entry in the growing catalog of sequence‐dependent structural effects that ma

ISSN:0006-3525    

DOI:10.1002/bip.360241203

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

年代:1985

数据来源: WILEY

摘要:

AbstractFive models of collagen molecular structure incorporating a variableh‐spacing were evaluated by comparing theoretical densitometric scans of segment long spacing (SLS) banding patterns with experimental densitometric scans. The five models tested assumed a shift in theh‐spacing of different residues: (1) proline only, (2) hydroxyproline only, (3) proline and hydroxyproline (in the same direction), (4) proline and hydroxyproline (in opposite directions), and (5) all residues shifted depending on their relative hydrophobicity. The best correlation coefficients were obtained when, in the theoretical models, the proline residues were expanded axially and/or the hydroxyproline residues were contracted. Using the hydrophobic model, the results showed that in general the more hydrophobic a residue is, the larger itsh‐spacing. Theorectical models with the α2‐chain in the A position of the triple helix (α2,α1,α1) correlated best with the experimental data. In conclusion, these studies suggest that variation exists in theh‐spacing of the amino acid residues proline and hydroxyproline in SLS prepared for electron microscopy and stained with phosphotungstic acid and uranyl acetate. Some of this variation may be due to drying and may not be present in hydra

ISSN:0006-3525    

DOI:10.1002/bip.360241204

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

年代:1985

数据来源: WILEY

摘要:

AbstractSpectroscopic data and conformational energy calculations are reported for eight oligosaccharides from ovarian cyst mucins and from human milk, the nonreducing terminals of which have fucose (α1 → 2)galactose linked either (β1 → 3) (type I) or (β1 → 4)(type II) toN‐acetylglucosamine or in (β1 → 3) linkage to galactosaminitol. The fully assigned proton nmr spectra are reported along with nuclear Overhauser enhancement (NOE) data. Amide proton coupling constants and vacuum‐uv CD spectra provide information on the amide plane orientation and amide environment. Our results imply that the fucosidic dihedral angles are similar for all three cases and that the substantial differences in the chemical shifts of the fucosyl protons of type I, type II, and 3‐ol chains result from different perturbations by the amide group of the residue to which the β‐galactose is linked. Stereopair diagrams of conformational models for both type I and II H chains are presented that are consistent with NOE, coupling constants, conformational energy calculations, and the CD data. While the temperature dependence of the observed NOE of penta‐ and hexasaccharides indicates that their rotational correlation times are strongly temperature dependent, we conclude that the conformations are essentially inde

ISSN:0006-3525    

DOI:10.1002/bip.360241205

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe intramolecular formation of multiple clusters of interacting helices has been characterized in a homopolymer. The configuration partition function permits the formation of clusters in which the number of interacting helices may be as large as the greatest integer inn/2, wherendenotes the number of amino acid residues in the chain. The theoretical formulation has its origin in a recent [Mattice, W. L.&Scheraga, H. A. (1984)Biopolymers23, 1701–1724], tractable matrix expression for the configuration partition function for intramolecular antiparallel β‐sheet formation. Reassignment of the expression for one of then(n+3)/2 elements in the sparse statistical weight matrix, along with a simple change in notation, converts that treatment into a matrix formulation of the configuration partition function for a chain containing multiple clusters of interacting antiparallel helices. The five statistical weights used are δ,fl,w, and the Zimm‐Bragg σ ands. Each tight bend that connects two interacting helices contributes a factor of δ,flis used in the weight for larger loops between interacting helices, andwarises from helix–helix interaction. The influence of the helix–helix interaction is well illustrated by two helix–coil transitions in a chain withn= 156 and σ = 0.001. In the absence of helix–helix interaction, the transition occurs by the nucleation and subsequent elongation of a small number of helices. When helix–helix interaction is attractive, the transition can occur by a different mechanism. Formation of a single pair of interacting helices is followed by addition of new helices to the initial cluster. In the latter process, individual helices experience relatively little growth a

ISSN:0006-3525    

DOI:10.1002/bip.360241206

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe electrophoresis of a series of DNA fragments ranging in size from 0.5 to 12 kilobase pairs, has been studied as a function of agarose gel concentration and electric field strength. The apparent mobility of all fragments decreased with decreasing electric field strength and with increasing gel concentration. When extrapolated to zero electric field strength and zero agarose concentration, the apparent mobility of all DNA fragments extrapolated to a common value (2.0 ± 0.1) × 10−4cm2/V s. The square roots of the retardation coefficients of the various fragments were found to be linearly related to the root‐mean‐square radii of gyration of the fragments, as predicted by pore‐size distribution theory. As predicted by reptation theory, the molecular weights of the various fragments were found to be linearly related to the reciprocal of the apparent mobilities. An equation is given for estimating the apparent pore size of agarose gels between 0.25 and 1.5% in conc

ISSN:0006-3525    

DOI:10.1002/bip.360241207

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe assignments of several1H lines in the spectrum of thelacrepressor DNA‐binding domain (or “headpiece”) are documented. These new assignments complement those obtained in a previous study [E.R.P. Zuiderweg, R. Kaptein, and K. Wüthrich (1983)Eur. J. Biochem.137, 279] and were made from pure absorption phase two‐dimensional nuclear Overhauser enhancement (2D NOE) spectra and1H 2D double‐quantum spectra of this protein. Based on the complete set of resonance assignments, a large number of interresidue NOEs are identified; these are documented and their relation with distance constraints is discussed. The identification of these NOEs is a prerequiste for the determination of the spatial structure of this protein, for which no crystallographic data are

ISSN:0006-3525    

DOI:10.1002/bip.360241208

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe low‐energy conformations accessible to dCpdG modified at guanine N2viatransepoxide opening by (+) and (−) 7β,8α‐dihydroxy‐9α,10α‐epoxy‐7,8,9,10‐tetrahydrobenzo(a)pyrene (anti‐BPDE) have been delineated by minimized semiempirical potential‐energy calculations with all torsion angles flexible. Nearly 4000 trials were made, representing a fairly thorough investigation of the conformation space of the adducts. Carcinogen–base stacked states and base–base stacked conformers were found in the low‐energy regions of both enantiomers. Many ω′, ω, ψ domains accommodate the two types of conformations, with B‐like backbones among the most preferred states in each case. The conformational differences between the two enantiomers on the dimer level reside in subtle distinctions in orientat

ISSN:0006-3525    

DOI:10.1002/bip.360241209

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

年代:1985

数据来源: WILEY

摘要:

AbstractPhysical studies and conformational analysis of human glycophorin A suggest a revised model for its molecular organization, self‐association, and interactions with the erythrocyte membrane. Intrinsic viscosity has been used to study, under more physiological conditions, the monomer–dimer equilibrium demonstrated previously by polyacrylamide–SDS gel electrophoresis. The results show that the equilibrium persists in the absence of detergent and support earlier indications that the dimer is probably the physiologically relevant form and that it is promoted by salt, inhibited by conventional denaturants, and abolished by carboxymethylation.Combined application of CD, fitted to the poly‐(L‐lysine) model spectra of Greenfield and Fasman, and conformational prediction, by the statistical method of Chou and Fasman and the stereochemical approach of Lim, suggests five helical sequences in glycophorin A: Arg‐39 to Tyr‐52 (A); Gln‐63 to Glu‐70 (B); Glu‐72 to Leu‐89 (C); Ile‐95 to Lys‐101 (D); and Leu‐118 to Asn‐125 (E). Sequence A occurs only at low pH and may be stabilized by favorable noncovalent interactions ofO‐linked tetrasaccharide side chains. The other four helices all occur in the dimeric form of glycophorin A at physiological pH and ionic strength. Sequence D is destroyed by trypsin, and is also lost on conversion to the monomeric form of the glycoprotein at low ionic strength. Sequence E is denatured by 6Mguanidine hydrochloride/4Murea. Sequences B and C, which are separated by a single proline residue, are stable under all these conditions.Dimerization of the major, hydrophobic helical sequence, (C) may be promoted and directed by an adjacent short sequence of intermolecular parallel β‐sheet (Leu‐90 to Tyr‐93). It is proposed that these two structures span the lipid bilayerin vivo, and that helices B and D lie, respectively, along the outer and inner surfaces of the membrane. Molecular organization in the N‐ and C‐terminal regions of the molecule is discussed in terms of evidence from the present

ISSN:0006-3525    

DOI:10.1002/bip.360241210

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

年代:1985

数据来源: WILEY

摘要:

Abstract13C‐nmr has been employed to probe the molecular conformation and crystal structure of (1 → 6)‐β‐D‐glucan (pustulan) in the solution, gel, and solid states. CP/MAS13C‐nmr spectra recorded for partially crystalline solid pustulan display a resonance near 82 ppm that is absent in solution spectra. The intensity and peak width of this resonance were found to depend on relative crystallinity as determined by x‐ray diffraction. CP/MAS spectra of aqueous pustulan gels also exhibit the 82‐ppm resonance, suggesting that the gelation mechanism may involve microcrystalline junction zones. Since the 82‐ppm resonance is absent in the CP/MAS spectrum of the (1 → 6)‐β‐linked dimer gentiobiose, we tentatively conclude the crystal structure of this dimer does not adequately model the yet undetermi

ISSN:0006-3525    

DOI:10.1002/bip.360241211

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

年代:1985

数据来源: WILEY