摘要:

AbstractMolecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2′‐endoregion and the phosphodiester conformations are (trans,gauche−), and the RNA helices have sugars in the C3′‐endoregion and the phosphodiester conformations are (gauche−,gauche−). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson‐Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson‐Crick duplex and the corresponding triple helix. © 1994 Jo

ISSN:0006-3525    

DOI:10.1002/bip.360341202

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe binding of polyamines, including spermidine (1) and spermine (2), to poly[d(G‐C) · d(G‐C) ] was probed using spectroscopic studies of anthracene‐9‐carbonyl‐N1‐spermine (3); data from normal absorption, linear dichroism (LD), and circular dichroism (CD) are reported. Ligand LD and CD for transitions located in the DNA region of the spectrum were used. The data show that3binds to DNA in a manner characteristic of both its amine and polycyclic aromatic parts. With poly [(dG‐dC) · (dG‐dC)], binding modes are occupied sequentially and different modes correspond to different structural perturbations of the DNA. The most stable binding mode for3with poly[d(G‐C) · d(G‐C)] has a site size of 6 ± 1 bases, and an equilibrium binding constant of (2.2 ± 1.1) × 107M−1with the anthracene moiety intercalated. It dominates the spectra from mixing ratios of approximately 133:1 until 6:1 DNA phosphate:3is reached. The analogous data for poly [d(A‐T) · d(A‐T)] between mixing ratios 36:1 and 7:1 indicates a site size of 8.3 ± 1.1 bases and an equilibrium binding constant of (6.6 ± 3.3) × 105M−1. Thus,3binds preferentially to poly [d(G‐C) · d(G‐C)] at these c

ISSN:0006-3525    

DOI:10.1002/bip.360341203

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

年代:1994

数据来源: WILEY

摘要:

AbstractWe report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing Cα,α‐diphenylglycine (Dph), namely Z‐Aib‐Dph‐Gly‐OMe (Aib: Cα,α‐dimethylgrycine) and Bz‐Dph‐Dph‐Gly‐OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the Cαatom, adopts the typical 310/α‐helical conformation. Gly residues, without substituents on the Cαatom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported.

ISSN:0006-3525    

DOI:10.1002/bip.360341204

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe anisotropic self‐diffusion coefficient of7Li+(I= 3/2) counterions has been studied in hydrated, macroscopically oriented Li‐(B)DNA fibers at relatively high water contents, corresponding to approximate DNA‐DNA helix axis distances of 22–35 Å, using the pulsed field gradient hmr spin‐echo method. Self‐diffusion coefficients parallel (D∥) and perpendicular (D⟂) to the DNA helix axis increase with increasing salt content and with increasing DNA‐DNA helix axis distance. The observed anisotropyD∥/D⟂decreases from 1.6 to 1.2 with the DNA‐DNA separation increasing from 22 to 35 Å in the salt‐free sample. This result can be understood by the obstruction effect caused by the DNA molecules themselves. The values of the Li+self‐diffusion coefficients in the most water‐rich system with no added salt (corresponding to an approximate distance of 35 Å between the DNA helix axes) wereD∥∼ 1.15 × 10−10m2s−1andD⟂∼ 0.98 × 10−10m2s−1, compared to 9.14 × 10−10m2s−1for the diffusion of Li+in an aqueous solution of LiCl (∼ 2.1M). The possible occurrence of restriction effects in the DNA fibers have also been studied by determining the self‐diffusion coefficient at different effective diffusion times. The self‐diffusion coefficient of Li+in the sample with the largest DNA‐DNA helix axis distance seems to be independent of the effective diffusion time, which indicates that the lithium ions are not trapped within impermeable barriers. The possibility of diffusion through permeable barriers has also b

ISSN:0006-3525    

DOI:10.1002/bip.360341205

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

年代:1994

数据来源: WILEY

摘要:

AbstractA proton magnetic resonance study of different cross‐linked collagens was performed as a function of water content and temperature. Collagens from three connective tissues (calf, steer, and cow) were chosen according to the different number of nonreducible multivalent cross‐links, which increases during the life of animal. Samples were hydrated under five well‐defined water activities (Aw) ranging from 0.44 to 0.85. The transverse and cross‐relaxation times of water protons were studied as a function of temperature from −20 up to 100°C. From the temperature dependence of relaxation rates, the dynamics of water molecules can be described according to different processes: exchange of protons at the higher temperatures and dipole‐dipole interactions that prevail at the lower temperatures. The exchange processes are analyzed as a function of the residence lifetime of water molecules at the protein interface and of the transfer of spin energy from water protons to macromolecule protons. The proton dipole‐dipole interactions are related to the relaxation parameters of protein and water protons. All the relaxation parameters showed specific behavior for the 0.44 water activity for every tissue. The collagen tissue from calf also showed distinct behavior in comparison with other tissues. © 1994 John

ISSN:0006-3525    

DOI:10.1002/bip.360341206

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

年代:1994

数据来源: WILEY

摘要:

AbstractIntact cells ofSaccharomyces cerevisiaewere examined as an aqueous paste by13C‐nmr spectroscopy with direct polarization and magic‐angle spinning. The spectra obtained were highly resolved, showing numerous resonances in the 60‐105 ppm range that were assigned to carbons of a liquid‐like domain of the cell wall glucan. Assignments were confirmed by running the spectrum ofS. cerevisiaein which the cell wall glucans were labeled with [13C] by feeding the cell [13C ] galactose. The spectra indicate that the glucan in the cell wall of intact S.cerevisiaeassumes a helical conformation and suggest that strain 17A fed with galactose preferentially incorporates the resulting glucose into β(1 → 3)‐linkages. © 1994 John Wi

ISSN:0006-3525    

DOI:10.1002/bip.360341207

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

年代:1994

数据来源: WILEY

摘要:

AbstractSequence analysis of msDNA from bacterium such asStigmatella aurantiaca, Myxococcus xanthusandEscherichia coli Brevealed that the guanine residue of the single‐stranded RNA is linked to the cytosine residue of the msDNA through a 2′–5′ instead of a conventional 3′–5′ phosphodiester bond. We have now obtained the crystal structure of the self‐complementary dimer guanylyl‐2′,5′‐cytidine (G2′p5′C) that occurs at the msDNA‐RNA junction. G2′p5′C crystallizes in the orthorhombic space group P212121witha= 8.376(2),b= 16.231(5),c= 18.671(4). CuK ∝ intensity data were collected on a diffractometer in the ω −2θ scan mode. The amount of 1699 out of 2354 reflections havingI≥ 3σ (F) were considered observed. The structure was solved by direct methods and refined by full‐matrix least squares to aRfactor of 0.054. The conformation of the guanine base about the glycosyl bond is syn (χ1= −54°) and that of cytosine is anti (χ2= 156°). The 5′ and 2′ and ribose moieties show C2′‐endoand C3‐endomixed puckering just like in A2′p5′A, A2′p5′C, A2′p5U, and dC3′p5′G. Charge neutralization in G2′p5′C is accomplished through protonation of the cytosine base. An important feature of G2′p5′C is the stacking of guanine on ribose 04′ of cytosine similar to that seen in other 2′–5′ dimers. G2′p5′C, unlike its 3′–5′ isomer, does not form a miniature double helix with the Watson‐Crick base‐pairing pattern. Comparison of G2′p5′C with A2′p5′C reveals that they are isostruct

ISSN:0006-3525    

DOI:10.1002/bip.360341208

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe pore‐lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993)Journal of Molecular Biology, Vol. 229, pp. 1101–1124]. We have performed molecular dynamics simulations of isolated 22‐residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2α and M2δ) were studied in this manner, resulting in a total often 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side‐chain atoms. Comparison with data from the literature on site‐directed mutagenesis of M2 residues suggests that such polar side‐chain to main‐chain H bonds may also contribute to kinking of M2 helices in the intact channel protein. © 1994 John

ISSN:0006-3525    

DOI:10.1002/bip.360341209

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

年代:1994

数据来源: WILEY

摘要:

AbstractCD studies are presented on thermal unfolding of coiled‐coil homodimers of two genetic variant chains of chicken gizzard tropomyosin (CG‐Tm). The experiments include the effects of cross‐linking both isoforms and the dependence on protein concentration of unfolding in both reduced isoforms, variables not examined in extant work. The general shapes of the unfolding curves for singly cross‐linked species depend on whether the crosslink is at C190 (its site on one isoform) or at C36 (its site on the other). These curves are compared with extant ones for various cross‐linked species of rabbit tropomyosin. The comparison supports the view that the unfolding behavior of cross‐linked species results from a complex interaction of strain at the cross‐link, local variations in structural stability, and loop entropy. The observed concentration dependence of the transition temperature for the uncross‐linked (reduced) species of CG‐Tm is very small (2.9°C) for one variant homodimer and unobservably small (<2°C) for the other in the 100‐fold concentration range (∼ 0.01–1.0 mg/mL) accessible here. These experimental values of ΔTmare much smaller than are predicted from extant values of the van't Hoff transition enthalpies, calling the latter into question.

ISSN:0006-3525    

DOI:10.1002/bip.360341210

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

年代:1994

数据来源: WILEY

摘要:

AbstractA two‐stage method is developed to search the conformational space of small protein segments for low energy structures. Central features of the method are efficient procedures for generating small, eight‐backbone atom, local moves in Cartesian coordinates and for introducing geometric constraints in adaptable Monte Carlo procedures. This allows natural implementation of an adaptive simulated annealing algorithm, which achieves an effective trade‐off between speed and acceptance ratio. The method is applied to the calculation of various immunoglobulin loops. We also develop data base derived rules for identifying constraint conditions, and show that the incorporation of an identified side‐chain constraint allows a 1.2 Å all‐backbone atom rms deviation prediction of a 9 residue long L1 loop. © 1994 John Wile

ISSN:0006-3525    

DOI:10.1002/bip.360341211

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

年代:1994

数据来源: WILEY