摘要:

AbstractFour‐arm DNA branched junctions are stable analogues of Holliday recombinational intermediates. A number of four‐arm DNA junctions synthesized from oligonucleotides have now been studied. Gel mobility or chemical footprinting experiments on several immobile four‐arm junctions indicate that in the presence of Mg2+, they assume a preferred conformation consisting of two helical domains, each formed by stacking a particular pair of arms on each other. We show here that a junction we designate as J1cthat has the same chemical composition as one we have previously studied in detail, J1, but is formed from the four strands complementary to those of the latter, exhibits the reverse stacking preference. The pattern of self‐protection of the strands of J1cexposed to Fe(II) · EDTA‐induced scission reveals that twofold symmetry is preserved, but the opposite pair of strands preferentially cross over. Moreover, the Fe(II) · EDTA scission profiles of J1cindicate that this junction exhibits a weaker bias as to which strands cross over than is observed in J1. The preference for the dominant species in J1 is 1.3 times greater than in J1cat 4°C and in the presence of 10 mMMg2+, based on chemical reactivity data. This is confirmed by a cleavage experiment using the resolvase enzyme, endonuclease I, from bacteriophage T7. This difference could reflect either sequence‐dependent differences in the equilibrium among isomers, or in the structure of these junctions. Chemical footprinting experiments using the probes MPE · Fe(II) and (OP)2Cu(I) show that the high‐affinity ligand binding site in immobile junctions is determined by

ISSN:0006-3525    

DOI:10.1002/bip.360310402

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

年代:1991

数据来源: WILEY

摘要:

AbstractCD and absorption spectra are sensitive to the secondary structure of RNAs. By fitting the spectra contained in our basis set to the CD and absorption spectra of an RNA of known sequence, we could determine the fractions of base pairs, the fractions of each of the nearest neighbor base pairs, and the fractions of the single‐stranded nucleotides in that RNA. The basis set included 58 CD and 58 absorption spectra. The fitting was done with a guided selection routine. The estimated error was about 0.05 for predicting the fractions of the nearest neighbor base pairs, 0.06 for predicting the fractions of A · U, G · C, and G · U base pairs, and 0.04 for predicting the fractions of the single‐stranded nucle

ISSN:0006-3525    

DOI:10.1002/bip.360310403

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

年代:1991

数据来源: WILEY

摘要:

AbstractWe analyzed the CD and uv absorption spectra of 5S RNA fromEscherichia coliusing the method developed in the preceding paper. The analysis of spectra of 5S RNA at 20°C in 0.1MNaClO4, 2.5 mMNa+(phosphate), pH 7.0, and 0.5 mMMgSO4gave 7 ± 3.6 A · U base pairs, 25 ± 3.6 G · C base pairs, and 7.5 ± 3.6 G · U base pairs. Estimates of nearest neighbor base pairs were more consistent with the Pieler–Erdmann and the Gewirth–Moore secondary structure models than with the Fox–Woese or the Burns–Luoma–Marshall models.We also examined the structure of 5S RNA as a function of temperature. The melting profile exhibited two transitions—one at about 35°C and one above 50°C. Our spectral data showed that helices I and II were stable during the first transition, and agreed with other data that helix III was the most likely helix to have melted. The results from this in‐depth study of 5S RNA indicate that our method of analysis should be useful for studying the secondary structures of other

ISSN:0006-3525    

DOI:10.1002/bip.360310404

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe synthetic peptide Gly‐L‐Ala‐L‐Val (C10H19N3O4·3H2O; GAV) crystallizes in the monoclinic space group P21, witha= 8.052(2),b= 6.032(2),c= 15.779(7) Å, β = 98.520(1)°,V= 757.8 Å3,Dx= 1.312 g cm−3, andZ= 2. The peptide Gly‐L‐Ala‐L‐Leu (C11H21N3O4·3H2O; GAL) crystallizes in the orthorhombic space group P212121, witha= 6.024(1),b= 8.171(1),c= 32.791(1) Å,V= 1614 Å3,Dx= 1.289 g cm−3, andZ= 4. Their crystal structures were solved by direct methods using the program SHELXS‐86, and refined to anRindex of 0.05 for 1489 reflections for GAV and to anRindex of 0.05 for 1563 reflections for GAL. The tripeptides exist as a zwitterion in the crystal and assume a near α‐helical backbone conformation with the following torsion angles: ψ1= −150.7°; ϕ2, ψ2= −68.7°, −38.1°; ϕ3, ψ31, ψ32, = −74.8°, −44.9°, 135.9° for GAV; ψ1= −150.3°; ϕ2, ψ2= −67.7°, −38.9°; ϕ3, ψ31, ψ32= −72.2°, −45.3°, 137.5°, for GAL. Both the peptide units in both of the tripeptides show significant deviation from planarity [ω1= −171.3(6)° and ω2= −172.0(6)° for GAV; ω1= −171.9(5)° and ω2= −173.2(6)° for GAL]. The sidechain conformational angles χ21and χ22are −61.7(5)° and 175.7(5)°, respectively, for valine, and the side‐chain conformations χ12and χ23's are −68.5(5)° and (−78.4(6)°, 159.1(5)°) respectively, for leucine. Each of the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH 3+and COO−groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bond

ISSN:0006-3525    

DOI:10.1002/bip.360310405

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

年代:1991

数据来源: WILEY

摘要:

AbstractDirect x‐ray analysis has been used to determine the crystal structure of [D‐Hyi2,L‐Hyi4]meso‐valinomycin {cyclo[‐D‐Val‐D‐Hyi‐L‐Val‐L‐Hyi‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐], C60H102N6O18}, which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cellZ= 3, cell parametersa=b= 15.2085 (8) Å,c= 29.3250 (9) Å, γ = 120°. The standard (R)and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six NH …︁ OC 4 → 1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast tomeso‐valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residuesD‐Val1andL‐Val3are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion‐binding center, it is inaccessible because the hydrophobic isopropyl groups of theD

ISSN:0006-3525    

DOI:10.1002/bip.360310406

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe crystal structure of a synthetic analogue of valinomycin, cyclo[‐(L‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)‐] ([L‐Val1,L‐Val5]meso‐valinomycin), C60H102N6O18, has been determined. Crystals grown from petroleum ether are orthorhombic, space group P212121, with cell parametersa= 16.41(1),b= 18.76(1),c= 25.86(1) Å, andZ= 4. The atomic coordinates for nonhydrogen atoms, except those of terminal carbons on one side chain, were refined in the anisotropic thermal motion approximation. The coordinate parameters of the H atoms were incorporated into the structure factor calculations at geometrically expected positions. Values of the standard and weightedRfactors after refinement are 0.074 and 0.083, respectively. The crystal structure of the molecule is asymmetric and adopts a conformation with four 4 → 1 type and one 6 → 1 type intramolecular hydrogen bonds between amide nitrogens and carbonyl oxygens. Valinomycin binds potassium more than 100 times strongly than theD,LStereoisomeric analogue, as a result of a different spatial orientatio

ISSN:0006-3525    

DOI:10.1002/bip.360310407

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe conductance of the gramicidin A single channels in glycerolmonooleate membranes is strongly reduced in the presence of Mn2+cations. The nmr experiments were performed for N‐terminal to N‐terminal gramicidin A dimer formed by two right‐handed single‐stranded helixes incorporated into the sodium dodecyl sulfate micelles in the presence of Mn2+ions. Dependence of the nonselective spin–lattice relaxation rates of the gramicidin A protons on Mn2+concentration was analyzed to determine coordinates of the divalent cation binding sites. It is inferred that Mn2+ions are bound at the channel mouths at distances of 6.4, 8.6, and 8.8 Å (±2 Å) from the oxygen atoms of exposed carbonyl groups ofD‐Leu 12, 14, and 10, respectively. The bounded Mn2+retains its hydrate shell, the size of which (≈ 6 Å) exceeds the inner pore diameter (≈ 4 Å). That makes the gramicidin A channel impermeable

ISSN:0006-3525    

DOI:10.1002/bip.360310408

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe effective sphere approximation for modeling electrophoretic transport of macromolecules in highly porous gels (the “Ogston model”) is examined, and contrasted with similar mobility models for stiff and flexible solutes. Calculation of segmental depletion near gel obstacles of various shapes demonstrates the limited applicability of the effective sphere approach. For highly flexible chains, both theory and experiment reveal a nonunique mapping between mobility and molecular size when the molecular radius is comparable to that of gel fibers. Turning to mobility behavior in more concentrated gels, neither flexible or stiff macromolecules behave as spheres; for the particular case of flexible chains, the presence of entropic barriers in concentrated gels can be understood in terms of a simple random planes model for the gel struct

ISSN:0006-3525    

DOI:10.1002/bip.360310409

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe solution conformation of tubulin‐β(422–434)‐NH2(YQQYQDATADEQG‐NH2) and its Nac‐DATADEQG‐NH2fragment has been studied by two‐dimensional1H‐nmr spectroscopy in CD3OH/H2O (90/10 v/v) at neutral and low pH. The 13 amino acid peptide is a segment of the C‐terminal region of tubulin, and is directly involved in the selective binding site with microtubule‐associated proteins MAP‐2 and the τ protein. Based on correlated spectroscopy, total correlation spectroscopy, and rotating frame nuclear Over‐hauser effect spectroscopy experiments, a complete assignment of all proton resonances was achieved, and the conformation of the backbone could be deduced from coupling constants, NH temperature coefficients, and nuclear Overhauser effects. The spectroscopic evidence indicates that the T8‐Q12section of both molecules forms one complete α‐helical turn, stabilized by a NH(Q12)‐CO(T8) hydrogen bond. Furthermore, strong pH‐dependent backfolding of the E11side chain to its own NH proton was found. In addition, close proximity between the aromatic side chains of Y1, Y4, and the α‐helical part, resulting in some substantial chemical shift changes when comparing the entire 13‐mer with the octamer, could be explained in terms of a nonclassical kink in the DATA section. The conformational space is dominated by extended structures and the nonextended conformers are only a minor, yet spectroscopically clearly discernible entity. The presence of the α‐helical region at the C‐terminus of the 13‐mer is important because binding studies of this peptide with MAP‐2 indicate that the D10‐E11‐Q

ISSN:0006-3525    

DOI:10.1002/bip.360310410

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe structure of the vasoactive intestinal peptide 1–28 in 40% 2,2,2‐trifluoroethanol was investigated by two‐dimensional1H‐nmr spectroscopy. All1H resonances, except the γ, δ, and ε protons of the lysine residues, could be sequentially assigned. Numerous intraresidual as well as short‐range interresidual nuclear Overhauser effect spectroscopy connectivities were observed. Using a variable‐target function minimization, a molecular model consisting of two helical stretches involving residues 7–15 and 19–27 connected by a region of undefined structure was calculated. The existence of an undefined structure between residues 16 and 18 confers mobility to th

ISSN:0006-3525    

DOI:10.1002/bip.360310411

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

年代:1991

数据来源: WILEY