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1.
Two closely related crystal forms of dimeric cytochrome c5 from Azotobacter rinelandii have been grown. The crystals belong to space groups (C2 with a = 45·0, b = 38·4, c = 41·3 A? and β = 101 ° 0′; and C1 (a centered triclinic cell) with a = 46·0, b = 37·6, c = 49·4 A?, α = 87 ° 20′, β = 96 ° 40′ and γ = 90 ° 0′. In C2 the 24,000 molecular weight dimer lies on a Crystallographic 2-fold axis; in C1 the entire dimer occupies the asymmetric unit.  相似文献   

2.
3.
Native DNA duplexes in fibers exist usually in one of three well-known (A, B and C) forms depending on relative humidity, type of cations and the amount of retained salt. To determine the precise influence of these factors and the effect of base composition, as well as base sequence, on DNA secondary structure, X-ray diffraction methods have been used to study all four synthetic DNA duplexes with repeated dinucleotide sequences, eight of the 12 with repeated trinucleotide sequences and seven analogues in which guanine was replaced with hypoxanthine. The results indicate that there are at least six additional allomorphs denoted by B′, C′, C″, D, E and S.The B′ form (h = 0.329 nm) observed for poly(dA) · poly(dT), poly(dI) · poly(dC) and poly[d(A-I)] · poly[d(C-T)] is a minor variant of the traditional B form (h = 0.338 nm) of native DNA. The two C-like forms C′ for poly[d(A-G-C)] · poly-[d(G-C-T)] and poly[d(G-G-T)] · poly[d(A-C-C)] and C″ for poly[d(A-G)] · poly-[d(C-T)] have, respectively, 91 and 92 symmetries which reflect repetition of trinucleotide and dinucleotide sequences, respectively. Although isocompositional with poly(dA) · poly(dT), the existence of the rather different D form (81) for poly[d(A-T)] · poly[d(A-T)] or for poly[d(A-A-T)] · poly[d(A-T-T)] is a clear demonstration of the sequence effect. The I · C pair generally mimics an A · T pair, but poly[d(I-I-T)] · poly[d(A-C-C)] provides a new (E) form with approximately 152 screw symmetry and with 〈h〉 = 0.325 nm and 〈t〉 = 48 dg per nucleotide. The S form (65) observed for poly[d(G-C)] · poly[d(G-C)] and poly[d(A-C)] · poly[d(G-T)] is an unusual left-handed polydinucleotide helix and is accessible to any alternating purine-pyrimidine sequence. In it the two nucleotides have quite different conformations and involve syn purine and anti pyrimidine nucleosides.  相似文献   

4.
We have targeted the d[G(AG)5] · d[C(TC)5] duplex for triplex formation at neutral pH with either d[G(AG)5] or d[G(TG)5]. Using a combination of gel electrophoresis, uv and CD spectra, mixing and melting curves, along with DNase I digestion studies, we have investigated the stability of the 2:1 pur*pur · pyr triplex, d[G(AG)5] * d[G(AG)5] · d[C(TC)5], in the presence of MgCl2. This triplex melts in a monophasic fashion at the same temperature as the underlying duplex. Although the uv spectrum changes little upon binding of the second purine strand, the CD spectrum shows significant changes in the wavelength range 200–230 nm and about a 7 nm shift in the positive band near 270 nm. In contrast, the 1:1:1 pur/pyr*pur · pyr triplex, d[G(TG)5] * d[G(AG)5] · d[C(TC)5], is considerably less stable thermally, melting at a much lower temperature than the underlying duplex, and possesses a CD spectrum that is entirely negative from 200 to 300 nm. Ethidium bromide undergoes a strong fluorescence enhancement upon binding to each of these triplexes, and significantly stabilizes the pur/pyr*pur · pyr triplex. The uv melting and differential scanning calorimetry analysis of the alternating sequence duplex and pur*pur · pyr triplex shows that they are lower in thermodynamic stability than the corresponding 10-mer d(G3A4G3) · d(C3T4C3) duplex and its pur*pur · pyr triplex under identical solution conditions. © 1997 John Wiley & Sons, Inc.  相似文献   

5.
Summary The actinomycin-D-d(A1-A2-A3-G4-C5-T6-T7-T8) complex (1 drug per duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. We have assigned the exchangeable and nonexchangeable proton resonances of Act and d(A3GCT3) in the complex and identified the intermolecular proton-proton NOES that define the alignment of the antitumor agent at its binding site on duplex DNA. The molecular dynamics calculations were guided by 70 intermolecular distance constraints between Act and nucleic acid protons in the complex. The phenoxazone chromophore of Act intercalates at the (G-C)I·(G-C)II step in the d(A3GCT3) duplex with the phenoxazone ring stacking selectively with the G4I and G4II purine bases but not with C4I and C4II pyrimidine bases at the intercalation site. There is a pronounced unwinding between the A3·T6 and G4·C5 base pairs which are the next steps located in either direction from the intercalation site in the Act-d(A3GCT3) complex. The Act cyclic pentapeptide ring conformations in the complex are similar to those for free Act in the crystal except for a change in orientation of the ester linkage connecting meVal and Thr residues. The cyclic pentapeptide rings are positioned in the minor groove with the established G-C sequence specificity of binding associated with intermolecular hydrogen bonds between the Thr backbone CO and NH groups to the NH2-2 and N3 positions of guanosine, respectively. Complex formation is also stabilized by van der Waals interactions between nonpolar groups on the cyclic pentapeptide rings and the sugar residues and base pair edges lining the widened minor groove of the (A3-G4-C5-T6)I·(A3-G4-C5-T6)II binding site segment of the DNA helix.Dedicated to the memory of Professor V.F. Bystrov  相似文献   

6.
This study establishes the bioenergetics budget of juvenile whitespotted bamboo shark Chiloscyllium plagiosum by estimating the standard metabolic rate (RS), measuring the effect of body size and temperature on the RS, and identifying the specific dynamic action (RSDA) magnitude and duration of that action in juvenile whitespotted bamboo sharks. The mean ±s .d . (RS) of six fish (500–620 g) measured in a circular closed respirometry system was 30·21 ± 5·68 mg O2 kg?1 h?1 at 18° C and 70·38 ± 14·81 mg O2 kg?1 h?1 at 28° C, respectively. There were no significant differences in RS between day and night at either 18 or 28° C (t‐test, P > 0·05). The mean ±s .d . Q10 for 18–28° C was 2·32 ± 0·06 (n = 6). The amount of oxygen consumed per hour changed predictably with body mass (M; 295–750 g) following the relationship: (n = 40, r2= 0·92, P < 0·05). The mean magnitude of RSDA was 95·28 ± 17·55 mg O2 kg?1 h?1. The amount of gross ingested energy (EI) expended as RSDA ranged from 6·32 to 12·78% with a mean ±s .d . of 8·01 ± 0·03%. The duration of the RSDA effect was 122 h. The energy content of juvenile whitespotted bamboo shark, squid and faeces determined by bomb calorimeter were 19·51, 20·3 and 18·62 kJ g dry mass?1. A mean bioenergetic budget for juvenile whitespotted bamboo sharks fed with squid at 18° C was 100C = 29·5G + 31·9RS+ 28·2RSDA+ 6·7F + 2·1E + 1·6U, where C = consumption, G = growth, F = egestion, E = excretion and U = unaccounted energy.  相似文献   

7.
Abstract

A single-point substitution of the O4′ oxygen by a CH2 group at the sugar residue of A 6 (i.e. 2′-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5′- d(C1G2C3G4A5A6T7T8C9G10C11G12)2 ?3, has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A 6:T7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)→←(1B): Keq = k1/k-1 = 0.56±0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k1 (298K) = 3.9± 0.8 sec?1; δH°? = 164±14 kJ/mol;-TδS°? (298K) = ?92 kJ/mol giving a δG298°? of 72 kJ/mol. Ea (k1) = 167±14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0±0.6 sec-1, δH°? = 153±13 kJ/mol;-TδS°? (298K) = ?82 kJ/mol giving a δG298°? of 71 kJ/mol. Ea (k-1) = 155±13 kJ/mol]. A comparison of δG298°? of the forward (k1) and backward (k-1) conversions, (1A)→←(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A 6:T7 Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition, 55 NMR-derived backbone dihedral constraints per strand were used for both structures. The main effect of the Hoogsteen basepairs in (1B) on the overall structure is a narrowing of the minor groove and a corresponding widening of the major groove. The Hoogsteen basepairing at the central A 6:T7 basepairs in (1B) has enforced a syn conformation on the glycosyl torsion of the 2′- deoxyaristeromycin moiety, A 6, as a result of substitution of the endocyclic 4′-oxygen in the natural sugar with a methylene group in A 6. A comparison of the Watson-Crick basepaired duplex (1A) to the Hoogsteen basepaired duplex (1B) shows that only a few changes, mainly in α, σ and γ torsions, in the sugar-phosphate backbone seem to be necessary to accommodate the Hoogsteen basepair.  相似文献   

8.
1. This study characterizes chlorophyll a-H2O adducts in vitro in order to establish their generic relationship to the recently proposed [15, 18–20, 31] primary molecular adduct in photosynthesis. The effects of water titration and temperature on the absorption, fluorescence, excitation, and redox properties of the various in vitro chlorophyll a aggregate species are investigated.2. From fluorescence measurements, we conclude that the driest chlorophyll a sample contains an equimolar amount of water. This conclusion is consistent with earlier experimental work [2, 3, 14, 17, 31], and clarifies the origin of the controversial [15] Katz model [14] of chlorophyll a-H2O interactions.3. With increasing water concentration or as the temperature is lowered below room temperature, the A-663 monohydrate chlorophyll a · H2O (species absorbing at 663 nm) is favored at the expense of the A-678 anhydrous aggregate according to the equilibrium 2H2O + chlorophyll a2ai 2 chlorophyll a · H2O. Under excess water conditions, A-663 is converted to A-743 (chlorophyll a · 2H2O)n.4. On slow sample cooling to T ? 200 °K, we observe the growth of A-700 at the expense of A-663. There is a direct correspondence between the increasing (decreasing) absorption by A-700 (A-663) and increasing (decreasing) fluorescence at 720 nm (664 nm).5. It is concluded that A-700 is most probably the dimer participating in the equilibrium 2 chlorophyll a · H2O ai (chlorophyll a · H2O)2. The A-700 band consists of two exciton components (separated by ≈ 280 cm?1) that are interpretable in terms of the dimeric origin of A-700.6. The deconvoluted A-700 absorption spectrum and the excitation spectrum of the 720 nm fluorescence are compared with the light-minus-dark spectra of P-700.7. It is found that A-700 is reversibly bleached by I2 (E0 = 0.54 V). The significance of this observation is discussed in terms of the redox properties of monomeric chlorophyll a and P-700.  相似文献   

9.
10.
Two kinds of conformational variability have been reported for left-handed Z-DNA: the Z to Z′ transition, which involves a change in guanine sugar pucker from C-3′-endo to C-1′-exo, and the ZIto ZII transition, which corresponds to a simple three-atom phosphate-group rotation. Neither of these motions substantially affects base stacking or helical twist, and this is because the degree of independent motion of phosphate groups, sugar molecules and base-pairs is greater in the left-handed Z helix than in right-handed B-DNA. Detailed considerations of Z helix geometry suggest that ZI, ZIIand Z′ are not separate species, but only samplings of the full range of conformation open to Z-DNA.  相似文献   

11.
Crystals of β-lactamase I from Bacillus cereus 569 are monoclinic, space group C2 with unit cell dimensions a = 143·0 (± 0·5), b = 35·8 (± 0·1), c = 52·7 (± 0·2) A?, β = 97·0 (± 0·1) °, and one molecule of molecular weight about 28,000 per asymmetric unit.  相似文献   

12.
A complex between EcoRI restriction endonuclease and cognate DNA fragment, 5′-G-A-A-T-T-C C-T-T-A-A-G-5′, has been crystallized. The space group is P4212 with a = b = 183.2A?, c = 49.7A?, α = β = γ = 90 °. The unit cell contains four enzyme monomers plus two duplex DNA fragments in an asymmetric unit. High quality crystals of the enzyme alone have also been obtained.  相似文献   

13.
The crystal and molecular structure of [UO2(DMB)2(H2O)2]·H2O (DMB = 2,6-dimethoxybenzoate), complex I, has been detcrmined by X-ray diffraction and refined to a final R value of 0.0411. The compound belongs to the space group P21/a with cell constants a = 12.649(4), b = 14.418(5), c = 13.460(4) Å and Z = 4. As in the analogous complex [UO2(DHB)2(H2O)2]·8H2O (DHB = 2,6- dihydroxybenzoate), compound II, the uranyl ion is bound to two bidentate carboxylate groups and two water molecules, but the point-symmetry is lower because the carboxylates, and the water molecules, are in vicinal positions. The lack of hydrogen- bonds between carboxylate groups and ortho-methoxy substituents and, possibly, steric factors account for the rotation of the phenyl rings with respect to the equatorial plane of the metal, the dihedral angle between the ‘best planes’ being about 77°. Detectable changes in the bond distances and angles within the carboxylate groups are produced by the non-planarity of the ligand. Spectroscopic and thermal properties of complexes I and II are also compared.  相似文献   

14.
Natural intergeneric hybrids betweenAster ageratoides subsp.ovatus (2n=36) andKalimeris incisa (2n=72) were found. All of the hybrids studied were found to have 2n=72, 18 more chromosomes than a regular F1 hybrid. The hybrids were found to be of two types: one having 18 large chromosomes ofovatus, and the other having 9 large chromosomes of the same subspecies. In meiosis of the PMCs of the hybrid with 18 large chromosomes, a regular chromosome configuration, 36II, was observed. In PMCs of the hybrid with 9 large chromosomes an irregularity of chromosome pairings was observed, showing varied chromosome configurations: 35II+2I, 34II+4I, 33II+6I, IIII+33II+3I, 1IV+32II+4I, 32II+8I, 31II+10I, 29II+14I, 3III+29II+5I. Most univalents were large, but a few were small. The hybrids with 18 large chromosomes were found to be partial amphidiploid and possessing double chromosome complements ofovatus. The hybrids with 9 large chromosomes were found to be the first backcrossed generation between the hybrid with 18 large chromosomes andK. incisa.  相似文献   

15.
Abstract

We examined the effects of 1–(2-deoxy -2-fluoro-β-D-arabinofuranosyl)-thymine (or FMAU, a potent antiviral nucleoside) on the stability of duplex and triplexes. When compared the stability of the self-complementary 5′-A5T5 duplex with 5′-A5X5 (X = FMAU), duplex containing FMAU has much higher melting temperature (Tm). 5′-A6T5T3X3T5F3X3 and T3X3T5A6T5F3X3 form the parallel and antiparallel triplexes T3X3: A6:X3X3, respectively. The former exhibited the typical T:A:T triplex behavior with only one melting temperature at 70 °C and 45 °c in 1.0 M and 0.2 M NaCl solution, respectively, whereas the latter has two Tm values at 56 °C and 28 °C in 1.0 M solution. FMAU clearly stabilize the triplex structure as A6T22 which forms the parallel triplex T6:A6:T6 has also only one Tm at 54 °C and 37 °C in high and iow salt concentration solutions, respectively. A 31mer 5′-TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT and 5′-TCCTCCTTTTTTAGGAGGATTTTTTX'X'TX'X'T (X' = 2′-deoxy-5-methylcytidine) were prepared to study their triplex forming potential. The former was found to have a week interaction of the Watson-Crick duplex with the mismatched third-strand at all pH. The latter formed a stable triplex at lower pH consistent with required protonation on the 5-methylcytosine base. For these studies we developed a simple PC desktop spreadsheet program to calculate the first derivative profile of the melting curve data.

This paper is dedicated to Prof. Jacques H. van Boom on the occasion of his 60th birthday.  相似文献   

16.
The αII-helix (? = ?70.47°, ψ = ?35.75°) is a structure having the same n and h as the (standard) αI-helix (? = ?57.37°, ψ = ?47.49°). Its conformational angles are commonly found in proteins. Using an improved α-helix force field, we have compared the vibrational frequencies of these two structures. Despite the small conformational differences, there are significant predicted differences in frequencies, particularly in the amide A, amide I, and amide II bands, and in the conformation-sensitive region below 900 cm?1. This analysis indicates that αII-helices are likely to be present in bacteriorhodopsin [Krimm, S. & Dwivedi, A. M. (1982) Science 216 , 407–408].  相似文献   

17.
Abstract

The non-exchangeable and imino proton NMR resonances of the non self-complementary decadeoxyribonucleotide d-[(GATCCGTATG) · (GATACGGATC)] as well as those of the 1:1 complex of the monocatonic bis-imidazole lexitropsin 1 to this sequence have been assigned by using a combination of NOE difference, COSY and NOESY techniques. Confirmation of complete annealing of the two non self-complementary decamer strands to give the duplex decadeoxyribonucleotide is obtained by the detection of ten imino protons. It is established that the sugar-base orientations of all the bases in the duplex decamer are anti. From NOE studies, it is concluded that the duplex oligomer is right-handed and adopts a conformation in solution that belongs to the B family. A population analysis reveals that the sugar moieties exist predominantly in the S-form (2′-endo-3′-exo). Addition of 1 to the DNA solution leads to doubling of the resonances for CH6(4,5), GH8(6), TH6(7) and T-CH3(7). The base, anomeric H1′ and imino proton signals for the base sequence 5′-CCGT undergo the most marked drug-induced chemical shift changes. These results provide evidence that the lexitropsin is bound to the sequence 5′-CCGT in the minor groove of the DNA NOE measurements between the amide protons (NH1 and NH4) and the imino proton (IV and V) signals confirmed the location and orientation of 1 in the 1:1 complex, with the amino terminus oriented to C(4). The specific binding of 1 to the sequence 5′-CCGT-3′ deduced in this study is in agreement with the footprinting data obtained using the Hind III/Nci I fragment from pBR322 DNA [Kissinger et al. 1987 (13)]. Intramolecular NOEs observed between H4 and H9 of the lexitropsin suggest that the molecule is not planar, but subjected to propeller twisting, in both the free and bound forms. Furthermore, NOE measurements permit assignment of the DNA duplex in the 1:1 complex to the B-form, which is similar to that of the free DNA The [(T7A8T9)· (A12T13A14)] segment of the DNA shows better stacking, by propeller twisting, compared to the rest of the molecule in the free as well as the complex forms. The intermolecular rate of exchange of 1 between the equivalent 5′-CCGT sites, at a concentration of 12 mM, is estimated to be ~88s?1 at 308°K with ΔG≠ of 63±5 K.J mol?1.  相似文献   

18.
Oxygen consumption rates (QO2) of laboratory reared stage one zoeae of Pandalus borealis (Krøyer) at 1.5, 3, 4.5, 6, and 9°C were 1.5, 2.2, 2.6, 3.6 and 4.1μ O2 · mg?1 · h?1, respectively. These values of QO2 correspond to 0.26, 0.38, 0.44, 0.60, and 0.70 μl O2 · individual?1 · h?1. At 10.5 °C oxygen consumption rates decreased suggesting thermally induced respiratory stress.The equation log10QO2 = 0.55 log10T°C + 0.086 describes the relationship between QO2 (μl O2 · mg?1 · h?1) and sea-water temperature between 1.5 and 9°C. Corresponding values of QO2 for an individual (μl O2 · h?1) exhibited the relationship log10QO2 = 0.55 log10T°C ?0.686.The minimum daily metabolic caloric requirements for an individual zoea ranged from 0.04 at 3 °C to 0.07 calories per day at 8 °C. The number of calories ingested daily ranged from 0.4 to 0.5 at 3 to 8 °C.  相似文献   

19.
Abstract

The 5-alkoxymethyl-2,2,7,8-tetramethyl-6-chromanols (II) are excellent antioxidants against autoxidising safflower oil (ASO), although not as good as 2,2,5,7,8-pentamethyl-6-chromanol (I), the model compound of -tocopherol. The aim of this work was to determine whether the rate of reaction of (II) with the radicals diphenylpicrylhydrazyl (DPP·) and galvinoxyl (ArO·) was directly proportional to their antioxidant activity against ASO. Compounds (II) reacted faster with DPP·. than with ArO·. but, in each case, slower than compound (I). The rates of reaction of I and II with both radicals followed the order I > II (R = H) > II (R = CH3) > II (R = other alkyls) and were directly proportional to their antioxidant activity against ASO.  相似文献   

20.
β-N-Acetylhexosaminidases were detected in 10 insects including species of Lepidoptera, Coleoptera, Hemiptera, and Orthoptera. Two enzymes were purified from the tobacco hornworm, Manduca sexta (L.). EI was detected in larval and pharate pupal molting fluid, integument, and pupal hemolymph while EII was found in larval and pupal hemolymphs. They are acidic hydrolases with similar molecular weights (6.1 × 104), molar extinction coefficients at 280 nm (1.9 × 105 liters mol?1 cm?1), and pH optima (pH 6). They differ in the number of polypeptide chains per molecule (EI is a single chain and EII consists of two polypeptide chains), amino acid composition, extent of glycosylation (EII is probably a glycoprotein), isoelectric point (pIEI = 5.9 and pIEII ~- 5.1), tissue distribution, and reactivities toward nitrophenylated N-acetylglucosamine (kcat,I = 328 s?1 and kcat,II = 103 s?1) and N,N′-diacetylchitobiose (kcat,I = 307 s?1 and kcat,II = 3 s?1). These results suggest that EI is a chitinase and that EII may function as a hexosaminidase in vivo.  相似文献   

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