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1.
The crystal structure of a synthetic analogue of meso-valinomycin, crystallized with two acetone molecules, has been solved by X-ray direct methods. The trigonal crystals belong to the P32 space group, with the number of molecules in the unit cell z = 3, and cell dimensions a = b = 15,2085 A, c = 29,3250 A, alpha = beta = 90 degrees, gamma = 120 degrees. The standard (R) and weighted (Rw) factors after the structure refinement of atoms C, N, O in anisotropic thermal motion approximation and with the contribution from H atoms taken into account are 0,070 and 0,082, respectively. The molecule adopts an asymmetric conformations stabilized by six amide intramolecular hydrogen bonds NH ... OC of the 4----4 type; one of those is strong and the other are weakened in different extent. The side chains occupy the external pseudoaxial positions towards the cyclic frame of the molecule, whereas six free ester carbonyl groups have different orientations. In contrast to meso-valinomycin, the analogue under study has no specific binding site for metal ions. The isopropyl side chains of D-Hyi(2) and Hyi(4) residues effectively shield, from both sides, the access to the inner molecular cavity.  相似文献   

2.
Direct 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 cell Z = 3, cell parameters a = b = 15.2085 (8) A, c = 29.3250 (9) A, gamma = 120 degrees. 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 to meso-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 residues D-Val1 and L-Val3 are 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 the D-Hyi2 and L-Hyi4 residues screen the molecular cavity on both sides.  相似文献   

3.
BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS: We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.  相似文献   

4.
The structure of the long-chain flavodoxin from the photosynthetic cyanobacterium Anabaena 7120 has been determined at 2 A resolution by the molecular replacement method using the atomic coordinates of the long-chain flavodoxin from Anacystis nidulans. The structure of a third long-chain flavodoxin from Chondrus crispus has recently been reported. Crystals of oxidized A. 7120 flavodoxin belong to the monoclinic space group P2(1) with a = 48.0, b = 32.0, c = 51.6 A, and beta = 92 degrees, and one molecule in the asymmetric unit. The 2 A intensity data were collected with oscillation films at the CHESS synchrotron source and processed to yield 9,795 independent intensities with Rmerg of 0.07. Of these, 8,493 reflections had I > 2 sigma and were used in the analysis. The model obtained by molecular replacement was initially refined by simulated annealing using the XPLOR program. Repeated refitting into omit maps and several rounds of conjugate gradient refinement led to an R-value of 0.185 for a model containing atoms for protein residues 2-169, flavin mononucleotide (FMN), and 104 solvent molecules. The FMN shows many interactions with the protein with the isoalloxazine ring, ribityl sugar, and the 5'-phosphate. The flavin ring has its pyrimidine end buried into the protein, and the functional dimethyl benzene edge is accessible to solvent. The FMN interactions in all three long-chain structures are similar except for the O4' of the ribityl chain, which interacts with the hydroxyl group of Thr 88 side chain in A. 7120, while with a water molecule in the other two. The phosphate group interacts with the atoms of the 9-15 loop as well as with NE1 of Trp 57. The N5 atom of flavin interacts with the amide NH of Ile 59 in A. 7120, whereas in A. nidulans it interacts with the amide NH of Val 59 in a similar manner. In C. crispus flavodoxin, N5 forms a hydrogen bond with the side chain hydroxyl group of the equivalent Thr 58. The hydrogen bond distances to the backbone NH groups in the first two flavodoxins are 3.6 A and 3.5 A, respectively, whereas in the third flavodoxin the distance is 3.1 A, close to the normal value. Even though the hydrogen bond distances are long in the first two cases, still they might have significant energy because their microenvironment in the protein is not accessible to solvent.(ABSTRACT TRUNCATED AT 400 WORDS)  相似文献   

5.
Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.  相似文献   

6.
The adsorptions of hydrogen molecule of the Fe?-?doped pristine and Stone?-?Wales defected armchair (5,5) single?-?walled carbon nanotubes (SWCNTs) compared with the pristine SWCNT were investigated by using the density functional theory at the B3LYP/LanL2DZ level. The doping of Fe atom into SWCNTs occurring via an exothermic process was found. The adsorptions of hydrogen molecule on the Fe?-?doped structures of either perfect or SW defected SWCNTs are stronger than on their corresponding undoped structures. The structural and electronic properties of the pristine and SW defected SWCNTs, their Fe?-?doped structures and their hydrogen molecule adsorptions are reported.  相似文献   

7.
Directly observed 15N NMR spectra of uniformly enriched proteins   总被引:1,自引:0,他引:1  
G M Smith  L P Yu  D J Domingues 《Biochemistry》1987,26(8):2202-2207
The proteins cytochrome c2, cytochrome c', and ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum were enriched in 15N by growth of the organism on 15NH4Cl. The proteins were purified to homogeneity and studied by 15N NMR. Longitudinal and transverse relaxation times as well as the nuclear Overhauser effects were determined for various groups of the proteins which vary in molecular weight from 13,000 to 114,000. The values of these parameters for the amide resonances or for groups thought to be rigid were consistent with the molecular weights of the proteins. Relaxation times of the amino-terminal alpha-amino groups and the side chain nitrogen atoms of arginine and lysine were consistent with much more rapid motion. Nitrogen atoms having bound protons were generally found to be decoupled from the protons by chemical exchange. Demonstrable 1H-15N coupling was taken as an indication that exchange was hindered, either by hydrogen bonding interactions or by inaccessibility of the group to solvent. Histidine side chain nitrogen atoms, which experience a large chemical shift upon protonation/deprotonation, were often found to be broadened beyond detectability by chemical exchange and tautomerization. Strategies for improving sensitivity and for obtaining specific peak assignments are also discussed.  相似文献   

8.
A comprehensive analysis of interfacial water molecules in the structures of 109 unique protein-DNA complexes is presented together with a new view on their role in protein-DNA recognition. Location of interfacial water molecules as reported in the crystal structures and as emerging from a series of molecular dynamics studies on protein-DNA complexes with explicit solvent and counterions, was analyzed based on their acceptor, donor hydrogen bond relationships with the atoms and residues of the macromolecules, electrostatic field calculations and packing density considerations. Water molecules for the purpose of this study have been categorized into four classes: viz. (I) those that contact both the protein and the DNA simultaneously and thus mediate recognition directly; (II) those that contact either the protein or the DNA exclusively via hydrogen bonds solvating each solute separately; (III) those that contact the hydrophobic groups in either the protein or the DNA; and, lastly (IV) those that contact another water molecule. Of the 17,963 crystallographic water molecules under examination, about 6% belong to class I and 76% belong to class II. About three-fourths of class I and class II water molecules are exclusively associated with hydrogen bond acceptor atoms of both protein and DNA. Noting that DNA is polyanionic, it is significant that a majority of the crystallographically observed water molecules as well as those from molecular dynamics simulations should be involved in facilitating binding by screening unfavorable electrostatics. Less than 2% of the reported water molecules occur between hydrogen bond donor atoms of protein and acceptor atoms of DNA. These represent cases where protein atoms cannot reach out to DNA to make favorable hydrogen bond interactions due to packing/structural restrictions and interfacial water molecules provide an extension to side-chains to accomplish hydrogen bonding.  相似文献   

9.
The functionalization of graphene with transition metals is of great interest due to its wide range of applications, such as hydrogen storage, spintronics, information storage, etc. Due to its magnetic property adsorption of Mn atom on graphene has a high consequence on the electronic properties of graphene. The increase in size of the graphene sheet with hydrogen termination has a high impact on the transformation of electronic properties of the graphene sheet. Hence in this work, we investigate the size as well as change in structural and electronic properties of pristine/defective graphene sheets on adsorption of Mn atom using density functional theory methods. From the results obtained a higher adsorption energy value of 3.04 eV is found for Mn adatom on the defected graphene sheet than the pristine, 1.85 eV. It is subject to the coverage effect which decreases on increasing number of carbon atoms. Moreover, a decrease in energy gap is observed in pristine and defected graphene sheets with a high number of carbon atoms. The density of states illustrates the significant effect for hydrogen termination in the conduction band of the Mn adsorbed graphene sheet with low carbon atoms.
Graphical Abstract Mn adatom on graphene at different sites
  相似文献   

10.
The present study addresses the effect of intracellular Na(+) and membrane potential on the binding of dopamine (DA) to the dopamine transporter (DAT). Perforation of plasma membranes of DAT-expressing cells with gramicidin diminished DA uptake and decreased the potency (increases K(i)) of DA in inhibiting the binding of cocaine analog [(3)H]2beta-carbomethoxy-3beta-(4-fluorophenyl)tropane (CFT). It also compromised the ability of external Na(+) to reduce DA K(i). No substantial effect on DA K(i) was observed upon gramicidin treatment in Na(+)-free buffer, membrane depolarization with high [K(+)](o), or elevation of [Na(+)](i) with monensin under non-depolarizing conditions. Elevation of DA K(i) was greater at more positive potentials when [Na(+)](i) was raised to a similar level, or at higher [Na(+)](i) when the membrane was depolarized to a similar level. In cells expressing D313N DAT, DA K(i) was significantly higher but less sensitive to gramicidin than that in wild-type (WT) cells. In contrast, DA K(i) in cell-free membranes was insensitive to Na(+), gramicidin, and D313N mutation. The data suggest that (i) intracellular Na(+) plays a role in affecting the external access to DA binding sites at DAT on depolarized plasma membranes of cells, and (ii) access to DA binding sites in cell-free membranes may occur from the intracellular side of the membrane. Unlike DA binding, CFT binding to both cells and membranes was sensitive to Na(+) and D313N mutation but insensitive to gramicidin, consistent with exclusively external access to sites that are different from but conformationally linked to those for DA.  相似文献   

11.
The dynamics of an electrical-driven linear nanopump, consisting of a carbon nanotube, a C60+ molecule and a graphene sheet, has been simulated via the application of the molecular dynamics method. In this nanopump, the nanotube and the graphene sheet are used as the sleeve of the pump and the boundary between the two sides of the nanopump, respectively. By exposing the nanopump to an external alternative electric field, the C60+ molecule will be oscillating linearly in the nanotube. We found that the linear oscillating motion of the C60+ molecule causes the gas atoms to flow through the nanotube, and a density gradient is generated between the two sides of the nanopump. Also, it was observed that the frequency of the external alternative electric field affected the pump performance in the generation of the density gradient amount. The maximum performance occurred at a specific frequency of the electric field. This specific frequency can be computed by an analytical formula for given materials and temperatures. Moreover, the results indicate that the length of the nanotube can affect the gas pumping.  相似文献   

12.
3,4-Dihydroxyphenyl- l -alanine (l- DOPA)-induced dyskinesia often develops as a side effect of chronic l -DOPA therapy. This study was undertaken to investigate dopamine (DA) release upon l -DOPA treatment. Chronoamperometric measurements were performed in unilaterally DA-depleted rats, chronically treated with l -DOPA, resulting in dyskinetic and non-dyskinetic animals. Normal and lesioned l -DOPA naïve animals were used as controls. Potassium-evoked DA releases were significantly reduced in intact sides of animals undertaken chronic l -DOPA treatment, independent on dyskinetic behavior. Acute l -DOPA further attenuated the amplitude of the DA release in the control sides. In DA-depleted striata, no difference was found in potassium-evoked DA releases, and acute l -DOPA did not affect the amplitude. While immunoreactivity to serotonin uptake transporter was higher in lesioned striata of animals displaying dyskinetic behavior, no correlation could be documented between serotonin transporter-positive nerve fiber density and the amplitude of released DA. In conclusions, the amplitude of potassium-evoked DA release is attenuated in intact striatum after chronic intermittent l -DOPA treatment. No change in amplitude was found in DA-denervated sides of either dyskinetic or non-dyskinetic animals, while release kinetics were changed. This indicates the importance of studying DA release dynamics for the understanding of both beneficial and adverse effects of l -DOPA replacement therapy.  相似文献   

13.
Abstract: The effect of selective inhibition of monoamine oxidase (MAO) subtypes A and B on striatal metabolism of DOPA to dopamine (DA), 3,4-dihydroxyphenylacetic acid (DOPAC), and 4-hydroxy-3-methoxyphenylacetic acid (homovanillic acid; HVA) was studied in halothane-anesthetized rats 3 weeks after unilateral 6-hydroxydopamine lesion of the substantia nigra. Implantation of bilateral microdialysis probes allowed simultaneous quantitation of metabolite production on lesioned and control sides. The DOPA was administered as a 15-min bolus of 1 m M solution in the striatal microdialysate. Rats were pretreated with the selective MAO-A inhibitor clorgyline, or the selective MAO-B inhibitors deprenyl or TVP-101 [2,3-dihydro- N -2-propynyl-1 H -inden-1-amine-(1 R )-hydrochloride]. Intrastriatal infusion of DOPA caused an increased efflux of DA, DOPAC, and HVA, which was greater on the intact side. Clorgyline, but not deprenyl or TVP-101, increased post-DOPA DA efflux on both intact and lesioned sides. Clorgyline also caused a marked suppression of post-DOPA DOPAC and HVA effluxes, whereas only mild effects were produced by the MAO-B inhibitors. There was no evidence for a differential effect of MAO-B inhibition on efflux of DA or metabolites in the lesioned as compared with the control striatum. The results indicate a major role for MAO-A in DA metabolism both intra- and extraneuronally in the rat striatum.  相似文献   

14.
The physisorption of bisphenol A (BPA) on pristine and oxidized graphene was studied theoretically via calculations performed at the PBE-D3 level (including dispersion force corrections). Three stable conformations of BPA on graphene were found. A lying-down configuration was energetically favored because the presence of π–π stacking and dispersion forces increased interactions. In addition, the adsorption of BPA on the edges of graphene oxide was enhanced when adsorption occurred on carboxyl and carbonyl groups, whereas the adsorption strength decreased when adsorption occurred on hydroxyl groups. The highest physisorption strength was obtained on the surface of graphene oxide due to the presence of π–π stacking and dispersion forces (which provided the greatest contribution to the adsorption energy) as well as hydrogen bonds (which provided a smaller contribution), indicating that oxidized graphene is a better candidate than pristine graphene for BPA removal. On the other hand, an increase in electrophilicity was observed after the physisorption of BPA in all systems (with respect to graphene and BPA in their isolated forms), with the adsorbent acting as the electron acceptor. Finally, molecular dynamics simulations performed using the PM6 Hamiltonian showed that the adsorption of BPA on graphene is stable.  相似文献   

15.
The complete unraveling of the proton nuclear magnetic resonance spectra at high field strength of Lasalocid (1) and its sodium salt (2) in different solvents allowed the definition of their solution conformations. The free acid, a lozengeshaped molecule of 17 × 13 × 9 Å is prefolded in a way almost identical to that of its sodium derivative, where the ion lies in the centre, surrounded by all the oxygen atoms in the molecule except for the phenolic one. Although the upper side of the molecule is rather accessible to hydrophilic approach, some alkyl substituents are arranged out- and upwards, thus shielding the ion from possible contact with lipophilic surroundings. The spatial picture suggests that the ion is trapped upon arrival at one side (the flat upper side) and is released either at the same or at the opposite side.  相似文献   

16.
Reactions between manganese agostic species having (Mn---C---H) interactions and molecular hydrogen have been investigated. Treatment of the bridging agostic cyclooctenylmanganese tricarbonyl, 3, and butenylmanganese tricarbonyl, 5, with hydrogen in benzene results in the formation of the cyclohexadienylmanganese tricarbonyl compound 4. This suggests that the hydrogen molecule is highly reactive toward organometallic manganese complexes containing an agostic C---H bond. In these reactions (η2-H2) bonded species are plausible intermediates but these are not detected by NMR. The results indicate that the suggested intermediates in the reactions may be useful as hydrogenation catalysts and as precursors to prepare new manganese compounds which may not be accessible by other pathways.  相似文献   

17.
Five pure cultures of bacteria (strains DA1-5) able to degrade 2,2-dichloropropionic acid (22DCPA) were isolated for the first time from pristine bulk soil samples. From 16S rDNA analysis, it was concluded that strains DA2, DA3 and DA4 were members of the Bradyrhizobium subgroup (alpha-Proteobacteria), strain DA5 clustered in the Brucella assemblage (alpha-Proteobacteria) and strain DA1 clustered in the beta-Proteobacteria. Biochemical and molecular analysis of the dehalogenases from the isolates showed that these enzymes were quite diverse. Several dehalogenases were closely related to group I and II alpha-halocarboxylic acid dehalogenases, and partial polymerase chain reaction (PCR) products were obtained from isolates DA1, 2, 3 and 4 using degenerate dehalogenase primers. However, no PCR products were obtained from isolate DA5 using either of the group I or II alpha-halocarboxylic acid dehalogenase primers. Isolates DA2 and DA4 contained putative silent dehalogenases. The investigation highlighted the endemic nature of these genes in pristine environments and how diverse these were even from spatially close samples.  相似文献   

18.
In voltage- and cyclic nucleotide-gated ion channels, the amino-acid loop that connects the S5 and S6 transmembrane domains, is a major component of the channel pore. It determines ion selectivity and participates in gating. In the alpha subunit of cyclic nucleotide-gated channels from bovine rod, the pore loop is formed by the residues R345-S371, here called R1-S27. These 24 residues were mutated one by one into a cysteine. Mutant channels were expressed in Xenopus laevis oocytes and currents were recorded from excised membrane patches. The accessibility of the substituted cysteines from both sides of the plasma membrane was tested with the thiol-specific reagents 2-aminoethyl methanethiosulfonate (MTSEA) and [2-(trimethylammonium)ethyl]methanethiosulfonate (MTSET). Residues V4C, T20C, and P22C were accessible to MTSET only from the external side of the plasma membrane, and to MTSEA from both sides of the plasma membrane. The effect of MTSEA applied to the inner side of T20C and P22C was prevented by adding 10 mM cysteine to the external side of the plasma membrane. W9C was accessible to MTSET from the internal side only. L7C residue was accessible to internal MTSET, but the inhibition was partial, approximately 50% when the MTS compound was applied in the absence of cGMP and 25% when it was applied in the presence of cGMP, suggesting that this residue is not located inside the pore lumen and that it changes its position during gating. Currents from T15C and T16C mutants were rapidly potentiated by intracellular MTSET. In T16C, a slower partial inhibition took place after the initial potentiation. Current from I17C progressively decayed in inside-out patches. The rundown was accelerated by inwardly applied MTSET. The accessibility results of MTSET indicate a well-defined topology of the channel pore in which residues between L7 and I17 are inwardly accessible, residue G18 and E19 form the narrowest section of the pore, and T20, P21, P22 and V4 are outwardly accessible.  相似文献   

19.
The crystal and molecular structures of an adenine-glycyl-glycine-copper(II) complex have been determined by X-ray diffraction. The chelating atoms, amino and amide nitrogen atoms, the carboxyl oxygen atom of the dipeptide, N(9) of adenine and one water molecule form a square-pyramid. The hydrogen-bonded adenine base-pairs stack with a distance of 3.8Å, while the dipeptides contact each other by NHO hydrogen bond to form a dimer.  相似文献   

20.
Model glycopeptides of the general formula Boc-Ala-Thr(G-D)-A(1)-A(2)-Leu-Leu-Lys(N)-Ala-OMe, where D = dansyl (dimethyl aminonaphthalenesulphonyl), G = glucosyl and N = naphthyl, while A(1)-A(2) = Ala-Leu or Aib-Aib, and denoted as D-G-Ala-N and D-G-Aib-N, respectively, were used to investigate glycoprotein-membrane interactions. They carry two fluorophores (D and N), covalently linked to the glucose ring and the lysine side chain, respectively, while the threonine side chain is O-glycosylated. CD spectra in different solvent media suggest that both glycopeptides attain an ordered structure, possibly a helix-like conformation. By combining FRET (fluorescence resonance energy transfer) experiments with molecular mechanics data, the most probable structures of both glycopeptides were built up, starting from both a right-handed (rh) alpha- and 3(10)-helix. They were found to populate an alpha-helical conformation, a result further confirmed by the very good agreement between theoretical and experimental quenching efficiency only observed when the backbone chain was in alpha-helix. The association of D-G-Ala-N with model membranes (liposomes) was studied by CD, fluorescence decay, fluorescence anisotropy, and collisional quenching experiments. The binding does not alter the structural features of the peptide because the CD spectral patterns are unaffected by the association. The peptide orientation inside the phospholipidic bilayer is guided by the polar glucose molecule lying in the water phase. The insertion of the hydrophobic backbone chain into the membrane, seeing the probes only partially accessible from the external solution, is characterized by a significant degree of heterogeneity, an increase in vesicles size, and a relevant stabilizing effect on the membrane itself against rupture by methanol.  相似文献   

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