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1.
In our previous study, we have observed that the chelation of various metal ions to the His‐tag motifs mostly involves the i and i+2 His residues for Ni2+, Cu2+, Zn2+ and Co2+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His‐tag motif with 6 His residues (His‐tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His‐tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni2+ and Cu2+.K+ was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe3+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni2+ exhibits the highest binding affinity towards His‐tag6 over the other metal ions. Most of the structural variations of the His‐tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.  相似文献   

2.
Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co2+ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an IzSz‐exchange experiment. The double‐histidine‐Co2+ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.  相似文献   

3.
In the title compounds, 4‐aminopyridinium 4‐aminobenzoate dihydrate, C7H6NO2·C5H7N2+·2H2O, (I), and 4‐aminopyridinium nicotinate, C5H7N2+·C6H4NO2, (II), the aromatic N atoms of the 4‐aminopyridinium cations are protonated. In (I), the asymmetric unit is composed of two 4‐aminopyridinium cations, two 4‐aminobenzoate anions and four water molecules, and the compound crystallizes in a noncentrosymmetric space group. The two sets of independent molecules of (I) are related by a centre of symmetry which is not part of the space group. In (I), the protonated pyridinium ring H atoms are involved in bifurcated hydrogen bonding with carboxylate O atoms to form an R12(4) ring motif. The water molecules link the ions to form a two‐dimensional network along the (10) plane. In (II), an intramolecular bifurcated hydrogen bond generates an R12(4) ring motif and inter‐ion hydrogen bonding generates an R42(16) ring motif. The packing of adduct (II) is consolidated via N—H...O and N—H...N hydrogen bonds to form a two‐dimensional network along the (10) plane.  相似文献   

4.
In the crystal structure of the title compound, C6H10N3+·C7H5O3, the asymmetric unit contains four crystallographically independent 2‐amino‐4,6‐dimethyl­pyrimidinium and salicylate ions (Z = 8). In each of these, one of the pyrimidine N atoms is protonated, and the carboxyl­ate group of the salicylate ion inter­acts with the pyrimidine group through a pair of N—H⋯O hydrogen bonds, forming an R22(8) motif. The pyrimidine cations also form base pairs via a pair of N—H⋯N hydrogen bonds (involving the amino group and the unprotonated ring N atom), forming another R22(8) motif. Three such R22(8) motifs, fused together, constitute a closed cyclic aggregate, and the linking of these aggregates, arranged in consecutive layers, can be analysed in terms of off‐face stacking inter­actions.  相似文献   

5.
The title compound, [Zn3(C9H21SiS)6] or [(iPr3SiS)Zn(μ‐SSiiPr3)2Zn(μ‐SSiiPr3)2Zn(SSiiPr3)], is the first structurally characterized homoleptic silanethiolate complex of zinc. A near‐linear arrangement of three ZnII ions is observed, the metals at the ends being three‐coordinate with one terminally bound silanethiolate ligand. The central ZnII ion is four‐coordinate and tetrahedral, with two bridging silanethiolate ligands joining it to each of the two peripheral ZnII ions. The nonbonding intermetallic distances are 3.1344 (11) and 3.2288 (12) Å, while the Zn...Zn...Zn angle is 172.34 (2)°. A trimetallic silanethiolate species of this type has not been previously identified by X‐ray crystallography for any element.  相似文献   

6.
The solid‐state structure of the title compound, [Na2Mn2(C32H56N2OSi2)2O2] or [1,8‐C10H6(NSiiPr3)2Mn(μ3‐O)Na(THF)]2, which lies across a crystallographic twofold axis, exhibits a central [Mn2O2Na2]4+ core, with two oxide groups, each triply bridging between the two MnIII ions and an Na+ ion. Additional coordination is provided to each MnIII centre by a 1,8‐C10H6(NSiiPr3)2 [1,8‐bis(triisopropylsilylamido)naphthalene] ligand and to the Na+ centres by a tetrahydrofuran molecule. The presence of an additional Na...H—C agostic interaction potentially contributes to the distortion around the bridging oxide group.  相似文献   

7.
The title compound, [Cd(NO3)2(C9H12N4)2]n, has a one‐dimensional double‐bridged chain polymer structure with a 16‐membered macrometallacyclic tetragonal structural motif. The CdII ion occupies a crystallographic inversion centre and is coordinated by four equatorial N atoms from four distinct bis(2‐methylimidazol‐1‐yl)methane ligands and two apical nitrate O atoms to form a slightly distorted octahedral coordination geometry.  相似文献   

8.
<!?tpct=1pt>Racemic malic acid and trimethoprim [5‐(3,4,5‐trimethoxybenzyl)pyrimidine‐2,4‐diamine] form a 1:2 salt (monoclinic, P21/c), 2C14H19N4O3+·C4H4O52−, in which the malate component is disordered across a centre of inversion. The crystal structure of the salt consists of protonated trimethoprim residues and a malate dianion. The carboxylate group of the malate ion interacts with the trimethoprim cation in a linear fashion through pairs of N—H...O hydrogen bonds to form a cyclic hydrogen‐bonded motif. This is similar to the carboxylate–trimethoprim cation interaction observed earlier in the complex of dihydrofolate reductase with trimethoprim. The structure of the salt of trimethoprim with racemic dl ‐malic acid reported here is the first of its kind. The present study investigates the conformations and the hydrogen‐bonding interactions, which are very important for biological functions. The pyrimidine plane makes a dihedral angle of 78.08 (7)° with the benzene ring of the trimethoprim cation. The cyclic hydrogen‐bonded motif observed in this structure is self‐organized, leading to novel types of hydrogen‐bonding motifs in supramolecular patterns.  相似文献   

9.
Rhodium(III) para‐benziporphyrin alters the fundamental reactivity of the built‐in para‐phenylene moiety. Due to additional macrocyclic stabilization, a sequence of intramolecular rearrangements are triggered to afford rhodium(III) 21‐carbaporphyrin, which incorporates the rhodacyclopropane motif. The peculiar reversible transformations of the bridging methylene unit provide an example of selective and reversible aliphatic C?H bond elimination. Rhodium(III) 21‐carbaporphyrin can be oxygenated to rhodium(III) 21‐oxy‐21‐carbaporphyrin, whereas the metal ion interacts with the C(21)?O(25) fragment in an η2 fashion. This species demonstrates a remarkable axial affinity toward alkenes.  相似文献   

10.
Ansa‐zirconocene diamide complex rac‐Me2Si(CMB)2Zr(NMe2)2 (rac‐1, CMB = 1‐C5H2‐2‐Me‐4‐tBu) reacts with AlR3 (R = Me, Et, i‐Bu) and then with [CPh3]+[B(C6F5)4] (2) in toluene in order to in situ generate cationic alkylzirconium species. In the sequential NMR‐scale reactions of rac‐1 with various amount of AlMe3 and 2, rac‐1 transforms first to rac‐Me2Si(CMB)2Zr(Me)(NMe2) (rac‐3) and rac‐Me2Si(CMB)2ZrMe2 (rac‐4) by the reaction with AlMe3, and then to [rac‐Me2Si(CMB)2ZrMe]+ (5+) cation by the reaction of the resulting mixtures with 2. The activities of propylene polymerizations by rac‐1/Al(i‐Bu)3/2 system are dependent on the type and concentration of AlR3, resulting in the order of activity: rac‐1/Al(i‐Bu)3/2 > rac‐1/AlEt3/2 > rac‐1/MAO ≫ rac‐1/AlMe3/2 system. The bulkier isobutyl substituents make inactive catalytic species sterically unfavorable and give rise to more separated ion pairs so that the monomers can easily access to the active sites. The dependence of the maximum rate (Rp, max) on polymerization temperature (Tp) obtained by rac‐1/Al(i‐Bu)3/2 system follows Arrhenius relation, and the overall activation energy corresponds to 0.34 kcal/mol. The molecular weight (MW) of the resulting isotactic polypropylene (iPP) is not sensitive to Al(i‐Bu)3 concentration. The analysis of regiochemical errors of iPP shows that the chain transfer to Al(i‐Bu)3 is a minor chain termination. The 1,3‐addition of propylene monomer is the main source of regiochemical sequence and the [mr] sequence is negligible, as a result the meso pentad ([mmmm]) values of iPPs are very high ([mmmm] > 94%). These results can explain the fact that rac‐1/Al(i‐Bu)3/2 system keeps high activity over a wide range of [Al(i‐Bu)3]/[Zr] ratio between 32 and 3,260. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1071–1082, 1999  相似文献   

11.
The solution structure of the self‐complementary deca‐ribonucleotide 5′‐r(GCGA*AUUCGC)‐3′ containing 9‐[2‐O‐(β‐D ‐ribofuranosyl)‐β‐D ‐ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAsiMet), was determined by NMR spectroscopy. Unexpectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3′)‐endo conformation and takes up a well‐defined position in the minor groove, which is in agreement with its position in tRNAsiMet as determined by X‐ray crystallography. Molecular‐dynamics simulations on the RNA duplex in H2O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H‐bonds (mediated by two H2O molecules) to the backbone of the complementary chain.  相似文献   

12.
The structures associated with halide (F?, Cl?, Br?) complexation inside CH hydrogen‐bonding macrocyclic receptors, called triazolophanes, are characterized using density functional theory (DFT). The associated binding energies in the gas and solution phases are evaluated. The ruffles in the empty triazolophane become smoothed‐out upon Cl?‐ and Br?‐ion binding directly into the middle of the cavity. The largely pre‐organized cavity morphs into an elliptical shape to facilitate shorter hydrogen bonds in the north and south regions and longer ones west and east. The smaller F? ion sits in, and flattens‐out, only the north (or south) region. The 1,2,3‐triazoles show shorter CH???Cl? contacts than for the phenylenes. Both Cl? and Br? show the same binding geometries but Cl? has a larger binding energy consistent with its stronger Lewis basicity. Model triads were used to decompose the overall binding energy into those of its components. In the course of this triad analysis, anion polarization was identified and its contribution to the triad???Cl? binding energy estimated. Consequently, the binding energies for the individual aryl units within the comparatively non‐polarized triazolophanes were estimated. The 1,2,3‐triazoles are twice as strong as the phenylenes thus contributing most of the interaction energy to Cl?‐ion binding. Therefore, the 1,2,3‐triazoles appear to approach the hydrogen bond strengths of the NH donors of pyrrole units.  相似文献   

13.
The title compound anilinium chloride–4‐bromo‐N‐phenyl­benzene­sulfonamide (1/1), C6H8N+·Cl·C12H10BrNO2S, displays a hydrogen‐bonded ladder motif with four independent N—H⋯Cl bonds in which both the NH group of the sulfonamide molecule and the NH3 group of the anilinium ion [N⋯Cl = 3.135 (3)–3.196 (2) Å and N—H⋯Cl = 151–167°] are involved. This hydrogen‐bonded chain contains two independent R42(8) rings and each chloride ion acts as an acceptor of four hydrogen bonds.  相似文献   

14.
The platinum complex [Pt(ItBuiPr′)(ItBuiPr)][BArF] interacts with tertiary silanes to form stable (<0 °C) mononuclear PtII σ‐SiH complexes [Pt(ItBuiPr′)(ItBuiPr)(η1‐HSiR3)][BArF]. These compounds have been fully characterized, including X‐ray diffraction methods, as the first examples for platinum. DFT calculations (including electronic topological analysis) support the interpretation of the coordination as an unusual η1‐SiH. However, the energies required for achieving a η2‐SiH mode are rather low, and is consistent with the propensity of these derivatives to undergo Si?H cleavage leading to the more stable silyl species [Pt(SiR3)(ItBuiPr)2][BArF] at room temperature.  相似文献   

15.
Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg2+, Co2+, Ni2+, Cu2+, and Zn2+. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co2+, Ni2+, and Cu2+ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.  相似文献   

16.
Helicobacter pylori 3‐deoxy‐D ‐manno‐2‐octulosonate‐8‐phosphate (KDO8P) synthase catalyzes the conversion of D ‐arabinose‐5‐phosphate (A5P) and phosphoenolpyruvate (PEP) to produce KDO8P and inorganic phosphate. Since this protein is absent in mammals, it might therefore be an attractive target for the development of new antibiotics. Unlike E. coli KDO8P synthase (class I), the H. pylori counterpart is a class II enzyme, where it requires a divalent transition metal ion for catalysis. Although the metal ions have been shown to be important for catalysis, their role in the structure is not understood. Using electrospray ionization mass spectrometry (ESI‐MS), the role of the metal ions in H. pylori KDO8P synthase has been investigated. This protein is found to be a tetramer in the gas phase but dissociates into the dimer with increasing declustering potential (DP2) suggesting an existence of a ‘structurally specific’ tetramer. An examination of mass spectra revealed that the tetrameric state of the Cd2+‐reconstituted enzyme is less stable than those of the Zn2+‐, Co2+‐ and Cu2+‐enzymes. The stoichiometry of metal binding to the protein depends on the nature of the metal ion. Taken together, our data suggest that divalent metal ions play an important role in the quaternary structure of the protein and the tetrameric state may be primarily responsible for catalysis. This study demonstrates the first structural characterization and stoichiometry of metal binding in class II KDO8P synthase using electrospray ionization quadrupole time‐of‐flight mass spectrometry under nondenaturing conditions. Copyright © 2009 John Wiley & Sons, Ltd.  相似文献   

17.
The title dipeptide, 1‐(tert‐butoxy­carbonyl‐d ‐alanyl)‐N‐iso­propyl‐l ‐pipecol­amide or Boc‐d ‐Ala‐l ‐Pip‐NHiPr (H‐Pip‐OH is pipecolic acid or piperidine‐2‐carboxylic acid), C17H31N3­O4, with a d –l heterochiral sequence, adopts a type II′β‐­turn conformation, with all‐trans amide functions, where the C‐terminal amide NH group interacts with the Boc carbonyl O atom to form a classical i+3 i intramolecular hydrogen bond. The Cα substituent takes an axial position [Hα (Pip) equatorial] and the trans pipecolamide function is nearly planar.  相似文献   

18.
The correlation between β2‐, β3‐, and β2,3‐amino acid‐residue configuration and stability of helix and hairpin‐turn secondary structures of peptides consisting of homologated proteinogenic amino acids is analyzed (Figs. 1–3). To test the power of Zn2+ ions in fortifying and/or enforcing secondary structures of β‐peptides, a β‐decapeptide, 1 , four β‐octapeptides, 2 – 5 , and a β‐hexadecapeptide, 10 , have been devised and synthesized. The design was such that the peptides would a) fold to a 14‐helix ( 1 and 3 ) or a hairpin turn ( 2 and 4 ), or form neither of these two secondary structures (i.e., 5 ), and b) carry the side chains of cysteine and histidine in positions, which will allow Zn2+ ions to use their extraordinary affinity for RS? and the imidazole N‐atoms for stabilizing or destabilizing the intrinsic secondary structures of the peptides. The β‐hexadecapeptide 10 was designed to a) fold to a turn, to which a 14‐helical structure is attached through a β‐dipeptide spacer, and b) contain two cysteine and two histidine side chains for Zn complexation, in order to possibly mimic a Zn‐finger motif. While CD spectra (Figs. 6–8 and 17) and ESI mass spectra (Figs. 9 and 18) are compatible with the expected effects of Zn2+ ions in all cases, it was shown by detailed NMR analyses of three of the peptides, i.e., 2, 3, 5 , in the absence and presence of ZnCl2, that i) β‐peptide 2 forms a hairpin turn in H2O, even without Zn complexation to the terminal β3hHis and β3hCys side chains (Fig. 11), ii) β‐peptide 3 , which is present as a 14‐helix in MeOH, is forced to a hairpin‐turn structure by Zn complexation in H2O (Fig. 12), and iii) β‐peptide 5 is poorly ordered in CD3OH (Fig. 13) and in H2O (Fig. 14), with far‐remote β3hCys and β3hHis residues, and has a distorted turn structure in the presence of Zn2+ ions in H2O, with proximate terminal Cys and His side chains (Fig. 15).  相似文献   

19.
The Bigenelli acid catalyzed condensation of 2‐trifluoromethylbenzaldehyde ( 1 ), urea ( 2 ) and an alkyl acetoacetate ( 3 ) afforded the respective alkyl (Me, Et, i‐Pr, i‐Bu) 6‐methyl‐4‐(2‐trifluoromethylphenyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylate ( 4‐7 ). Subsequent N3‐nitration of the alkyl esters ( 4‐7 ) using Cu(NO3)2 3H2O and Ac2O furnished the target alkyl 6‐methyl‐3‐nitro‐4‐(2‐trifluoromethylphenyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylates ( 8‐11 ). The N3‐nitro compounds ( 8‐11 ) were less potent calcium channel antagonists (IC50 values in the 1.9 × 10?7 to 3.9 × 10?6 M range) on guinea pig ileal longitudinal smooth muscle than the reference drug nifedipine (Adalat®, IC50 = 1.4 × 10?8 M). In vitro calcium channel modulation studies on guinea pig left atrium (GPLA) showed that the methyl and ethyl esters ( 8‐9 ) induced a weak‐to‐modest positive inotropic (agonist) effect, and that the inactive isopropyl ( 10 ) and isobutyl ( 11 ) esters did not alter the cardiac contractile force of GPLA.  相似文献   

20.
Asymmetric anionic polymerizations of 7‐cyano‐7‐alkoxycarbonyl‐1,4‐benzoquinone methides ( 1 ) with various alkoxy groups were performed using chiral initiators such as lithium isopropylphenoxide (iPrPhOLi)/(S)‐(–)‐2,2′‐isopropylidene‐bis(4‐phenyl‐2‐oxazoline) ((–)‐PhBox) and lithium isopropylphenoxide (iPrPhOLi)/(–)‐sparteine ((–)‐Sp) to investigate the effect of the alkoxy groups of alkoxycarbonyl substituent in the monomers 1 and chiral ligands of chiral initiators on the control of chiral center in the formation of polymers. Molar optical rotation values of the polymers were significantly dependent upon alkoxy groups, and the polymers with higher molar optical rotation were obtained in monomers with primary alkoxy groups. The asymmetric anionic oligomerizations of the quinone methides having methoxy( 1a ), ethoxy( 1b ), and n‐propoxy( 1c ) groups with chiral initiators were carried out. Both 1‐mers and 2‐mers were isolated and their optical resolutions were performed to determine the extent of stereocontrol. High stereoselectivity was observed at the propagation reaction, but not at the initiation reaction. The effect of the counterion on the control of chiral center in the formation of the polymer was investigated in the asymmetric anionic polymerizations of 1b with iPrPhOM(M = Li, Na, K)/(–)‐Sp and iPrPhOM(M = Li, Na, K)/(–)‐PhBox initiators and discussed. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011  相似文献   

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