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Tomoaki Nishimura Yoshito Sasaki Yoshimitsu Tachi Shuichi Suzuki Keiji Okada Masatoshi Kozaki 《化学:亚洲杂志》2020,15(5):594-600
A stimulus‐responsive receptor 1 was designed and prepared to control the ligand‐binding ability of three active sites, two zinc tetraphenylporphyrin units (P1) and one zinc diethynyldiphenylporphyrin unit (P2), with one effector molecule 2 . Bulky hexarylbenzene units were incorporated as shielding panels in the middle of the flexible side arms of 1 . Spectroscopic titrations indicated that a stable supramolecular complex 1 ? 2 (K 1 ? 2 =6.7×106 m ?1) was produced by the cooperative formation of multiple hydrogen and coordination bonds. As a result, the binding of a ligand to P1 was inhibited by 2 in a competitive manner. Additionally, the formation of 1 ? 2 brought about conformational restriction of the side arms to cover both faces of P2 with the shielding panels. The binding constant of 4‐phenylpyridine with P2 in 1 ? 2 decreased to 8.9 % of that in 1 . Namely, the ligand‐binding ability of P2 was inhibited according to an allosteric mechanism. 相似文献
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Five metallocycles 1 a-e have been self-assembled from S-shaped bispyridyl ligands 2 a-e and a palladium complex, [Pd(dppp)(OTf)(2)] (dppp=1,3-bis(diphenylphosphanyl)propane), and have been characterized by elemental analysis and various spectroscopic methods including (1)H NMR spectroscopy and electrospray ionization (ESI) mass spectrometry. These metallocycles all are monocyclic compounds, but can fold to generate two binding domains bearing hydrogen-bonding sites based on pyridine-2,6-dicarboxamide units. The binding properties of the metallocycles with N,N,N',N'-tetramethylterephthalamide (G) have been probed by means of ESI mass spectrometry and (1)H NMR spectroscopy. The results both in the gas phase and in solution are consistent with the fact that the metallocycles accommodate two molecules of the guest G. Thus, the ESI mass spectra clearly show fragments corresponding to the 1:2 complexes in all cases. (1)H NMR studies on 1 a and G support the formation of a 1:2 complex in solution; the titration curves are nicely fitted to a 1:2 binding isotherm, but not to a 1:1 binding isotherm. In addition, a Job plot also suggests a 1:2 binding mode between 1 a and G, showing maximum complexation at approximately 0.33 mol fraction of the metallocycle 1 a in CDCl(3). The binding constants K(1) and K(2) are calculated to be 1600 and 1400 M(-1) (+/-10 %), respectively, at 25 degrees C in CDCl(3), indicative of positively cooperative binding. This positive cooperativity was confirmed by the Hill equation, affording a Hill coefficient of n = 1.6. Owing to insufficient solubility in CDCl(3), for comparison purposes the binding properties of the metallocycles 1 b-e were investigated in a more polar medium, 3 % CD(3)CN/CDCl(3). (1)H NMR titrations revealed that the metallocycles all bind two molecules of the guest G with Hill coefficients ranging from 1.4 to 1.8. This positive cooperativity may be attributed to a structural reorganization of the second binding cavity when the first guest binds to either one of the subcavities present in the metallocycles. 相似文献
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Ute F. Röhrig Aurélien Grosdidier Vincent Zoete Olivier Michielin 《Journal of computational chemistry》2009,30(14):2305-2315
In silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron–ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme‐containing complexes with iron‐ligand contact. By introducing Morse‐like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand–water interactions in the X‐ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross‐docking studies. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 相似文献
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Intramolecular Oxidative O‐Demethylation of an Oxoferryl Porphyrin Complexed with a Per‐O‐methylated β‐Cyclodextrin Dimer
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The intramolecular oxidation of ROCH3 to ROCH2OH, where the latter compound spontaneously decomposed to ROH and HCHO, was observed during the reaction of the supramolecular complex (met‐hemoCD3) with cumene hydroperoxide in aqueous solution. Met‐hemoCD3 is composed of meso‐tetrakis(4‐sulfonatophenyl)porphinatoiron(III) (FeIIITPPS) and a per‐O‐methylated β‐cyclodextrin dimer having an ‐OCH2PyCH2O‐ linker (Py=pyridine‐3,5‐diyl). The O=FeIVTPPS complex was formed by the reaction of met‐hemoCD3 with cumene hydroperoxide, and isolated by gel‐filtration chromatography. Although the isolated O=FeIVTPPS complex in the cyclodextrin cage was stable in aqueous solution at 25 °C, it was gradually converted to FeIITPPS (t1/2=7.6 h). This conversion was accompanied by oxidative O‐demethylation of an OCH3 group in the cyclodextrin dimer. The results indicated that hydrogen abstraction by O=FeIVTPPS from ROCH3 yields HO‐FeIIITPPS and ROCH2.. This was followed by radical coupling to afford FeIITPPS and ROCH2OH. The hemiacetal (ROCH2OH) immediately decomposed to ROH and HCHO. This study revealed the ability of oxoferryl porphyrin to induce two‐electron oxidation. 相似文献
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Mulder A Juković A van Leeuwen FW Kooijman H Spek AL Huskens J Reinhoudt DN 《Chemistry (Weinheim an der Bergstrasse, Germany)》2004,10(5):1114-1123
Two photoswitchable dithienylethene-tethered beta-cyclodextrin dimers were synthesized to function as host molecules with an externally controllable binding affinity. The cyclodextrin cavities of these dimers are linked through their secondary sides by a photochromic dithienylethene unit that is connected to the secondary rim either directly (4) or through propyl spacers (9). Irradiation with light switches these dimers between a relatively flexible (open) and a rigid (closed) form. The binding properties of the dimers depend on the configuration of the dithienylethene spacer, as is shown by microcalorimetry performed with tetrakis-sulfonatophenyl porphyrin (TSPP) as a guest molecule. The differences in binding properties are most pronounced for the more rigid dimer 4, which binds TSPP 35 times more strongly in the open form (4 a) than in the closed form (4 b). The values found for the enthalpy of binding (deltaH degrees ) indicate that this difference in binding is due to the loss of cooperativity between the two beta-cyclodextrin cavities in the closed form. Molecular modeling shows that 4 b is not able to bind TSPP effectively in both cyclodextrin cavities. The open and closed forms of the more flexible dimer 9 show no substantial difference in their binding of TSPP. Thermodynamic values indicative of strong binding of TSPP by two beta-cyclodextrin cavities were measured for both forms of the dimer, and molecular modeling confirms that both are flexible enough to tightly bind TSPP. The binding differences between the forms of dimer 4 allow the photocontrolled release and uptake of TSPP, which renders control of the ratio of complexed to free TSPP in solution possible. 相似文献
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Laurent SA Robert A Meunier B 《Angewandte Chemie (International ed. in English)》2005,44(14):2060-3; author reply 2064-5
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Using the Population‐Shift Mechanism to Rationally Introduce “Hill‐type” Cooperativity into a Normally Non‐Cooperative Receptor
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Anna J. Simon Prof. Dr. Alexis Vallée‐Bélisle Prof. Dr. Francesco Ricci Dr. Herschel M. Watkins Prof. Dr. Kevin W. Plaxco 《Angewandte Chemie (International ed. in English)》2014,53(36):9471-9475
Allosteric cooperativity, which nature uses to improve the sensitivity with which biomolecular receptors respond to small changes in ligand concentration, could likewise be of use in improving the responsiveness of artificial biosystems. Thus motivated, we demonstrate here the rational design of cooperative molecular beacons, a widely employed DNA sensor, using a generalizable population‐shift approach in which we engineer receptors that equilibrate between a low‐affinity state and a high‐affinity state exposing two binding sites. Doing so we achieve cooperativity within error of ideal behavior, greatly steepening the beacon’s binding curve relative to that of the parent receptor. The ability to rationally engineer cooperativity should prove useful in applications such as biosensors, synthetic biology and “smart” biomaterials, in which improved responsiveness is of value. 相似文献
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Li J Peng Q Barabanschikov A Pavlik JW Alp EE Sturhahn W Zhao J Schulz CE Sage JT Scheidt WR 《Chemistry (Weinheim an der Bergstrasse, Germany)》2011,17(40):11178-11185
We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations. 相似文献
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Henry Dube Dr. Besnik Kasumaj Carlos Calle Dr. Beatrice Felber Dr. Makoto Saito Dr. Gunnar Jeschke Prof. Dr. François Diederich Prof. Dr. 《Chemistry (Weinheim an der Bergstrasse, Germany)》2009,15(1):125-135
Distal hydrogen bonding in natural dioxygen binding proteins is crucial for the discrimination between different potential ligands such as O2 or CO. In the present study, we probe the chemical requirements for proper distal hydrogen bonding in a series of synthetic model compounds for dioxygen‐binding heme proteins. The model compounds 1‐Co to 7‐Co bear different distal residues. The hydrogen bonding in their corresponding dioxygen adducts is directly measured by pulse EPR spectroscopy. The geometrical requirements for this interaction to take place were found to be narrow and very specific. Only two model complexes, 1‐Co and 7‐Co , form a hydrogen bond to bound dioxygen, which was characterized in terms of geometry and nature of the bond. The geometry and dipolar nature of this interaction in 1‐Co ‐O2 is more similar to the one in natural cobalt myoglobin (Co‐Mb), making 1‐Co the best model compound in the entire series. 相似文献
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Tani F Matsu-ura M Ariyama K Setoyama T Shimada T Kobayashi S Hayashi T Matsuo T Hisaeda Y Naruta Y 《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(4):862-870
Inspired by the observation of polar interactions between CO and O(2) ligands and the peptide residues at the active site of hemoglobin and myoglobin, we synthesized two kinds of superstructured porphyrins: TCP-IM, which contains a linked imidazole ligand, and TCP-PY, which contains a linked pyridine ligand, and examined the thermodynamic, kinetic, and spectroscopic (UV/Vis, IR, NMR, and resonance Raman) properties of their CO and O(2) complexes. On both sides of each porphyrin plane, bulky binaphthyl bridges form hydrophobic cavities that are suitable for the binding of small molecules. In the proximal site, an imidazole or pyridine residue is covalently fixed and coordinates axially to the central iron atom. In the distal site, two naphtholic hydroxyl groups overhang toward the center above the heme. The CO affinities of TCPs are significantly lower than those of other heme models. In contrast, TCPs have moderate O(2) binding ability. Compared with reported model hemes, the binding selectivity of O(2) over CO in TCP-IM and TCP-PY complexes is greatly improved. The high O(2) selectivity of the TCPs is mainly attributable to a low CO affinity. The comparison of k(on)(CO) values of TCPs with those of unhindered hemes indicates the absence of steric hindrance to the intrinsically linear CO coordination to Fe(II) in TCP-IM and TCP-PY. The abnormally large k(off)(CO) values are responsible for the low CO affinities. In contrast, k(off)(O(2)) of TCP-PY is smaller than those of other pyridine-coordinated model hemes. For the CO adducts of TCPs, unusually low nu(Fe-CO) and unusually high nu(C-O) frequencies are observed. These results can be ascribed to decreased back-bonding from the iron atom to the bound CO. The lone pairs of the oxygen atoms of the hydroxyl groups prevent back-bonding by exertion of a strong negative electrostatic interaction. On the other hand, high nu(Fe-O(2)) frequencies are observed for the O(2) adducts of TCPs. In the resonance Raman (RR) spectrum of oxy-TCP-IM, we observed simultaneous enhancement of the Fe-O(2) and O-O stretching modes. Furthermore, direct evidence for hydrogen bonding between the hydroxyl groups and bound dioxygen was obtained by RR and IR spectroscopy. These spectroscopic data strongly suggest that O(2) and CO binding to TCPs is controlled mainly by the two different electrostatic effects exerted by the overhanging OH groups: destabilization of CO binding by decreasing back-bonding and stabilization of O(2) binding by hydrogen bonding. 相似文献
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Jung Su Park Franck Le Derf Dr. Christopher M. Bejger Vincent M. Lynch Dr. Jonathan L. Sessler Prof. Kent A. Nielsen Dr. Carsten Johnsen Jan O. Jeppesen Prof. 《Chemistry (Weinheim an der Bergstrasse, Germany)》2010,16(3):848-854
The study of positive homotropic allosterism in supramolecular receptors is important for elucidating design strategies that can lead to increased sensitivity in various molecular recognition applications. In this work, the cooperative relationship between tetrathiafulvalene (TTF)‐calix[4]pyrroles and several nitroaromatic guests is examined. The design and synthesis of new annulated TTF‐calix[4]pyrrole receptors with the goal of rigidifying the system to accommodate better nitroaromatic guests is outlined. These new derivatives, which display significant improvement in terms of binding constants, also display a positive homotropic allosteric relationship, as borne out from the sigmoidal nature of the binding isotherms and analysis by using the Hill equation, Adair equation, and Scatchard plots. The host–guest complexes themselves have been characterized by single‐crystal X‐ray diffraction analyses and studied by means of UV‐spectroscopic titrations. Investigations into the electronic nature of the receptors were made by using cyclic voltammetry; this revealed that the binding efficiency was not strictly related to the redox potential of the receptor. On the other hand, this work serves to illustrate how cooperative effects may be used to enhance the recognition ability of TTF‐calix[4]pyrrole receptors. It has led to new allosteric systems that function as rudimentary colorimetric chemosensors for common nitroaromatic‐based explosives, and which are effective even in the presence of potentially interfering anions. 相似文献
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HNO‐Binding in Heme Proteins: Effects of Iron Oxidation State,Axial Ligand,and Protein Environment
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Dr. Rahul L. Khade Yuwei Yang Yelu Shi Prof. Dr. Yong Zhang 《Angewandte Chemie (International ed. in English)》2016,55(48):15058-15061
HNO plays significant roles in many biological processes. Numerous heme proteins bind HNO, an important step for its biological functions. A systematic computational study was performed to provide the first detailed trends and origins of the effects of iron oxidation state, axial ligand, and protein environment on HNO binding. The results show that HNO binds much weaker with ferric porphyrins than corresponding ferrous systems, offering strong thermodynamic driving force for experimentally observed reductive nitrosylation. The axial ligand was found to influence HNO binding through its trans effect and charge donation effect. The protein environment significantly affects the HNO hydrogen bonding structures and properties. The predicted NMR and vibrational data are in excellent agreement with experiment. This broad range of results shall facilitate studies of HNO binding in many heme proteins, models, and related metalloproteins. 相似文献