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1.
Photoisomerization of the retinylidene chromophore of rhodopsin is the starting point in the vision cascade. A counterion switch mechanism that stabilizes the retinal protonated Schiff base (PSB) has been proposed to be an essential step in rhodopsin activation. On the basis of vibrational and UV-visible spectroscopy, two counterion switch models have emerged. In the first model, the PSB is stabilized by Glu181 in the meta I state, while in the most recent proposal, it is stabilized by Glu113 as well as Glu181. We assess these models by conducting a pair of microsecond scale, all-atom molecular dynamics simulations of rhodopsin embedded in a 99-lipid bilayer of SDPC, SDPE, and cholesterol (2:2:1 ratio) varying the starting protonation state of Glu181. Theoretical simulations gave different orientations of retinal for the two counterion switch mechanisms, which were used to simulate experimental 2H NMR spectra for the C5, C9, and C13 methyl groups. Comparison of the simulated 2H NMR spectra with experimental data supports the complex-counterion mechanism. Hence, our results indicate that Glu113 and Glu181 stabilize the retinal PSB in the meta I state prior to activation of rhodopsin.  相似文献   

2.
Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state 2H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific 2H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability 2H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C3) axes with an order parameter for the off‐axial motion of For the dark state, the 2H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, 2H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state 2H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.  相似文献   

3.
An increasing number of diseases, including Alzheimer's, have been found to be a result of the formation of amyloid aggregates that are practically independent of the original primary sequence of the protein(s). (Eakin, C. M.; Berman, A. J.; Miranker, A. D. Nat. Struct. Mol. Biol. 2006, 13, 202-208.) Consequently, the driving force of the transformation from original to disordered amyloid fold is expected to lie in the protein backbone, which is common to all proteins. (Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. O.; Riekel, C.; Grothe, R.; Eisenberg, D. Nature 2005, 435, 773-778. Wright, C. F.; Teichmann, S. A.; Clarke, J.; Dobson, C. M. Nature 2005, 438, 878-881.) However, the exact explanation for the existence of such a "dead-end" structure is still unknown. Using systematic first principle calculations on carefully selected but large enough systems modeling the protein backbone we show that the beta-pleated sheet structure, the building block of amyloid fibers, is the thermodynamically most stable supramolecular arrangement of all the possible peptide dimers and oligomers both in vacuum and in aqueous environments. Even in a crystalline state (periodical, tight peptide attechment), the beta-pleated sheet assembly remains the most stable superstructure. The present theoretical study provides a quantum-level explanation for why proteins can take the amyloid state when local structural preferences jeopardize the functional native global fold and why it is a beta-pleated sheetlike structure they prefer.  相似文献   

4.
It was previously shown that opsin can be regenerated with the newly synthesized 11‐cis‐7‐methyl‐retinal forming an artificial visual pigment. We now extend this study to include mutants at positions close to the retinal to further dissect the interactions of native and artificial chromophores with opsin. Several mutants at M207, W265 and Y268 have been obtained and regenerated with 11‐cis‐retinal and the 7‐methyl analog. M207 is the site of the point mutation M207R associated with the retinal degenerative disease retinitis pigmentosa. All the studied mutants regenerated with 11‐cis‐retinal except for M207C which proved to be completely misfolded. The naturally occurring M207R mutant formed a pigment with an unprotonated Schiff base linkage, altered photobleaching and low MetarhodopsinII stability. Mutants regenerated with the 7‐methyl analog showed altered photobleaching reflecting a structural perturbation in the vicinity of M207. The newly obtained mutants at M207 also showed reduced levels of transducin activation with M207R showing essentially no transducin activation. Our results highlight the tight coupling of the vicinity of C7 of retinal and M207 and support the involvement of this amino acid residue in the conformational changes associated with rhodopsin photoactivation.  相似文献   

5.
Side-chain 2H and backbone 15N relaxation data have been collected at multiple temperatures in the samples of the SH3 domain from alpha-spectrin. Combined analyses of the data allowed for determination of the temperature-dependent correlation times tauf characterizing fast methyl motion. Molecular dynamics simulations confirmed that tauf are dominated by methyl rotation; the corresponding activation energies approximate methyl rotation barriers. For 33 methyl groups in the alpha-spectrin SH3 domain the average barrier height was thus determined to be 2.8 +/- 0.9 kcal/mol. This value is deemed representative of the "fluid" hydrophobic protein core where some barriers are increased and others are lowered because of the contacts with surrounding atoms, but there is no local order that could produce systematically higher (lower) barriers. For comparison, the MD simulation predicts the average barrier of 3.1 kcal/mol (calculated via the potential of mean force) or 3.4-3.5 kcal/mol (rigid barriers after appropriate averaging over multiple MD snapshots). The latter result prompted us to investigate rigid methyl rotation barriers in a series of NMR structures from the Protein Databank. In most cases the barriers proved to be higher than expected, 4-6 kcal/mol. To a certain degree, this is caused by tight packing of the side chains in the NMR structures and stems from the structure calculation procedure where the coordinates are first annealed toward the temperature of 0 K and then subjected to energy minimization. In several cases the barriers >10 kcal/mol are indicative of van der Waals violations. The notable exceptions are (i) the structures solved using the GROMOS force field where tight methyl packing is avoided (3.0-3.6 kcal/mol) and (ii) the structure solved by means of the dynamic ensemble refinement method (Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Nature 2005, 433, 128) (3.5 kcal/mol). These results demonstrate that methyl rotation barriers, derived from the experiments that are traditionally associated with studies of protein dynamics, can be also used in the context of structural work. This is particularly interesting in view of the recent efforts to incorporate dynamics data in the process of protein structure elucidation.  相似文献   

6.
For the structural analysis of oriented polymers and other macromolecular systems, we present a solid state 2H NMR technique capable of measuring the orientations of individual chemical bond vectors with high accuracy. When an immobilized uniaxially oriented sample is aligned along the spectrometer magnetic field direction, the angle between a deuterium-labelled methyl group and the axis of ordering can be calculated from the spectral quadrupole splitting. However, since positive and negative splittings are indistinguishable, there may be two solutions. We show how these may be discriminated by acquiring additional spectra at different sample inclinations (Ref 1). The analysis of the resulting complex lineshapes is aided by computer simulation, which furthermore allows a characterization of the orientational distribution function of the sample. The 2H NMR method has been developed around the membrane protein bacteriorhodopsin as a biological model system that can be prepared in uniaxially oriented films. The overall orientation and molecular conformation of the retinal chromophore were resolved from the individual orientations of its five labelled methyl groups (Refs 2, 3). Structural changes were detected in an intermediate of the photocycle (M), which provide insight into the mechanism of the protein as a proton pump (Ref 4).  相似文献   

7.
The yellow-green luminescence from firefly luciferase has long been understood to be the emission from enol-oxyluciferin. However, a recent experiment showed that an oxyluciferin constrained to the keto form produced a yellow-green emission in luciferase (Branchini, B. R.; Murtiashaw, M. H.; Magyar, R. A.; Portier, N. C.; Ruggiero, M. C.; Stroh, J. G. J. Am. Chem. Soc. 2002, 124, 2112-2113). The present quantum mechanical/molecular mechanical and symmetry-adapted cluster-configuration interaction (SAC-CI) theoretical study supports the keto-form to be the yellow-green bioluminescence state in luciferase. We give the theoretically optimized structure of the excited state of oxyluciferin within luciferase, which gives luminescence calculated by the SAC-CI method that is close to the experimental value. Coulombic interactions with neighboring residues, in particular Arg218 and the phosphate group of AMP, play important roles in the color-tuning mechanism. Transformation to the enol form is energetically unfavorable in the luciferase environment. The twisted intramolecular charge-transfer (TICT) state is meta stable and would be easily relaxed to the co-planer structure. Further analyses were performed to verify the spectral-tuning mechanism based on the protonation state and the resonance structure of oxyluciferin.  相似文献   

8.
Ab initio molecular dynamics (AIMD) simulations were performed on the closed D(2h) and open C(2v) isomers of tetrasulfur. After a careful calibration of the electronic structure method, the calculations were done using the BPW91/aug-cc-pVTZ method. This combination of method/basis set adequately reproduces the relative benchmark CCSD(T) energy difference [Matus, M.; Dixon, D.; Peterson, K. A.; Harkless, J. A. W.; Francisco, J. S. J. Chem. Phys. 2007, 127, 174305] between these two isomers and, crucially, the fact that the D(2h) structure is a transition state linking two equivalent (mirror images) C(2v) isomers. The trajectories show that the symmetric open C(2v) isomers interconvert when passing through the D(2h) closed transition state structure and that, unlike tetraoxygen, no three-dimensional structures arise. The dynamic vibrational analysis yields peaks in good agreement with the static CCSD(T) harmonic frequencies and explains higher peaks as overtones, thus showing that unlike previous AIMD DFT-based approaches, carefully calibrated exchange-correlation functionals can produce reliable molecular dynamics results for complex PESs as the one corresponding to the lowest singlet of S(4).  相似文献   

9.
10.
Solution 1H NMR has been used to assign a major portion of the heme environment and the substrate-binding pocket of resting state horseradish peroxidase, HRP, despite the high-spin iron(III) paramagnetism, and a quantitative interpretive basis of the hyperfine shifts is established. The effective assignment protocol included 2D NMR over a wide range of temperatures to locate residues shifted by paramagnetism, relaxation analysis, and use of dipolar shifts predicted from the crystal structure by an axial paramagnetic susceptibility tensor normal to the heme. The most effective use of the dipolar shifts, however, is in the form of their temperature gradients, rather than by their direct estimation as the difference of observed and diamagnetic shifts. The extensive assignments allowed the quantitative determination of the axial magnetic anisotropy, Deltachi(ax) = -2.50 x 10(-8) m(3)/mol, oriented essentially normal to the heme. The value of Deltachi(ax) together with the confirmed T(-2) dependence allow an estimate of the zero-field splitting constant D = 15.3 cm(-1), which is consistent with pentacoordination of HRP. The solution structure was generally indistinguishable from that in the crystal (Gajhede, M.; Schuller, D. J.; Henriksen, A.; Smith, A. T.; Poulos, T. L. Nature Structural Biology 1997, 4, 1032-1038) except for Phe68 of the substrate-binding pocket, which was found turned into the pocket as found in the crystal only upon substrate binding (Henriksen, A.; Schuller, D. J.; Meno, K.; Welinder, K. G.; Smith, A. T.; Gajhede, M. Biochemistry 1998, 37, 8054-8060). The reorientation of several rings in the aromatic cluster adjacent to the proximal His170 is found to be slow on the NMR time scale, confirming a dense, closely packed, and dynamically stable proximal side up to 55 degrees C. Similar assignments on the H42A-HRP mutant reveal conserved orientations for the majority of residues, and only a very small decrease in Deltachi(ax) or D, which dictates that five-coordination is retained in the mutant. The two residues adjacent to residue 42, Ile53 and Leu138, reorient slightly in the mutant H42A protein. It is concluded that effective and very informative 1H NMR studies of the effect of either substrate binding or mutation can be carried out on resting state heme peroxidases.  相似文献   

11.
Abstract— A visual chromophore analogue, 10-methyl-13-demethyl (dm) retinal, was synthesized and reconstituted with bleached bovine rhodopsin to form a visual pigment derivative with absorbance maximum at 505 nm. The investigations with this new compound were stimulated from recent results using 13-dm retinal as a chromophore that revealed a remarkable loss in quantum efficiency (φ of 13-dm retinal-containing rhodopsin: 0.30, Ternieden and Gartner, J. Photochem. Photobiol. B Biol. 33, 83–86, 1996). The quantum efficiency of the new pigment was determined as 0.59 by quantitative bleaching using reconstituted rhodopsin as a reference. The very similar quantum efficiencies of rhodopsin and the new pigment give experimental support for the recently presented hypothesis that a steric hindrance between the substituents at positions 10 and 13 in 11- cis -retinal is elevated during the photoisomerization and thus facilitates the rapid photoisomerization of the visual chromophore (Peteanu et al., Proc. Natl. Acad. Sci. USA 90, 11762–11766, 1993). Such steric hindrance is removed from the molecule by the elimination of the methyl group from position 13 and can be re-established via a rearrangement of the substitution pattern by introducing a methyl group at position 10 of 13-dm retinal.  相似文献   

12.
Possible mechanisms for degrading chloromethylmercury (CH(3)HgCl) and dimethylmercury [(CH3)2Hg] involving thiol and ammonium residues were investigated by DFT and atoms-in-molecules (QTAIM) calculations. Using H2S and HS- as models for thiol and thiolate groups RSH and RS-, respectively, we obtained transition states and energy barriers for possible decomposition routes to Hg(SH)2 based on a model proposed by Moore and Pitts (Moore, M. J.; Distefano, M. D.; Zydowsky, L. D.; Cummings, R. T.; Walsh, C. T. Acc. Chem. Res. 1990, 23, 301. Pitts, K. E.; Summers, A. O. Biochemistry 2002, 41, 10287). Demethylation was found to be a multistep process that involved initial substitution of Cl- by RS-. We found that successive coordination of Hg with thiolates leads to increased negative charge on the methyl group and facilitates the protonolysis of the Hg-C bond by H-SH. This was also found to be the case for (CH3)2Hg. We found that NH4(+) readily protonolyzes the Hg-C bond of these thiolate complexes, suggesting that ammonium residues of protonated amino acids might also act as effective proton donors.  相似文献   

13.
Planar supported lipid bilayers that are stable under ambient atmospheric and ultra-high-vacuum conditions were prepared by cross-linking polymerization of bis-sorbylphosphatidylcholine (bis-SorbPC). X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were employed to investigate bilayers that were cross-linked using either redox-initiated radical polymerization or ultraviolet photopolymerization. The redox method yields a more structurally intact bilayer; however, the UV method is more compatible with incorporation of transmembrane proteins. UV polymerization was therefore used to prepare cross-linked bilayers with incorporated bovine rhodopsin, a light-activated, G-protein-coupled receptor (GPCR). A previous study (Subramaniam, V.; Alves, I. D.; Salgado, G. F. J.; Lau, P. W.; Wysocki, R. J.; Salamon, Z.; Tollin, G.; Hruby, V. J.; Brown, M. F.; Saavedra, S. S. J. Am. Chem. Soc. 2005, 127, 5320-5321) showed that rhodopsin retains photoactivity after incorporation into UV-polymerized bis-SorbPC, but did not address how the protein is associated with the bilayer. In this study, we show that rhodopsin is retained in supported bilayers of poly(bis-SorbPC) under ultra-high-vacuum conditions, on the basis of the increase in the XPS nitrogen concentration and the presence of characteristic amino acid peaks in the ToF-SIMS data. Angle-resolved XPS data show that the protein is inserted into the bilayer, rather than adsorbed on the bilayer surface. This is the first study to demonstrate the use of ultra-high-vacuum techniques for structural studies of supported proteolipid bilayers.  相似文献   

14.
Abstract— Squid opsin which is capable of combining with 11- cis or 9- cis retinal to reconstitute photo-pigment has been prepared by irradiation of rhabdomal membranes with orange light (> 530 nm) in the presence of 0.2 M hydroxylamine. When the irradiation is carried out either at concentrations of hydroxylamine higher than 0.2 M or with light of wavelength shorter than 530 nm, rhodopsin in the membranes is bleached quickly, but the ability of the resultant opsin to form rhodopsin is greatly reduced.
The optimum pH for rhodopsin regeneration in rhabdomal membranes was found to be between 6.5 and 8.5. The rate of regeneration of rhodopsin increases with raising temperature, and at about 20°C it is almost the same as that of isorhodopsin. Even after solubilization in digitonin solution, opsin still preserves the ability to reform rhodopsin.
All- trans retinal can be incorporated into retinochrome-bearing membranes, in which it is isomerized into 11- cis isomer by the photoisomerase activity of retinochrome. Rhabdomal membranes retaining active opsin can take up 11- cis retinal from retinochrome membranes so as to synthesize rhodopsin.  相似文献   

15.
The structure of the laser-light-induced metastable state MS(1) of the [Ru(NO(2))(4)(OH)(NO)](2)(-) anion in K(2)[Ru(NO(2))(4)(OH)(NO)] was determined by X-ray analysis at 50 K of a crystal with a 16% excited-state population. Results of an independent determination of the ground-state structure were used in the analysis. The most pronounced geometrical change upon excitation was an increase of the Ru-(NO) distance by 0.097(11) ?, significantly larger than the change of the corresponding distance in sodium nitroprusside (Pressprich, M. R.; White, M. A.; Vekhter, Y.; Coppens, P. J. Am. Chem. Soc. 1994, 116, 5233-5238). A decrease in the angleRu-(N-O) angle from 174.0(2) to 169(1) degrees was observed. The diffraction results provide evidence that the photoinduced state MS(1) of the transition metal nitrosyl complexes is a linkage isomer in which the NO group is attached to the metal atom through the oxygen, instead of through the nitrogen atom, rather than an electronic excited state as reported previously.  相似文献   

16.
Anthocyanins are a class of phytochemicals that confer color to flowers, fruits, vegetables and leaves. They are part of our regular diet and serve as dietary supplements because of numerous health benefits, including improved vision. Recent studies have shown that the anthocyanin cyanidin‐3‐O‐glucoside (C3G) increased regeneration of the dim‐light photoreceptor rhodopsin (Matsumoto et al. [2003] J. Agric. Food Chem., 51 , 3560–3563). In an accompanying study (Yanamala et al. [2009] Photochem. Photobiol.), we show that C3G directly binds to rhodopsin in a pH‐dependent manner. In this study, we investigated the functional consequences of C3G binding to rhodopsin. As observed previously in rod outer segments, regeneration of purified rhodopsin in detergent micelles is also accelerated in the presence of C3G. Thermal denaturation and stability studies using circular dichroism, fluorescence and UV/visible absorbance spectroscopy show that C3G exerts a destabilizing effect on rhodopsin structure while it only modestly alters G‐protein activation and the rates at which the light‐activated Metarhodopsin II state decays to opsin and free retinal. These results indicate that the mechanism of C3G‐enhanced regeneration may be based on changes in opsin structure promoting access to the retinal binding pocket.  相似文献   

17.
Abstract— We showed by spectrophotometry and HPLC that a photoproduct having 7-cis retinal (1-cis photoproduct) can be derived from the photoisomerization of frog lumirhodopsin (L) and metarhodopsin I (M I). The efficiency of the isomerization was higher in M I than in L. The absorption maximum of the 1-cis photoproduct at -20°C is at 455 nm, and its maximum absorbance 1.1 times as large as that of rhodopsin. The photoproduct exhibited two positive CD bands at 450 nm α-band) and 320 nm (β-band); the molecular ellipticity at a-band ([θ] = 73000) being larger than that of rhodopsin ([θ] = 61000). Re-examination of the absorption spectra of rhodopsin intermediates gave the absorption maxima of L. M 1 and M 111 to be 522, 482 and 475 nm, respectively.  相似文献   

18.
Nickel(II) chloride forms a complex with tetrahydrofuran, NiCl(2)(THF)(1.5), that can be used to prepare nickel chloride complexes of a bulky beta-diketiminate ligand L(Me). [L(Me)NiCl](2) and L(Me)NiCl(2)LiTHF(2), which have tetrahedral geometries in the solid state, are in equilibrium with three-coordinate L(Me)NiCl. Thermodynamic parameters for the equilibrium between [L(Me)NiCl](2) and L(Me)NiCl are DeltaH = 51(5) kJ/mol and DeltaS = 116(11) J/(mol.K). L(Me)NiCl forms a tetrahydrofuran complex with a binding constant of 1.2(2) M(-)(1) at 21 degrees C. The chloride complexes were used to generate a three-coordinate nickel(II)-amido complex. This amido complex, L(Me)NiN(SiMe(3))(2), is compared with L(Me)MN(SiMe(3))(2) (M = Mn, Fe, Co) (Panda, A.; Stender, M.; Wright, R. J.; Olmstead, M. M.; Klavins, P.; Power, P. P. Inorg. Chem. 2002, 41, 3909-3916). Trends in the metrical parameters of the three-coordinate L(Me)M(II) amido compounds are similar to the trends in three-coordinate L(tBu)M(II) chloride compounds (Holland, P. L.; Cundari, T. R.; Perez, L. L.; Eckert, N. A.; Lachicotte, R. J. J. Am. Chem. Soc. 2002, 124, 14416-14424).  相似文献   

19.
Rabbit metallothionein (MT) 2A complexes with Cd(II), Zn(II), Ag(I), Cu(I), Hg(II), arsenite, monomethylarsonous acid (MMA), and dimethylarsinous acid (DMA) have been examined using ion-mobility measurements and mass spectrometry in a triple-quadrupole mass spectrometer equipped with a segmented second quadrupole that doubled as an ion-mobility cell [Guo, Y.; Wang, J.; Javahery, G.; Thomson, B. A.; Siu, K. W. M. An Ion-Mobility Spectrometer with Radial Collisional Focusing. Anal. Chem.2005, 77, 266-275]. The metal ions confer conformational rigidity on the MT complexes, which counteracts Coulombic repulsion among protons added as a result of electrospray. Triply and quadruply protonated Cd(7)MT2A have smaller cross-sections than the Cd(7)MT2A structure deduced from published NMR data. For the 6+ ions, the As(6)MT2A complex has a cross-section of 790 A(2); the MMA(10)MT2A complex, 920 A(2); and the DMA(20)MT2A complex, 1220 A(2). This increase in cross-section of the As(III) species, from As(3+) to MMA to DMA, is interpreted as a consequence of decreasing multiple coordination and increasing number of methyl groups.  相似文献   

20.
In our previous study (Wang, Y. Q.; Yang, C.-M.; Zibrowius, B.; Spliethoff, B.; Lindén, M.; Schüth, F. Chem. Mater. 2003, 15, 5029), mesoporous vinyl-functionalized silica (vinyl silica) with hexagonal P6mm and cubic Ia3d structures has been synthesized at different loadings of vinyl groups and at different concentrations of sodium chloride when triblock copolymer P123 was used as a template. Our further investigations presented in this article reveal that at a loading of 10% vinyl groups, well-ordered cubic Ia3d structure was obtained at a low concentration of Na2SO4 (0.5 M) and the hexagonal structure was produced at 1.0 M NaCl. When NaNO3 was used as the inorganic salt, the hexagonal structure was still maintained even at a salt concentration of 2.0 M. The result is in accordance with the Hofmeister series order (salting-out effect): SO4(2-) > Cl- > NO3(-). The lowering of the acidity also induced the formation of the cubic Ia3d structure. At 20% loading, hexagonal structure can be obtained by adding the more hydrophilic Pluronic F127 (EO106PO70EO106) to the acidic solutions of P123, but the hexagonal structure cannot be produced with pure P123 under the synthesis conditions investigated. All of these results can be rationalized through hydrophilic-hydrophobic balance and the change in micellar curvature. Furthermore, 10% mercaptopropyl-functionalized mesoporous silica with cubic Ia3d structure was designed and synthesized successfully with the assistance of an inorganic salt (NaCl) in an acidic solution of P123, which is the first example of mercaptopropyl-functionalized large-pore mesoporous silica with high loadings.  相似文献   

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