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1.
AHb1 is a hexacoordinated type 1 nonsymbiotic hemoglobin recently discovered in Arabidopsis thaliana. To gain insight into the ligand migration inside the protein, we studied the CO rebinding kinetics of AHb1 encapsulated in silica gels, in the presence of glycerol. The CO rebinding kinetics after nanosecond laser flash photolysis exhibits complex ligand migration patterns, consistent with the existence of discrete docking sites in which ligands can temporarily be stored before rebinding to the heme at different times. This finding may be of relevance to the physiological NO dioxygenase activity of this protein, which requires sequential binding of two substrates, NO and O2, to the heme.  相似文献   

2.
CO rebinding kinetics after nanosecond photolysis of myoglobin encapsulated in wet silica gels exhibits an enhanced geminate phase that allows the determination of the microscopic rate constants and the activation barriers for distinct ligand docking sites inside the protein matrix. Using a maximum entropy method, we demonstrate that the geminate phase can be well-described by a biphasic lifetime distribution, reflecting rebinding from the distal and proximal sites. Microscopic rates and activation barriers were estimated using a four-state model.  相似文献   

3.
The rebinding kinetics of an amino acid ligand to ferrous microperoxidase-11 (MP11) after photolysis of aggregated ferrous MP11 was measured in aqueous solution with femtosecond transient visible absorption spectroscopy. The kinetics of CO rebinding to ferrous MP11 after photolysis of MP11CO was also measured in aqueous solution with femtosecond transient visible absorption spectroscopy. From these measurements, we found that either Val-11 or Lys-13 rebinds to ferrous MP11 exponentially with an 8 picosecond time constant in aggregated ferrous MP11 solution and that CO rebinds to ferrous MP11 nonexponentially with subnanosecond time scale in MP11CO solution. The kinetics of both the amino acid and CO rebinding to ferrous MP11 in MP11 system mimics that in carbon monoxide oxidation activator protein (CooA) or carboxymethyl cytochrome c (CmCytC) system. We also measured the kinetics of CO rebinding to ferrous MP11 in aqueous solution at different MP11CO concentrations and found that MP11CO concentration has an obvious effect on the kinetics of CO rebinding to ferrous MP11, where both the germinate yield and rate of CO rebinding to ferrous MP11 increase with the increase of MP11CO concentration. These findings suggested that the picosecond amino acid ligand rebinding process could disturb the proximal heme-ligand structure that possibly leads to the subnanosecond CO rebinding kinetics in MP11CO, CooACO and CmCytCCO systems.  相似文献   

4.
Encapsulation of hemoglobin (Hb) in silica gel preserves structure and function but greatly slows protein motion, thereby providing access to intermediates along the allosteric pathway that are inaccessible in solution. Resonance Raman (RR) spectroscopy with visible and ultraviolet laser excitation provides probes of heme reactivity and of key tertiary and quaternary contacts. These probes were monitored in gels after deoxygenation of oxyHb and after CO binding to deoxyHb, which initiate conformational change in the R-T and T-R directions, respectively. The spectra establish that quaternary structure change in the gel takes a week or more but that the evolution of heme reactivity, as monitored by the Fe-histidine stretching vibration, ν(FeHis), is completed within two days, and is therefore uncoupled from the quaternary structure. Within each quaternary structure, the evolving ν(FeHis) frequencies span the full range of values between those previously associated with the high- and low-affinity end states, R and T. This result supports the tertiary two-state (TTS) model, in which the Hb subunits can adopt high- and low-affinity tertiary structures, r and t, within each quaternary state. The spectra also reveal different tertiary pathways, involving the breaking and reformation of E and F interhelical contacts in the R-T direction but not the T-R direction. In the latter, tertiary motions are restricted by the T quaternary contacts.  相似文献   

5.
In this letter we report the first experimental evidence for CO rebinding to human hemoglobin from multiple geminate states. The analysis of the rebinding kinetics using a maximum entropy method allowed the identification of two distinct rebinding states within the protein matrix, which become populated under conditions of increased viscosity in a silica gel at high glycerol concentration. Our findings suggest the presence of at least two distinct docking sites for the photolyzed ligand. Assuming a minimal four-state model, we estimate the microscopic rates and the activation energies for the elementary processes.  相似文献   

6.
NO is an important signaling molecule in human tissue. However, the mechanisms by which this molecule is controlled and directed are currently little understood. Nitrophorins (NPs) comprise a group of ferriheme proteins originating from blood-sucking insects that are tailored to protect and deliver NO via coordination to and release from the heme iron. Therefore, the kinetics of the association and dissociation reactions were studied in this work using the ferroheme-CO complexes of NP4, NP4(D30N), and NP7 as isoelectronic models for the ferriheme-NO complexes. The kinetic measurements performed by nanosecond laser-flash-photolysis and stopped-flow are accompanied by resonance Raman and FT-IR spectroscopy to characterize the carbonyl species. Careful analysis of the CO rebinding kinetics reveals that in NP4 and, to a larger extent, NP7 internal gas binding cavities are located, which temporarily trap photodissociated ligands. Moreover, changes in the free energy barriers throughout the rebinding and release pathway upon increase of the pH are surprisingly small in case of NP4. Also in case of NP4, a heterogeneous kinetic trace is obtained at pH 7.5, which corresponds to the presence of two carbonyl species in the heme cavity that are seen in vibrational spectroscopy and that are due to the change of the distal heme pocket polarity. Quantification of the two species from FT-IR spectra allowed the fitting of the kinetic traces as two processes, corresponding to the previously reported open and closed conformation of the A-B and G-H loops. With the use of the A-B loop mutant NP4(D30N), it was confirmed that the kinetic heterogeneity is controlled by pH through the disruption of the H-bond between the Asp30 side chain and the Leu130 backbone carbonyl. Overall, this first study on the slow phase of the dynamics of diatomic gas molecule interaction with NPs comprises an important experimental contribution for the understanding of the dynamics involved in the binding/release processes of NO/CO in NPs.  相似文献   

7.
Picosecond to millisecond laser time-resolved transient absorption spectroscopy was used to study molecular oxygen (O2) rebinding and conformational relaxation following O2 photodissociation in the α and β subunits within human hemoglobin in the quaternary R-like structure. Oxy-cyanomet valency hybrids, α2(Fe2+–O22(Fe3+–CN) and α2(Fe3+–CN)β2(Fe2+–O2), were used as models for oxygenated R-state hemoglobin. An extended kinetic model for geminate O2 rebinding in the ferrous hemoglobin subunits, ligand migration between the primary and secondary docking site(s), and nonexponential tertiary relaxation within the R quaternary structure, was introduced and discussed. Significant functional non-equivalence of the α and β subunits in both the geminate O2 rebinding and concomitant structural relaxation was revealed. For the β subunits, the rate constant for the geminate O2 rebinding to the unrelaxed tertiary structure and the tertiary transition rate were found to be greater than the corresponding values for the α subunits. The conformational relaxation following the O2 photodissociation in the α and β subunits was found to decrease the rate constant for the geminate O2 rebinding, this effect being more than one order of magnitude greater for the β subunits than for the α subunits. Evidence was provided for the modulation of the O2 rebinding to the individual α and β subunits within human hemoglobin in the R-state structure by the intrinsic heme reactivity through a change in proximal constraints upon the relaxation of the tertiary structure on a picosecond to microsecond time scale. Our results demonstrate that, for native R-state oxyhemoglobin, O2 rebinding properties and spectral changes following the O2 photodissociation can be adequately described as the sum of those for the α and β subunits within the valency hybrids. The isolated β chains (hemoglobin H) show similar behavior to the β subunits within the valency hybrids and can be used as a model for the β subunits within the R-state oxyhemoglobin. At the same time, the isolated α chains behave differently to the α subunits within the valency hybrids.

O2 rebinding and conformational relaxation following O2 photodissociation were studied on picosecond to millisecond time scale in the α and β subunits within human hemoglobin in the quaternary R-like structure.  相似文献   

8.
Biphasic geminate rebinding of CO to myoglobin upon flash photolysis has been associated to ligand distribution in hydrophobic cavities, structurally detected by time-resolved crystallography, xenon occupancy, and molecular simulations. We show that the time course of CO rebinding to human hemoglobin also exhibits a biphasic geminate rebinding when the protein is entrapped in wet nanoporous silica gel. A simple branched kinetic scheme, involving the bound state A, the primary docking site C, and a secondary binding site B was used to calculate the microscopic rates and the time-dependent population of the intermediate species. The activation enthalpies of the associated transitions were determined in the absence and presence of 80% glycerol. Potential hydrophobic docking cavities within the alpha and beta chains of hemoglobin were identified by computational modeling using xenon as a probe. A hydrophobic pocket on the distal side of the heme, corresponding to Xe4 in Mb, and a nearby site that does not have a correspondence in Mb were detected. Neither potential xenon sites on the proximal side nor a migration channel from the distal to proximal site was located. The small enthalpic barriers between states B and C are in very good agreement with the location of the xenon sites on the distal side. Furthermore, the connection between the two xenon sites is relatively open, explaining why the decreased mobility of the protein with viscosity only slightly perturbs the energetics of ligand migration between the two sites.  相似文献   

9.
The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H(p), to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: DeltaG(D) approximately 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin ( approximately 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H(D) approximately 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).  相似文献   

10.
It was established that linear polymers with quaternary ammonium groups are obtained by the reaction of chloromethylated polystyrene (CMPS) with hydroxyalkylic tertiary amines when the amines contain one or two hydroxyl groups, and that crosslinked polymers are obtained with aminoether groups when the amines have three hydroxyl groups, i.e., tris(2-hydroxyethy1)amine. The aminoether units appear by intramolecular rearrangement of quaternary ammonium structural units. Kinetic studies on the synthesis of polymers with quaternary ammonium groups from CMPS, poly(N,N-dimethylamino-ethylmethacrylate), and poly(N,N-dimethylaminopropylacrylamide), were performed. The main factors which influence the kinetics of reactions are steric hindrance of near neighboring groups, hydrophilic effect for hydroxyalkylamines and polymer-solvent interaction.  相似文献   

11.
The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.  相似文献   

12.
[reaction: see text] We have recently developed a new class of chiral phosphorus ligands: P-chirogenic diaminophosphine oxides. These pentavalent phosphorus compounds have been successfully applied to Pd-catalyzed asymmetric construction of tertiary and quaternary carbons. The actual ligand structure was the trivalent phosphorus species 17, which was generated in situ by BSA-induced P(V) to P(III) transformation of 6, the preligand. Detailed mechanistic studies, including asymmetric amplification and initial rate kinetics, revealed that complex 18 [Pd-17 (1:2) complex] was the active catalyst. The important function of the nitrogen atom on the sidearm in the ligands was also clarified. The source of enantioselection in the construction of asymmetric quaternary carbons was the secondary ligand substrate interaction mediated by N-Zn coordination.  相似文献   

13.
The nonsymbiotic hemoglobins, AHb1 and AHb2, have recently been isolated from Arabidopsis thaliana. Using steady-state and time-resolved spectroscopic methods, we show that Fe2+ AHb1 contains a mixture of penta- and hexacoordinated heme, while Fe2+ AHb2 is fully hexacoordinated. In the CO complexes, polar interactions and H-bonds with the ligand are stronger for AHb1 than for AHb2. The ligand binding kinetics are substantially different, reflecting the distribution between the penta- and hexacoordinated species, and indicate that protein dynamics and ligand migration pathways are very specific for each of the two proteins. In particular, a very small, non-exponential geminate rebinding observed in AHb1 suggests that the distal heme cavity is connected with the exterior by a relatively open channel. The large, temperature-dependent geminate rebinding observed for AHb2 implies a major role of protein dynamics in the ligand migration from the distal cavity to the solvent. The structures of AHb1 and AHb2, modeled on the basis of the homologous rice hemoglobin, exhibit a different cavity system that is fully compatible with the observed ligand binding kinetics. Overall, these kinetic and structural data are consistent with the putative NO-dioxygenase activity previously attributed to AHb1, whereas the role of AHb2 remains elusive.  相似文献   

14.
时间分辨拉曼光谱研究一氧化氮与肌红蛋白的结合过程   总被引:1,自引:0,他引:1  
纳秒瞬态拉曼光谱技术是研究分子结构变化超快动态过程的重要实验手段之一.而肌红蛋白(Mb)与小分子配体的结合过程一直是人们研究的焦点.本文旨在利用纳秒瞬态拉曼光谱技术研究小分子配体NO与肌红蛋白结合的动力学过程.通过考察MbNO光解后产物脱氧肌红蛋白(DeoxyMb)与反应物MbNO的ν4特征振动峰的强度比值随激光激发功率的变化,阐述了利用纳秒瞬态拉曼光谱技术研究MbNO体系中NO与DeoxyMb结合过程的可行性.利用纳秒瞬态拉曼光谱技术,获得了与皮秒时间分辨拉曼和皮秒时间分辨吸收相一致的结合动力学实验结果.为研究其它复杂体系的超快结合动力学过程提供了一种新的思路.  相似文献   

15.
Extraction of some trivalent actinides and lanthanides from 11.9 M LiCl (pH 2.0) by some primary, secondary, tertiary and quaternary amines in xylene has been studied. Negligible extraction of the metal ions was found with primary and secondary amines whereas they are appreciably extracted with tertiary and quaternary amines, the trivalent actinides always being extracted to a greater extent. The separation factors Kd An(III)/Kd Ln(III) for several trivalent actinides with respect to Eu(III) and Tm(III) are found to be much greater when tertiary amines are used as extractants compared to when quaternary amines are used which has been ascribed to the extraction of higher chloro complexes of the metal ions by tertiary amines. Absorption spectra of Am(III) and Nd(III) extracted into the long chain amines from 11.0 M LiCl (pH 2.0) indicate that octahedral hexachloro complexes are present in the tertiary amine extracts whereas lower complexes are predominantly extracted by the quaternary amines leading to the observed lower separation factors for the trivalent actinides with reference to the lanthanides. Possible role of hydrogen bonding in the stabilization of chloro complexes extracted by tertiary amines as well as the extraction of hydrated chloro complexes by the quaternary amines are discussed.  相似文献   

16.
A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.  相似文献   

17.
Femtosecond vibrational coherence spectroscopy was used to investigate the low-frequency vibrational dynamics of the heme in the carbon monoxide oxidation activator protein (CooA) from the thermophilic anaerobic bacterium Carboxydothermus hydrogenoformans (Ch-CooA). Low frequency vibrational modes are important because they are excited by the ambient thermal bath (k(B)T = 200 cm(-1)) and participate in thermally activated barrier crossing events. However, such modes are nearly impossible to detect in the aqueous phase using traditional spectroscopic methods. Here, we present the low frequency coherence spectra of the ferric, ferrous, and CO-bound forms of Ch-CooA in order to compare the protein-induced heme distortions in its active and inactive states. Distortions take place predominantly along the coordinates of low-frequency modes because of their weak force constants, and such distortions are reflected in the intensity of the vibrational coherence signals. A strong mode near ~90 cm(-1) in the ferrous form of Ch-CooA is suggested to contain a large component of heme ruffling, consistent with the imidazole-bound ferrous heme crystal structure, which shows a significant protein-induced heme distortion along this coordinate. A mode observed at ~228 cm(-1) in the six-coordinate ferrous state is proposed to be the ν(Fe-His) stretching vibration. The observation of the Fe-His mode indicates that photolysis of the N-terminal α-amino axial ligand takes place. This is followed by a rapid (~8.5 ps) transient absorption recovery, analogous to methionine rebinding in photolyzed ferrous cytochrome c. We have also studied CO photolysis in CooA, which revealed very strong photoproduct state coherent oscillations. The observation of heme-CO photoproduct oscillations is unusual because most other heme systems have CO rebinding kinetics that are too slow to make the measurement possible. The low frequency coherence spectrum of the CO-bound form of Ch-CooA shows a strong vibration at ~230 cm(-1) that is broadened and up-shifted compared to the ν(Fe-His) of Rr-CooA (216 cm(-1)). We propose that the stronger Fe-His bond is related to the enhanced thermal stability of Ch-CooA and that there is a smaller (time dependent) tilt of the histidine ring with respect to the heme plane in Ch-CooA. The appearance of strong modes at ~48 cm(-1) in both the ferrous and CO-bound forms of Ch-CooA is consistent with coupling of the heme doming distortion to the photolysis reaction in both samples. Upon CO binding and protein activation, a heme mode near 112 ± 5 cm(-1) disappears, probably indicating a decreased heme saddling distortion. This reflects changes in the heme environment and geometry that must be associated with the conformational transition activating the DNA-binding domain. Protein-specific DNA binding to the CO-bound form of Ch-CooA was also investigated, and although the CO rebinding kinetics are significantly perturbed, there are negligible changes in the low-frequency vibrational spectrum of the heme.  相似文献   

18.
Under prolonged X-ray irradiation, the ferrous heme of nitrosylated human adult hemoglobin derivative (HbNO) undergoes a reversible transition generating a 5-coordinate species, due to release of the Fe-NO bond. The overall process can be investigated using X-ray absorption near edge structure (XANES) spectroscopy. In this work, Fe K-edge XANES spectra were measured at T < 15 K, pH 9.2, i.e., on a high-affinity state (R-HbNO) where all the hemes are 6-coordinate, and at pH 6.5 in the presence of inositol hexakis-phosphate (IHP), i.e., on a low-affinity ligated state (T-HbNO) where the iron-hemes of the α-chains are 5-coordinate due to breaking of the Fe-proximal histidine bond. Under X-ray irradiation, 5-coordinate Fe-hemes are populated in both R-HbNO and T-HbNO, the Fe-NO bond lysis induced in T-HbNO involving rebinding of the proximal histidine to the transiently populated 4-coordinate hemes of the α-chains. A detailed analysis of the spectra confirms that different intermediate states in the ligand binding cooperative process of hemoglobin can be populated by X-ray irradiation, and that the part of the energy associated to the R-T quaternary transition, that is transmitted to the heme site, can be monitored by XANES spectroscopy.  相似文献   

19.
In this work we present the separation of FTIR difference signals induced by electron transfer to/from the redox centers of the cytochrome c oxidase from P. denitrificans and compare electrochemically induced FTIR difference spectra with those induced by CO photolysis. FTIR difference spectra of rebinding of CO to the half reduced (mixed valence) form of the cytochrome c oxidase after photolysis reflect the conformational changes induced by the rebinding of CO and by electron transfer reactions from heme a3 to heme a and further on to CUA. During this process, heme a3 (and CUB) are oxidized, whereas heme a and CuA are reduced. By subtracting these difference spectra from an electrochemically induced FTIR difference spectrum, where all four cofactors are reduced, the contributions for heme a3 (and CuB) could be separated. Correspondingly, the spectral contributions of heme a and CuA have been separated. The comparison of these spectra with the spectra calculated for the hemes on the basis of their redox dependent changes previously published in Hellwig et al., (Biochemistry 38, (1999) 1685-1694) show a high degree of similarity, except for additional signals coupled to the reorganization of the binuclear center upon CO rebinding. The separated spectra clearly show that the signals attributed to Glu278, an amino acid discussed to be crucial for proton pumping, is coupled to electron transfer to/from heme a and the binuclear heme a3-CuB center.  相似文献   

20.
Iodobenzene is shown to catalyze the 5-exo-dig cyclization of δ-alkynyl β-ketoesters under oxidative conditions that generate hypervalent iodine species in situ. The cyclopentane products contain adjacent quaternary and tertiary stereocenters which are generated with excellent diastereoselectivity.  相似文献   

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