血红素C十一肽含氰络合物的共振喇曼光谱

我们研究了血红素C+-肽含氰络合物的共振喇曼光谱。我们的实验结果证明,氰化物可以很高的亲和力与血红素C+-肽生成低自旋三价铁的络合物其Fe(Ⅲ)-CN~-伸缩振动频率为462cm~(-1),它比血红素C+-肽一氧化碳络合物中的Fe(Ⅱ)-CO伸缩振动频率509cm~(-1)要低47cm~(-1)     

Characterization of the effects of nonspecific xenon-protein interactions on (129)Xe chemical shifts in aqueous solution: further development of xenon as a biomolecular probe

The sensitivity of (129)Xe chemical shifts to weak nonspecific xenon-protein interactions has suggested the use of xenon to probe biomolecular structure and interactions. The realization of this potential necessitates a further understanding of how different macromolecular properties influence the (129)Xe chemical shift in aqueous solution. Toward this goal, we have acquired (129)Xe NMR spectra of xenon dissolved in amino acid, peptide, and protein solutions under both native and denaturing conditions. In general, these cosolutes induce (129)Xe chemical shifts that are downfield relative to the shift in water, as they deshield the xenon nucleus through weak, diffusion-mediated interactions. Correlations between the extent of deshielding and molecular properties including chemical identity, structure, and charge are reported. Xenon deshielding was found to depend linearly on protein size under denaturing solution conditions; the denaturant itself has a characteristic effect on the (129)Xe chemical shift that likely results from a change in the xenon solvation shell structure. In native protein solutions, contributions to the overall (129)Xe chemical shift arise from the presence of weak xenon binding either in cavities or at the protein surface. Potential applications of xenon as a probe of biological systems including the detection of conformational changes and the possible quantification of buried surface area at protein-protein interfaces are discussed.     

Resonance Raman spectroscopic investigation of structural changes of CO‐heme in soluble guanylate cyclase generated by effectors and substrate

The influence of the effectors YC‐1 and BAY on the CO‐heme structure of bovine lung soluble guanylate cyclase (sGC) was investigated with resonance Raman spectroscopy. The effectors produced a five‐coordinate (5c) CO‐heme in addition to the His‐bound six‐coordinate (6c) CO‐heme, and both their Soret maxima were determined by simulation. On the basis of the absorption intensity, the amount of the 5c species was not dominant, in contrast to the high activity. The heme structural features common to the 5c and 6c CO‐hemes generated by effectors are that the vinyl and propionate side chains are more coplanar to the pyrrole rings. The out‐of‐plane Raman bands were observed only for the 5c species, for which the saddling and propeller distortions of heme were deduced to be large. The Fe CO stretching bands of the 5c species at 522 cm⁻¹ and of the 6c species at 488 cm⁻¹ were most enhanced upon excitation at 407 and 422 nm, respectively, which is consistent with the simulated spectra. Unexpectedly, the ¹³C¹⁸O isotope sensitivity appeared in low wavenumber porphyrin modes. From these observations, we propose that the high catalytic activity of sGC‐CO in the presence of effectors is a result of the concerted effects of protein conformational changes triggered by certain local interactions between the heme side chains and effectors/substrate in the heme pocket, which partly induce the cleavage of the Fe Hisβ 105 bond. Copyright © 2010 John Wiley & Sons, Ltd.     

Sub‐picosecond Raman spectrometer for time‐resolved studies of structural dynamics in heme proteins

We describe a pump–probe Raman spectrometer based on a femtosecond Ti:sapphire laser, an optical parametric generator and two optical parametric amplifiers for time‐resolved studies, with emphasis on the structural dynamics in heme proteins. The system provides a 100‐fs pump pulse tunable in the range 500–600 nm and a transform‐limited sub‐picosecond probe pulse tunable in the range 390–450 nm. The spectrometer has spectral (25 cm⁻¹) and temporal (∼0.7 ps) resolutions which constitute an effective compromise for identifying transient heme protein species and for following their structural evolution by spontaneous Raman scattering in the time range 0.5 ps to 2 ns. This apparatus was applied to time‐resolved studies of a broad range of heme proteins, monitoring the primary dynamics of photoinduced heme coordination state and structural changes, its interaction with protein side‐chains and diatomic gaseous ligands, as well as heme vibrational cooling. The treatment of transient Raman spectra is described in detail, and the advantages and shortcomings of spontaneous resonance Raman spectroscopy for ultrafast heme proteins studies are discussed. We demonstrate the efficiency of the constructed spectrometer by measuring Raman spectra in the sub‐picosecond and picosecond time ranges for the oxygen‐storage heme protein myoglobin and for the oxygen‐sensor heme protein FixLH in interaction with the diatomic gaseous ligands CO, NO, and O₂. Copyright © 2010 John Wiley & Sons, Ltd.     

Comparison of ligand migration and binding in heme proteins of the globin family

The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins(via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family.     

Infrared spectra of the Kr—CO and Xe—CO van der Waals complexes

The infrared spectra of the weakly bound complexes Kr—CO and Xe—CO have been studied in the region of the CO stretching vibration (4.7 μm) using a high-resolution tuneable diode laser probe. The complexes were observed in a long path (200 m) low temperature (76 K) gas cell (Kr—CO) and in a pulsed supersonic jet expansion (Kr—CO and Xe—CO). Previous long path cell measurements on these complexes at lower resolution analysed only the K = 0 and 1 stacks of rotational levels in the ground intermolecular vibrational state. The new data extend up to K = 3 (Xe—CO) or 4 (Kr—CO), and also include K = 0 and 1 stacks in the excited bending state, ν₂ = 1. The bending frequencies for Kr—CO and Xe—CO (in the ν_co = 1 upper state) were determined to be 13.156cm_?1 and 13.794cm^?1, respectively. Detailed molecular parameters were determined to describe the rotational energy levels of each complex using a simple empirical Hamiltonian. These results enable parameters to be compared for the entire series of rare gas—carbon monoxide complexes, from He—CO to Xe—CO. Also they will guide the future development and evaluation of accurate intermolecular potential energy surfaces for Kr—CO and Xe—CO.     

Electron spin-lattice relaxation rates for high-spin Fe(III) complexes in glassy solvents at temperatures between 6 and 298 K

The temperature dependence of spin-lattice relaxation rates was analyzed for four high-spin nonheme iron proteins between 5 and 20 K, for three high-spin iron porphyrins between 5 and 118 K, and for four high-spin heme proteins between 5 and 150 to 298 K. For the nonheme proteins the zero-field splittings, D, are less than 0.7 cm(-1), and the relaxation is dominated by the Orbach and Raman processes. For the iron porphyrins and heme proteins D is between 4 and 12 cm(-1) and the relaxation is dominated by the Orbach process between about 5 and 100 K and by a local mode at higher temperatures. The relaxation rates for the heme proteins in glassy matrices extrapolated to values at room temperature that are similar to values obtained by NMR relaxivity in fluid solution. This similarity suggests that for high-spin Fe(III) heme proteins with effective intramolecular spin-lattice relaxation processes, the additional motional freedom gained when a relatively large protein goes from glassy solid to liquid solution at room temperature has little impact on spin-lattice relaxation.     

The human brain hexacoordinated neuroglobin three-dimensional structure

Neuroglobin, mainly expressed in vertebrate brain and retina, is a recently identified member of the globin superfamily. Augmenting O2 supply, neuroglobin promotes survival of neurons upon hypoxic injury, potentially limiting brain damage. In the absence of exogenous ligands, neuroglobin displays a six-coordinated heme. O2 and CO bind to the heme-iron, displacing the endogenous HisE7 heme distal ligand. Hexacoordinated human neuroglobin displays a classical globin fold, adapted to host the reversible bis-histidyl heme complex, and an elongated protein matrix cavity, held to facilitate O2 diffusion to the heme. The structure of neuroglobin suggests that the classical globin fold is endowed with striking adaptability, indicating that hemoglobin and myoglobin are just two examples within a wide and functionally diversified protein homology superfamily.     

AFM method for investigation of irradiated polymers

Tracks of swift heavy ions (Xe and Bi) at the surface of polymer (PET) were studied using AFM and surface defects—cavities (for Xe) and hillocks with cavities on its top (for Bi) were found. Thermal behavior of these Bi-irradiated samples (during annealing from 70°C to 180°C) was investigated. It was found that low-temperature annealing does not change the shape of surface defects, while high-temperature annealing leads to slow disappearance of these defects.

Irradiation of a stack of ultra-thin PET films by fission fragments was carried out and some sheets were then investigated separately. Two types of defects, corresponding to two main types of incident fragments (according to average energy distribution) were found. The deep structure of a track was studied and the ranges for two types of fragments were estimated. The increase of area of destruction was found at the depth 10–12 μm, which may be associated with changing of mechanism of interaction of passing particle with polymer and the dominant role of nuclear interaction. The obtained results are supported by a model calculation.     

CO vibration as a probe of ligand dissociation and transfer in myoglobin

We report femtosecond visible pump, midinfrared probe, spectrally integrated experiments resolving the dynamics of CO in myoglobin upon photodissociation. Our results show a progressive change in absorption strength of the CO vibrational transition during its transfer from the heme to the docking site, whereas the vibrational frequency change is faster than our time resolution. A phenomenological model gives good qualitative agreement with our data for a time constant of 400 fs for the change in oscillator strength. Density-functional calculations demonstrate that indeed vibrational frequency and absorption strength are not linearly coupled and that the absorption strength varies in a slower manner due to charge transfer from the heme iron to CO.     

光谱法研究高铁肌红蛋白活性中心与一氧化氮的配位反应

蛋白质与配体作用的瞬时性对调节生物功能的正常发挥至关重要。采用紫外-可见吸收光谱法(UV-Vis)和圆二色光谱法(CD)研究了高铁肌红蛋白(metMyoglobin,metMb)与一氧化氮的配位反应过程,论证了metMb与NO配位反应机理以及影响配位反应的因素。结果表明：metMb能与NO发生配位反应,420,534和568 nm处特征峰的出现,表明metMb与NO结合并生成一种新的配合物——亚硝基高铁肌红蛋白(nitrosylmetmyoglobin,metMbNO)。随着时间的推移,溶液中NO浓度逐渐减小,metMbNO配合物中Fe—N配位键在大量H₂O分子的进攻下断裂,NO慢慢地脱离,metMbNO配合物完成解离过程并重新生成metMb。实验中还发现metMb与NO配位反应的进行受到缓冲介质类型、离子强度、pH及温度等外界因素的影响。并且在0.01 mol·L-1磷酸盐缓冲液近中性条件时,metMb与NO配位反应最先达到平衡;当温度较低为280 K时,更易于metMb与NO配位反应的进行。此外,CD数据表明NO只与metMb血红素中心的铁原子发生配位反应而对蛋白二级结构影响甚微。探讨metMb与NO配位反应机制对于进一步研究生物体内NO功能的发挥有着重要的指导意义。     

FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2))

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (E(bond)) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). The results indicate that an accurate prediction of E(bond) for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield E(bond) values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O(2), respectively, which are in reasonable agreement with experimental data (0.78 - 0.85 eV for CO, 0.99 eV for NO, and 0.44 - 0.53 eV for O(2)). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined.     

A REMPI study of the correlation of internal excitations and substrate-adsorbate coupling for CO molecules desorbed by electron impact

We compare vibrational, translational and rotational excitations of CO molecules desorbed by electron impact, and the yield of oxygen and carbon atoms from electron-induced fragmentation of CO molecules for: (1) CO monolayers on bare transition metals [Ru(001) and Pt(111)]; (2) CO monolayers coadsorbed with well-ordered oxygen atoms; (3) weakly bound CO monolayers on epitaxially grown silver films; and (4) CO monolayers decoupled from the metallic substrate by mono-atomic xenon spacer layers. For all but the last system, we find CO molecules which are vibrationally extremely hot. This is explained by the excitation of strongly antibonding multi-electron states which are quenched in the vicinity of the metal surface before enough translational energy is acquired by the nuclei to complete dissociation. For CO/Xe/Ag(111), vibrationally hot CO molecules are missing among the desorbing particles, whereas strong fragment signals persist. Because of the isolating Xe layer, the substrate-adsorbate coupling is too weak to terminate the dissociation reaction which is induced by the electron impact before the rupture of the molecular bond.     

The adsorption of Xe and CO on Au(100)

The adsorption of Xe and CO on Au(100) has been studied by LEED, Auger electron spectroscopy, electron energy loss spectroscopy (EELS) and surface potential measurements. The physical adsorption of xenon showed successive stages preceding the completion of a monolayer. The heat of adsorption was 22 (±2) kJ mol^?1 and the maximum surface potential was 0.45 V. Carbon monoxide gave a surface potential of 0.85 V at the highest coverage reached. The heat of adsorption showed a continuous fall from an initial value of 58 (±3) kJ mol^?1 as the coverage increased. Ordered adsorption structures were not observed in LEED for either Xe or CO. The EEL spectrum of clean Au(100) agreed well with spectra of polycrystalline gold. New loss features observed with adsorbed Xe and CO are discussed.     

CO adsorbed on a Xe covered Cu(100) surface studied by infrared spectroscopy

When a Cu(100) surface covered by a full Xe monolayer is exposed to CO at 60 K no infrared absorption associated with the CO vibration is observed. If the temperature is increased to 90 K, when the Xe atoms are desorbed, the ordinary CO spectrum develops. This observation can be explained, if the CO molecules on the Xe covered surface are oriented on the average with their molecular axes parallel to the surface.     

The adsorption of Xe and CO on Ag(111)

The adsorption of Xe and CO on Ag(111) in the range 66 to 123 K and 10^?7 to 10^?1 Pa has been studied by surface potential, low energy electron diffraction (LEED), Auger electron spectroscopy (AES) and electron energy loss spectroscopic (EELS) measurements. Isotherms derived from both surface potential and AES measurements for submonolayer Xe adsorption reveal successive stages and a two-dimensional phase change. Isosteric heats were 18 ± 1 kJ mol^?1. Temkin isotherms were observed for CO, the heat falling linearly with coverage from an initial value of 27 ± 1.5 kj mol^?1. No ordered CO overlayer structure could be detected. EEL spectra of clean Ag(111) agree with previous studies. Additional loss peaks were recorded for Xe and CO overlayers, and the assignment of the substrate loss features is discussed in relation to the effects of adsorption.     

Quantitative analysis of x-ray absorption near edge structure data by a full multiple scattering procedure: the Fe-CO geometry in photolyzed carbonmonoxy-myoglobin single crystal

We report the first quantitative analysis of the Fe K-edge polarized x-ray absorption near edge structure of the iron protein carbonmonoxy-myoglobin (MbCO) single crystal and of its cryogenic photoproduct Mb(*)CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure based on the full multiple scattering approach. The extracted local structure of Mb(*)CO includes a Fe-CO distance of (3.08+/-0.07) A, with a tilting angle between the heme normal and the Fe-C vector of (37+/-7) degrees, and a bending angle between the Fe-C vector and the C-O bond of (31+/-5) degrees.     

H2O on Pt(111): structure and stability of the first wetting layer

We study the structure and stability of the first water layer on Pt(111) by variable-temperature scanning tunneling microscopy. We find that a high Pt step edge density considerably increases the long-range order of the equilibrium √37 × √37R25.3°- and √39 × √39R16.1°-superstructures, presumably due to the capability of step edges to trap residual adsorbates from the surface. Passivating the step edges with CO or preparing a flat metal surface leads to the formation of disordered structures, which still show the same structural elements as the ordered ones. Coadsorption of Xe and CO proves that the water layer covers the metal surface completely. Moreover, we determine the two-dimensional crystal structure of Xe on top of the chemisorbed water layer which exhibits an Xe-Xe distance close to the one in bulk Xe and a rotation angle of 90° between the close-packed directions of Xe and the close-packed directions of the underlying water layer. CO is shown to replace H(2)O on the Pt(111) surface as has been deduced previously. In addition, we demonstrate that tunneling of electrons into the antibonding state or from the bonding state of H(2)O leads to dissociation of the molecules and a corresponding reordering of the adlayer into a √3 × √3R30°-structure. Finally, a so far not understood restructuring of the adlayer by an increased tunneling current has been observed.     

P450血红素与CO、NO 和O2结合性质的密度泛涵研究

用两种模型在B3LYP/6-31G(d)水平上研究了双原子分子CO、NO和O2 (通称XO) 与P450血红素的结合性质. 在模型M2中考虑了双原子分子XO附近的丝氨酸残基对其的影响. 结果表明血红素附近的丝氨酸使得XO与血红素的结合更加牢固. 频率分析表明，当XO与血红素结合后X{O伸缩振动频率降低.同时讨论了复合物的HOMO和LUMO轨道的组成.     

Electron impact desorption of Xe from the tungsten (110) plane

The electron stimulated desorption of Xe adsorbed on the clean and on oxygen and CO covered tungsten (110) surfaces has been investigated. Only neutral Xe desorption was observed; for Xe on clean W a very small initial regime with cross section 10^?17cm² is followed by a slow decay with cross section 3×10^?19cm². The Xe yield varies nonlinearly with coverage, suggesting desorption from edges of islands or from sites with less than their full complement of nearest neighbor Xe atoms. Desorption from oxygen or CO covered surfaces results in an apparent desorption cross section identical to that of the underlying adsorbate. This results from a kicking off of Xe by electron desorbed O or CO. The true cross sections for these processes are ～10^?14cm² for Xe-0 and ～10^?15 cm² for Xe-CO. Some speculations about the mechanism, particularly the absence of ions are presented.