Mössbauer studies of the dynamics of biopolymers and model systems

In this survey, the scales and correlation times of the motion of iron atoms in the active site of myoglobin and hemoglobin, in the iron containing core, in iron storage proteins, and model polymer systems, and the average fragmental motion of protein globules of myoglobin and human serum albumin are considered. Models of intramolecular protein mobility are presented.     

可见光谱法研究肌红蛋白血红素铁与金属离子相互作用(Ⅰ)

肌红蛋白(Myoglobin,Mb)是哺乳动物细胞主要是肌细胞贮存和分配氧的蛋白质, 由一条多肽链和一个血红素辅基构成,其血红素铁在氧气的传递和运输中起到关键作用。文章利用紫外-可见光谱法对肌红蛋白的血红素铁和外加金属离子M(Ⅱ)[Cu(Ⅱ), Zn(Ⅱ)和Co(Ⅱ)] 的直接相互作用进行了研究。结果发现, 金属离子M(Ⅱ)与肌红蛋白活性中心的Fe(Ⅱ)发生了直接相互作用,外加金属离子将铁离子从肌红蛋白中“拖拽”出来,形成部分空位肌红蛋白衍生物。同时研究了外界条件,如离子浓度对这种相互作用的影响,发现随着外加金属离子量的增加这种相互作用逐渐增强,其作用强度依次为Co(Ⅱ)＞Zn(Ⅱ)＞Cu(Ⅱ)。 研究证实了肌红蛋白的血红素铁与金属离子之间存在直接相互作用,并且离子浓度对这种相互作用有影响。     

Conversion Electron Moessbauer Spectroscopie Studies on Ion Implanted Iron Layers

Conversion electron Moessbauer spectroscopy (CEMS) is a method very suitable for the study of ion implanted iron. It is demonstrated on nitrogen and phosphorus implanted iron layers. Using this technique not the 14.4-keV-gamma-rays as in the case of the conventional Moessbauer transmission experiments but the conversion and Auger electrons are detected. These electrons have a maximum energy of 7.3 keV. The Moessbauer signal can be obtained from a surface layer of about 300 nm. But the main fraction of the signal, namely 65%, comes from the first 50 nm. This range is just interesting for ion implantation. Depending on the test conditions different iron nitrides are formed by the nitrogen implantation and the phosphorus implantation can result in both amorphization and compound formation in the implanted layer.     

The effect of protein internal cavities on ligand migration and binding in myoglobin

Using Fourier Transform Infrared Spectroscopy at cryogenic temperatures, we have studied carbon monoxide (CO) migration in the interior of sperm whale myoglobin and binding to teh heme iron. The effect of protein internal cavities was examined by comparing the wild-type protein with mutants in which the cavities were blocked by bulky amino acid sidechains. After photodissociation at 3 K, CO ligands reside in the primary docking site (B) from where they can migrate to other sites (C, D) that were identified as the Xe4 and Xe1 cavities. These studies were complemented by flash photolysis experiments at room temperature, which revealed that the protein cavities enable efficient excape of ligands from the protein after dissociation from the heme iron.     

Influence of Zinc Ions on the Geminal and Bimolecular Stages of the Horse-Myoglobin Oxygenation

The kinetics of nanosecond geminal recombination and bimolar association of molecular oxygen with the horse-heart myoglobin has been investigated by laser flash photolysis. The influence of Zn(II) ions on the dioxygenation and rebonding of myoglobin to a ligand has been considered. The kinetics of the geminal recombination was analyzed within the framework of the model of four states with a side path of ligand motion in the protein matrix. It is shown that an increase in the affinity of myoglobin to O₂ in the presence of Zn(II) ions is predominantly caused by an increase in the rate constant of recombination of molecular oxygen from the primary intraprotein site. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 72, No. 5, pp. 670–677, September–October, 2005.     

光谱法结合分子动力学模拟研究臭氧对肌红蛋白结构的作用机制

臭氧(O₃)是一种具有强氧化性作用的杀菌消毒剂,因其安全无害等特点已被广泛用于肉制品生产加工的减菌处理,但O₃减菌处理对红肉色泽具有较强的负面作用,且其作用机制尚缺乏研究。针对肌红蛋白（Mb）存在状态是决定红色肉色泽关键因素的基础,通过紫外-可见吸收光谱法、荧光光谱法和圆二色光谱法（CD）研究O₃作用下Mb的光谱特性变化,结合蛋白质氧化特征指标分析和分子动力学模拟技术探究O₃对Mb分子的作用效果与机制。光谱研究结果表明,O₃处理可使Mb的紫外-可见光谱图在412 nm左右处的铁卟啉环特征峰及540和580 nm附近的氧合肌红蛋白（OMb）特征峰的强度减弱,其中铁卟啉环特征峰发生蓝移;利用固定激发波长280 nm下测定Mb内源性荧光和同步荧光光谱表明O₃会降低Mb的荧光强度,增大铁卟啉基团贡献的荧光峰强度和造成酪氨酸残基荧光光谱特征峰的蓝移;O₃作用使Mb三维荧光光谱特征峰强度的下降及光散射强度的增加。以上变化推断出O₃会促进Mb的氧化,造成其氨基酸残基疏水基团裸露,使Mb所处微环境及其蛋白构象改变;CD分析表明O₃与肌红蛋白接触时间越久,蛋白质二级结构变化越明显,造成α-螺旋的含量下降,无规则卷曲增加。辅以检测不同强度O₃处理Mb的含量及性质的变化,可知O₃处理使OMb含量下降,高铁肌红蛋白（MMb）含量增加,同时O₃处理Mb的羰基含量增加和巯基含量下降,这也进一步证实O₃作用促进了Mb的氧化,此外,O₃处理Mb表面疏水性的增强,说明O₃造成Mb体系微环境的极性变化。分子动力学模拟结果显示O₃会提高Mb肽链的RMSD值,影响Mb肽链的稳定性,减弱铁卟啉环与Mb肽链的相互作用;RMSF结果表明Mb活性口袋附近氨基酸残基的变化较大;蛋白质二级结构分析与光谱学试验研究结果一致,Mb的α-螺旋的含量下降,无规则卷曲增加。总而言之,O₃可作用于Mb的氨基酸残基,导致蛋白质二级结构和疏水性改变,并发生蛋白氧化及铁卟啉环暴露,进而引起红色肉色泽发生改变。该研究可为生鲜红肉护色技术制定等提供一定理论依据。     

Principal components of the protein dynamical transition

Proteins exhibit a solvent-driven dynamical transition at 180-220 K, manifested by nonlinearity in the temperature dependence of the average mean-square displacement. Here, molecular dynamics simulations of hydrated myoglobin show that the onset of the transition at approximately 180 K is characterized by the appearance of a single double-well principal component mode involving a global motion of two groups of helices. As the temperature is raised a few more quasiharmonic and multiminimum components successively appear. The results indicate an underlying simplicity in the protein dynamical transition.     

Stiffness,resilience, compressibility

The flexibility of a protein is an important component of its functionality. We use nuclear resonance vibrational spectroscopy (NRVS) to quantify the flexibility of the heme iron environment in the electron-carrying protein cytochrome c by measuring the stiffness and the resilience. These quantities are sensitive to structural differences between the active sites of different proteins, as illustrated by a comparative analysis with myoglobin. The elasticity of the entire protein, on the other hand, can be probed quantitatively from NRVS and high energy-resolution inelastic X-ray scattering (IXS) measurements, an approach that we used to extract the bulk modulus of cytochrome c.     

Conformational changes in hemoglobin triggered by changing the iron charge

In this work the hemoglobin conformational changes induced by changing the iron charge have been studied and compared with Myoglobin. Mössbauer spectroscopy was used to follow the change of the iron conformation. In order to compare the conformational relaxation of hemoglobin and myoglobin, and to study a possible influence of the quaternary structure, an intermediate metastable state of hemoglobin has been created by low temperature X-ray irradiation of methemoglobin. The irradiation reduces the Fe(III) of the heme groups to Fe(II) Low Spin, where the water is still bound on the sixth coordination. Heating cycles performed at temperatures from 140 K to 200 K allow the molecules to overcome an activation energy barrier and to relax into a stable conformation such as deoxy-hemoglobin or carboxy-hemoglobin, if CO is present. Slightly different structures (conformational substates) reveal themselves as a distribution of energy barriers (ΔG^#). The distribution of the activation energy, for the decay of the Fe(II) Low Spin intermediate, has been fitted with a Gaussian. For comparison, published myoglobin data were re-analysed in the same way. The average energy value at characteristic temperature is very similar in case of myoglobin and hemoglobin. The larger Gaussian energy distribution for myoglobin with respect to hemoglobin shows that more conformational substates are available. This may be caused by a larger area exposed to water. In hemoglobin, part of the surface of the chains is not water accessible due to the quaternary structure.     

Cryoradiolytic reduction of crystalline heme proteins: analysis by UV‐Vis spectroscopy and X‐ray crystallography

The X‐ray crystallographic analysis of redox‐active systems may be complicated by photoreduction. Although radiolytic reduction by the probing X‐ray beam may be exploited to generate otherwise short‐lived reaction intermediates of metalloproteins, it is generally an undesired feature. Here, the X‐ray‐induced reduction of the three heme proteins myoglobin, cytochrome P450cam and chloroperoxidase has been followed by on‐line UV‐Vis absorption spectroscopy. All three systems showed a very rapid reduction of the heme iron. In chloroperoxidase the change of the ionization state from ferric to ferrous heme is associated with a movement of the heme‐coordinating water molecule. The influence of the energy of the incident X‐ray photons and of the presence of scavengers on the apparent reduction rate of ferric myoglobin crystals was analyzed.     

荧光光谱法研究咖啡因与肌红蛋白的相互作用

采用荧光光谱法在生理pH 7.4条件下研究了药物咖啡因与肌红蛋白分子间的相互作用,表明这种相互作用能使肌红蛋白的内源荧光猝灭。通过猝灭常数,结合常数和结合位点数的计算,证明此猝灭为静态猝灭机制。咖啡因和肌红蛋白形成1∶1稳定配合物,形成常数(18 ℃)K_A=1.82×104 L·mol-1;根据热力学参数确定了它们之间的主要作用力为疏水力和静电力。利用同步荧光光谱法研究了咖啡因对肌红蛋白构象的影响。咖啡因能使肌红蛋白的构象发生改变,导致蛋白质分子中色氨酸和酪氨酸残基所处微环境由原来的疏水环境不同程度地向亲水环境转变。     

Mössbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Mössbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Mössbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.     

Optical manipulation of proteins in aqueous solution

Optical trapping of lysozyme, cytochrome c, or myoglobin based on photon pressure generated by focusing 1064 nm laser beam in an aqueous solution was explored. For all the proteins, microparticle formation was observed at the focal point under an optical microscope. Furthermore, the microparticles were identified to the molecular assemblies of the corresponding protein by means of confocal Raman microspectroscopy. For lysozyme, molecular clusters in solution were optically trapped to form the microparticle and it took more than 1 h to produce the microparticle. By contrast, molecular assembling proceeded within 1 min for cytochrome c and myoglobin. Since heme in cytochrome c or myoglobin would have a high polarizability, that would contribute to rapid assembling of the protein. Thus we demonstrated that a focused laser beam was a powerful tool to manipulate protein molecules in solution.     

Spin fluctuation rates in myoglobin azide: Comparison of Mössbauer and EPR results

We have analyzed the Mössbauer spectra of low-spin ferric myoglobin azide, taken in small applied field from 30 K to 200 K, in terms of a dynamic lineshape model [1]. Our results show fluctuation rates having a temperature dependence which is different from that measured using EPR forT<10 K [2–4] and shed new light on the vibrational modes coupling to the spinS=1/2 of the heme iron.     

Angular dependent rayleigh scattering of Mössbauer radiation on proteins

RSMR experiments with⁵⁷Fe radiation were performed on myoglobin. An areasensitive detector was employed for simultaneous angular dependent collection of the scattered quanta up to a maximum angle 2θ of 17‡. Experimental data of polycrystalline and lyophilized myoglobin are compared with computer calculations of the scattering which are based on the atomic coordinates determined by X-ray structure analysis. Special attention has been paid to the influence of coherence effects from collectively moving parts of the protein. A simple model is introduced in order to take into account these segmental motions. Our first results indicate that the sizes of collectively moving segments are comparable with spheres of about 6 å in diameter in dry myoglobin. In myoglobin crystals, where the molecules are surrounded by large hydration shells, the movements appear to be correlated in segments with sizes comparable to helices.

     

Protein dynamics studied on myoglobin

Two methods of inelastic scattering of synchrotron radiation were used to measure the dynamics of myoglobin in the temperature range from T = 60 K to 300 K. The inelastic Rayleigh scattering of metmyoglobin was analyzed by delayed elastic nuclear forward scattering of an iron foil. This yields averaged information on all phonons within the sample. The mean square displacement of the atoms due to this dynamics is 〈x〉 ²/T = 2.1 · 10^—4 Ų K^—1 on average. Complementary information was obtained by phonon assisted nuclear scattering on deoxymyoglobin. This method selects the phonons coupling to the iron atom in the active center of the protein. The mean square displacement of the iron was measured to be 〈x〉 ²/T = 0.6· 10^—4 Ų K^—1. The results are in agreement with Mössbauer absorption experiments in the low temperature range. Above 200 K the results allow one to distinguish between harmonic and quasidiffusive dynamics within the protein. A comparison with Raman spectroscopy is made.

     

Application of X-ray radiography to study the segregation process of iron from silicate under high pressure and high temperature

X-ray radiography was applied to observe the segregation process of iron from silicate at high pressure and high temperature in mixtures containing light elements. As the temperature of the hydrogen-containing sample increases, the molten iron becomes coherent. Small droplets of iron sink to the bottom of the chamber, where they merge into a single, large droplet. The small iron droplets exhibit complex motion, moving in random directions. Markedly different behavior is found in the sulfur-containing sample, where no clear motion of the molten iron is observed. Instead, as the sample temperature is increased, the concentration of iron near the wall of the sample chamber gradually increases. These observations demonstrate that the behavior of molten iron changes according to the dissolved elements. This X-ray radiography experiment represents a powerful technique to study the segregation process of molten iron from solid or partially molten silicate, particularly when combined with high-resolution tomography techniques.     

Molecular Dynamics Simulation of Myoglobin Collision with Low Energy Ions

Collisions of a low energy heavy ion with a myoglobin in water are simulated by molecular dynamics model. The increase of total energy is very small. The mean squared fluctuation decreases at 300 K and increases at 250K. This is an important novel cooling effect that protects the protein from ion damage. The possible collision side effect is the change of tertiary structure that blocks the normal functions of the myoglobin.     

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.