Probing Proteins in Solution by Xe NMR Spectroscopy

The interaction of xenon with different proteins in aqueous solution is investigated by ¹²⁹Xe NMR spectroscopy. Chemical shifts are measured in horse metmyoglobin, hen egg white lysozyme, and horse cytochrome c solutions as a function of xenon concentration. In these systems, xenon is in fast exchange between all possible environments. The results suggest that nonspecific interactions exist between xenon and the protein exteriors and the data are analyzed in term of parameters which characterize the protein surfaces. The experimental data for horse metmyoglobin are interpreted using a model in which xenon forms a 1:1 complex with the protein and the chemical shift of the complexed xenon is reported (Locci et al., Keystone Symposia “Frontiers of NMR in Molecular Biology VI”, Jan. 9–15, 1999, Breckenridge, CO, Abstract E216, p. 53; Locci et al., XeMAT 2000 “Optical Polarization and Xenon NMR of Materials”, June 28–30, 2000, Sestri Levante, Italy, p. 46).     

TOF-SIMS structural characterization of self-assembly monolayer of cytochrome b5 onto gold substrate

Orientation and three-dimensional structure of immobilized proteins on bio-devices are very important to assure their high performance. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is able to analyze upper surface of one layer of molecules. Orientation of immobilized proteins can be evaluated based on determination of a partial structure, representing ensemble of amino acids, on the surface part. In this study, a monolayer of cytochrome b5 was reconstituted onto gold substrate and investigated by surface plasmon resonance (SPR). After freeze-drying, the resulted protein self-assembly was evaluated using TOF-SIMS with the bismuth cluster ion source, and then TOF-SIMS spectra were analyzed to select peaks specific to cytochrome b5 and identify their chemical formula and ensembles of amino acids. The results from TOF-SIMS spectra analysis were compared to the amino acid sequence of the modified cytochrome b5 and three-dimensional structure of cytochrome b5 registered in the protein data bank. Finally, fragment-ion-generating parts of the immobilized-cytochrome b5 are determined based on the suggested residues and three-dimensional structure. These results suggest the actual structure and confirm the expected orientation of immobilized protein.     

蛋白质支链动力学快运动的核磁共振研究

蛋白质的功能不仅取决于其结构,而且受到其构像及其变化的影响. 许多生物化学过程就是由于蛋白质结构的一些动力学变化而完成,如蛋白质-蛋白质,蛋白质-药物配体之间的相互作用. 因此分析蛋白质的动力学变化,就能够对其参与的生化过程进行分析. 作为动力学研究的有力工具之一,核磁共振能够分辨到原子范围内的从千秒到皮秒时间范围的运动过程,因此在动力学研究中有着不可替代的作用. 本文仅就核磁共振在蛋白质支链快运动方法（ps-ns）研究方面的进展进行总结,以期阐明核磁共振的在支链动力学研究中的发展现状.     

Ultrasound exposure in the presence of hematoporphyrin induced loss of membrane integral proteins and inactivity of cell proliferation associated enzymes in sarcoma 180 cells in vitro

Ultrasonically induced effects of hematoporphyrin (HPD) on cell damage and membrane protein alteration of S180 isolated tumor cells in vitro were investigated, and the potential mechanisms of sonodynamic therapy (SDT) inhibiting tumor growth were discussed. Tumor cells suspended in air-saturated PBS (pH 7.2) were exposed to ultrasound at 1.8 MHz for up to 180 s in the presence and absence of HPD. The viability of cells was determined by a trypan blue exclusion test. To estimate the damage effects of SDT on plasma membrane of tumor cells primarily, membrane integral proteins (EGFR, Ras, Fas, FasL) and cell proliferation associated enzymes (adenylate cyclase and guanylate cyclase) were checked with immunochemical methods. The results indicated that the intensity threshold for ultrasonically induced cell damage at 1.8 MHz was 3 W/cm². At this condition, the expression of the integral proteins was obviously inhibited and the activity of the enzymes was decreased post ultrasound treatment in the presence of 20 μg/ml HPD. Loss of the membrane proteins and inactivity of AC and GC post SDT was time-dependent. This paper reveals SDT can cause the loss of tumor cell membrane integral proteins and inactivity of the enzymes associated with cell proliferation which might be attributed to a sonochemical activation mechanism. The mechanisms by that tumor growth is inhibited by SDT can be understood as that the growth signaling pathway is partially interdicted and the resistance of tumor cells to the specifically activated immune cells is weakened.     

Effect of unfolding on the thickness of the hydration layer of a protein

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the folding-unfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.      

Improvement of the relative entropy based protein folding method

The “relative entropy” has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm. Contributed equally to this work Supported by the National Natural Science Foundation of China (Grant No. 30670497), the Beijing Natural Science Foundation (Grant No. 5072002), and the Specialized Research Foundation for the Doctoral Program of Higher Education (Grant No. 200800050003)     

胆结石中蛋白质的傅里叶变换红外光谱和表面增强拉曼光谱研究

用氯仿、乙醚、乙醇和盐酸等溶剂溶解一组人体胆结石，获取难溶物；用傅里叶变换红外光谱和表面增强拉曼光谱对难溶剩余物进行研究。结果显示，结石难溶物主要由胆红素盐和蛋白质组成，结石中的蛋白质的二级结构以α螺旋和无规卷曲构象为主，其中α螺旋构象成分较多。讨论了蛋白质在胆结石形成中的作用。     

Geometrical analysis of cytochrome c unfolding

A geometrical model has been developed to study the unfolding of iso-1 cytochrome c. The model draws on the crystallographic data reported for this protein. These data were used to calculate the distance between specific residues in the folded state, and in a sequence of extended states defined by n?=?3, 5, 7, 9, 11, 13, and 15 residue units. Exact calculations carried out for each of the 103 residues in the polypeptide chain demonstrate that different regions of the chain have different unfolding histories. Regions where there is a persistence of compact structures can be identified, and this geometrical characterization is fully consistent with analyses of time-resolved fluorescence energy-transfer (TrFET) data using dansyl-derivatized cysteine side-chain probes at positions 39, 50, 66, 85, and 99. The calculations were carried out assuming that different regions of the polypeptide chain unfold synchronously. To test this assumption, lattice Monte Carlo simulations were performed to study systematically the possible importance of asynchronicity. Calculations show that small departures from synchronous dynamics can arise if displacements of residues in the main body of the chain are much more sluggish than near-terminal residues.     

基于NMR自旋弛豫技术的蛋白质动力学研究

蛋白质的三维结构在很多情况下不能很好地解释其在生理过程中的作用机制. 动力学研究能够获悉蛋白质在不同时间尺度下的内运动信息,建立起动态结构和生物功能的联系. 该文综述了通过NMR自旋弛豫技术研究蛋白质动力学的原理和方法：ps~ns的快运动分析主要采用约化谱密度函数映射和Modelfree方法;μs~ms的慢运动涉及化学/构象交换过程,常借助CPMG和R_1ρ弛豫色散手段. 基于NMR的蛋白质动力学研究,将蛋白质科学从三维空间结构推进到四维时空结构的新层面.     

光敏蛋白菌紫质分子及其在光电器件中的应用

紫膜菌紫质是一类新型的光敏蛋白分子,本文在介绍菌紫质分子结构和光致色变特性的基础上,重点讨论了它们在光探测器,全息材料,空间光调制器,光盘,条纹相机等光电器件中的潜在应用。