固氮酶金属原子簇对其结构和功能的影响

一、 △nifZ MoFe蛋白的纯化、特性及晶体生长 从缺失nifZ的棕色因氮菌突变种DJ194中，经离子交换层析和凝胶过滤提纯得到△nifZ MoFe蛋白，其纯度可达SDS凝胶电泳纯。它的Fe、Mo含量分别为野生型OP MoFe蛋白的56.6%和75.0%左右;C_2H_2、H~+还原活性和△H_2均只有OP MoFe蛋白的14.6%、21.7%和21.7%;其可见吸收光谱、CD及AR谱都与OP MoFe蛋白有较大差异，其中，可以反应P-cluster氧还状态和含量的ε_(450nm)、ε_(700nm)及△ε_(450nm)均要比OP MoFe蛋白低;由紫外CD谱反映的△nifZ MoFe蛋白的构象也与OP MoFe蛋白有所不同。由此我们推测，nifZ可能与固氮酶MoFe蛋白中P-cluster的合成或组装有关。为进一步阐明△nifZ MoFe蛋白的结构和功能特性，我们对△nifZ MoFe蛋白的晶体生长进行了研究，通过对沉淀剂浓度、缓冲体系和pH、蛋白浓度以及温度等条件的不断优化组合，目前我们已获得棕色短斜四棱柱形△nifZ MoFe蛋白的最大晶体为0.15 * 0.09mm。 二、 MoFe(C,O)与含Mo、Mn和Cr重组液重组的比较研究 MoFe(R)经O_2和o-phen共同处理后，成为部分缺失FeMoco和P-cluster的不全蛋白(MoFe(C,O))，其C_2H_2还原活性降至MoFe(R)的40%左右，将其分别与含Mo、Cr和Mn的重组液进行保温重组，其C_2H_2还原活性及光谱学特征都得到明显恢复。通过对不同重组液及与MoFe(C,O)形成的重组蛋白的比较，我们认为：1)MoFe(R)中的Fe和Mo原子可能是逐步被鳌合除去的，且不同蛋白中的Fe和Mo原子的缺失程度不同，因而MoFe(C,O)会以多种状态存在;2)在重组液配制过程中，发生的一系列颜色变化及沉淀反应与其是否具有重组激活能力具有相关性，重组液中可能已合成一些简单的含M(M=Mo或Cr或Mn或V)的铁硫化物，但不可能形成完整的金属原子簇;3)含M(M=Mo或Cr或Mn)的重组液均能使MoFe(C,O)中遭到破坏的FeMoco和P-cluster及其连接部分得以重新组装和修复，进而恢复其底物还原活性和光谱学特征。 三、 含锰固氮酶的初步探索 棕色固氮菌突变种UW_3(nifH~-)不能在含钼的培养中固氮生长，但能在含MnSO_4的无氮培养基中固氮生长。用含MnSO_4的无钼无氮培养基培养该突变种从中纯化得到的固氮酶组分1蛋白，其C_2H_2及H~+还原活性约相当于MoFe(R)的20%左右，Mn元素含量测定表明，其中已经含有Mn元素，Fe/Mn比值比OP MoFe蛋白中的Fe/Mo低。这些结果表明：UW_3突变种在该种条件下可能已表达了不同于已发现的三种固氮酶的新的固氮酶组分1蛋白，并且其中含有Mn元素。

An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Feasibility of Protein a for the Oriented Immobilization of Immunoglobulin on Silicon Surface for a Biosensor with Imaging Ellipsometry

The feasibility of using protein A to immobilize antibody on silicon surface for a biosensor with imaging ellipsometry was presented in this study. The amount of human IgG bound with anti-IgG immobilized by the protein A on silicon surface was much more than that bound with anti-IgG immobilized by physical adsorption. The result indicated that the protein A could be used to immobilize antibody molecules in a highly oriented manner and maintain antibody molecular functional configuration on the silicon surface. High reproducibility of the amount of antibody immobilization and homogenous antibody adsorption layer on surfaces could be obtained by this immobilization method. Imaging ellipsometry has been proven to be a fast and reliable detection method and sensitive enough to detect small changes in a molecular monolayer level. The combination of imaging ellipsometry and surface modification with protein A has the potential to be further developed into an efficient immunoassay protein chip.

Application of Optical Protein-chip in Detecting Phage M13KO7

Abstract: Avidin layer was bound on the substrate surface of Silicon wafer modified with aldehyde. The interaction between avidin and biotin was adopted for the immobilization of mouse monoclonal biotin-anti-M13 (antibody GP3)-labeled biotin. The surface was incubated in a solution containing phage M13KO7, which was trapped by the antibody GP3 with the interaction between phage M13KO7 and antibody GP3, resulting in a variation of layer thickness that was detected by imaging ellipsometry. The results showed a saturated layer of antibody GP3 with a thickness about 6.9 nm on the surface of the silicon wafer. The specific interaction between phage M13KO7 and antibody GP3 resulted in a variation of layer thickness. The layer of phage M13KO7 bound with antibody GP3 was 17.5 nm in the concentration of 1.1×1010 pfu/mL. Each variation of the layer thickness corresponded to a concentration of phage M13KO7 in the range of 0.1×1010–2.5×1010 pfu/mL, with the sensitivity of 109 pfu/mL. Compared with other methods, the optical protein-chip, requiring only short measurement time, label free, is a quantitative test, and can be visualized. This study could be significant on the interactions between the antibody and the virus, showing potential in the early diagnosis of virosis.

Competitive protein adsorption studied with atomic force microscopy and imaging ellipsometry

The adsorption and competitive adsorption of collagen and bovine serum albumin (BSA) were directly visualized and quantified using atomic force microscopy (AFM) and imaging ellipsometry. Chemically modified silicon surfaces were used as hydrophilic and hydrophobic substrates. The results showed that collagen and BSA in single component solution adsorbed onto a hydrophobic surface two times more than that onto a hydrophilic surface. The competitive adsorption between collagen and BSA showed that serum albumin preferentially adsorbed onto a hydrophobic surface, while collagen on a hydrophilic surface. In the binary solution of BSA (1 mg/ml BSA) and collagen (0.1 mg/ml), nearly 100% of the protein adsorbed onto the hydrophobic surface was BSA, but on the hydrophilic surface only about 6% was BSA. Surface affinity was the main factor controlling the competitive adsorption.

A Label-Free Protein Microfluidic Array for Parallel Immunoassays

A label-free protein microfluidic array for immunoassays based on the combination of imaging ellipsometry and an integrated microfluidic system is presented. Proteins can be patterned homogeneously on substrate in array format by the microfluidic system simultaneously. After preparation, the protein array can be packed in the microfluidic system which is full of buffer so that proteins are not exposed to denaturing conditions. With simple microfluidic channel junction, the protein microfluidic array can be used in serial or parallel format to analyze single or multiple samples simultaneously. Imaging ellipsometry is used for the protein array reading with a label-free format. The biological and medical applications of the label-free protein microfluidic array are demonstrated by screening for antibody–antigen interactions, measuring the concentration of the protein solution and detecting five markers of hepatitis B.

Micro-systems for Optical Protein-Chip

Protein-Chip as micro-assays for the determination of protein interaction, the analysis, the identification and the purification of proteins has large potential applications. The Optical Protein-Chip is able to detect the multi-interaction of proteins and multi-bio-activities of molecules directly and simultaneously with no labeling. The chip is a small matrix on solid substrate containing multi-micro-area prepared by microfabrication with photolithography or soft lithography for surface patterning, and processed with surface modification which includes the physical, chemical, and bio-chemical modifications, etc. The ligand immobilization, such as protein immobilization, especially the oriented immobilization with low steric hindrance and high bio-specific binding activity between ligand and receptor is used to form a sensing surface. Each area of the pattern is corresponding to only one bioactivity. The interval between the areas is non-bioactive and optically extinctive. The affinity between proteins is used to realize non-labeling microassays for the determination of protein identification and protein interaction. The sampling of the chip is non-disturbing, performed with imaging ellipsometry and image processing on a database of proteins.

Observation Of Diffusion Process Of A Water Droplet Immersed In Protein Solution In Microgravity

Pure liquid - liquid diffusion driven by concentration gradients is hard to study in a normal gravity environment since convection and sedimentation also contribute to the mass transfer process. We employ a Mach - Zehnder interferometer to monitor the mass transfer process of a water droplet in EAFP protein solution under microgravity condition provided by the Satellite Shi Jian No 8. A series of the evolution charts of mass distribution during the diffusion process of the liquid droplet are presented and the relevant diffusion coefficient is determined.

The Fluid Phenomena In the Crystallization Of the Protein Crystal

This paper reports that an optical diagnostic system consisting of Mach-Zehnder interferometer with a phase shift device and image processor has been used for study of the kinetics of protein crystal growing process. The crystallization process of protein crystal by vapour diffusion is investigated. The interference fringes are observed in real time. The present experiment demonstrates that the diffusion and the sedimentation influence the crystallization of protein crystal which grows in solution, and the concentration capillary convection associated with surface tension occurs at the vicinity of free surface of the protein mother liquor, and directly affects on the outcome of protein crystallization. So far the detailed analysis and the important role of the fluid phenomena in protein crystallization have been discussed a little in both space- and ground-based crystal growth experiments. It is also found that these fluid phenomena affect the outcome of protein crystallization, regular growth, and crystal quality. This may explain the fact that many results of space-based investigation do not show overall improvement.

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Investigation of Interactions between Two Monoclonal Antibodies and SARS Virus with a Label-Free Protein Array

The investigation of interactions between two kinds of monoclonal antibodies and SARS virus with a label-free protein array technique were presented in this paper. The performance consists of three parts: a surface modification for ligand immobilization/surface, a protein array fabrication with an integrated microfluidic system for patterning, packaging and liquid handling, and a protein array reader of imaging ellipsometer. This revealed the technique could be used as an immunoassay for qualitative and quantitative detection as wen as kinetic analysis of biomolecule interaction.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Outline and computational approaches of protein misfolding.

Protein misfolding is a general causation of classical conformational diseases and many pathogenic changes that are the result of structural conversion. Here I review recent progress in clinical and computational approaches for each stage of the misfolding process, aiming to present readers an outline for swift comprehension of this field.