Glu101对保持中心蛋白正常构象作用的研究——光谱法研究稀土离子与八肋游仆虫中心蛋白作用对蛋白构象的影响

通过位点直接突变法将八肋游仆虫中心蛋白101位保守的Glu突变成Lys,得到突变蛋白E101K.利用疏水性探针TN S研究了突变对Tb^3＋与蛋白作用时蛋白构象变化的影响.结果表明,相对于钙饱和的蛋白,铽的饱和对蛋白构象变化的影响更大.同时,共振光散射研究表明,Glu101对保持蛋白适当的构象变化行为起着至关重要的作用.     

The molten globule protein conformation probed by disulphide bonds

The molten globule is a compact protein conformation that has a secondary structure content like that of the native protein, but poorly defined tertiary structure. It is a stable state for a few proteins under particular conditions and could be a ubiquitous kinetic intermediate in protein folding. The extent to which native interactions, above the level of the secondary structure, are preserved in this conformation is not so far known. Here we report that alpha-lactalbumin can adopt a molten globule conformation when one of its four disulphide bonds is reduced. In this state, the three other disulphide bonds rearrange spontaneously, at the same rate as when the protein is fully unfolded, to a number of different disulphide bond isomers that tend to maintain the molten globule conformation. That the molten globule state is compatible with a variety of disulphide bond pairings suggests that it is unlikely to be stabilized by many specific tertiary interactions.     

Structure of an ABC transporter in complex with its binding protein

ATP-binding cassette (ABC) transporter proteins carry diverse substrates across cell membranes. Whereas clinically relevant ABC exporters are implicated in various diseases or cause multidrug resistance of cancer cells, bacterial ABC importers are essential for the uptake of nutrients, including rare elements such as molybdenum. A detailed understanding of their mechanisms requires direct visualization at high resolution and in distinct conformations. Our recent structure of the multidrug ABC exporter Sav1866 has revealed an outward-facing conformation of the transmembrane domains coupled to a closed conformation of the nucleotide-binding domains, reflecting the ATP-bound state. Here we present the 3.1 A crystal structure of a putative molybdate transporter (ModB2C2) from Archaeoglobus fulgidus in complex with its binding protein (ModA). Twelve transmembrane helices of the ModB subunits provide an inward-facing conformation, with a closed gate near the external membrane boundary. The ATP-hydrolysing ModC subunits reveal a nucleotide-free, open conformation, whereas the attached binding protein aligns the substrate-binding cleft with the entrance to the presumed translocation pathway. Structural comparison of ModB2C2A with Sav1866 suggests a common alternating access and release mechanism, with binding of ATP promoting an outward-facing conformation and dissociation of the hydrolysis products promoting an inward-facing conformation.     

Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics

Folding simulations are often time-consuming or highly sensitive to the initial conformation of the simulation even for mini protein like the Trp-cage. Here, we present a multiscale molecular dynamics method which appears to be both efficient and insensitive to the starting conformation based on the testing results from the Trp-cage protein. In this method the simulated system is simultaneously mod- eled on atoms and coarse-grained particles with incremental coarsening levels. The dynamics of coarse-grained particles are adapted to the recent trajectories of finer-grained particles instead of fixed and parameterized energy functions as used in previous coarse-grained models. In addition, the compositions of coarse-grained particles are allowed to be updated automatically based on the coherence during its history. Starting from the fully extended conformation and other several different conformations of the Trp-cage protein, our method successfully finds out the native-like conformations of the Trp-cage protein in the largest cluster of the trajectories in all of the eight performed simulations within at most 10 ns simulation time. The results show that approaches based on multiscale modeling are promising for ab initio protein structure prediction.     

A bacterial calcium-binding protein homologous to calmodulin

Many of the effects of calcium ions in eukaryotic cells are mediated by calcium-binding regulatory proteins such as calmodulin, in which each calcium-binding site has a distinctive helix-loop-helix conformation termed the EF hand. Protein S from the spore coat of the Gram-negative bacterium Myxococcus xanthus has been shown to resemble calmodulin in its internally-duplicated structure and ability to bind calcium. However, it has a beta-sheet secondary structure rather than the helix-loop-helix arrangement of the eukaryotic proteins. We have determined the complete amino-acid sequence of a calcium-binding protein from the Gram-positive bacterium "Streptomyces erythraeus" by cloning and sequencing the corresponding gene. It contains four EF-hand motifs bearing remarkable sequence similarity to the calcium-binding sites in calmodulin. This implies that the EF-hand super-family may have evolved from ancient proteins present in prokaryotes.     

Rational screenning in combinatorial peptide libraries of protein functional loop

Redesigning the sequences of protein loops is a frequent practice in protein design. Based on the new results of protein loop database analysis, a rational computer simulation strategy is proposed to obtain functional proteins, which exploits a fast and accurate program to calculate the protein loop conformation, and at the same time, combines molecular docking method with combinatorial chemistry strategy to screen the combinatorial peptide library of protein loops. A characteristic of this method is that it separates the conformation computation of backbone from that of side chain and incorporates side chain growth into the docking procedure and therefore greatly reduces the computation by converting the huge computation on explosive conformations to relatively small computation on limited canonical backbone structures and side chain growth. This method can be practically used in screening combinatorial peptide libraries of protein loops.     

蛋白质分子中多紧密接触对的几率特征

利用无规飞行高斯模型，研究四个分离的紧密接触对的分子链构象，推导了四紧密接触对的12种不同拓扑构象的几率分布理论表达式，计算了相应的几率分布的相关函数。这为理论上研究生物高分子结构特征和动力特征提供一种非常有效的方法。     

结构几何构造分析规律的灵活应用

分析了“三角”规律与结构几何构造分析四大规律的相互转化关系,以实例说明了“三角”规律在实际工程计算简图中的分析应用。     

分子伴侣及其作用机理的研究概况

分子伴侣为一类与其他蛋白不稳定构象结合并使之稳定的蛋白质,广泛分布于各种生物体内。本文对分子伴侣的最新研究作一综述。     

Transfer of a beta-turn structure to a new protein context

Four-residue beta-turns and larger loop structures represent a significant fraction of globular protein surfaces and play an important role in determining the conformation and specificity of enzyme active sites and antibody-combining sites. Turns are an attractive starting point to develop protein design methods, as they involve a small number of consecutive residues, adopt a limited number of defined conformations and are minimally constrained by packing interactions with the remainder of the protein. The ability to substitute one beta-turn geometry for another will extend protein engineering beyond the redecoration of fixed backbone conformations to include local restructuring and the repositioning of surface side chains. To determine the feasibility and to examine the effect of such a structural modification on the fold and thermodynamic stability of a globular protein, we have substituted a five-residue turn sequence from concanavalin A for a type I' beta-turn in staphylococcal nuclease. The resulting hybrid protein is folded and has full nuclease enzymatic activity but reduced thermodynamic stability. The crystal structure of the hybrid protein reveals that the guest turn sequence retains the conformation of the parent concanavalin A structure when substituted in the nuclease host.     

钙离子对S100A1蛋白聚合形式的影响

S100A1是钙结合蛋白家族S100亚家族中一个小分子量的酸性蛋白．研究S100A1蛋白分子在溶液中的构象均一性随不同钙高于浓度的变化规律，发现钙离子浓度的提高促使S100A1蛋白的寡聚化，稳定蛋白质分子的构象。     

Prediction of protein structure from amino acid sequence.

In principle, it is possible to predict theoretically the three-dimensional structure of a protein from its amino acid sequence. Recently substantial progress towards this goal has been made by the use of simple models to represent protein conformation and interatomic interactions, together with the knowledge gained form analyses of know protein structures.     

Crystal structure of a catalytic intermediate of the maltose transporter

The maltose uptake system of Escherichia coli is a well-characterized member of the ATP-binding cassette transporter superfamily. Here we present the 2.8-A crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP. This structure, stabilized by a mutation that prevents ATP hydrolysis, captures the ATP-binding cassette dimer in a closed, ATP-bound conformation. Maltose is occluded within a solvent-filled cavity at the interface of the two transmembrane subunits, about halfway into the lipid bilayer. The binding protein docks onto the entrance of the cavity in an open conformation and serves as a cap to ensure unidirectional translocation of the sugar molecule. These results provide direct evidence for a concerted mechanism of transport in which solute is transferred from the binding protein to the transmembrane subunits when the cassette dimer closes to hydrolyse ATP.     

Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB

Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation. Here we report the 3.2-A-resolution structure of the tRNA-like domain of tmRNA (tmRNA(Delta)) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNA(Delta) is a 90 degrees rotation of the TPsiC-arm around the helical axis. Owing to this unusual conformation, the SmpB-tmRNA(Delta) complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.     

Respective roles of short-and long-range interactions in protein folding

A new method was presented to discuss the respective roles of short- and long-range interactions in protein folding. It‘s based on an off-lattice model, which is also being called as toy model. Simulated annealing algorithm was used to search its native conformation. When it is applied to analysis proteins lagt and laho, we find that helical segment catmot fold into native conformation without the influence of long-range interactions. That‘s to say that long-range interactions are the main determinants in protein folding.     

遗传算法在蛋白质结构预测中的应用

蛋白质结构预测在生物信息学研究中占有重要地位,此文对遗传算法（GAs)在蛋白质结构预测中的应用作一评述,首先,简要地介绍了遗传算法和一般的蛋白质构象搜索问题,然后对近年来用遗传算法解决蛋白质结构预测的研究作了回顾,并分析了算法的效果和特点,最后,展望了用遗传算法解决蛋白质结构预测问题的前景。     

大阪鲫鱼两种卵黄蛋白紫外吸收特性的研究

采用大柱制备电泳的办法从大阪鲫鱼卵巢中提纯出两种蛋白质:卵黄脂磷蛋白和类似于卵黄高磷蛋白的卵黄蛋白L。分析了两种蛋白的氨基酸组成,并对两种蛋白的紫外吸收和紫外吸收四阶导数谱特性进行了分析研究。发现卵黄脂磷蛋白在溶液的pH改变(pH3.12-8.12-11.00)时。紫外吸收谱和四阶导数谱未发生明显变化,而卵黄蛋白L在溶液的pH改变(pH7,66-9,35-11,89)时,其紫外吸收谱最大吸收波长红移,紫外吸收四阶导数谱出现新的未知峰,发生显著变化。这表明卵黄脂磷蛋白所含的大量脂类存在于蛋白质分子的表面,从而影响了蛋白质分子中产生紫外吸收的氨基酸—酪氮酸、色氨酸、苯丙氨酸的紫外吸收。在卵黄蛋白L中,这几种氨基酸则位于蛋白质分子的表面,从而对溶液pH的变化尤为敏感。     

蛋白质力学及其力-化关系研究

基于分子生物力学方法详细介绍了蛋白质结构功能域的力学理论分析。首先,从力学、物理学和医学角度阐述了蛋白质中铰运动、蛋白质功能域的铺展变形和受体-配体的接合,最后详细讨论了蛋白质在机械力作用下发生的运动和变形与生物学及生物化学之间相耦合的基本原理,旨在探索力学和生物化学之间的联系及其生理学意义。     

TCP1 complex is a molecular chaperone in tubulin biogenesis.

A role in folding of newly translated proteins in the cytosol of eukaryotes has been proposed for t-complex polypeptide-1 (TCP1), although its molecular targets have not yet been identified. Tubulin is a major cytosolic protein whose assembly into microtubules is critical to many cellular processes. Although numerous studies have focused on the expression of tubulin, little is known about the processes whereby newly translated tubulin subunits acquire conformations that enable them to form alpha-beta-heterodimers. We examined the biogenesis of alpha- and beta-tubulin in rabbit reticulocyte lysate, and report here that newly translated tubulin subunits entered a 900K complex in a protease-sensitive conformation. Addition of Mg-ATP, but not nonhydrolysable analogues, released the tubulin subunits as assembly-competent protein with a conformation that was relatively protease-resistant. The 900K complex purified from reticulocyte lysate contained as its major constituent a 58K protein that cross-reacted with a monoclonal antiserum against mouse TCP1. We conclude that TCP1 functions as a cytosolic chaperone in the biogenesis of tubulin.     

蛋白质的挤压组织化改性─—大豆蛋白在挤压过程中的物理、化学变化

将挤压过程用于蛋白质改性，使大豆浓缩蛋白经挤压组织化处理后，成为一种具有一定组织特性的功能蛋白质。由缓冲液浸出试验、聚丙烯酰胺凝胶电泳分析，并结合傅立叶变换红外差谱测试结果可知：大豆浓缩蛋白在挤压组织化过程中，发生了二硫键交换反应，但并未形成异肽键，蛋白质的相对分子质量也无变化。维持组织蛋白结构的主要空间构象力是二硫键和疏水相互作用。