Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme

Measurements of changes in structure and stability caused by 13 different substitutions for threonine 157 in phage T4 lysozyme show that the most stable lysozyme variants contain hydrogen bonds analogous to those in the wild-type enzyme and that structural adjustments allow the protein to be surprisingly tolerant of amino-acid substitutions.     

A mutant T4 lysozyme displays five different crystal conformations

Phage T4 lysozyme consists of two domains between which is formed the active-site cleft of the enzyme. The crystallographically determined thermal displacement parameters for the protein suggested that the amino terminal of the two domains undergoes 'hinge-bending' motion about an axis passing through the waist of the molecule. Such conformational mobility may be important in allowing access of substrates to the active site of the enzyme. We report here a crystallographic study of a mutant T4 lysozyme which demonstrates further the conformational flexibility of the protein. A mutant form of the enzyme with a methionine residue (Met 6) replaced by isoleucine crystallizes with four independent molecules in the crystal lattice. These four molecules have distinctly different conformations. The mutant protein can also crystallize in standard form with a structure very similar to the wild-type protein. Thus the mutant protein can adopt five different crystal conformations. The isoleucine for methionine substitution at the intersection of the two domains of T4 lysozyme apparently enhances the hinge-bending motion presumed to occur in the wild-type protein, without significantly affecting the catalytic activity or thermal stability of the protein.     

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.     

Protein-disulphide isomerase and prolyl isomerase act differently and independently as catalysts of protein folding

Two enzymes are now known that catalyse slow steps in protein folding. Peptidyl-prolyl cis-trans isomerase catalyses the cis-trans isomerization of Xaa-Pro peptide bonds in oligopeptides and during the refolding of several proteins. The other enzyme, protein-disulphide isomerase, accelerates the reactivation of reduced proteins, presumably by catalysis of thiol-disulphide exchange reactions. Recent evidence indicates that the beta-subunit of prolyl 4-hydroxylase, an enzyme involved in collagen biosynthesis, is identical with disulphide isomerase. On the basis of this important finding, it was suggested that disulphide isomerase accelerates protein folding, not by 'reshuffling' incorrect disulphide bonds, but in the same way as prolyl isomerase by catalysing proline isomerization which is known to be important for the folding of collagen and other proteins. Here we show that the catalytic activities of these two enzymes are different. Disulphide isomerase accelerates the reformation of native disulphide bonds during protein reoxidation. We find no evidence that this enzyme can catalyse the isomerization of proline peptide bonds, a reaction efficiently accelerated by prolyl isomerase. When both enzymes are present simultaneously during protein folding, they act independently of one another.     

Glycoproteins form mixed disulphides with oxidoreductases during folding in living cells

The formation of intra- and interchain disulphide bonds constitutes an integral part of the maturation of most secretory and membrane-bound proteins in the endoplasmic reticulum. Evidence indicates that members of the protein disulphide isomerase (PDI) superfamily are part of the machinery needed for proper oxidation and isomerization of disulphide bonds. Models based on in vitro studies predict that the formation of mixed disulphide bonds between oxidoreductase and substrate is intermediate in the generation of the native intrachain disulphide bond in the substrate polypeptide. Whether this is how thiol oxidoreductases work inside the endoplasmic reticulum is not clear. Nor has it been established which of the many members of the PDI superfamily interacts directly with newly synthesized substrate proteins, because transient mixed disulphides have never been observed in the mammalian endoplasmic reticulum during oxidative protein folding. Here we describe the mechanisms involved in co- and post-translational protein oxidation in vivo. We show that the endoplasmic-reticulum-resident oxidoreductases PDI and ERp57 are directly involved in disulphide oxidation and isomerization, and, together with the lectins calnexin and calreticulin, are central in glycoprotein folding in the endoplasmic reticulum of mammalian cells.     

Defective co-translational formation of disulphide bonds in protein disulphide-isomerase-deficient microsomes

The formation of disulphide bonds in mammalian secretory and cell-surface proteins occurs in the lumen of the endoplasmic reticulum and is believed to be catalysed by the enzyme protein disulphide-isomerase (PDI). The evidence for this physiological role for PDI is circumstantial and relates to the cell and tissue distribution of the enzyme, its developmental behaviour and its catalytic properties in vitro. A clear requirement for PDI in the correct folding or assembly of disulphide-bonded proteins during biosynthesis has not been demonstrated. We have prepared dog pancreas microsomes which are deficient in soluble lumenal proteins, including PDI, but which are still able to translocate and process proteins synthesized in vitro. Using the formation of intramolecular disulphide bonds during the in vitro synthesis of gamma-gliadin, a wheat storage protein, as a model, we have demonstrated that these microsomes are defective in co-translational formation of disulphide bonds. Reconstitution of these microsomes with purified PDI reverses this defect.     

Role of ATP and disulphide bonds during protein folding in the endoplasmic reticulum.

Being topologically equivalent to the extracellular space, the lumen of the endoplasmic reticulum (ER) provides a unique folding environment for newly synthesized proteins. Unlike other compartments in the cell where folding occurs, the ER is oxidizing and therefore can promote the formation of disulphide bonds. The reducing agent dithiothreitol, when added to living cells, inhibits disulphide formation with profound effects on folding. Taking advantage of this effect, we demonstrate here that folding of influenza haemagglutinin is energy dependent. Metabolic energy is required to support the correct folding and disulphide bond formation in this well characterized viral glycoprotein, to rescue misfolded proteins from disulphide-linked aggregates, and to maintain the oxidized protein in its folded and oligomerization-competent state.     

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。     

Sequence of protein disulphide isomerase and implications of its relationship to thioredoxin

The formation of disulphide bonds is essential to the structure and function of proteins. These bonds rapidly form either cotranslationally or immediately post-translationally in the lumen of the endoplasmic reticulum. Native disulphide pairing for such proteins has been achieved in vitro; however, the rates of reassembly are slow and the conditions non-physiological. To account for these observations, Anfinsen et al. proposed that a 'disulphide interchange protein' was the in vivo catalyst of disulphide bond rearrangement. Other groups discovered an activity with similar characteristics that catalysed the reductive cleavage of insulin and may be associated with insulin degradation, although this result has been disputed. The enzyme involved, protein disulphide isomerase (PDI; EC 5.3.4.1), may be the in vivo catalyst of disulphide bond formation. Here we describe the sequence of cloned rat liver PDI complementary DNA which predicts a protein with two distinct regions homologous with Escherichia coli thioredoxin, a known cofactor in oxidation-reduction reactions. Each of these regions contains the presumed active site sequence Trp-Cys-Gly-His-Cys-Lys, suggesting that PDI, similar in action to thioredoxin, catalyses disulphide bond interchange via an internal disulphide-sulphydryl interchange. The cDNA predicts a signal peptide consistent with the view that PDI is a luminal endoplasmic reticulum protein. PDI messenger RNA, although ubiquitous, is more highly concentrated in secretory cells.     

氯化镁促进溶菌酶淀粉样聚集的分子机制研究

高浓度氯化镁能够在一定的条件下促进溶菌酶发生聚集,但其具体的作用机制尚不明确.采用分子生物学实验和分子动力学模拟相结合的方法研究了鸡溶菌酶在不同浓度的MgCl2溶液中的聚集特性和结构稳定性.分子生物学实验结果表明,200 mmol/L MgCl2能够显著促进鸡溶菌酶形成二聚体和三聚体,但效果没有NaCl显著.分子动力学模拟分析显示,200 mmol/L MgCl2能够引起螺旋3和螺旋4的显著偏移,同时能够减弱溶菌酶聚集关键区域（40-110位残基）内二硫键Cys76-Cys94的结合强度;另一方面,MgCl2也能减少疏水核心内部氢键的数量,促使疏水核心的稳定性显著降低,从而促进了溶菌酶分子间的相互作用.     

Demonstration by NMR of folding domains in lysozyme

Although there has been much speculation on the pathways of protein folding, only recently have experimental data on the topic been available. The study of proteins under conditions where species intermediate between the fully folded and unfolded states are stable has provided important information, for example about the disulphide intermediates in BPTI, cis/trans proline isomers of RNase A3 and the molten globule state of alpha-lactalbumin. An alternative approach to investigating folding pathways has involved detection and characterization of transient conformers in refolding studies using stopped-flow methods coupled with NMR measurements of hydrogen exchange. The formation of intermediate structures has been detected in the early stages of folding of cytochrome c, RNaseA and barnase. For alpha-lactalbumin, hydrogen exchange kinetics monitored by NMR proved to be crucial for identifying native-like structural features in the stable molten globule state. An analogous partially folded protein stable under equilibrium conditions has not been observed for the structurally homologous protein hen egg-white lysozyme, although there is evidence that a similar but transient state is formed during refolding. Here we describe NMR experiments based on competition between hydrogen exchange and the refolding process which not only support the existence of such a transient species for lysozyme, but enable its structural characteristics to be defined. The results indicate that the two structural domains of lysozyme are distinct folding domains, in that they differ significantly in the extent to which compact, probably native-like, structure is present in the early stages of folding.     

A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme

Amyloid diseases are characterized by an aberrant assembly of a specific protein or protein fragment into fibrils and plaques that are deposited in various organs and tissues, often with serious pathological consequences. Non-neuropathic systemic amyloidosis is associated with single point mutations in the gene coding for human lysozyme. Here we report that a single-domain fragment of a camelid antibody raised against wild-type human lysozyme inhibits the in vitro aggregation of its amyloidogenic variant, D67H. Our structural studies reveal that the epitope includes neither the site of mutation nor most residues in the region of the protein structure that is destabilized by the mutation. Instead, the binding of the antibody fragment achieves its effect by restoring the structural cooperativity characteristic of the wild-type protein. This appears to occur at least in part through the transmission of long-range conformational effects to the interface between the two structural domains of the protein. Thus, reducing the ability of an amyloidogenic protein to form partly unfolded species can be an effective method of preventing its aggregation, suggesting approaches to the rational design of therapeutic agents directed against protein deposition diseases.     

Role of a subdomain in the folding of bovine pancreatic trypsin inhibitor.

The disulphide-bonded intermediates that accumulate in the oxidative folding of bovine pancreatic trypsin inhibitor (BPTI) were characterized some time ago. Structural characterization of these intermediates would provide an explanation of the kinetically preferred pathways of folding for BPTI. When folding occurs under strongly oxidizing conditions, more than half the molecules become trapped in an intermediate, designated N*, which is similar to the native protein but lacks the 30-51 disulphide bond. We have tested the hypothesis that the precursor to N* is the one-disulphide intermediate [5-55], which contains the most stable disulphide in BPTI, and present evidence here that this is the case. A peptide model of [5-55], corresponding to a subdomain of BPTI, seems to fold into a native-like conformation, explaining why [5-55] does not lead to native protein and why it folds rapidly to N*. A native-like subdomain structure in a peptide model of [30-51], the other crucial one-disulphide intermediate, may explain the route by which [30-51] folds to native protein. Thus, much of the folding pathway of BPTI can be explained by the formation of a native-like subdomain in these two early intermediates. This suggests that a large part of the protein folding problem can be reduced to identifying and understanding subdomains of native proteins.     

拟南芥RING finger结构域ABRv1基因的功能初步研究

拟南芥ABscisic acid responsive RING-v protein 1基因（ABRv1）编码一个含有RING finger结构域的E3连接酶。为了分析ABRv1的基因功能,我们首先构建了高表达载体pBI121- ABRv1,经农杆菌转化,花序浸染后得到T0代转基因种子,并经卡那霉素板筛选得到转基因苗,再经过两代的筛选获取了纯合的高表达株系ABRv1。通过DNA及RNA水平鉴定了该基因的T –DNA插入突变体abrv1。对突变体、高表达转基因株系及野生型进行ABA诱导处理,检测其萌发率、气孔关闭情况进行,发现ABA处理后突变体的萌发率降低,过表达株系萌发率升高;突变体株系气孔几乎未关闭,过表达株系气孔关闭非常明显。以上结果表明ABRv1基因在拟南芥的ABA信号应答响应中可能起负调控作用,为深入分析该基因的功能打下基础。     

Reverse hydrophobic effects relieved by amino-acid substitutions at a protein surface

It is rare for amino-acid substitutions on the surface of proteins to have large stabilizing or destabilizing effects. Nevertheless, one substitution of this type, the Tyr 26----Cys mutation in lambda Cro, increases the melting temperature of the protein by 11 degrees C and the stability by 2.2 kcal mol-1. Here we show that the stability of Cro can be increased by many different amino-acid substitutions at position 26, with increasing stability showing a good correlation with decreasing side-chain hydrophobicity. As Tyr 26 is hyper-exposed to solvent in the Cro crystal structure, we suggest that wild-type and variant proteins with other hydrophobic side chains at position 26 are destabilized as a result of a reverse hydrophobic effect caused by the side chain being more exposed to solvent in the native than in the denatured state.     

Cumulative effect of intragenic amino-acid replacements on the thermostability of a protein

The marginal net stability of a folded protein is thought to depend on a small difference between large, compensating individual forces. Therefore, the net free energy of stabilization of proteins is unexpectedly small (approximately 10 kcal mol-1). The contribution of individual forces such as hydrogen bonds and salt bridges to the stabilization is evaluated as 1-3 kcal mol-1, and several additional forces are thought to be sufficient to account for the extra thermostability of thermophilic proteins. The native conformation of a protein is determined by the total number of interatomic interactions and hence by the amino-acid sequence. If the few amino-acid residues that individually contribute to the stabilization could be implemented concurrently into the sequence, the multiple replacement would enhance the overall stability of the protein molecule. Here we report evidence to support this argument. Thermal inactivation kinetics and proteolytic resistance for mutants of a kanamycin nucleotidyltransferase reveal that a few intragenic amino-acid replacements stabilize the protein cumulatively. Our experiments not only demonstrate the feasibility of elevating the thermostability of a protein but also lead to better understanding of the forces that are responsible for protein stability.     

偶氮类食品着色剂诱惑红与蛋溶菌酶的相互作用研究

采用荧光光谱、紫外吸收光谱和计算机模拟分子对接研究了偶氮类食品着色剂诱惑红与蛋溶菌酶的相互作用.讨论了诱惑红对蛋溶菌酶荧光的猝灭机理,属于静态猝灭.测定了诱惑红与蛋溶菌酶反应体系的结合常数和结合位点数,根据热力学参数焓变(ΔH>0)和熵变(ΔS>0)可推断诱惑红和蛋溶菌酶的相互作用力为典型的疏水作用力.在298、304、310 K温度下,两者间的结合常数分别为17897、19865、23267.     

盐酸溶液中溶菌酶对Q235钢的缓蚀作用

运用失重法、动电位极化曲线法、交流阻抗法研究了溶菌酶在盐酸溶液中对Q235钢的缓蚀作用和吸附行为,并用扫描电子显微镜(SEM)观察腐蚀表面的形貌.结果表明,溶菌酶是一种缓蚀效果显著的混合型缓蚀剂,缓蚀效率受温度影响较小,吸附行为属于自发的单分子层化学吸附,符合Langmuir等温吸附式.     

A six-armed oligomer isolated from cell surface fibronectin preparations

Fibronectins are adhesive glycoproteins thought to mediate the attachment of cells to various substrates. Plasma fibronectin (PFN) is a dimer comprising subunits of molecular weight 220,000, connected by one or two disulphide bonds. Electron microscopy shows that PFN is a long, flexible strand, 2-3 nm in diameter and 140 nm long. Many cells in tissue culture elaborate an extracellular matrix of insoluble (highly cross-linked by disulphide bonds) fibronectin, and a variable amount of 'cell surface fibronectin' (CSFN) that can be extracted by mild urea treatment. This CSFN, soluble in 1 M urea and at high pH, is a mixture of dimers and disulphide-bonded oligomers. In the present study we have examined the structure of these molecules by electron microscopy. Oligomers were separated from dimers and contaminating proteins by zone sedimentation through glycerol gradients. We report that the CSFN dimers are identical in structure to PFN. In contrast, the oligomers have an elaborate and well defined structure that we call a 'hexabrachion': six arms emanating from a central globular particle. The arms are similar to PFN in being long, thin and flexible, but have several distinctly different features.     

Disruption of the actin cytoskeleton in yeast capping protein mutants

Capping protein controls the addition of actin subunits to the barbed end of actin filaments and nucleates actin polymerization in vitro. Capping protein has been identified in all eukaryotic cells examined so far; it is a heterodimer with subunits of relative molecular masses 32,000-36,000 (alpha-subunit) and 28,000-32,000 (beta-subunit). In skeletal muscle, capping protein (CapZ) probably binds the barbed ends of actin filaments at the Z line. The in vivo role of this protein in non-muscle cells is not known. We report here the characterization of CAP2, the single gene encoding the beta-subunit of capping protein in Saccharomyces cerevisiae. Yeast cells in which the CAP2 gene was disrupted by an insertion or a deletion had an abnormal actin distribution, including the loss of actin cables. The mutant cells were round and large, with a heterogeneous size distribution, and, although viable, grew more slowly than congenic wild-type cells. Chitin, a cell wall component restricted to the mother-bud junction in wild-type budding yeast, was found on the entire mother cell surface in the mutants. The phenotype of CAP2 disruption resembled that of temperature-sensitive mutations in the yeast actin gene ACT1, indicating that capping protein regulates actin-filament distribution in vivo.