A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene.

The hydrophobic cores of proteins are generally well packed, with few cavities. Mutations in which a bulky buried residue such as leucine or phenylalanine is replaced with a small residue such as alanine can create cavities in the core of a protein (our unpublished results). The sizes and shapes of such cavities can vary substantially depending on factors such as local geometry, whether or not a cavity already exists at the site of substitution, and the degree to which the protein structure relaxes to occupy the space vacated by the substituted residue. We show by crystallographic and thermodynamic analysis that the cavity created by the replacement Leu 99----Ala in T4 lysozyme is large enough to bind benzene and that ligand binding increases the melting temperature of the protein by 6.0 degrees C at pH 3.0. Benzene does not, however, bind to the cavity created by the Phe 153----Ala replacement. The results show that cavities can be engineered in proteins and suggest that such cavities might be tailored to bind specific ligands. The binding of benzene at an internal site 7 A from the molecular surface also illustrates the dynamic nature of proteins, even in crystals.     

Do general anaesthetics act by competitive binding to specific receptors?

Most proteins are insensitive to the presence of anaesthetics at concentrations which induce general anaesthesia, while some are inhibited by certain agents but not others. Here we show that, over a 100,000-fold range of potencies, the activity of a pure soluble protein (firefly luciferase) can be inhibited by 50% at anaesthetic concentrations which are essentially identical to those which anaesthetize animals. This identity holds for inhalational agents (such as halothane, methoxyflurane and chloroform), aliphatic and aromatic alcohols, ketones, ethers and alkanes. This finding is all the more striking in view of the fact that the inhibition is shown to be competitive in nature, with anaesthetic molecules competing with substrate (luciferin) molecules for binding to the protein. We show that the anaesthetic-binding site can accommodate only one large, but more than one small, anaesthetic molecule. The obvious mechanism suggested by our results is that general anaesthetics, despite their chemical and structural diversity, act by competing with endogenous ligands for binding to specific receptors.     

A novel calcium binding site in the galactose-binding protein of bacterial transport and chemotaxis

The refined 1.9-A resolution structure of the periplasmic D-galactose-binding protein (GBP) reveals a calcium ion surrounded by seven ligands, all protein oxygen atoms. A nine-residue loop (amino-acid positions 134-142), which is preceded by a beta-turn and followed by a beta-strand, provides five ligands from every second residue. The last two ligands are supplied by the carboxylate group of Glu 205. The entire GBP Ca2+-binding site adopts a conformation very similar to the site in the 'helix-loop-helix' or 'EF-hand' unit commonly found in intracellular calcium-binding proteins, but without the two helices. Structural analyses have also uncovered the sugar-binding site some 30 A from the calcium and a site for interacting with the membrane-bound trg chemotactic signal transducer approximately 45 A from the calcium. Our results show that a common tight calcium binding site of ancient origin can be tethered to different secondary structures. They also provide the first demonstration of a metal-binding site in a protein which is involved in bacterial active transport and chemotaxis.     

Heat shock in Escherichia coli alters the protein-binding properties of the chaperonin groEL by inducing its phosphorylation.

When bacterial or eukaryotic cells are exposed to high temperatures or other harsh conditions, they respond by synthesis of a specific set of heat-shock proteins. Certain heat-shock proteins such as groEL, called 'chaperonins', can prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under harmful conditions. We report here a new aspect of the heat-shock response in Escherichia coli: at high temperatures a fraction of groEL becomes modified covalently, altering its interaction with unfolded proteins. The heat-modified form can be eluted with ATP from an unfolded protein more easily than normal groEL. The critical heat-induced modification seems to be phosphorylation, which is reversed on return to low temperature. Treatment of the modified groEL with phosphatases caused its apparent size, charge and binding properties to resemble those of the unmodified form. Thus during heat shock some groEL is reversibly phosphorylated, which allows its ATP-dependent release from protein substrates in the absence of its usual cofactor (groES), and probably promotes the repair of damaged polypeptides.     

A reversibly antigen-responsive hydrogel.

Stimuli-responsive hydrogels that undergo abrupt changes in volume in response to external stimuli such as pH, temperature and solvent composition have potential applications in biomedicine and the creation of 'intelligent' materials systems, for example as media for drug delivery, separation processes and protein immobilization. Hydrogels have been reported that respond to pH, temperature, electric fields and saccharides. For some biomedical applications it would be very useful to have a material whose swelling response was dictated by a specific protein. Here we report such a material, which swells reversibly in a buffer solution in response to a specific antigen. The hydrogel was prepared by grafting the antigen and corresponding antibody to the polymer network, so that binding between the two introduces crosslinks in the network. Competitive binding of the free antigen triggers a change in gel volume owing to breaking of these non-covalent crosslinks. In addition, we show that the hydrogel displays shape-memory behaviour, and that stepwise changes in antigen concentration can induce pulsatile permeation of a protein through the network.     

通过小试样的控制冷却模拟大截面模块淬火硬度的分布

采用有限差分数值解法,计算了4Cr2MoVNi钢400mm×400mm×400mm大截面模块淬火过程的温度场;设计制造了一套冷却模拟装置,该装置可精确模拟大截面钢件淬火过程内部任意指定处的冷却过程,并以小试样冷却模拟计算获得的大模块内部指定处的温度随时间的变化曲线;通过对小试样硬度的测定,实现对大截面模块内部淬火硬度分布的预测·这种预测大截面钢件淬火过程内部淬火硬度分布的方法精确、适用面宽、简便易行·     

Molecular imprinted polymer with positively charged assistant recognition polymer chains for adsorption/enrichment of low content target protein

Here, we introduce a new type of molecular imprinted polymer （MIP） with immobilized assistant recognition polymer chains （ARPCs） to create effective recognition sites and with bacterial cloned protein as template for adsorbing the low content target protein from cell extract. In this work, cloned pig cyclophilin 18 （pCyP18）, a peptidyl-prolyl cis/trans-isomerase, was used as template. The template protein was selectively assembled with ARPCs from their library, which consists of numerous limited length polymer chains with randomly distributed recognition sites of positively charged amino groups and immobilizing sites. These assemblies were adsorbed by porous microsphers and immobilized on them. After removing the template, binding sites complementary to the target protein in size, shape and the position of recognition groups were exposed, and their confirmation was preserved by the cross-linked structure. The synthesized MIP was used to adsorb the cellular pCyP18, and its proportional content was enriched more than hundred times. The extended experiment on imprinting bovine serum albumin （BSA） with ARPCs shows that this method is also suitable for large protein.     

A substrate-specific inhibitor of protein translocation into the endoplasmic reticulum

The segregation of secretory and membrane proteins to the mammalian endoplasmic reticulum is mediated by remarkably diverse signal sequences that have little or no homology with each other. Despite such sequence diversity, these signals are all recognized and interpreted by a highly conserved protein-conducting channel composed of the Sec61 complex. Signal recognition by Sec61 is essential for productive insertion of the nascent polypeptide into the translocation site, channel gating and initiation of transport. Although subtle differences in these steps can be detected between different substrates, it is not known whether they can be exploited to modulate protein translocation selectively. Here we describe cotransin, a small molecule that inhibits protein translocation into the endoplasmic reticulum. Cotransin acts in a signal-sequence-discriminatory manner to prevent the stable insertion of select nascent chains into the Sec61 translocation channel. Thus, the range of substrates accommodated by the channel can be specifically and reversibly modulated by a cell-permeable small molecule that alters the interaction between signal sequences and the Sec61 complex.     

Signal sequence mutations disrupt feedback between secretion of an exported protein and its synthesis in E. coli

Recent studies in a eukaryotic system indicate that a block in secretion can lead to a block in the translation of secretory proteins. This feedback on protein synthesis is thought to be a result of an interaction of the signal recognition particle with the signal sequences of nascent proteins. Genetic studies in the prokaryote Escherichia coli suggest that a complex secretion machinery and a similar feedback mechanism exist. In addition, mutations affecting two genes, secA and secC, thought to encode components of the bacterial secretion machinery, selectively interfere with the synthesis of exported proteins. This selective interference with translation may be a result of recognition by the secretion machinery of signal sequences. If so, alteration of the signal sequence of a particular protein by mutation should eliminate the block in synthesis for that protein. We show here that signal sequence mutants for an exported protein, maltose binding protein, prevent the block in synthesis of this protein in a secA mutant.     

动物体液中的胞外钙调素结合蛋白（快报）

利用以生物素标记钙调素为探针的凝胶覆盖技术检测动物体液中胞外钙调素结合蛋白（ＣａＭＢＰ）。结果，人的唾液中检测到至少３种分子量分别为１４ｋＤ，２４ｋＤ和５２ｋＤ的ＣａＭＢＰｓ。其中，５２ｋＤ蛋白与ＣａＭ的结合依赖于Ｃａ２＋的存在，而２４ｋＤ和１４ｋＤ蛋白则不依赖于Ｃａ２＋。在鸡血清里，检测到以９４ｋＤ，４４／４５ｋＤ蛋白为主的４～５种胞外ＣａＭＢＰｓ，所有的这些蛋白与ＣａＭ的结合都依赖于Ｃａ２－。此外，在牛奶中也检出胞外ＣａＭＢＰｓ。以上结果，证明了在动物中普遍存在胞外ＣａＭＢＰｓ，为胞外钙调素的作用机理提供了新线索。     

Myb DNA binding inhibited by phosphorylation at a site deleted during oncogenic activation

The c-Myb nuclear oncoprotein is phosphorylated in vitro and in vivo at an N-terminal site near its DNA-binding domain by casein kinase II (CK-II) or a CK-II-like activity. This in vitro phosphorylation reversibly inhibits the sequence-specific binding of c-Myb to DNA. The site of this phosphorylation is deleted in nearly all oncogenically activated Myb proteins, resulting in DNA-binding that is independent of CK-II. Because CK-II activity is modulated by growth factors, loss of the site could uncouple c-Myb from its normal physiological regulator.     

Molecular heterogeneity of benzodiazepine receptors

Benzodiazepines exhibit reversible, stereospecific high affinity binding to mammalian brain membranes, and the respective binding sites for 3H-flunitrazepam represent pharmacologically and clinically relevant receptors for benzodiazepines. Recently it has been demonstrated that reversibly bound 3H-flunitrazepam becomes irreversibly attached to a specific membrane protein with apparent molecular weight of 50,000 when incubations are performed in the presence of UV light. Irreversible binding of 3H-flunitrazepam to this protein had pharmacological properties similar to reversible benzodiazepine receptor binding, indicating that 3H-flunitrazepam is a photoaffinity label for the benzodiazepine receptor. Using irreversible binding of 3H-flunitrazepam and subsequent electrophoretic separation of the labelled proteins in SDS-gels followed by fluorography, we found that in hippocampus and several other brain regions at least two different types of benzodiazepine receptors exist. Each seems to be associated with a gamma-aminobutyric acid (GABA) receptor.     

Structural basis for the regulated protease and chaperone function of DegP

All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.     

Ligand binding and conformational motions in myoglobin

Myoglobin, a small globular haem protein that binds gaseous ligands such as O2, CO and NO reversibly at the haem iron, serves as a model for studying structural and dynamic aspects of protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand revealed a complex ligand-binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe the structural changes induced by ligand dissociation, we have carried out X-ray crystallographic investigations of carbon monoxy-myoglobin (MbCO mutant L29W) crystals illuminated below and above 180 K, complemented by time-resolved infrared spectroscopy of CO rebinding. Here we show that below 180 K photodissociated ligands migrate to specific sites within an internal cavity--the distal haem pocket--of an essentially immobilized, frozen protein, from where they subsequently rebind by thermally activated barrier crossing. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. We recover most of the ligands in a cavity on the opposite side of the haem group.     

去污剂／聚合物双水相体系在膜蛋白分离中的应用

去污剂／聚合物双水相体系主要依靠胶束和聚合物分子间作用力来实现成相,具有对疏水膜蛋白增溶作用、成相物浓度低、萃取环境温和及操作简单等特点,可以克服传统膜蛋白提取工艺的一些缺陷;工艺开发过程中疏水膜蛋白以疏水作用富集于去污剂相,亲水蛋白以体积排阻效应富集于聚合物相,从而实现对膜蛋白的分离纯化。     

Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units

Electrostatic interactions are of considerable importance in protein structure and function, and in a variety of cellular and biochemical processes. Here we report three similar findings from highly refined atomic structures of periplasmic binding proteins. Hydrogen bonds, acting primarily through backbone peptide units, are mainly responsible for the involvement of the positively charged arginine 151 residue in the ligand site of the arabinose-binding protein, for the association between teh sulphate-binding protein and the completely buried sulphate dianion, and for the formation of the complex of the leucine/isoleucine/valine-binding protein with the leucine zwitterion. We propose a general mechanism in which the isolated charges on the various buried, desolvated ionic groups are stabilized by the polarized peptide units. This mechanism also has broad application to processes requiring binding of uncompensated ions and charged ligands and stabilization of enzyme reaction charged intermediates, as well as activation of catalytic residues.     

亮氨酸拉链结构蛋白在大肠杆菌重组子中的表达

酵母转录因子GCN4是通过亮氨酸拉链(bZIP)结构结合DNA的蛋白质之一，当GCN4二聚体与DNA结合时，亮氨酸拉链区的2个单体结合为平行的卷曲螺旋结构，而其基区由无规线团结构变为α螺旋．为探讨亮氨酸拉链蛋白与DNA的结合机理，设计了含有GCN4亮氨酸拉链蛋白基区结合DNA的必需氨基酸的折叠片段，并将其克隆到Escherichia coli BL21，讨论了此亮氨酸拉链蛋白的表达条件．在蛋白质的小量表达试验中，重组子Escherichia coli BL21于5mL含有50μg／mL氨节青霉素和34μg／mL氯霉素的LB液体培养基中培养至对数期，加入不同浓度的IPTG，继续培养以诱导蛋白质的表达，在不同的时间(如：诱导前，诱导2，4，6，8h)取样100μL到1．5mL离心管中、离心收集沉淀，将沉淀悬浮于样品缓冲液中，用10％SDS-PAGE检测；在10L含氨苄青霉素和氯霉素的LB液体培养基中进行了大量表达，根据小量表达的试验结果确定了IPTG的浓度和诱导时间．结果表明：含有这种拉链蛋白质的重组子Escherichia coli BL21在37℃下小量培养时，0．1-0．8mmol的IPTG均可在2-10h内诱导该蛋白质表达；而大量培养时，0．2mmol和0．4mmol的IPTG在37℃均不可能诱导表达，只在28℃时才表达；小量培养和大量培养的最佳诱导时间为4-6h，诱导剂IPTG的浓度为0．2mmol，大量表达的温度为28℃而不是37℃．     

Brefeldin A inhibits Golgi membrane-catalysed exchange of guanine nucleotide onto ARF protein.

The fungal metabolite brefeldin A is a powerful tool for investigating membrane traffic in eukaryotic cells. The effects of brefeldin A on traffic are partly explained by its ability to prevent binding of cytosolic coat proteins onto membranes. The non-clathrin coatomer complex binds reversibly to Golgi membranes in a GTP-controlled cycle. The low-molecular-mass GTP-binding protein ADP-ribosylation factor (ARF), which also associates reversibly with Golgi membranes, is required for coatomer binding and probably accounts for the control by guanine nucleotide of the coatomer-membrane interaction. Brefeldin A prevents the assembly of coatomer onto the membrane by inhibiting the GTP-dependent interaction of ARF with the Golgi membrane, but the nature of this interaction has not been established. Here we demonstrate that Golgi membranes can specifically catalyse the exchange of GTP onto ARF and that brefeldin A prevents this function.