Designing small-molecule switches for protein-protein interactions

Mutations introduced into human growth hormone (hGH) (Thr175 --> Gly-hGH) and the extracellular domain of the hGH receptor (Trp104 --> Gly-hGHbp) created a cavity at the protein-protein interface that resulted in binding affinity being reduced by a factor of 10(6). A small library of indole analogs was screened for small molecules that bind the cavity created by the mutations and restore binding affinity. The ligand 5-chloro-2-trichloromethylimidazole was found to increase the affinity of the mutant hormone for its receptor more than 1000-fold. Cell proliferation and JAK2 phosphorylation assays showed that the mutant hGH activates growth hormone signaling in the presence of added ligand. This approach may allow other protein-protein and protein-nucleic acid interactions to be switched on or off by the addition or depletion of exogenous small molecules.     

哺乳动物抗菌肽研究进展

抗菌肽是生物长期进化过程中保留的先天免疫系统或原生宿主防卫机制中重要的活性分子。其在生物界广泛分布,目前已从细菌、昆虫、植物以及动物中分离到多种抗菌肽。抗菌肽的抗菌谱广泛,可以抗细菌、真菌、被膜病毒等多种微生物,还对支原体、衣原体、螺旋体及一些恶性肿瘤和艾滋病毒具有杀伤作用;但不破坏动物及人体正常的体细胞,是吞噬细胞、嗜中性白细胞和巨噬细胞中防御系统的重要活性物质。由于抗菌肽的选择性效应和分子量小、无抗原性等特点,在面临抗药性和筛选新的抗生素较为困难的今天,有望成为新一代的抗菌、抗癌药物。     

Progress in modeling of protein structures and interactions

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.     

Long-range interactions within a nonnative protein

Protein folding and unfolding are coupled to a range of biological phenomena, from the regulation of cellular activity to the onset of neurodegenerative diseases. Defining the nature of the conformations sampled in nonnative proteins is crucial for understanding the origins of such phenomena. We have used a combination of nuclear magnetic resonance (NMR) spectroscopy and site-directed mutagenesis to study unfolded states of the protein lysozyme. Extensive clusters of hydrophobic structure exist within the wild-type protein even under strongly denaturing conditions. These clusters involve distinct regions of the sequence but are all disrupted by a single point mutation that replaced residue Trp62 with Gly located at the interface of the two major structural domains in the native state. Thus, nativelike structure in the denatured protein is stabilized by the involvement of Trp62 in nonnative and long-range interactions.     

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure

Catechol-O-methyltransferase (COMT) is a key regulator of pain perception, cognitive function, and affective mood. Three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, code for differences in COMT enzymatic activity and are associated with pain sensitivity. Haplotypes divergent in synonymous changes exhibited the largest difference in COMT enzymatic activity, due to a reduced amount of translated protein. The major COMT haplotypes varied with respect to messenger RNA local stem-loop structures, such that the most stable structure was associated with the lowest protein levels and enzymatic activity. Site-directed mutagenesis that eliminated the stable structure restored the amount of translated protein. These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations.     

Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic

Resistance to antibiotics is increasing in some groups of clinically important pathogens. For instance, high vancomycin resistance has emerged in enterococci. Promising alternative antibiotics are the peptide antibiotics, abundant in host defense systems, which kill their targets by permeabilizing the plasma membrane. These peptides generally do not act via specific receptors and are active in the micromolar range. Here it is shown that vancomycin and the antibacterial peptide nisin Z use the same target: the membrane-anchored cell wall precursor Lipid II. Nisin combines high affinity for Lipid II with its pore-forming ability, thus causing the peptide to be highly active (in the nanomolar range).     

抗菌肽Dermaseptin S4体外抑制猪繁殖与呼吸障碍综合征病毒的活性

探讨抗菌肽Dermaseptin S4(DS4)体外对猪繁殖与呼吸障碍综合征病毒(PRRSV)的抑制作用,为研制抗PRRSV病毒药物提供理论依据.该研究以Marc-145细胞培养增殖的PRRSV为研究对象,采用不同的给药方式(同时、感染前、感染后),运用噻唑篮(MTT)比色法观察细胞病变,测定最大无毒浓度TC0和半数细胞感染量(TCID50),以吸光度值(OD490nm)、细胞存活率和DS4对PRRSV的抑制率为指标,确定DS4对PRRSV的抑制强度.结果表明:抗菌肽Dermaseptin S4体外对PRRSV的直接灭活效果最好,与药物拉米夫定对照组相当,且抑制强度与其浓度呈显著正相关,R2=0.998 3.     

Frataxin acts as an iron chaperone protein to modulate mitochondrial aconitase activity

Numerous degenerative disorders are associated with elevated levels of prooxidants and declines in mitochondrial aconitase activity. Deficiency in the mitochondrial iron-binding protein frataxin results in diminished activity of various mitochondrial iron-sulfur proteins including aconitase. We found that aconitase can undergo reversible citrate-dependent modulation in activity in response to pro-oxidants. Frataxin interacted with aconitase in a citrate-dependent fashion, reduced the level of oxidant-induced inactivation, and converted inactive [3Fe-4S]1+ enzyme to the active [4Fe-4S]2+ form of the protein. Thus, frataxin is an iron chaperone protein that protects the aconitase [4Fe-4S]2+ cluster from disassembly and promotes enzyme reactivation.     

Synthetic amphiphilic peptide models for protein ion channels

Ion channel proteins are important for the conduction of ions across biological membranes. Recent analyses of their sequences have suggested that they are composed of bundles of alpha-helices that associate to form ion-conducting channels. To gain insight into the mechanisms by which alpha-helices can aggregate and conduct ions, three model peptides containing only leucine and serine residues were synthesized and characterized. A 21-residue peptide, H2N-(Leu-Ser-Ser-Leu-Leu-Ser-Leu)3-CONH2, which was designed to be a membrane-spanning amphiphilic alpha-helix, formed well-defined ion channels with ion permeability and lifetime characteristics resembling the acetylcholine receptor. In contrast, a 14-residue version of this peptide, which was too short to span the phospolipid bilayer as an alpha-helix, failed to form discrete, stable channels. A third peptide, H2N-(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3-CONH2, in which one serine per heptad repeat was replaced by leucine, produced proton-selective channels. Computer graphics and energy minimization were used to create molecular models that were consistent with the observed properties of the channels.     

Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation

Cells reuse signaling proteins in multiple pathways, raising the potential for improper cross talk. Scaffold proteins are thought to insulate against such miscommunication by sequestering proteins into distinct physical complexes. We show that the scaffold protein Ste5, which organizes the yeast mating mitogen-activated protein kinase (MAPK) pathway, does not use sequestration to prevent misactivation of the mating response. Instead, Ste5 appears to use a conformation mechanism: Under basal conditions, an intramolecular interaction of the pleckstrin homology (PH) domain with the von Willebrand type A (VWA) domain blocks the ability to coactivate the mating-specific MAPK Fus3. Pheromone-induced membrane binding of Ste5 triggers release of this autoinhibition. Thus, in addition to serving as a conduit guiding kinase communication, Ste5 directly receives input information to decide if and when signal can be transmitted to mating output.     

酶水解制备鲤鱼肉蛋白抗氧化肽

采用碱性蛋白酶、风味蛋白酶、中性蛋白酶和胰蛋白酶分别在最适条件下对鲤鱼肉蛋白进行水解,研究在不同水解条件下水解物的抗氧化能力.用pH-Stat法测定水解产物的水解度,通过测定水解产物对卵磷脂脂质氧化体系的抑制作用和还原能力(FRAP)来研究水解产物的抗氧化能力.结果表明,鲤鱼肉蛋白水解产物的抗氧化能力与酶的种类、水解度...     

Conformational equilibria in spin-labeled hemoglobin

A component characteristic of deoxyhemoglobin appears in the paramagnetic resonance spectrum of spin-labeled oxyhemoglobin, and vice versa, under conditions of pH and ionic strength consistent with the interpretation that the spectrum is sensitive to the conformational equilibrium of the carboxy-terminal histidines. The oxygenation-induced change in the resonance spectrum is discussed in terms of shifts in this equilibrium.     

Signal peptide for protein secretion directing glycophospholipid membrane anchor attachment

Decay accelerating factor (DAF) is anchored to the plasma membrane by a glycophospholipid (GPI) membrane anchor covalently attached to the COOH-terminus of the protein. A hydrophobic domain located at the COOH-terminus is required for anchor attachment; DAF molecules lacking this domain are secreted. Replacement of the COOH-terminal hydrophobic domain with a signal peptide that normally functions in membrane translocation, or with a random hydrophobic sequence, results in efficient and correct processing, producing GPI-anchored DAF on the cell surface. The structural requirements for GPI anchor attachment and for membrane translocation are therefore similar, presumably depending on overall hydrophobicity rather than specific sequences.     

泥鳅蛋白抗氧化肽的Plastein反应修饰研究

采用中性蛋白酶水解泥鳅蛋白制备抗氧化肽,以DPPH自由基清除能力为指标,用木瓜白酶对泥鳅蛋白抗氧化肽进行Plastein反应修饰研究。通过单因素试验研究了外源氨基酸种类、pH值、时间、E/S、温度和外源氨基酸的添加量对泥鳅蛋白抗氧化肽Plastein反应修饰的影响,在此基础上采用响应面法对泥鳅蛋白抗氧化肽Plastein反应修饰工艺进行了优化。结果表明,泥鳅蛋白抗氧化肽Plastein反应修饰的最佳条件为:底物浓度40%、组氨酸添加量为0.5 mmol·g^-1、E/S为1 782.49 U·g^-1 、pH值9.0、温度35 ℃、时间3 h,此条件下制备的Plastein反应修饰产物的抗氧化活性是修饰前的1.99倍,其对DPPH自由基的清除率为(77.98±0.08)%。     

菜籽粕蛋白肽制备工艺条件优化

试验改进了菜籽粕蛋白的酶解工艺,并对改进后的工艺条件进行了优化。采用2709碱性蛋白酶水解菜籽粕蛋白,分别考察了pH值、酶用量、酶解时间、温度、底物浓度对蛋白回收率的影响规律,在此基础上,利用响应面分析法对菜籽粕蛋白的酶解条件进行了优化。结果表明,2709碱性蛋白酶水解菜籽粕蛋白的较优条件为pH11.5、温度50℃、底物浓度4%、水解时间173min、酶用量5778U·g-1,此时蛋白回收率可达87.18%。     

Random peptide libraries: a source of specific protein binding molecules

Libraries of random peptide sequences were constructed and screened to identify peptides that specifically bind to proteins. In one of these about 2 X 10(7) different 15-residue peptide sequences were expressed on the surface of the coliphage M13. Each phage encoded a single random sequence and expressed it as a fusion complex with pIII, a minor coat protein present at five molecules per phage. Phage encoding nine different streptavidin-binding peptide sequences were isolated from this library. The core consensus sequence was His-Pro-Gln and binding of these phage to streptavidin was inhibited by biotin. This type of library makes it possible to identify peptides that bind to proteins (or other macromolecules) that have no previously known affinity for peptides.     

小麦谷氨酰胺合成酶基因克隆与其表达特性分析

为了研究小麦谷氨酰胺合成酶(Glutamine synthetase,GS)的功能,利用RACE及RT-PCR技术克隆了小麦GS1(GenBank登录号:HQ840647)和GS2(GenBank登录号:JF894116)基因的全长cDNA.小麦GS1的cDNA全长为1 494 bp,GS2的cDNA全长为1 631 bp,并利用生物信息软件对GS1和GS2的基因序列以及所表达的蛋白特性进行了分析.利用半定量PCR和Western-bolt技术分别分析了小麦苗期叶片发育过程中GS同工酶基因转录和表达特点,结果表明,GS1在叶片开始衰老时转录和表达水平较高,GS2从叶片伸长期到定长期转录和表达水平最高.     

Probing steric and hydrophobic effects on enzyme-substrate interactions by protein engineering

Steric and hydrophobic effects on substrate specificity were probed by protein engineering of subtilisin. Subtilisin has broad peptidase specificity and contains a large hydrophobic substrate binding cleft. A conserved glycine (Gly(166)), located at the bottom of the substrate binding left, was replaced by 12 nonionic amino acids by the cassette mutagenesis method. Mutant enzymes showed large changes in specificity toward substrates of increasing size and hydrophobicity. In general, the catalytic efficiency (k(cat)/K(m)) toward small hydrophobic substrates was increased (up to 16 times) by hydrophobic substitutions at position 166 in the binding cleft. Exceeding the optimal binding volume of the cleft ( approximately 160 A(3)), by enlarging either the substrate side chain or the side chain at position 166, evoked precipitous drops in catalytic efficiency (k(cat)/K(m)) (up to 5000 times) as a result of steric hindrance.