化学裂解结合生物质谱对多肽二硫键的定位

二硫键是一种与多肽及蛋白质结构和功能密切相关的化学键. 当多肽中存在多个半胱氨酸时, 形成的二硫键可能会存在多种配对方式. 快速且精准地定位多肽中多对二硫键对研究多肽的结构与功能间的关系十分重要. 本文开发了一种基于化学裂解和生物质谱的新方法, 对利那洛肽中3对二硫键进行了精准定位. 通过解析裂解后特异肽段的二级质谱图, 确定利那洛肽中3对二硫键的配对方式分别为Cys1-Cys6, Cys2-Cys10和Cys5-Cys13. 该方法为二硫键的定位研究提供了新思路.     

Discovery, structure and biological activities of the cyclotides

The cyclotides are a family of small disulfide rich proteins that have a cyclic peptide backbone and a cystine knot formed by three conserved disulfide bonds. The combination of these two structural motifs contributes to the exceptional chemical, thermal and enzymatic stability of the cyclotides, which retain bioactivity after boiling. They were initially discovered based on native medicine or screening studies associated with some of their various activities, which include uterotonic action, anti-HIV activity, neurotensin antagonism, and cytotoxicity. They are present in plants from the Rubiaceae, Violaceae and Cucurbitaceae families and their natural function in plants appears to be in host defense: they have potent activity against certain insect pests and they also have antimicrobial activity. There are currently around 50 published sequences of cyclotides and their rate of discovery has been increasing over recent years. Ultimately the family may comprise thousands of members. This article describes the background to the discovery of the cyclotides, their structural characterization, chemical synthesis, genetic origin, biological activities and potential applications in the pharmaceutical and agricultural industries. Their unique topological features make them interesting from a protein folding perspective. Because of their highly stable peptide framework they might make useful templates in drug design programs, and their insecticidal activity opens the possibility of applications in crop protection.     

On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin

Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80 % (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.      

Synthesis of Disulfide Surrogate Peptides Incorporating Large-Span Surrogate Bridges Through a Native-Chemical-Ligation-Assisted Diaminodiacid Strategy

The use of synthetic bridges as surrogates for disulfide bonds has emerged as a practical strategy to obviate the poor stability of some disulfide-containing peptides. However, peptides incorporating large-span synthetic bridges are still beyond the reach of existing methods. Herein, we report a native chemical ligation (NCL)-assisted diaminodiacid (DADA) strategy that enables the robust generation of disulfide surrogate peptides incorporating surrogate bridges up to 50 amino acids in length. This strategy provides access to some highly desirable but otherwise impossible-to-obtain disulfide surrogates of bioactive peptide. The bioactivities and structures of the synthetic disulfide surrogates were verified by voltage clamp assays, NMR, and X-ray crystallography; and stability studies established that the disulfide replacements effectively overcame the problems of disulfide reduction and scrambling that often plague these pharmacologically important peptides.     

Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation

Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.     

Structure and function of annexin V-decorsin fusion

Decorsin is an antagonist of fibrinogen receptor on platelets and Annexin V is able to recognize stimulated platelets. Two recombinant proteins, Annexin V plus Decorsin (AnnV-D39) and Annexin V plus the C terminal 27 amino acids variant of Decorsin (AnnV-D27), were constructed, expressed, and purified. Platelet Aggregation assay results appear that AnnV-D39 shows good anti-platelet aggregation activity, but AnnV-D27 no such activities in any platelet aggregation assay test. And computational simulations reveal that AnnV-D39 showed good anti-platelet aggregation activity as a new antagonist of fibrinogen receptor, while Annv-D27 needs re-modification. Despite the AnnV_D39 fusion is more than decorsin, the former maintains the binding sites of decorsin interacton with its receptor, which contains Asp10, Arg28-Asp33, and Tyr37-Glu39. And the addition of Annexin V could not influence the interaction between its decorsin part with its receptor GPIIb–IIIa due to the linkage peptide (GGGGSGGGGS). Although the AnnV_D27 fusion is similar to the AnnV_D39 fusion, there are differences between them, where the former is in shortage of the linkage peptide and the N-terminal segment of decorsin whose one residue (Asp10) contribution to its interaction with GPIIb–IIIa. Meanwhile, these complex models suggest that decorsin plays a role in antiplatelet aggregation not only by its RGD motif interaction with its GPIIb–IIIa receptor, but also by other residues, especially Asp10 of its N-terminal segment and Tyr37-Glu39 of its C-terminal segment. On the other hand, the linkage peptide acts as avoidance of influence and blockage between domains of fusion. This is the cause that AnnV-D39 shows good anti-platelet aggregation activity.     

Mass spectrometric mapping of disulfide bonds in recombinant human interleukin-13

Interleukin 13 (IL-13), a member of the a-helical family of cytokines, has approximately 30% primary sequence homology with IL-4 and shares a common receptor component. The biologically active rhIL-13 is monomeric and non-glycosylated, and contains two disulfide bonds as determined by comparative electrospray mass spectrometric (MS) analysis of the protein before and after reduction with dithiothreitol-dithioerythritol. A trypsin-resistant core peptide of rhIL-13 was isolated and analyzed by plasma desorption (PD) MS, identifying a disulfide-linked core peptide. Subsequent digestion of this core peptide by pepsin, followed by PDMS analysis of the resulting cystine-containing peptic fragments, provided rapid determination of the existing disulfide bonds between cysteine residues 28-56 and 44-70. This disulfide arrangement is similar to that observed for the analogous four internal cysteine residues in hIL-4. The conservation of disulfide bond arrangements between hIL-13 and hIL-4, coupled with their alpha-helical structure and sequence homologies, confirms that IL-13 and IL-4 are structural homologues. It is also consistent with their reported similarities in biological function and receptor binding kinetics.     

Synthesis of Disulfide Surrogate Peptides Incorporating Large‐Span Surrogate Bridges Through a Native‐Chemical‐Ligation‐Assisted Diaminodiacid Strategy

The use of synthetic bridges as surrogates for disulfide bonds has emerged as a practical strategy to obviate the poor stability of some disulfide‐containing peptides. However, peptides incorporating large‐span synthetic bridges are still beyond the reach of existing methods. Herein, we report a native chemical ligation (NCL)‐assisted diaminodiacid (DADA) strategy that enables the robust generation of disulfide surrogate peptides incorporating surrogate bridges up to 50 amino acids in length. This strategy provides access to some highly desirable but otherwise impossible‐to‐obtain disulfide surrogates of bioactive peptide. The bioactivities and structures of the synthetic disulfide surrogates were verified by voltage clamp assays, NMR, and X‐ray crystallography; and stability studies established that the disulfide replacements effectively overcame the problems of disulfide reduction and scrambling that often plague these pharmacologically important peptides.     

Syntheses and biological activity of amamistatin B and analogs

Amamistatins A and B, natural products isolated from a strain of Nocardia, showed growth inhibition against three human tumor cell lines (IC(50) 0.24-0.56 microM). Structurally related mycobactins affect the growth of both mycobacterial and human cells through interference with iron chelation. To further probe the biological activity of this class of compounds, the total syntheses of amamistatin B and two analogs were completed, and the synthetic samples were screened for tumor cell growth inhibition, HDAC inhibition, and Mycobacterium tuberculosis growth inhibition. Amamistatin B (15) and diastereomer 18 were both active against MCF-7 cells (IC(50) 0.12-0.20 microM), and less so against PC-3 cells (IC(50) 8-13 microM). Amamistatin B only moderately inhibited the growth of M. tuberculosis (MIC 47 microM) but showed growth promotion of Mycobacterium smegmatis and other bacteria.     

Extracellular SH3 domain containing proteins--features of a new protein family

In the year 1994, the protein MIA (melanoma inhibitory activity) was found to be strongly expressed and secreted by malignant melanomas and subsequent studies revealed that MIA has an important function in melanoma development and invasion. Multidimensional NMR-spectroscopy and x-ray crystallography revealed that recombinant human MIA adopts a Src homology 3 (SH3) domain-like fold in solution, a structure with two perpendicular antiparallel three- and five-stranded beta-sheets. SH3 domains are protein modules that are found in many intracellular signalling proteins and mediate protein-protein interactions by binding to proline-rich peptide sequences. Unlike previously described protein structures with SH3 domain folds, MIA is a secreted single-domain protein of 12 kDa that contains an additional antiparallel beta-sheet and two disulfide bonds. Furthermore, the charge surrounding the canonical binding site differs from that of classical SH3 domains. The two disulfide bonds are crucial for correct folding and function as revealed by mutation analysis. Therefore, MIA appears to be the first extracellular protein adopting an SH3 domain-like fold. MIA was shown to interact with fibronectin, and MIA-interacting peptide ligands identified by phage display screening are similar to the consensus sequence of type III human fibronectin repeats, especially FN14. Interestingly, recent data revealed that MIA can also directly bind to integrin alpha 4 beta 1 and alpha 5 beta1 and that it modulates integrin activity negatively. These findings suggest an interesting role of the SH3-domain proteins in the extracellular compartment. Recently, MIA homologous proteins with a sequence identity of 44% and a sequence homology of approximately 80% were determined (TANGO, MIA-2, OTOR). This clearly suggests that this structural device is used more frequently, in processes ranging from developmental changes to the interference of cell attachment in the extracellular matrix. Detailed studies are necessary to determine the exact function of the MIA homologous proteins. It will be interesting to know whether additional protein families can be identified which are secreted and carry SH3 domain-like modules, in addition to elucidate what the specific physiological targets of this protein family are.     

A two disulfide bridge Kazal domain from <Emphasis Type="Italic">Phytophthora</Emphasis> exhibits stable inhibitory activity against serine proteases of the subtilisin family

Background  

Kazal-like serine protease inhibitors are defined by a conserved sequence motif. A typical Kazal domain contains six cysteine residues leading to three disulfide bonds with a 1–5/2–4/3–6 pattern. Most Kazal domains described so far belong to this class. However, a novel class of Kazal domains with two disulfide bridges resulting from the absence of the third and sixth cysteines have been found in biologically important molecules, such as human LEKTI, a 15-domain inhibitor associated with the severe congenital disease Netherton syndrome. These domains are referred to as atypical Kazal domains. Previously, EPI1, a Kazal-like protease inhibitor from the oomycete plant pathogen Phytophthora infestans, was shown to be a tight-binding inhibitor of subtilisin A. EPI1 also inhibits and interacts with the pathogenesis-related P69B subtilase of the host plant tomato, suggesting a role in virulence. EPI1 is composed of two Kazal domains, the four-cysteine atypical domain EPI1a and the typical domain EPI1b.     

部分还原和分步序列测定法定位虎纹捕鸟蛛毒素-Ⅳ二硫键

结合部分还原和分步序列测定法确定了虎纹捕鸟蛛毒素-的二硫键配对方式.在pH=3和40℃的条件下与还原剂三羧甲基磷酸(TCEP)反应10min,利用RP-HPLC分离并分别收集含有一对和两对二硫键被还原的中间体,分别与0.5mol/L碘乙酰胺溶液(pH=8.3)反应1min,使游离巯基烷基化后,测定各中间体的氨基酸序列,从而确定虎纹捕鸟蛛毒素-的3对二硫键分别为Cys2-Cys17,Cys9-Cys24和Cys-Cys31(1-4,2-5和3-6).     

PDI-Regulated Disulfide Bond Formation in Protein Folding and Biomolecular Assembly

Disulfide bonds play a pivotal role in maintaining the natural structures of proteins to ensure their performance of normal biological functions. Moreover, biological molecular assembly, such as the gluten network, is also largely dependent on the intermolecular crosslinking via disulfide bonds. In eukaryotes, the formation and rearrangement of most intra- and intermolecular disulfide bonds in the endoplasmic reticulum (ER) are mediated by protein disulfide isomerases (PDIs), which consist of multiple thioredoxin-like domains. These domains assist correct folding of proteins, as well as effectively prevent the aggregation of misfolded ones. Protein misfolding often leads to the formation of pathological protein aggregations that cause many diseases. On the other hand, glutenin aggregation and subsequent crosslinking are required for the formation of a rheologically dominating gluten network. Herein, the mechanism of PDI-regulated disulfide bond formation is important for understanding not only protein folding and associated diseases, but also the formation of functional biomolecular assembly. This review systematically illustrated the process of human protein disulfide isomerase (hPDI) mediated disulfide bond formation and complemented this with the current mechanism of wheat protein disulfide isomerase (wPDI) catalyzed formation of gluten networks.     

A Protein from Aloe vera that Inhibits the Cleavage of Human Fibrin(ogen) by Plasmin

A protease inhibitor protein with the molecular mass of 11,804.931 Da (analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) was isolated from Aloe vera leaf gel and designated as AVPI-12. The isoelectric point of the protein is about 7.43. The first ten amino acid sequence from the N-terminal was found to be R–D–W–A–E–P–N–D–G–Y, which did not match other protease inhibitors in database searches and other publications, indicating AVPI-12 is a novel protease inhibitor. The band protein of AVPI-12 migrated further on nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) than reducing SDS-PAGE. This result indicated that the molecule of AVPI-12 did not contain interchain disulfide bonds, but appeared to have intrachain disulfide bonds instead. AVPI-12 strongly resisted digestion by the serine proteases human plasmin and bovine trypsin. The protein could protect the γ-subunit of human fibrinogen from plasmin and trypsin digestion, similar to the natural plasma serine protease inhibitor α₂-macroglobulin. The protein also could protect the γ-subunit of fibrinogen from the cysteine protease papain. AVPI-12 also exhibited dose-dependent inhibition of the fibrinogenolytic activity of plasmin, similar to α₂-macroglobulin. The fibrinolytic inhibitory activity of AVPI-12 and the small-angle X-ray scattering showed that the protein could protect human fibrin clot from complete degradation by plasmin. The inhibition of the fibrinogenolytic and fibrinolytic activities of plasmin by AVPI-12 suggests that the inhibitor has potential for use in antifibrinolytic treatment.     

Protein Engineering III: Computer Aided Design of Disulfide-Bond Free Cobra Venom Cardiotoxin with a Novel Conformation and Biological Activity from Synthetic Peptides

Using the crystal structure of cobra venom cardiotoxin as a templet, a computer designed peptide with a novel conformation and biological activity has been synthesized chemically. The designed peptide utilized two calcium coordination sites instead of disulfide bridges to hold the conformation. The coordination sites were introduced at the cleft of three β-sheet strands by replacing the residues of Leu-1, Leu-26, Ser-28, Leu-48, and Ser-55 with Glu and using their γ-carboxyl groups as legends. The residues of Cys at positions 3, 14, 21, 38, 42, 53, 54, and 59 of the four disulfide bridges were changed with Gly to remove all the disulfide bonds. Circular dichroism spectra showed that the synthesized peptide has a conformation similar to that of the native cardiotoxin of a defined structure only in aqueous solutions with the presence of calcium ions. Immunoprecipitation assay, using the anti-cardiotoxin V, showed that in the presence of calcium ion the peptide had same cross reaction as that of native cardiotoxin. Hemolysis assay in the presence of calcium ion (150–250 mmol) and phospholipase A₂ showed that the peptide had 65–70% as much cytolytic activity as the native toxin.     

KIO3存在下溶菌酶的极谱催化波研究与应用

研究了溶菌酶(Lysozyme,LE)在KIO₃存在下的极谱催化波.在0.1mol/LHAc-NaAc(pH4.7±0.1)缓冲液中,LE有1个由Cys6～Cys127间双硫键还原产生的可逆波.其峰电位为-0.51V(vs.Ag/AgCl).当KIO₃存在时,在原电位处产生了LE的极谱催化波.该催化波是由于KIO₃及其中间价态衍生质点(包括自由基IO^-·,IO_{2^{-·)氧化LE还原产物巯基成双硫键所致.这是蛋白质极谱催化波的一种新类型.在0.1mol/LHAc-NaAc(pH4.7±0.1)-1×10-3mol/LKIO3支持电解质中,LE催化波的灵敏度比其还原波的高两个数量级,峰电流与LE浓度在2×10-7～1.0×10-6mol/L范围内有线性关系.100倍半胱氨酸和胱氨酸不干扰1.0×10-6mol/LLE的测定.}}     

Improvement of Drosophila acetylcholinesterase stability by elimination of a free cysteine

Background

Acetylcholinesterase is irreversibly inhibited by organophosphate and carbamate insecticides allowing its use for residue detection with biosensors. Drosophila acetylcholinesterase is the most sensitive enzyme known and has been improved by in vitro mutagenesis. However, it is not sufficiently stable for extensive utilization. It is a homodimer in which both subunits contain 8 cysteine residues. Six are involved in conserved intramolecular disulfide bridges and one is involved in an interchain disulfide bridge. The 8^th cysteine is not conserved and is present at position 290 as a free thiol pointing toward the center of the protein.

Results

The free cysteine has been mutated to valine and the resulting protein has been assayed for stability using various denaturing agents: temperature, urea, acetonitrile, freezing, proteases and spontaneous-denaturation at room temperature. It was found that the C290V mutation rendered the protein 1.1 to 2.7 fold more stable depending on the denaturing agent.

Conclusion

It seems that stabilization resulting from the cysteine to valine mutation originates from a decrease of thiol-disulfide interchanges and from an increase in the hydrophobicity of the buried side chain.     

蛋白质中二硫键的定位及其质谱分析*

二硫键是一种常见的蛋白质翻译后修饰,对稳定蛋白质的空间结构,保持及调节其生物活性等都有着非常重要的作用。因此,确定二硫键在蛋白质中的位置是全面了解含二硫键蛋白化学结构的重要方面。在众多实验方法中,现代质谱技术因其操作简单、快速、灵敏等优点而成为分析二硫键的重要手段。本文介绍了目前主要的定位二硫键的方法,以及质谱在二硫键定位分析中的应用与进展。     

Novel strategies for isolation and characterization of cyclotides: the discovery of bioactive macrocyclic plant polypeptides in the Violaceae

This review focuses on the discovery of cyclotides in the Violaceae, their isolation and their anti-cancer effects. These macrocyclic plant peptides consist of about 30 amino acids, including three conserved disulfide bonds in a cystine knotted arrangement, which renders them a remarkable stability. Their unique structure, combined with a wide array of biological activities, makes them of great interest as possible leads in drug development or as carriers of grafted peptide sequences. Here we describe the work conducted in our laboratory, which started with the overall aim of identifying peptides and small proteins of the size 10-50 amino acid residues in plants with novel chemical structures and biological profiles with a potential for drug development or for use as pharmacological tools. Thus we developed a fractionation protocol to directly address major challenges encountered when dealing with plant material, such as removal of chlorophyll, polyphenols, and low molecular compounds omnipresent in plants. Using this protocol, we then discovered a suite of cyclotides, the varv peptides, from the plant Viola arvensis (Violaceae). Following this, separation methods directly targeting cyclotides were developed, e.g. by adsorption, ion exchange chromatography and solvent-solvent partitioning, which then were used in the isolation of additional cyclotides. To structurally examine cyclotides we have also developed methods based on mass spectrometry for cyclotide sequencing and mapping of disulfide bonds. Finally, to assess structure-activity relationships, regarding their anti-cancer and cytotoxic effects that we focus upon, we have also characterized the three dimensional structure of cyclotides by homology modeling techniques.     

RTD-1mimic containing γPNA scaffold exhibits broad-spectrum antibacterial activities

Macrocyclic peptides with multiple disulfide cross-linkages, such as those produced by plants and those found in nonhuman primates, as components of the innate immunity, hold great promise for molecular therapy because of their broad biological activities and high chemical, thermal, and enzymatic stability. However, for some, because of their intricate spatial arrangement and elaborate interstrand cross-linkages, they are difficult to prepare de novo in large quantities and high purity, due to the nonselective nature of disulfide-bond formation. We show that the disulfide bridges of RTD-1, a member of the θ-defensin subfamily, could be replaced with noncovalent Watson-Crick hydrogen bonds without significantly affecting its biological activities. The work provides a general strategy for engineering conformationally rigid, cyclic peptides without the need for disulfide-bond reinforcement.