分子电性作用矢量法定量预测单质子化肽段离子迁移谱碰撞截面

基于分子二维图形特征得到了一种新的结构参数化方法:分子电性作用矢量(MEIV)。将其应用于113个单质子化肽段样本集的结构表征及离子迁移谱碰撞截面模拟和预测当中,通过严格检验所得到3个回归模型的复相关系数Rcum及交叉验证Q分别为:0.984、0.981、0.980和0.979、0.979、0.978。结果表明MEIV对有机分子结构及其性质具有良好的表达和预测能力。     

Sortase-Mediated Transpeptidation for Site-Specific Modification of Peptides,Glycopeptides, and Proteins

Sortases are a family of transpeptidases found in gram-positive bacteria responsible for covalent anchoring of cell surface proteins to bacterial cell walls. It has been discovered that sortase A (SrtA) of Staphylococcus aureus origin is rather promiscuous and can accept various molecules as substrates. As a result, SrtA has been widely used to ligate peptides and proteins with a variety of nucleophiles, and the ligation products are useful for research in chemical biology, proteomics, biomedicine, etc. This review summarizes the recent applications of SrtA with special emphasis on SrtA-catalyzed ligation of carbohydrates with peptides and proteins.     

Sortase-Mediated Transpeptidation for Site-Specific Modification of Peptides, Glycopeptides, and Proteins

Sortases are a family of transpeptidases found in Gram-positive bacteria responsible for covalent anchoring of cell surface proteins to bacterial cell walls. It has been discovered that sortase A (SrtA) of Staphylococcus aureus origin is rather promiscuous and can accept various molecules as substrates. As a result, SrtA has been widely used to ligate peptides and proteins with a variety of nucleophiles, and the ligation products are useful for research in chemical biology, proteomics, biomedicine, etc. This review summarizes the recent applications of SrtA with special emphasis on SrtA-catalyzed ligation of carbohydrates with peptides and proteins.     

氢氘交换质谱技术在蛋白质和蛋白复合物结构研究中的应用进展

蛋白质是生命功能的执行者,其功能的发挥受自身结构动态变化、与其他生物分子的相互作用及修饰等因素的调节。因此,对蛋白质及蛋白复合物结构的研究有助于揭示重要生命过程中的分子机理与机制。氢氘交换质谱(Hydrogen deuterium exchange mass spectrometry,HDX-MS)是研究蛋白质结构、动态变化和相互作用的强有力工具,也是传统生物物理手段的重要补充。该文综述了HDX-MS的基本原理、机制、实验方法和研究最新进展,并从蛋白质自身动态变化、蛋白质-小分子相互作用、蛋白质-蛋白质相互作用3个方面介绍了近年来HDX-MS在蛋白及蛋白复合物研究中的应用进展。     

A Rapid Gas-Chromatography/Mass-Spectrometry Technique for Determining Odour Activity Values of Volatile Compounds in Plant Proteins: Soy,and Allergen-Free Pea and Brown Rice Protein

Plant-based protein sources have a characteristic aroma that limits their usage in various meat-alternative formulations. Despite being the most popular plant-based protein, the allergenicity of soy protein severely restricts the potential adoption of soy protein as an animal substitute. Thereby, allergen-free plant-protein sources need to be characterized. Herein, we demonstrate a rapid solid-phase-microextraction gas-chromatography/mass-spectrometry (SPME-GC/MS) technique for comparing the volatile aroma profile concentration of two different allergen-free plant-protein sources (brown rice and pea) and comparing them with soy protein. The extraction procedure consisted of making a 1:7 w/v aqueous plant protein slurry, and then absorbing the volatile compounds on an SPME fibre under agitation for 10 min at 40 °C, which was subsequently injected onto a GC column coupled to an MS system. Observed volatile concentrations were used in conjunction with odour threshold values to generate a Total Volatile Aroma Score for each protein sample. A total of 76 volatile compounds were identified. Aldehydes and furans were determined to be the most dominant volatiles present in the plant proteins. Both brown rice protein and pea protein contained 64% aldehydes and 18% furans, with minor contents of alcohols, ketones and other compounds. On the other hand, soy protein consisted of fewer aldehydes (46%), but a more significant proportion of furans (42%). However, in terms of total concentration, brown rice protein contained the highest intensity and number of volatile compounds. Based on the calculated odour activity values of the detected compounds, our study concludes that pea proteins could be used as a suitable alternative to soy proteins in applications for allergen-free vegan protein products without interfering with the taste or flavour of the product.     

A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins

Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF₃)ppy)₂(dNMe₃bpy)]Cl₃, is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.     

Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

Analysis of Proteins,Protein Complexes,and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein–protein and protein–ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes).

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Online Capillary Electrophoresis Reaction for Interaction Study of Amino Acid Modified Peptide Nucleic Acid and Proteins

Peptide nucleic acid (PNA) is a nucleic acid analog which consists of purines, pyrimidines bases, and a neutrally charged peptide backbone. The PNA has the potential as a very useful biological probe for protein analysis since it has more in vivo biological stability as compared to DNA- or RNA-based aptamers. Usually, the addition of amino acids or peptide to the PNA backbone is used to improve its water-solubility and cell-permeability, but these modifications may affect the interaction between PNA and proteins. To date, the investigation of the interaction between PNA and proteins is rare, and there is no reported study about the effects of modifications. In this work, we designed two types of amino acid modified PNAs, (Lys)₂-PNA and (Glu)₂-PNA, which kept the same base sequence with 15-mer thrombin aptamer and had two basic lysine and two acidic glutamic acid residues on N-terminal of the peptide backbone, respectively. To rapidly assess the binding affinity and specificity of modified PNA and proteins, the online CE reaction method was developed to analyze the interactions of (Lys)₂-PNA/(Glu)₂-PNA and three proteins: thrombin (THB), single-strand DNA-binding protein (SSB) and human serum albumin (HSA). Meanwhile, the interactions of (Lys)₂-PNA/(Glu)₂-PNA and thrombin were compared with that of the corresponding complementary base sequence (Lys)₂-cPNA/(Glu)₂-cPNA and thrombin. The online CE reaction results showed that the interaction of (Lys)₂-PNA and (Glu)₂-PNA with three proteins was in the order of THB > SSB > HSA. However, (Lys)₂-PNA and (Lys)₂-cPNA showed similar binding affinity with thrombin; while the binding affinity of (Glu)₂-PNA with thrombin was stronger than that of (Glu)₂-cPNA with thrombin. Moreover, the binding constant K_b of (Glu)₂-PNA and three proteins was determined by affinity capillary electrophoresis (ACE). The online CE reaction eliminates the requirement of incubation, and thus it is fast in detection, and easy to operate with minimum cost. The method is particularly suitable for the interaction studies of expensive modified PNAs and proteins, and can assist the design of PNA probe that binds to proteins.     

稀土三元配合物的低热固相合成、表征及抑菌活性研究

首次在室温条件下通过固相反应制得了镧稀土水杨酸8-羟基喹啉三元配合物La(Hsal)2(hq)(hq=C9H6NO^-;Hsal^-=C7H5COO^-)。采用元素分析、红外光谱、X射线粉末衍射、热重-差热分析等手段对配合物进行了表征。同时还初步分析了固相反应的机理。抑菌实验表明该配合物对大肠杆菌、金黄色葡萄球菌、白色念珠菌、芽孢杆菌都有很好的抑菌效果。     

一种新多肽表征方法及支持向量机用于肽HPLC定量结构-保留建模预测

从20种天然氨基酸的1369种性质参数经主成分分析得出一种新多肽序列表征方法——SZOTT. 将其用于71个不同长度肽序列表征, 以偏最小二乘(PLS)和支持向量机(SVM)建立定量结构-保留模型(QSRM). 研究表明, SZOTT能够较好表征71个肽序列特征, 其含信息量大且易操作, 与PLS相比, SVM对lgk建模预测表现出较强的拟合能力和良好外部预测能力, SZOTT表征方法和SVM建模可进一步用于肽HPLC保留行为研究.     

Noncovalent Chirality Sensing Ensembles for the Detection and Reaction Monitoring of Amino Acids,Peptides, Proteins,and Aromatic Drugs

Ternary complexes between the macrocyclic host cucurbit[8]uril, dicationic dyes, and chiral aromatic analytes afford strong induced circular dichroism (ICD) signals in the near‐UV and visible regions. This allows for chirality sensing and peptide‐sequence recognition in water at low micromolar analyte concentrations. The reversible and noncovalent mode of binding ensures an immediate response to concentration changes, which allows the real‐time monitoring of chemical reactions. The introduced supramolecular method is likely to find applications in bioanalytical chemistry, especially enzyme assays, for drug‐related analytical applications, and for continuous monitoring of enantioselective reactions, particularly asymmetric catalysis.     

基质辅助激光解析电离质谱用于多肽和蛋白质亚硝基化修饰研究

亚硝基阴离子是生物体内重要的生物调控小分子,广泛分布于生物体的血液和组织中,能使蛋白质发生硝基化和亚硝基化修饰,并且调控生物体的多种生理过程.本研究应用高灵敏度的基质辅助激光解析电离-飞行时间串联质谱(MALDI-TOF-MS)技术,以合成的标准肽段和肌红蛋白为模型系统.研究了蛋白质和多肽主链N端氨基与赖氨酸侧链氨基对HNO2反应的敏感性,并考察了反应体系和不同的反应时间对HNO2与多肽的反应完全程度的影响.结果表明,HNO2能与肽段N端的伯氨基发生重氮化反应,形成的叠氮化中间产物不稳定,放出氮气形成碳正离子,碳正离子可进一步发生取代或消除反应.发生取代反应,水溶液中的羟基取代N-末端氨基形成M+1产物,既使得产物比原肽段分子量多1 Da;发生消除反应,脱掉1分子的氨,又生成M-17烯烃衍生物,从而使产物比原肽段分子量少17 Da.当采用1 mol/L乙酸和1 mol/L的亚硝酸钠作为反应体系时,反应5 min, 肽段的N端氨基即可完全与HNO2反应生成羟基取代产物和烯烃衍生物.而在上述条件下,未发现赖氨酸侧链氨基与HNO2反应,说明HNO2主要与肽段和蛋白的N端氨基发生反应.     

A ZINDO／1-CI Study of Substituted Triphenylamines for Use as Charge Transfer Materials

Electronic spectra of substituted triphenylamines are investigated in this paper by time dependent perturbation theory and ZINDO/1-CI calculation.     

N-亚水杨基苄胺过渡金属配合物的合成、结构与抑菌性能研究(英)

N-salicylidene-benzylamineato M(Ⅱ) complexes (ZnL₂, CuL₂ and CdL₂) were synthesized, characterized and valued for antimicrobial activities against bacterial strands using the agar diffusion method. The crystal of ZnL₂ was determined by X-ray diffraction. It crystallizes in the Monoclinic system, space group C2/c with a=2.269 1(3), b=0.918 2(1), c=1.239 5(2) nm, β=117.89(2), Z=4, R₁=0.049 4, wR₂=0.138 2. The complexes were found to be active against Staphylococcus aureus and Eschierichia Coli. CCDC: 249474.     

Site‐Specific Labeling of Proteins with a Chemically Stable,High‐Affinity Tag for Protein Study

Site‐specific labeling of proteins with paramagnetic lanthanides offers unique opportunities by virtue of NMR spectroscopy in structural biology. In particular, these paramagnetic data, generated by the anisotropic paramagnetism including pseudocontact shifts (PCS), residual dipolar couplings (RDC), and paramagnetic relaxation enhancement (PRE), are highly valuable in structure determination and mobility studies of proteins and protein–ligand complexes. Herein, we present a new way to label proteins in a site‐specific manner with a high‐affinity and chemically stable tag, 4‐vinyl(pyridine‐2,6‐diyl)bismethylenenitrilo tetrakis(acetic acid) (4VPyMTA), through thiol alkylation. Its performance has been demonstrated in G47C and E64C mutants of human ubiquitin both in vitro and in a crowded environment. In comparison with the published tags, 4VPyMTA has several interesting features: 1) it has a very high binding affinity for lanthanides (higher than EDTA), 2) there is no heterogeneity in complexes with lanthanides, 3) the derivatized protein is stable and potentially applicable to the in situ analysis of proteins.     

Interplay of Charge Transfer, Dimensionality, and Amide Hydrogen Bond Network Adaptability in TCNQF4 Complexes of EDO-TTF-CONH2 and EDT-TTF-CONH2

[EDO-TTF-CONH₂][TCNQF₄], triclinic system, space group P-1, a=8.2479(12) Å, b=12.282(2) Å, c=12.6842(18) Å, α=113.850(17)°, β=106.420(17)°, γ=90.284(19)°, V=1116.8(4) ų; and [EDT-TTF-CONH₂]₂[TCNQF₄], triclinic system, space group P-1, a=6.5858(9) Å, b=11.699(2) Å, c=12.2281(18) Å, α=104.000(19)°, β=93.611(17)°, γ=98.279(19)°, V=899.9(3) ų, whose π-donor molecules, (ethylenedioxo)-carbamoyltetrathiafulvalene and (ethylenedithio)-carbamoyltetrathiafulvalene, respectively, differ solely by the nature of the chalcogen atoms in their outer ethylene dichalcogeno bridge, yet form very different charge-transfer complexes with the same π-acceptor. [EDO-TTF-CONH₂^•+]₂ [TCNQF₄^•−]₂ is a diamagnetic insulating ionic salt with a three-dimensional rock-salt-type structure based on discrete dimers while in the semi-conducting mixed-valence complex, [EDT-TTF-CONH₂]₂^•+[TCNQF₄^•−], the mixed-valence dimers aggregate into infinite chains interspersed within parallel rows of non-interacting radical anions. It is shown how the robust and adaptable supramolecular amide hydrogen bond tweezers-like motifs common to the two solids simply comply to the 3-to-1 dimensionality reduction upon substitution of O for S.     

Rare-Earth Metal Complexes of the Antibacterial Drug Oxolinic Acid: Synthesis,Characterization, DNA/Protein Binding and Cytotoxicity Studies

“Drug repositioning” is a current trend which proved useful in the search for new applications for existing, failed, no longer in use or abandoned drugs, particularly when addressing issues such as bacterial or cancer cells resistance to current therapeutic approaches. In this context, six new complexes of the first-generation quinolone oxolinic acid with rare-earth metal cations (Y³⁺, La³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺) have been synthesized and characterized. The experimental data suggest that the quinolone acts as a bidentate ligand, binding to the metal ion via the keto and carboxylate oxygen atoms; these findings are supported by DFT (density functional theory) calculations for the Sm³⁺ complex. The cytotoxic activity of the complexes, as well as the ligand, has been studied on MDA-MB 231 (human breast adenocarcinoma), LoVo (human colon adenocarcinoma) and HUVEC (normal human umbilical vein endothelial cells) cell lines. UV-Vis spectroscopy and competitive binding studies show that the complexes display binding affinities (K_b) towards double stranded DNA in the range of 9.33 × 10⁴ − 10.72 × 10⁵. Major and minor groove-binding most likely play a significant role in the interactions of the complexes with DNA. Moreover, the complexes bind human serum albumin more avidly than apo-transferrin.     

A Study of the Interaction,Morphology, and Structure in Trypsin-Epigallocatechin-3-Gallate Complexes

Understanding the interaction between proteins and polyphenols is of significance to food industries. The aim of this research was to investigate the mode of aggregation for trypsin-EGCG (Epigallocatechin-3-gallate) complexes. For this, the complex was characterized by fluorescence spectroscopy, circular dichroism (CD) spectra, small-angel X-ray scattering (SAXS), and atomic force microscope (AFM) techniques. The results showed that the fluorescence intensity of trypsin-EGCG complexes decreased with increasing the concentration of EGCG, indicating that the interaction between trypsin and EGCG resulted in changes in the microenvironment around fluorescent amino acid residues. The results of CD analysis showed conformational changes in trypsin after binding with EGCG. The results from SAXS analysis showed that the addition of EGCG results in the formation of aggregates of trypsin-EGCG complexes, and increasing the concentration of EGCG resulted in larger aggregates. AFM images showed that the trypsin-EGCG complex formed aggregates of irregular ellipsoidal shapes with the size of about 200 × 400 × 200 nm, with EGCG interconnecting the trypsin particles. Overall, according to these results, it was concluded that the large aggregates of trypsin-EGCG complexes are formed from several small aggregates that are interconnected. The results of this study shed some light on the interaction between digestive enzymes and EGCG.