1
|
JIANG B, GAO B, WEI S, LIANG Z, ZHANG L, ZHANG Y. [Progress in enrichment methods for protein N-phosphorylation]. Se Pu 2024; 42:623-631. [PMID: 38966971 PMCID: PMC11224942 DOI: 10.3724/sp.j.1123.2024.04029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Indexed: 07/06/2024] Open
Abstract
Protein phosphorylation is one of the most common and important post-translational modifications that regulates almost all life processes. In particular, protein phosphorylation regulates the development of major diseases such as tumors, neurodegenerative diseases, and diabetes. For example, excessive phosphorylation of Tau protein can cause neurofibrillary tangles, leading to Alzheimer's disease. Therefore, large-scale methods for identifying protein phosphorylation must be developed. Rapid developmentin efficient enrichment methods and biological mass spectrometry technologies have enabled the large-scale identification of low-abundance protein O-phosphorylation modifications in, allowing for a more thorough study of their biological functions. The N-phosphorylation modifications that occur on the side-chain amino groups of histidine, arginine, and lysine have recently received increased attention. For example, the biological function of histidine phosphorylation in prokaryotes has been well studied; this type of modification regulates signal transduction and sugar metabolism. Two mammalian pHis kinases (NME1 and NME2) and three pHis phosphatases (PHPT1, LHPP, and PGAM5) have been successfully identified using various biological methods. N-Phosphorylation is involved in multiple biological processes, and its functions cannot be ignored. However, N-phosphorylation is unstable under acidic and thermal conditions owing to the poor chemical stability of the P-N bond. Unfortunately, the current O-phosphorylation enrichment method, which relies on acidic conditions, is unsuitable for N-phosphorylation enrichment, resulting in a serious lag in the large-scale identification of protein N-phosphorylation. The lack of enrichment methods has also seriously hindered studies on the biological functions of N-phosphorylation. Therefore, the development of efficient enrichment methods that target protein N-phosphorylation is an urgent undertaking. Research on N-phosphorylation proteome enrichment methods is limited, hindering functional research. Thus, summarizing such methods is necessary to promote further functional research. This article introduces the structural characteristics and reported biological functions of protein N-phosphorylation, reviews the protein N-phosphorylation modification enrichment methods developed over the past two decades, and analyzes the advantages and disadvantages of each method. In this study, both antibody-based and nonantibody-dependent methods are described in detail. Owing to the stability of the molecular structure of histidine, the antibody method is currently limited to histidine phosphorylation enrichment research. Future studies will focus on the development of new enrichment ligands. Moreover, research on ligands will promote studies on other nonconventional phosphorylation targets, such as two acyl-phosphates (pAsp, pGlu) and S-phosphate (pCys). In summary, this review provides a detailed analysis of the history and development directions of N-phosphorylation enrichment methods.
Collapse
|
2
|
Li M, Xiong Y, Qing G. Innovative Chemical Tools to Address Analytical Challenges of Protein Phosphorylation and Glycosylation. Acc Chem Res 2023; 56:2514-2525. [PMID: 37638729 DOI: 10.1021/acs.accounts.3c00397] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
- School of Chemistry and Materials Science, East China University of Technology, Nanchang, Jiangxi 330013, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| |
Collapse
|
3
|
Zhai Z, Dong X, Qi H, Tao R, Zhang P. Carbon Quantum Dots with High Photothermal Conversion Efficiency and Their Application in Photothermal Modulated Reversible Deformation of Poly( N-isopropylacrylamide) Hydrogel. ACS APPLIED BIO MATERIALS 2023; 6:3395-3405. [PMID: 37133748 DOI: 10.1021/acsabm.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The fluorescence of carbon quantum dots (CQDs) has been paid a lot of attention, but its photothermal performance attracts less attention since preparing CQDs with high photothermal conversion efficiency (PCE) is a big challenge. In this work, CQDs with an average size of 2.3 nm and a PCE of up to 59.4% under 650 nm laser irradiation were synthesized by a simple one-pot microwave-assisted solvothermal method using citric acid (CA) and urea (UR) as the precursors and N,N-dimethylformamide as the solvent under an optimized condition (CA/UR = 1/7, 150 °C, and 1 h). The as-prepared CQDs were demonstrated to have unique surface chemical states; i.e., abundant pyrrole, amide, carboxyl, and hydroxyl groups were found on the surfaces of CQDs, which ensure a high PCE. These CQDs were introduced into a thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) to form a CQDs@PNIPAM nanocomposite, and then, a bilayer hydrogel composed of CQDs@PNIPAM and polyacrylamide (PAM) was fabricated. The bilayer hydrogel can be reversibly deformed just by a light switching on/off operation. Based on the excellent photothermal performance, the developed CQDs are expected to be used in photothermal therapy, photoacoustic imaging, and other biomedical fields, and the CQDs@PNIPAM hydrogel nanocomposite is promising to be applied in intelligent device systems as a light-driven smart flexible material.
Collapse
Affiliation(s)
- Zizhuo Zhai
- College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xipeng Dong
- College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongxia Qi
- College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ranting Tao
- Analysis and Test Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Pudun Zhang
- College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
- Analysis and Test Center, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
4
|
Wang L, Zhang Z, Yu D, Yang L, Li L, He Y, Shi J. Recent research of BTK inhibitors: Methods of structural design, pharmacological activities, manmade derivatives and structure-activity relationship. Bioorg Chem 2023; 138:106577. [PMID: 37178649 DOI: 10.1016/j.bioorg.2023.106577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Protein kinases constitute the largest group within the kinase family, and mutations and translocations of protein kinases due to genetic alterations are intimately linked to the pathogenesis of numerous diseases. Bruton's tyrosine kinase (BTK) is a member of the protein kinases and plays a pivotal role in the development and function of B cells. BTK belongs to the tyrosine TEC family. The aberrant activation of BTK is closely associated with the pathogenesis of B-cell lymphoma. Consequently, BTK has always been a critical target for treating hematological malignancies. To date, two generations of small-molecule covalent irreversible BTK inhibitors have been employed to treat malignant B-cell tumors, and have exhibited clinical efficacy in hitherto refractory diseases. However, these drugs are covalent BTK inhibitors, which inevitably lead to drug resistance after prolonged use, resulting in poor tolerance in patients. The third-generation non-covalent BTK inhibitor Pirtobrutinib has obtained approval for marketing in the United States, thereby circumventing drug resistance caused by C481 mutation. Currently, enhancing safety and tolerance constitutes the primary issue in developing novel BTK inhibitors. This article systematically summarizes recently discovered covalent and non-covalent BTK inhibitors and classifies them according to their structures. This article also provides a detailed discussion of binding modes, structural features, pharmacological activities, advantages and limitations of typical compounds within each structure type, providing valuable references and insights for developing safer, more effective and more targeted BTK inhibitors in future studies.
Collapse
Affiliation(s)
- Lin Wang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Zhengjie Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Dongke Yu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Liuqing Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Ling Li
- School of Comprehensive Health Management, Xihua University, Chengdu, Sichuan 610039, China.
| | - Yuxin He
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China.
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China.
| |
Collapse
|
5
|
Zhao Y, Xu W, Zheng H, Jia Q. Light, pH, and Temperature Triple-Responsive Magnetic Composites for Highly Efficient Phosphopeptide Enrichment. Anal Chem 2023. [PMID: 37262441 DOI: 10.1021/acs.analchem.3c01330] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Smart materials can dynamically and reversibly change their structures and functions in response to external stimuli. In this study, we designed a smart magnetic composite (MNP-pSPA-b-pNIPAm) with a triple response to ultraviolet (UV) light, pH, and temperature. Relying on the response of spiropyranyl acrylate (SPA) and N-isopropylacrylamide (NIPAm) to external stimuli (light, pH, and temperature), MNP-pSPA-b-pNIPAm was used for the controlled capture and release of phosphopeptides. The established phosphopeptide enrichment platform exhibits high sensitivity (detection limit of 0.04 fmol), high selectivity (BSA/β-casein, 1000:1), and good reusability (6 cycles). In addition, the method was also applied to the enrichment of phosphopeptides in real samples (skim milk, human saliva, and serum), demonstrating the feasibility of this method for phosphoproteomic analysis. After enriching from human nonsmall cell lung cancer cell (A549) lysates with MNP-pSPA-b-pNIPAm, 2595 phosphopeptides corresponding to 2281 phosphoproteins were identified. The novel responsive enrichment probe is highly specific for phosphoproteomic analysis and provides an effective method for studying the significance of protein phosphorylation in complex biological samples.
Collapse
Affiliation(s)
- Yanqing Zhao
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Wenhui Xu
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Haijiao Zheng
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China
| |
Collapse
|
6
|
Yu J, Wang X, Ren F, Zhang J, Shen J, Liu H, Zhou J. An easy and straightforward synthesized nano calcium phosphate for highly capture of multiply phosphorylated peptides. Anal Chim Acta 2023; 1257:341150. [PMID: 37062565 DOI: 10.1016/j.aca.2023.341150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 04/18/2023]
Abstract
Multisite phosphorylation of proteins regulates various cellular life activities, however, the capture of low abundance multi-phosphopeptides from biosamples and identification of phosphorylation sites are largely limited due to the limited enrichment materials and their unclear interactions with multi-phosphopeptides. Here we propose using two cheap raw materials (CaCl2·2H2O and Na2HPO4·12H2O) in 10 min at room temperature to synthesize the structurally simple Nanometric Calcium Phosphate (CaP) to resolve this challenge. The current results showed that the "simple" CaP has good selection specificity, high sensitivity and stability for multi-phosphopeptides enrichment and the identification of phosphorylation sites, which facilitate the popularization and application of phosphoproteomics research. Further, the interaction of CaP and multi-phosphopeptides were qualitatively characterized at the molecular/atomic level and the high affinity between them was quantified by the isothermal titration microcalorimeter based on the laws of thermodynamics. The results indicated that the interaction was a spontaneous (ΔG < 0) exothermic reaction with enthalpy reduction (ΔH < 0) and driven mainly by hydrogen bond and electrostatic interaction process.
Collapse
Affiliation(s)
- Jialin Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xinhui Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Fangkun Ren
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyi Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jian Shen
- College of Chemistry and Materials Science, Jiangsu Key Laboratory Biofunctional Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Hailong Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Jiahong Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| |
Collapse
|
7
|
Xiong Y, Li M, Cao Y, Li Z, Chang Y, Zhao X, Qing G. Nanofluidic Device for Detection of Lysine Methylpeptides and Sensing of Lysine Methylation. Anal Chem 2023; 95:7761-7769. [PMID: 37140051 DOI: 10.1021/acs.analchem.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein methylation is the smallest possible yet vitally important post-translational modification (PTM). This small and chemically inert addition in proteins makes the analysis of methylation more challenging, thus calling for an efficient tool for the sake of recognition and detection. Herein, we present a nanofluidic electric sensing device based on a functionalized nanochannel that was constructed by introducing monotriazole-containing p-sulfonatocalix[4]arene (TSC) into a single asymmetric polymeric nanochannel via click chemistry. The device can selectively detect lysine methylpeptides with subpicomole sensitivity, distinguish between different lysine methylation states, and monitor the lysine methylation process by methyltransferase at the peptide level in real time. The introduced TSC molecule, with its confined asymmetric configuration, presents the remarkable ability to selectively bind to lysine methylpeptides, which, coupled with the release of the complexed Cu ions, allows the device to transform the molecular-level recognition to the discernible change in ionic current of the nanofluidic electric device, thus enabling detection. This work could serve as a stepping stone to the development of a new methyltransferase assay and the chemical that specifically targets lysine methylation in PTM proteomics.
Collapse
Affiliation(s)
- Yuting Xiong
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
| | - Minmin Li
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yongxin Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| |
Collapse
|
8
|
Zhang J, Xu W, Ma J, Jia Q. Design of reversibly charge-changeable rhodamine B modified magnetic nanoparticles to enrich phosphopeptides. J Chromatogr A 2023; 1697:463992. [PMID: 37080009 DOI: 10.1016/j.chroma.2023.463992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
In the present study, by employing ethylenediaminetetraacetic acid (EDTA), tetraethylene pentaamine (TEPA), and rhodamine B (Rb), we designed and synthesized a magnetic adsorbent (Fe3O4@EDTA@TEPA@Rb) on the basis of reversible charge change of Rb and applied to capture phosphopeptides. Rb existing in open planarized zwitterion form when stimulated by acidic loading buffer adsorbs negative phosphopeptides via electrostatic interaction. Under the stimulation of alkalic eluent, ring-closed structure of Rb is formed to elute the enriched phosphopeptides. TEPA containing rich amino groups is used as a crosslinking agent, which is also protonated in acidic loading buffer to bond phosphopeptides. Then phosphopeptides are eluted when TEPA deprotonates in alkalic eluent. Coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) detection, phosphopeptide signals originated from 0.4 fmol/μL β-casein digests were successfully detected. In addition, Fe3O4@EDTA@TEPA@Rb can also efficiently enrich phosphopeptides from skimmed milk, human serum and saliva samples (26, 4, 39 phosphopeptides, respectively), opening a new gallery for phosphopeptides-related analysis. In general, the developed adsorbent has the great potential for further application in the near future.
Collapse
Affiliation(s)
- Jinfeng Zhang
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Wenhui Xu
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
| |
Collapse
|
9
|
Wang H, Tang R, Jia S, Ma S, Gong B, Ou J. Monodisperse Ti 4+-immobilized macroporous adsorbent resins with polymer brush for improved multi-phosphopeptides enrichment in milk. Mikrochim Acta 2022; 189:405. [PMID: 36197509 DOI: 10.1007/s00604-022-05500-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/15/2022] [Indexed: 10/10/2022]
Abstract
Enrichment of phosphopeptides before mass spectrometry (MS) analysis is essential due to the limitations of low abundance and poor ionization efficiency in complex biological samples. Immobilized metal affinity chromatography (IMAC), especially titanium ion (Ti4+)-IMAC, has become a popular strategy for enrichment of phosphopeptides due to high selectivity and sensitivity. Conventional Ti4+-immobilized macroporous adsorption resin (MAR) fabricated by monolayer modification can preferentially capture mono-phosphopeptide over multi-phosphopeptides, which takes on more functions in the regulation of cell behaviors of organism. In this paper, a kind of monodisperse MAR microsphere with functional polymer brush (Ti4+-Brush@MAR) was prepared and modified via surface-initiated atom transfer radical polymerization (SI-ATRP). Compared with common Ti4+-MAR without polymer brush, Ti4+-Brush@MAR exhibited high enrichment specificity not only for mono-phosphopeptides but also for multi-phosphopeptides in β-casein or milk digest samples. As a result, a total of 93 unique phosphopeptides mapped to 18 phosphoproteins were identified from 5 μL milk, and the limit of detection is 10 fmol. It is expected that Ti4+-Brush@MAR would be utilized to enrich both multi-phosphopeptides and mono-phosphopeptides in additional biological or food samples.
Collapse
Affiliation(s)
- Hongwei Wang
- School of Chemistry and Chemical Engineering, Key Laboratory for Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, 750021, China
| | - Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Shicong Jia
- School of Chemistry and Chemical Engineering, Key Laboratory for Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, 750021, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Bolin Gong
- School of Chemistry and Chemical Engineering, Key Laboratory for Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, 750021, China.
| | - Junjie Ou
- School of Chemistry and Chemical Engineering, Key Laboratory for Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, 750021, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
10
|
Xu Z, Wu Y, Hu X, Deng C, Sun N. Inherently hydrophilic mesoporous channel coupled with metal oxide for fishing endogenous salivary glycopeptides and phosphopeptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.12.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
11
|
ZHAO Y, XU W, JIA Q. [Application of smart responsive materials in phosphopeptide and glycopeptide enrichment]. Se Pu 2022; 40:862-871. [PMID: 36222249 PMCID: PMC9577696 DOI: 10.3724/sp.j.1123.2022.06026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 11/12/2022] Open
Abstract
Phosphorylation and glycosylation of proteins, two of the most widely studied post-translational modifications (PTMs), have shown increasing potential in the early non-invasive diagnosis, prognosis, and therapeutic evaluation of diseases. Besides regulating the function of cell membranes and intracellular signal transduction, protein phosphorylation participates in mitochondrial function and cellular and transcriptional metabolism. Protein glycosylation plays an important role in both intracellular and extracellular signal transduction and intracellular endocytosis. Aberrant phosphorylation and glycosylation of proteins are frequently observed in clinical proteomic studies and in the discovery of disease-related biomarkers. There are generally three methods for detecting protein phosphorylation/glycosylation: isotope radiolabeling, western blotting, and mass spectrometry. Mass spectrometry has become the most important and advantageous detection method due to its high throughput and time- and labor-efficiency. However, phosphopeptides and glycopeptides have low stoichiometry and ionization efficiency, and a large number of non-phosphopeptides and -glycopeptides interference. These issues make it difficult to directly detect phosphopeptides and glycopeptides by mass spectrometry. Therefore, the enrichment of phosphopeptides and glycopeptides before mass spectrometry detection is a key step. At present, a variety of materials have been developed for enrichment studies of phosphopeptides and glycopeptides. For example, immobilized metal affinity (IMAC) and metal oxide affinity chromatography (MOAC) methods are mostly used for the enrichment of phosphopeptides. The IMAC mainly uses positively charged metal ions and negatively charged phosphate groups to attract each other for the purpose of enriching phosphopeptides. MOAC materials rely on the chelation of metal atoms and phosphate oxygens to capture phosphopeptides. IMAC and MOAC materials rely on strong interactions between metals and phosphate groups, which often lead to difficult elution. The enrichment method for glycopeptides is mainly based on the difference in hydrophilicity between glycopeptides and non-glycopeptides, which are mainly enriched by hydrophilic interaction chromatography (HILIC). In addition, materials containing compounds such as boronic acid and lectin materials are also widely used for the separation and enrichment of glycopeptides. Smart responsive materials have also been successively reported for the enrichment of phosphopeptides and glycopeptides due to their unique responsiveness and reversibility. Smart responsive materials can respond to external stimuli; undergo structural and property changes; and convert signals such as optical, electrical, thermal, and mechanical into biochemical signals. Responsive molecules are a prerequisite for determining the response properties of smart responsive materials, and their reversible isomerization under different stimuli (such as temperature, pH, light, mechanical stress, and electromagnetic field) will lead to dynamic changes in the physical and chemical properties of materials. Compared with traditional materials, smart responsive materials can be reversibly "turned on" and "off" with better controllability. Exogenous stimuli, including temperature, light, ultrasound, electromagnetic field, and mechanical stress, can be implemented in a specific time and space. Exogenous responsive materials do not depend on changes in the reaction system itself and are non-invasive. Enzymes, pH, redox, solution polarity, and ionic strength are endogenous stimuli. Endogenous responsive materials depend on changes in the reaction system itself, and sometimes the regulation process requires the introduction of other chemicals into the reaction system. The identification, capture, and release of phosphopeptides or glycopeptides can be achieved by modulating the interactions between smart responsive materials and phosphopeptides or glycopeptides (such as hydrogen bonds, and electrostatic and hydrophobic interactions). This review classifies smart responsive materials according to the types of stimuli, which are specifically divided into exogenous and endogenous responsive materials. The enrichment of phosphopeptides and glycopeptides of exogenous/endogenous responsive materials and endogenous/exogenous co-responsive materials are summarized. In addition, we discuss the development prospects of smart responsive materials in the enrichment of phosphopeptides and glycopeptides, and also raised the challenges existing in the application of smart responsive materials in other protein post-translational modifications.
Collapse
|
12
|
Leong YX, Tan EX, Leong SX, Lin Koh CS, Thanh Nguyen LB, Ting Chen JR, Xia K, Ling XY. Where Nanosensors Meet Machine Learning: Prospects and Challenges in Detecting Disease X. ACS NANO 2022; 16:13279-13293. [PMID: 36067337 DOI: 10.1021/acsnano.2c05731] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Disease X is a hypothetical unknown disease that has the potential to cause an epidemic or pandemic outbreak in the future. Nanosensors are attractive portable devices that can swiftly screen disease biomarkers on site, reducing the reliance on laboratory-based analyses. However, conventional data analytics limit the progress of nanosensor research. In this Perspective, we highlight the integral role of machine learning (ML) algorithms in advancing nanosensing strategies toward Disease X detection. We first summarize recent progress in utilizing ML algorithms for the smart design and fabrication of custom nanosensor platforms as well as realizing rapid on-site prediction of infection statuses. Subsequently, we discuss promising prospects in further harnessing the potential of ML algorithms in other aspects of nanosensor development and biomarker detection.
Collapse
Affiliation(s)
- Yong Xiang Leong
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Emily Xi Tan
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Shi Xuan Leong
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Charlynn Sher Lin Koh
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Lam Bang Thanh Nguyen
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Jaslyn Ru Ting Chen
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Xing Yi Ling
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| |
Collapse
|
13
|
Jiang D, Lv S, Qi R, Liu J, Duan L. Design of two-dimensional molybdenum trioxide-immobilized magnetic graphite nitride nanocomposites with multiple affinity sites for phosphopeptide enrichment. J Chromatogr A 2022; 1678:463374. [DOI: 10.1016/j.chroma.2022.463374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 11/30/2022]
|
14
|
Zn(II)-DPA functionalized graphene oxide two-dimensional nanocomposites for N-phosphoproteins enrichment. Talanta 2022; 243:123384. [DOI: 10.1016/j.talanta.2022.123384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/15/2022]
|
15
|
Synthesis of a metal oxide affinity chromatography magnetic mesoporous nanomaterial and development of a one-step selective phosphopeptide enrichment strategy for analysis of phosphorylated proteins. Anal Chim Acta 2022; 1195:339430. [DOI: 10.1016/j.aca.2022.339430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/05/2021] [Accepted: 01/01/2022] [Indexed: 11/23/2022]
|
16
|
Enrichment of IgG and HRP glycoprotein by dipeptide-based polymeric material. Talanta 2022; 241:123223. [PMID: 35030500 DOI: 10.1016/j.talanta.2022.123223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/30/2022]
Abstract
Separation, purification, and identification of glycoproteins are essential for understanding their vital roles in biological and pathological processes. However, glycoproteins are difficult to be captured due to their low abundance, strong interference from non-glycosylated proteins. Here, we report a promising dipeptide-based saccharide recognition platform to selectively enrich two typical glycoproteins, named immunoglobin G (IgG) and horseradish peroxidase (HRP). Different from the conventional glycoprotein enrichment method based on boronic acid affinity or hydrophilic interaction with glycans, the present method was established based on affinity between Pro-Glu (PE) dipeptide and mannose, which is a key unit in the pentasaccharide core of the IgG and HRP glycans. The prepared PE homopolymer surface was proved to selectively bind IgG and HRP superior to that of bovine serum albumin (BSA). Benefiting from this feature, selective enrichment of IgG and HRP was achieved from a protein mixture containing 200-fold BSA interference by using polyPE@SiO2 under a dispersive solid-phase extraction (dSPE) mode. High adsorption capacity, controllable and selective adsorption behaviors, as well as satisfactory recovery demonstrated the high potential of the dipeptide-based polymeric material in IgG and HRP enrichment. This study might provide a new insight to solve the challenging problem of glycoprotein separation.
Collapse
|
17
|
A novel graphene oxide/chitosan foam incorporated with metal–organic framework stationary phase for simultaneous enrichment of glycopeptide and phosphopeptide with high efficiency. Anal Bioanal Chem 2022; 414:2251-2263. [DOI: 10.1007/s00216-021-03861-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 01/07/2023]
|
18
|
Zhao Y, Li Z, Ma J, Jia Q. Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:55806-55814. [PMID: 34786943 DOI: 10.1021/acsami.1c14739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Smart responsive materials have attractive application prospects due to their tunable behaviors. In this work, we design novel spiropyran (SP)-based magnetic nanoparticles (MNP-SP) with dual response to ultraviolet light and pH and apply them to the enrichment of phosphopeptides. SP is modified on the surface of magnetic nanoparticles through a simple esterification reaction, based on which an MNP-SP-MS phosphopeptide identification platform is established. The capture and release of phosphopeptides are facilely adjusted by changing external light and the pH of the solution. The smart responsive MNP-SP has fast magnetic response performance, high sensitivity (detection limit of 0.4 fmol), and good reusability (6 cycles). In addition, MNP-SP is used for the enrichment of phosphopeptides in skimmed milk, human saliva, and human serum samples, indicating that it is an ideal adsorbent for enriching low-abundance phosphopeptides in complex biological environments.
Collapse
Affiliation(s)
- Yanqing Zhao
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Zheng Li
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China
| |
Collapse
|
19
|
Yu L, Luo B, Zhou X, Liu Y, Lan F, Wu Y. In Situ Controllable Fabrication of Two-Dimensional Magnetic Fe 3O 4/TiO 2@Ti 3C 2T x Composites for Highly Efficient Phosphopeptides Enrichment. ACS APPLIED MATERIALS & INTERFACES 2021; 13:54665-54676. [PMID: 34762403 DOI: 10.1021/acsami.1c13936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Highly efficient enrichment of phosphopeptides is of great significance for phosphoproteomics-related biological and pathological processes research, but it remains challenging due to the lack of affinity materials which hold high enrichment efficiency and capacity. Ti3C2Tx MXene, a novel two-dimensional material with outstanding physicochemical properties, has attracted wide research interests for application in various fields. However, there are few reports on the use of MXene-derived materials for phosphopeptides separation in the biomedical field. In this work, we proposed a facile one-pot method that in situ oxidation and modification of Ti3C2Tx MXene, to prepare two-dimensional (2D) magnetic Fe3O4/TiO2@Ti3C2Tx composites for potential application in phosphopeptides enrichment. Benefiting from the outstanding magnetic responsiveness and multiaffinity sites (Ti-O, Fe-O, and NH2 groups), the Fe3O4/TiO2@Ti3C2Tx composites possessed excellent enrichment performance with high sensitivity (0.1 fmol μL-1), excellent selectivity (β-casein: bovine serum albumin = 1:5000, molar ratio), good repeatability (5 times), and high enrichment capacity (200 mg g-1). Moreover, the results of selective enrichment of phosphopeptides from nonfat milk, human saliva, human serum, and rat brain lysates indicated the great potential of Fe3O4/TiO2@Ti3C2Tx composites in low-abundance phosphopeptides enrichment from complex biological samples. This work has put forward a versatile method to prepare magnetic MXene composites and promoted the use of MXene composites in phosphoproteome in biomedicine.
Collapse
Affiliation(s)
- Lingzhu Yu
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| | - Bin Luo
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| | - Xiaoxi Zhou
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| | - Yicheng Liu
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu610064, P. R. China
| |
Collapse
|
20
|
He Y, Huang W, Zheng Q, Huang H, Ouyang D, Zhang S, Yan X, Ji Y, Wu Y, Lin Z. Two-dimensional guanidinium-based covalent organic nanosheets for controllable recognition and specific enrichment of global/multi-phosphopeptides. Talanta 2021; 233:122497. [PMID: 34215115 DOI: 10.1016/j.talanta.2021.122497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/15/2022]
Abstract
Highly specific capture of phosphopeptides, especially multi-phosphopeptides, from complex biological samples is critical for comprehensive phosphoproteomic analysis, but it still poses great challenges due to the lack of affinity material with ideal enrichment efficiency. Here, two-dimensional (2D) covalent organic framework (COFs) nanosheets was applied for selective separation of phosphopeptides for the first time. Particularly, by incorporating guanidinium units, the 2D guanidinium-based COF nanosheets (denoted as TpTGCl CONs) exhibited controllable and specific enrichment performance towards global/multi-phosphopeptides. TpTGCl CONs was easy to prepare and showed large surface area, low steric hindrance, abundant accessible interaction sites and high chemical stability. Taking these merits together, TpTGCl CONs exhibited excellent efficiency for phosphopeptide enrichment, such as low detection limits (0.05 fmol μL-1 for global phosphopeptides and 0.1 fmol μL-1 for multi-phosphopeptides), high selectivity (1:5000 of molar ratios of β-casein/BSA for both global and multi-phosphopeptides), high adsorption capacity (100 mg g-1 for global phosphopeptides and 50 mg g-1 for multi-phosphopeptides). Furthermore, TpTGCl CONs could be reused due to the high chemical stability. In addition, TpTGCl CONs were successfully applied to controllable and specific capture of endogenous global/multi-phosphopeptides from human serum and human saliva, indicating its good potential in rapid and sensitive detection of biomarkers from biological fluid. Finally, rat liver protein digest was used to confirm the high specificity of TpTGCl CONs towards multi-phosphopeptides and demonstrated its potential as an ideal enrichment probe for comprehensive phosphoproteomic analysis.
Collapse
Affiliation(s)
- Yanting He
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Weini Huang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Qiong Zheng
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Huan Huang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Dan Ouyang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Shasha Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Xi Yan
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yin Ji
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yijing Wu
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Zian Lin
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
| |
Collapse
|
21
|
Kwon G, Kim M, Jung WH, Park S, Tam TTH, Oh SH, Choi SH, Ahn DJ, Lee SH, Kim BS. Designing Cooperative Hydrogen Bonding in Polyethers with Carboxylic Acid Pendants. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Geehwan Kwon
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Minseong Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Woo Hyuk Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Suebin Park
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Thi-Thanh Huynh Tam
- Center for Advanced Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan 44412, Republic of Korea
| | - Seung-Hwan Oh
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea
| | - Dong June Ahn
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Sang-Ho Lee
- Center for Advanced Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan 44412, Republic of Korea
| | - Byeong-Su Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
22
|
Luo B, Yan S, Zhang Y, Zhou J, Lan F, Wu Y. Bifunctional magnetic covalent organic framework for simultaneous enrichment of phosphopeptides and glycopeptides. Anal Chim Acta 2021; 1177:338761. [PMID: 34482887 DOI: 10.1016/j.aca.2021.338761] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023]
Abstract
Protein phosphorylation and glycosylation, which are closely related to various diseases, have been extensively studied recently. Mass spectrometry (MS) based phosphoproteomics and glycoproteomics analysis rely heavily on the pre-treatment. Due to the differences in enrichment conditions, there are still huge challenges in designing and preparing a single affinity material to achieve efficient simultaneous capture and elution of phosphopeptides and glycopeptides. Herein, a novel magnetic covalent organic framework, which was modified with functional molecule 4-(3-(2-(methacryloyloxy)ethyl)-ureido)benzoic acid (MUBA), was designed as a bifunctional enrichment platform for glycopeptides and phosphopeptides. Thanks to the multiple hydrogen bonding interactions between MUBA and hydrogen phosphates, the material possessed excellent enrichment performance for phosphopeptides. In addition, the hydrophilicity of the COF structure and modified molecules endowed this material recognition capability towards glycopeptides based on hydrophilic interaction chromatography. Combining with the inherent properties of COF structure, the established platform achieved simultaneous enrichment of phosphopeptides and glycopeptides with excellent selectivity (1:1:1000 M ratio of α-casein/IgG/BSA), high sensitivity (0.05 fmol/μL α-casein; 0.05 fmol/μL IgG), and good size-exclusion effect (α-casein digests/IgG digests/BSA, 1:1:500). More excitingly, the method was used for the identification of glycopeptides and phosphopeptides from rat liver tissue and the exosomes extracted from liver cancer patients' plasma, proving its specific phosphoproteomics and glycoproteomics study in complex biosamples.
Collapse
Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China
| | - Shuang Yan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China
| | - Yujia Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China.
| |
Collapse
|
23
|
Xu H, Zhang Z, Wang Y, Lu W, Min Q. Engineering of nanomaterials for mass spectrometry analysis of biomolecules. Analyst 2021; 146:5779-5799. [PMID: 34397044 DOI: 10.1039/d1an00860a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) based analysis has received intense attention in diverse biological fields. However, direct MS interrogation of target biomolecules in complex biological samples is still challenging, due to the extremely low abundance and poor ionization potency of target biological species. Innovations in nanomaterials create new auxiliary tools for deep and comprehensive MS characterization of biomolecules. More recently, growing research interest has been directed to the compositional and structural engineering of nanomaterials for enriching target biomolecules prior to MS analysis, enhancing the ionization efficiency in MS detection and designing biosensing nanoprobes in sensitive MS readout. In this review, we mainly focus on the recent advances in the engineering of nanomaterials towards their applications in sample pre-treatment, desorption/ionization matrices and ion signal amplification for MS profiling of biomolecules. This review will provide a toolbox of nanomaterials for researchers devoted to developing analytical methods and practical applications in the biological MS field.
Collapse
Affiliation(s)
- Hongmei Xu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China. and Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yihan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Weifeng Lu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| |
Collapse
|
24
|
[Advances in enrichment of phosphorylated peptides and glycopeptides by smart polymer-based materials]. Se Pu 2021; 39:15-25. [PMID: 34227355 PMCID: PMC9274847 DOI: 10.3724/sp.j.1123.2020.05036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如磷酸化肽和糖肽)丰度很低,且存在着强烈的背景干扰,很难直接用质谱进行分析,因此迫切需要开发高效的富集材料和技术来选择性富集翻译后修饰产物。近年来,智能聚合物基材料通过外部物理、化学或生物刺激可逆地改变其结构和功能,实现对磷酸化肽和糖肽高度可控的吸附和脱附,进而衍生开发出一系列新颖的富集方法,极大地吸引研究者们的兴趣。一方面,智能聚合物基材料的响应变化包括材料疏水性的增加或减少、形状和形貌的改变、表面电荷的重新分布以及亲和配体的暴露或隐藏等特性。这些特性使得目标物和智能聚合物基材料之间的亲和力可以通过简单改变外部条件(如温度、pH值、溶剂极性和生物分子等)实现更可控和更智能的精细调节。另一方面,智能聚合物基材料为集成功能模块提供了便捷的可扩展平台,例如特定的识别组件,显著提高了目标物质的分离选择性。智能聚合物基材料在分离方面展现出巨大的潜力,这为蛋白质翻译后修饰产物的分析和研究带来了希望。围绕上述主题,该文依据Web of Science近20年来近50篇代表性文献,概述了智能聚合物基材料在磷酸化肽和糖肽分离及富集中的发展方向。
Collapse
|
25
|
Poly amidoamine functionalized poly (styrene-divinylbenzene-glycidylmethacrylate) composites for the rapid enrichment and determination of N-phosphoryl peptides. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
26
|
Chen LJ, Humphrey SJ, Zhu JL, Zhu FF, Wang XQ, Wang X, Wen J, Yang HB, Gale PA. A Two-Dimensional Metallacycle Cross-Linked Switchable Polymer for Fast and Highly Efficient Phosphorylated Peptide Enrichment. J Am Chem Soc 2021; 143:8295-8304. [PMID: 34042430 PMCID: PMC8193630 DOI: 10.1021/jacs.0c12904] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The selective and
efficient capture of phosphopeptides is critical
for comprehensive and in-depth phosphoproteome analysis. Here we report
a new switchable two-dimensional (2D) supramolecular polymer that
serves as an ideal platform for the enrichment of phosphopeptides.
A well-defined, positively charged metallacycle incorporated into
the polymer endows the resultant polymer with a high affinity for
phosphopeptides. Importantly, the stimuli-responsive nature of the
polymer facilitates switchable binding affinity of phosphopeptides,
thus resulting in an excellent performance in phosphopeptide enrichment
and separation from model proteins. The polymer has a high enrichment
capacity (165 mg/g) and detection sensitivity (2 fmol), high enrichment
recovery (88%), excellent specificity, and rapid enrichment and separation
properties. Additionally, we have demonstrated the capture of phosphopeptides
from the tryptic digest of real biosamples, thus illustrating the
potential of this polymeric material in phosphoproteomic studies.
Collapse
Affiliation(s)
- Li-Jun Chen
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jun-Long Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Fan-Fan Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xu-Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiang Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials & College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Jin Wen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials & College of Materials Science and Engineering, Donghua University, Shanghai 201620, China.,Institute of Theoretical Chemistry, Faculty of Vienna, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Philip A Gale
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
27
|
Cabral AD, Radu TB, de Araujo ED, Gunning PT. Optical chemosensors for the detection of proximally phosphorylated peptides and proteins. RSC Chem Biol 2021; 2:815-829. [PMID: 34458812 PMCID: PMC8341930 DOI: 10.1039/d1cb00055a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Proximal multi-site phosphorylation is a critical post-translational modification in protein biology. The additive effects of multiple phosphosite clusters in close spatial proximity triggers integrative and cooperative effects on protein conformation and activity. Proximal phosphorylation has been shown to modulate signal transduction pathways and gene expression, and as a result, is implicated in a broad range of disease states through altered protein function and/or localization including enzyme overactivation or protein aggregation. The role of proximal multi-phosphorylation events is becoming increasingly recognized as mechanistically important, although breakthroughs are limited due to a lack of detection technologies. To date, there is a limited selection of facile and robust sensing tools for proximal phosphorylation. Nonetheless, there have been considerable efforts in developing optical chemosensors for the detection of proximal phosphorylation motifs on peptides and proteins in recent years. This review provides a comprehensive overview of optical chemosensors for proximal phosphorylation, with the majority of work being reported in the past two decades. Optical sensors, in the form of fluorescent and luminescent chemosensors, hybrid biosensors, and inorganic nanoparticles, are described. Emphasis is placed on the rationale behind sensor scaffolds, relevant protein motifs, and applications in protein biology.
Collapse
Affiliation(s)
- Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
| |
Collapse
|
28
|
Kawasue S, Sakaguchi Y, Koga R, Hayama T, Yoshida H, Nohta H. Multiple phosphorylated protein selective analysis via fluorous derivatization and liquid chromatography-electrospray ionization-mass spectrometry analysis. Anal Biochem 2021; 628:114247. [PMID: 33965426 DOI: 10.1016/j.ab.2021.114247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/27/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
Post-translational modification of proteins is involved in protein function and higher-order structure. Among such modification, phosphorylation is an important intracellular signal transduction pathway. Many studies on phosphorylated protein analysis using liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) have been developed. However, there are few reports on the analysis of highly phosphorylated proteins because of their handling difficulty. Hence, we developed an analytical method that converts multiple phosphate groups contained in the peptides into perfluoroalkyl groups for selective analysis using fluorous affinity. Here, tryptic digested β-casein fragment peptides [RELEELNVPGEIVE(pSer)L(pSer)(pSer)(pSer)EESITR and FQ(pSer)EEQQQTEDELQDK] were used as model phosphorylated peptides. 1H,1H,2H,2H-Perfluorooctanethiol (PFOT) and 2,2,2-trifluoroethanethiol (TFET) were used as derivatization reagents for mono-phosphorylated peptides and multi-phosphorylated peptides, respectively, to derivatize via β-elimination/Michael addition. The derivatives were analyzed by LC-ESI-MS. A fluorous LC column is typically used to selectively retain the fluorous-derivatized peptides, which are expected to be separated from contaminants and non-phosphorylated peptides. When this method was applied to β-casein, TFET- and PFOT-derivatized peptides were strongly retained in the fluorous LC column and clearly separated from non-phosphorylated peptides on the chromatogram. Therefore, the developed method enables quantification of mono- and multi-phosphorylated peptides and is suitable for application in proteomics.
Collapse
Affiliation(s)
- Shimba Kawasue
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan
| | - Yohei Sakaguchi
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan
| | - Reiko Koga
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan
| | - Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan
| | - Hideyuki Yoshida
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan
| | - Hitoshi Nohta
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka, 814-0180, Japan.
| |
Collapse
|
29
|
Qi H, Li Z, Zheng H, Jia Q. Carnosine functionalized magnetic metal-organic framework nanocomposites for synergistic enrichment of phosphopeptides. Anal Chim Acta 2021; 1157:338383. [PMID: 33832591 DOI: 10.1016/j.aca.2021.338383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 10/21/2022]
Abstract
Protein phosphorylation regulates the conformations and function of proteins, which plays an important part in organisms. However, systematic and in-depth analysis of phosphorylation often hinders on account of the low abundance and suppressed ionization of phosphopeptides. Various materials based on single enrichment mechanism show potential in phosphopeptides enrichment, but the enrichment performance is typically not satisfactory. Herein, we developed a carnosine (Car) functionalized magnetic metal organic framework designed as Fe3O4@NH2@ZIF-90@Car. Benefiting from the multiple recognition groups of Car and massive metal ions site of ZIF-90, the as-fabricated Fe3O4@NH2@ZIF-90@Car was utilized as a multifunctional material with synergistic effect for phosphopeptides enrichment. On the basis of combined immobilized metal ion affinity chromatography (IMAC) and amine-based affinity enrichment mechanism, Fe3O4@NH2@ZIF-90@Car exhibited higher enrichment performance of phosphopeptides compared with Fe3O4@NH2@ZIF-90 (single IMAC mechanism). Besides, the feasibility of Fe3O4@NH2@ZIF-90@Car nanocomposites in complicated samples was further verified by enriching phosphopeptides from nonfat milk, human fluids such as serum and saliva, demonstrating its bright application prospects in phosphoproteomics analysis.
Collapse
Affiliation(s)
- He Qi
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zheng Li
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Haijiao Zheng
- College of Chemistry, Jilin University, Changchun, 130012, China.
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun, 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China.
| |
Collapse
|
30
|
|
31
|
Sheng Q, Wang C, Li X, Qin H, Ye M, Xiong Y, Wang X, Li X, Lan M, Li J, Ke Y, Qing G, Liang X. Highly Efficient Separation of Methylated Peptides Utilizing Selective Complexation between Lysine and 18-Crown-6. Anal Chem 2020; 92:15663-15670. [PMID: 33169968 DOI: 10.1021/acs.analchem.0c04158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein methylation is one of the most common and important post-translational modifications, and it plays vital roles in epigenetic regulation, signal transduction, and chromatin metabolism. However, due to the diversity of methylation forms, slight difference between methylated sites and nonmodified ones, and ultralow abundance, it is extraordinarily challenging to capture and separate methylated peptides from biological samples. Here, we introduce a simple and highly efficient method to separate methylated and nonmethylated peptides using 18-crown-6 as a mobile phase additive in high-performance liquid chromatography. Selective complexation between lysine and 18-crown-6 remarkably increases the retention of the peptides on a C18 stationary phase, leading to an excellent baseline separation between the lysine methylated and nonmethylated peptides. A possible binding mechanism is verified by nuclear magnetic resonance titration, biolayer interferometry technology, and quantum chemistry calculation. Through establishment of a simple enrichment methodology, a good selectivity is achieved and four methylated peptides with greatly improved signal-to-noise (S/N) ratios are successfully separated from a complex peptide sample containing 10-fold bovine serum albumin tryptic digests. By selecting rLys N as an enzyme to digest histone, methylation information in the histone could be well identified based on our enrichment method. This study will open an avenue and provide a novel insight for selective enrichment of lysine methylated peptides in post-translational modification proteomics.
Collapse
Affiliation(s)
- Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiaopei Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yuting Xiong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xue Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junyan Li
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yanxiong Ke
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| |
Collapse
|
32
|
Luo B, Yu L, Li Z, He J, Li C, Lan F, Wu Y. Complementary multiple hydrogen-bond-based magnetic composite microspheres for high coverage and efficient phosphopeptide enrichment in bio-samples. J Mater Chem B 2020; 8:8414-8421. [PMID: 32966536 DOI: 10.1039/d0tb01410a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Due to the number of phosphorylation sites, mono- and multiple-phosphopeptides exhibit significantly different biological effects. Therefore, comprehensive profiles of mono- and multiple-phosphopeptides are vital for the analysis of these biological and pathological processes. However, the most commonly used affinity materials based on metal oxide affinity chromatography (MOAC) show stronger selectivity toward mono-phosphopeptides, thus losing most information on multiple-phosphopeptides. Herein, we report polymer functionalized magnetic nanocomposite microspheres as an ideal platform to efficiently enrich both mono- and multiple-phosphopeptides from complex biological samples. Driven by complementary multiple hydrogen bonding interactions, the composite microspheres exhibited remarkable performance for phosphopeptide enrichment from model proteins and real bio-samples. Excellent selectivity (the molar ratio of nonphosphopeptides/phosphopeptides was 5000 : 1), high enrichment sensitivity (2 fmol) and coverage, as well as high capture rates of multiple-phosphopeptides revealed their great potential in comprehensive phosphoproteomics studies. More importantly, we successfully captured the cancer related phosphopeptides (from the phosphoprotein Stathmin-1) and identified their relevant phosphorylation sites from oral carcinoma patients' saliva and tissue lysate, demonstrating the potential of this material for phosphorylated disease marker detection and discovery.
Collapse
Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Lingzhu Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Zhiyu Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Jia He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Chunjie Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610064, P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| |
Collapse
|
33
|
Liu Y, Xia C, Fan Z, Jiao F, Gao F, Xie Y, He Z, Zhang W, Zhang Y, Shen Y, Qian X, Qin W. Novel Two-Dimensional MoS 2-Ti 4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry. Anal Chem 2020; 92:12801-12808. [PMID: 32966065 DOI: 10.1021/acs.analchem.0c00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS2-Ti4+ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS2 nanosheets and Ti4+. The MoS2-Ti4+ nanomaterials have the advantage of the combined affinity of Ti4+ and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS2-Ti4+ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS2-Ti4+ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS2-Ti4+ nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.
Collapse
Affiliation(s)
- Yuanyuan Liu
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Chaoshuang Xia
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China.,Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Zhiya Fan
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fenglong Jiao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fangyuan Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yuping Xie
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Zhongmei He
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yehua Shen
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| |
Collapse
|
34
|
Li M, Xiong Y, Lu W, Wang X, Liu Y, Na B, Qin H, Tang M, Qin H, Ye M, Liang X, Qing G. Functional Nanochannels for Sensing Tyrosine Phosphorylation. J Am Chem Soc 2020; 142:16324-16333. [PMID: 32894673 DOI: 10.1021/jacs.0c06510] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Tyrosine phosphorylation (pTyr), much of which occurred on localized multiple sites, initiates cellular signaling, governs cellular functions, and its dysregulation is implicated in many diseases, especially cancers. pTyr-specific sensing is of great significance for understanding disease states and developing targeted anticancer drugs, however, it is very challenging due to the slight difference from serine (pSer) or threonine phosphorylation (pThr). Here we present polyethylenimine-g-phenylguanidine (PEI-PG)-modified nanochannels that can address the challenge. Rich guanidinium groups enabled PEI-PG to form multiple interactions with phosphorylated residues, especially pTyr residue, which triggered the conformational change of PEI-PG. By taking advantage of the "OFF-ON" change of the ion flux arising from the conformational shrinkage of the grafted PEI-PG, the nanochannels could distinguish phosphorylated peptide (PP) from nonmodified peptide, recognize PPs with pSer, pThr, or pTyr residue and PPs with different numbers of identical residues, and importantly could sense pTyr peptides in a biosample. Benefiting from the strong interaction between the guanidinium group and the pTyr side-chain, the specific sensing of pTyr peptide was achieved by performing a simple logic operation based on PEI-PG-modified nanochannels when Ca2+ was introduced as an interferent. The excellent pTyr sensing capacity makes the nanochannels available for real-time monitoring of the pTyr process by c-Abl kinase on a peptide substrate, even under complicated conditions, and the proof-of-concept study of monitoring the kinase activity demonstrates its potential in kinase inhibitor screening.
Collapse
Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Wenqi Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xue Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yunhai Liu
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Bing Na
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, East China University of Technology, Nanchang 330013, P. R. China
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Mingliang Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| |
Collapse
|
35
|
Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
Collapse
Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
| |
Collapse
|
36
|
Lu Q, Chen C, Xiong Y, Li G, Zhang X, Zhang Y, Wang D, Zhu Z, Li X, Qing G, Sun T, Liang X. High-Efficiency Phosphopeptide and Glycopeptide Simultaneous Enrichment by Hydrogen Bond–based Bifunctional Smart Polymer. Anal Chem 2020; 92:6269-6277. [DOI: 10.1021/acs.analchem.9b02643] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
- Research & Development Center, Jushi Group. Co., Ltd, 669 Wenhua Road, Tongxiang 314500, China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yuting Xiong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Guodong Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yahui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhichao Zhu
- College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| |
Collapse
|
37
|
|
38
|
Selective enrichment of sialylated glycopeptides with mesoporous poly-melamine-formaldehyde (mPMF) material. Anal Bioanal Chem 2020; 412:1497-1508. [PMID: 32025769 DOI: 10.1007/s00216-020-02415-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/31/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022]
Abstract
Analysis of glycoprotein sialylation is challenging due to the relatively low abundance of sialylated glycopeptides (SGPs) in complex biosamples and low signals of SGPs in mass spectrometry. In this study, a mesoporous poly-melamine-formaldehyde (mPMF) polymer was prepared and utilized as the high-efficiency sorbent for SGPs. The mPMF polymer featured high surface area (755.4 m2 g-1) and high density of amine and triazine functional groups. This polymer demonstrated high enrichment selectivity (resistant to 100 molar fold interference of BSA) and superior adsorption capacity (560 mg g-1) for SGPs. The high performance of mPMF toward SGPs ascribes to the unique physicochemical properties of mPMF and high density of accessible binding sites for glycopeptides. Further application of mPMF to HeLa S3 cell lysate resulted in 576 characterized glycopeptides with 218 unique glycosylation sites. This finding provides a new choice of promising extraction approach for characterization of protein glycosylation. Graphical abstract A mesoporous poly-melamine-formaldehyde (mPMF) polymer was prepared and utilized as the high-efficiency enrichment sorbent for sialylated glycopeptides (SGPs).
Collapse
|
39
|
Xiong F, Jiang L, Jia Q. Facile synthesis of guanidyl-based magnetic ionic covalent organic framework composites for selective enrichment of phosphopeptides. Anal Chim Acta 2020; 1099:103-110. [DOI: 10.1016/j.aca.2019.11.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/17/2019] [Accepted: 11/23/2019] [Indexed: 11/15/2022]
|
40
|
Yu L, Luo B, Li Z, He J, Lan F, Wu Y. PAMAM–PMAA brush-functionalized magnetic composite nanospheres: a smart nanoprobe with tunable selectivity for effective enrichment of mono-, multi-, or global phosphopeptides. J Mater Chem B 2020; 8:1266-1276. [DOI: 10.1039/c9tb02577d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel PAMAM–PMAA brush functionalized magnetic composite nanosphere was successfully prepared for selective enrichment of mono-, multi-, or global phosphopeptides by modulating buffer polarity and acidity.
Collapse
Affiliation(s)
- Lingzhu Yu
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Bin Luo
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Zhiyu Li
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Jia He
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials
- Sichuan University
- Chengdu 610064
- P. R. China
| |
Collapse
|
41
|
Zhang W, Gao G, Ma Z, Luo Z, He M, Sun T. Au 23(CR) 14 nanocluster restores fibril Aβ's unfolded state with abolished cytotoxicity and dissolves endogenous Aβ plaques. Natl Sci Rev 2019; 7:763-774. [PMID: 34692095 PMCID: PMC8289031 DOI: 10.1093/nsr/nwz215] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022] Open
Abstract
The misfolding of amyloid-β (Aβ) peptides from the natural unfolded state to β-sheet structure is a critical step, leading to abnormal fibrillation and formation of endogenous Aβ plaques in Alzheimer's disease (AD). Previous studies have reported inhibition of Aβ fibrillation or disassembly of exogenous Aβ fibrils in vitro. However, soluble Aβ oligomers have been reported with increased cytotoxicity; this might partly explain why current clinical trials targeting disassembly of Aβ fibrils by anti-Aβ antibodies have failed so far. Here we show that Au23(CR)14 (a new Au nanocluster modified by Cys-Arg (CR) dipeptide) is able to completely dissolve exogenous mature Aβ fibrils into monomers and restore the natural unfolded state of Aβ peptides from misfolded β-sheets. Furthermore, the cytotoxicity of Aβ40 fibrils when dissolved by Au23(CR)14 is fully abolished. More importantly, Au23(CR)14 is able to completely dissolve endogenous Aβ plaques in brain slices from transgenic AD model mice. In addition, Au23(CR)14 has good biocompatibility and infiltration ability across the blood-brain barrier. Taken together, this work presents a promising therapeutics candidate for AD treatment, and manifests the potential of nanotechnological approaches in the development of nanomedicines.
Collapse
Affiliation(s)
- Wenkang Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Zhongjie Ma
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Zhuoying Luo
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Meng He
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| |
Collapse
|
42
|
Varadwaj PR. Does Oxygen Feature Chalcogen Bonding? Molecules 2019; 24:E3166. [PMID: 31480378 PMCID: PMC6749412 DOI: 10.3390/molecules24173166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 01/29/2023] Open
Abstract
Using the second-order Møller-Plesset perturbation theory (MP2), together with Dunning's all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R-M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.
Collapse
Affiliation(s)
- Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan.
- The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8560, Japan.
| |
Collapse
|
43
|
Jiang D, Li Z, Jia Q. A sensitive and selective phosphopeptide enrichment strategy by combining polyoxometalates and cysteamine hydrochloride-modified chitosan through layer-by-layer assembly. Anal Chim Acta 2019; 1066:58-68. [DOI: 10.1016/j.aca.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 02/04/2023]
|
44
|
Zhang X, Lu Q, Chen C, Li X, Qing G, Sun T, Liang X. Smart polymers driven by multiple and tunable hydrogen bonds for intact phosphoprotein enrichment. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2019; 20:858-869. [PMID: 31497179 PMCID: PMC6720224 DOI: 10.1080/14686996.2019.1643259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 05/04/2023]
Abstract
Separation of phosphoproteins is essential for understanding their vital roles in biological processes and pathology. Transition metal-based receptors and antibodies, the routinely used materials for phosphoproteins enrichment, both suffer from low sensitivity, low recovery and coverage. In this work, a novel smart copolymer material was synthesized by modifying porous silica gel with a poly[(N-isopropylacrylamide-co-4-(3-acryloylthioureido) benzoic acid)0.35] (denoted as NIPAAm-co-ATBA0.35@SiO2). Driven by the hydrogen bonds complexation of ATBA monomers with phosphate groups, the copolymer-modified surface exhibited a remarkable adsorption toward native α-casein (a model phosphoprotein), accompanied with significant changes in surface viscoelasticity and roughness. Moreover, this adsorption was tunable and critically dependent on the polarity of carrier solvent. Benefiting from these features, selective enrichment of phosphoprotein was obtained using NIPAAm-co-ATBA0.35@SiO2 under a dispersive solid-phase extraction (dSPE) mode. This result displays a good potential of smart polymeric materials in phosphoprotein enrichment, which may facilitate top-down phosphoproteomics studies.
Collapse
Affiliation(s)
- Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P. R. China
- Research & Development Center, Jushi Group. Co., P. R. China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| |
Collapse
|
45
|
Xiao J, Yang SS, Wu JX, Wang H, Yu X, Shang W, Chen GQ, Gu ZY. Highly Selective Capture of Monophosphopeptides by Two-Dimensional Metal–Organic Framework Nanosheets. Anal Chem 2019; 91:9093-9101. [DOI: 10.1021/acs.analchem.9b01581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - He Wang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
46
|
Mirza MR, Rainer M, Duran S, Moin ST, Choudhary MI, Bonn GK. Highly selective enrichment of phosphopeptides using poly(dibenzo‐18‐crown‐6) as a solid‐phase extraction material. Biomed Chromatogr 2019; 33:e4567. [DOI: 10.1002/bmc.4567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/25/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Munazza Raza Mirza
- Institute of Analytical Chemistry and RadiochemistryLeopold‐Franzens University of Innsbruck Innsbruck Austria
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological SciencesUniversity of Karachi Karachi Pakistan
| | - Matthias Rainer
- Institute of Analytical Chemistry and RadiochemistryLeopold‐Franzens University of Innsbruck Innsbruck Austria
| | - Shahid Duran
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological SciencesUniversity of Karachi Karachi Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological SciencesUniversity of Karachi Karachi Pakistan
| | - M. Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological SciencesUniversity of Karachi Karachi Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological SciencesUniversity of Karachi Karachi Pakistan
| | - Günther K. Bonn
- Institute of Analytical Chemistry and RadiochemistryLeopold‐Franzens University of Innsbruck Innsbruck Austria
| |
Collapse
|
47
|
Maeda M, Kojima T, Song Y, Takayama S. DNA-Based Biomaterials for Immunoengineering. Adv Healthc Mater 2019; 8:e1801243. [PMID: 30516349 PMCID: PMC6407644 DOI: 10.1002/adhm.201801243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/05/2018] [Indexed: 12/19/2022]
Abstract
Man-made DNA materials hold the potential to modulate specific immune pathways toward immunoactivating or immunosuppressive cascades. DNA-based biomaterials introduce DNA into the extracellular environment during implantation or delivery, and subsequently intracellularly upon phagocytosis or degradation of the material. Therefore, the immunogenic functionality of biological and synthetic extracellular DNA should be considered to achieve desired immune responses. In vivo, extracellular DNA from both endogenous and exogenous sources holds immunoactivating functions which can be traced back to the molecular features of DNA, such as sequence and length. Extracellular DNA is recognized as damage-associated molecular patterns (DAMPs), or pathogen-associated molecular patterns (PAMPs), by immune cell receptors, activating either proinflammatory signaling pathways or immunosuppressive cell functions. Although extracellular DNA promotes protective immune responses during early inflammation such as bacterial killing, recent advances demonstrate that unresolved and elevated DNA concentrations may contribute to the pathogenesis of autoimmune diseases, cancer, and fibrosis. Therefore, addressing the immunogenicity of DNA enables immune responses to be engineered by optimizing their activating and suppressive performance per application. To this end, emerging biology relevant to the generation of extracellular DNA, DNA sensors, and its role concerning existing and future synthetic DNA biomaterials are reviewed.
Collapse
Affiliation(s)
- Midori Maeda
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Dr NW. Atlanta, GA 30332 USA
- The Parker H Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta GA 30332 USA
| | - Taisuke Kojima
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Dr NW. Atlanta, GA 30332 USA
- The Parker H Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta GA 30332 USA
| | - Yang Song
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Dr NW. Atlanta, GA 30332 USA
- The Parker H Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta GA 30332 USA
| | - Shuichi Takayama
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Dr NW. Atlanta, GA 30332 USA
- The Parker H Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta GA 30332 USA,
| |
Collapse
|
48
|
Chen Z, Sun T, Qing G. cAMP-modulated biomimetic ionic nanochannels based on a smart polymer. J Mater Chem B 2019. [DOI: 10.1039/c9tb00639g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dynamic gating behaviour of ionic nanochannel is precisely manipulated by cyclic 3′,5′-adenosine monophosphate (cAMP) by taking advantage of reversible conformational transition of the smart polymer chains in response to cAMP specific adsorption, which provides a new idea for developing smart nanochannels regulated by crucial signal-biomolecules.
Collapse
Affiliation(s)
- Zhixiang Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
- Key Laboratory of Separation Science for Analytical Chemistry
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| |
Collapse
|
49
|
Peng J, Niu H, Zhang H, Yao Y, Zhao X, Zhou X, Wan L, Kang X, Wu R. Highly Specific Enrichment of Multi-phosphopeptides by the Diphosphorylated Fructose-Modified Dual-Metal-Centered Zirconium-Organic Framework. ACS APPLIED MATERIALS & INTERFACES 2018; 10:32613-32621. [PMID: 30156824 DOI: 10.1021/acsami.8b11138] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multisite phosphorylation of a protein, generally occurring in biological processes, plays important roles in the regulation of cellular functions. However, the identification of multi-phosphopeptides especially at low abundance is a big challenge as the extreme hydrophilicity and poor ionization efficiency of the multiphosphorylated peptides restrict the deep inspection of multisite phosphorylation processes. In this study, the highly specific enrichment of multiphosphorylated peptides was achieved via the modification of the dual-metal-centered zirconium-organic framework with the diphosphorylated fructose. The diphosphorylated fructose-modified dual-metal-centered zirconium-organic framework (DZMOF-FDP) demonstrated the highly specific affinity to the multiple phosphorylated peptides, with the density functional theory calculations explaining the plausible mechanism for multi-phosphopeptides on the DZMOF-FDP. The selective capture of multi-phosphopeptides from mimic samples confirmed the superior performance of the DZMOF-FDP, with comprehensive comparisons to other modification agents, such as orthophosphate and pyrophosphate. A number of 1871 multiphosphorylated peptides captured by DZMOF-FDP from tryptic digests of HeLa cell lysate could be identified, significantly higher than that by the pristine DZMOF. The deliberately designed modification with diphosphorylated fructose for the dual-zirconium-centered metal-organic framework materials suggests an efficient strategy to develop new enrichment methods in the selective capture of target analytes by judiciously optimizing specific modifiers for adsorbents.
Collapse
Affiliation(s)
- Jiaxi Peng
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Huan Niu
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongyan Zhang
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yating Yao
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xingyun Zhao
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiaoyu Zhou
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Lihong Wan
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
| | - Xiaohui Kang
- College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Ren'an Wu
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
| |
Collapse
|
50
|
Hong Y, Zhan Q, Pu C, Sheng Q, Zhao H, Lan M. Highly efficient enrichment of phosphopeptides from HeLa cells using hollow magnetic macro/mesoporous TiO2 nanoparticles. Talanta 2018; 187:223-230. [DOI: 10.1016/j.talanta.2018.05.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/12/2018] [Accepted: 05/08/2018] [Indexed: 02/02/2023]
|