Current Biotechnology ›› 2022, Vol. 12 ›› Issue (2): 161-167.DOI: 10.19586/j.2095-2341.2021.0137
• Reviews • Next Articles
Ruixue SUN1,2(
), Wei MI2(
), Zihong YE1(
)
Received:2021-07-17
Accepted:2021-11-08
Online:2022-03-25
Published:2022-03-25
Contact:
Wei MI,Zihong YE
通讯作者:
米薇,叶子弘
作者简介:孙瑞雪 E-mail: 2528041495@qq.com
基金资助:CLC Number:
Ruixue SUN, Wei MI, Zihong YE. Research Advances in Protein Interactions Based on Mass Spectrometry[J]. Current Biotechnology, 2022, 12(2): 161-167.
孙瑞雪, 米薇, 叶子弘. 基于质谱技术的蛋白质互作研究进展[J]. 生物技术进展, 2022, 12(2): 161-167.
| 经典蛋白质互作方法 | 优点 | 缺点 |
|---|---|---|
| 酵母双杂交技术 | 能捕获到微弱或瞬时的蛋白质互作且性价比高 | 假阳性率高,转化率低 |
| 蛋白质芯片技术 | 通量高 | 特异性低 |
| 表面等离子共振技术 | 可快速测试、可用于蛋白质互作的定量分析 | 易受温度、样品组成等条件干扰 |
| 荧光共振能量转移技术 | 可以直接在活细胞环境中使用;检测相互作用位点;监测复杂的相互作用动力学 | 易受自发荧光、光学噪声和检测器噪声干扰 |
| 串联亲和纯化法 | 可信度高、能降低非特异性结合、假阳性率和假阴性率低 | 不能高效识别较弱/瞬时蛋白质互作,且价格昂贵 |
| 双分子荧光互补技术 | 灵敏度高,可用于不同的生物体,设置简单,成本效益高 | 不能实时反映蛋白的互作情况 |
| 免疫共沉淀技术 | 操作简单,蛋白互作复合物可在天然状态下获得 | 需要特定的抗体或标签的蛋白质 |
| 噬菌体展示技术 | 高通量、容易操控 | 难以有效表达和展示有毒分子 |
| 谷胱甘肽转移酶沉淀实验 | 体外验证蛋白质互作特异性强 | 无法解释天然蛋白质互作 |
| 蛋白片段互补 | 灵敏度高且能检测瞬时互作蛋白 | 易产生假阳性结果,外源蛋白质的过量表达会对细胞产生毒害 |
Table 1 Advantages and disadvantages of classical protein interaction methods
| 经典蛋白质互作方法 | 优点 | 缺点 |
|---|---|---|
| 酵母双杂交技术 | 能捕获到微弱或瞬时的蛋白质互作且性价比高 | 假阳性率高,转化率低 |
| 蛋白质芯片技术 | 通量高 | 特异性低 |
| 表面等离子共振技术 | 可快速测试、可用于蛋白质互作的定量分析 | 易受温度、样品组成等条件干扰 |
| 荧光共振能量转移技术 | 可以直接在活细胞环境中使用;检测相互作用位点;监测复杂的相互作用动力学 | 易受自发荧光、光学噪声和检测器噪声干扰 |
| 串联亲和纯化法 | 可信度高、能降低非特异性结合、假阳性率和假阴性率低 | 不能高效识别较弱/瞬时蛋白质互作,且价格昂贵 |
| 双分子荧光互补技术 | 灵敏度高,可用于不同的生物体,设置简单,成本效益高 | 不能实时反映蛋白的互作情况 |
| 免疫共沉淀技术 | 操作简单,蛋白互作复合物可在天然状态下获得 | 需要特定的抗体或标签的蛋白质 |
| 噬菌体展示技术 | 高通量、容易操控 | 难以有效表达和展示有毒分子 |
| 谷胱甘肽转移酶沉淀实验 | 体外验证蛋白质互作特异性强 | 无法解释天然蛋白质互作 |
| 蛋白片段互补 | 灵敏度高且能检测瞬时互作蛋白 | 易产生假阳性结果,外源蛋白质的过量表达会对细胞产生毒害 |
| 基于质谱的蛋白质互作方法 | 优点 | 缺点 |
|---|---|---|
| 亲和纯化⁃质谱 | 可以得到高度可靠的蛋白质互作数据,可以捕获和鉴定目的蛋白的直接和间接结合因子 | 不能轻易区分直接和间接相互作用 |
| 生物素鉴定⁃质谱 | 允许检测可溶性蛋白和膜蛋白中的PPI | 过氧化物酶可能会与生物素⁃苯酚和过氧化氢反应,产生反应性自由基,导致细胞毒性 |
氢氘交换质谱法 | 对样品及纯度要求低,研究对象不是晶体构象,而是溶液中的蛋白质天然构象 | 存在氢和氘回交的现象,这会对实验结果的准确性产生不利影响,需将温度和pH控制在最低回交反应系数的范围内 |
化学交联质谱法 | 通量高;分析速度快;应用范围广;部分交联剂可进行细胞内交联;无需对蛋白质进行特殊的化学标记 | 交联剂反应位点具有特异性、交联肽段丰度低、交联肽段谱图复杂、解析困难 |
Table 2 Advantages and disadvantages of protein interaction methods based on mass spectrometry
| 基于质谱的蛋白质互作方法 | 优点 | 缺点 |
|---|---|---|
| 亲和纯化⁃质谱 | 可以得到高度可靠的蛋白质互作数据,可以捕获和鉴定目的蛋白的直接和间接结合因子 | 不能轻易区分直接和间接相互作用 |
| 生物素鉴定⁃质谱 | 允许检测可溶性蛋白和膜蛋白中的PPI | 过氧化物酶可能会与生物素⁃苯酚和过氧化氢反应,产生反应性自由基,导致细胞毒性 |
氢氘交换质谱法 | 对样品及纯度要求低,研究对象不是晶体构象,而是溶液中的蛋白质天然构象 | 存在氢和氘回交的现象,这会对实验结果的准确性产生不利影响,需将温度和pH控制在最低回交反应系数的范围内 |
化学交联质谱法 | 通量高;分析速度快;应用范围广;部分交联剂可进行细胞内交联;无需对蛋白质进行特殊的化学标记 | 交联剂反应位点具有特异性、交联肽段丰度低、交联肽段谱图复杂、解析困难 |
| 1 | BISSANTZ C, KUHN B, STAHL M. A medicinal chemist's guide to molecular interactions[J]. J. Med. Chem., 2010, 53 (14):5061-5084. |
| 2 | WANG W, SINGH S, ZENG D L, et al.. Antibody structure, instability, and formulation[J]. J. Pharm Sci., 2007, 96(1): 1-26. |
| 3 | BECK A, WURCH T, BAILLY C, et al.. Strategies and challenges for the next generation of therapeutic antibodies[J]. Nat. Rev. Immunol., 2010, 10(5):345-352. |
| 4 | 吴梅,刘小云.生物质谱在蛋白-蛋白相互作用研究中的应用[J].生命的化学,2017,37(1):2-8. |
| 5 | FAINI M, STENGEL F, AEBERSOLD R, et al.. The evolving contribution of mass spectrometry to integrative structural biology[J]. J. Am. Soc. Mass Spectrom., 2016, 27(6): 966-974. |
| 6 | MA L, YANG F, ZHENG J. Application of fluorescence resonance energy transfer in protein studies[J]. J. Mol. Struct., 2017, 1077: 87-100. |
| 7 | STROTH N. A surface plasmon resonance-based method for monitoring interactions between G protein-coupled receptors and interacting proteins[J]. J. Biol. Methods, 2016,3(1): 1-9. |
| 8 | HOMOLA J. Surface plasmon resonance sensors for detection of chemical and biological species[J]. Chem. Rev., 2008, 108(2):462-493. |
| 9 | LUR M, HWANG Y C, LIU I J, et al.. Development of therapeutic antibodies for the treatment of diseases[J]. J. Biomed. Sci., 2020, 27(1): 1-27. |
| 10 | MILLER K E, KIM Y, HUH W K, et al.. Bimolecular fluorescence complementation (BiFC) analysis: advances and recent applications for genome-wide interaction studies[J]. J. Mol. Biol., 2015, 427(11): 2039-2055. |
| 11 | POLGE C, LENTZE N, AUERBACH D, et al.. Two-hybrid, a powerful tool for systems biology[J]. Int. J. Mol. Sci., 2009, 10(6): 2763-2788. |
| 12 | HAMDI A, COLAS P. Yeast two-hybrid methods and their applications in drug discovery[J]. Trends Pharmacol. Sci., 2012, 33(2): 109-118. |
| 13 | 王婷,葛怀娜,郭宏.酵母双杂交技术应用进展[J].生物技术进展,2015,5(5):392-396. |
| 14 | FERRO E, TRABALZINI L. The yeast two-hybrid and related methods as powerful tools to study plant cell signalling[J]. Plant Mol. Biol., 2013, 83(4-5): 287-301. |
| 15 | DUNHAM W H, MULLIN M, GINGRAS A C. Affinity-purification coupled to mass spectrometry: basic principles and strategies[J]. Proteomics, 2012,12(10): 1576-1590. |
| 16 | MANN M. Functional and quantitative proteomics using SILAC[J]. Nat. Rev. Mol. Cell Biol., 2006,7(12):952-958. |
| 17 | VERMEULEN M, HUBNER N C, MANN M. High confidence determination of specific protein-protein interactions using quantitative mass spectrometry[J]. Curr. Opin. Biotechnol., 2008,19(4): 331-337. |
| 18 | TRINKLE-MULCAHY, BOULON S, LAM Y W, et al.. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes[J]. J. Cell Biol., 2008,183(2): 223-239. |
| 19 | XU X, SONG Y, LI Y, et al.. The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification[J]. Protein Expr. Purif., 2010, 72(2):149-156. |
| 20 | ROUX K J, KIM D I, RAIDA M, et al.. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells[J]. J. Cell Biol., 2012, 196(6): 801-810. |
| 21 | SNIDER J, KOTLYAR M, SARAONET P, et al.. Fundamentals of protein interaction network mapping[J/OL]. Mol. Syst. Biol., 2015, 11(12):848[2021-08-26]. . |
| 22 | 陈学明,刘姿,马亮.活细胞内临近标记技术BioID在蛋白质相互作用研究中的进展[J].生命的化学,2021,41(5):996-1002. |
| 23 | LEE J J, PARK Y S, LEE K J. Hydrogen-deuterium exchange mass spectrometry for determining protein structural changes in drug discovery[J]. Arch. Pharm. Res., 2015, 38(10):1737-1745. |
| 24 | PUCHADES C, KUKRER B, DIEFENBACH O, et al.. Epitope mapping of diverse influenza Hemagglutinin drug candidates using HDX-MS[J/OL]. Sci. Rep., 2019,9(1):4735[2021-08-26].. |
| 25 | DENG B, LENTO C, WILSON D J. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development-A review[J]. Anal. Chim. Acta., 2016, 940: 8-20. |
| 26 | KONERMANN L, RODRIGUEZ A D, SOWOLE M A. Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein-ligand complexes[J]. Analyst, 2014, 139(23):6078-6087. |
| 27 | WEI H, MO J, TAO L, et al.. Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications[J]. Drug Discov. Today, 2014, 19(1):95-102. |
| 28 | ZHANG H, CUI W, GROSS M L. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies[J]. FEBS Lett., 2014, 588(2):308-317. |
| 29 | ABBOTT W M, DAMSCHRODER M M, LOWE D C. Current approaches to fine mapping of antigen antibody interactions[J]. Immunology, 2014, 142(4):526-535. |
| 30 | PAN L Y, SALAS-SOLANO O, VALLIERE-DOUGLASS J F. Conformation and dynamics of interchain cysteine-linked antibody-drug conjugates as revealed by hydrogen/deuterium exchange mass spectrometry[J]. Anal. Chem., 2014, 86(5):2657-2664. |
| 31 | HUANG R Y, KUHNE M, DESHPANDE S, et al.. Mapping binding epitopes of monoclonal antibodies targeting major histocompatibility complex class I chain related a (MICA) with hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry[J]. Anal. Bioanal. Chem., 2020,412(7):1693-1700. |
| 32 | MCKENZIE-COE A, SHORTT R, JONES L M. The making of a footprint in protein footprinting: a review in honor of Michael L. Gross [J]. Mass Spectrom. Rev., 2021, 40(3):177-200. |
| 33 | YANG D, FREGO L, LASARO M, et al.. Efficient qualitative and quantitative determination of antigen-induced immune responses[J]. J. Biol. Chem., 2016, 291(31): 16361-16374. |
| 34 | DOMINA M, CARICCIO V L, BENFATTO S, et al.. Epitope mapping of a monoclonal antibody directed against neisserial heparin binding antigen using next generation sequencing of antigen-specific libraries[J]. PLoS ONE, 2016,11 (8): 1-17. |
| 35 | RAFALIK M, SPODZIEJA M, KOLODZIEJCZYK A S, et al.. The identification of discontinuous epitope in the human cystatin C-monoclonal antibody HCC3 complex[J]. J. Proteome., 2019, 191:58-67. |
| 36 | CALVARESI V, REDSTED A, NORAIS N, et al.. Hydrogen-Deuterium exchange mass spectrometry with integrated size-exclusion chromatography for analysis of complex protein samples[J]. Anal. Chem., 2021, 93(33): 11406-11414. |
| 37 | HUANG R Y, KUHNE M, DESHPANDE S, et al.. Mapping binding epitopes of monoclonal antibodies targeting major histocompatibility complex class I chain-related A (MICA) with hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry[J]. Anal. Bioanal. Chem., 2020, 412(7): 1693-1700. |
| 38 | BERESZCZAK J Z, ROSE R J, WATTS N R, et al.. Epitope-distal effects accompany the binding of two distinct antibodies to hepatitis B virus capsids[J]. J. Am. Chem. Soc., 2013,135(17):6504-6512. |
| 39 | FERNANDEZ E, KOSE N, EDELING M A, et al.. Mouse and human monoclonal antibodies protect against infection by multiple genotypes of Japanese encepha-litis virus[J/OL]. MBio, 2018,9(1):e00008-18[2022-01-24]. . |
| 40 | SPERRY J B, SMITH C L, CAPARON M G, et al.. Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes [J]. Biochemistry, 2011, 5(19):4038-4045. |
| 41 | 樊盛博,吴妍洁,杨兵 等.蛋白质结构与相互作用研究新方法-交联质谱技术[J].生物化学与生物物理进展,2014,41(11):1109-1125. |
| 42 | CHAVEZ J D, LEE C F, CAUDAL A, et al.. Chemical crosslinking mass spectrometry analysis of protein conformations and super complexes in heart tissue[J]. Cell Syst., 2018, 6(1):136-141. |
| 43 | HUANG B X, KIM H Y, DASS C. Probing three-dimensional structure of bovine serum albumin by chemical cross-linking and mass spectrometry[J]. J. Am. Soc. Mass Spectrom., 2004,15(8):1237-1247. |
| 44 | KAAKE R M, WANG X, BURKE A, et al.. A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells[J]. Mol. Cell Proteomics., 2014, 13(12): 3533-3543. |
| 45 | LIU F, RIJKERS D T, POST H, et al.. Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry[J]. Nat. Methods, 2015, 12(12): 1179-1184. |
| 46 | XU W, BEEBE K, CHAVEZ J D, et al.. Hsp90 middle domain phosphorylation initiates a complex conformational program to recruit the ATPase-stimulating cochaperone Aha1[J/OL]. Nat. Commun., 2019, 10(1): 2574[2021-08-26].. |
| 47 | CHAVEZ J D, ENG J K. SCHWEPPE D K,et al.. A general method for targeted quantitative cross-linking mass spectrometry[J]. PLoS ONE, 2016, 11(12):1-14. |
| 48 | PIERSIMONI L, SINZ A. Cross-linking/mass spectrometry at the crossroads[J]. Anal. Bioanal. Chem., 2020, 412(24): 5981-5987. |
| 49 | LIU F, HECK A J. Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry[J]. Curr. Opin. Struct., Biol., 2015,35:100-108. |
| 50 | YU C, HUANG L. Cross-linking mass spectrometry: an emerging technology for interactomics and structural biology[J]. Anal. Chem., 2018, 90(1): 144-165. |
| 51 | COUROUBLE V V, DEY S K, YADAV R, et al.. Revealing the structural plasticity of SARS-CoV-2 nsp7 and nsp8 using structural proteomics[J]. J. Am. Soc. Mass Spectrom., 2021, 32(7): 1618-1630. |
| 52 | ZHANG M M, ADHIKARI J, BENO B R, et al.. An integrated approach for determining a protein-protein binding interface in solution and an evaluation of hydrogen-deuterium exchange kinetics for adjudicating candidate docking models[J]. Anal. Chem., 2019, 91(24): 15709-15717. |
| 53 | DE JONG L, BUNCHERD H, ROSEBOOM W, et al.. In-culture cross-linking of bacterial cells reveals large-scale dynamic protein-protein interactions at the peptide level[J]. J. Proteome Res., 2017, 16(7):2457-2471. |
| 54 | WALKER-GRAY R, STENGEL F, GOLD M G, et al.. Mechanisms for restraining cAMP-dependent protein kinase revealed by subunit quantitation and cross-linking approaches[J]. Proc. Natl. Acad. Sci. USA, 2017, 114(39):10414-10419. |
| 55 | LEITNER A, FAINI M, STENGEL F, et al.. Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines[J]. Trends Biochem. Sci., 2016, 41(1):20-32. |
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