基于质谱技术的蛋白质互作研究进展

doi:10.19586/j.2095-2341.2021.0137

生物技术进展 ›› 2022, Vol. 12 ›› Issue (2): 161-167.DOI: 10.19586/j.2095-2341.2021.0137

• 进展评述 • 下一篇

基于质谱技术的蛋白质互作研究进展

孙瑞雪¹^,²(), 米薇²(), 叶子弘¹()

^1.中国计量大学生命科学学院，杭州 310018
^2.中国计量科学研究院，北京 100029

收稿日期:2021-07-17 接受日期:2021-11-08 出版日期:2022-03-25 发布日期:2022-03-25
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:
国家重点研发计划项目(2021YFF0600803);国家市场监督管理总局技术保障专项项目(2020YJ054)

Research Advances in Protein Interactions Based on Mass Spectrometry

Ruixue SUN¹^,²(), Wei MI²(), Zihong YE¹()

^1.College of Life Sciences，China Jiliang University，Hangzhou 310018，China
^2.National Institute of Metrology，Beijing 100029，China

Received:2021-07-17 Accepted:2021-11-08 Online:2022-03-25 Published:2022-03-25
Contact: Wei MI,Zihong YE

摘要/Abstract

摘要：

蛋白质作为生命活动的执行者，其功能往往体现在与其他蛋白质的相互作用中，研究蛋白-蛋白相互作用对于人们深入了解和预防传染病、靶向治疗多基因疾病、阐明蛋白质的分子作用机制及各种复杂的生命现象具有重要意义。目前，有多种技术被用来研究蛋白间的相互作用，研究难点在于实时捕获瞬时或弱蛋白质间的相互作用，质谱技术（mass spectrometry, MS）可在某种程度上解决该难点。由于质谱技术可研究简单的蛋白质复合物再到大规模的蛋白质组实验，基于质谱技术研究蛋白质间相互作用被越来越多地应用于科学研究中。综述了蛋白质间相互作用检测方法的研究进展，重点介绍了氢氘交换质谱法和化学交联质谱法研究蛋白质间相互作用的优缺点及其应用，最后对基于质谱技术研究蛋白质间相互作用进行了总结与展望，以期为深入开展相关研究提供借鉴。

关键词: 蛋白-蛋白相互作用, 蛋白质结构, 氢氘交换质谱法, 化学交联质谱法

Abstract:

As the executor of life activities， the protein function is often reflected in the interaction with other proteins. The study of protein-protein interaction is of great significance for people to understand the prevention of infectious diseases， targeted treatment of multi-gene diseases， and elucidate the molecular mechanism of protein and various complex life phenomena. At present， a variety of techniques have been used to study protein-protein interactions. The difficulty lies in real-time capture of transient or weak protein-protein interactions， mass spectrometry （MS） can solve this difficulty to some extent. Because mass spectrometry can be used to study simple protein complexes and large-scale proteome experiments， the study of protein interactions based on mass spectrometry has been increasingly applied in scientific research. In this paper， the research progress of protein-protein interaction detection methods was reviewed， and the advantages and disadvantages of hydrogen deuterium exchange mass spectrometry and chemical crosslinking mass spectrometry and their applications were emphasized. Finally， the research on protein-protein interaction based on mass spectrometry was summarized and prospected， which aimed to provide reference for further research.

Key words: protein-protein interaction, protein structure, hydrogen deuterium exchange mass spectrometry, chemical cross-linking mass spectrometry

中图分类号:

Q816

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.

Ruixue SUN, Wei MI, Zihong YE. Research Advances in Protein Interactions Based on Mass Spectrometry[J]. Current Biotechnology, 2022, 12(2): 161-167.

图/表 2

参考文献 55

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.

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

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

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

基于质谱技术的蛋白质互作研究进展

Research Advances in Protein Interactions Based on Mass Spectrometry

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