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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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2
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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Polymeric sorbents modified with gold and silver nanoparticles for solid-phase extraction of proteins followed by MALDI-TOF analysis. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2168-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jagusztyn-Krynicka EK, Dadlez M, Grabowska A, Roszczenko P. Proteomic technology in the design of new effective antibacterial vaccines. Expert Rev Proteomics 2014; 6:315-30. [DOI: 10.1586/epr.09.47] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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6
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Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues. Nat Protoc 2012. [PMID: 23196971 DOI: 10.1038/nprot.2012.129] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to the low abundance of signaling proteins and transcription factors, their protein complexes are not easily identified by classical proteomics. The isolation of these protein complexes from endogenous plant tissues (rather than plant cell cultures) is therefore an important technical challenge. Here, we describe a sensitive, quantitative proteomics-based procedure to determine the composition of plant protein complexes. The method makes use of fluorophore-tagged protein immunoprecipitation (IP) and label-free mass spectrometry (MS)-based quantification to correct for nonspecifically precipitated proteins. We provide procedures for the isolation of membrane-bound receptor complexes and transcriptional regulators from nuclei. The protocol consists of an IP step (~6 h) and sample preparation for liquid chromatography-tandem MS (LC-MS/MS; 2 d). We also provide a guide for data analysis. Our single-step affinity purification protocol is a good alternative to two-step tandem affinity purification (TAP), as it is shorter and relatively easy to perform. The data analysis by label-free quantification (LFQ) requires a cheaper and less challenging experimental setup compared with known labeling techniques in plants.
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Wang X, Chen G, Zhao Z, Wang X, Li Z. Proteomics-based Characterization of Protein Complexes from Human Pancreatic Cancer Cell Line. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Tian R, Hoa XD, Lambert JP, Pezacki JP, Veres T, Figeys D. Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions. Anal Chem 2011; 83:4095-102. [PMID: 21520965 DOI: 10.1021/ac200194d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry-based proteomics techniques have been very successful for the identification and study of protein-protein interactions. Typically, immunopurification of protein complexes is conducted, followed by protein separation by gel electrophoresis and in-gel protein digestion, and finally, mass spectrometry is performed to identify the interacting partners. However, the manual processing of the samples is time-consuming and error-prone. Here, we developed a polymer-based microfluidic proteomic reactor aimed at the parallel analysis of minute amounts of protein samples obtained from immunoprecipitation. The design of the proteomic reactor allows for the simultaneous processing of multiple samples on the same devices. Each proteomic reactor on the device consists of SCX beads packed and restricted into a 1 cm microchannel by two integrated pillar frits. The device is fabricated using a combination of low-cost hard cyclic olefin copolymer thermoplastic and elastomeric thermoplastic materials (styrene/(ethylene/butylenes)/styrene) using rapid hot-embossing replication techniques with a polymer-based stamp. Three immunopurified protein samples are simultaneously captured, reduced, alkylated, and digested on the device within 2-3 h instead of the days required for the conventional protein-protein interaction studies. The limit of detection of the microfluidic proteomic reactor was shown to be lower than 2 ng of protein. Furthermore, the application of the microfluidic proteomic reactor was demonstrated for the simultaneous processing of the interactome of the histone variant Htz1 in wild-type yeast and in a swr1Δ yeast strain compared to an untagged control using a novel three-channel microfluidic proteomic reactor.
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Affiliation(s)
- Ruijun Tian
- Ottawa Institute of Systems Biology, National Research Council, Boucherville, QC, Canada J4B 6Y4
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Adamczyk-Poplawska M, Markowicz S, Jagusztyn-Krynicka EK. Proteomics for development of vaccine. J Proteomics 2011; 74:2596-616. [PMID: 21310271 DOI: 10.1016/j.jprot.2011.01.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 12/20/2022]
Abstract
The success of genome projects has provided us with a vast amount of information on genes of many pathogenic species and has raised hopes for rapid progress in combating infectious diseases, both by construction of new effective vaccines and by creating a new generation of therapeutic drugs. Proteomics, a strategy complementary to the genomic-based approach, when combined with immunomics (looking for immunogenic proteins) and vaccinomics (characterization of host response to immunization), delivers valuable information on pathogen-host cell interaction. It also speeds the identification and detailed characterization of new antigens, which are potential candidates for vaccine development. This review begins with an overview of the global status of vaccinology based on WHO data. The main part of this review describes the impact of proteomic strategies on advancements in constructing effective antibacterial, antiviral and anticancer vaccines. Diverse aspects of disease mechanisms and disease preventions have been investigated by proteomics.
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Affiliation(s)
- Monika Adamczyk-Poplawska
- Department of Virology, Institute of Microbiology, Biology Faculty, Warsaw University, Warsaw, Poland
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Liu R, Duan JA, Wang M, Shang E, Guo J, Tang Y. Analysis of active components of rhinoceros, water buffalo and yak horns using two-dimensional electrophoresis and ethnopharmacological evaluation. J Sep Sci 2011; 34:354-62. [DOI: 10.1002/jssc.201000617] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Balch WE, Yates JR. Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis. Methods Mol Biol 2011; 742:227-247. [PMID: 21547736 DOI: 10.1007/978-1-61779-120-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.
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Affiliation(s)
- William E Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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13
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Terentiev AA, Moldogazieva NT, Shaitan KV. Dynamic proteomics in modeling of the living cell. Protein-protein interactions. BIOCHEMISTRY (MOSCOW) 2010; 74:1586-607. [DOI: 10.1134/s0006297909130112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wilkins MR. Hares and tortoises: the high- versus low-throughput proteomic race. Electrophoresis 2009; 30 Suppl 1:S150-5. [PMID: 19441020 DOI: 10.1002/elps.200900175] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The analysis of the proteome can be undertaken with parallel, high-throughput techniques or those that analyze proteins in a serial, one-at-a-time manner. The former include 2-D gels and shotgun MS/MS; the latter includes libraries containing fusion proteins (GST, green fluorescent protein, TAP-tag and others) that are engineered onto each protein in a proteome and then studied one by one. In this review, we explore the progress that these scientifically contrasting paradigms have made in measuring protein abundance, half-life, post-translational modifications, localization in cells and tissues and in protein membership of complexes, pathways and networks. We find that our understanding of the yeast proteome has been furthered more substantially by the slower "tortoise techniques" than the "high-throughput hares". A number of aspects of the human proteome are also likely to be elucidated most accurately with low-throughput approaches. However, the high-throughput techniques are expected to remain crucial for comparative analyses and most studies of proteome dynamics. This review also briefly explores how electrophoretic separations can continue to support the field of proteomics.
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Affiliation(s)
- Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Edwards AN, Fowlkes JD, Owens ET, Standaert RF, Pelletier DA, Hurst GB, Doktycz MJ, Morrell-Falvey JL. An in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities. Anal Biochem 2009; 395:166-77. [PMID: 19698693 DOI: 10.1016/j.ab.2009.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 08/13/2009] [Accepted: 08/17/2009] [Indexed: 11/28/2022]
Abstract
Identifying and characterizing protein interactions are fundamental steps toward understanding and modeling biological networks. Methods that detect protein interactions in intact cells rather than buffered solutions are likely more relevant to natural systems since molecular crowding events in the cytosol can influence the diffusion and reactivity of individual proteins. One in vivo, imaging-based method relies on the colocalization of two proteins of interest fused to DivIVA, a cell division protein from Bacillus subtilis, and green fluorescent protein (GFP). We have modified this imaging-based assay to facilitate rapid cloning by constructing new vectors encoding N- and C-terminal DivIVA or GFP molecular tag fusions based on site-specific recombination technology. The sensitivity of the assay was defined using a well-characterized protein interaction system involving the eukaryotic nuclear import receptor subunit, Importin alpha (Imp alpha), and variant nuclear localization signals (NLS) representing a range of binding affinities. These data demonstrate that the modified colocalization assay is sensitive enough to detect protein interactions with K(d) values that span over four orders of magnitude (1 nM to 15 microM). Lastly, this assay was used to confirm numerous protein interactions identified from mass spectrometry-based analyses of affinity isolates as part of an interactome mapping project in Rhodopseudomonas palustris.
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Affiliation(s)
- A Nicole Edwards
- University of Tennessee-Oak Ridge National Laboratory, Graduate School of Genome Science and Technology, Knoxville, TN 37996, USA
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Brennan K, Jefferies CA. Proteomic analysis of protein complexes in Toll-like receptor biology. Methods Mol Biol 2009; 517:91-104. [PMID: 19378014 DOI: 10.1007/978-1-59745-541-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Purification of protein complexes and identification of the constituent components therein have been made relatively simple by the recent advances in proteomics. Uniting good biochemical and protein chemistry techniques with protein identification by mass spectrometry (MS) has resulted in advances in this field that are unprecedented. Our knowledge of Toll-like receptor (TLR) biology has been considerably advanced through the use of such techniques, with key intermediates such as TRAF3, TANK, RIP1 all being identified using proteomic strategies. Applying these techniques to key questions in TLR -biology will undoubtedly serve to further advance the field.
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Affiliation(s)
- Kiva Brennan
- RCSI Research Institute, Royal College of Surgeons in Ireland, Stephen's Green, Dublin 2, Ireland
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Dormeyer W, van Hoof D, Mummery CL, Krijgsveld J, Heck AJR. A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics 2008; 8:4036-53. [DOI: 10.1002/pmic.200800143] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Xu X, Veenstra TD. Analysis of biofluids for biomarker research. Proteomics Clin Appl 2008; 2:1403-12. [DOI: 10.1002/prca.200780173] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Indexed: 01/11/2023]
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Li J, Ge J, Yin Y, Zhong W. Multiplexed affinity-based protein complex purification. Anal Chem 2008; 80:7068-74. [PMID: 18715017 DOI: 10.1021/ac801251y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Here we proved the principle of a multiplexed affinity-based protein complex purification (MAPcP) technique that targets simultaneous extraction of multiple protein complexes with superior purity. Microspheres of various sizes and coupled with different affinity probes extract several protein complexes concurrently and specifically. After the coextraction, flow-field flow fractionation (Fl-FFF) rapidly washes the microspheres as well as separates them based on their sizes to recover the clean individual complex for downstream analysis. Demonstration of the parallel extraction of two immuno-complexes from the yeast whole cell lysate showed that MAPcP can enhance the sample purity significantly compared to the traditional centrifugation and magnetic pull-down methods used for small scale protein purification. Simultaneous isolation of multiple protein complexes can facilitate the elucidation of the functional relationship among protein complexes and improve our understanding of the biological network.
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Affiliation(s)
- Jishan Li
- Department of Chemistry, University of California, Riverside, California 92521, USA
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Guzman NA, Blanc T, Phillips TM. Immunoaffinity capillary electrophoresis as a powerful strategy for the quantification of low-abundance biomarkers, drugs, and metabolites in biological matrices. Electrophoresis 2008; 29:3259-78. [PMID: 18646282 PMCID: PMC2659498 DOI: 10.1002/elps.200800058] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the last few years, there has been a greater appreciation by the scientific community of how separation science has contributed to the advancement of biomedical research. Despite past contributions in facilitating several biomedical breakthroughs, separation sciences still urgently need the development of improved methods for the separation and detection of biological and chemical substances. In particular, the challenging task of quantifying small molecules and biomolecules, found in low abundance in complex matrices (e.g., serum), is a particular area in need of new high-efficiency techniques. The tandem or on-line coupling of highly selective antibody capture agents with the high-resolving power of CE is being recognized as a powerful analytical tool for the enrichment and quantification of ultra-low abundance analytes in complex matrices. This development will have a significant impact on the identification and characterization of many putative biomarkers and on biomedical research in general. Immunoaffinity CE (IACE) technology is rapidly emerging as the most promising method for the analysis of low-abundance biomarkers; its power comes from a three-step procedure: (i) bioselective adsorption and (ii) subsequent recovery of compounds from an immobilized affinity ligand followed by (iii) separation of the enriched compounds. This technology is highly suited to automation and can be engineered to as a multiplex instrument capable of routinely performing hundreds of assays per day. Furthermore, a significant enhancement in sensitivity can be achieved for the purified and enriched affinity targeted analytes. Thus, a compound that exists in a complex biological matrix at a concentration far below its LOD is easily brought to well within its range of quantification. The present review summarizes several applications of IACE, as well as a chronological description of the improvements made in the fabrication of the analyte concentrator-microreactor device leading to the development of a multidimensional biomarker analyzer.
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Affiliation(s)
- Norberto A Guzman
- Biomarker Laboratory, Princeton Biochemicals, Inc., Princeton, NJ 08543, USA.
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Josic D, Kovač S. Application of proteomics in biotechnology – Microbial proteomics. Biotechnol J 2008; 3:496-509. [DOI: 10.1002/biot.200700234] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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