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Shu X, Asghar S, Yang F, Li ST, Wu H, Yang B. Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids. Front Chem 2022; 10:815991. [PMID: 35252115 PMCID: PMC8894327 DOI: 10.3389/fchem.2022.815991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/27/2022] [Indexed: 11/15/2022] Open
Abstract
Genetically encoded non-canonical amino acids (ncAAs) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These ncAAs, including a series of alkyl bromide-based ncAAs, mainly target cysteine residues to form protein-protein cross-links. Although some reactivities towards lysine and tyrosine residues have been reported, a comprehensive understanding of their reactivity towards a broad range of nucleophilic amino acids is lacking. Here we used a recently developed OpenUaa search engine to perform an in-depth analysis of mass spec data generated for Thioredoxin and its direct binding proteins cross-linked with an alkyl bromide-based ncAA, BprY. The analysis showed that, besides cysteine residues, BprY also targeted a broad range of nucleophilic amino acids. We validated this broad reactivity of BprY with Affibody/Z protein complex. We then successfully applied BprY to map a binding interface between SUMO2 and SUMO-interacting motifs (SIMs). BprY was further applied to probe SUMO2 interaction partners. We identified 264 SUMO2 binders, including several validated SUMO2 binders and many new binders. Our data demonstrated that BprY can be effectively used to probe protein-protein interaction interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.
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Affiliation(s)
- Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Sana Asghar
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shang-Tong Li
- Glbizzia Biosciences Co., Ltd, Beijing, China
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, United States
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
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52
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Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022; 9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
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Affiliation(s)
- Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alisa Potter
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Felix Evers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, Netherlands.,Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Konoplev G, Agafonova D, Bakhchova L, Mukhin N, Kurachkina M, Schmidt MP, Verlov N, Sidorov A, Oseev A, Stepanova O, Kozyrev A, Dmitriev A, Hirsch S. Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures. Biomedicines 2022; 10:207. [PMID: 35203416 PMCID: PMC8868674 DOI: 10.3390/biomedicines10020207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/01/2022] [Accepted: 01/11/2022] [Indexed: 12/25/2022] Open
Abstract
Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.
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Affiliation(s)
- Georgii Konoplev
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
| | - Darina Agafonova
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
| | - Liubov Bakhchova
- Institute for Automation Technology, Otto-von-Guericke-University Magdeburg, 39106 Magdeburg, Germany;
| | - Nikolay Mukhin
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
- Department of Engineering, University of Applied Sciences Brandenburg, 14770 Brandenburg an der Havel, Germany; (M.K.); (S.H.)
| | - Marharyta Kurachkina
- Department of Engineering, University of Applied Sciences Brandenburg, 14770 Brandenburg an der Havel, Germany; (M.K.); (S.H.)
| | - Marc-Peter Schmidt
- Faculty of Electrical Engineering, University of Applied Sciences Dresden, 01069 Dresden, Germany;
| | - Nikolay Verlov
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov, National Research Centre Kurchatov Institute, 188300 Gatchina, Russia;
| | - Alexander Sidorov
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
- Fuculty of Photonics, ITMO University, 197101 Saint Petersburg, Russia
| | - Aleksandr Oseev
- FEMTO-ST Institute, CNRS UMR-6174, University Bourgogne Franche-Comté, 25000 Besançon, France;
| | - Oksana Stepanova
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
| | - Andrey Kozyrev
- Faculty of Electronics, Saint Petersburg Electrotechnical University “LETI”, 197376 Saint Petersburg, Russia; (D.A.); (A.S.); (O.S.); (A.K.)
| | - Alexander Dmitriev
- Department of Ecological Physiology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine” (FSBSI “IEM”), 197376 Saint Petersburg, Russia;
| | - Soeren Hirsch
- Department of Engineering, University of Applied Sciences Brandenburg, 14770 Brandenburg an der Havel, Germany; (M.K.); (S.H.)
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Chen Y, Zhou W, Li X, Yang K, Liang Z, Zhang L, Zhang Y. Research Progress of Protein-Protein Interaction Based on Liquid Chromatography Mass Spectrometry ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a22010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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55
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Kim W, Nott J, Kim S, Krishnan HB. Soybean seed proteomics: Methods for the isolation, detection, and identification of low abundance proteins. Methods Enzymol 2022; 676:325-345. [DOI: 10.1016/bs.mie.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Graziadei A, Rappsilber J. Leveraging crosslinking mass spectrometry in structural and cell biology. Structure 2021; 30:37-54. [PMID: 34895473 DOI: 10.1016/j.str.2021.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/11/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein structures proposed by other methods and have helped derive models of protein complexes by integrative structural biology approaches. The use of crosslinking-MS in integrative approaches is underpinned by progress in estimating error rates in crosslinking-MS data and in combining these data with other information. The flexible and high-throughput nature of crosslinking-MS has allowed it to complement the ongoing resolution revolution in electron microscopy by providing system-wide residue-residue distance restraints, especially for flexible regions or systems. Here, we review how crosslinking-MS information has been leveraged in structural model validation and integrative modeling. Crosslinking-MS has also been a key technology for cell biology studies and structural systems biology where, in conjunction with cryoelectron tomography, it can provide structural and mechanistic insights directly in situ.
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Affiliation(s)
- Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
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Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021; 22:ijms22157809. [PMID: 34360575 PMCID: PMC8346016 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.
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