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Li S, Zhu C, Zhao Q, Zhang ZM, Sun P, Li Z. Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells. ACS Chem Biol 2023; 18:1405-1415. [PMID: 37231651 DOI: 10.1021/acschembio.3c00149] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for the study of protein structure and protein-protein interactions (PPIs). However, the chemical probes used in the CXMS are limited to bidentate reactive warheads, and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonyl ynamide, was developed as a new zero-length cross-linker that can connect high-abundance carboxyl residues (D/E) with lysine (K) to form amide bonds in the absence of any catalyst. Significant improvement in the cross-linking efficiency and specificity in comparison with traditional EDC/NHS was achieved with model proteins, which includes inter- and intramolecular conjugations. The cross-linked structures were validated by X-ray crystallography. Importantly, this coupling reagent can be successfully used to capture interacting proteins in the whole proteome and can be a useful reagent for probing potential protein-protein interactions in situ.
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Affiliation(s)
- Shengrong Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengjun Zhu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Pinghua Sun
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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2
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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3
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Lees JA, Dias JM, Han S. Applications of Cryo-EM in small molecule and biologics drug design. Biochem Soc Trans 2021; 49:2627-2638. [PMID: 34812853 PMCID: PMC8786282 DOI: 10.1042/bst20210444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is a powerful technique for the structural characterization of biological macromolecules, enabling high-resolution analysis of targets once inaccessible to structural interrogation. In recent years, pharmaceutical companies have begun to utilize cryo-EM for structure-based drug design. Structural analysis of integral membrane proteins, which comprise a large proportion of druggable targets and pose particular challenges for X-ray crystallography, by cryo-EM has enabled insights into important drug target families such as G protein-coupled receptors (GPCRs), ion channels, and solute carrier (SLCs) proteins. Structural characterization of biologics, such as vaccines, viral vectors, and gene therapy agents, has also become significantly more tractable. As a result, cryo-EM has begun to make major impacts in bringing critical therapeutics to market. In this review, we discuss recent instructive examples of impacts from cryo-EM in therapeutics design, focusing largely on its implementation at Pfizer. We also discuss the opportunities afforded by emerging technological advances in cryo-EM, and the prospects for future development of the technique.
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Affiliation(s)
- Joshua A. Lees
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Joao M. Dias
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Seungil Han
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
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4
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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Belsom A, Rappsilber J. Anatomy of a crosslinker. Curr Opin Chem Biol 2020; 60:39-46. [PMID: 32829152 DOI: 10.1016/j.cbpa.2020.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/17/2022]
Abstract
Crosslinking mass spectrometry has become a core technology in structural biology and is expanding its reach towards systems biology. Its appeal lies in a rapid workflow, high sensitivity and the ability to provide data on proteins in complex systems, even in whole cells. The technology depends heavily on crosslinking reagents. The anatomy of crosslinkers can be modular, sometimes comprising combinations of functional groups. These groups are defined by concepts including: reaction selectivity to increase information density, enrichability to improve detection, cleavability to enhance the identification process and isotope-labelling for quantification. Here, we argue that both concepts and functional groups need more thorough experimental evaluation, so that we can show exactly how and where they are useful when applied to crosslinkers. Crosslinker design should be driven by data, not only concepts. We focus on two crosslinker concepts with large consequences for the technology, namely reactive group reaction kinetics and enrichment groups.
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Affiliation(s)
- Adam Belsom
- 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, Edinburgh, EH9 3BF, UK.
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