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Kim S, Kim E, Park M, Kim SH, Kim BG, Na S, Sadongo VW, Wijesinghe WCB, Eom YG, Yoon G, Jeong H, Hwang E, Lee C, Myung K, Kim CU, Choi JM, Min SK, Kwon TH, Min D. Hidden route of protein damage through oxygen-confined photooxidation. Nat Commun 2024; 15:10873. [PMID: 39738007 DOI: 10.1038/s41467-024-55168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 12/04/2024] [Indexed: 01/01/2025] Open
Abstract
Oxidative modifications can disrupt protein folds and functions, and are strongly associated with human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), which primarily attack the protein surface. Yet, it remains unclear whether and how internal protein folds capable of trapping oxygen (O2) contribute to oxidative damage. Here, we report a hidden pathway of protein damage, which we refer to as O2-confined photooxidation. In this process, O2 is captured in protein cavities and subsequently converted into multiple ROS, primarily mediated by tryptophan residues under blue light irradiation. The generated ROS then attack the protein interior through constrained diffusion, causing protein damage. The effects of this photooxidative reaction appear to be extensive, impacting a wide range of cellular proteins, as supported by whole-cell proteomic analysis. This photooxidative mechanism may represent a latent oxidation pathway in human tissues directly exposed to visible light, such as skin and eyes.
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Affiliation(s)
- Seoyoon Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Eojin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Mingyu Park
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Seong Ho Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Seungjin Na
- Digital Omics Research Center, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Victor W Sadongo
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan, 46241, Republic of Korea
| | - Gwangsu Yoon
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hannah Jeong
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Eunhye Hwang
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Chaiheon Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan, 46241, Republic of Korea
- Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Tae-Hyuk Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- X-Dynamic Research Center, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- X-Dynamic Research Center, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
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2
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Lee C, Park M, Wijesinghe WCB, Na S, Lee CG, Hwang E, Yoon G, Lee JK, Roh DH, Kwon YH, Yang J, Hughes SA, Vince JE, Seo JK, Min D, Kwon TH. Oxidative photocatalysis on membranes triggers non-canonical pyroptosis. Nat Commun 2024; 15:4025. [PMID: 38740804 DOI: 10.1038/s41467-024-47634-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Intracellular membranes composing organelles of eukaryotes include membrane proteins playing crucial roles in physiological functions. However, a comprehensive understanding of the cellular responses triggered by intracellular membrane-focused oxidative stress remains elusive. Herein, we report an amphiphilic photocatalyst localised in intracellular membranes to damage membrane proteins oxidatively, resulting in non-canonical pyroptosis. Our developed photocatalysis generates hydroxyl radicals and hydrogen peroxides via water oxidation, which is accelerated under hypoxia. Single-molecule magnetic tweezers reveal that photocatalysis-induced oxidation markedly destabilised membrane protein folding. In cell environment, label-free quantification reveals that oxidative damage occurs primarily in membrane proteins related to protein quality control, thereby aggravating mitochondrial and endoplasmic reticulum stress and inducing lytic cell death. Notably, the photocatalysis activates non-canonical inflammasome caspases, resulting in gasdermin D cleavage to its pore-forming fragment and subsequent pyroptosis. These findings suggest that the oxidation of intracellular membrane proteins triggers non-canonical pyroptosis.
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Affiliation(s)
- Chaiheon Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Mingyu Park
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - W C Bhashini Wijesinghe
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Seungjin Na
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Chae Gyu Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Eunhye Hwang
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Gwangsu Yoon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Jeong Kyeong Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Deok-Ho Roh
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Yoon Hee Kwon
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Jihyeon Yang
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Sebastian A Hughes
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jeong Kon Seo
- Research Center, O2MEDi inc., Ulsan, Republic of Korea.
- UNIST Central Research Facility, UNIST, Ulsan, Republic of Korea.
| | - Duyoung Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea.
| | - Tae-Hyuk Kwon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea.
- Research Center, O2MEDi inc., Ulsan, Republic of Korea.
- Graduate School of Carbon Neutrality, UNIST, Ulsan, Republic of Korea.
- Graduate School of Semiconductor Materials and Device Engineering, UNIST, Ulsan, Republic of Korea.
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van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K. Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell Rep 2024; 43:114110. [PMID: 38607912 DOI: 10.1016/j.celrep.2024.114110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Transmembrane transporter proteins are essential for maintaining cellular homeostasis and, as such, are key drug targets. Many transmembrane transporter proteins are known to undergo large structural rearrangements during their functional cycles. Despite the wealth of detailed structural and functional data available for these systems, our understanding of their dynamics and, consequently, how they function is generally limited. We introduce an innovative approach that enables us to directly measure the dynamics and stability of interdomain interactions of transmembrane proteins using optical tweezers. Focusing on the osmoregulatory ATP-binding cassette transporter OpuA from Lactococcus lactis, we examine the mechanical properties and potential interactions of its substrate-binding domains. Our measurements are performed in lipid nanodiscs, providing a native-mimicking environment for the transmembrane protein. The technique provides high spatial and temporal resolution and allows us to study the functionally relevant motions and interdomain interactions of individual transmembrane transporter proteins in real time in a lipid bilayer.
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Affiliation(s)
- Lyan van der Sleen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Jan A Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Kasia Tych
- Chemical Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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4
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Min D. Folding speeds of helical membrane proteins. Biochem Soc Trans 2024; 52:491-501. [PMID: 38385525 PMCID: PMC10903471 DOI: 10.1042/bst20231315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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5
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Yu M, Jiang C, Lai B, Zhang K. Exploring Novel Sensor Design Ideas through Concentration-Induced Conformational Changes in PEG Single Chains. SENSORS (BASEL, SWITZERLAND) 2024; 24:883. [PMID: 38339600 PMCID: PMC10856974 DOI: 10.3390/s24030883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Polyethylene glycol (PEG) is an artificial polymer with good biocompatibility and a low cost, which has a wide range of applications. In this study, the dynamic response of PEG single chains to different ion concentrations was investigated from a microscopic point of view based on single-molecule force spectroscopy, revealing unique interactions that go beyond the traditional sensor-design paradigm. Under low concentrations of potassium chloride, PEG single chains exhibit a gradual reduction in rigidity, while, conversely, high concentrations induce a progressive increase in rigidity. This dichotomy serves as the cornerstone for a profound understanding of PEG conformational dynamics under diverse ion environments. Capitalizing on the remarkable sensitivity of PEG single chains to ion concentration shifts, we introduce innovative sensor-design ideas. Rooted in the adaptive nature of PEG single chains, these sensor designs extend beyond the traditional applications, promising advancements in environmental monitoring, healthcare, and materials science.
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Affiliation(s)
- Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Chong Jiang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Bing Lai
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
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6
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Kim S, Min D. Robust magnetic tweezers for membrane protein folding studies. Methods Enzymol 2024; 694:285-301. [PMID: 38492955 DOI: 10.1016/bs.mie.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Single-molecule magnetic tweezers have recently been adapted for monitoring the interactions between transmembrane helices of membrane proteins within lipid bilayers. In this chapter, we describe the procedures of conducting studies on membrane protein folding using a robust magnetic tweezer method. This tweezer method is capable of observing thousands of (un)folding transitions over extended periods of several to tens of hours. Using this approach, we can dissect the folding pathways of membrane proteins, determine their folding time scales, and map the folding energy landscapes, with a higher statistical reliability. Our robust magnetic tweezers also allow for estimating the folding speed limit of helical membrane proteins, which serves as a link between the kinetics and barrier energies.
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Affiliation(s)
- Seoyoon Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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Lee D, Min D. Single-molecule tethering methods for membrane proteins. Methods Enzymol 2024; 694:263-284. [PMID: 38492954 DOI: 10.1016/bs.mie.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Molecular tethering of a single membrane protein between the glass surface and a magnetic bead is essential for studying the structural dynamics of membrane proteins using magnetic tweezers. However, the force-induced bond breakage of the widely-used digoxigenin-antidigoxigenin tether complex has imposed limitations on its stable observation. In this chapter, we describe the procedures of constructing highly stable single-molecule tethering methods for membrane proteins. These methods are established using dibenzocyclooctyne click chemistry, traptavidin-biotin binding, SpyCatcher-SpyTag conjugation, and SnoopCatcher-SnoopTag conjugation. The molecular tethering approaches allow for more stable observation of structural transitions in membrane proteins under force.
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Affiliation(s)
- Daehyo Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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Kim E, Min D. Chaperoning the major facilitator superfamily at single-molecule level. Structure 2023; 31:1291-1294. [PMID: 37922865 DOI: 10.1016/j.str.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
In this issue of Structure, Blaimschein et al. elucidate the chaperoning function of the insertase YidC during the insertion and folding of the melibiose permease MelB. Their single-molecule forced unfolding approach reveals that YidC significantly reduces the misfolding and enhances the folding of helices near the interface of two folding cores.
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Affiliation(s)
- Eojin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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