1
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Liu H, Yan P, Zhang Z, Han H, Zhou Q, Zheng J, Zhang J, Xu F, Shui W. Structural Mass Spectrometry Captures Residue-Resolved Comprehensive Conformational Rearrangements of a G Protein-Coupled Receptor. J Am Chem Soc 2024; 146:20045-20058. [PMID: 39001877 DOI: 10.1021/jacs.4c03922] [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: 07/15/2024]
Abstract
G protein-coupled receptor (GPCR) structural studies with in-solution spectroscopic approaches have offered distinctive insights into GPCR activation and signaling that highly complement those yielded from structural snapshots by crystallography or cryo-EM. While most current spectroscopic approaches allow for probing structural changes at selected residues or loop regions, they are not suitable for capturing a holistic view of GPCR conformational rearrangements across multiple domains. Herein, we develop an approach based on limited proteolysis mass spectrometry (LiP-MS) to simultaneously monitor conformational alterations of a large number of residues spanning both flexible loops and structured transmembrane domains for a given GPCR. To benchmark LiP-MS for GPCR conformational profiling, we studied the adenosine 2A receptor (A2AR) in response to different ligand binding (agonist/antagonist/allosteric modulators) and G protein coupling. Systematic and residue-resolved profiling of A2AR conformational rearrangements by LiP-MS precisely captures structural mechanisms in multiple domains underlying ligand engagement, receptor activation, and allostery, and may also reflect local conformational flexibility. Furthermore, these residue-resolution structural fingerprints of the A2AR protein allow us to readily classify ligands of different pharmacology and distinguish the G protein-coupled state. Thus, our study provides a new structural MS approach that would be generalizable to characterizing conformational transition and plasticity for challenging integral membrane proteins.
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Affiliation(s)
- Hongyue Liu
- 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
| | - Pengfei Yan
- 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
| | - Zhaoyu Zhang
- 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
| | - Hongbo Han
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jie Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, 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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2
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James VK, Voss BJ, Helms A, Trent MS, Brodbelt JS. Investigating Lipid Transporter Protein and Lipid Interactions Using Variable Temperature Electrospray Ionization, Ultraviolet Photodissociation Mass Spectrometry, and Collision Cross Section Analysis. Anal Chem 2024. [PMID: 39038171 DOI: 10.1021/acs.analchem.4c01392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Gram-negative bacteria develop and exhibit resistance to antibiotics, owing to their highly asymmetric outer membrane maintained by a group of six proteins comprising the Mla (maintenance of lipid asymmetry) pathway. Here, we investigate the lipid binding preferences of one Mla protein, MlaC, which transports lipids through the periplasm. We used ultraviolet photodissociation (UVPD) to identify and characterize modifications of lipids endogenously bound to MlaC expressed in three different bacteria strains. UVPD was also used to localize lipid binding to MlaC residues 130-140, consistent with the crystal structure reported for lipid-bound MlaC. The impact of removing the bound lipid from MlaC on its structure was monitored based on collision cross section measurements, revealing that the protein unfolded prior to release of the lipid. The lipid selectivity of MlaC was evaluated based on titrimetric experiments, indicating that MlaC-bound lipids in various classes (sphingolipids, glycerophospholipids, and fatty acids) as long as they possessed no more than two acyl chains.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Bradley J Voss
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Zhang T, Lyu J, Yang B, Yun SD, Scott E, Zhao M, Laganowsky A. Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids. Nat Commun 2024; 15:5946. [PMID: 39009687 PMCID: PMC11251056 DOI: 10.1038/s41467-024-50350-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 07/07/2024] [Indexed: 07/17/2024] Open
Abstract
The ATP-binding cassette (ABC) transporter, MsbA, plays a pivotal role in lipopolysaccharide (LPS) biogenesis by facilitating the transport of the LPS precursor lipooligosaccharide (LOS) from the cytoplasmic to the periplasmic leaflet of the inner membrane. Despite multiple studies shedding light on MsbA, the role of lipids in modulating MsbA-nucleotide interactions remains poorly understood. Here we use native mass spectrometry (MS) to investigate and resolve nucleotide and lipid binding to MsbA, demonstrating that the transporter has a higher affinity for adenosine 5'-diphosphate (ADP). Moreover, native MS shows the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL) can tune the selectivity of MsbA for adenosine 5'-triphosphate (ATP) over ADP. Guided by these studies, four open, inward-facing structures of MsbA are determined that vary in their openness. We also report a 2.7 Å-resolution structure of MsbA in an open, outward-facing conformation that is not only bound to KDL at the exterior site, but with the nucleotide binding domains (NBDs) adopting a distinct nucleotide-free structure. The results obtained from this study offer valuable insight and snapshots of MsbA during the transport cycle.
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Affiliation(s)
- Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Bowei Yang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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4
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Kettel P, Karagöz GE. Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response. Int J Biochem Cell Biol 2024; 172:106598. [PMID: 38768891 DOI: 10.1016/j.biocel.2024.106598] [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: 03/18/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The endoplasmic reticulum (ER) regulates essential cellular processes, including protein folding, lipid synthesis, and calcium homeostasis. The ER homeostasis is maintained by a conserved set of signaling cascades called the Unfolded Protein Response (UPR). How the UPR senses perturbations in ER homeostasis has been the subject of active research for decades. In metazoans, the UPR consists of three ER-membrane embedded sensors: IRE1, PERK and ATF6. These sensors detect the accumulation of misfolded proteins in the ER lumen and adjust protein folding capacity according to cellular needs. Early work revealed that the ER-resident chaperone BiP binds to all three UPR sensors in higher eukaryotes and BiP binding was suggested to regulate their activity. More recent data have shown that in higher eukaryotes the interaction of the UPR sensors with a complex network of chaperones and misfolded proteins modulates their activation and deactivation dynamics. Furthermore, emerging evidence suggests that the UPR monitors ER membrane integrity beyond protein folding defects. However, the mechanistic and structural basis of UPR activation by proteotoxic and lipid bilayer stress in higher eukaryotes remains only partially understood. Here, we review the current understanding of novel protein interaction networks and the contribution of the lipid membrane environment to UPR activation.
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Affiliation(s)
- Paulina Kettel
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Medical University of Vienna, Vienna, Austria.
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5
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Bai Z, Wang X, Liang T, Xu G, Cai J, Xu W, Yang K, Hu L, Pei P. Harnessing Bacterial Membrane Components for Tumor Vaccines: Strategies and Perspectives. Adv Healthc Mater 2024:e2401615. [PMID: 38935934 DOI: 10.1002/adhm.202401615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/17/2024] [Indexed: 06/29/2024]
Abstract
Tumor vaccines stand at the vanguard of tumor immunotherapy, demonstrating significant potential and promise in recent years. While tumor vaccines have achieved breakthroughs in the treatment of cancer, they still encounter numerous challenges, including improving the immunogenicity of vaccines and expanding the scope of vaccine application. As natural immune activators, bacterial components offer inherent advantages in tumor vaccines. Bacterial membrane components, with their safer profile, easy extraction, purification, and engineering, along with their diverse array of immune components, activate the immune system and improve tumor vaccine efficacy. This review systematically summarizes the mechanism of action and therapeutic effects of bacterial membranes and its derivatives (including bacterial membrane vesicles and hybrid membrane biomaterials) in tumor vaccines. Subsequently, the authors delve into the preparation and advantages of tumor vaccines based on bacterial membranes and hybrid membrane biomaterials. Following this, the immune effects of tumor vaccines based on bacterial outer membrane vesicles are elucidated, and their mechanisms are explained. Moreover, their advantages in tumor combination therapy are analyzed. Last, the challenges and trends in this field are discussed. This comprehensive analysis aims to offer a more informed reference and scientific foundation for the design and implementation of bacterial membrane-based tumor vaccines.
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Affiliation(s)
- Zhenxin Bai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xuanyu Wang
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, People's Republic of China
| | - Tianming Liang
- Jiangsu Provincial Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, P.R. China
| | - Guangyu Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jinzhou Cai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Wei Xu
- Jiangsu Provincial Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, P.R. China
| | - Kai Yang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Lin Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Pei Pei
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, People's Republic of China
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6
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. Simultaneous Native Mass Spectrometry Analysis of Single and Double Mutants To Probe Lipid Binding to Membrane Proteins. Anal Chem 2024; 96:10426-10433. [PMID: 38859611 PMCID: PMC11215972 DOI: 10.1021/acs.analchem.4c01704] [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] [Indexed: 06/12/2024]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into the binding of lipids to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Farhana Afrin Mohona
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Megan Ewbank
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
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7
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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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8
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Umegawa Y, Kato S, Seo S, Shinoda W, Kawatake S, Matsuoka S, Murata M. Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Biophys Chem 2024; 308:107204. [PMID: 38412762 DOI: 10.1016/j.bpc.2024.107204] [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: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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Affiliation(s)
- Yuichi Umegawa
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Sho Kato
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Division of Supercomputing, Korea Institute of Science and Technology Information, 245 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1, Tsushima-naka, Okayama 700-8530, Japan
| | - Satoshi Kawatake
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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9
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Jandu RS, Yu H, Zhao Z, Le HT, Kim S, Huan T, Duong van Hoa F. Capture of endogenous lipids in peptidiscs and effect on protein stability and activity. iScience 2024; 27:109382. [PMID: 38577106 PMCID: PMC10993126 DOI: 10.1016/j.isci.2024.109382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Compared to protein-protein and protein-nucleic acid interactions, our knowledge of protein-lipid interactions remains limited. This is primarily due to the inherent insolubility of membrane proteins (MPs) in aqueous solution. The traditional use of detergents to overcome the solubility barrier destabilizes MPs and strips away certain lipids that are increasingly recognized as crucial for protein function. Recently, membrane mimetics have been developed to circumvent the limitations. In this study, using the peptidisc, we find that MPs in different lipid states can be isolated based on protein purification and reconstitution methods, leading to observable effects on MP activity and stability. Peptidisc also enables re-incorporating specific lipids to fine-tune the protein microenvironment and assess the impact on downstream protein associations. This study offers a first look at the illusive protein-lipid interaction specificity, laying the path for a systematic evaluation of lipid identity and contributions to membrane protein function.
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Affiliation(s)
- Rupinder Singh Jandu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Huaxu Yu
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hai Tuong Le
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sehyeon Kim
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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10
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Urner LH, Fiorentino F, Shutin D, Sauer JB, Agasid MT, El-Baba TJ, Bolla JR, Stansfeld PJ, Robinson CV. Detergents with Scalable Properties Identify Noncanonical Lipopolysaccharide Binding to Bacterial Inner Membrane Proteins. J Am Chem Soc 2024; 146. [PMID: 38604609 PMCID: PMC11046432 DOI: 10.1021/jacs.3c14358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 04/13/2024]
Abstract
Lipopolysaccharide (LPS) is vital for maintaining the outer membrane barrier in Gram-negative bacteria. LPS is also frequently obtained in complex with the inner membrane proteins after detergent purification. The question of whether or not LPS binding to inner membrane proteins not involved in outer membrane biogenesis reflects native lipid environments remains unclear. Here, we leverage the control of the hydrophilic-lipophilic balance and packing parameter concepts to chemically tune detergents that can be used to qualitatively differentiate the degree to which proteins copurify with phospholipids (PLs) and/or LPS. Given the scalable properties of these detergents, we demonstrate a detergent fine-tuning that enables the facile investigation of intact proteins and their complexes with lipids by native mass spectrometry (nMS). We conclude that LPS, a lipid that is believed to be important for outer membranes, can also affect the activity of membrane proteins that are currently not assigned to be involved in outer membrane biogenesis. Our results deliver a scalable detergent chemistry for a streamlined biophysical characterization of protein-lipid interactions, provide a rationale for the high affinity of LPS-protein binding, and identify noncanonical associations between LPS and inner membrane proteins with relevance for membrane biology and antibiotic research.
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Affiliation(s)
- Leonhard H. Urner
- TU
Dortmund University, Department of Chemistry
and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Francesco Fiorentino
- Department
of Drug Chemistry and Technologies, Sapienza
University Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Denis Shutin
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Joshua B. Sauer
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mark T. Agasid
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Tarick J. El-Baba
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jani R. Bolla
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Phillip J. Stansfeld
- School
of Life Sciences, Gibbet Hill Campus, The
University of Warwick, Coventry CV4 7AL, United
Kingdom
| | - Carol V. Robinson
- Kavli
Institute for Nanoscience Discovery,
South Parks Road, Oxford OX1 3QU, United Kingdom
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11
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Sandberg JW, Santiago-McRae E, Ennis J, Brannigan G. The density-threshold affinity: Calculating lipid binding affinities from unbiased coarse-grained molecular dynamics simulations. Methods Enzymol 2024; 701:47-82. [PMID: 39025580 DOI: 10.1016/bs.mie.2024.03.008] [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: 07/20/2024]
Abstract
Many membrane proteins are sensitive to their local lipid environment. As structural methods for membrane proteins have improved, there is growing evidence of direct, specific binding of lipids to protein surfaces. Unfortunately the workhorse of understanding protein-small molecule interactions, the binding affinity for a given site, is experimentally inaccessible for these systems. Coarse-grained molecular dynamics simulations can be used to bridge this gap, and are relatively straightforward to learn. Such simulations allow users to observe spontaneous binding of lipids to membrane proteins and quantify localized densities of individual lipids or lipid fragments. In this chapter we outline a protocol for extracting binding affinities from these localized distributions, known as the "density threshold affinity." The density threshold affinity uses an adaptive and flexible definition of site occupancy that alleviates the need to distinguish between "bound'' lipids and bulk lipids that are simply diffusing through the site. Furthermore, the method allows "bead-level" resolution that is suitable for the case where lipids share binding sites, and circumvents ambiguities about a relevant reference state. This approach provides a convenient and straightforward method for comparing affinities of a single lipid species for multiple sites, multiple lipids for a single site, and/or a single lipid species modeled using multiple forcefields.
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Affiliation(s)
- Jesse W Sandberg
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Jahmal Ennis
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States; Department of Physics, Rutgers University, Camden, NJ, United States.
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12
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Newstead S. Future opportunities in solute carrier structural biology. Nat Struct Mol Biol 2024; 31:587-590. [PMID: 38637662 DOI: 10.1038/s41594-024-01271-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024]
Abstract
Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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13
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Gu Y, Liu M, Ma L, Quinn RJ. Identification of Ligands for Ion Channels: TRPM2. Chembiochem 2024; 25:e202300790. [PMID: 38242853 DOI: 10.1002/cbic.202300790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable, nonselective cation channel with a widespread distribution throughout the body. It is involved in many pathological and physiological processes, making it a potential therapeutic target for various diseases, including Alzheimer's disease, Parkinson's disease, and cancers. New analytical techniques are beneficial for gaining a deeper understanding of its involvement in disease pathogenesis and for advancing the drug discovery for TRPM2-related diseases. In this work, we present the application of collision-induced affinity selection mass spectrometry (CIAS-MS) for the direct identification of ligands binding to TRPM2. CIAS-MS circumvents the need for high mass detection typically associated with mass spectrometry of large membrane proteins. Instead, it focuses on the detection of small molecules dissociated from the ligand-protein-detergent complexes. This affinity selection approach consolidates all affinity selection steps within the mass spectrometer, resulting in a streamlined process. We showed the direct identification of a known TRPM2 ligand dissociated from the protein-ligand complex. We demonstrated that CIAS-MS can identify binding ligands from complex mixtures of compounds and screened a compound library against TRPM2. We investigated the impact of voltage increments and ligand concentrations on the dissociation behavior of the binding ligand, revealing a dose-dependent relationship.
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Affiliation(s)
- Yushu Gu
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
- School of Environment and Science, Griffith University, N34 1.29, Nathan Campus, Brisbane, Queensland, 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
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14
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. eLife 2024; 12:RP91094. [PMID: 38252560 PMCID: PMC10945598 DOI: 10.7554/elife.91094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of ArizonaTucsonUnited States
| | - David Clemmer
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - David H Russell
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
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15
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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16
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Yun S, Scott E, Laganowsky A. Biophysical Characterization of RAS-SOS Complexes by Native Mass Spectrometry. Methods Mol Biol 2024; 2797:177-193. [PMID: 38570460 DOI: 10.1007/978-1-0716-3822-4_13] [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: 04/05/2024]
Abstract
RAS is regulated by specific guanine nucleotide exchange factors, such as Son of Sevenless (SOS), that activates RAS by facilitating the exchange of inactive, GDP-bound RAS with GTP. The catalytic activity of SOS is known to be allosterically modulated by an active, GTP-bound RAS. However, it remains poorly understood how oncogenic RAS mutants interact with SOS and modulate its activity. In this chapter, we describe the application of native mass spectrometry (MS) to monitor the assembly of the catalytic domain of SOS (SOScat) with RAS and cancer-associated mutants. Results from this approach have led to the discovery of different molecular assemblies and distinct conformers of SOScat engaging KRAS. It was also found that KRASG13D exhibits high affinity for SOScat and is a potent allosteric modulator of its SOScat activity. KRASG13D-GTP can allosterically increase the nucleotide exchange rate of KRAS at the active site by more than twofold compared to the wild-type protein. Furthermore, small-molecule RAS•SOS disruptors fail to dissociate KRASG13D•SOScat complexes, underscoring the need for more potent disruptors targeting oncogenic RAS mutants. Taken together, native MS will be instrumental in better understanding the interaction between oncogenic RAS mutants and SOS, which is of crucial importance for development of improved therapeutics.
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Affiliation(s)
- Sangho Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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17
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. SIMULTANEOUS NATIVE MASS SPECTROMETRY ANALYSIS OF SINGLE AND DOUBLE MUTANTS TO PROBE LIPID BINDING TO MEMBRANE PROTEINS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558516. [PMID: 37781586 PMCID: PMC10541089 DOI: 10.1101/2023.09.19.558516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that the W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into lipid binding to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Farhana Afrin Mohona
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Megan Ewbank
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Michael T. Marty
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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18
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Kundlacz T, Schmidt C. Deciphering Solution and Gas-Phase Interactions between Peptides and Lipids by Native Mass Spectrometry. Anal Chem 2023; 95:17292-17299. [PMID: 37956985 PMCID: PMC10688224 DOI: 10.1021/acs.analchem.3c03428] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023]
Abstract
Many biological processes depend on the interactions between proteins and lipids. Accordingly, the analysis of protein-lipid complexes has become increasingly important. Native mass spectrometry is often used to identify and characterize specific protein-lipid interactions. However, it requires the transfer of the analytes into the gas phase, where electrostatic interactions are enhanced and hydrophobic interactions do not exist. Accordingly, the question remains whether interactions that are observed in the gas phase accurately reflect interactions that are formed in solution. Here, we systematically explore noncovalent interactions between the antimicrobial peptide LL-37 and glycerophospholipids containing different headgroups or varying in fatty acyl chain length. We observe differences in peak intensities for different peptide-lipid complexes, as well as their relative binding strength in the gas phase. Accordingly, we found that ion intensities and gas-phase stability correlate well for complexes formed by electrostatic interactions. Probing hydrophobic interactions by varying the length of fatty acyl chains, we detected differences in ion intensities based on hydrophobic interactions formed in solution. The relative binding strength of these peptide-lipid complexes revealed only minor differences originating from van der Waals interactions and different binding modes of lipid headgroups in solution. In summary, our results demonstrate that hydrophobic interactions are reflected by ion intensities, while electrostatic interactions, including van der Waals interactions, determine the gas-phase stability of complexes.
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Affiliation(s)
- Til Kundlacz
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Institute
of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Department
of Chemistry—Biochemistry, Johannes
Gutenberg University Mainz, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
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19
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Liu W, Jayasekera HS, Sanders JD, Zhang G, Viner R, Marty MT. Online Buffer Exchange Enables Automated Membrane Protein Analysis by Native Mass Spectrometry. Anal Chem 2023; 95:17212-17219. [PMID: 37963237 PMCID: PMC10696660 DOI: 10.1021/acs.analchem.3c02164] [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] [Indexed: 11/16/2023]
Abstract
Membrane proteins represent the majority of clinical drug targets and are actively involved in a range of cellular processes. However, the complexity of membrane mimetics for membrane protein solubilization poses challenges for native mass spectrometry (MS) analyses. The most common approach for native MS analyses of membrane proteins remains offline buffer exchange into native MS-compatible buffers prior to manual sample loading into static nano-ESI emitters. This laborious process requires relatively high sample consumption and optimization for the individual proteins. Here, we developed online buffer exchange coupled to native mass spectrometry (OBE-nMS) for analyzing membrane proteins in different membrane mimetics, including detergent micelles and nanodiscs. Detergent screening for OBE-nMS reveals that mobile phases containing ammonium acetate with lauryl-dimethylamine oxide are most universal for characterizing both bacterial and mammalian membrane proteins in detergent. Membrane proteins in nanodiscs simply require ammonium acetate as the mobile phase. To preserve the intact nanodiscs, a novel switching electrospray approach was used to capture the high-flow separation on the column with a low-flow injection to MS. Rapid OBE-nMS completes each membrane protein measurement within minutes and thus enables higher-throughput assessment of membrane protein integrity prior to its structural elucidation.
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Affiliation(s)
- Weijing Liu
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134
| | - Hiruni S. Jayasekera
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - James D. Sanders
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
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20
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Zhang T, Lyu J, Zhu Y, Laganowsky A. Cardiolipin Regulates the Activity of the Mitochondrial ABC Transporter ABCB10. Biochemistry 2023; 62:3159-3165. [PMID: 37807693 PMCID: PMC10634319 DOI: 10.1021/acs.biochem.3c00417] [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: 08/08/2023] [Revised: 09/22/2023] [Indexed: 10/10/2023]
Abstract
The ATP-binding cassette (ABC) transporter ABCB10 resides in the inner membrane of mitochondria and is implicated in erythropoiesis. Mitochondria from different cell types share some specific characteristics, one of which is the high abundance of cardiolipin. Although previous studies have provided insight into ABCB10, the affinity and selectivity of this transporter toward lipids, particularly those found in the mitochondria, remain poorly understood. Here, native mass spectrometry is used to directly monitor the binding events of lipids to human ABCB10. The results reveal that ABCB10 binds avidly to cardiolipin with an affinity significantly higher than that of other phospholipids. The first three binding events of cardiolipin display positive cooperativity, which is suggestive of specific cardiolipin-binding sites on ABCB10. Phosphatidic acid is the second-best binder of the lipids investigated. The bulk lipids, phosphatidylcholine and phosphatidylethanolamine, display the weakest binding affinity for ABCB10. Other lipids bind ABCB10 with a similar affinity. Functional assays show that cardiolipin regulates the ATPase activity of ABCB10 in a dose-dependent fashion. ATPase activity of ABCB10 was also impacted in the presence of other lipids but to a lesser extent than cardiolipin. Taken together, ABCB10 has a high binding affinity for cardiolipin, and this lipid also regulates the ATPase activity of the transporter.
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Affiliation(s)
- Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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21
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547565. [PMID: 37461710 PMCID: PMC10350010 DOI: 10.1101/2023.07.03.547565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of Arizona, Tucson, AZ 85721
| | - David Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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22
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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23
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Zhu Y, Odenkirk MT, Qiao P, Zhang T, Schrecke S, Zhou M, Marty MT, Baker ES, Laganowsky A. Combining native mass spectrometry and lipidomics to uncover specific membrane protein-lipid interactions from natural lipid sources. Chem Sci 2023; 14:8570-8582. [PMID: 37593000 PMCID: PMC10430552 DOI: 10.1039/d3sc01482g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
While it is known that lipids play an essential role in regulating membrane protein structure and function, it remains challenging to identify specific protein-lipid interactions. Here, we present an innovative approach that combines native mass spectrometry (MS) and lipidomics to identify lipids retained by membrane proteins from natural lipid extracts. Our results reveal that the bacterial ammonia channel (AmtB) enriches specific cardiolipin (CDL) and phosphatidylethanolamine (PE) from natural headgroup extracts. When the two extracts are mixed, AmtB retains more species, wherein selectivity is tuned to bias headgroup selection. Using a series of natural headgroup extracts, we show TRAAK, a two-pore domain K+ channel (K2P), retains specific acyl chains that is independent of the headgroup. A brain polar lipid extract was then combined with the K2Ps, TRAAK and TREK2, to understand lipid specificity. More than a hundred lipids demonstrated affinity for each protein, and both channels were found to retain specific fatty acids and lysophospholipids known to stimulate channel activity, even after several column washes. Natural lipid extracts provide the unique opportunity to not only present natural lipid diversity to purified membrane proteins but also identify lipids that may be important for membrane protein structure and function.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University Raleigh NC 27695 USA
| | - Pei Qiao
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine Houston TX 77030 USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona Tucson AZ 85721 USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina Chapel Hill NC 27514 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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24
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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25
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Urbančič I, Eggeling C, Sezgin E. Do lipids tune B cell signaling? Nat Chem Biol 2023; 19:669-670. [PMID: 36997648 DOI: 10.1038/s41589-023-01303-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Affiliation(s)
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany.
- Leibniz Institute of Photonic Technology, Jena, Germany.
- Jena Center for Soft Matter, Jena, Germany.
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
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26
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Du Z, Zhou X, Lai Y, Xu J, Zhang Y, Zhou S, Feng Z, Yu L, Tang Y, Wang W, Yu L, Tian C, Ran T, Chen H, Guddat LW, Liu F, Gao Y, Rao Z, Gong H. Structure of the human respiratory complex II. Proc Natl Acad Sci U S A 2023; 120:e2216713120. [PMID: 37098072 PMCID: PMC10161127 DOI: 10.1073/pnas.2216713120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease.
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Affiliation(s)
- Zhanqiang Du
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Xiaoting Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Jinxu Xu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Ziyan Feng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Long Yu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Ting Ran
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Hongming Chen
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Fengjiang Liu
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
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27
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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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28
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Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward. Essays Biochem 2023; 67:187-200. [PMID: 36876893 PMCID: PMC10070480 DOI: 10.1042/ebc20220173] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 03/07/2023]
Abstract
Integral membrane proteins (IMPs) perform a range of diverse functions and their dysfunction underlies numerous pathological conditions. Consequently, IMPs constitute most drug targets, and the elucidation of their mechanism of action has become an intense field of research. Historically, IMP studies have relied on their extraction from membranes using detergents, which have the potential to perturbate their structure and dynamics. To circumnavigate this issue, an array of membrane mimetics has been developed that aim to reconstitute IMPs into native-like lipid environments that more accurately represent the biological membrane. Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a versatile tool for probing protein dynamics in solution. The continued development of HDX-MS methodology has allowed practitioners to investigate IMPs using increasingly native-like membrane mimetics, and even pushing the study of IMPs into the in vivo cellular environment. Consequently, HDX-MS has come of age and is playing an ever-increasingly important role in the IMP structural biologist toolkit. In the present mini-review, we discuss the evolution of membrane mimetics in the HDX-MS context, focusing on seminal publications and recent innovations that have led to this point. We also discuss state-of-the-art methodological and instrumental advancements that are likely to play a significant role in the generation of high-quality HDX-MS data of IMPs in the future.
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29
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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30
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Biou V. Lipid-membrane protein interaction visualised by cryo-EM: A review. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184068. [PMID: 36216098 DOI: 10.1016/j.bbamem.2022.184068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Membrane proteins reside at interfaces between aqueous and lipid media and solving their molecular structure relies most of the time on removing them from the membrane using detergent. Luckily, this solubilization process does not strip them from all the associated lipids and single-particle cryo-transmission electron microscopy (SP-TEM) has proved a very good tool to visualise both protein high-resolution structure and, often, many of its associated lipids. In this review, we observe membrane protein structures from the Protein DataBank and their associated maps in the Electron Microscopy DataBase and determine how the SP-TEM maps allow lipid visualization, the type of binding sites, the influence of symmetry, resolution and other factors. We illustrate lipid visualization around and inside the protein core, show that some lipid bilayers in the core can be shifted with respect to the membrane and how some proteins can actively bend the lipid bilayer that binds to them. We conclude that resolution improvement in SP-TEM will likely enable many more discoveries regarding the role of lipids bound to proteins.
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Affiliation(s)
- Valérie Biou
- Université de Paris, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
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31
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Villacob RA, Egbejiogu BC, Feizi N, Hogan C, Murray KK, Solouki T. Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2215-2225. [PMID: 36346890 DOI: 10.1021/jasms.2c00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.
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Affiliation(s)
| | | | - Neda Feizi
- Baylor University, Waco, Texas 76706, United States
| | - Cole Hogan
- Baylor University, Waco, Texas 76706, United States
| | - Kermit K Murray
- Louisiana State University, Baton Rouge, Louisiana 70803, United States
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32
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Lyu J, Liu C, Zhang T, Schrecke S, Elam NP, Packianathan C, Hochberg GKA, Russell D, Zhao M, Laganowsky A. Structural basis for lipid and copper regulation of the ABC transporter MsbA. Nat Commun 2022; 13:7291. [PMID: 36435815 PMCID: PMC9701195 DOI: 10.1038/s41467-022-34905-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
A critical step in lipopolysaccharide (LPS) biogenesis involves flipping lipooligosaccharide, an LPS precursor, from the cytoplasmic to the periplasmic leaflet of the inner membrane, an operation carried out by the ATP-binding cassette transporter MsbA. Although LPS binding to the inner cavity of MsbA is well established, the selectivity of MsbA-lipid interactions at other site(s) remains poorly understood. Here we use native mass spectrometry (MS) to characterize MsbA-lipid interactions and guide structural studies. We show the transporter co-purifies with copper(II) and metal binding modulates protein-lipid interactions. A 2.15 Å resolution structure of an N-terminal region of MsbA in complex with copper(II) is presented, revealing a structure reminiscent of the GHK peptide, a high-affinity copper(II) chelator. Our results demonstrate conformation-dependent lipid binding affinities, particularly for the LPS-precursor, 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). We report a 3.6 Å-resolution structure of MsbA trapped in an open, outward-facing conformation with adenosine 5'-diphosphate and vanadate, revealing a distinct KDL binding site, wherein the lipid forms extensive interactions with the transporter. Additional studies provide evidence that the exterior KDL binding site is conserved and a positive allosteric modulator of ATPase activity, serving as a feedforward activation mechanism to couple transporter activity with LPS biosynthesis.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Chang Liu
- Department of Biochemistry and Molecular biology, University of Chicago, Chicago, 60637, IL, USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Nicklaus P Elam
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Charles Packianathan
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
- Walter Reed Army Institute of Research, Pilot Bioproduction Facility, Silver Spring, 20910, MD, USA
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology and Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, University of Marburg, Marburg, Germany
| | - David Russell
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular biology, University of Chicago, Chicago, 60637, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA.
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33
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Randolph CE, Beveridge CH, Iyer S, Blanksby SJ, McLuckey SA, Chopra G. Identification of Monomethyl Branched-Chain Lipids by a Combination of Liquid Chromatography Tandem Mass Spectrometry and Charge-Switching Chemistries. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2156-2164. [PMID: 36218280 PMCID: PMC10173259 DOI: 10.1021/jasms.2c00225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions. Subsequent activation of these charge inverted anions yields mass spectra that differentiate anteiso-branched- from straight-chain and iso-branched-chain FA isomers with the predictable fragmentation enabling de novo assignment of anteiso branch points. The application of these charge-inversion chemistries in both gas- and solution-phase modalities is demonstrated to assign the position of anteiso-methyl branch-points in FAs and, with the aid of liquid chromatography, can be extended to de novo assignment of additional branching sites via predictable fragmentation patterns as methyl branching site(s) move closer to the carboxyl carbon. The gas-phase approach is shown to be compatible with top-down structure elucidation of complex lipids such as phosphatidylcholines, while the integration of solution-phase charge-inversion with reversed phase liquid chromatography enables separation and unambiguous identification of FA structures within isomeric mixtures. Taken together, the presented charge-switching MS-based technique, in combination with liquid chromatography, enables the structural identification of branched-chain FA without the requirement of authentic methyl-branched FA reference standards.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Connor H. Beveridge
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Sanjay Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Stephen J. Blanksby
- Central Analytical Research Facility and the School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
- Department of Computer Science (by courtesy), Purdue Institutes of Drug Discovery and Integrative Neuroscience, Purdue Center for Cancer Research, West Lafayette, Indiana, 47907, USA
- Address reprint requests to: Dr. Gaurav Chopra, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 496-6108, Fax: (765) 494-0239,
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34
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Umegawa Y, Shimonishi T, Tsuchikawa H, Murata M. LnDOTA-d 8 , a versatile chemical-shift thermometer for 2 H solid-state NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1005-1013. [PMID: 35938541 DOI: 10.1002/mrc.5303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
2 H solid-state nuclear magnetic resonance (NMR) is a method for examining the mobility and orientation of molecules in the field of biophysics. In studies on lipid bilayer membranes, 2 H NMR is often adopted to detect a phase transition from the gel to the liquid-crystal phase, which is observed as a change in spectral shape, and to evaluate the ordering of lipid alkyl chains using quadrupole coupling values. Because the mobility of membrane lipids is highly temperature dependent, precise temperature control is a prerequisite for evaluating the physical properties of membranes. Generally, NMR instruments monitor the temperature of the variable temperature (VT) gas. The temperature inside the sample tube and the VT gas match only when the heat generated by the radio frequency (rf) pulse emitted from the coil or magic angle spinning is significantly lower than the cooling capacity of the VT gas. In other words, the sample temperature inside the tube depends on the measurement method. Therefore, in this study, we took advantage of temperature-dependent changes in the chemical shift of a paramagnetic metal-ligand complex. We designed and synthesized a deuterated ligand complex and evaluated its temperature dependence as a thermometer for 2 H solid-state NMR spectroscopy. We chose Tb, Dy, Ho, and Er as the paramagnetic central metals. We then measured the 2 H NMR spectrum of each metal complex and confirmed the 2 H chemical shift to be temperature dependent. Furthermore, with the use of the thermometer molecule with Er, we succeeded in accurately evaluating the segmental melting of an alkyl chain in lipid bilayers with 0.1°C accuracy.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
| | - Takeshi Shimonishi
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
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35
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Korn P, Schwieger C, Gruhle K, Garamus VM, Meister A, Ihling C, Drescher S. Azide- and diazirine-modified membrane lipids: Physicochemistry and applicability to study peptide/lipid interactions via cross-linking/mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184004. [PMID: 35841926 DOI: 10.1016/j.bbamem.2022.184004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Although the incorporation of photo-activatable lipids into membranes potentially opens new avenues for studying interactions with peptides and proteins, the question of whether azide- or diazirine-modified lipids are suitable for such studies remains controversial. We have recently shown that diazirine-modified lipids can indeed form cross-links to membrane peptides after UV activation and that these cross-links can be precisely determined in their position by mass spectrometry (MS). However, we also observed an unexpected backfolding of the lipid's diazirine-containing stearoyl chain to the membrane interface challenging the potential application of this modified lipid for future cross-linking (XL)-MS studies of protein/lipid interactions. In this work, we compared an azide- (AzidoPC) and a diazirine-modified (DiazPC) membrane lipid regarding their self-assembly properties, their mixing behavior with saturated bilayer-forming phospholipids, and their reactivity upon UV activation using differential scanning calorimetry (DSC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and MS. Mixtures of both modified lipids with DMPC were further used for photo-chemically induced XL experiments with a transmembrane model peptide (KLAW23) to elucidate similarities and differences between the azide and the diazirine moiety. We showed that both photo-reactive lipids can be used to study lipid/peptide and lipid/protein interactions. The AzidoPC proved easier to handle, whereas the DiazPC had fewer degradation products and a higher cross-linking yield. However, the problem of backfolding occurs in both lipids; thus, it seems to be a general phenomenon.
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Affiliation(s)
- Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Schwieger
- Institute of Chemistry, MLU Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology-Physical Biotechnology, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany; Phospholipid Research Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany.
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36
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Kumar S, Zhu Y, Stover L, Laganowsky A. Step toward Probing the Nonannular Belt of Membrane Proteins. Anal Chem 2022; 94:13906-13912. [PMID: 36170465 DOI: 10.1021/acs.analchem.2c02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integral membrane proteins are embedded in the biological membrane, where they carry out numerous biological processes. Although lipids present in the membrane are crucial for membrane protein function, it remains difficult to characterize many lipid binding events to membrane proteins, such as those that form the annular belt. Here, we use native mass spectrometry along with the charge-reducing properties of trimethylamine N-oxide (TMAO) to characterize a large number of lipid binding events to the bacterial ammonia channel (AmtB). In the absence of TMAO, significant peak overlap between neighboring charge states is observed, resulting in erroneous abundances for different molecular species. With the addition of TMAO, the weighted average charge state (Zavg) was decreased. In addition, the increased spacing between nearby charge states enabled a higher number of lipid binding species to be observed while minimizing mass spectral peak overlap. These conditions helped us to determine the equilibrium binding constants (Kd) for up to 16 lipid binding events. The binding constants for the first few lipid binding events display the highest affinity, whereas the binding constants for higher lipid binding events converge to a similar value. These findings suggest a transition from nonannular to annular lipid binding to AmtB.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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37
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Advances in membrane mimetics and mass spectrometry for understanding membrane structure and function. Curr Opin Chem Biol 2022; 69:102157. [DOI: 10.1016/j.cbpa.2022.102157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/19/2022]
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38
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Clarke A, Groschner K, Stockner T. Exploring TRPC3 Interaction with Cholesterol through Coarse-Grained Molecular Dynamics Simulations. Biomolecules 2022; 12:biom12070890. [PMID: 35883446 PMCID: PMC9313397 DOI: 10.3390/biom12070890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transient receptor potential canonical 3 (TRPC3) channel belongs to the superfamily of transient receptor potential (TRP) channels which mediate Ca2+ influx into the cell. These channels constitute essential elements of cellular signalling and have been implicated in a wide range of diseases. TRPC3 is primarily gated by lipids and its surface expression has been shown to be dependent on cholesterol, yet a comprehensive exploration of its interaction with this lipid has thus far not emerged. Here, through 80 µs of coarse-grained molecular dynamics simulations, we show that cholesterol interacts with multiple elements of the transmembrane machinery of TRPC3. Through our approach, we identify an annular binding site for cholesterol on the pre-S1 helix and a non-annular site at the interface between the voltage-sensor-like domain and pore domains. Here, cholesterol interacts with exposed polar residues and possibly acts to stabilise the domain interface.
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Affiliation(s)
- Amy Clarke
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr., 13A, 1090 Vienna, Austria;
| | - Klaus Groschner
- Gottfried Schatz Research Center, Division of Biophysics, Medical University of Graz, 8010 Graz, Austria;
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr., 13A, 1090 Vienna, Austria;
- Correspondence:
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Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
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Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
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40
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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41
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Zhu Y, Schrecke S, Tang S, Odenkirk MT, Walker T, Stover L, Lyu J, Zhang T, Russell D, Baker ES, Yan X, Laganowsky A. Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions. J Am Chem Soc 2022; 144:7048-7053. [PMID: 35421309 DOI: 10.1021/jacs.2c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TRAAK and TREK2 are two-pore domain K+ (K2P) channels and are modulated by diverse factors including temperature, membrane stretching, and lipids, such as phosphatidic acid. In addition, copper and zinc, both of which are essential for life, are known to regulate TREK2 and a number of other ion channels. However, the role of ions in the association of lipids with integral membrane proteins is poorly understood. Here, we discover cupric ions selectively modulate the binding of phosphatidylserine (PS) to TRAAK but not TREK2. Other divalent cations (Ca2+, Mg2+, and Zn2+) bind both channels but have no impact on binding PS and other lipids. Additionally, TRAAK binds more avidly to Cu2+ and Zn2+ than TREK2. In the presence of Cu2+, TRAAK binds similarly to PS with different acyl chains, indicating a crucial role of the serine headgroup in coordinating Cu2+. High-resolution native mass spectrometry (MS) enables the determination of equilibrium binding constants for distinct Cu2+-bound stoichiometries and uncovered the highest coupling factor corresponds to a 1:1 PS-to-Cu2+ ratio. Interestingly, the next three highest coupling factors had a ∼1.5:1 PS-to-Cu2+ ratio. Our findings bring forth the role of cupric ions as an essential cofactor in selective TRAAK-PS interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shuli Tang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xin Yan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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42
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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43
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Frequency chasing of individual megadalton ions in an Orbitrap analyser improves precision of analysis in single-molecule mass spectrometry. Nat Chem 2022; 14:515-522. [PMID: 35273389 PMCID: PMC9068510 DOI: 10.1038/s41557-022-00897-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
To enhance the performance of charge-detection mass spectrometry, we investigated the behaviour of macromolecular single ions on their paths towards and within the Orbitrap analyser. Ions with a mass beyond one megadalton reach a plateau of stability and can be successfully trapped for seconds, travelling a path length of multiple kilometres, thereby enabling precise mass analysis with an effective resolution of greater than 100,000 at a mass-to-charge ratio of 35,000. Through monitoring the frequency of individual ions, we show that these high-mass ions, rather than being lost from the trap, can gradually lose residual solvent molecules and, in rare cases, a single elementary charge. We also demonstrate that the frequency drift of single ions due to desolvation and charge stripping can be corrected, which improves the effective ion sampling 23-fold and gives a twofold improvement in mass precision and resolution. ![]()
The mass precision and resolution in charge-detection mass spectrometry can be improved by correcting frequency drifts of single ions. Now, chasing these individual ions for seconds in an Orbitrap mass spectrometer has revealed the exceptional stability of ultra-high-mass ions, culminating in an effective resolution of greater than 100,000 at m/z = 35,000.
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44
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Verteporfin is a Substrate-Selective γ-Secretase Inhibitor that Binds the Amyloid Precursor Protein Transmembrane Domain. J Biol Chem 2022; 298:101792. [PMID: 35247387 PMCID: PMC8968665 DOI: 10.1016/j.jbc.2022.101792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 11/23/2022] Open
Abstract
This work reports substrate-selective inhibition of a protease with broad substrate specificity based on direct binding of a small molecule inhibitor to the substrate. The target for these studies was γ-secretase protease, which cleaves dozens of different single span membrane protein substrates, including both the C99 domain of the human amyloid precursor protein and the Notch receptor. Substrate-specific inhibition of C99 cleavage is desirable to reduce production of the amyloid-β polypeptide without inhibiting Notch cleavage, a major source of toxicity associated with broad specificity γ-secretase inhibitors. In order to identify a C99-selective inhibitors of the human γ-secretase, we conducted an NMR-based screen of FDA-approved drugs against C99 in model membranes. From this screen, we identified the small molecule verteporfin with these properties. We observed that verteporfin formed a direct 1:1 complex with C99, with a KD of 15-47 μM (depending on the membrane mimetic used), and that it did not bind the transmembrane domain of the Notch-1 receptor. Biochemical assays showed that direct binding of verteporfin to C99 inhibits γ-secretase cleavage of C99 with IC50 values in the range of 15- 164 μM, while Notch-1 cleavage was inhibited only at higher concentrations, and likely via a mechanism that does not involve binding to Notch-1. This work documents a robust NMR-based approach to discovery of small molecule binders to single-span membrane proteins and confirmed that it is possible to inhibit γ-secretase in a substrate-specific manner.
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45
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Protein Lipidation Types: Current Strategies for Enrichment and Characterization. Int J Mol Sci 2022; 23:ijms23042365. [PMID: 35216483 PMCID: PMC8880637 DOI: 10.3390/ijms23042365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.
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46
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It Takes More than Two to Tango: Complex, Hierarchal, and Membrane-Modulated Interactions in the Regulation of Receptor Tyrosine Kinases. Cancers (Basel) 2022; 14:cancers14040944. [PMID: 35205690 PMCID: PMC8869822 DOI: 10.3390/cancers14040944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022] Open
Abstract
The search for an understanding of how cell fate and motility are regulated is not a purely scientific undertaking, but it can also lead to rationally designed therapies against cancer. The discovery of tyrosine kinases about half a century ago, the subsequent characterization of certain transmembrane receptors harboring tyrosine kinase activity, and their connection to the development of human cancer ushered in a new age with the hope of finding a treatment for malignant diseases in the foreseeable future. However, painstaking efforts were required to uncover the principles of how these receptors with intrinsic tyrosine kinase activity are regulated. Developments in molecular and structural biology and biophysical approaches paved the way towards better understanding of these pathways. Discoveries in the past twenty years first resulted in the formulation of textbook dogmas, such as dimerization-driven receptor association, which were followed by fine-tuning the model. In this review, the role of molecular interactions taking place during the activation of receptor tyrosine kinases, with special attention to the epidermal growth factor receptor family, will be discussed. The fact that these receptors are anchored in the membrane provides ample opportunities for modulatory lipid-protein interactions that will be considered in detail in the second part of the manuscript. Although qualitative and quantitative alterations in lipids in cancer are not sufficient in their own right to drive the malignant transformation, they both contribute to tumor formation and also provide ways to treat cancer. The review will be concluded with a summary of these medical aspects of lipid-protein interactions.
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47
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Daggubati V, Raleigh DR, Sever N. Sterol regulation of developmental and oncogenic Hedgehog signaling. Biochem Pharmacol 2022; 196:114647. [PMID: 34111427 PMCID: PMC8648856 DOI: 10.1016/j.bcp.2021.114647] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/03/2023]
Abstract
The Hedgehog (Hh) family of lipid-modified signaling proteins directs embryonic tissue patterning and postembryonic tissue homeostasis, and dysregulated Hh signaling drives familial and sporadic cancers. Hh ligands bind to and inhibit the tumor suppressor Patched and allow the oncoprotein Smoothened (SMO) to accumulate in cilia, which in turn activates the GLI family of transcription factors. Recent work has demonstrated that endogenous cholesterol and oxidized cholesterol derivatives (oxysterols) bind and modulate SMO activity. Here we discuss the myriad sterols that activate or inhibit the Hh pathway, with emphasis on endogenous 24(S),25-epoxycholesterol and 3β,5α-dihydroxycholest-7-en-6-one, and propose models of sterol regulation of SMO. Synthetic inhibitors of SMO have long been the focus of drug development efforts. Here, we discuss the possible utility of steroidal SMO ligands or inhibitors of enzymes involved in sterol metabolism as cancer therapeutics.
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Affiliation(s)
- Vikas Daggubati
- Departments of Radiation Oncology and Neurological Surgery, and Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA,Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - David R. Raleigh
- Departments of Radiation Oncology and Neurological Surgery, and Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Navdar Sever
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA,Corresponding author: Navdar Sever, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB 405, Boston, MA 02115, USA, , Telephone: (617) 432-1612
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48
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Uncoupling Proteins and Regulated Proton Leak in Mitochondria. Int J Mol Sci 2022; 23:ijms23031528. [PMID: 35163451 PMCID: PMC8835771 DOI: 10.3390/ijms23031528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
Abstract
Higher concentration of protons in the mitochondrial intermembrane space compared to the matrix results in an electrochemical potential causing the back flux of protons to the matrix. This proton transport can take place through ATP synthase complex (leading to formation of ATP) or can occur via proton transporters of the mitochondrial carrier superfamily and/or membrane lipids. Some mitochondrial proton transporters, such as uncoupling proteins (UCPs), transport protons as their general regulating function; while others are symporters or antiporters, which use the proton gradient as a driving force to co-transport other substrates across the mitochondrial inner membrane (such as phosphate carrier, a symporter; or aspartate/glutamate transporter, an antiporter). Passage (or leakage) of protons across the inner membrane to matrix from any route other than ATP synthase negatively impacts ATP synthesis. The focus of this review is on regulated proton transport by UCPs. Recent findings on the structure and function of UCPs, and the related research methodologies, are also critically reviewed. Due to structural similarity of members of the mitochondrial carrier superfamily, several of the known structural features are potentially expandable to all members. Overall, this report provides a brief, yet comprehensive, overview of the current knowledge in the field.
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49
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Insights into lipid-protein interactions from computer simulations. Biophys Rev 2022; 13:1019-1027. [PMID: 35047089 PMCID: PMC8724345 DOI: 10.1007/s12551-021-00876-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022] Open
Abstract
Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.
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50
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Klykov O, Kopylov M, Carragher B, Heck AJ, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding author for cryo-EM/ET/FIB-SEM: Alex J. Noble, tel: (+1) 212-939-0660;
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands,Corresponding author for MS: Richard A. Scheltema, tel: (+31) 30 253 6804;
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