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Shang Z, Zhao J, Yang M, Xiao Y, Chu W, Xu S, Zhang X, Yi X, Lin M, Xia F. Precise control of transmembrane current via regulating bionic lipid membrane composition. SCIENCE ADVANCES 2024; 10:eadq0118. [PMID: 39213352 PMCID: PMC11364097 DOI: 10.1126/sciadv.adq0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The transport of ions through biological ion channels is regulated not only by their structural characteristics but also by the composition of the phospholipid membrane, which serves as a carrier for nanochannels. Inspired by the modulation of ion currents by lipid membrane composition, exemplified by the activation of the K+ channel of Streptomyces A by anionic lipids, we present a biomimetic nanochannel system based on combining DNA nanotechnology with two-dimensional graphene oxide (GO) nanosheets. By designing multibranched DNA nanowires, we assemble programmable DNA scaffold networks (DSNs) on the GO surface to precisely control membrane composition. Modulating the DSN layers from one to five enhances DNA composition, yielding a maximum 12-fold enhancement in ion current, primarily due to charge effects. Incorporating DNAzymes facilitates reversible modulation of membrane composition, enabling cyclic conversion of ion current. This approach offers a pathway for creating devices with highly efficient, tunable ion transport, applicable in diverse fields like mass transport, environmental protection, biomimetic channels, and biosensors.
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Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jing Zhao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yuling Xiao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wenjing Chu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shijun Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Wu D, Tang H, Qiu X, Song S, Chen S, Robinson CV. Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters. Nat Protoc 2024:10.1038/s41596-024-01037-4. [PMID: 39174660 DOI: 10.1038/s41596-024-01037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/06/2024] [Indexed: 08/24/2024]
Abstract
The mammalian membrane is composed of various eukaryotic lipids interacting with extensively post-translationally modified proteins. Probing interactions between these mammalian membrane proteins and their diverse and heterogeneous lipid cohort remains challenging. Recently, native mass spectrometry (MS) combined with bottom-up 'omics' approaches has provided valuable information to relate structural and functional lipids to membrane protein assemblies in eukaryotic membranes. Here we provide a step-by-step protocol to identify and provide relative quantification for endogenous lipids bound to mammalian membrane proteins and their complexes. Using native MS to guide our lipidomics strategies, we describe the necessary sample preparation steps, followed by native MS data acquisition, tailored lipidomics and data interpretation. We also highlight considerations for the integration of different levels of information from native MS and lipidomics and how to deal with the various challenges that arise during the experiments. This protocol begins with the preparation of membrane proteins from mammalian cells and tissues for native MS. The results enable not only direct assessment of copurified endogenous lipids but also determination of the apparent affinities of specific lipids. Detailed sample preparation for lipidomics analysis is also covered, along with comprehensive settings for liquid chromatography-MS analysis. This protocol is suitable for the identification and quantification of endogenous lipids, including fatty acids, sterols, glycerolipids, phospholipids and glycolipids and can be used to interrogate proteins from recombinant sources to native membranes.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyun Chen
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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3
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Krygier M, Ziętkiewicz S, Talaśka-Liczbik W, Chylińska M, Walczak A, Kostrzewa G, Płoski R, Mazurkiewicz-Bełdzińska M. The epilepsy phenotype of KCNK4-related neurodevelopmental disease. Seizure 2024; 121:114-122. [PMID: 39146707 DOI: 10.1016/j.seizure.2024.08.008] [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: 06/04/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
INTRODUCTION Potassium ion channels play a crucial role in maintaining cellular electrical stability and are implicated in various epilepsies. Heterozygous pathogenic variants in KCNK4 cause a recognizable neurodevelopmental syndrome with facial dysmorphism, hypertrichosis, epilepsy, intellectual disability (ID), and gingival overgrowth (FHEIG). To date, no more than nine patients with FHEIG have been described worldwide and still little is known about epileptic phenotype in KCNK4-related disease. METHODS We identified a novel de novo p.(Gly139Arg) variant in KCNK4 in a patient with drug-resistant nocturnal seizures, mild ID, and dysmorphic features. In silico analyses of the variant strongly suggest a gain-of-function effect. We conducted a retrospective review of previously published cases, focusing on the epileptic features and response to various treatments. RESULTS To date, epilepsy has been reported in 8/10 patients with KCNK4-related disease. The mean age of seizure onset was 1.8 years, and the most common seizure type was focal to bilateral tonic-clonic (5/8). Sodium channel blockers and valproate were effective in the majority of patients, but in 3/8 the epilepsy was drug-resistant. Our patient showed improved seizure control after treatment with the carbonic anhydrase inhibitor sulthiame. Interestingly, the patient showed features of peripheral nerve hyperexcitability syndrome, a phenomenon not previously described in potassium channelopathies caused by increased K+ conductance. CONCLUSION Gain-of-function variants in KCNK4 cause a spectrum of epilepsies, ranging from benign isolated epilepsy to epileptic encephalopathy, with focal to bilateral tonic-clonic seizures being the most commonly observed. Importantly, a subgroup of patients present with a mild extra-neurological phenotype without characteristic facial dysmorphism or generalized hypertrichosis. This report expands the phenotypic spectrum of KNCK4-associated disease and provides new insights into the clinical heterogeneity of this rare neurodevelopmental syndrome.
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Affiliation(s)
- Magdalena Krygier
- Department of Developmental Neurology, Medical University of Gdansk, Gdansk, Poland.
| | - Szymon Ziętkiewicz
- Laboratory of Protein Biochemistry, Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
| | | | | | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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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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5
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Stover L, Zhu Y, Schrecke S, Laganowsky A. TREK2 Lipid Binding Preferences Revealed by Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1516-1522. [PMID: 38843438 PMCID: PMC11228984 DOI: 10.1021/jasms.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
TREK2, a two-pore domain potassium channel, is recognized for its regulation by various stimuli, including lipids. While previous members of the TREK subfamily, TREK1 and TRAAK, have been investigated to elucidate their lipid affinity and selectivity, TREK2 has not been similarly studied in this regard. Our findings indicate that while TRAAK and TREK2 exhibit similarities in terms of electrostatics and share an overall structural resemblance, there are notable distinctions in their interaction with lipids. Specifically, SAPI(4,5)P2,1-stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate) exhibits a strong affinity for TREK2, surpassing that of dOPI(4,5)P2,1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate), which differs in its acyl chains. TREK2 displays lipid binding preferences not only for the headgroup of lipids but also toward the acyl chains. Functional studies draw a correlation for lipid binding affinity and activity of the channel. These findings provide important insight into elucidating the molecular prerequisites for specific lipid binding to TREK2 important for function.
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Affiliation(s)
- Lauren Stover
- 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
| | - Samantha Schrecke
- 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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6
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Thomas N, Combs W, Mandadapu KK, Agrawal A. Preferential electrostatic interactions of phosphatidic acid with arginines. SOFT MATTER 2024; 20:2998-3006. [PMID: 38482724 DOI: 10.1039/d4sm00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Phosphatidic acid (PA) is an anionic lipid that preferentially interacts with proteins in a diverse set of cellular processes such as transport, apoptosis, and neurotransmission. One such interaction is that of the PA lipids with the proteins of voltage-sensitive ion channels. In comparison to several other similarly charged anionic lipids, PA lipids exhibit much stronger interactions. Intrigued and motivated by this finding, we sought out to gain deeper understanding into the electrostatic interactions of anionic lipids with charged proteins. Using the voltage sensor domain (VSD) of the KvAP channel as a model system, we performed long-timescale atomistic simulations to analyze the interactions of POPA, POPG, and POPI lipids with arginines (ARGs). Our simulations reveal two mechanisms. First, POPA is able to interact not only with surface ARGs but is able to snorkel and interact with a buried arginine. POPG and POPI lipids on the other hand show weak interactions even with both the surface and buried ARGs. Second, deprotonated POPA with -2 charge is able to break the salt-bridge connection between VSD protein segments and establish its own electrostatic bond with the ARG. Based on these findings, we propose a headgroup size hypothesis for preferential solvation of proteins by charged lipids. These findings may be valuable in understanding how PA lipids could be modulating kinematics of transmembrane proteins in cellular membranes.
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Affiliation(s)
- Nidhin Thomas
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA.
| | - Wesley Combs
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA.
| | - Kranthi K Mandadapu
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Ashutosh Agrawal
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA.
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7
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Zhu Y, Yun SD, Zhang T, Chang JY, Stover L, Laganowsky A. Native mass spectrometry of proteoliposomes containing integral and peripheral membrane proteins. Chem Sci 2023; 14:14243-14255. [PMID: 38098719 PMCID: PMC10718073 DOI: 10.1039/d3sc04938h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Cellular membranes are critical to the function of membrane proteins, whether they are associated (peripheral) or embedded (integral) within the bilayer. While detergents have contributed to our understanding of membrane protein structure and function, there remains challenges in characterizing protein-lipid interactions within the context of an intact membrane. Here, we developed a method to prepare proteoliposomes for native mass spectrometry (MS) studies. We first use native MS to detect the encapsulation of soluble proteins within liposomes. We then find the peripheral Gβ1γ2 complex associated with the membrane can be ejected and analyzed using native MS. Four different integral membrane proteins (AmtB, AqpZ, TRAAK, and TREK2), all of which have previously been characterized in detergent, eject from the proteoliposomes as intact complexes bound to lipids that have been shown to tightly associate in detergent, drawing a correlation between the two approaches. We also show the utility of more complex lipid environments, such as a brain polar lipid extract, and show TRAAK ejects from liposomes of this extract bound to lipids. These findings underscore the capability to eject protein complexes from membranes bound to both lipids and metal ions, and this approach will be instrumental in the identification of key protein-lipid interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Sangho D Yun
- 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
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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8
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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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9
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Zhu Y, Peng BJ, Kumar S, Stover L, Chang JY, Lyu J, Zhang T, Schrecke S, Azizov D, Russell DH, Fang L, Laganowsky A. Polyamine detergents tailored for native mass spectrometry studies of membrane proteins. Nat Commun 2023; 14:5676. [PMID: 37709761 PMCID: PMC10502129 DOI: 10.1038/s41467-023-41429-w] [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: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Native mass spectrometry (MS) is a powerful technique for interrogating membrane protein complexes and their interactions with other molecules. A key aspect of the technique is the ability to preserve native-like structures and noncovalent interactions, which can be challenging depending on the choice of detergent. Different strategies have been employed to reduce charge on protein complexes to minimize activation and preserve non-covalent interactions. Here, we report the synthesis of a class of polyamine detergents tailored for native MS studies of membrane proteins. These detergents, a series of spermine covalently attached to various alkyl tails, are exceptional charge-reducing molecules, exhibiting a ten-fold enhanced potency over spermine. Addition of polyamine detergents to proteins solubilized in maltoside detergents results in improved, charge-reduced native mass spectra and reduced dissociation of subunits. Polyamine detergents open new opportunities to investigate membrane proteins in different detergent environments that have thwarted previous native MS studies.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Bo-Ji Peng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jixing Lyu
- 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
| | - Djavdat Azizov
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
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10
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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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11
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Tang H, Li H, Prakaash D, Pedebos C, Qiu X, Sauer DB, Khalid S, Duerr K, Robinson CV. The solute carrier SPNS2 recruits PI(4,5)P 2 to synergistically regulate transport of sphingosine-1-phosphate. Mol Cell 2023; 83:2739-2752.e5. [PMID: 37499662 PMCID: PMC10790328 DOI: 10.1016/j.molcel.2023.06.033] [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: 11/30/2022] [Revised: 05/11/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Solute carrier spinster homolog 2 (SPNS2), one of only four known major facilitator superfamily (MFS) lysolipid transporters in humans, exports sphingosine-1-phosphate (S1P) across cell membranes. Here, we explore the synergistic effects of lipid binding and conformational dynamics on SPNS2's transport mechanism. Using mass spectrometry, we discovered that SPNS2 interacts preferentially with PI(4,5)P2. Together with functional studies and molecular dynamics (MD) simulations, we identified potential PI(4,5)P2 binding sites. Mutagenesis of proposed lipid binding sites and inhibition of PI(4,5)P2 synthesis reduce S1P transport, whereas the absence of the N terminus renders the transporter essentially inactive. Probing the conformational dynamics of SPNS2, we show how synergistic binding of PI(4,5)P2 and S1P facilitates transport, increases dynamics of the extracellular gate, and stabilizes the intracellular gate. Given that SPNS2 transports a key signaling lipid, our results have implications for therapeutic targeting and also illustrate a regulatory mechanism for MFS transporters.
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Affiliation(s)
- Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina Duerr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK; OMass Therapeutics, Ltd., Oxford OX4 2GX, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK.
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12
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Goodman MB, Haswell ES, Vásquez V. Mechanosensitive membrane proteins: Usual and unusual suspects in mediating mechanotransduction. J Gen Physiol 2023; 155:e202213248. [PMID: 36696153 PMCID: PMC9930137 DOI: 10.1085/jgp.202213248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This Viewpoint, which accompanies a Special Issue focusing on membrane mechanosensors, discusses unifying and unique features of both established and emerging mechanosensitive (MS) membrane proteins, their distribution across protein families and phyla, and current and future challenges in the study of these important proteins and their partners. MS membrane proteins are essential for tissue development, cellular motion, osmotic homeostasis, and sensing external and self-generated mechanical cues like those responsible for touch and proprioception. Though researchers' attention and this Viewpoint focus on a few famous ion channels that are considered the usual suspects as MS mechanosensors, we also discuss some of the more unusual suspects, such as G-protein coupled receptors. As the field continues to grow, so too will the list of proteins suspected to function as mechanosensors and the diversity of known MS membrane proteins.
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Affiliation(s)
- Miriam B. Goodman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Elizabeth S. Haswell
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Valeria Vásquez
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
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13
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Schmidpeter PAM, Petroff JT, Khajoueinejad L, Wague A, Frankfater C, Cheng WWL, Nimigean CM, Riegelhaupt PM. Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1. Nat Commun 2023; 14:1077. [PMID: 36841877 PMCID: PMC9968290 DOI: 10.1038/s41467-023-36765-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators.
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Affiliation(s)
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Leila Khajoueinejad
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Aboubacar Wague
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Cheryl Frankfater
- Department of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Paul M Riegelhaupt
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
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14
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Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
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15
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Yuan Z, Hansen SB. Cholesterol Regulation of Membrane Proteins Revealed by Two-Color Super-Resolution Imaging. MEMBRANES 2023; 13:membranes13020250. [PMID: 36837753 PMCID: PMC9966874 DOI: 10.3390/membranes13020250] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 05/15/2023]
Abstract
Cholesterol and phosphatidyl inositol 4,5-bisphosphate (PIP2) are hydrophobic molecules that regulate protein function in the plasma membrane of all cells. In this review, we discuss how changes in cholesterol concentration cause nanoscopic (<200 nm) movements of membrane proteins to regulate their function. Cholesterol is known to cluster many membrane proteins (often palmitoylated proteins) with long-chain saturated lipids. Although PIP2 is better known for gating ion channels, in this review, we will discuss a second independent function as a regulator of nanoscopic protein movement that opposes cholesterol clustering. The understanding of the movement of proteins between nanoscopic lipid domains emerged largely through the recent advent of super-resolution imaging and the establishment of two-color techniques to label lipids separate from proteins. We discuss the labeling techniques for imaging, their strengths and weakness, and how they are used to reveal novel mechanisms for an ion channel, transporter, and enzyme function. Among the mechanisms, we describe substrate and ligand presentation and their ability to activate enzymes, gate channels, and transporters rapidly and potently. Finally, we define cholesterol-regulated proteins (CRP) and discuss the role of PIP2 in opposing the regulation of cholesterol, as seen through super-resolution imaging.
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Affiliation(s)
- Zixuan Yuan
- Department of Molecular Medicine, Department of Neuroscience, UF Scripps, Jupiter, FL 33458, USA
- Department of Neuroscience UF Scripps, Jupiter, FL 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Scott B. Hansen
- Department of Molecular Medicine, Department of Neuroscience, UF Scripps, Jupiter, FL 33458, USA
- Department of Neuroscience UF Scripps, Jupiter, FL 33458, USA
- Correspondence:
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16
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Schmidpeter PAM, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat Struct Mol Biol 2022; 29:1092-1100. [PMID: 36352139 PMCID: PMC10022520 DOI: 10.1038/s41594-022-00851-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/25/2022] [Indexed: 11/11/2022]
Abstract
Lipids play important roles in regulating membrane protein function, but the molecular mechanisms used are elusive. Here we investigated how anionic lipids modulate SthK, a bacterial pacemaker channel homolog, and HCN2, whose activity contributes to pacemaking in the heart and brain. Using SthK allowed the reconstitution of purified channels in controlled lipid compositions for functional and structural assays that are not available for the eukaryotic channels. We identified anionic lipids bound tightly to SthK and their exact binding locations and determined that they potentiate channel activity. Cryo-EM structures in the most potentiating lipids revealed an open state and identified a nonannular lipid bound with its headgroup near an intersubunit salt bridge that clamps the intracellular channel gate shut. Breaking this conserved salt bridge abolished lipid modulation in SthK and eukaryotic HCN2 channels, indicating that anionic membrane lipids facilitate channel opening by destabilizing these interactions. Our findings underline the importance of state-dependent protein-lipid interactions.
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Affiliation(s)
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
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17
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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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18
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Shrestha A, Kahraman O, Haselwandter CA. Mechanochemical coupling of lipid organization and protein function through membrane thickness deformations. Phys Rev E 2022; 105:054410. [PMID: 35706253 DOI: 10.1103/physreve.105.054410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Cell membranes are composed of a great variety of protein and lipid species with distinct unperturbed hydrophobic thicknesses. To achieve hydrophobic matching, the lipid bilayer tends to deform around membrane proteins so as to match the protein hydrophobic thickness at bilayer-protein interfaces. Such protein-induced distortions of the lipid bilayer hydrophobic thickness incur a substantial energy cost that depends critically on the bilayer-protein hydrophobic mismatch, while distinct conformational states of membrane proteins often show distinct hydrophobic thicknesses. As a result, hydrophobic interactions between membrane proteins and lipids can yield a rich interplay of lipid-protein organization and transitions in protein conformational state. We combine here the membrane elasticity theory of protein-induced lipid bilayer thickness deformations with the Landau-Ginzburg theory of lipid domain formation to systematically explore the coupling between local lipid organization, lipid and protein hydrophobic thickness, and protein-induced lipid bilayer thickness deformations in membranes with heterogeneous lipid composition. We allow for a purely mechanical coupling of lipid and protein composition through the energetics of protein-induced lipid bilayer thickness deformations as well as a chemical coupling driven by preferential interactions between particular lipid and protein species. We find that the resulting lipid-protein organization can endow membrane proteins with diverse and controlled mechanical environments that, via protein-induced lipid bilayer thickness deformations, can strongly influence protein function. The theoretical approach employed here provides a general framework for the quantitative prediction of how membrane thickness deformations influence the joint organization and function of lipids and proteins in cell membranes.
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Affiliation(s)
- Ahis Shrestha
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Osman Kahraman
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Christoph A Haselwandter
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
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19
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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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20
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Riel EB, Jürs BC, Cordeiro S, Musinszki M, Schewe M, Baukrowitz T. The versatile regulation of K2P channels by polyanionic lipids of the phosphoinositide and fatty acid metabolism. J Gen Physiol 2022; 154:212926. [PMID: 34928298 PMCID: PMC8693234 DOI: 10.1085/jgp.202112989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/01/2021] [Indexed: 12/29/2022] Open
Abstract
Work over the past three decades has greatly advanced our understanding of the regulation of Kir K+ channels by polyanionic lipids of the phosphoinositide (e.g., PIP2) and fatty acid metabolism (e.g., oleoyl-CoA). However, comparatively little is known regarding the regulation of the K2P channel family by phosphoinositides and by long-chain fatty acid–CoA esters, such as oleoyl-CoA. We screened 12 mammalian K2P channels and report effects of polyanionic lipids on all tested channels. We observed activation of members of the TREK, TALK, and THIK subfamilies, with the strongest activation by PIP2 for TRAAK and the strongest activation by oleoyl-CoA for TALK-2. By contrast, we observed inhibition for members of the TASK and TRESK subfamilies. Our results reveal that TASK-2 channels have both activatory and inhibitory PIP2 sites with different affinities. Finally, we provided evidence that PIP2 inhibition of TASK-1 and TASK-3 channels is mediated by closure of the recently identified lower X-gate as critical mutations within the gate (i.e., L244A, R245A) prevent PIP2-induced inhibition. Our findings establish that K+ channels of the K2P family are highly sensitive to polyanionic lipids, extending our knowledge of the mechanisms of lipid regulation and implicating the metabolism of these lipids as possible effector pathways to regulate K2P channel activity.
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Affiliation(s)
- Elena B Riel
- Institute of Physiology, Kiel University, Kiel, Germany
| | - Björn C Jürs
- Institute of Physiology, Kiel University, Kiel, Germany.,Medical School Hamburg, University of Applied Sciences and Medical University, Hamburg, Germany
| | | | | | - Marcus Schewe
- Institute of Physiology, Kiel University, Kiel, Germany
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21
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McCoull D, Veale EL, Walsh Y, Byrom L, Avkiran T, Large JM, Vaitone E, Gaffey F, Jerman J, Mathie A, Wright PD. Aprepitant is a novel, selective activator of the K2P channel TRAAK. Biochem Biophys Res Commun 2021; 588:41-46. [PMID: 34942533 DOI: 10.1016/j.bbrc.2021.12.031] [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: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 11/02/2022]
Abstract
TRAAK (KCNK4, K2P4.1) is a mechanosensitive two-pore domain potassium (K2P) channel. Due to its expression within sensory neurons and genetic link to neuropathic pain it represents a promising potential target for novel analgesics. In common with many other channels in the wider K2P sub-family, there remains a paucity of small molecule pharmacological tools. Specifically, there is a lack of molecules selective for TRAAK over the other members of the TREK subfamily of K2P channels. We developed a thallium flux assay to allow high throughput screening of compounds and facilitate the identification of novel TRAAK activators. Using a library of ∼1200 drug like molecules we identified Aprepitant as a small molecule activator of TRAAK. Aprepitant is an NK-1 antagonist used to treat nausea and vomiting. Close structural analogues of Aprepitant and a range of NK-1 antagonists were also selected or designed for purchase or brief chemical synthesis and screened for their ability to activate TRAAK. Electrophysiology experiments confirmed that Aprepitant activates both the 'long' and 'short' transcript variants of TRAAK. We also demonstrated that Aprepitant is selective and does not activate other members of the K2P superfamily. This work describes the development of a high throughput assay to identify potential TRAAK activators and subsequent identification and confirmation of the novel TRAAK activator Aprepitant. This discovery identifies a useful tool compound which can be used to further probe the function of TRAAK K2P channels.
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Affiliation(s)
- D McCoull
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK.
| | - E L Veale
- Medway School of Pharmacy, University of Greenwich and University of Kent, Anson Building, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Y Walsh
- Medway School of Pharmacy, University of Greenwich and University of Kent, Anson Building, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - L Byrom
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - T Avkiran
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - J M Large
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - E Vaitone
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - F Gaffey
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - J Jerman
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - A Mathie
- Medway School of Pharmacy, University of Greenwich and University of Kent, Anson Building, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK; School of Engineering, Arts, Science and Technology, University of Suffolk, Ipswich, IP4 1QJ, UK
| | - P D Wright
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
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22
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McCabe JW, Jones BJ, Walker TE, Schrader RL, Huntley AP, Lyu J, Hoffman NM, Anderson GA, Reilly PTA, Laganowsky A, Wysocki VH, Russell DH. Implementing Digital-Waveform Technology for Extended m/ z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2812-2820. [PMID: 34797072 PMCID: PMC9026758 DOI: 10.1021/jasms.1c00245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Here, we describe a digital-waveform dual-quadrupole mass spectrometer that enhances the performance of our drift tube FT-IMS high-resolution Orbitrap mass spectrometer (MS). The dual-quadrupole analyzer enhances the instrument capabilities for studies of large protein and protein complexes. The first quadrupole (q) provides a means for performing low-energy collisional activation of ions to reduce or eliminate noncovalent adducts, viz., salts, buffers, detergents, and/or endogenous ligands. The second quadrupole (Q) is used to mass-select ions of interest for further interrogation by ion mobility spectrometry and/or collision-induced dissociation (CID). Q is operated using digital-waveform technology (DWT) to improve the mass selection compared to that achieved using traditional sinusoidal waveforms at floated DC potentials (>500 V DC). DWT allows for increased precision of the waveform for a fraction of the cost of conventional RF drivers and with readily programmable operation and precision (Hoffman, N. M. . A comparison-based digital-waveform generator for high-resolution duty cycle. Review of Scientific Instruments 2018, 89, 084101).
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert L Schrader
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Adam P Huntley
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nathan M Hoffman
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | | | - Peter T A Reilly
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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23
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Gulezian E, Crivello C, Bednenko J, Zafra C, Zhang Y, Colussi P, Hussain S. Membrane protein production and formulation for drug discovery. Trends Pharmacol Sci 2021; 42:657-674. [PMID: 34270922 DOI: 10.1016/j.tips.2021.05.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (MPs) are important drug targets across most fields of medicine, but historically have posed a major challenge for drug discovery due to difficulties in producing them in functional forms. We review the state of the art in drug discovery strategies using recombinant multipass MPs, and outline methods to successfully express, stabilize, and formulate them for small-molecule and monoclonal antibody therapeutics development. Advances in structure-based drug design and high-throughput screening are allowing access to previously intractable targets such as ion channels and transporters, propelling the field towards the development of highly specific therapies targeting desired conformations.
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Affiliation(s)
- Ellen Gulezian
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA
| | | | - Janna Bednenko
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA
| | - Claudia Zafra
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA
| | - Yihui Zhang
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA
| | - Paul Colussi
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA
| | - Sunyia Hussain
- TetraGenetics Inc., 91 Mystic Street, Arlington, MA 02474, USA.
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24
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Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins. Int J Mol Sci 2021; 22:ijms22169026. [PMID: 34445730 PMCID: PMC8396450 DOI: 10.3390/ijms22169026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
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25
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Pipatpolkai T, Quetschlich D, Stansfeld PJ. From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels. J Mol Biol 2021; 433:167105. [PMID: 34139216 PMCID: PMC8361781 DOI: 10.1016/j.jmb.2021.167105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022]
Abstract
Potassium (K+) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K+ conductance, returning a cell to its resting potential. K+ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K+ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K+ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K+ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Physiology Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, UK
| | - Daniel Quetschlich
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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26
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Cecchetti C, Strauss J, Stohrer C, Naylor C, Pryor E, Hobbs J, Tanley S, Goldman A, Byrne B. A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution. PLoS One 2021; 16:e0254118. [PMID: 34252116 PMCID: PMC8274869 DOI: 10.1371/journal.pone.0254118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/20/2021] [Indexed: 12/29/2022] Open
Abstract
Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.
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Affiliation(s)
- Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Claudia Stohrer
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Edward Pryor
- Anatrace, Maumee, Ohio, United States of America
| | | | | | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- MIBS, Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail: (AG); (BB)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (AG); (BB)
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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Agasid MT, Robinson CV. Probing membrane protein-lipid interactions. Curr Opin Struct Biol 2021; 69:78-85. [PMID: 33930613 DOI: 10.1016/j.sbi.2021.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 12/15/2022]
Abstract
Structure determination of membrane proteins has highlighted the many roles played by lipids in influencing overall protein architecture. It is now widely accepted that lipids surrounding membrane proteins play crucial roles by modulating their conformational, structural, and functional properties. Capturing often transient lipid interactions and defining their chemical identity, however, remains challenging. Recent advances in mass spectrometry have resolved questions concerning lipid interactions by providing the molecular composition of intact complexes in association with lipids. Together with other biophysical tools, a picture is emerging of the dynamic nature of lipid-mediated interactions and their effects on conformation, interactions, and signaling.
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Affiliation(s)
- Mark T Agasid
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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29
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Natale AM, Deal PE, Minor DL. Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels. J Mol Biol 2021; 433:166995. [PMID: 33887333 PMCID: PMC8436263 DOI: 10.1016/j.jmb.2021.166995] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 01/10/2023]
Abstract
Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K2Ps contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K2Ps have established the basic architecture of this channel family, revealed key moving parts involved in K2P function, uncovered the importance of asymmetric pinching and dilation motions in the K2P selectivity filter (SF) C-type gate, and defined two K2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K2P:modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K2P activity. Such knowledge should catalyze development of new K2P modulators to probe function and treat a wide range of disorders.
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Affiliation(s)
- Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Parker E Deal
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience University of California, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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