1
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Wu D, Yan R, Song S, Swansiger AK, Li Y, Prell JS, Zhou Q, Robinson CV. The complete assembly of human LAT1-4F2hc complex provides insights into its regulation, function and localisation. Nat Commun 2024; 15:3711. [PMID: 38697966 PMCID: PMC11065870 DOI: 10.1038/s41467-024-47948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
The LAT1-4F2hc complex (SLC7A5-SLC3A2) facilitates uptake of essential amino acids, hormones and drugs. Its dysfunction is associated with many cancers and immune/neurological disorders. Here, we apply native mass spectrometry (MS)-based approaches to provide evidence of super-dimer formation (LAT1-4F2hc)2. When combined with lipidomics, and site-directed mutagenesis, we discover four endogenous phosphatidylethanolamine (PE) molecules at the interface and C-terminus of both LAT1 subunits. We find that interfacial PE binding is regulated by 4F2hc-R183 and is critical for regulation of palmitoylation on neighbouring LAT1-C187. Combining native MS with mass photometry (MP), we reveal that super-dimerization is sensitive to pH, and modulated by complex N-glycans on the 4F2hc subunit. We further validate the dynamic assemblies of LAT1-4F2hc on plasma membrane and in the lysosome. Together our results link PTM and lipid binding with regulation and localisation of the LAT1-4F2hc super-dimer.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Qiang Zhou
- Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
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2
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Yan Y, Xiao J, Huang F, Xian W, Yu B, Cheng R, Wu H, Lu X, Wang X, Huang W, Li J, Oyejobi GK, Robinson CV, Wu H, Wu D, Liu X, Wang L, Zhu B. Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway. Nat Microbiol 2024:10.1038/s41564-024-01684-z. [PMID: 38649411 DOI: 10.1038/s41564-024-01684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP-AMP synthase (cGAS) and CBASS-associated proteins, CBASS uses cyclic oligonucleotides to activate antiviral immunity. One major class of CBASS contains a homologue of eukaryotic ubiquitin-conjugating enzymes, which is either an E1-E2 fusion or a single E2. However, the functions of single E2s in CBASS remain elusive. Here, using biochemical, genetic, cryo-electron microscopy and mass spectrometry investigations, we discover that the E2 enzyme from Serratia marcescens regulates cGAS by imitating the ubiquitination cascade. This includes the processing of the cGAS C terminus, conjugation of cGAS to a cysteine residue, ligation of cGAS to a lysine residue, cleavage of the isopeptide bond and poly-cGASylation. The poly-cGASylation activates cGAS to produce cGAMP, which acts as an antiviral signal and leads to cell death. Thus, our findings reveal a unique regulatory role of E2 in CBASS.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Xiao
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
| | - Wei Xian
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjing Huang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Li
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Greater Kayode Oyejobi
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Xiaoyun Liu
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
| | - Longfei Wang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Du G, Healy LB, David L, Walker C, El-Baba TJ, Lutomski CA, Goh B, Gu B, Pi X, Devant P, Fontana P, Dong Y, Ma X, Miao R, Balasubramanian A, Puthenveetil R, Banerjee A, Luo HR, Kagan JC, Oh SF, Robinson CV, Lieberman J, Wu H. ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D. Nature 2024:10.1038/s41586-024-07373-5. [PMID: 38599239 DOI: 10.1038/s41586-024-07373-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation and was previously shown to form large transmembrane pores upon cleavage by inflammatory caspases to generate the GSDMD N-terminal domain (GSDMD-NT)1-10. Here we report that GSDMD Cys191 is S-palmitoylated and palmitoylation is required for pore formation. S-palmitoylation, which does not affect GSDMD cleavage, is augmented by mitochondria-generated reactive oxygen species (ROS). Surprisingly, cleavage-deficient D275A GSDMD is also palmitoylated after inflammasome stimulation or treatment with ROS activators, and causes pyroptosis, although less efficiently than palmitoylated GSDMD-NT. Palmitoylated, but not unpalmitoylated, full-length GSDMD induces liposome leakage, and forms a pore similar in structure to GSDMD-NT pores shown by cryogenic electron microscopy. zDHHC5 and zDHHC9 are the major palmitoyltransferases that mediate GSDMD palmitoylation, and their expression is upregulated by inflammasome activation and ROS. The other human gasdermins are also palmitoylated in their N-termini. These data challenge the concept that cleavage is the only trigger for GSDMD activation. They suggest that reversible palmitoylation is a checkpoint for pore formation by both GSDMD-NT and intact GSDMD that serves as a general switch for the activation of this pore-forming family.
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Affiliation(s)
- Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Liam B Healy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Caitlin Walker
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Seqirus, Cambridge, MA, USA
| | - Tarick J El-Baba
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, United Kingdom
| | - Corinne A Lutomski
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, United Kingdom
| | - Byoungsook Goh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Bowen Gu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Pascal Devant
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Xiyu Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Miao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Arumugam Balasubramanian
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Robbins Puthenveetil
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Hongbo R Luo
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan C Kagan
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Sungwhan F Oh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, United Kingdom
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
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5
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Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y. Constitutive activation mechanism of a class C GPCR. Nat Struct Mol Biol 2024; 31:678-687. [PMID: 38332368 DOI: 10.1038/s41594-024-01224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Class C G-protein-coupled receptors (GPCRs) are activated through binding of agonists to the large extracellular domain (ECD) followed by rearrangement of the transmembrane domains (TMDs). GPR156, a class C orphan GPCR, is unique because it lacks an ECD and exhibits constitutive activity. Impaired GPR156-Gi signaling contributes to loss of hearing. Here we present the cryo-electron microscopy structures of human GPR156 in the Go-free and Go-coupled states. We found that an endogenous phospholipid molecule is located within each TMD of the GPR156 dimer. Asymmetric binding of Gα to the phospholipid-bound GPR156 dimer restructures the first and second intracellular loops and the carboxy-terminal part of the elongated transmembrane 7 (TM7) without altering dimer conformation. Our findings reveal that GPR156 is a transducer for phospholipid signaling. Constant binding of abundant phospholipid molecules and the G-protein-induced reshaping of the cytoplasmic face provide a basis for the constitutive activation of GPR156.
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Affiliation(s)
- Jinwoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Junhyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jieun Jeong
- Department of Applied Chemistry, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea
| | - Jordy Homing Lam
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Kuglae Kim
- Department of Pharmacy, Yonsei University, Incheon, Republic of Korea
| | - Joo-Youn Lee
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jaekyung Hyun
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea.
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea.
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Medical Science and Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
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6
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Oluwole A, Hernández-Rocamora VM, Cao Y, Li X, Vollmer W, Robinson CV, Bolla JR. Real-Time Biosynthetic Reaction Monitoring Informs the Mechanism of Action of Antibiotics. J Am Chem Soc 2024; 146:7007-7017. [PMID: 38428018 PMCID: PMC10941186 DOI: 10.1021/jacs.4c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The rapid spread of drug-resistant pathogens and the declining discovery of new antibiotics have created a global health crisis and heightened interest in the search for novel antibiotics. Beyond their discovery, elucidating mechanisms of action has necessitated new approaches, especially for antibiotics that interact with lipidic substrates and membrane proteins. Here, we develop a methodology for real-time reaction monitoring of the activities of two bacterial membrane phosphatases, UppP and PgpB. We then show how we can inhibit their activities using existing and newly discovered antibiotics such as bacitracin and teixobactin. Additionally, we found that the UppP dimer is stabilized by phosphatidylethanolamine, which, unexpectedly, enhanced the speed of substrate processing. Overall, our results demonstrate the potential of native mass spectrometry for real-time biosynthetic reaction monitoring of membrane enzymes, as well as their in situ inhibition and cofactor binding, to inform the mode of action of emerging antibiotics.
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Affiliation(s)
- Abraham
O. Oluwole
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Víctor M. Hernández-Rocamora
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
| | - Yihui Cao
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Xuechen Li
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
- Institute
for Molecular Bioscience, University of
Queensland, Carmody Road, Brisbane, Queensland 4072, Australia
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Jani R. Bolla
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K.
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7
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. Sci Adv 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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8
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Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience 2024; 27:108785. [PMID: 38303728 PMCID: PMC10831248 DOI: 10.1016/j.isci.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Membrane proteins perform numerous critical functions in the cell, making many of them primary drug targets. However, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using the ABC transporter BtuCD, we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.
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Affiliation(s)
- John William Young
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emanuel Pfitzner
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raman van Wee
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Carla Kirschbaum
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philipp Kukura
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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9
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Gerle C, Misumi Y, Kawamoto A, Tanaka H, Kubota-Kawai H, Tokutsu R, Kim E, Chorev D, Abe K, Robinson CV, Mitsuoka K, Minagawa J, Kurisu G. Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin. Biochim Biophys Acta Bioenerg 2023; 1864:148986. [PMID: 37270022 DOI: 10.1016/j.bbabio.2023.148986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023]
Abstract
Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.
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Affiliation(s)
- Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Hyogo, Japan; Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| | - Yuko Misumi
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Akihiro Kawamoto
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hideaki Tanaka
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hisako Kubota-Kawai
- Faculty of Science, Department of Science, Yamagata University, Yamagata, Japan; National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Ryutaro Tokutsu
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Eunchul Kim
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Dror Chorev
- Chemistry Research Laboratory, South Parks Road, Oxford University, United Kingdom
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan; Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Carol V Robinson
- Chemistry Research Laboratory, South Parks Road, Oxford University, United Kingdom
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Ibaraki, Osaka, Japan
| | - Jun Minagawa
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan; Department of Basic Biology, School of Life Science, the Graduate University for Advanced Studies, Sokendai, Okazaki, Japan
| | - Genji Kurisu
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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10
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Chi G, Dietz L, Tang H, Snee M, Scacioc A, Wang D, Mckinley G, Mukhopadhyay SM, Pike AC, Chalk R, Burgess-Brown NA, Timmermans JP, van Putte W, Robinson CV, Dürr KL. Structural characterization of human urea transporters UT-A and UT-B and their inhibition. Sci Adv 2023; 9:eadg8229. [PMID: 37774028 PMCID: PMC10541013 DOI: 10.1126/sciadv.adg8229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
In this study, we present the structures of human urea transporters UT-A and UT-B to characterize them at molecular level and to detail the mechanism of UT-B inhibition by its selective inhibitor, UTBinh-14. High-resolution structures of both transporters establish the structural basis for the inhibitor's selectivity to UT-B, and the identification of multiple binding sites for the inhibitor will aid with the development of drug lead molecules targeting both transporters. Our study also discovers phospholipids associating with the urea transporters by combining structural observations, native MS, and lipidomics analysis. These insights improve our understanding of urea transporter function at a molecular level and provide a blueprint for a structure-guided design of therapeutics targeting these transporters.
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Affiliation(s)
- Gamma Chi
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Larissa Dietz
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Matthew Snee
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Andreea Scacioc
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Dong Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Gavin Mckinley
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Shubhashish M. M. Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Ashley C. W. Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Rod Chalk
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology (CBH) at Antwerp Centre for Advanced Microscopy (ACAM), Department of Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wouter van Putte
- Laboratory of Cell Biology and Histology (CBH) at Antwerp Centre for Advanced Microscopy (ACAM), Department of Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- PUXANO, Ottergemsesteenweg Zuid 713, 9000 Gent, Belgium
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina L. Dürr
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
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11
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Int Ed Engl 2023; 62:e202305694. [PMID: 37329506 PMCID: PMC7615181 DOI: 10.1002/anie.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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12
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Weinheim Bergstr Ger 2023; 135:e202305694. [PMID: 38516403 PMCID: PMC10953453 DOI: 10.1002/ange.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 03/23/2024]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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13
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Hu H, van Roon AMM, Ghanim GE, Ahsan B, Oluwole AO, Peak-Chew SY, Robinson CV, Nguyen THD. Structural basis of telomeric nucleosome recognition by shelterin factor TRF1. Sci Adv 2023; 9:eadi4148. [PMID: 37624885 PMCID: PMC10456876 DOI: 10.1126/sciadv.adi4148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription.
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Affiliation(s)
- Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | | | - Bilal Ahsan
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Abraham O. Oluwole
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | | | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
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14
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Durbin KR, Robey MT, Voong LN, Fellers RT, Lutomski CA, El-Baba TJ, Robinson CV, Kelleher NL. ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data. J Proteome Res 2023; 22:2660-2668. [PMID: 37436406 PMCID: PMC10407923 DOI: 10.1021/acs.jproteome.3c00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 07/13/2023]
Abstract
Native mass spectrometry has recently moved alongside traditional structural biology techniques in its ability to provide clear insights into the composition of protein complexes. However, to date, limited software tools are available for the comprehensive analysis of native mass spectrometry data on protein complexes, particularly for experiments aimed at elucidating the composition of an intact protein complex. Here, we introduce ProSight Native as a start-to-finish informatics platform for analyzing native protein and protein complex data. Combining mass determination via spectral deconvolution with a top-down database search and stoichiometry calculations, ProSight Native can determine the complete composition of protein complexes. To demonstrate its features, we used ProSight Native to successfully determine the composition of the homotetrameric membrane complex Aquaporin Z. We also revisited previously published spectra and were able to decipher the composition of a heterodimer complex bound with two noncovalently associated ligands. In addition to determining complex composition, we developed new tools in the software for validating native mass spectrometry fragment ions and mapping top-down fragmentation data onto three-dimensional protein structures. Taken together, ProSight Native will reduce the informatics burden on the growing field of native mass spectrometry, enabling the technology to further its reach.
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Affiliation(s)
| | | | - Lilien N. Voong
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
| | - Ryan T. Fellers
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
| | - Corinne A. Lutomski
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Tarick J. El-Baba
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Neil L. Kelleher
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Smithers L, Degtjarik O, Weichert D, Huang CY, Boland C, Bowen K, Oluwole A, Lutomski C, Robinson CV, Scanlan EM, Wang M, Olieric V, Shalev-Benami M, Caffrey M. Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N-acyltransferase. Sci Adv 2023; 9:eadf5799. [PMID: 37390210 PMCID: PMC10313180 DOI: 10.1126/sciadv.adf5799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein N-acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.
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Affiliation(s)
- Luke Smithers
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Oksana Degtjarik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Abraham Oluwole
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Corinne Lutomski
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
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17
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Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant. bioRxiv 2023:2023.05.05.539595. [PMID: 37205478 PMCID: PMC10187269 DOI: 10.1101/2023.05.05.539595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
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Affiliation(s)
- Nanami Senoo
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dinesh K. Chinthapalli
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Matthew G. Baile
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vinaya K. Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bodhisattwa Saha
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Oluwaseun B. Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A. Saba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Teona Munteanu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yllka Valdez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kevin Whited
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dror Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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18
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Hardy BJ, Martin Hermosilla A, Chinthapalli DK, Robinson CV, Anderson JLR, Curnow P. Cellular production of a de novo membrane cytochrome. Proc Natl Acad Sci U S A 2023; 120:e2300137120. [PMID: 37036998 PMCID: PMC10120048 DOI: 10.1073/pnas.2300137120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Heme-containing integral membrane proteins are at the heart of many bioenergetic complexes and electron transport chains. The importance of these electron relay hubs across biology has inspired the design of de novo proteins that recreate their core features within robust, versatile, and tractable protein folds. To this end, we report here the computational design and in-cell production of a minimal diheme membrane cytochrome which successfully integrates into the cellular membrane of live bacteria. This synthetic construct emulates a four-helix bundle found in modern respiratory complexes but has no sequence homology to any polypeptide sequence found in nature. The two b-type hemes, which appear to be recruited from the endogenous heme pool, have distinct split redox potentials with values close to those of natural membrane-spanning cytochromes. The purified protein can engage in rapid biomimetic electron transport with small molecules, with other redox proteins, and with biologically relevant diffusive electron carriers. We thus report an artificial membrane metalloprotein with the potential to serve as a functional electron transfer module in both synthetic protocells and living systems.
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Affiliation(s)
- Benjamin J Hardy
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
| | | | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
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19
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Ottonello A, Wyllie JA, Yahiaoui O, Sun S, Koelln RA, Homer JA, Johnson RM, Murray E, Williams P, Bolla JR, Robinson CV, Fallon T, Soares da Costa TP, Moses JE. Shapeshifting bullvalene-linked vancomycin dimers as effective antibiotics against multidrug-resistant gram-positive bacteria. Proc Natl Acad Sci U S A 2023; 120:e2208737120. [PMID: 37011186 PMCID: PMC10104512 DOI: 10.1073/pnas.2208737120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 02/24/2023] [Indexed: 04/05/2023] Open
Abstract
The alarming rise in superbugs that are resistant to drugs of last resort, including vancomycin-resistant enterococci and staphylococci, has become a significant global health hazard. Here, we report the click chemistry synthesis of an unprecedented class of shapeshifting vancomycin dimers (SVDs) that display potent activity against bacteria that are resistant to the parent drug, including the ESKAPE pathogens, vancomycin-resistant Enterococcus (VRE), methicillin-resistant Staphylococcus aureus (MRSA), as well as vancomycin-resistant S. aureus (VRSA). The shapeshifting modality of the dimers is powered by a triazole-linked bullvalene core, exploiting the dynamic covalent rearrangements of the fluxional carbon cage and creating ligands with the capacity to inhibit bacterial cell wall biosynthesis. The new shapeshifting antibiotics are not disadvantaged by the common mechanism of vancomycin resistance resulting from the alteration of the C-terminal dipeptide with the corresponding d-Ala-d-Lac depsipeptide. Further, evidence suggests that the shapeshifting ligands destabilize the complex formed between the flippase MurJ and lipid II, implying the potential for a new mode of action for polyvalent glycopeptides. The SVDs show little propensity for acquired resistance by enterococci, suggesting that this new class of shapeshifting antibiotic will display durable antimicrobial activity not prone to rapidly acquired clinical resistance.
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Affiliation(s)
- Alessandra Ottonello
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Jessica A. Wyllie
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Oussama Yahiaoui
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Shoujun Sun
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Rebecca A. Koelln
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Robert M. Johnson
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Ewan Murray
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, NottinghamNG7 2RD, U.K.
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, NottinghamNG7 2RD, U.K.
| | - Jani R. Bolla
- Department of Biology, University of Oxford, OxfordOX1 3RB, U.K.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, OxfordOX1 3QU, U.K.
| | - Carol V. Robinson
- The Kavli Institute for Nanoscience Discovery, University of Oxford, OxfordOX1 3QU, U.K.
- Physical and Theoretical Chemistry Laboratory, University of Oxford, OxfordOX1 3QZ, U.K.
| | - Thomas Fallon
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | | | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
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20
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Matsuoka R, Fudim R, Jung S, Zhang C, Bazzone A, Chatzikyriakidou Y, Robinson CV, Nomura N, Iwata S, Landreh M, Orellana L, Beckstein O, Drew D. Author Correction: Structure, mechanism and lipid-mediated remodeling of the mammalian Na +/H + exchanger NHA2. Nat Struct Mol Biol 2023; 30:565. [PMID: 37029209 PMCID: PMC10113147 DOI: 10.1038/s41594-023-00970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Affiliation(s)
- Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roman Fudim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Sukkyeong Jung
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Chenou Zhang
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Orellana
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA.
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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21
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El-Baba TJ, Lutomski CA, Burnap SA, Bolla JR, Baker LA, Baldwin AJ, Struwe WB, Robinson CV. Uncovering the Role of N-Glycan Occupancy on the Cooperative Assembly of Spike and Angiotensin Converting Enzyme 2 Complexes: Insights from Glycoengineering and Native Mass Spectrometry. J Am Chem Soc 2023; 145:8021-8032. [PMID: 37000485 PMCID: PMC10103161 DOI: 10.1021/jacs.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address these unanswered questions by combining a glycoengineering strategy with high-resolution native mass spectrometry (MS) to investigate the impact of N-glycan occupancy on the assembly of multiple Spike-ACE2 complexes. We confirmed that intact Spike trimers have all 66 N-linked sites occupied. For monomeric ACE2, all seven N-linked glycan sites are occupied to various degrees; six sites have >90% occupancy, while the seventh site (Asn690) is only partially occupied (∼30%). By resolving the glycoforms on ACE2, we deciphered the influence of each N-glycan on ACE2 dimerization. Unexpectedly, we found that Asn432 plays a role in mediating dimerization, a result confirmed by site-directed mutagenesis. We also found that glycosylated dimeric ACE2 and Spike trimers form complexes with multiple stoichiometries (Spike-ACE2 and Spike2-ACE2) with dissociation constants (Kds) of ∼500 and <100 nM, respectively. Comparing these values indicates that positive cooperativity may drive ACE2 dimers to complex with multiple Spike trimers. Overall, our results show that occupancy has a key regulatory role in mediating interactions between ACE2 dimers and Spike trimers. More generally, since soluble ACE2 (sACE2) retains an intact SARS-CoV-2 interaction site, the importance of glycosylation in ACE2 dimerization and the propensity for Spike and ACE2 to assemble into higher oligomers are molecular details important for developing strategies for neutralizing the virus.
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Affiliation(s)
- Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Corinne A Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Sean A Burnap
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Lindsay A Baker
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
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22
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Noske GD, Song Y, Fernandes RS, Chalk R, Elmassoudi H, Koekemoer L, Owen CD, El-Baba TJ, Robinson CV, Oliva G, Godoy AS. An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition. Nat Commun 2023; 14:1545. [PMID: 36941262 PMCID: PMC10027274 DOI: 10.1038/s41467-023-37035-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The main protease from SARS-CoV-2 (Mpro) is responsible for cleavage of the viral polyprotein. Mpro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S Mpro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of Mpro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the Mpro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.
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Affiliation(s)
- Gabriela Dias Noske
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Yun Song
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rafaela Sachetto Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Rod Chalk
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Haitem Elmassoudi
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - C David Owen
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Andre Schutzer Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil.
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23
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Yen HY, Jazayeri A, Robinson CV. G protein-coupled receptor pharmacology - insights from mass spectrometry. Pharmacol Rev 2023; 75:397-415. [PMID: 36918259 DOI: 10.1124/pharmrev.120.000237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 03/16/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are key drug targets due to their involvement in many physiological processes. The complexity of receptor pharmacology however is influenced by multiple interactions with various types of ligands and protein transducers representing significant challenges for drug discovery. The ability of mass spectrometry to observe both the binding of ligand molecules such as lipids, ions or drugs and their impact on interaction with transducers provides an exciting opportunity to probe many aspects that are difficult to track directly in cell-based systems. From the early days, when hydrogen deuterium exchange (HDX) experiments were used to probe the different conformations of GPCRs, through to the most recent insights in which the intact receptor-G protein/arrestin complexes associated with small molecules can be preserved by mass spectrometry, this review highlights the potential of mass spectrometry techniques for in-depth investigations of GPCR biology. Herein, we will describe the utility of mass spectrometry (MS) including HDX-MS, cross-linking and native-MS, in investigating GPCR pharmacology. Specifically, we will include ligand/drug interactions and Gi/s protein-coupling and illustrate and how these techniques can lead to the discovery of endogenous allosteric ligands and thereby offer a new perspective for drug discovery of GPCRs. Significance Statement GPCRs represent the largest family of druggable protein targets that interact with a diverse array of ligands, from metal ions and small molecules through to peptides and proteins. These extracellular stimuli are translated allosterically into intracellular signals mediated by transducer proteins. Typically, activation of GPCRs relies on binding of endogenous or exogenous agonists to stabilize the receptors in active conformations. Recent developments in MS enable capture of the extent of GPCR activation and discovery of allosteric modulators of downstream signaling.
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24
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Urner LH, Junge F, Fiorentino F, El-Baba TJ, Shutin D, Nölte G, Haag R, Robinson CV. Rationalizing the Optimization of Detergents for Membrane Protein Purification. Chemistry 2023; 29:e202300159. [PMID: 36897295 DOI: 10.1002/chem.202300159] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/11/2023]
Abstract
Membrane protein purification by means of detergents is key to isolating membrane-bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed preparations, and thereby raising costs. Here we evaluate the utility of the hydrophilic-lipophilic balance (HLB) concept, which was introduced by Griffin in 1949, for guiding the optimization of the hydrophobic tail in first-generation, dendritic oligoglycerol detergents ([G1] OGDs). Our findings deliver qualitative HLB guidelines for rationalizing the optimization of detergents. Moreover, [G1] OGDs exhibit strongly delipidating properties, regardless of the structure of the hydrophobic tail, which delivers a methodological enabling step for investigating binding strengths of endogenous lipids and their role for membrane protein oligomerization. Our findings will facilitate the analysis of challenging drug targets in the future.
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Affiliation(s)
- Leonhard Hagen Urner
- TU Dortmund University: Technische Universitat Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Straße 6, 44227, Dortmund, GERMANY
| | - Florian Junge
- Freie Universität Berlin: Freie Universitat Berlin, Institute of Chemistry and Biochemistry, GERMANY
| | - Francesco Fiorentino
- Sapienza Università di Roma: Universita degli Studi di Roma La Sapienza, Department of Drug Chemistry and Technologies, ITALY
| | - Tarick J El-Baba
- University of Oxford, Kavli Institute for Nanoscience Discovery, UNITED KINGDOM
| | - Denis Shutin
- University of Oxford, Kavli Institute for Nanoscience Discovery, UNITED KINGDOM
| | - Gideon Nölte
- Freie Universität Berlin: Freie Universitat Berlin, Institute of Chemistry and Biochemistry, GERMANY
| | - Rainer Haag
- Freie Universitat Berlin, Institute of Chemistry and Biochemistry, GERMANY
| | - Carol V Robinson
- University of Oxford, Kavli Institute for Nanoscience Discovery, UNITED KINGDOM
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25
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Wu D, Guo M, Robinson CV. Connecting single-nucleotide polymorphisms, glycosylation status, and interactions of plasma serine protease inhibitors. Chem 2023; 9:665-681. [PMID: 38455847 PMCID: PMC10914678 DOI: 10.1016/j.chempr.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/06/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Understanding the combined impacts of genetic variances and post-translational modifications requires new approaches. Here, we delineate proteoforms of plasma serine protease inhibitors and relate specific proteoforms to their interactions in complexes through the use of native mass spectrometry (MS). First, we dissect the proteoform repertoire of an acute-phase plasma protein, serine protease inhibitor A1 (SERPINA1), resolving four SERPINA1 variants (M1V, M1A, M2, and M3) with common single-nucleotide polymorphisms (SNPs). Investigating the glycosylation status of these variants and their ability to form complexes with a serine protease, elastase, we find that fucosylation stabilizes the interaction of the SERPINA1 M1V variant through its core fucosylation on Asn271. In contrast, antennary fucosylation on Asn271 destabilizes SERPINA1-elastase interactions. We unveil the same opposing effects of core and antennary fucosylation on SERPINA3 interactions with chymotrypsin. Together, our native MS results highlight the modulating effects of fucosylation with different linkages on glycoprotein interactions.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Manman Guo
- Botnar Research Centre, NIHR Biomedical Research Unit Oxford, Nuffield Department of Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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26
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Kjølbye LR, Sørensen L, Yan J, Berglund NA, Ferkinghoff-Borg J, Robinson CV, Schiøtt B. Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4,5)P 2 Lipids. J Chem Inf Model 2022; 62:6788-6802. [PMID: 36036575 DOI: 10.1021/acs.jcim.2c00635] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) lipids have been shown to stabilize an active conformation of class A G-protein coupled receptors (GPCRs) through a conserved binding site, not present in class B GPCRs. For class B GPCRs, previous molecular dynamics (MD) simulation studies have shown PI(4,5)P2 interacting with the Glucagon receptor (GCGR), which constitutes an important target for diabetes and obesity therapeutics. In this work, we applied MD simulations supported by native mass spectrometry (nMS) to study lipid interactions with GCGR. We demonstrate how tail composition plays a role in modulating the binding of PI(4,5)P2 lipids to GCGR. Specifically, we find the PI(4,5)P2 lipids to have a higher affinity toward the inactive conformation of GCGR. Interestingly, we find that in contrast to class A GPCRs, PI(4,5)P2 appear to stabilize the inactive conformation of GCGR through a binding site conserved across class B GPCRs but absent in class A GPCRs. This suggests differences in the regulatory function of PI(4,5)P2 between class A and class B GPCRs.
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Affiliation(s)
- Lisbeth R Kjølbye
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Lars Sørensen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Jun Yan
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Nils A Berglund
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C, Denmark
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27
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Wu D, Robinson CV. Native Top-Down Mass Spectrometry Reveals a Role for Interfacial Glycans on Therapeutic Cytokine and Hormone Assemblies. Angew Chem Weinheim Bergstr Ger 2022; 134:e202213170. [PMID: 38504999 PMCID: PMC10947189 DOI: 10.1002/ange.202213170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Oligomerization and glycosylation modulate therapeutic glycoprotein stability and efficacy. The interplay between these two critical attributes on therapeutic glycoproteins, is however often hard to define. Here, we present a native top-down mass spectrometry (MS) approach to assess the glycosylation status of therapeutic cytokine and hormone assemblies and relate interfacial glycan occupancy to complex stability. We found that interfacial O-glycan stabilizes tumor necrosis factor-α trimer. On the contrary, interferon-β1a dimerization is independent of glycosylation. Moreover, we discovered a unique distribution of N-glycans on the follicle-stimulating hormone α subunit. We found that the interfacial N-glycan, at Asn52 of the α subunit, interacts extensively with the β subunit to regulate the dimer assembly. Overall, we have exemplified a method to link glycosylation with assembly status, for cytokines and hormones, critical for informing optimal stability and bioavailability.
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Affiliation(s)
- Di Wu
- Department of ChemistryUniversity of OxfordOxfordOX1 3QZUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordOX1 3QUUK
| | - Carol V. Robinson
- Department of ChemistryUniversity of OxfordOxfordOX1 3QZUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordOX1 3QUUK
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28
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Yen HY, Liko I, Song W, Kapoor P, Almeida F, Toporowska J, Gherbi K, Hopper JTS, Charlton SJ, Politis A, Sansom MSP, Jazayeri A, Robinson CV. Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor. Nat Chem 2022; 14:1375-1382. [PMID: 36357787 PMCID: PMC9758051 DOI: 10.1038/s41557-022-01041-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor-Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor-Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
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Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- OMass Therapeutics, Oxford, UK.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
- Rahko, London, UK
| | | | | | | | | | | | - Steven J Charlton
- OMass Therapeutics, Oxford, UK
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, London, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, Oxford, UK.
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29
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Yao X, Wang Y, Wang Z, Fan X, Wu D, Huang J, Mueller A, Gao S, Hu M, Robinson CV, Yu Y, Gao S, Yan N. Structures of the R-type human Ca v2.3 channel reveal conformational crosstalk of the intracellular segments. Nat Commun 2022; 13:7358. [PMID: 36446785 PMCID: PMC9708679 DOI: 10.1038/s41467-022-35026-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
The R-type voltage-gated Ca2+ (Cav) channels Cav2.3, widely expressed in neuronal and neuroendocrine cells, represent potential drug targets for pain, seizures, epilepsy, and Parkinson's disease. Despite their physiological importance, there have lacked selective small-molecule inhibitors targeting these channels. High-resolution structures may aid rational drug design. Here, we report the cryo-EM structure of human Cav2.3 in complex with α2δ-1 and β3 subunits at an overall resolution of 3.1 Å. The structure is nearly identical to that of Cav2.2, with VSDII in the down state and the other three VSDs up. A phosphatidylinositol 4,5-bisphosphate (PIP2) molecule binds to the interface of VSDII and the tightly closed pore domain. We also determined the cryo-EM structure of a Cav2.3 mutant in which a Cav2-unique cytosolic helix in repeat II (designated the CH2II helix) is deleted. This mutant, named ΔCH2, still reserves a down VSDII, but PIP2 is invisible and the juxtamembrane region on the cytosolic side is barely discernible. Our structural and electrophysiological characterizations of the wild type and ΔCH2 Cav2.3 show that the CH2II helix stabilizes the inactivated conformation of the channel by tightening the cytosolic juxtamembrane segments, while CH2II helix is not necessary for locking the down state of VSDII.
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Affiliation(s)
- Xia Yao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Yan Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Zhifei Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Xiao Fan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Di Wu
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Jian Huang
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Alexander Mueller
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Sarah Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Miaohui Hu
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Carol V. Robinson
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Yong Yu
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Shuai Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA ,grid.49470.3e0000 0001 2331 6153Present Address: Department of Radiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Nieng Yan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
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30
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Wu D, Robinson CV. Native Top‐Down Mass Spectrometry Reveals a Role for Interfacial Glycans on Therapeutic Cytokine and Hormone Assemblies. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202215767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Di Wu
- Department of Chemistry University of Oxford Oxford OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery University of Oxford Oxford OX1 3QU UK
| | - Carol V. Robinson
- Department of Chemistry University of Oxford Oxford OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery University of Oxford Oxford OX1 3QU UK
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31
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Wu D, Robinson CV. Native Top‐Down Mass Spectrometry Reveals a Role for Interfacial Glycans on Therapeutic Cytokine and Hormone Assemblies. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202215767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Di Wu
- Department of Chemistry University of Oxford Oxford OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery University of Oxford Oxford OX1 3QU UK
| | - Carol V. Robinson
- Department of Chemistry University of Oxford Oxford OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery University of Oxford Oxford OX1 3QU UK
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32
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Webby MN, Oluwole AO, Pedebos C, Inns PG, Olerinyova A, Prakaash D, Housden NG, Benn G, Sun D, Hoogenboom BW, Kukura P, Mohammed S, Robinson CV, Khalid S, Kleanthous C. Lipids mediate supramolecular outer membrane protein assembly in bacteria. Sci Adv 2022; 8:eadc9566. [PMID: 36322653 PMCID: PMC9629720 DOI: 10.1126/sciadv.adc9566] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
β Barrel outer membrane proteins (OMPs) cluster into supramolecular assemblies that give function to the outer membrane (OM) of Gram-negative bacteria. How such assemblies form is unknown. Here, through photoactivatable cross-linking into the Escherichia coli OM, coupled with simulations, and biochemical and biophysical analysis, we uncover the basis for OMP clustering in vivo. OMPs are typically surrounded by an annular shell of asymmetric lipids that mediate higher-order complexes with neighboring OMPs. OMP assemblies center on the abundant porins OmpF and OmpC, against which low-abundance monomeric β barrels, such as TonB-dependent transporters, are packed. Our study reveals OMP-lipid-OMP complexes to be the basic unit of supramolecular OMP assembly that, by extending across the entire cell surface, couples the requisite multifunctionality of the OM to its stability and impermeability.
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Affiliation(s)
- Melissa N. Webby
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Abraham O. Oluwole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Conrado Pedebos
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick G. Inns
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Nicholas G. Housden
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Georgina Benn
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Dawei Sun
- Structural Biology, Genentech Inc., South San Francisco, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Physics and Astronomy, University College London, WC1E 6BT London, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Mechanistic Proteomics, Rosalind Franklin Institute, Harwell Campus, Didcot OX11 OFA, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Syma Khalid
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
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33
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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34
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Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL. CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7. Life Sci Alliance 2022; 5:5/11/e202201527. [PMID: 35794005 PMCID: PMC9263379 DOI: 10.26508/lsa.202201527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 12/18/2022] Open
Abstract
The structure of mammalian V-ATPase with mEAK-7 shows how a TLDc domain-containing protein can bind the proton pump to form an activity-sensitive interaction. V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7’s TLDc domain interacts with V-ATPase’s stator, whereas its C-terminal α helix binds V-ATPase’s rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme’s activity.
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Affiliation(s)
- Yong Zi Tan
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Yazan M Abbas
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Jing Ze Wu
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Kristine A Keon
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Sergio Grinstein
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada .,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
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35
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Wu D, Robinson CV. Native Top‐Down Mass Spectrometry Reveals a Role for Interfacial Glycans on Therapeutic Cytokine and Hormone Assemblies. Angew Chem Int Ed Engl 2022; 61:e202213170. [PMID: 36260431 PMCID: PMC10100379 DOI: 10.1002/anie.202213170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 11/06/2022]
Abstract
Oligomerization and glycosylation modulate therapeutic glycoprotein stability and efficacy. The interplay between these two critical attributes on therapeutic glycoproteins, is however often hard to define. Here, we present a native top-down mass spectrometry (MS) approach to assess the glycosylation status of therapeutic cytokine and hormone assemblies and relate interfacial glycan occupancy to complex stability. We found that interfacial O-glycan stabilizes tumor necrosis factor-α trimer. On the contrary, interferon-β1a dimerization is independent of glycosylation. Moreover, we discovered a unique distribution of N-glycans on the follicle-stimulating hormone α subunit. We found that the interfacial N-glycan, at Asn52 of the α subunit, interacts extensively with the β subunit to regulate the dimer assembly. Overall, we have exemplified a method to link glycosylation with assembly status, for cytokines and hormones, critical for informing optimal stability and bioavailability.
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Affiliation(s)
- Di Wu
- Department of ChemistryUniversity of OxfordOxfordOX1 3QZUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordOX1 3QUUK
| | - Carol V. Robinson
- Department of ChemistryUniversity of OxfordOxfordOX1 3QZUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordOX1 3QUUK
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36
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Akkermans O, Delloye-Bourgeois C, Peregrina C, Carrasquero-Ordaz M, Kokolaki M, Berbeira-Santana M, Chavent M, Reynaud F, Raj R, Agirre J, Aksu M, White ES, Lowe E, Ben Amar D, Zaballa S, Huo J, Pakos I, McCubbin PT, Comoletti D, Owens RJ, Robinson CV, Castellani V, del Toro D, Seiradake E. GPC3-Unc5 receptor complex structure and role in cell migration. Cell 2022; 185:3931-3949.e26. [PMID: 36240740 PMCID: PMC9596381 DOI: 10.1016/j.cell.2022.09.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/22/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Neural migration is a critical step during brain development that requires the interactions of cell-surface guidance receptors. Cancer cells often hijack these mechanisms to disseminate. Here, we reveal crystal structures of Uncoordinated-5 receptor D (Unc5D) in complex with morphogen receptor glypican-3 (GPC3), forming an octameric glycoprotein complex. In the complex, four Unc5D molecules pack into an antiparallel bundle, flanked by four GPC3 molecules. Central glycan-glycan interactions are formed by N-linked glycans emanating from GPC3 (N241 in human) and C-mannosylated tryptophans of the Unc5D thrombospondin-like domains. MD simulations, mass spectrometry and structure-based mutants validate the crystallographic data. Anti-GPC3 nanobodies enhance or weaken Unc5-GPC3 binding and, together with mutant proteins, show that Unc5/GPC3 guide migrating pyramidal neurons in the mouse cortex, and cancer cells in an embryonic xenograft neuroblastoma model. The results demonstrate a conserved structural mechanism of cell guidance, where finely balanced Unc5-GPC3 interactions regulate cell migration.
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Affiliation(s)
- Onno Akkermans
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Céline Delloye-Bourgeois
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Claudia Peregrina
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Maria Carrasquero-Ordaz
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Maria Kokolaki
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Miguel Berbeira-Santana
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, Toulouse, France
| | - Florie Reynaud
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Ritu Raj
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Metin Aksu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eleanor S. White
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Edward Lowe
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Dounia Ben Amar
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Sofia Zaballa
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK,Division of Structural Biology, University of Oxford, Oxford, UK
| | - Irene Pakos
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Patrick T.N. McCubbin
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK,Division of Structural Biology, University of Oxford, Oxford, UK
| | - Carol V. Robinson
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK,Department of Chemistry, University of Oxford, Oxford, UK
| | - Valérie Castellani
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France,Corresponding author
| | - Daniel del Toro
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain,Corresponding author
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, Oxford, UK,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK,Corresponding author
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37
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Urner LH, Liko I, Pagel K, Haag R, Robinson CV. Non-ionic hybrid detergents for protein delipidation. Biochim Biophys Acta Biomembr 2022; 1864:183958. [PMID: 35551920 DOI: 10.1016/j.bbamem.2022.183958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/05/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023]
Abstract
Non-ionic detergents are important tools for the investigation of interactions between membrane proteins and lipid membranes. Recent studies led to the question as to whether the ability to capture protein-lipid interactions depends on the properties of detergents or their concentration in purification buffers. To address this question, we present the synthesis of an asymmetric, hybrid detergent that combines the head groups of detergents with opposing delipidating properties. We discuss detergent properties and protein purification outcomes to reveal whether the properties of detergent micelles or the detergent concentration in purification buffers drive membrane protein delipidation. We anticipate that our findings will enable the development of rationally design detergents for future applications in membrane protein research.
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Affiliation(s)
- Leonhard H Urner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany; University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX13QZ, United Kingdom; TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany.
| | - Idlir Liko
- University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX13QZ, United Kingdom
| | - Kevin Pagel
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany
| | - Rainer Haag
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany
| | - Carol V Robinson
- University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX13QZ, United Kingdom
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38
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS Nexus 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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39
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Lutomski CA, El-Baba TJ, Robinson CV, Riek R, Scheres SHW, Yan N, AlQuraishi M, Gan L. The next decade of protein structure. Cell 2022; 185:2617-2620. [PMID: 35868264 DOI: 10.1016/j.cell.2022.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
Abstract
With recent dramatic advances in various techniques used for protein structure research, we asked researchers to comment on the next exciting questions for the field and about how these techniques will advance our knowledge not only about proteins but also about human health and diseases.
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40
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Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
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Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
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41
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Khera R, Mehdipour AR, Bolla JR, Kahnt J, Welsch S, Ermler U, Muenke C, Robinson CV, Hummer G, Xie H, Michel H. Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. EMBO J 2022; 41:e109990. [PMID: 35698912 PMCID: PMC9475539 DOI: 10.15252/embj.2021109990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022] Open
Abstract
Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.
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Affiliation(s)
- Radhika Khera
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Centre for molecular modelling, Ghent University, Zwijnaarde, Belgium
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Joerg Kahnt
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ulrich Ermler
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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42
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Wu D, Robinson CV. Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry. Curr Opin Struct Biol 2022; 74:102351. [DOI: 10.1016/j.sbi.2022.102351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
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43
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Lang PA, Raj R, Tumber A, Lohans CT, Rabe P, Robinson CV, Brem J, Schofield CJ. Studies on enmetazobactam clarify mechanisms of widely used β-lactamase inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2117310119. [PMID: 35486701 PMCID: PMC9170034 DOI: 10.1073/pnas.2117310119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
β-Lactams are the most important class of antibacterials, but their use is increasingly compromised by resistance, most importantly via serine β-lactamase (SBL)-catalyzed hydrolysis. The scope of β-lactam antibacterial activity can be substantially extended by coadministration with a penicillin-derived SBL inhibitor (SBLi), i.e., the penam sulfones tazobactam and sulbactam, which are mechanism-based inhibitors working by acylation of the nucleophilic serine. The new SBLi enmetazobactam, an N-methylated tazobactam derivative, has recently completed clinical trials. Biophysical studies on the mechanism of SBL inhibition by enmetazobactam reveal that it inhibits representatives of all SBL classes without undergoing substantial scaffold fragmentation, a finding that contrasts with previous reports on SBL inhibition by tazobactam and sulbactam. We therefore reinvestigated the mechanisms of tazobactam and sulbactam using mass spectrometry under denaturing and nondenaturing conditions, X-ray crystallography, and NMR spectroscopy. The results imply that the reported extensive fragmentation of penam sulfone–derived acyl–enzyme complexes does not substantially contribute to SBL inhibition. In addition to observation of previously identified inhibitor-induced SBL modifications, the results reveal that prolonged reaction of penam sulfones with SBLs can induce dehydration of the nucleophilic serine to give a dehydroalanine residue that undergoes reaction to give a previously unobserved lysinoalanine cross-link. The results clarify the mechanisms of action of widely clinically used SBLi, reveal limitations on the interpretation of mass spectrometry studies concerning mechanisms of SBLi, and will inform the development of new SBLi working by reaction to form hydrolytically stable acyl–enzyme complexes.
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Affiliation(s)
- Pauline A. Lang
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Ritu Raj
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher T. Lohans
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
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44
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Oluwole AO, Corey RA, Brown CM, Hernández-Rocamora VM, Stansfeld PJ, Vollmer W, Bolla JR, Robinson CV. Peptidoglycan biosynthesis is driven by lipid transfer along enzyme-substrate affinity gradients. Nat Commun 2022; 13:2278. [PMID: 35477938 PMCID: PMC9046198 DOI: 10.1038/s41467-022-29836-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/31/2022] [Indexed: 01/02/2023] Open
Abstract
Maintenance of bacterial cell shape and resistance to osmotic stress by the peptidoglycan (PG) renders PG biosynthetic enzymes and precursors attractive targets for combating bacterial infections. Here, by applying native mass spectrometry, we elucidate the effects of lipid substrates on the PG membrane enzymes MraY, MurG, and MurJ. We show that dimerization of MraY is coupled with binding of the carrier lipid substrate undecaprenyl phosphate (C55-P). Further, we demonstrate the use of native MS for biosynthetic reaction monitoring and find that the passage of substrates and products is controlled by the relative binding affinities of the different membrane enzymes. Overall, we provide a molecular view of how PG membrane enzymes convey lipid precursors through favourable binding events and highlight possible opportunities for intervention. Bacterial cell wall enzymes and their precursors are critical targets for antibiotic development. Here, the authors investigate several biosynthetic enzymes with their substrates and show that the passage of substrates and products in the pathway is controlled by their relative binding affinities.
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Affiliation(s)
- Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Chelsea M Brown
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Victor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jani R Bolla
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK. .,Department of Plant Sciences/Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK. .,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK.
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45
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Affiliation(s)
- Tara Pukala
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom.,Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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46
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Yen HY, Abramsson ML, Agasid MT, Lama D, Gault J, Liko I, Kaldmäe M, Saluri M, Qureshi AA, Suades A, Drew D, Degiacomi MT, Marklund EG, Allison TM, Robinson CV, Landreh M. Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Adv 2022; 12:9671-9680. [PMID: 35424940 PMCID: PMC8972943 DOI: 10.1039/d2ra01282k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we show that the final charge of membrane proteins can be predicted by their molecular weight when released from the non-charge reducing saccharide detergents. Our data indicate that PEG detergents lower the charge depending on the number of detergent molecules in the surrounding micelle, whereas fos-choline detergents may additionally participate in ion–ion reactions after desolvation. The supercharging reagent sulfolane, on the other hand, has no discernible effect on the charge of detergent-free membrane proteins. Taking our observations into the context of protein-detergent interactions in the gas phase, we propose a charge equilibration model for the generation of native-like membrane protein ions. During ionization of the protein-detergent complex, the ESI charges are distributed between detergent and protein according to proton affinity of the detergent, number of detergent molecules, and surface area of the protein. Charge equilibration influenced by detergents determines the final charge state of membrane proteins. This process likely contributes to maintaining a native-like fold after detergent release and can be harnessed to stabilize particularly labile membrane protein complexes in the gas phase. The electrospray ionization mechanism contributes to preserving the structures and interactions of membrane protein complexes in native mass spectrometry.![]()
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Affiliation(s)
- Hsin-Yung Yen
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Institute of Biological Chemistry, Academia Sinica 128, Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Mia L Abramsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mark T Agasid
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Joseph Gault
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Abdul Aziz Qureshi
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | | | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University Box 576 75123 Uppsala Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury Christchurch 8140 New Zealand
| | - Carol V Robinson
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
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47
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Matsuoka R, Fudim R, Jung S, Zhang C, Bazzone A, Chatzikyriakidou Y, Robinson CV, Nomura N, Iwata S, Landreh M, Orellana L, Beckstein O, Drew D. Structure, mechanism and lipid-mediated remodeling of the mammalian Na +/H + exchanger NHA2. Nat Struct Mol Biol 2022; 29:108-120. [PMID: 35173351 PMCID: PMC8850199 DOI: 10.1038/s41594-022-00738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The Na+/H+ exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na+/Li+ exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na+/H+ exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.
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Affiliation(s)
- Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roman Fudim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Sukkyeong Jung
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Chenou Zhang
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Orellana
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA.
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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48
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Schmidpeter P, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gate of pacemaker channels. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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49
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Jin R, He S, Black KA, Clarke OB, Wu D, Bolla JR, Johnson P, Periasamy A, Wardak A, Czabotar P, Colman PM, Robinson CV, Laver D, Smith BJ, Gulbis JM. Ion currents through Kir potassium channels are gated by anionic lipids. Nat Commun 2022; 13:490. [PMID: 35079013 PMCID: PMC8789855 DOI: 10.1038/s41467-022-28148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
AbstractIon currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook gate of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this gate is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.
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50
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Patil DN, Singh S, Laboute T, Strutzenberg TS, Qiu X, Wu D, Novick SJ, Robinson CV, Griffin PR, Hunt JF, Izard T, Singh AK, Martemyanov KA. Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex. Science 2022; 375:86-91. [PMID: 34793198 PMCID: PMC8926151 DOI: 10.1126/science.abl4732] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GPR158 is an orphan G protein–coupled receptor (GPCR) highly expressed in the brain, where it controls synapse formation and function. GPR158 has also been implicated in depression, carcinogenesis, and cognition. However, the structural organization and signaling mechanisms of GPR158 are largely unknown. We used single-particle cryo–electron microscopy (cryo-EM) to determine the structures of human GPR158 alone and bound to an RGS signaling complex. The structures reveal a homodimeric organization stabilized by a pair of phospholipids and the presence of an extracellular Cache domain, an unusual ligand-binding domain in GPCRs. We further demonstrate the structural basis of GPR158 coupling to RGS7-Gβ5. Together, these results provide insights into the unusual biology of orphan receptors and the formation of GPCR-RGS complexes.
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Affiliation(s)
- Dipak N. Patil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Shikha Singh
- Department of Biological Sciences, Columbia University New York, NY 10027
| | - Thibaut Laboute
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Xingyu Qiu
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Di Wu
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Scott J. Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - John F. Hunt
- Department of Biological Sciences, Columbia University New York, NY 10027
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Appu K. Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India,Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India,Co-corresponding authors: Dr. Kirill A. Martemyanov, ; Dr. Appu K. Singh,
| | - Kirill A. Martemyanov
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA,Co-corresponding authors: Dr. Kirill A. Martemyanov, ; Dr. Appu K. Singh,
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