1
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Attanayake K, Mahmud S, Banerjee C, Sharif D, Rahman M, Majuta S, DeBastiani A, Sultana MN, Foroushani SH, Li C, Li P, Valentine SJ. Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 499:117231. [PMID: 38854816 PMCID: PMC11156224 DOI: 10.1016/j.ijms.2024.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.
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Affiliation(s)
- Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Chandrima Banerjee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sandra Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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2
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Zuo J, Zheng W, Shi N, Song R, Han F, Yang C, Li J, Peng C, Li B, Chen Y. Study on the Thermal Stability of the Sweet-Tasting Protein Brazzein Based on Its Structure-Sweetness Relationship. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7374-7382. [PMID: 38526016 DOI: 10.1021/acs.jafc.3c09616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Brazzein (Brz) is a sweet-tasting protein composed of 54 amino acids and is considered as a potential sugar substitute. The current methods for obtaining brazzein are complicated, and limited information is available regarding its thermal stability. In this study, we successfully expressed recombinant brazzein, achieving a sweetness threshold of 15.2 μg/mL. Subsequently, we conducted heat treatments at temperatures of 80, 90, 95, and 100 °C for a duration of 2 h to investigate the structural changes in the protein. Furthermore, we employed hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) to analyze the effect of heating on the protein structure-sweetness relationships. Our results indicated that the thermal inactivation process primarily affects residues 6-14 and 36-45 of brazzein, especially key residues Tyr8, Tyr11, Ser14, Glu36, and Arg43, which are closely associated with its sweetness. These findings have significant implications for improving the thermal stability of brazzein.
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Affiliation(s)
- Jingnan Zuo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Shi
- Xianning Vocational Technical College, Xianning 437100, China
| | - Rong Song
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Yang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijie Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China
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3
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Lambert T, Gramlich M, Stutzke L, Smith L, Deng D, Kaiser PD, Rothbauer U, Benesch JLP, Wagner C, Koenig M, Pompach P, Novak P, Zeck A, Rand KD. Development of a PNGase Rc Column for Online Deglycosylation of Complex Glycoproteins during HDX-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2556-2566. [PMID: 37756257 PMCID: PMC10623573 DOI: 10.1021/jasms.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Protein glycosylation is one of the most common PTMs and many cell surface receptors, extracellular proteins, and biopharmaceuticals are glycosylated. However, HDX-MS analysis of such important glycoproteins has so far been limited by difficulties in determining the HDX of the protein segments that contain glycans. We have developed a column containing immobilized PNGase Rc (from Rudaea cellulosilytica) that can readily be implemented into a conventional HDX-MS setup to allow improved analysis of glycoproteins. We show that HDX-MS with the PNGase Rc column enables efficient online removal of N-linked glycans and the determination of the HDX of glycosylated regions in several complex glycoproteins. Additionally, we use the PNGase Rc column to perform a comprehensive HDX-MS mapping of the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Importantly, the column retains high activity in the presence of common quench-buffer additives like TCEP and urea and performed consistent across 114 days of extensive use. Overall, our work shows that HDX-MS with the integrated PNGase Rc column can enable fast and efficient online deglycosylation at harsh quench conditions to provide comprehensive analysis of complex glycoproteins.
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Affiliation(s)
- Thomas Lambert
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Marius Gramlich
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Luisa Stutzke
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Luke Smith
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Dingyu Deng
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Philipp D. Kaiser
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Pharmaceutical
Biotechnology, Eberhard Karls University, 72074 Tübingen, Germany
| | - Justin L. P. Benesch
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Cornelia Wagner
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maximiliane Koenig
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Petr Pompach
- BioCev,
Institute of Biotechnology of the CAS, 252 50 Prumyslova, Czech Republic
| | - Petr Novak
- BioCeV,
Institute of Microbiology of the CAS, 142 20 Prumyslova, Czech Republic
| | - Anne Zeck
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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4
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Shaaban M, Clapperton JA, Ding S, Kunzelmann S, Mäeots ME, Maslen SL, Skehel JM, Enchev RI. Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange. Mol Cell 2023:S1097-2765(23)00418-5. [PMID: 37339624 DOI: 10.1016/j.molcel.2023.05.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023]
Abstract
Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation.
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Affiliation(s)
- Mohammed Shaaban
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Julie A Clapperton
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Shan Ding
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Märt-Erik Mäeots
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Radoslav I Enchev
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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5
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Ahn D, Provasi D, Duc NM, Xu J, Salas-Estrada L, Spasic A, Yun MW, Kang J, Gim D, Lee J, Du Y, Filizola M, Chung KY. Gαs slow conformational transition upon GTP binding and a novel Gαs regulator. iScience 2023; 26:106603. [PMID: 37128611 PMCID: PMC10148139 DOI: 10.1016/j.isci.2023.106603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023] Open
Abstract
G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR-G protein complex formation and guanosine diphosphate (GDP) release have been reported, no information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling framework that combines data from hydrogen-deuterium exchange mass spectrometry, tryptophan-induced fluorescence quenching, and metadynamics simulations to derive a kinetic model and atomic-level characterization of stepwise conformational changes incurred by the β2-adrenergic receptor (β2AR)-Gs complex after GDP release and GTP binding. Our data suggest rapid GTP binding and GTP-induced dissociation of Gαs from β2AR and Gβγ, as opposed to a slow closing of the Gαs α-helical domain (AHD). Yeast-two-hybrid screening using Gαs AHD as bait identified melanoma-associated antigen D2 (MAGE D2) as a novel AHD-binding protein, which was also shown to accelerate the GTP-induced closing of the Gαs AHD.
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Affiliation(s)
- Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Min Woo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Juyeong Kang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dongmin Gim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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6
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Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape. iScience 2023; 26:106282. [PMID: 36910327 PMCID: PMC9968663 DOI: 10.1016/j.isci.2023.106282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.
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7
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Han F, Shen Q, Zheng W, Zuo J, Zhu X, Li J, Peng C, Li B, Chen Y. The Conformational Changes of Bovine Serum Albumin at the Air/Water Interface: HDX-MS and Interfacial Rheology Analysis. Foods 2023; 12:foods12081601. [PMID: 37107396 PMCID: PMC10137346 DOI: 10.3390/foods12081601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
The characterization and dynamics of protein structures upon adsorption at the air/water interface are important for understanding the mechanism of the foamability of proteins. Hydrogen-deuterium exchange, coupled with mass spectrometry (HDX-MS), is an advantageous technique for providing conformational information for proteins. In this work, an air/water interface, HDX-MS, for the adsorbed proteins at the interface was developed. The model protein bovine serum albumin (BSA) was deuterium-labeled at the air/water interface in situ for different predetermined times (10 min and 4 h), and then the resulting mass shifts were analyzed by MS. The results indicated that peptides 54-63, 227-236, and 355-366 of BSA might be involved in the adsorption to the air/water interface. Moreover, the residues L55, H63, R232, A233, L234, K235, A236, R359, and V366 of these peptides might interact with the air/water interface through hydrophobic and electrostatic interactions. Meanwhile, the results showed that conformational changes of peptides 54-63, 227-236, and 355-366 could lead to structural changes in their surrounding peptides, 204-208 and 349-354, which could cause the reduction of the content of helical structures in the rearrangement process of interfacial proteins. Therefore, our air/water interface HDX-MS method could provide new and meaningful insights into the spatial conformational changes of proteins at the air/water interface, which could help us to further understand the mechanism of protein foaming properties.
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Affiliation(s)
- Fei Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Shen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingnan Zuo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijie Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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8
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Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE. ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure 2023; 31:343-354.e3. [PMID: 36758543 DOI: 10.1016/j.str.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
Akt is a master regulator of pro-growth signaling in the cell. Akt is activated by phosphoinositides that disrupt the autoinhibitory interface between the kinase and pleckstrin homology (PH) domains and then is phosphorylated at T308 and S473. Akt hyperactivation is oncogenic, which has spurred development of potent and selective inhibitors as therapeutics. Using hydrogen deuterium exchange mass spectrometry (HDX-MS), we interrogated the conformational changes upon binding Akt ATP-competitive and allosteric inhibitors. We compared inhibitors against three different states of Akt1. The allosteric inhibitor caused substantive conformational changes and restricts membrane binding. ATP-competitive inhibitors caused extensive allosteric conformational changes, altering the autoinhibitory interface and leading to increased membrane binding, suggesting that the PH domain is more accessible for membrane binding. This work provides unique insight into the autoinhibitory conformation of the PH and kinase domain and conformational changes induced by Akt inhibitors and has important implications for the design of Akt targeted therapeutics.
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Affiliation(s)
- Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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9
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Gao S, Zhang W, Barrow SL, Iavarone AT, Klinman JP. Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks. J Biol Chem 2022; 298:102350. [PMID: 35933011 PMCID: PMC9483566 DOI: 10.1016/j.jbc.2022.102350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend temperature-dependent hydrogen deuterium exchange from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different hydrogen deuterium exchange-mass spectrometry properties for the two ligands, as expected from their 106-fold differences in strength of binding. By contrast, analogous patterns for temperature-dependent hydrogen deuterium exchange mass spectrometry emerge in the presence of both 1-deaza-adenosine and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended temperature-dependent hydrogen deuterium exchange to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility versus site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Samuel L Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
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10
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Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about the structural determinants of hydrogen exchange itself, such data have successfully helped guide the structural modeling of challenging molecular systems, such as membrane proteins or large macromolecular complexes. As hydrogen-exchange monitoring provides information on the dynamics of molecules in solution, it can complement other experimental techniques in so-called integrative modeling approaches. However, hydrogen-exchange data have often only been used to qualitatively assess molecular structures produced by computational modeling tools. In this paper, we look beyond qualitative approaches and survey the various paradigms under which hydrogen-exchange data have been used to quantitatively guide the computational modeling of molecular structures. Although numerous prediction models have been proposed to link molecular structure and hydrogen exchange, none of them has been widely accepted by the structural biology community. Here, we present as many hydrogen-exchange prediction models as we could find in the literature, with the aim of providing the first exhaustive list of its kind. From purely structure-based models to so-called fractional-population models or knowledge-based models, the field is quite vast. We aspire for this paper to become a resource for practitioners to gain a broader perspective on the field and guide research toward the definition of better prediction models. This will eventually improve synergies between hydrogen-exchange monitoring and molecular modeling.
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Affiliation(s)
- Didier Devaurs
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77005, United States
| | - Antoni J Borysik
- Department of Chemistry, King's College London, London SE1 1DB, U.K
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11
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Comamala G, Krogh CC, Nielsen VS, Kutter JP, Voglmeir J, Rand KD. Hydrogen/Deuterium Exchange Mass Spectrometry with Integrated Electrochemical Reduction and Microchip-Enabled Deglycosylation for Epitope Mapping of Heavily Glycosylated and Disulfide-Bonded Proteins. Anal Chem 2021; 93:16330-16340. [PMID: 34843209 DOI: 10.1021/acs.analchem.1c01728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a recognized method to study protein conformational dynamics and interactions. Proteins encompassing post-translational modifications (PTMs), such as disulfide bonds and glycosylations, present challenges to HDX-MS, as disulfide bond reduction and deglycosylation is often required to extract HDX information from regions containing these PTMs. In-solution deglycosylation with peptide-N4-(N-acetyl-β-d-glucosaminyl)-asparagine amidase A (PNGase A) or PNGase H+ combined with chemical reduction using tris-(2-carboxyethyl)phosphine (TCEP) has previously been used for HDX-MS analysis of disulfide-linked glycoproteins. However, this workflow requires extensive manual sample preparation and consumes large amounts of enzyme. Furthermore, large amounts of TCEP and glycosidases often result in suboptimal liquid chromatography-mass spectrometry (LC-MS) performance. Here, we compare the in-solution activity of PNGase A, PNGase H+, and the newly discovered PNGase Dj under quench conditions and immobilize them onto thiol-ene microfluidic chips to create HDX-MS-compatible immobilized microfluidic enzyme reactors (IMERs). The IMERS retain deglycosylation activity, also following repeated use and long-term storage. Furthermore, we combine a PNGase Dj IMER, a pepsin IMER, and an electrochemical cell to develop an HDX-MS setup capable of efficient online disulfide-bond reduction, deglycosylation, and proteolysis. We demonstrate the applicability of this setup by mapping the epitope of a monoclonal antibody (mAb) on the heavily disulfide-bonded and glycosylated sema-domain of the tyrosine-protein kinase Met (SD c-Met). We achieve near-complete sequence coverage and extract HDX data to identify regions of SD c-Met involved in mAb binding. The described methodology thus presents an integrated and online workflow for improved HDX-MS analysis of challenging PTM-rich proteins.
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Affiliation(s)
- Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Camilla C Krogh
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Vibe S Nielsen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jörg P Kutter
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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12
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Calvaresi V, Truelsen LT, Larsen SB, Petersen NHT, Kirkegaard T, Rand KD. Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments. Commun Biol 2021; 4:1369. [PMID: 34876699 PMCID: PMC8651726 DOI: 10.1038/s42003-021-02892-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 11/10/2021] [Indexed: 11/21/2022] Open
Abstract
The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. However, the conformational features of this protein-lipid complex remain unclear. Here, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the dynamics of the full-length Hsp70 in the cytosol and its conformational changes upon translocation into lysosomes. Using wild-type and W90F mutant proteins, we also map and discriminate the interaction of Hsp70 with BMP and other lipid components of the lysosomal membrane. We identify the N-terminal of the nucleotide binding domain (residues 87-118) as the primary orchestrator of BMP interaction. We show that the conformation of this domain is significantly reorganized in the W90F mutant, explaining its inability to stabilize lysosomal membranes. Overall, our results reveal important new molecular details of the protective effect of Hsp70 in lysosomal storage diseases, which, in turn, could guide future drug development.
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Affiliation(s)
- Valeria Calvaresi
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Line T. Truelsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Sidsel B. Larsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | | | | | - Kasper D. Rand
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
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13
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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14
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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15
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Huang L, So PK, Chen YW, Leung YC, Yao ZP. Interdomain flexibility and interfacial integrity of β-lactamase inhibitory protein (BLIP) modulate its binding to class A β-lactamases. J Biol Chem 2021; 297:100980. [PMID: 34302811 PMCID: PMC8363833 DOI: 10.1016/j.jbc.2021.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 11/05/2022] Open
Abstract
β-Lactamase inhibitory protein (BLIP) consists of a tandem repeat of αβ domains conjugated by an interdomain loop and can effectively bind and inactivate class A β-lactamases, which are responsible for resistance of bacteria to β-lactam antibiotics. The varied ability of BLIP to bind different β-lactamases and the structural determinants for significant enhancement of BLIP variants with a point mutation are poorly understood. Here, we investigated the conformational dynamics of BLIP upon binding to three clinically prevalent class A β-lactamases (TEM1, SHV1, and PC1) with dissociation constants between subnanomolar and micromolar. Hydrogen deuterium exchange mass spectrometry revealed that the flexibility of the interdomain region was significantly suppressed upon strong binding to TEM1, but was not significantly changed upon weak binding to SHV1 or PC1. E73M and K74G mutations in the interdomain region improved binding affinity toward SHV1 and PC1, respectively, showing significantly increased flexibility of the interdomain region compared to the wild-type and favorable conformational changes upon binding. In contrast, more rigidity of the interfacial loop 135–145 was observed in these BLIP mutants in both free and bound states. Consistently, molecular dynamics simulations of BLIP exhibited drastic changes in the flexibility of the loop 135–145 in all complexes. Our results indicated for the first time that higher flexibility of the interdomain linker, as well as more rigidity of the interfacial loop 135–145, could be desirable determinants for enhancing inhibition of BLIP to class A β-lactamases. Together, these findings provide unique insights into the design of enhanced inhibitors.
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Affiliation(s)
- Liwen Huang
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yu Wai Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, China.
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16
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Stariha JTB, Hoffmann RM, Hamelin DJ, Burke JE. Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Methods Mol Biol 2021; 2263:465-485. [PMID: 33877613 DOI: 10.1007/978-1-0716-1197-5_22] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular membranes are a central hub for initiation and execution of many signaling processes. Integral to these processes being accomplished appropriately is the highly controlled recruitment and assembly of proteins at membrane surfaces. The study of the molecular mechanisms that mediate protein-membrane interactions can be facilitated by utilizing hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS is a robust analytical technique that allows for the measurement of the exchange rate of backbone amide hydrogens with solvent to make inferences about protein structure and conformation. This chapter discusses the use of HDX-MS as a tool to study the conformational changes that occur within peripheral membrane proteins upon association with membrane. Particular reference will be made to the analysis of the protein kinase Akt and its activation upon binding phosphatidylinositol (3,4,5) tris-phosphate (PIP3)-containing membranes to illustrate specific methodological principles.
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Affiliation(s)
- Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada. .,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada.
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17
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Lentini G, Ben Chaabene R, Vadas O, Ramakrishnan C, Mukherjee B, Mehta V, Lunghi M, Grossmann J, Maco B, Visentin R, Hehl AB, Korkhov VM, Soldati-Favre D. Structural insights into an atypical secretory pathway kinase crucial for Toxoplasma gondii invasion. Nat Commun 2021; 12:3788. [PMID: 34145271 PMCID: PMC8213820 DOI: 10.1038/s41467-021-24083-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Active host cell invasion by the obligate intracellular apicomplexan parasites relies on the formation of a moving junction, which connects parasite and host cell plasma membranes during entry. Invading Toxoplasma gondii tachyzoites secrete their rhoptry content and insert a complex of RON proteins on the cytoplasmic side of the host cell membrane providing an anchor to which the parasite tethers. Here we show that a rhoptry-resident kinase RON13 is a key virulence factor that plays a crucial role in host cell entry. Cryo-EM, kinase assays, phosphoproteomics and cellular analyses reveal that RON13 is a secretory pathway kinase of atypical structure that phosphorylates rhoptry proteins including the components of the RON complex. Ultimately, RON13 kinase activity controls host cell invasion by anchoring the moving junction at the parasite-host cell interface.
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Affiliation(s)
- Gaëlle Lentini
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Rouaa Ben Chaabene
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Chandra Ramakrishnan
- grid.7400.30000 0004 1937 0650Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Budhaditya Mukherjee
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland ,grid.429017.90000 0001 0153 2859Present Address: School of Medical Science and Technology, IIT Kharagpur, India
| | - Ved Mehta
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Matteo Lunghi
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Jonas Grossmann
- grid.7400.30000 0004 1937 0650Functional Genomic Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland ,grid.419765.80000 0001 2223 3006The Swiss Institute of Bioinformatics, SIB, Lausanne, Switzerland
| | - Bohumil Maco
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Rémy Visentin
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Adrian B. Hehl
- grid.7400.30000 0004 1937 0650Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Volodymyr M. Korkhov
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland ,grid.5991.40000 0001 1090 7501Paul Scherrer Institute, Villigen, Switzerland
| | - Dominique Soldati-Favre
- grid.8591.50000 0001 2322 4988Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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18
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Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res 2021; 20:1133-1152. [PMID: 33464917 PMCID: PMC7839417 DOI: 10.1021/acs.jproteome.0c00764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 12/17/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.
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Affiliation(s)
- Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robyn M. Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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19
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Fang M, Wang Z, Cupp-Sutton KA, Welborn T, Smith K, Wu S. High-throughput hydrogen deuterium exchange mass spectrometry (HDX-MS) coupled with subzero-temperature ultrahigh pressure liquid chromatography (UPLC) separation for complex sample analysis. Anal Chim Acta 2021; 1143:65-72. [PMID: 33384131 PMCID: PMC8265693 DOI: 10.1016/j.aca.2020.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/31/2020] [Accepted: 11/16/2020] [Indexed: 11/23/2022]
Abstract
Hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) is a powerful technique for the characterization of protein dynamics and protein interactions. Recent technological developments in the HDX-MS field, such as sub-zero LC separations, large-scale data analysis tools, and efficient protein digestion methods, have allowed for the application of HDX-MS to the analysis of multi protein systems in addition to pure protein analysis. Still, high-throughput HDX-MS analysis of complex samples is not widespread because the co-elution of peptides combined with increased peak complexity after labeling makes peak de-convolution extremely difficult. Here, for the first time, we evaluated and optimized long gradient subzero-temperature ultra-high-pressure liquid chromatography (UPLC) separation conditions for the HDX-MS analysis of complex protein samples such as E. coli cell lysate digest. Under the optimized conditions, we identified 1419 deuterated peptides from 320 proteins at -10 °C, which is about 3-fold more when compared with a 15-min gradient separation under the same conditions. Interestingly, our results suggested that the peptides eluted late in the gradient are well-protected by peptide-column interactions at -10 °C so that peptides eluted even at the end of the gradient maintain high levels of deuteration. Overall, our study suggests that the optimized, sub-zero, long-gradient UPLC separation is capable of characterizing thousands of peptides in a single HDX-MS analysis with low back-exchange rates. As a result, this technique holds great potential for characterizing complex samples such as cell lysates using HDX-MS.
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Affiliation(s)
- Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Thomas Welborn
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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20
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Ham D, Ahn D, Ashim J, Cho Y, Kim HR, Yu W, Chung KY. Conformational switch that induces GDP release from Gi. J Struct Biol 2021; 213:107694. [PMID: 33418033 DOI: 10.1016/j.jsb.2020.107694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are composed of α, β, and γ subunits. Gα switches between guanosine diphosphate (GDP)-bound inactive and guanosine triphosphate (GTP)-bound active states, and Gβγ interacts with the GDP-bound state. The GDP-binding regions are composed of two sites: the phosphate-binding and guanine-binding regions. The turnover of GDP and GTP is induced by guanine nucleotide-exchange factors (GEFs), including G protein-coupled receptors (GPCRs), Ric8A, and GIV/Girdin. However, the key structural factors for stabilizing the GDP-bound state of G proteins and the direct structural event for GDP release remain unclear. In this study, we investigated structural factors affecting GDP release by introducing point mutations in selected, conserved residues in Gαi3. We examined the effects of these mutations on the GDP/GTP turnover rate and the overall conformation of Gαi3 as well as the binding free energy between Gαi3 and GDP. We found that dynamic changes in the phosphate-binding regions are an immediate factor for the release of GDP.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Janbolat Ashim
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea
| | - Yejin Cho
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea; Core Protein Resources Center, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.
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21
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Ozohanics O, Ambrus A. Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes. Life (Basel) 2020; 10:E286. [PMID: 33203161 PMCID: PMC7696067 DOI: 10.3390/life10110286] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.
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Affiliation(s)
- Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
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Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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23
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Kammari R, Topp EM. Effects of Secondary Structure on Solid-State Hydrogen–Deuterium Exchange in Model α-Helix and β-Sheet Peptides. Mol Pharm 2020; 17:3501-3512. [DOI: 10.1021/acs.molpharmaceut.0c00521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajashekar Kammari
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Elizabeth M. Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Co., Dublin A94 X099, Ireland
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24
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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25
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Xiong Y, Zhang Y, Liu X, Yao J, Lu H. A novel method for large-scale confirmation of protein structures and surface accessible modification sites. Talanta 2020; 211:120697. [DOI: 10.1016/j.talanta.2019.120697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/24/2022]
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26
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Hodge EA, Benhaim MA, Lee KK. Bridging protein structure, dynamics, and function using hydrogen/deuterium-exchange mass spectrometry. Protein Sci 2020; 29:843-855. [PMID: 31721348 PMCID: PMC7096709 DOI: 10.1002/pro.3790] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
Abstract
Much of our understanding of protein structure and mechanistic function has been derived from static high-resolution structures. As structural biology has continued to evolve it has become clear that high-resolution structures alone are unable to fully capture the mechanistic basis for protein structure and function in solution. Recently Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has developed into a powerful and versatile tool for structural biologists that provides novel insights into protein structure and function. HDX-MS enables direct monitoring of a protein's structural fluctuations and conformational changes under native conditions in solution even as it is carrying out its functions. In this review, we focus on the use of HDX-MS to monitor these dynamic changes in proteins. We examine how HDX-MS has been applied to study protein structure and function in systems ranging from large, complex assemblies to intrinsically disordered proteins, and we discuss its use in probing conformational changes during protein folding and catalytic function. STATEMENT FOR A BROAD AUDIENCE: The biophysical and structural characterization of proteins provides novel insight into their functionalities. Protein motions, ranging from small scale local fluctuations to larger concerted structural rearrangements, often determine protein function. Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has proven a powerful biophysical tool capable of probing changes in protein structure and dynamic protein motions that are often invisible to most other techniques.
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Affiliation(s)
- Edgar A. Hodge
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashington
| | - Mark A. Benhaim
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashington
| | - Kelly K. Lee
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashington
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27
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Martens C, Shekhar M, Lau AM, Tajkhorshid E, Politis A. Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. Nat Protoc 2019; 14:3183-3204. [PMID: 31605097 PMCID: PMC7058097 DOI: 10.1038/s41596-019-0219-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022]
Abstract
Biological membranes define the boundaries of cells and are composed primarily of phospholipids and membrane proteins. It has become increasingly evident that direct interactions of membrane proteins with their surrounding lipids play key roles in regulating both protein conformations and function. However, the exact nature and structural consequences of these interactions remain difficult to track at the molecular level. Here, we present a protocol that specifically addresses this challenge. First, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of membrane proteins incorporated into nanodiscs of controlled lipid composition is used to obtain information on the lipid species that are involved in modulating the conformational changes in the membrane protein. Then molecular dynamics (MD) simulations in lipid bilayers are used to pinpoint likely lipid-protein interactions, which can be tested experimentally using HDX-MS. By bringing together the MD predictions with the conformational readouts from HDX-MS, we have uncovered key lipid-protein interactions implicated in stabilizing important functional conformations. This protocol can be applied to virtually any integral membrane protein amenable to classic biophysical studies and for which a near-atomic-resolution structure or homology model is available. This protocol takes ~4 d to complete, excluding the time for data analysis and MD simulations, which depends on the size of the protein under investigation.
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Affiliation(s)
- Chloe Martens
- Department of Chemistry, King's College London, London, UK
- Department of Chemistry, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy M Lau
- Department of Chemistry, King's College London, London, UK
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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28
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Szymkowicz L, Lento C, Wilson DJ. Impact of Cardiolipin and Phosphatidylcholine Interactions on the Conformational Ensemble of Cytochrome c. Biochemistry 2019; 58:3617-3626. [DOI: 10.1021/acs.biochem.9b00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lisa Szymkowicz
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
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29
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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30
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Liu H, Wang D, Zhang Q, Zhao Y, Mamonova T, Wang L, Zhang C, Li S, Friedman PA, Xiao K. Parallel Post-Translational Modification Scanning Enhancing Hydrogen-Deuterium Exchange-Mass Spectrometry Coverage of Key Structural Regions. Anal Chem 2019; 91:6976-6980. [PMID: 31082219 DOI: 10.1021/acs.analchem.9b01410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-deuterium exchange-mass spectrometry (HDXMS) is a powerful technology to characterize conformations and conformational dynamics of proteins and protein complexes. HDXMS has been widely used in the field of therapeutics for the development of protein drugs. Although sufficient sequence coverage is critical to the success of HDXMS, it is sometimes difficult to achieve. In this study, we developed a HDXMS data analysis strategy that includes parallel post-translational modification (PTM) scanning in HDXMS analysis. Using a membrane-delimited G protein-coupled receptor (vasopressin type 2 receptor; V2R) and a cytosolic protein (Na+/H+ exchanger regulatory factor-1; NHERF1) as examples, we demonstrate that this strategy substantially improves protein sequence coverage, especially in key structural regions likely including PTMs themselves that play important roles in protein conformational dynamics and function.
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Affiliation(s)
| | | | | | | | | | | | | | - Sheng Li
- Department of Medicine , University of California San Diego , La Jolla , California 92093 , United States
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31
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Du Y, Duc NM, Rasmussen SGF, Hilger D, Kubiak X, Wang L, Bohon J, Kim HR, Wegrecki M, Asuru A, Jeong KM, Lee J, Chance MR, Lodowski DT, Kobilka BK, Chung KY. Assembly of a GPCR-G Protein Complex. Cell 2019; 177:1232-1242.e11. [PMID: 31080064 DOI: 10.1016/j.cell.2019.04.022] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/25/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
The activation of G proteins by G protein-coupled receptors (GPCRs) underlies the majority of transmembrane signaling by hormones and neurotransmitters. Recent structures of GPCR-G protein complexes obtained by crystallography and cryoelectron microscopy (cryo-EM) reveal similar interactions between GPCRs and the alpha subunit of different G protein isoforms. While some G protein subtype-specific differences are observed, there is no clear structural explanation for G protein subtype-selectivity. All of these complexes are stabilized in the nucleotide-free state, a condition that does not exist in living cells. In an effort to better understand the structural basis of coupling specificity, we used time-resolved structural mass spectrometry techniques to investigate GPCR-G protein complex formation and G-protein activation. Our results suggest that coupling specificity is determined by one or more transient intermediate states that serve as selectivity filters and precede the formation of the stable nucleotide-free GPCR-G protein complexes observed in crystal and cryo-EM structures.
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Affiliation(s)
- Yang Du
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Daniel Hilger
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Xavier Kubiak
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Liwen Wang
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jennifer Bohon
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Marcin Wegrecki
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Awuri Asuru
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kyung Min Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeongmi Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Mark R Chance
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - David T Lodowski
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Brian K Kobilka
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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33
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Markwick PRL, Peacock RB, Komives EA. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophys J 2018; 116:49-56. [PMID: 30558884 DOI: 10.1016/j.bpj.2018.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022] Open
Abstract
Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of proteins has become extremely popular for identifying ligand-binding sites, protein-protein interactions, intrinsic disorder, and allosteric changes upon protein modification. Such phenomena are revealed when amide exchange is measured in the fast limit, that is, within a few minutes of exchange in deuterated buffer. The HDXMS data have a resolution of the length of peptides and are difficult to interpret because many different phenomena lead to changes in hydrogen/deuterium exchange. We present a quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data. Comparative analysis of thrombin and a single-point mutant reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation. In addition, the results provide a deeper understanding of the underlying changes in dynamics revealed by the HDXMS that extend far from the site of mutation.
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Affiliation(s)
- Phineus R L Markwick
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California
| | - Riley B Peacock
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California.
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34
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Trabjerg E, Nazari ZE, Rand KD. Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): Challenges and emerging solutions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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36
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Fassler R, Edinger N, Rimon O, Reichmann D. Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry. J Vis Exp 2018. [PMID: 29939186 DOI: 10.3791/57806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Living organisms regularly need to cope with fluctuating environments during their life cycle, including changes in temperature, pH, the accumulation of reactive oxygen species, and more. These fluctuations can lead to a widespread protein unfolding, aggregation, and cell death. Therefore, cells have evolved a dynamic and stress-specific network of molecular chaperones, which maintain a "healthy" proteome during stress conditions. ATP-independent chaperones constitute one major class of molecular chaperones, which serve as first-line defense molecules, protecting against protein aggregation in a stress-dependent manner. One feature these chaperones have in common is their ability to utilize structural plasticity for their stress-specific activation, recognition, and release of the misfolded client. In this paper, we focus on the functional and structural analysis of one such intrinsically disordered chaperone, the bacterial redox-regulated Hsp33, which protects proteins against aggregation during oxidative stress. Here, we present a toolbox of diverse techniques for studying redox-regulated chaperone activity, as well as for mapping conformational changes of the chaperone, underlying its activity. Specifically, we describe a workflow which includes the preparation of fully reduced and fully oxidized proteins, followed by an analysis of the chaperone anti-aggregation activity in vitro using light-scattering, focusing on the degree of the anti-aggregation activity and its kinetics. To overcome frequent outliers accumulated during aggregation assays, we describe the usage of Kfits, a novel graphical tool which allows easy processing of kinetic measurements. This tool can be easily applied to other types of kinetic measurements for removing outliers and fitting kinetic parameters. To correlate the function with the protein structure, we describe the setup and workflow of a structural mass spectrometry technique, hydrogen-deuterium exchange mass spectrometry, that allows the mapping of conformational changes on the chaperone and substrate during different stages of Hsp33 activity. The same methodology can be applied to other protein-protein and protein-ligand interactions.
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Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Oded Rimon
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem;
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37
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Abstract
Mutations in the E3 ubiquitin ligase parkin (PARK2, also known as PRKN) and the protein kinase PINK1 (also known as PARK6) are linked to autosomal-recessive juvenile parkinsonism (AR-JP)1,2; at the cellular level, these mutations cause defects in mitophagy, the process that organizes the destruction of damaged mitochondria3,4. Parkin is autoinhibited, and requires activation by PINK1, which phosphorylates Ser65 in ubiquitin and in the parkin ubiquitin-like (Ubl) domain. Parkin binds phospho-ubiquitin, which enables efficient parkin phosphorylation; however, the enzyme remains autoinhibited with an inaccessible active site5,6. It is unclear how phosphorylation of parkin activates the molecule. Here we follow the activation of full-length human parkin by hydrogen-deuterium exchange mass spectrometry, and reveal large-scale domain rearrangement in the activation process, during which the phospho-Ubl rebinds to the parkin core and releases the catalytic RING2 domain. A 1.8 Å crystal structure of phosphorylated human parkin reveals the binding site of the phospho-Ubl on the unique parkin domain (UPD), involving a phosphate-binding pocket lined by AR-JP mutations. Notably, a conserved linker region between Ubl and the UPD acts as an activating element (ACT) that contributes to RING2 release by mimicking RING2 interactions on the UPD, explaining further AR-JP mutations. Our data show how autoinhibition in parkin is resolved, and suggest a mechanism for how parkin ubiquitinates its substrates via an untethered RING2 domain. These findings open new avenues for the design of parkin activators for clinical use.
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38
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Sinz A. Cross‐Linking/Mass Spectrometry for Studying Protein Structures and Protein–Protein Interactions: Where Are We Now and Where Should We Go from Here? Angew Chem Int Ed Engl 2018; 57:6390-6396. [DOI: 10.1002/anie.201709559] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/06/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of PharmacyMartin Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle (Saale) Germany
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39
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Lučić I, Rathinaswamy MK, Truebestein L, Hamelin DJ, Burke JE, Leonard TA. Conformational sampling of membranes by Akt controls its activation and inactivation. Proc Natl Acad Sci U S A 2018; 115:E3940-E3949. [PMID: 29632185 PMCID: PMC5924885 DOI: 10.1073/pnas.1716109115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The protein kinase Akt controls myriad signaling processes in cells, ranging from growth and proliferation to differentiation and metabolism. Akt is activated by a combination of binding to the lipid second messenger PI(3,4,5)P3 and its subsequent phosphorylation by phosphoinositide-dependent kinase 1 and mechanistic target of rapamycin complex 2. The relative contributions of these mechanisms to Akt activity and signaling have hitherto not been understood. Here, we show that phosphorylation and activation by membrane binding are mutually interdependent. Moreover, the converse is also true: Akt is more rapidly dephosphorylated in the absence of PIP3, an autoinhibitory process driven by the interaction of its PH and kinase domains. We present biophysical evidence for the conformational changes in Akt that accompany its activation on membranes, show that Akt is robustly autoinhibited in the absence of PIP3 irrespective of its phosphorylation, and map the autoinhibitory PH-kinase interface. Finally, we present a model for the activation and inactivation of Akt by an ordered series of membrane binding, phosphorylation, dissociation, and dephosphorylation events.
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Affiliation(s)
- Iva Lučić
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria;
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
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40
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Sinz A. Vernetzung/Massenspektrometrie zur Untersuchung von Proteinstrukturen und Protein‐Protein‐Wechselwirkungen: Wo stehen wir und welchen Weg wollen wir einschlagen? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Sinz
- Abteilung für Pharmazeutische Chemie & BioanalytikInstitut für PharmazieMartin-Luther-Universität Halle-Wittenberg Wolfgang-Langenbeck-Straße 4 06120 Halle (Saale) Deutschland
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41
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Nnadi CI, Jenkins ML, Gentile DR, Bateman LA, Zaidman D, Balius TE, Nomura DK, Burke JE, Shokat KM, London N. Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model 2018; 58:464-471. [PMID: 29320178 DOI: 10.1021/acs.jcim.7b00399] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The success of targeted covalent inhibitors in the global pharmaceutical industry has led to a resurgence of covalent drug discovery. However, covalent inhibitor design for flexible binding sites remains a difficult task due to a lack of methodological development. Here, we compared covalent docking to empirical electrophile screening against the highly dynamic target K-RasG12C. While the overall hit rate of both methods was comparable, we were able to rapidly progress a docking hit to a potent irreversible covalent binder that modifies the inactive, GDP-bound state of K-RasG12C. Hydrogen-deuterium exchange mass spectrometry was used to probe the protein dynamics of compound binding to the switch-II pocket and subsequent destabilization of the nucleotide-binding region. SOS-mediated nucleotide exchange assays showed that, contrary to prior switch-II pocket inhibitors, these new compounds appear to accelerate nucleotide exchange. This study highlights the efficiency of covalent docking as a tool for the discovery of chemically novel hits against challenging targets.
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Affiliation(s)
- Chimno I Nnadi
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology. University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Daniel R Gentile
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States
| | - Daniel Zaidman
- Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States
| | - John E Burke
- Department of Biochemistry and Microbiology. University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Nir London
- Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel
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42
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Abstract
The Aichi RNA virus remodels host membranes by conscripting two host proteins, PI4KIIIβ (to generate PI4P in the remodeled vesicle) and ACBD3 (that tightly binds PI4KIIIβ), and localizing them on target membranes via Aichi protein 3A. In this issue of Structure, McPhail et al. (2017) reveal structural glimpses of the interfaces involved in this protein threesome using HDX-MS.
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Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
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43
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Bhat JY, Miličić G, Thieulin-Pardo G, Bracher A, Maxwell A, Ciniawsky S, Mueller-Cajar O, Engen JR, Hartl FU, Wendler P, Hayer-Hartl M. Mechanism of Enzyme Repair by the AAA + Chaperone Rubisco Activase. Mol Cell 2017; 67:744-756.e6. [PMID: 28803776 DOI: 10.1016/j.molcel.2017.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/07/2017] [Accepted: 07/01/2017] [Indexed: 01/16/2023]
Abstract
How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.
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Affiliation(s)
- Javaid Y Bhat
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Goran Miličić
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gabriel Thieulin-Pardo
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andrew Maxwell
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Susanne Ciniawsky
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Oliver Mueller-Cajar
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Petra Wendler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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44
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Integrative modelling of cellular assemblies. Curr Opin Struct Biol 2017; 46:102-109. [PMID: 28735107 DOI: 10.1016/j.sbi.2017.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023]
Abstract
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively. We highlight general concepts in integrative modelling and discuss the need for careful formulation and merging of different types of information.
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45
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Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE. Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data. Front Mol Biosci 2017; 4:13. [PMID: 28344973 PMCID: PMC5344923 DOI: 10.3389/fmolb.2017.00013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a single conformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | | | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Broad Institute of MIT & HarvardCambridge, MA, USA
| | - Mark Moll
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Department of Pharmaceutical Sciences, University of BaselBasel, Switzerland
| | - John D. Lambris
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
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46
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Conformational disruption of PI3Kδ regulation by immunodeficiency mutations in PIK3CD and PIK3R1. Proc Natl Acad Sci U S A 2017; 114:1982-1987. [PMID: 28167755 DOI: 10.1073/pnas.1617244114] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Activated PI3K Delta Syndrome (APDS) is a primary immunodeficiency disease caused by activating mutations in either the leukocyte-restricted p110δ catalytic (PIK3CD) subunit or the ubiquitously expressed p85α regulatory (PIK3R1) subunit of class IA phosphoinositide 3-kinases (PI3Ks). There are two classes of APDS: APDS1 that arises from p110δ mutations that are analogous to oncogenic mutations found in the broadly expressed p110α subunit and APDS2 that occurs from a splice mutation resulting in p85α with a central deletion (Δ434-475). As p85 regulatory subunits associate with and inhibit all class IA catalytic subunits, APDS2 mutations are expected to similarly activate p110α, β, and δ, yet APDS2 largely phenocopies APDS1 without dramatic effects outside the immune system. We have examined the molecular mechanism of activation of both classes of APDS mutations using a combination of biochemical assays and hydrogen-deuterium exchange mass spectrometry. Intriguingly, we find that an APDS2 mutation in p85α leads to substantial basal activation of p110δ (>300-fold) and disrupts inhibitory interactions from the nSH2, iSH2, and cSH2 domains of p85, whereas p110α is only minimally basally activated (∼2-fold) when associated with mutated p85α. APDS1 mutations in p110δ (N334K, E525K, E1021K) mimic the activation mechanisms previously discovered for oncogenic mutations in p110α. All APDS mutations were potently inhibited by the Food and Drug Administration-approved p110δ inhibitor idelalisib. Our results define the molecular basis of how PIK3CD and PIK3R1 mutations result in APDS and reveal a potential path to treatment for all APDS patients.
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47
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McPhail JA, Ottosen EH, Jenkins ML, Burke JE. The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIβ, PI4KB, through ACBD3. Structure 2016; 25:121-131. [PMID: 27989622 DOI: 10.1016/j.str.2016.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/19/2016] [Accepted: 11/18/2016] [Indexed: 01/12/2023]
Abstract
Phosphatidylinositol 4-kinase III beta (PI4KIIIβ) is an essential enzyme in mediating membrane transport, and plays key roles in facilitating viral infection. Many pathogenic positive-sense single-stranded RNA viruses activate PI4KIIIβ to generate phosphatidylinositol 4-phosphate (PI4P)-enriched organelles for viral replication. The molecular basis for PI4KIIIβ activation during viral infection has remained largely unclear. We describe the biochemical reconstitution and characterization of the complex of PI4KIIIβ with the Golgi protein Acyl-coenzyme A binding domain containing protein 3 (ACBD3) and Aichi virus 3A protein on membranes. We find that 3A directly activates PI4KIIIβ, and this activation is sensitized by ACBD3. The interfaces between PI4KIIIβ-ACBD3 and ACBD3-3A were mapped with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Determination of the crystal structure of the ACBD3 GOLD domain revealed a unique N terminus that mediates the interaction with 3A. Rationally designed complex-disrupting mutations in both ACBD3 and PI4KIIIβ completely abrogated the sensitization of 3A activation by ACBD3.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Erik H Ottosen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada.
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