1
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Narkhede Y, Saxena R, Sharma T, Conarty JP, Ramirez VT, Motsa BB, Amiar S, Li S, Chapagain PP, Wiest O, Stahelin RV. Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Sci 2024; 33:e4978. [PMID: 38591637 PMCID: PMC11002992 DOI: 10.1002/pro.4978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/01/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
The Ebola virus (EBOV) is a lipid-enveloped virus with a negative sense RNA genome that can cause severe and often fatal viral hemorrhagic fever. The assembly and budding of EBOV is regulated by the matrix protein, VP40, which is a peripheral protein that associates with anionic lipids at the inner leaflet of the plasma membrane. VP40 is sufficient to form virus-like particles (VLPs) from cells, which are nearly indistinguishable from authentic virions. Due to the restrictions of studying EBOV in BSL-4 facilities, VP40 has served as a surrogate in cellular studies to examine the EBOV assembly and budding process from the host cell plasma membrane. VP40 is a dimer where inhibition of dimer formation halts budding and formation of new VLPs as well as VP40 localization to the plasma membrane inner leaflet. To better understand VP40 dimer stability and critical amino acids to VP40 dimer formation, we integrated computational approaches with experimental validation. Site saturation/alanine scanning calculation, combined with molecular mechanics-based generalized Born with Poisson-Boltzmann surface area (MM-GB/PBSA) method and molecular dynamics simulations were used to predict the energetic contribution of amino acids to VP40 dimer stability and the hydrogen bonding network across the dimer interface. These studies revealed several previously unknown interactions and critical residues predicted to impact VP40 dimer formation. In vitro and cellular studies were then pursued for a subset of VP40 mutations demonstrating reduction in dimer formation (in vitro) or plasma membrane localization (in cells). Together, the computational and experimental approaches revealed critical residues for VP40 dimer stability in an alpha-helical interface (between residues 106-117) as well as in a loop region (between residues 52-61) below this alpha-helical region. This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability.
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Affiliation(s)
- Yogesh Narkhede
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Roopashi Saxena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Tej Sharma
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | - Jacob P. Conarty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Valentina Toro Ramirez
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
- Pharmaceutical ChemistryUniversidad CESMedellínColombia
| | - Balindile B. Motsa
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Souad Amiar
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Sheng Li
- Department of MedicineUniversity of CaliforniaSan DiegoCaliforniaUSA
| | - Prem P. Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences Institute, Florida International UniversityMiamiFloridaUSA
| | - Olaf Wiest
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Robert V. Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
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2
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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1213-1222. [PMID: 38174900 PMCID: PMC10843815 DOI: 10.1021/acs.langmuir.3c02609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of significant interest because it impacts an organism's response to a nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. A residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Lysine methylation experiments reveal subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX rates become slower overall in the presence of PSNPs. However, some regions of the R2ab protein exhibit faster than average exchange rates in the presence of PSNPs, while others are slower than the average behavior, suggesting conformational changes upon binding. HDX rates and methylation ratios support a recently proposed "adsorbotope" model for PSNPs, wherein adsorbed proteins consist of unfolded anchor points interspersed with partially structured regions. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how R2ab adsorbs onto PSNP surfaces, this research emphasizes the need for advanced methods to comprehend residue-level interactions in the nanoparticle corona.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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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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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.554951. [PMID: 37693402 PMCID: PMC10491123 DOI: 10.1101/2023.08.28.554951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of high interest because it impacts the organism's response to the nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. Ultimately, a residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Through lysine methylation, we observe subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX measurements reveal that certain regions of the R2ab protein undergo faster exchange rates in the presence of PSNPs, suggesting conformational changes upon binding. Both results support a recently proposed "adsorbotope" model, wherein adsorbed proteins consist of unfolded anchor points interspersed with regions of partial structure. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how proteins respond to nanoparticle surfaces, this research emphasizes the need for advanced methods to comprehend these intricate interactions fully at the residue level.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
| | | | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
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5
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Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochem Soc Trans 2022; 50:1607-1617. [DOI: 10.1042/bst20220206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022]
Abstract
A large amount of the human proteome is composed of highly dynamic regions that do not adopt a single static conformation. These regions are defined as intrinsically disordered, and they are found in a third of all eukaryotic proteins. They play instrumental roles in many aspects of protein signaling, but can be challenging to characterize by biophysical methods. Intriguingly, many of these regions can adopt stable secondary structure upon interaction with a variety of binding partners, including proteins, lipids, and ligands. This review will discuss the application of Hydrogen-deuterium exchange mass spectrometry (HDX-MS) as a powerful biophysical tool that is particularly well suited for structural and functional characterization of intrinsically disordered regions in proteins. A focus will be on the theory of hydrogen exchange, and its practical application to identify disordered regions, as well as characterize how they participate in protein–protein and protein–membrane interfaces. A particular emphasis will be on how HDX-MS data can be presented specifically tailored for analysis of intrinsically disordered regions, as well as the technical aspects that are critical to consider when designing HDX-MS experiments for proteins containing intrinsically disordered regions.
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6
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Sheetz JB, Lemmon MA, Tsutsui Y. Dynamics of protein kinases and pseudokinases by HDX-MS. Methods Enzymol 2022; 667:303-338. [PMID: 35525545 PMCID: PMC9148214 DOI: 10.1016/bs.mie.2022.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dynamics of the protein kinase fold are deeply intertwined with its structure. The past three decades of kinase biophysical studies revealed key dynamic features of the kinase domain and, more recently, how these features may endow catalytically impaired kinases-or pseudokinases-with signaling properties. Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is proving to be a valuable approach for studies of kinase and pseudokinase domain dynamics. Here, we briefly discuss the methods that have provided insights into protein kinase dynamics, describe how HDX-MS is being used to answer questions in the kinase/pseudokinase field, and provide a detailed protocol for collecting an HDX-MS dataset to study the impacts of small molecule binding to a pseudokinase domain. As more small molecules are discovered that can disrupt pseudokinase conformations, HDX-MS is likely to be a powerful approach for exploring drug-induced changes in pseudokinase dynamics and structure.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States
| | - Mark A Lemmon
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
| | - Yuko Tsutsui
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
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7
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Wang Y, Tortorella M. Molecular design of dual inhibitors of PI3K and potential molecular target of cancer for its treatment: A review. Eur J Med Chem 2022; 228:114039. [PMID: 34894440 DOI: 10.1016/j.ejmech.2021.114039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022]
Abstract
Aberrant activation of the phosphoinositide 3-kinase (PI3K) signaling network is a key event in many human cancers and therefore enormous efforts have been made in the development of PI3K inhibitors. However, due to intrinsic and acquired resistance as well as poor drug tolerance, limited therapeutic efficacy has been achieved with these agents. In view of the fact that PI3K inhibitors can show synergistic antitumor effects with other cancer agents, namely mammalian target of rapamycin (mTOR) inhibitors, histone deacetylase (HDAC) inhibitors and mitogen-activated protein kinase (MEK) inhibitors, dual inhibition of both targets by a single-molecule is regarded as a promising complementary or alternative therapeutic strategy to overcome the drawbacks of just PI3K monotherapy. In this review, we discuss the theoretical foundation for designing PI3K-based dual-target inhibitors and summarize the structure-activity relationships and clinical progress of these dual-binding agents.
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Affiliation(s)
- Yuanze Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, 510530, PR China.
| | - Micky Tortorella
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, 510530, PR China
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8
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Elmenier FM, Lasheen DS, Abouzid KAM. Design, synthesis, and biological evaluation of new thieno[2,3- d] pyrimidine derivatives as targeted therapy for PI3K with molecular modelling study. J Enzyme Inhib Med Chem 2021; 37:315-332. [PMID: 34955086 PMCID: PMC8725920 DOI: 10.1080/14756366.2021.2010729] [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] [Indexed: 11/15/2022] Open
Abstract
Cancer is one of the most aggressive diseases characterised by abnormal growth and uncontrolled cell division. PI3K is a lipid kinase involved in cancer progression which makes it fruitful target for cancer control. 28 new morpholine based thieno[2,3-d] pyrimidine derivatives were designed and synthesised as anti-PI3K agents maintaining the common pharmacophoric features of several potent PI3K inhibitors. Their antiproliferative activity on NCI 60 cell lines as well as their enzymatic activity against PI3K isoforms were evaluated. Three compounds revealed good cytotoxic activities against breast cancer cell lines, especially T-47D. Compound VIb exhibited the best enzymatic inhibitory activity (72% & 84% on PI3Kβ & PI3Kγ), respectively and good activity on most NCI cell lines especially those with over expressed PI3K. Docking was carried out into PI3K active site which showed comparable binding mode to that of the PI-103 inhibitor. Compound VIb could be optimised to serve as a new chemical entity for discovering new anticancer agents.
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Affiliation(s)
- Fatma M Elmenier
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt
| | - Deena S Lasheen
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt
| | - Khaled A M Abouzid
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt.,Faculty of Pharmacy, Department of Organic and Medicinal Chemistry, University of Sadat City, Menoufia, Egypt
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9
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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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10
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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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11
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Nguyen TT, Marzolf DR, Seffernick JT, Heinze S, Lindert S. Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR. Structure 2021; 30:313-320.e3. [PMID: 34739840 DOI: 10.1016/j.str.2021.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/04/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022]
Abstract
Hydrogen-deuterium exchange (HDX) measured by nuclear magnetic resonance (NMR) provides structural information for proteins relating to solvent accessibility and flexibility. While this structural information is beneficial, the data cannot be used exclusively to elucidate structures. However, the structural information provided by the HDX-NMR data can be supplemented by computational methods. In previous work, we developed an algorithm in Rosetta to predict structures using qualitative HDX-NMR data (categories of exchange rate). Here we expand on the effort, and utilize quantitative protection factors (PFs) from HDX-NMR for structure prediction. From observed correlations between PFs and solvent accessibility/flexibility measures, we present a scoring function to quantify the agreement with HDX data. Using a benchmark set of 10 proteins, an average improvement of 5.13 Å in root-mean-square deviation (RMSD) is observed for cases of inaccurate Rosetta predictions. Ultimately, seven out of 10 predictions are accurate without including HDX data, and nine out of 10 are accurate when using our PF-based HDX score.
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Affiliation(s)
- Tung T Nguyen
- Department of Chemistry and Biochemistry, Denison University, Granville, OH 43023, USA
| | - Daniel R Marzolf
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18(th) Avenue, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18(th) Avenue, Columbus, OH 43210, USA
| | - Sten Heinze
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18(th) Avenue, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18(th) Avenue, Columbus, OH 43210, USA.
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12
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Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021; 93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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 powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.
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Affiliation(s)
- Jochem H Smit
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Bindu Y Srinivasu
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Rinky Parakra
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
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13
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Gu W, Gao S, Wang H, Fleming KD, Hoffmann RM, Yang JW, Patel NM, Choi YM, Burke JE, Reue K, Airola MV. The middle lipin domain adopts a membrane-binding dimeric protein fold. Nat Commun 2021; 12:4718. [PMID: 34354069 PMCID: PMC8342540 DOI: 10.1038/s41467-021-24929-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
Phospholipid synthesis and fat storage as triglycerides are regulated by lipin phosphatidic acid phosphatases (PAPs), whose enzymatic PAP function requires association with cellular membranes. Using hydrogen deuterium exchange mass spectrometry, we find mouse lipin 1 binds membranes through an N-terminal amphipathic helix, the Ig-like domain and HAD phosphatase catalytic core, and a middle lipin (M-Lip) domain that is conserved in mammalian and mammalian-like lipins. Crystal structures of the M-Lip domain reveal a previously unrecognized protein fold that dimerizes. The isolated M-Lip domain binds membranes both in vitro and in cells through conserved basic and hydrophobic residues. Deletion of the M-Lip domain in lipin 1 reduces PAP activity, membrane association, and oligomerization, alters subcellular localization, diminishes acceleration of adipocyte differentiation, but does not affect transcriptional co-activation. This establishes the M-Lip domain as a dimeric protein fold that binds membranes and is critical for full functionality of mammalian lipins.
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Affiliation(s)
- Weijing Gu
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
| | - Shujuan Gao
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
| | - Huan Wang
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Kaelin D. Fleming
- grid.143640.40000 0004 1936 9465Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC Canada
| | - Reece M. Hoffmann
- grid.143640.40000 0004 1936 9465Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC Canada
| | - Jong Won Yang
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
| | - Nimi M. Patel
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
| | - Yong Mi Choi
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
| | - John E. Burke
- grid.143640.40000 0004 1936 9465Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC Canada
| | - Karen Reue
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Michael V. Airola
- grid.36425.360000 0001 2216 9681Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY USA
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14
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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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15
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A nexus of intrinsic dynamics underlies translocase priming. Structure 2021; 29:846-858.e7. [PMID: 33852897 DOI: 10.1016/j.str.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/06/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022]
Abstract
The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We show that priming exploits a nexus of intrinsic dynamics in SecA. Using atomistic simulations, smFRET, and HDX-MS, we reveal multiple dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are functionally important and conserved. Central to the nexus is a slender stem through which rotation of the preprotein clamp of SecA is biased by ATPase domain motions between open and closed clamping states. An H-bonded framework covering most of SecA enables multi-tier dynamics and conformational alterations with minimal energy input. As a result, cognate ligands select preexisting conformations and alter local dynamics to regulate catalytic activity and clamp motions. These events prime the translocase for high-affinity reception of non-folded preprotein clients. Dynamics nexuses are likely universal and essential in multi-liganded proteins.
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16
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Marzolf DR, Seffernick JT, Lindert S. Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. J Chem Theory Comput 2021; 17:2619-2629. [PMID: 33780620 DOI: 10.1021/acs.jctc.1c00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amide hydrogen-deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse for full structural characterization. Experiments that measure HDX rates, such as HDX-NMR, have far higher throughput compared to structure determination via X-ray crystallography, cryo-EM, or a full suite of NMR experiments. Data from HDX-NMR experiments encode information on the protein structure, making HDX a prime candidate to be supplemented by computational algorithms for protein structure prediction. We have developed a methodology to incorporate HDX-NMR data into ab initio protein structure prediction using the Rosetta software framework to predict structures based on experimental agreement. To demonstrate the efficacy of our algorithm, we examined 38 proteins with HDX-NMR data available, comparing the predicted model with and without the incorporation of HDX data into scoring. The root-mean-square deviation (rmsd, a measure of the average atomic distance between superimposed models) of the predicted model improved by 1.42 Å on average after incorporating the HDX-NMR data into scoring. The average rmsd improvement for the proteins where the selected model rmsd changed after incorporating HDX data was 3.63 Å, including one improvement of more than 11 Å and seven proteins improving by greater than 4 Å, with 12/15 proteins improving overall. Additionally, for independent verification, two proteins that were not part of the original benchmark were scored including HDX data, with a dramatic improvement of the selected model rmsd of nearly 9 Å for one of the proteins. Moreover, we have developed a confidence metric allowing us to successfully identify near-native models in the absence of a native structure. Improvement in model selection with a strong confidence measure demonstrates that protein structure prediction with HDX-NMR is a powerful tool which can be performed with minimal additional computational strain and expense.
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Affiliation(s)
- Daniel R Marzolf
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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17
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Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. Nat Commun 2020; 11:6162. [PMID: 33268777 PMCID: PMC7710758 DOI: 10.1038/s41467-020-20032-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Proton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport. XylE is a bacterial xylose transporter and homologue of human glucose transporters GLUTs 1-4. HDX-MS, mutagenesis and MD simulations suggest that protonation of a conserved aspartate triggers conformational transition from outward- to inward facing state only in the presence of substrate xylose. In contrast, inhibitor glucose locks the transporter in the outward facing state.
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18
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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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19
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Dobbs JM, Jenkins ML, Burke JE. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2202-2209. [PMID: 32869988 DOI: 10.1021/jasms.0c00283] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filtering of nonspecifically binding contaminant proteins from affinity purification mass spectrometry (AP-MS) data is a well-established strategy to improve statistical confidence in identified proteins. The CRAPome (contaminant repository for affinity purification) describes the contaminating background content present in many purification strategies. However, full contaminant lists for nickel-nitrilotriacetic acid (NiNTA) and glutathione S-transferase (GST) affinity matrices are lacking. Similarly, no Spodoptera frugiperda (Sf9) contaminants are available, and only the FLAG-purified contaminants are described for Escherichia coli. For MS experiments that use recombinant protein, such as structural mass spectrometry experiments (hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking, and radical foot-printing), failing to include these contaminants in the search database during the initial tandem MS (MS/MS) identification stage can result in complications in peptide identification. We have created contaminant FASTA databases for Sf9 and E. coli NiNTA or GST purification strategies and show that the use of these databases can effectively improve HDX-MS protein coverage, fragment count, and confidence in peptide identification. This approach provides a robust strategy toward the design of contaminant databases for any purification approach that will expand the complexity of systems able to be interrogated by HDX-MS.
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Affiliation(s)
- Joseph M Dobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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20
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Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
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Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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21
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McPhail JA, Lyoo H, Pemberton JG, Hoffmann RM, van Elst W, Strating JRPM, Jenkins ML, Stariha JTB, Powell CJ, Boulanger MJ, Balla T, van Kuppeveld FJM, Burke JE. Characterization of the c10orf76-PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication. EMBO Rep 2020; 21:e48441. [PMID: 31829496 PMCID: PMC7001497 DOI: 10.15252/embr.201948441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/25/2019] [Accepted: 11/11/2019] [Indexed: 11/09/2022] Open
Abstract
The lipid kinase PI4KB, which generates phosphatidylinositol 4-phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi and is essential for the viral replication of specific enteroviruses. We used hydrogen-deuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complex-disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76-dependent enteroviruses. Intriguingly, c10orf76 also contributed to proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Heyrhyoung Lyoo
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Joshua G Pemberton
- Section on Molecular Signal TransductionEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMDUSA
| | - Reece M Hoffmann
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Wendy van Elst
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Jeroen RPM Strating
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Meredith L Jenkins
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Jordan TB Stariha
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Cameron J Powell
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Martin J Boulanger
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
| | - Tamas Balla
- Section on Molecular Signal TransductionEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMDUSA
| | - Frank JM van Kuppeveld
- Department of Infectious Diseases & ImmunologyVirology DivisionFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - John E Burke
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
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22
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Defining How Oncogenic and Developmental Mutations of PIK3R1 Alter the Regulation of Class IA Phosphoinositide 3-Kinases. Structure 2019; 28:145-156.e5. [PMID: 31831213 DOI: 10.1016/j.str.2019.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022]
Abstract
The class I phosphoinositide 3-kinases (PI3Ks) are key signaling enzymes composed of a heterodimer of a p110 catalytic subunit and a p85 regulatory subunit, with PI3K mutations being causative of multiple human diseases including cancer, primary immunodeficiencies, and developmental disorders. Mutations in the p85α regulatory subunit encoded by PIK3R1 can both activate PI3K through oncogenic truncations in the iSH2 domain, or inhibit PI3K through developmental disorder mutations in the cSH2 domain. Using a combined biochemical and hydrogen deuterium exchange mass spectrometry approach we have defined the molecular basis for how these mutations alter the activity of p110α/p110δ catalytic subunits. We find that the oncogenic Q572∗ truncation of PIK3R1 disrupts all p85-inhibitory inputs, with p110α being hyper-activated compared with p110δ. In addition, we find that the R649W mutation in the cSH2 of PIK3R1 decreases sensitivity to activation by receptor tyrosine kinases. This work reveals unique insight into isoform-specific regulation of p110s by p85α.
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23
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Phosphatidylinositol 3 kinase (PI3K) inhibitors as new weapon to combat cancer. Eur J Med Chem 2019; 183:111718. [DOI: 10.1016/j.ejmech.2019.111718] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
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24
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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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25
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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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26
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Abstract
Since I started doing scientific research, I've been fascinated by the interplay of protein structure and dynamics and how they together mediate protein function. A particular area of interest has been in understanding the mechanistic basis of how lipid-signaling enzymes function on membrane surfaces. In this award lecture article, I will describe my laboratory's studies on the structure and dynamics of lipid-signaling enzymes on membrane surfaces. This is important, as many lipid-signaling enzymes are regulated through dynamic regulatory mechanisms that control their enzymatic activity. This article will discuss my continued enthusiasm in using a synergistic application of hydrogen-deuterium exchange MS (HDX-MS) with other structural biology techniques to probe the mechanistic basis for how membrane-localized signaling enzymes are regulated and how these approaches can be used to understand how they are misregulated in disease. I will discuss specific examples of how we have used HDX-MS to study phosphoinositide kinases and the protein kinase Akt. An important focus will be on a description of how HDX-MS can be used as a powerful tool to optimize the design of constructs for X-ray crystallography and EM. The use of a diverse toolbox of biophysical methods has revealed novel insight into the complex and varied regulatory networks that control the function of lipid-signaling enzymes and enabled unique insight into the mechanics of membrane recruitment.
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Affiliation(s)
- John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
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27
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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28
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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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29
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Dornan GL, Dalwadi U, Hamelin DJ, Hoffmann RM, Yip CK, Burke JE. Probing the Architecture, Dynamics, and Inhibition of the PI4KIIIα/TTC7/FAM126 Complex. J Mol Biol 2018; 430:3129-3142. [PMID: 30031006 DOI: 10.1016/j.jmb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα) is the lipid kinase primarily responsible for generating the lipid phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, which acts as the substrate for generation of the signaling lipids PIP2 and PIP3. PI4KIIIα forms a large heterotrimeric complex with two regulatory partners, TTC7 and FAM126. We describe using an integrated electron microscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) approach to probe the architecture and dynamics of the complex of PI4KIIIα/TTC7/FAM126. HDX-MS reveals that the majority of the PI4KIIIα sequence was protected from exchange in short deuterium pulse experiments, suggesting presence of secondary structure, even in putative unstructured regions. Negative stain electron microscopy reveals the shape and architecture of the full-length complex, revealing an overall dimer of PI4KIIIα/TTC7/FAM126 trimers. HDX-MS reveals conformational changes in the TTC7/FAM126 complex upon binding PI4KIIIα, including both at the direct TTC7-PI4KIIIα interface and at the putative membrane binding surface. Finally, HDX-MS experiments of PI4KIIIα bound to the highly potent and selective inhibitor GSK-A1 compared to that bound to the non-specific inhibitor PIK93 revealed substantial conformational changes throughout an extended region of the kinase domain. Many of these changes were distant from the putative inhibitor binding site, showing a large degree of allosteric conformational changes that occur upon inhibitor binding. Overall, our results reveal novel insight into the regulation of PI4KIIIα by its regulatory proteins TTC7/FAM126, as well as additional dynamic information on how selective inhibition of PI4KIIIα is achieved.
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Affiliation(s)
- Gillian L Dornan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2.
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Wang H, Lo WT, Vujičić Žagar A, Gulluni F, Lehmann M, Scapozza L, Haucke V, Vadas O. Autoregulation of Class II Alpha PI3K Activity by Its Lipid-Binding PX-C2 Domain Module. Mol Cell 2018; 71:343-351.e4. [DOI: 10.1016/j.molcel.2018.06.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/14/2018] [Accepted: 06/27/2018] [Indexed: 11/30/2022]
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Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS Synth Biol 2018; 7:1152-1162. [PMID: 29609459 DOI: 10.1021/acssynbio.8b00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.
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Affiliation(s)
- Christine E. Kaiser
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Juan Pablo Rincon Pabon
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - M. Paola Castaldi
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Structure and Biophysics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - David D. Weis
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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Dornan GL, Burke JE. Molecular Mechanisms of Human Disease Mediated by Oncogenic and Primary Immunodeficiency Mutations in Class IA Phosphoinositide 3-Kinases. Front Immunol 2018; 9:575. [PMID: 29616047 PMCID: PMC5868324 DOI: 10.3389/fimmu.2018.00575] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022] Open
Abstract
The signaling lipid phosphatidylinositol 3,4,5, trisphosphate (PIP3) is an essential mediator of many vital cellular processes, including growth, survival, and metabolism. PIP3 is generated through the action of the class I phosphoinositide 3-kinases (PI3K), and their activity is tightly controlled through interactions with regulatory proteins and activating stimuli. The class IA PI3Ks are composed of three distinct p110 catalytic subunits (p110α, p110β, and p110δ), and they play different roles in specific tissues due to disparities in both expression and engagement downstream of cell-surface receptors. Disruption of PI3K regulation is a frequent driver of numerous human diseases. Activating mutations in the PIK3CA gene encoding the p110α catalytic subunit of class IA PI3K are frequently mutated in several cancer types, and mutations in the PIK3CD gene encoding the p110δ catalytic subunit have been identified in primary immunodeficiency patients. All class IA p110 subunits interact with p85 regulatory subunits, and mutations/deletions in different p85 regulatory subunits have been identified in both cancer and primary immunodeficiencies. In this review, we will summarize our current understanding for the molecular basis of how class IA PI3K catalytic activity is regulated by p85 regulatory subunits, and how activating mutations in the PI3K catalytic subunits PIK3CA and PIK3CD (p110α, p110δ) and regulatory subunits PIK3R1 (p85α) mediate PI3K activation and human disease.
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Affiliation(s)
- Gillian L Dornan
- 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
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34
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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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Pulkoski-Gross MJ, Jenkins ML, Truman JP, Salama MF, Clarke CJ, Burke JE, Hannun YA, Obeid LM. An intrinsic lipid-binding interface controls sphingosine kinase 1 function. J Lipid Res 2018; 59:462-474. [PMID: 29326159 DOI: 10.1194/jlr.m081307] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/04/2018] [Indexed: 12/15/2022] Open
Abstract
Sphingosine kinase 1 (SK1) is required for production of sphingosine-1-phosphate (S1P) and thereby regulates many cellular processes, including cellular growth, immune cell trafficking, and inflammation. To produce S1P, SK1 must access sphingosine directly from membranes. However, the molecular mechanisms underlying SK1's direct membrane interactions remain unclear. We used hydrogen/deuterium exchange MS to study interactions of SK1 with membrane vesicles. Using the CRISPR/Cas9 technique to generate HCT116 cells lacking SK1, we explored the effects of membrane interface disruption and the function of the SK1 interaction site. Disrupting the interface resulted in reduced membrane association and decreased cellular SK1 activity. Moreover, SK1-dependent signaling, including cell invasion and endocytosis, was abolished upon mutation of the membrane-binding interface. Of note, we identified a positively charged motif on SK1 that is responsible for electrostatic interactions with membranes. Furthermore, we demonstrated that SK1 uses a single contiguous interface, consisting of an electrostatic site and a hydrophobic site, to interact with membrane-associated anionic phospholipids. Altogether, these results define a composite domain in SK1 that regulates its intrinsic ability to bind membranes and indicate that this binding is critical for proper SK1 function. This work will allow for a new line of thinking for targeting SK1 in disease.
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Affiliation(s)
- Michael J Pulkoski-Gross
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11790.,Department of Medicine and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11790
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8N 1A1, Canada
| | - Jean-Philip Truman
- Department of Medicine and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11790
| | - Mohamed F Salama
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35511, Egypt
| | - Christopher J Clarke
- Department of Medicine and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11790
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8N 1A1, Canada
| | - Yusuf A Hannun
- Department of Medicine and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11790
| | - Lina M Obeid
- Department of Medicine and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11790 .,Northport Veterans Affairs Medical Center, Northport, NY 11768
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Chandra B, Maity BK, Das A, Maiti S. Fluorescence quenching by lipid encased nanoparticles shows that amyloid-β has a preferred orientation in the membrane. Chem Commun (Camb) 2018; 54:7750-7753. [DOI: 10.1039/c8cc02108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Short range plasmonic fields around a nanoparticle can modulate fluorescence or Raman processes.
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Affiliation(s)
| | | | - Anirban Das
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
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Gentile DR, Rathinaswamy MK, Jenkins ML, Moss SM, Siempelkamp BD, Renslo AR, Burke JE, Shokat KM. Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. Cell Chem Biol 2017; 24:1455-1466.e14. [PMID: 29033317 PMCID: PMC5915340 DOI: 10.1016/j.chembiol.2017.08.025] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 12/31/2022]
Abstract
Covalent inhibitors of K-Ras(G12C) have been reported that exclusively recognize the GDP state. Here, we utilize disulfide tethering of a non-natural cysteine (K-Ras(M72C)) to identify a new switch-II pocket (S-IIP) binding ligand (2C07) that engages the active GTP state. Co-crystal structures of 2C07 bound to H-Ras(M72C) reveal binding in a cryptic groove we term S-IIG. In the GppNHp state, 2C07 binding to a modified S-IIP pushes switch I away from the nucleotide, breaking the network of polar contacts essential for adopting the canonical GTP state. Biochemical studies show that 2C07 alters nucleotide preference and inhibits SOS binding and catalyzed nucleotide exchange. 2C07 was converted to irreversible covalent analogs, which target both nucleotide states, inhibit PI3K activation in vitro, and function as occupancy probes to detect reversible engagement in competition assays. Targeting both nucleotide states opens the possibility of inhibiting oncogenic mutants of Ras, which exist predominantly in the GTP state in cells.
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Affiliation(s)
- Daniel R Gentile
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Braden D Siempelkamp
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Adam R Renslo
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - 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, CA 94158, USA.
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Lo WT, Vujičić Žagar A, Gerth F, Lehmann M, Puchkov D, Krylova O, Freund C, Scapozza L, Vadas O, Haucke V. A Coincidence Detection Mechanism Controls PX-BAR Domain-Mediated Endocytic Membrane Remodeling via an Allosteric Structural Switch. Dev Cell 2017; 43:522-529.e4. [PMID: 29161595 DOI: 10.1016/j.devcel.2017.10.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/14/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Clathrin-mediated endocytosis occurs by bending and remodeling of the membrane underneath the coat. Bin-amphiphysin-rvs (BAR) domain proteins are crucial for endocytic membrane remodeling, but how their activity is spatiotemporally controlled is largely unknown. We demonstrate that the membrane remodeling activity of sorting nexin 9 (SNX9), a late-acting endocytic PX-BAR domain protein required for constriction of U-shaped endocytic intermediates, is controlled by an allosteric structural switch involving coincident detection of the clathrin adaptor AP2 and phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) at endocytic sites. Structural, biochemical, and cell biological data show that SNX9 is autoinhibited in solution. Binding to PI(3,4)P2 via its PX-BAR domain, and concomitant association with AP2 via sequences in the linker region, releases SNX9 autoinhibitory contacts to enable membrane constriction. Our results reveal a mechanism for restricting the latent membrane remodeling activity of BAR domain proteins to allow spatiotemporal coupling of membrane constriction to the progression of the endocytic pathway.
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Affiliation(s)
- Wen-Ting Lo
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | | | - Fabian Gerth
- Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dymtro Puchkov
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Oxana Krylova
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Leonardo Scapozza
- University of Geneva, Section of Pharmaceutical Sciences, 1206 Geneva, Switzerland
| | - Oscar Vadas
- University of Geneva, Section of Pharmaceutical Sciences, 1206 Geneva, Switzerland.
| | - Volker Haucke
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany.
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Masson GR, Jenkins ML, Burke JE. An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery. Expert Opin Drug Discov 2017; 12:981-994. [PMID: 28770632 DOI: 10.1080/17460441.2017.1363734] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered: This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions. Expert opinion: HDX-MS has been widely accepted within the pharmaceutical industry for the characterization of bio-therapeutics as well as in the mapping of antibody drug epitopes. However, there is room for this technique to be more widely used in the drug discovery process. This is particularly true in the use of HDX-MS as a complement to other high-resolution structural approaches, as well as in the development of small molecule therapeutics that can target both active-site and allosteric binding sites.
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Affiliation(s)
- Glenn R Masson
- a Protein and Nucleic Acid Chemistry Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Meredith L Jenkins
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
| | - John E Burke
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
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40
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Design and purification of active truncated phosphoinositide 3-kinase gamma protein constructs for structural studies. Protein Expr Purif 2017; 135:1-7. [DOI: 10.1016/j.pep.2017.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 11/19/2022]
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Siempelkamp BD, Rathinaswamy MK, Jenkins ML, Burke JE. Molecular mechanism of activation of class IA phosphoinositide 3-kinases (PI3Ks) by membrane-localized HRas. J Biol Chem 2017; 292:12256-12266. [PMID: 28515318 DOI: 10.1074/jbc.m117.789263] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Class IA PI3Ks are involved in the generation of the key lipid signaling molecule phosphatidylinositol 3,4,5-trisphosphate (PIP3), and inappropriate activation of this pathway is implicated in a multitude of human diseases, including cancer, inflammation, and primary immunodeficiencies. Class IA PI3Ks are activated downstream of the Ras superfamily of GTPases, and Ras-PI3K interaction plays a key role in promoting tumor formation and maintenance in Ras-driven tumors. Investigating the detailed molecular events in the Ras-PI3K interaction has been challenging because it occurs on a membrane surface. Here, using maleimide-functionalized lipid vesicles, we successfully generated membrane-resident HRas and evaluated its effect on PI3K signaling in lipid kinase assays and through analysis with hydrogen-deuterium exchange MS. We screened all class IA PI3K isoforms and found that HRas activates both p110α and p110δ isoforms but does not activate p110β. The p110α and p110δ activation by Ras was synergistic with activation by a soluble phosphopeptide derived from receptor tyrosine kinases. Hydrogen-deuterium exchange MS revealed that membrane-resident HRas, but not soluble HRas, enhances conformational changes associated with membrane binding by increasing membrane recruitment of both p110α and p110δ. Together, these results afford detailed molecular insight into the Ras-PI3K signaling complex, provide a framework for screening Ras inhibitors, and shed light on the isoform specificity of Ras-PI3K interactions in a native membrane context.
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Affiliation(s)
- Braden D Siempelkamp
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada.
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42
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Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry. Biochem J 2017; 474:1867-1877. [PMID: 28381646 PMCID: PMC5544108 DOI: 10.1042/bcj20170127] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/22/2022]
Abstract
Until recently, one of the major limitations of hydrogen/deuterium exchange mass spectrometry (HDX-MS) was the peptide-level resolution afforded by proteolytic digestion. This limitation can be selectively overcome through the use of electron-transfer dissociation to fragment peptides in a manner that allows the retention of the deuterium signal to produce hydrogen/deuterium exchange tandem mass spectrometry (HDX-MS/MS). Here, we describe the application of HDX-MS/MS to structurally screen inhibitors of the oncogene phosphoinositide 3-kinase catalytic p110α subunit. HDX-MS/MS analysis is able to discern a conserved mechanism of inhibition common to a range of inhibitors. Owing to the relatively minor amounts of protein required, this technique may be utilised in pharmaceutical development for screening potential therapeutics.
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43
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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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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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Vadas O, Jenkins ML, Dornan GL, Burke JE. Using Hydrogen-Deuterium Exchange Mass Spectrometry to Examine Protein-Membrane Interactions. Methods Enzymol 2016; 583:143-172. [PMID: 28063489 DOI: 10.1016/bs.mie.2016.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS experiments measure protein conformational dynamics in their native state, based on the rate of exchange of amide hydrogens with solvent. This review discusses the use of HDX-MS as a tool to identify the interfaces of proteins with membranes and membrane-associated proteins, as well as define conformational changes elicited by membrane recruitment. Specific examples will focus on the use of HDX-MS to examine how large macromolecular protein complexes are recruited and activated on membranes, and how both posttranslational modifications and cancer-linked oncogenic mutations affect these processes.
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Affiliation(s)
- O Vadas
- Pharmaceutical Sciences Section, University of Geneva, Geneva, Switzerland
| | | | - G L Dornan
- University of Victoria, Victoria BC, Canada
| | - J E Burke
- University of Victoria, Victoria BC, Canada.
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Ohashi Y, Soler N, García Ortegón M, Zhang L, Kirsten ML, Perisic O, Masson GR, Burke JE, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL. Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex. Autophagy 2016; 12:2129-2144. [PMID: 27630019 PMCID: PMC5103362 DOI: 10.1080/15548627.2016.1226736] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.
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Affiliation(s)
- Yohei Ohashi
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Nicolas Soler
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | | | - Lufei Zhang
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Marie L Kirsten
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Olga Perisic
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Glenn R Masson
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - John E Burke
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Arjen J Jakobi
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany.,c European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | | | | | - Maki Ohashi
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | | | - Carsten Sachse
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Roger L Williams
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
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Harrison RA, Engen JR. Conformational insight into multi-protein signaling assemblies by hydrogen-deuterium exchange mass spectrometry. Curr Opin Struct Biol 2016; 41:187-193. [PMID: 27552080 DOI: 10.1016/j.sbi.2016.08.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/08/2016] [Accepted: 08/08/2016] [Indexed: 01/14/2023]
Abstract
Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide information about proteins that can be challenging to obtain by other means. Structure/function relationships, binding interactions, and the effects of modification have all been measured with HDX MS for a diverse and growing array of signaling proteins and multiprotein signaling complexes. As a result of hardware and software improvements, receptors and complexes involved in cellular signaling-including those associated with membranes-can now be studied. The growing body of HDX MS studies of signaling complexes at membranes is particularly exciting. Recent examples are presented to illustrate what can be learned about signaling proteins with this technique.
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Affiliation(s)
- Rane A Harrison
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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