1
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Kellogg GE. Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins. Molecules 2024; 29:2838. [PMID: 38930903 PMCID: PMC11207109 DOI: 10.3390/molecules29122838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
A method is described to deconstruct the network of hydropathic interactions within and between a protein's sidechain and its environment into residue-based three-dimensional maps. These maps encode favorable and unfavorable hydrophobic and polar interactions, in terms of spatial positions for optimal interactions, relative interaction strength, as well as character. In addition, these maps are backbone angle-dependent. After map calculation and clustering, a finite number of unique residue sidechain interaction maps exist for each backbone conformation, with the number related to the residue's size and interaction complexity. Structures for soluble proteins (~749,000 residues) and membrane proteins (~387,000 residues) were analyzed, with the latter group being subdivided into three subsets related to the residue's position in the membrane protein: soluble domain, core-facing transmembrane domain, and lipid-facing transmembrane domain. This work suggests that maps representing residue types and their backbone conformation can be reassembled to optimize the medium-to-high resolution details of a protein structure. In particular, the information encoded in maps constructed from the lipid-facing transmembrane residues appears to paint a clear picture of the protein-lipid interactions that are difficult to obtain experimentally.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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2
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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3
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Belghit H, Spivak M, Dauchez M, Baaden M, Jonquet-Prevoteau J. From complex data to clear insights: visualizing molecular dynamics trajectories. FRONTIERS IN BIOINFORMATICS 2024; 4:1356659. [PMID: 38665177 PMCID: PMC11043564 DOI: 10.3389/fbinf.2024.1356659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
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Affiliation(s)
- Hayet Belghit
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Mariano Spivak
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Marc Baaden
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
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4
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Shorthouse D, Zhuang L, Rahrmann EP, Kosmidou C, Wickham Rahrmann K, Hall M, Greenwood B, Devonshire G, Gilbertson RJ, Fitzgerald RC, Hall BA. KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas. Life Sci Alliance 2023; 6:e202302124. [PMID: 37748809 PMCID: PMC10520261 DOI: 10.26508/lsa.202302124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023] Open
Abstract
Voltage-sensitive potassium channels play an important role in controlling membrane potential and ionic homeostasis in the gut and have been implicated in gastrointestinal (GI) cancers. Through large-scale analysis of 897 patients with gastro-oesophageal adenocarcinomas (GOAs) coupled with in vitro models, we find KCNQ family genes are mutated in ∼30% of patients, and play therapeutically targetable roles in GOA cancer growth. KCNQ1 and KCNQ3 mediate the WNT pathway and MYC to increase proliferation through resultant effects on cadherin junctions. This also highlights novel roles of KCNQ3 in non-excitable tissues. We also discover that activity of KCNQ3 sensitises cancer cells to existing potassium channel inhibitors and that inhibition of KCNQ activity reduces proliferation of GOA cancer cells. These findings reveal a novel and exploitable role of potassium channels in the advancement of human cancer, and highlight that supplemental treatments for GOAs may exist through KCNQ inhibitors.
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Affiliation(s)
- David Shorthouse
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
| | - Lizhe Zhuang
- Institute for Early Detection, CRUK Cambridge Centre, Cambridge, UK
| | - Eric P Rahrmann
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | | | - Michael Hall
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Benedict Greenwood
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Benjamin A Hall
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
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5
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Zhang Y, Zhou J, Ni X, Wang Q, Jia Y, Xu X, Wu H, Fu P, Wen H, Guo Y, Yang G. Structural basis for the activity regulation of Salt Overly Sensitive 1 in Arabidopsis salt tolerance. NATURE PLANTS 2023; 9:1915-1923. [PMID: 37884652 DOI: 10.1038/s41477-023-01550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
The plasma membrane Na+/H+ exchanger Salt Overly Sensitive 1 (SOS1) is crucial for plant salt tolerance. Unlike typical sodium/proton exchangers, SOS1 contains a large cytoplasmic domain (CPD) that regulates Na+/H+ exchange activity. However, the underlying modulation mechanism remains unclear. Here we report the structures of SOS1 from Arabidopsis thaliana in two conformations, primarily differing in CPD flexibility. The CPD comprises an interfacial domain, a cyclic nucleotide-binding domain-like domain (CNBD-like domain) and an autoinhibition domain. Through yeast cell-based Na+ tolerance test, we reveal the regulatory role of the interfacial domain and the activation role of the CNBD-like domain. The CPD forms a negatively charged cavity that is connected to the ion binding site. The transport of Na+ may be coupled with the conformational change of CPD. These findings provide structural and functional insight into SOS1 activity regulation.
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Affiliation(s)
- Yanming Zhang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiaqi Zhou
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuping Ni
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | | | - Yutian Jia
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xia Xu
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haoyang Wu
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Peng Fu
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Han Wen
- DP Technology, Beijing, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guanghui Yang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
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6
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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7
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Ansell TB, Corey RA, Viti LV, Kinnebrew M, Rohatgi R, Siebold C, Sansom MS. The energetics and ion coupling of cholesterol transport through Patched1. SCIENCE ADVANCES 2023; 9:eadh1609. [PMID: 37611095 PMCID: PMC10446486 DOI: 10.1126/sciadv.adh1609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
Patched1 (PTCH1) is a tumor suppressor protein of the mammalian Hedgehog (HH) signaling pathway, implicated in embryogenesis and tissue homeostasis. PTCH1 inhibits the G protein-coupled receptor Smoothened (SMO) via a debated mechanism involving modulating ciliary cholesterol accessibility. Using extensive molecular dynamics simulations and free energy calculations to evaluate cholesterol transport through PTCH1, we find an energetic barrier of ~15 to 20 kilojoule per mole for cholesterol export. In silico data are coupled to in vivo biochemical assays of PTCH1 mutants to probe coupling between cation binding sites, transmembrane motions, and PTCH1 activity. Using complementary simulations of Dispatched1, we find that transition between "inward-open" and solvent "occluded" states is accompanied by Na+-induced pinching of intracellular helical segments. Thus, our findings illuminate the energetics and ion coupling stoichiometries of PTCH1 transport mechanisms, whereby one to three Na+ or two to three K+ couple to cholesterol export, and provide the first molecular description of transitions between distinct transport states.
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Affiliation(s)
- T. Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robin A. Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, Bristol University, Bristol BS8 1TD, UK
| | - Lucrezia Vittoria Viti
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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8
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Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
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Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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9
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Deptuła P, Fiedoruk K, Wasilewska M, Suprewicz Ł, Cieśluk M, Żeliszewska P, Oćwieja M, Adamczyk Z, Pogoda K, Bucki R. Physicochemical Nature of SARS-CoV-2 Spike Protein Binding to Human Vimentin. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37413693 PMCID: PMC10360031 DOI: 10.1021/acsami.3c03347] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Vimentin, a protein that builds part of the cytoskeleton and is involved in many aspects of cellular function, was recently identified as a cell surface attachment site for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The present study investigated the physicochemical nature of the binding between the SARS-CoV-2 S1 glycoprotein receptor binding domain (S1 RBD) and human vimentin using atomic force microscopy and a quartz crystal microbalance. The molecular interactions of S1 RBD and vimentin proteins were quantified using vimentin monolayers attached to the cleaved mica or a gold microbalance sensor as well as in its native extracellular form present on the live cell surface. The presence of specific interactions between vimentin and S1 RBD was also confirmed using in silico studies. This work provides new evidence that cell-surface vimentin (CSV) functions as a site for SARS-CoV-2 virus attachment and is involved in the pathogenesis of Covid-19, providing a potential target for therapeutic countermeasures.
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Affiliation(s)
- Piotr Deptuła
- Independent Laboratory of Nanomedicine, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Monika Wasilewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Mateusz Cieśluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Paulina Żeliszewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Magdalena Oćwieja
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Zbigniew Adamczyk
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
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10
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Kobayashi K, Kawakami K, Kusakizako T, Tomita A, Nishimura M, Sawada K, Okamoto HH, Hiratsuka S, Nakamura G, Kuwabara R, Noda H, Muramatsu H, Shimizu M, Taguchi T, Inoue A, Murata T, Nureki O. Class B1 GPCR activation by an intracellular agonist. Nature 2023; 618:1085-1093. [PMID: 37286611 PMCID: PMC10307627 DOI: 10.1038/s41586-023-06169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the activation of intracellular transducers, G proteins and β-arrestins. Because these signals often induce adverse effects, the selective activation mechanism for each transducer must be elucidated. Thus, many orthosteric-biased agonists have been developed, and intracellular-biased agonists have recently attracted broad interest. These agonists bind within the receptor intracellular cavity and preferentially tune the specific signalling pathway over other signalling pathways, without allosteric rearrangement of the receptor from the extracellular side1-3. However, only antagonist-bound structures are currently available1,4-6, and there is no evidence to support that biased agonist binding occurs within the intracellular cavity. This limits the comprehension of intracellular-biased agonism and potential drug development. Here we report the cryogenic electron microscopy structure of a complex of Gs and the human parathyroid hormone type 1 receptor (PTH1R) bound to a PTH1R agonist, PCO371. PCO371 binds within an intracellular pocket of PTH1R and directly interacts with Gs. The PCO371-binding mode rearranges the intracellular region towards the active conformation without extracellularly induced allosteric signal propagation. PCO371 stabilizes the significantly outward-bent conformation of transmembrane helix 6, which facilitates binding to G proteins rather than β-arrestins. Furthermore, PCO371 binds within the highly conserved intracellular pocket, activating 7 out of the 15 class B1 GPCRs. Our study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signalling mechanism that targets the receptor-transducer interface.
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Affiliation(s)
- Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Preferred Networks, Tokyo, Japan
| | - Michihiro Nishimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sawada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suzune Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Riku Kuwabara
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hiroshi Noda
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | | | - Masaru Shimizu
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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11
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AL Mughram MH, Catalano C, Herrington NB, Safo MK, Kellogg GE. 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins. Front Mol Biosci 2023; 10:1116868. [PMID: 37056722 PMCID: PMC10086146 DOI: 10.3389/fmolb.2023.1116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.
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Affiliation(s)
- Mohammed H. AL Mughram
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Noah B. Herrington
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Glen E. Kellogg
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Glen E. Kellogg,
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12
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Lanrezac A, Baaden M. UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. MEMBRANES 2023; 13:362. [PMID: 36984749 PMCID: PMC10054542 DOI: 10.3390/membranes13030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
The insertion of proteins into membranes is crucial for understanding their function in many biological processes. In this work, we present UNILIPID, a universal implicit lipid-protein description as a methodology for dealing with implicit membranes. UNILIPID is independent of the scale of representation and can be applied at the level of all atoms, coarse-grained particles down to the level of a single bead per amino acid. We provide example implementations for these scales and demonstrate the versatility of our approach by accurately reflecting the free energy of transfer for each amino acid. In addition to single membranes, we describe the analytical implementation of double membranes and show that UNILIPID is well suited for modeling at multiple scales. We generalize to membranes of arbitrary shape. With UNILIPID, we provide a methodological framework for a simple and general parameterization tuned to reproduce a selected reference hydrophobicity scale. The software we provide along with the methodological description is optimized for specific user features such as real-time response, live visual analysis, and virtual reality experiences.
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13
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Ansell TB, Corey RA, Viti LV, Kinnebrew M, Rohatgi R, Siebold C, Sansom MSP. The Energetics and Ion Coupling of Cholesterol Transport Through Patched1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528445. [PMID: 36824746 PMCID: PMC9949057 DOI: 10.1101/2023.02.14.528445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Patched1 (PTCH1) is the principal tumour suppressor protein of the mammalian Hedgehog (HH) signalling pathway, implicated in embryogenesis and tissue homeostasis. PTCH1 inhibits the Class F G protein-coupled receptor Smoothened (SMO) via a debated mechanism involving modulating accessible cholesterol levels within ciliary membranes. Using extensive molecular dynamics (MD) simulations and free energy calculations to evaluate cholesterol transport through PTCH1, we find an energetic barrier of ~15-20 kJ mol -1 for cholesterol export. In simulations we identify cation binding sites within the PTCH1 transmembrane domain (TMD) which may provide the energetic impetus for cholesterol transport. In silico data are coupled to in vivo biochemical assays of PTCH1 mutants to probe coupling between transmembrane motions and PTCH1 activity. Using complementary simulations of Dispatched1 (DISP1) we find that transition between 'inward-open' and solvent 'occluded' states is accompanied by Na + induced pinching of intracellular helical segments. Thus, our findings illuminate the energetics and ion-coupling stoichiometries of PTCH1 transport mechanisms, whereby 1-3 Na + or 2-3 K + couple to cholesterol export, and provide the first molecular description of transitions between distinct transport states.
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Affiliation(s)
- T. Bertie Ansell
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK
| | - Robin A. Corey
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK
| | - Lucrezia Vittoria Viti
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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14
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Kang K, Wang L, Song C. ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. J Chem Inf Model 2023; 63:1058-1065. [PMID: 36693122 DOI: 10.1021/acs.jcim.2c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Solvent accessibility has been extensively used to characterize and predict the chemical properties of the surface residues of soluble proteins. However, there is not yet a widely accepted quantity of the same dimension for the study of lipid-accessible residues of membrane proteins. In this study, we propose that lipid accessibility, defined in a similar way to solvent accessibility, can be used to characterize the lipid-accessible residues of membrane proteins. Moreover, we developed a deep learning-based method, ProtRAP (Protein Relative Accessibility Predictor), to predict the relative lipid accessibility and relative solvent accessibility of residues from a given protein sequence, which can infer which residues are likely accessible to lipids, accessible to solvent, or buried in the protein interior in one run.
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Affiliation(s)
- Kai Kang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
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15
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Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023; 21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins mediate a wide spectrum of biological processes, such as signal transduction and cell communication. Due to the arduous and costly nature inherent to the experimental process, membrane proteins have long been devoid of well-resolved atomic-level tertiary structures and, consequently, the understanding of their functional roles underlying a multitude of life activities has been hampered. Currently, computational tools dedicated to furthering the structure-function understanding are primarily focused on utilizing intelligent algorithms to address a variety of site-wise prediction problems (e.g., topology and interaction sites), but are scattered across different computing sources. Moreover, the recent advent of deep learning techniques has immensely expedited the development of computational tools for membrane protein-related prediction problems. Given the growing number of applications optimized particularly by manifold deep neural networks, we herein provide a review on the current status of computational strategies mainly in membrane protein type classification, topology identification, interaction site detection, and pathogenic effect prediction. Meanwhile, we provide an overview of how the entire prediction process proceeds, including database collection, data pre-processing, feature extraction, and method selection. This review is expected to be useful for developing more extendable computational tools specific to membrane proteins.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7LD, UK
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Kai Hu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India,Corresponding authors.
| | - Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China,Corresponding authors.
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16
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Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT. Catalysts 2023. [DOI: 10.3390/catal13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The enzyme OmpT of the outer membrane of Escherichia coli shows proteolytic activity and cleaves peptides and proteins. Using molecular dynamics simulations in a fully hydrated lipid bilayer on a time scale of hundreds of nanoseconds, we draw a detailed atomic picture of substrate recognition in the OmpT-holo enzyme complex. Hydrogen bonds and salt bridges are essential for maintaining the integrity of the active site and play a central role for OmpT in recognizing its substrate. Electrostatic interactions are critical at all stages from approaching the substrate to docking at the active site. Computational alanine scanning based on the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach confirms the importance of multiple residues in the active site that form salt bridges. The substrate fluctuates along the axis of the β-barrel, which is associated with oscillations of the binding cleft formed by the residue pairs D210-H212 and D83-D85. Principal component analysis suggests that substrate and protein movements are correlated. We observe the transient presence of putative catalytic water molecules near the active site, which may be involved in the nucleophilic attack on the cleavable peptide bond of the substrate.
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17
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Butler TJ, Smith SM. Strategies for the Purification of Membrane Proteins. Methods Mol Biol 2023; 2699:477-491. [PMID: 37647009 DOI: 10.1007/978-1-0716-3362-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Membrane proteins account for approximately 30% of the coding regions of all sequenced genomes, and they play crucial roles in many fundamental cell processes. However, there are relatively few membrane proteins with known three-dimensional structures. This is likely due to technical challenges associated with membrane protein extraction, solubilization, and purification. Membrane proteins are classified based on the level of interaction with membrane lipid bilayers, with peripheral membrane proteins associating non-covalently with the membrane, and integral membrane proteins associating more strongly by means of hydrophobic interactions. Generally speaking, peripheral membrane proteins can be purified by milder techniques than integral membrane proteins, with the latter's extraction requiring phospholipid bilayer disruption using detergents or organic solvents. In this chapter, important considerations for membrane protein purification are addressed, with a focus on the initial stages of membrane protein solubilization, where problems are most frequently encountered. Protocols are outlined for the extraction of peripheral membrane proteins, solubilization of integral membrane proteins, and sample clean-up and concentration.
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Affiliation(s)
- Thomas J Butler
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sinéad Marian Smith
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin, Ireland.
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18
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Rahrmann EP, Shorthouse D, Jassim A, Hu LP, Ortiz M, Mahler-Araujo B, Vogel P, Paez-Ribes M, Fatemi A, Hannon GJ, Iyer R, Blundon JA, Lourenço FC, Kay J, Nazarian RM, Hall BA, Zakharenko SS, Winton DJ, Zhu L, Gilbertson RJ. The NALCN channel regulates metastasis and nonmalignant cell dissemination. Nat Genet 2022; 54:1827-1838. [PMID: 36175792 PMCID: PMC9729110 DOI: 10.1038/s41588-022-01182-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 02/07/2023]
Abstract
We identify the sodium leak channel non-selective protein (NALCN) as a key regulator of cancer metastasis and nonmalignant cell dissemination. Among 10,022 human cancers, NALCN loss-of-function mutations were enriched in gastric and colorectal cancers. Deletion of Nalcn from gastric, intestinal or pancreatic adenocarcinomas in mice did not alter tumor incidence, but markedly increased the number of circulating tumor cells (CTCs) and metastases. Treatment of these mice with gadolinium-a NALCN channel blocker-similarly increased CTCs and metastases. Deletion of Nalcn from mice that lacked oncogenic mutations and never developed cancer caused shedding of epithelial cells into the blood at levels equivalent to those seen in tumor-bearing animals. These cells trafficked to distant organs to form normal structures including lung epithelium, and kidney glomeruli and tubules. Thus, NALCN regulates cell shedding from solid tissues independent of cancer, divorcing this process from tumorigenesis and unmasking a potential new target for antimetastatic therapies.
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Affiliation(s)
- Eric P Rahrmann
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - David Shorthouse
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Amir Jassim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Linda P Hu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Mariaestela Ortiz
- Molecular Pharmacology Lab, Organoid Models Research and Biology, National Cancer Institute, Leidos Biomedical Research, Frederick, MD, USA
| | - Betania Mahler-Araujo
- Wellcome-MRC Institute of Metabolic Science, Histopathology Core, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Peter Vogel
- Veterinary Pathology Core Laboratory, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Marta Paez-Ribes
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Atefeh Fatemi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Radhika Iyer
- Texas Children's Cancer and Hematology Centers, Houston, TX, USA
| | - Jay A Blundon
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Filipe C Lourenço
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jonathan Kay
- Departments of Medicine and of Population and Quantitative Health Sciences, University of Massachusetts Medical School and UMass Memorial Medical Center, Worcester, MA, USA
| | - Rosalynn M Nazarian
- Massachusetts General Hospital, Pathology Service, Dermatopathology Unit, Boston, MA, USA
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Stanislav S Zakharenko
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Liqin Zhu
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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19
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Collantes TMA, Clark CM, Musarrat F, Jambunathan N, Jois S, Kousoulas KG. Predicted Structure and Functions of the Prototypic Alphaherpesvirus Herpes Simplex Virus Type-1 UL37 Tegument Protein. Viruses 2022; 14:2189. [PMID: 36298744 PMCID: PMC9608200 DOI: 10.3390/v14102189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
The alphaherpesvirus UL37 tegument protein is a highly conserved, multi-functional protein. Mutagenesis analysis delineated the UL37 domains necessary for retrograde transport and viral replication. Specifically, the amino-terminal 480 amino acids are dispensable for virus replication in epithelial cell culture, but it is unknown whether this amino-terminal deletion affects UL37 structure and intracellular transport in epithelial cells and neurons. To investigate the structure and function of UL37, we utilized multiple computational approaches to predict and characterize the secondary and tertiary structure and other functional features. The structure of HSV-1 UL37 and Δ481N were deduced using publicly available predictive algorithms. The predicted model of HSV-1 UL37 is a stable, multi-functional, globular monomer, rich in alpha helices, with unfolded regions within the linker and the C-tail domains. The highly flexible C-tail contains predicted binding sites to the dynein intermediate chain, as well as DNA and RNA. Predicted interactions with the cytoplasmic surface of the lipid membrane suggest UL37 is a peripheral membrane protein. The Δ481N truncation did not alter the predicted structure of the UL37 C-terminus protein and its predicted interaction with dynein. We validated these models by examining the replication kinetics and transport of the Δ481N virus toward the nuclei of infected epithelial and neuronal cells. The Δ481N virus had substantial defects in virus spread; however, it exhibited no apparent defects in virus entry and intracellular transport. Using computational analyses, we identified several key features of UL37, particularly the flexible unstructured tail; we then demonstrated that the UL37 C-terminus alone is sufficient to effectively transport the virus towards the nucleus of infected epithelial and neuronal cells.
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Affiliation(s)
- Therese Marie A. Collantes
- Division of Biotechnology and Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- College of Veterinary Medicine, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Carolyn M. Clark
- Division of Biotechnology and Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Farhana Musarrat
- Division of Biotechnology and Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA 71201, USA
| | - Konstantin G. Kousoulas
- Division of Biotechnology and Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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20
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Khelashvili G, Kots E, Cheng X, Levine MV, Weinstein H. The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase. Commun Biol 2022; 5:990. [PMID: 36123525 PMCID: PMC9484709 DOI: 10.1038/s42003-022-03930-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
TMEM16F is a Ca2+-activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids. Molecular dynamics simulations reveal the allosteric mechanism leading to an open, lipid scrambling competent state of a mammalian TMEM16F.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Michael V Levine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
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21
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Kobayashi K, Kawakami K, Kusakizako T, Miyauchi H, Tomita A, Kobayashi K, Shihoya W, Yamashita K, Nishizawa T, Kato HE, Inoue A, Nureki O. Endogenous ligand recognition and structural transition of a human PTH receptor. Mol Cell 2022; 82:3468-3483.e5. [PMID: 35932760 DOI: 10.1016/j.molcel.2022.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/07/2021] [Accepted: 07/11/2022] [Indexed: 11/18/2022]
Abstract
Endogenous parathyroid hormone (PTH) and PTH-related peptide (PTHrP) bind to the parathyroid hormone receptor 1 (PTH1R) and activate the stimulatory G-protein (Gs) signaling pathway. Intriguingly, the two ligands have distinct signaling and physiological properties: PTH evokes prolonged Gs activation, whereas PTHrP evokes transient Gs activation with reduced bone-resorption effects. The distinct molecular actions are ascribed to the differences in ligand recognition and dissociation kinetics. Here, we report cryoelectron microscopic structures of six forms of the human PTH1R-Gs complex in the presence of PTH or PTHrP at resolutions of 2.8 -4.1 Å. A comparison of the PTH-bound and PTHrP-bound structures reveals distinct ligand-receptor interactions underlying the ligand affinity and selectivity. Furthermore, five distinct PTH-bound structures, combined with computational analyses, provide insights into the unique and complex process of ligand dissociation from the receptor and shed light on the distinct durations of signaling induced by PTH and PTHrP.
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Affiliation(s)
- Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hirotake Miyauchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hideaki E Kato
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; Komaba Institute for Science, the University of Tokyo, Meguro, Tokyo 153-8505, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
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22
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Nakao H, Nakano M. Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides. Chem Pharm Bull (Tokyo) 2022; 70:519-523. [DOI: 10.1248/cpb.c22-00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
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23
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Sun L, Pan F, Li S. Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties. MEMBRANES 2022; 12:membranes12080730. [PMID: 35893448 PMCID: PMC9394357 DOI: 10.3390/membranes12080730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023]
Abstract
The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions.
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Affiliation(s)
| | - Fan Pan
- Correspondence: (F.P.); (S.L.)
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24
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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25
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Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. TMEM16 scramblases thin the membrane to enable lipid scrambling. Nat Commun 2022; 13:2604. [PMID: 35562175 PMCID: PMC9095706 DOI: 10.1038/s41467-022-30300-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca2+-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove's intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove.
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Affiliation(s)
- Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Omar E Alvarenga
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - ByoungCheol Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Eva Fortea
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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26
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Wang L, Zhang J, Wang D, Song C. Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins. PLoS Comput Biol 2022; 18:e1009972. [PMID: 35353812 PMCID: PMC9000120 DOI: 10.1371/journal.pcbi.1009972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/11/2022] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
One of the unique traits of membrane proteins is that a significant fraction of their hydrophobic amino acids is exposed to the hydrophobic core of lipid bilayers rather than being embedded in the protein interior, which is often not explicitly considered in the protein structure and function predictions. Here, we propose a characteristic and predictive quantity, the membrane contact probability (MCP), to describe the likelihood of the amino acids of a given sequence being in direct contact with the acyl chains of lipid molecules. We show that MCP is complementary to solvent accessibility in characterizing the outer surface of membrane proteins, and it can be predicted for any given sequence with a machine learning-based method by utilizing a training dataset extracted from MemProtMD, a database generated from molecular dynamics simulations for the membrane proteins with a known structure. As the first of many potential applications, we demonstrate that MCP can be used to systematically improve the prediction precision of the protein contact maps and structures. The distribution of residues on protein surfaces is largely determined by the surrounding environment. For soluble proteins, most of the residues on the outer surface are hydrophilic, and people use the quantity “solvent accessibility” to describe and predict these surface residues. In contrast, for membrane proteins that are embedded in a lipid bilayer, many of their surface residues are hydrophobic and membrane-contacting, but there is yet a widely-accepted quantity for the description or prediction of this characteristic property. Here, we propose a new quantity termed “membrane contact probability (MCP)”, which can be used to describe and predict the membrane-contacting surface residues of proteins. We also propose a machine learning-based method to predict MCP from protein sequences, utilizing the dataset generated by physics-based computer simulations. We demonstrate that a quantity such as MCP is helpful for protein structure prediction, and we believe that it will find broad applications in the structure and function studies of membrane proteins.
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Affiliation(s)
- Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
| | - Jiangguo Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Dali Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail:
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27
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401,;
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,;
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28
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Suenaga R, Takemoto M, Inoue A, Ishitani R, Nureki O. Lateral access mechanism of LPA receptor probed by molecular dynamics simulation. PLoS One 2022; 17:e0263296. [PMID: 35113924 PMCID: PMC8812926 DOI: 10.1371/journal.pone.0263296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/17/2022] [Indexed: 11/23/2022] Open
Abstract
G-protein-coupled receptors (GPCR) are a family of membrane receptors that play important roles in the regulation of various physiological phenomena. LPA receptors (LPA1-6) are members of the class A GPCRs, which transduce a lysophosphatidic acid (LPA) signal across the cell membrane and evoke various responses, including cellular survival, proliferation, differentiation, and migration. The crystal structure of LPA6 revealed a gap between its transmembrane helices (TMs), which is opened toward the membrane side. This led to the proposal of the “lateral access model,” in which its lipophilic ligand directly enters the binding pocket through the gap structure at the membrane. In this study, we performed molecular dynamics (MD) simulations and Markov state model (MSM) analyses of LPA6 and LPA, to elucidate the long timescale dynamics of the ligand binding process. The results from the 71.4-μs MD simulation suggested that the flexibility of the TMs constituting the gap structure enables the lateral entrance of the ligand, and the key interactions between the receptor and ligand facilitate the transition state of the ligand binding process.
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Affiliation(s)
- Rieko Suenaga
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Mizuki Takemoto
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (RI); (ON)
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (RI); (ON)
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29
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Polymodal Control of TMEM16x Channels and Scramblases. Int J Mol Sci 2022; 23:ijms23031580. [PMID: 35163502 PMCID: PMC8835819 DOI: 10.3390/ijms23031580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The TMEM16A/anoctamin-1 calcium-activated chloride channel (CaCC) contributes to a range of vital functions, such as the control of vascular tone and epithelial ion transport. The channel is a founding member of a family of 10 proteins (TMEM16x) with varied functions; some members (i.e., TMEM16A and TMEM16B) serve as CaCCs, while others are lipid scramblases, combine channel and scramblase function, or perform additional cellular roles. TMEM16x proteins are typically activated by agonist-induced Ca2+ release evoked by Gq-protein-coupled receptor (GqPCR) activation; thus, TMEM16x proteins link Ca2+-signalling with cell electrical activity and/or lipid transport. Recent studies demonstrate that a range of other cellular factors—including plasmalemmal lipids, pH, hypoxia, ATP and auxiliary proteins—also control the activity of the TMEM16A channel and its paralogues, suggesting that the TMEM16x proteins are effectively polymodal sensors of cellular homeostasis. Here, we review the molecular pathophysiology, structural biology, and mechanisms of regulation of TMEM16x proteins by multiple cellular factors.
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30
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Prediction of molecular interactions and physicochemical properties relevant for vasopressin V2 receptor antagonism. J Mol Model 2022; 28:31. [PMID: 34997307 DOI: 10.1007/s00894-021-05022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
We have developed two ligand- and receptor-based computational approaches to study the physicochemical properties relevant to the biological activity of vasopressin V2 receptor (V2R) antagonist and eventually to predict the expected binding mode to V2R. The obtained quantitative structure activity relationship (QSAR) model showed a correlation of the antagonist activity with the hydration energy (EH2O), the polarizability (P), and the calculated partial charge on atom N7 (q6) of the common substructure. The first two descriptors showed a positive contribution to antagonist activity, while the third one had a negative contribution. V2R was modeled and further relaxed on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocoline (POPC) membrane by molecular dynamics simulations. The receptor antagonist complexes were guessed by molecular docking, and the stability of the most relevant structures was also evaluated by molecular dynamics simulations. As a result, amino acid residues Q96, W99, F105, K116, F178, A194, F307, and M311 were identified with the probably most relevant antagonist-receptor interactions on the studied complexes. The proposed QSAR model could explain the molecular properties relevant to the antagonist activity. The contributions to the antagonist-receptor interaction appeared also in agreement with the binding mode of the complexes obtained by molecular docking and molecular dynamics. These models will be used in further studies to look for new V2R potential antagonist molecules.
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31
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Lomize AL, Todd SC, Pogozheva ID. Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. Protein Sci 2022; 31:209-220. [PMID: 34716622 PMCID: PMC8740824 DOI: 10.1002/pro.4219] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 01/03/2023]
Abstract
Cellular protrusions, invaginations, and many intracellular organelles have strongly curved membrane regions. Transmembrane and peripheral membrane proteins that induce, sense, or stabilize such regions cannot be properly fitted into a single flat bilayer. To treat such proteins, we developed a new method and a web tool, PPM 3.0, for positioning proteins in curved or planar, single or multiple membranes. This method determines the energetically optimal spatial position, the hydrophobic thickness, and the radius of intrinsic curvature of a membrane-deforming protein structure by arranging it in a single or several sphere-shaped or planar membrane sections. In addition, it can define the lipid-embedded regions of a protein that simultaneously spans several membranes or determine the optimal position of a peptide in a spherical micelle. The PPM 3.0 web server operates with 17 types of biological membranes and 4 types of artificial bilayers. It is publicly available at https://opm.phar.umich.edu/ppm_server3. PPM 3.0 was applied to identify and characterize arrangements in membranes of 128 proteins with a significant intrinsic curvature, such as BAR domains, annexins, Piezo, and MscS mechanosensitive channels, cation-chloride cotransporters, as well as mitochondrial ATP synthases, calcium uniporters, and TOM complexes. These proteins form large complexes that are mainly localized in mitochondria, plasma membranes, and endosomes. Structures of bacterial drug efflux pumps, AcrAB-TolC, MexAB-OrpM, and MacAB-TolC, were positioned in both membranes of the bacterial cell envelop, while structures of multimeric gap-junction channels were arranged in two opposed cellular membranes.
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Affiliation(s)
- Andrei L. Lomize
- College of Pharmacy, Department of Medicinal ChemistryUniversity of MichiganAnn ArborMichiganUSA
| | - Spencer C. Todd
- Department of Electrical Engineering and Computer Science, College of EngineeringUniversity of MichiganAnn ArborMichiganUSA
| | - Irina D. Pogozheva
- College of Pharmacy, Department of Medicinal ChemistryUniversity of MichiganAnn ArborMichiganUSA
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32
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Lynch CI, Klesse G, Rao S, Tucker SJ, Sansom MSP. Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models. ACS NANO 2021; 15:19098-19108. [PMID: 34784172 PMCID: PMC7612143 DOI: 10.1021/acsnano.1c06443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a "vapor lock" if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.
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Affiliation(s)
- Charlotte I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Gianni Klesse
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
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33
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Tomita A, Daiho T, Kusakizako T, Yamashita K, Ogasawara S, Murata T, Nishizawa T, Nureki O. Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2. Mol Cell 2021; 81:4799-4809.e5. [PMID: 34798056 DOI: 10.1016/j.molcel.2021.11.001] [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] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 11/01/2021] [Indexed: 01/11/2023]
Abstract
The cytoplasmic polyamine maintains cellular homeostasis by chelating toxic metal cations, regulating transcriptional activity, and protecting DNA. ATP13A2 was identified as a lysosomal polyamine exporter responsible for polyamine release into the cytosol, and its dysfunction is associated with Alzheimer's disease and other neural degradation diseases. ATP13A2 belongs to the P5 subfamily of the P-type ATPase family, but its mechanisms remain unknown. Here, we report the cryoelectron microscopy (cryo-EM) structures of human ATP13A2 under four different conditions, revealing the structural coupling between the polyamine binding and the dephosphorylation. Polyamine is bound at the luminal tunnel and recognized through numerous electrostatic and π-cation interactions, explaining its broad specificity. The unique N-terminal domain is anchored to the lipid membrane to stabilize the E2P conformation, thereby accelerating the E1P-to-E2P transition. These findings reveal the distinct mechanism of P5B ATPases, thereby paving the way for neuroprotective therapy by activating ATP13A2.
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Affiliation(s)
- Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Daiho
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Tsurumi, Yokohama 230-0045, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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34
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Ansell TB, Curran L, Horrell MR, Pipatpolkai T, Letham SC, Song W, Siebold C, Stansfeld PJ, Sansom MSP, Corey RA. Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:6548-6558. [PMID: 34523933 PMCID: PMC8515805 DOI: 10.1021/acs.jctc.1c00547] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 12/18/2022]
Abstract
Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities.
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Affiliation(s)
- T. Bertie Ansell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Luke Curran
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Michael R. Horrell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Tanadet Pipatpolkai
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, South Parks
Road, Oxford, OX1 3PT, U.K.
| | - Suzanne C. Letham
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford, OX1 3RE, U.K.
| | - Wanling Song
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Christian Siebold
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, U.K.
| | - Phillip J. Stansfeld
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Robin A. Corey
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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35
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Catalano C, AL Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Curr Res Struct Biol 2021; 3:239-256. [PMID: 34693344 PMCID: PMC8517007 DOI: 10.1016/j.crstbi.2021.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery. Unfortunately, this data is often unavailable for some of the most interesting and therapeutically important proteins. Thus, computational tools for building native-like structural models from less-than-ideal experimental data are needed. To this end, interaction homology exploits the character, strength and loci of the sets of interactions that define a structure. Each residue type has its own limited set of backbone angle-dependent interaction motifs, as defined by their environments. In this work, we characterize the interactions of serine, cysteine and S-bridged cysteine in terms of 3D hydropathic environment maps. As a result, we explore several intriguing questions. Are the environments different between the isosteric serine and cysteine residues? Do some environments promote the formation of cystine S-S bonds? With the increasing availability of structural data for water-insoluble membrane proteins, are there environmental differences for these residues between soluble and membrane proteins? The environments surrounding serine and cysteine residues are dramatically different: serine residues are about 50% solvent exposed, while cysteines are only 10% exposed; the latter are more involved in hydrophobic interactions although there are backbone angle-dependent differences. Our analysis suggests that one driving force for -S-S- bond formation is a rather substantial increase in burial and hydrophobic interactions in cystines. Serine and cysteine become less and more, respectively, solvent-exposed in membrane proteins. 3D hydropathic environment maps are an evolving structure analysis tool showing promise as elements in a new protein structure prediction paradigm.
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Affiliation(s)
- Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed H. AL Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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36
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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37
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Corey RA, Song W, Duncan AL, Ansell TB, Sansom MSP, Stansfeld PJ. Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins. SCIENCE ADVANCES 2021; 7:eabh2217. [PMID: 34417182 PMCID: PMC8378812 DOI: 10.1126/sciadv.abh2217] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Integral membrane proteins are localized and/or regulated by lipids present in the surrounding bilayer. While bacteria have relatively simple membranes, there is ample evidence that many bacterial proteins bind to specific lipids, especially the anionic lipid cardiolipin. Here, we apply molecular dynamics simulations to assess lipid binding to 42 different Escherichia coli inner membrane proteins. Our data reveal an asymmetry between the membrane leaflets, with increased anionic lipid binding to the inner leaflet regions of the proteins, particularly for cardiolipin. From our simulations, we identify >700 independent cardiolipin binding sites, allowing us to identify the molecular basis of a prototypical cardiolipin binding site, which we validate against structures of bacterial proteins bound to cardiolipin. This allows us to construct a set of metrics for defining a high-affinity cardiolipin binding site on bacterial membrane proteins, paving the way for a heuristic approach to defining other protein-lipid interactions.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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38
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Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. SCIENCE ADVANCES 2021; 7:eabh3355. [PMID: 34433568 PMCID: PMC8386928 DOI: 10.1126/sciadv.abh3355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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39
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Nagiri C, Kobayashi K, Tomita A, Kato M, Kobayashi K, Yamashita K, Nishizawa T, Inoue A, Shihoya W, Nureki O. Cryo-EM structure of the β3-adrenergic receptor reveals the molecular basis of subtype selectivity. Mol Cell 2021; 81:3205-3215.e5. [PMID: 34314699 DOI: 10.1016/j.molcel.2021.06.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/17/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
The β3-adrenergic receptor (β3AR) is predominantly expressed in adipose tissue and urinary bladder and has emerged as an attractive drug target for the treatment of type 2 diabetes, obesity, and overactive bladder (OAB). Here, we report the cryogenic electron microscopy structure of the β3AR-Gs signaling complex with the selective agonist mirabegron, a first-in-class drug for OAB. Comparison of this structure with the previously reported β1AR and β2AR structures reveals a receptor activation mechanism upon mirabegron binding to the orthosteric site. Notably, the narrower exosite in β3AR creates a perpendicular pocket for mirabegron. Mutational analyses suggest that a combination of both the exosite shape and the amino-acid-residue substitutions defines the drug selectivity of the βAR agonists. Our findings provide a molecular basis for βAR subtype selectivity, allowing the design of more-selective agents with fewer adverse effects.
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Affiliation(s)
- Chisae Nagiri
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiko Kato
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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40
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Straub MS, Alvadia C, Sawicka M, Dutzler R. Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. eLife 2021; 10:e69800. [PMID: 34263724 PMCID: PMC8298096 DOI: 10.7554/elife.69800] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/11/2021] [Indexed: 12/17/2022] Open
Abstract
The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The protein XKR9 is a member of a conserved family that has been associated with apoptotic lipid scrambling. Here, we describe structures of full-length and caspase-treated XKR9 from Rattus norvegicus in complex with a synthetic nanobody determined by cryo-electron microscopy. The 43 kDa monomeric membrane protein can be divided into two structurally related repeats, each containing four membrane-spanning segments and a helix that is partly inserted into the lipid bilayer. In the full-length protein, the C-terminus interacts with a hydrophobic pocket located at the intracellular side acting as an inhibitor of protein function. Cleavage by caspase-3 at a specific site releases 16 residues of the C-terminus, thus making the pocket accessible to the cytoplasm. Collectively, the work has revealed the unknown architecture of the XKR family and has provided initial insight into its activation by caspases.
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Affiliation(s)
- Monique S Straub
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Marta Sawicka
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Raimund Dutzler
- Department of Biochemistry, University of ZurichZurichSwitzerland
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41
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Lemberg MK, Strisovsky K. Maintenance of organellar protein homeostasis by ER-associated degradation and related mechanisms. Mol Cell 2021; 81:2507-2519. [PMID: 34107306 DOI: 10.1016/j.molcel.2021.05.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Protein homeostasis mechanisms are fundamentally important to match cellular needs and to counteract stress conditions. A fundamental challenge is to understand how defective proteins are recognized and extracted from cellular organelles to be degraded in the cytoplasm. The endoplasmic reticulum (ER)-associated degradation (ERAD) pathway is the best-understood organellar protein quality control system. Here, we review new insights into the mechanism of recognition and retrotranslocation of client proteins in ERAD. In addition to the membrane-integral ERAD E3 ubiquitin ligases, we highlight one protein family that is remarkably often involved in various aspects of membrane protein quality control and protein dislocation: the rhomboid superfamily, which includes derlins and intramembrane serine proteases. Rhomboid-like proteins have been found to control protein homeostasis in the ER, but also in other eukaryotic organelles and in bacteria, pointing toward conserved principles of membrane protein quality control across organelles and evolution.
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Affiliation(s)
- Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany.
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czechia.
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42
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Torrens-Fontanals M, Stepniewski TM, Gloriam DE, Selent J. Structural dynamics bridge the gap between the genetic and functional levels of GPCRs. Curr Opin Struct Biol 2021; 69:150-159. [PMID: 34052782 DOI: 10.1016/j.sbi.2021.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 04/19/2021] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are implicated in nearly all physiological processes in the human body and represent an important drug targeting class. The genes encoding the different GPCR (sub)types determine their specific functionality, which can be altered by natural genetic variants and isoforms. Deciphering the molecular link between sequence diversity and its functional consequences is a current challenge and critical for the comprehension of the physiological response of GPCRs. It requires a global understanding of how protein sequence translates into protein structure, how this impacts the structural motions of the protein, and, finally, how all these factors determine the receptor functionality. Here, we discuss available resources and state-of-the-art computational approaches to address this question.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics (GRIB), Hospital Del Mar Medical Research Institute (IMIM)-Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Tomasz M Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital Del Mar Medical Research Institute (IMIM)-Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; InterAx Biotech AG, PARK InnovAARE, 5234 Villigen, Switzerland; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital Del Mar Medical Research Institute (IMIM)-Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain.
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43
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Hayatshahi HS, Luedtke RR, Taylor M, Chen PJ, Blass BE, Liu J. Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes. J Chem Inf Model 2021; 61:2829-2843. [PMID: 33988991 DOI: 10.1021/acs.jcim.1c00036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the D3 dopamine receptor (D3R) is a promising pharmacotherapeutic strategy for the treatment of many disorders. The structure of the D3R is similar to the D2 dopamine receptor (D2R), especially in the transmembrane spanning regions that form the orthosteric binding site, making it difficult to identify D3R selective pharmacotherapeutic agents. Here, we examine the molecular basis for the high affinity D3R binding and D3R vs D2R binding selectivity of substituted phenylpiperazine thiopheneamides. We show that removing the thiophenearylamide portion of the ligand consistently decreases the affinity of these ligands at D3R, while not affecting their affinity at the D2R. Our long (>10 μs) molecular dynamics simulations demonstrated that both dopamine receptor subtypes adopt two major conformations that we refer to as closed or open conformations, with D3R sampling the open conformation more frequently than D2R. The binding of ligands with conjoined orthosteric-allosteric binding moieties causes the closed conformation to populate more often in the trajectories. Also, significant differences were observed in the extracellular loops (ECL) of these two receptor subtypes leading to the identification of several residues that contribute differently to the ligand binding for the two receptors that could potentially contribute to ligand binding selectivity. Our observations also suggest that the displacement of ordered water in the binding pocket of D3R contributes to the affinity of the compounds containing an allosteric binding motif. These studies provide a better understanding of how a bitopic mode of engagement can determine ligands that bind selectively to D2 and D3 dopamine receptor subtypes.
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Affiliation(s)
- Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Robert R Luedtke
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Michelle Taylor
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Peng-Jen Chen
- Moulder Center for Drug Discovery Research, Department of Pharmaceutical Sciences, Temple University School of Pharmacy, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Benjamin E Blass
- Moulder Center for Drug Discovery Research, Department of Pharmaceutical Sciences, Temple University School of Pharmacy, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
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44
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Weber DK, Reddy UV, Wang S, Larsen EK, Gopinath T, Gustavsson MB, Cornea RL, Thomas DD, De Simone A, Veglia G. Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by Ca 2+ and phosphorylation. eLife 2021; 10:66226. [PMID: 33978571 PMCID: PMC8184213 DOI: 10.7554/elife.66226] [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: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023] Open
Abstract
Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca2+-transport response to β-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation by cAMP-dependent protein kinase A or increase in Ca2+ concentration reverses the inhibitory effects through an unknown mechanism. Using oriented-sample solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we reveal that phosphorylation of PLN's cytoplasmic regulatory domain signals the disruption of several inhibitory contacts at the transmembrane binding interface of the SERCA-PLN complex that are propagated to the enzyme's active site, augmenting Ca2+ transport. Our findings address long-standing questions about SERCA regulation, epitomizing a signal transduction mechanism operated by posttranslationally modified bitopic membrane proteins.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, United States
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Martin B Gustavsson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom.,Department of Pharmacy, University of Naples 'Federico II', Naples, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States.,Department of Chemistry, University of Minnesota, Minneapolis, United States
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45
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The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction. J Mol Biol 2021; 433:166941. [PMID: 33741412 DOI: 10.1016/j.jmb.2021.166941] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022]
Abstract
The TMEM16 family of membrane proteins displays a remarkable functional dichotomy - while some family members function as Ca2+-activated anion channels, the majority of characterized TMEM16 homologs are Ca2+-activated lipid scramblases, which catalyze the exchange of phospholipids between the two membrane leaflets. Furthermore, some TMEM16 scramblases can also function as channels. Due to their involvement in important physiological processes, the family has been actively studied ever since their molecular identity was unraveled. In this review, we will summarize the recent advances in the field and how they influenced our view of TMEM16 family function and evolution. Structural, functional and computational studies reveal how relatively small rearrangements in the permeation pathway are responsible for the observed functional duality: while TMEM16 scramblases can adopt both ion- and lipid conductive conformations, TMEM16 channels can only populate the former. Recent data further provides the molecular details of a stepwise activation mechanism, which is initiated by Ca2+ binding and modulated by various cellular factors, including lipids. TMEM16 function and the surrounding membrane properties are inextricably intertwined, with the protein inducing bilayer deformations associated with scrambling, while the surrounding lipids modulate TMEM16 conformation and activity.
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46
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Visualizing protein structures - tools and trends. Biochem Soc Trans 2021; 48:499-506. [PMID: 32196545 DOI: 10.1042/bst20190621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
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47
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Rosário-Ferreira N, Marques-Pereira C, Gouveia RP, Mourão J, Moreira IS. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. Methods Mol Biol 2021; 2315:3-28. [PMID: 34302667 DOI: 10.1007/978-1-0716-1468-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins (MPs) encompass a large family of proteins with distinct cellular functions, and although representing over 50% of existing pharmaceutical drug targets, their structural and functional information is still very scarce. Over the last years, in silico analysis and algorithm development were essential to characterize MPs and overcome some limitations of experimental approaches. The optimization and improvement of these methods remain an ongoing process, with key advances in MPs' structure, folding, and interface prediction being continuously tackled. Herein, we discuss the latest trends in computational methods toward a deeper understanding of the atomistic and mechanistic details of MPs.
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Affiliation(s)
- Nícia Rosário-Ferreira
- Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Catarina Marques-Pereira
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Raquel P Gouveia
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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48
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Le SC, Yang H. Structure-Function of TMEM16 Ion Channels and Lipid Scramblases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1349:87-109. [PMID: 35138612 PMCID: PMC11020148 DOI: 10.1007/978-981-16-4254-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The TMEM16 protein family comprises two novel classes of structurally conserved but functionally distinct membrane transporters that function as Ca2+-dependent Cl- channels (CaCCs) or dual functional Ca2+-dependent ion channels and phospholipid scramblases. Extensive functional and structural studies have advanced our understanding of TMEM16 molecular mechanisms and physiological functions. TMEM16A and TMEM16B CaCCs control transepithelial fluid transport, smooth muscle contraction, and neuronal excitability, whereas TMEM16 phospholipid scramblases mediate the flip-flop of phospholipids across the membrane to allow phosphatidylserine externalization, which is essential in a plethora of important processes such as blood coagulation, bone development, and viral and cell fusion. In this chapter, we summarize the major methods in studying TMEM16 ion channels and scramblases and then focus on the current mechanistic understanding of TMEM16 Ca2+- and voltage-dependent channel gating as well as their ion and phospholipid permeation.
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Affiliation(s)
- Son C Le
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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49
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Flegler VJ, Rasmussen A, Rao S, Wu N, Zenobi R, Sansom MSP, Hedrich R, Rasmussen T, Böttcher B. The MscS-like channel YnaI has a gating mechanism based on flexible pore helices. Proc Natl Acad Sci U S A 2020; 117:28754-28762. [PMID: 33148804 PMCID: PMC7682570 DOI: 10.1073/pnas.2005641117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanosensitive channel of small conductance (MscS) is the prototype of an evolutionarily diversified large family that fine-tunes osmoregulation but is likely to fulfill additional functions. Escherichia coli has six osmoprotective paralogs with different numbers of transmembrane helices. These helices are important for gating and sensing in MscS but the role of the additional helices in the paralogs is not understood. The medium-sized channel YnaI was extracted and delivered in native nanodiscs in closed-like and open-like conformations using the copolymer diisobutylene/maleic acid (DIBMA) for structural studies. Here we show by electron cryomicroscopy that YnaI has an extended sensor paddle that during gating relocates relative to the pore concomitant with bending of a GGxGG motif in the pore helices. YnaI is the only one of the six paralogs that has this GGxGG motif allowing the sensor paddle to move outward. Access to the pore is through a vestibule on the cytosolic side that is fenestrated by side portals. In YnaI, these portals are obstructed by aromatic side chains but are still fully hydrated and thus support conductance. For comparison with large-sized channels, we determined the structure of YbiO, which showed larger portals and a wider pore with no GGxGG motif. Further in silico comparison of MscS, YnaI, and YbiO highlighted differences in the hydrophobicity and wettability of their pores and vestibule interiors. Thus, MscS-like channels of different sizes have a common core architecture but show different gating mechanisms and fine-tuned conductive properties.
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Affiliation(s)
- Vanessa Judith Flegler
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
| | - Akiko Rasmussen
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
| | - Na Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
| | - Rainer Hedrich
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Tim Rasmussen
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany;
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
| | - Bettina Böttcher
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany;
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
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Pipatpolkai T, Corey RA, Proks P, Ashcroft FM, Stansfeld PJ. Evaluating inositol phospholipid interactions with inward rectifier potassium channels and characterising their role in disease. Commun Chem 2020; 3:147. [PMID: 36703430 PMCID: PMC9814360 DOI: 10.1038/s42004-020-00391-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/17/2020] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins are frequently modulated by specific protein-lipid interactions. The activation of human inward rectifying potassium (hKir) channels by phosphoinositides (PI) has been well characterised. Here, we apply a coarse-grained molecular dynamics free-energy perturbation (CG-FEP) protocol to capture the energetics of binding of PI lipids to hKir channels. By using either a single- or multi-step approach, we establish a consistent value for the binding of PIP2 to hKir channels, relative to the binding of the bulk phosphatidylcholine phospholipid. Furthermore, by perturbing amino acid side chains on hKir6.2, we show that the neonatal diabetes mutation E179K increases PIP2 affinity, while the congenital hyperinsulinism mutation K67N results in a reduced affinity. We show good agreement with electrophysiological data where E179K exhibits a reduction in neomycin sensitivity, implying that PIP2 binds more tightly E179K channels. This illustrates the application of CG-FEP to compare affinities between lipid species, and for annotating amino acid residues.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Physiology Anatomy and Genetics, Parks Road, Oxford, OX1 3PT, UK
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, OX1 3PT, UK
| | - Robin A Corey
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter Proks
- Department of Physiology Anatomy and Genetics, Parks Road, Oxford, OX1 3PT, UK
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, OX1 3PT, UK
| | - Frances M Ashcroft
- Department of Physiology Anatomy and Genetics, Parks Road, Oxford, OX1 3PT, UK.
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, OX1 3PT, UK.
| | - Phillip J Stansfeld
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK.
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, OX1 3PT, UK.
- Department of Chemistry, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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