1
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Rommelaere S, Carboni A, Bada Juarez JF, Boquete JP, Abriata LA, Teixeira Pinto Meireles F, Rukes V, Vincent C, Kondo S, Dionne MS, Dal Peraro M, Cao C, Lemaitre B. A humoral stress response protects Drosophila tissues from antimicrobial peptides. Curr Biol 2024; 34:1426-1437.e6. [PMID: 38484734 DOI: 10.1016/j.cub.2024.02.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
7An efficient immune system must provide protection against a broad range of pathogens without causing excessive collateral tissue damage. While immune effectors have been well characterized, we know less about the resilience mechanisms protecting the host from its own immune response. Antimicrobial peptides (AMPs) are small, cationic peptides that contribute to innate defenses by targeting negatively charged membranes of microbes. While protective against pathogens, AMPs can be cytotoxic to host cells. Here, we reveal that a family of stress-induced proteins, the Turandots, protect the Drosophila respiratory system from AMPs, increasing resilience to stress. Flies lacking Turandot genes are susceptible to environmental stresses due to AMP-induced tracheal apoptosis. Turandot proteins bind to host cell membranes and mask negatively charged phospholipids, protecting them from cationic pore-forming AMPs. Collectively, these data demonstrate that Turandot stress proteins mitigate AMP cytotoxicity to host tissues and therefore improve their efficacy.
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Affiliation(s)
- Samuel Rommelaere
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Alexia Carboni
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Juan F Bada Juarez
- Institute of Bioengineering, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jean-Philippe Boquete
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Fernando Teixeira Pinto Meireles
- Institute of Bioengineering, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Verena Rukes
- Institute of Bioengineering, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Crystal Vincent
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS London, UK
| | - Shu Kondo
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 162-8601 Tokyo, Japan
| | - Marc S Dionne
- Centre for Bacterial Resistance Biology and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Department of Inorganic and Analytical Chemistry, Chemistry and Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Bruno Lemaitre
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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2
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Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Dalton Trans 2024; 53:1794-1808. [PMID: 38170898 PMCID: PMC10804444 DOI: 10.1039/d3dt03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.
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Affiliation(s)
- Magali Roger
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Philippe Leone
- CNRS, Aix-Marseille University, Laboratoire d'Ingénierie des Systèmes Macromoléculaires, LISM UMR7255, 13009 Marseille, France
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sam Horrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Frédéric Biaso
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Marie-Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Sciara
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
- Aix Marseille Univ, INRAE, BBF UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Marianne Ilbert
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
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3
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Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
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Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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4
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von der Malsburg A, Sapp GM, Zuccaro KE, von Appen A, Moss FR, Kalia R, Bennett JA, Abriata LA, Dal Peraro M, van der Laan M, Frost A, Aydin H. Structural mechanism of mitochondrial membrane remodelling by human OPA1. Nature 2023; 620:1101-1108. [PMID: 37612504 PMCID: PMC10875962 DOI: 10.1038/s41586-023-06441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate1-3. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fusion of the mitochondrial inner membrane4,5. Despite its fundamental importance, the molecular mechanisms by which OPA1 modulates mitochondrial morphology are unclear. Here, using a combination of cellular and structural analyses, we illuminate the molecular mechanisms that are key to OPA1-dependent membrane remodelling and fusion. Human OPA1 embeds itself into cardiolipin-containing membranes through a lipid-binding paddle domain. A conserved loop within the paddle domain inserts deeply into the bilayer, further stabilizing the interactions with cardiolipin-enriched membranes. OPA1 dimerization through the paddle domain promotes the helical assembly of a flexible OPA1 lattice on the membrane, which drives mitochondrial fusion in cells. Moreover, the membrane-bending OPA1 oligomer undergoes conformational changes that pull the membrane-inserting loop out of the outer leaflet and contribute to the mechanics of membrane remodelling. Our findings provide a structural framework for understanding how human OPA1 shapes mitochondrial morphology and show us how human disease mutations compromise OPA1 functions.
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Affiliation(s)
- Alexander von der Malsburg
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Gracie M Sapp
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Kelly E Zuccaro
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Alexander von Appen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank R Moss
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA
| | - Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy A Bennett
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin van der Laan
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Halil Aydin
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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5
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Gehin C, Lone MA, Lee W, Capolupo L, Ho S, Adeyemi AM, Gerkes EH, Stegmann AP, López-Martín E, Bermejo-Sánchez E, Martínez-Delgado B, Zweier C, Kraus C, Popp B, Strehlow V, Gräfe D, Knerr I, Jones ER, Zamuner S, Abriata LA, Kunnathully V, Moeller BE, Vocat A, Rommelaere S, Bocquete JP, Ruchti E, Limoni G, Van Campenhoudt M, Bourgeat S, Henklein P, Gilissen C, van Bon BW, Pfundt R, Willemsen MH, Schieving JH, Leonardi E, Soli F, Murgia A, Guo H, Zhang Q, Xia K, Fagerberg CR, Beier CP, Larsen MJ, Valenzuela I, Fernández-Álvarez P, Xiong S, Śmigiel R, López-González V, Armengol L, Morleo M, Selicorni A, Torella A, Blyth M, Cooper NS, Wilson V, Oegema R, Herenger Y, Garde A, Bruel AL, Tran Mau-Them F, Maddocks AB, Bain JM, Bhat MA, Costain G, Kannu P, Marwaha A, Champaigne NL, Friez MJ, Richardson EB, Gowda VK, Srinivasan VM, Gupta Y, Lim TY, Sanna-Cherchi S, Lemaitre B, Yamaji T, Hanada K, Burke JE, Jakšić AM, McCabe BD, De Los Rios P, Hornemann T, D’Angelo G, Gennarino VA. CERT1 mutations perturb human development by disrupting sphingolipid homeostasis. J Clin Invest 2023; 133:e165019. [PMID: 36976648 PMCID: PMC10178846 DOI: 10.1172/jci165019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are associated with intellectual disability, but the pathogenic mechanism remains obscure. Here, we characterize 31 individuals with de novo missense variants in CERT1. Several variants fall into a previously uncharacterized dimeric helical domain that enables CERT homeostatic inactivation, without which sphingolipid production goes unchecked. The clinical severity reflects the degree to which CERT autoregulation is disrupted, and inhibiting CERT pharmacologically corrects morphological and motor abnormalities in a Drosophila model of the disease, which we call ceramide transporter (CerTra) syndrome. These findings uncover a central role for CERT autoregulation in the control of sphingolipid biosynthetic flux, provide unexpected insight into the structural organization of CERT, and suggest a possible therapeutic approach for patients with CerTra syndrome.
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Affiliation(s)
- Charlotte Gehin
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Museer A. Lone
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Winston Lee
- Department of Genetics and Development and
- Department Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Laura Capolupo
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylvia Ho
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Adekemi M. Adeyemi
- Department of Medical Genetics, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada
| | - Erica H. Gerkes
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Alexander P.A. Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, Netherlands
| | - Estrella López-Martín
- Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III, Madrid, Spain
| | - Eva Bermejo-Sánchez
- Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Center of Functional Genomics, Berlin, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Daniel Gräfe
- Department of Pediatric Radiology, University Hospital Leipzig, Leipzig, Leipzig, Germany
| | - Ina Knerr
- National Centre for Inherited Metabolic Disorders, Children’s Health Ireland (CHI) at Temple Street, Dublin, Ireland
- UCD School of Medicine, Dublin, Ireland
| | - Eppie R. Jones
- Genuity Science, Cherrywood Business Park, Dublin, Ireland
| | - Stefano Zamuner
- Institute of Physics, School of Basic Sciences, École Polytechnique Féderale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A. Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Facility, EPFL and Swiss Institute of Bioinformatics, Lausanne Switzerland
| | - Vidya Kunnathully
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
| | - Brandon E. Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Anthony Vocat
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | | | - Evelyne Ruchti
- Brain Mind Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Greta Limoni
- Brain Mind Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Samuel Bourgeat
- Brain Mind Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Petra Henklein
- Berlin Institute of Health, Institut für Biochemie, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Gilissen
- Radboud University Medical Center, Department of Human Genetics, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | - Bregje W. van Bon
- Radboud University Medical Center, Department of Human Genetics, Nijmegen, Netherlands
| | - Rolph Pfundt
- Radboud University Medical Center, Department of Human Genetics, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | | | - Jolanda H. Schieving
- Radboud University Medical Center, Department of Pediatric Neurology, Amalia Children’s Hospital and Donders Institute for Brain, Cognition and Behavior, Nijmegen, Netherlands
| | - Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Fiorenza Soli
- Medical Genetics Department, APSS Trento, Trento, Italy
| | - Alessandra Murgia
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Christina R. Fagerberg
- Department of Neurology, Odense University Hospital, and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Christoph P. Beier
- Department of Neurology, Odense University Hospital, and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J. Larsen
- Department of Neurology, Odense University Hospital, and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, University Hospital Vall d′Hebron, Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Paula Fernández-Álvarez
- Department of Clinical and Molecular Genetics, University Hospital Vall d′Hebron, Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Shiyi Xiong
- Fetal Medicine Unit and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Robert Śmigiel
- Department of Family and Pediatric Nursing, Medical University, Wroclaw, Poland
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER-ISCIII, Murcia, Spain
| | - Lluís Armengol
- Quantitative Genomic Medicine Laboratories, S.L., CSO & CEO, Esplugues del Llobregat, Barcelona, Catalunya, Spain
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples, Italy
| | - Angelo Selicorni
- Department of Pediatrics, ASST Lariana Sant’ Anna Hospital, San Fermo Della Battaglia, Como, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples, Italy
| | - Moira Blyth
- North of Scotland Regional Genetics Service, Clinical Genetics Centre, Ashgrove House, Foresterhill, Aberdeen, United Kingdom
| | - Nicola S. Cooper
- W Midlands Clinical Genetics Service, Birmingham Women’s Hospital, Edgbaston Birmingham, United Kingdom
| | - Valerie Wilson
- Northern Regional Genetics Laboratory, Newcastle upon Tyne, United Kingdom
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Yvan Herenger
- Genetica AG, Humangenetisches Labor und Beratungsstelle, Zürich, Switzerland
| | - Aurore Garde
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d’Enfants, CHU Dijon, Dijon, France
- UMR1231 GAD, INSERM – Université Bourgogne-Franche Comté, Dijon, France
| | - Ange-Line Bruel
- UMR1231 GAD, INSERM – Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frederic Tran Mau-Them
- UMR1231 GAD, INSERM – Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Alexis B.R. Maddocks
- Department of Radiology at Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer M. Bain
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, Columbia University Medical Center, New York, New York, USA
| | - Musadiq A. Bhat
- Institute of Pharmacology and Toxicology University of Zürich, Zürich, Switzerland
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ashish Marwaha
- Department of Medical Genetics, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada
| | - Neena L. Champaigne
- Greenwood Genetic Center and the Medical University of South Carolina, Greenwood, South Carolina, USA
| | - Michael J. Friez
- Greenwood Genetic Center and the Medical University of South Carolina, Greenwood, South Carolina, USA
| | - Ellen B. Richardson
- Greenwood Genetic Center and the Medical University of South Carolina, Greenwood, South Carolina, USA
| | - Vykuntaraju K. Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Yask Gupta
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York, USA
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York, USA
| | | | - Toshiyuki Yamaji
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - John E. Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ana Marjia Jakšić
- Brain Mind Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Brian D. McCabe
- Brain Mind Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Paolo De Los Rios
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Physics, School of Basic Sciences, École Polytechnique Féderale de Lausanne (EPFL), Lausanne, Switzerland
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Giovanni D’Angelo
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
- Global Health Institute, School of Life Sciences and
| | - Vincenzo A. Gennarino
- Department of Genetics and Development and
- Department of Pediatrics
- Department of Neurology
- Columbia Stem Cell Initiative, and
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, New York, USA
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6
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Krapp LF, Abriata LA, Cortés Rodriguez F, Dal Peraro M. PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces. Nat Commun 2023; 14:2175. [PMID: 37072397 PMCID: PMC10113261 DOI: 10.1038/s41467-023-37701-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Proteins are essential molecular building blocks of life, responsible for most biological functions as a result of their specific molecular interactions. However, predicting their binding interfaces remains a challenge. In this study, we present a geometric transformer that acts directly on atomic coordinates labeled only with element names. The resulting model-the Protein Structure Transformer, PeSTo-surpasses the current state of the art in predicting protein-protein interfaces and can also predict and differentiate between interfaces involving nucleic acids, lipids, ions, and small molecules with high confidence. Its low computational cost enables processing high volumes of structural data, such as molecular dynamics ensembles allowing for the discovery of interfaces that remain otherwise inconspicuous in static experimentally solved structures. Moreover, the growing foldome provided by de novo structural predictions can be easily analyzed, providing new opportunities to uncover unexplored biology.
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Affiliation(s)
- Lucien F Krapp
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Fabio Cortés Rodriguez
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland.
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7
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Val DS, Marchisio F, Di Nardo L, Peirú S, Aguirre A, Abriata LA, Palacios LE, Rasia RM, Castelli ME, Menzella HG. Sustainable Refining of Vegetable Oil Made Easy with a Designer Phospholipase C Enzyme. J Agric Food Chem 2023; 71:5275-5282. [PMID: 36961295 DOI: 10.1021/acs.jafc.2c09176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The increasing demand pressures the vegetable oil industry to develop novel refining methods. Degumming with type C phospholipases (PLCs) is a green technology and provides extra oil. However, natural PLCs are not active under the harsh conditions used in oil refining plants, requiring additional unit operations. These upfront capital expenditures and the associated operational costs hinder the adoption of this method. Here, we present a process based on ChPLC, a synthetic PLC obtained by consensus sequence design, possessing superior thermal stability and catalytic properties. Using ChPLC, crude soybean oil degumming was completed at 80 °C in 30 min, the temperature and residence time imposed by the design of existing oil refining plants. Remarkably, an extra yield of oil of 2% was obtained using 60% of the dose recommended for PLCs marketed today, saving upfront investments and reducing the operational cost of degumming. A techno-economic analysis indicates that, for medium size plants, ChPLC reduces the overall cost of soybean oil enzymatic degumming by 58%. The process presented here facilitates the implementation of enzymatic technologies to oil producers, regardless of their processing capacity, bringing potential annual benefits in the billion-dollar range for the global economy.
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Affiliation(s)
- Diego S Val
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | - Fiorela Marchisio
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | - Luisina Di Nardo
- Instituto de Biología Celular y Molecular de Rosario (IBR), Fbioyf-UNR-CONICET. Ocampo y Esmeralda, 2000 Rosario, Argentina
| | | | | | - Luciano A Abriata
- Ecole Polytechnique Federale de Lausanne, Rte Cantonale, 1015 Lausanne, Switzerland
| | - Luis E Palacios
- Industrial Innovation and Technology Development, Conde 1820, 1428 CABA Buenos Aires, Argentina
| | - Rodolfo M Rasia
- Plataforma Argentina de Biología Estructural y Metabolómica, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - María E Castelli
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | - Hugo G Menzella
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
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8
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Sandoz PA, Denhardt-Eriksson RA, Abrami L, Abriata LA, Spreemann G, Maclachlan C, Ho S, Kunz B, Hess K, Knott G, S Mesquita F, Hatzimanikatis V, van der Goot FG. Dynamics of CLIMP-63 S-acylation control ER morphology. Nat Commun 2023; 14:264. [PMID: 36650170 PMCID: PMC9844198 DOI: 10.1038/s41467-023-35921-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
The complex architecture of the endoplasmic reticulum (ER) comprises distinct dynamic features, many at the nanoscale, that enable the coexistence of the nuclear envelope, regions of dense sheets and a branched tubular network that spans the cytoplasm. A key player in the formation of ER sheets is cytoskeleton-linking membrane protein 63 (CLIMP-63). The mechanisms by which CLIMP-63 coordinates ER structure remain elusive. Here, we address the impact of S-acylation, a reversible post-translational lipid modification, on CLIMP-63 cellular distribution and function. Combining native mass-spectrometry, with kinetic analysis of acylation and deacylation, and data-driven mathematical modelling, we obtain in-depth understanding of the CLIMP-63 life cycle. In the ER, it assembles into trimeric units. These occasionally exit the ER to reach the plasma membrane. However, the majority undergoes S-acylation by ZDHHC6 in the ER where they further assemble into highly stable super-complexes. Using super-resolution microscopy and focused ion beam electron microscopy, we show that CLIMP-63 acylation-deacylation controls the abundance and fenestration of ER sheets. Overall, this study uncovers a dynamic lipid post-translational regulation of ER architecture.
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Affiliation(s)
- Patrick A Sandoz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modelling, Institute of Bioengineering, EPFL and Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Protein Production and Structure Core Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | | | - Sylvia Ho
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Béatrice Kunz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Kathryn Hess
- Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Graham Knott
- BioEM Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
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9
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Manicki M, Aydin H, Abriata LA, Overmyer KA, Guerra RM, Coon JJ, Dal Peraro M, Frost A, Pagliarini DJ. Structure and functionality of a multimeric human COQ7:COQ9 complex. Mol Cell 2022; 82:4307-4323.e10. [PMID: 36306796 PMCID: PMC10058641 DOI: 10.1016/j.molcel.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/01/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.
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Affiliation(s)
- Mateusz Manicki
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Halil Aydin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53506, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub and Altos Labs Bay Area Institute of Science, San Francisco, CA, USA.
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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10
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Affiliation(s)
- Suiyang Liao
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Lixia Wei
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Luciano A. Abriata
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
- Interfaculty Bioengineering Institute, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
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11
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Mesquita FS, Abrami L, Sergeeva O, Turelli P, Qing E, Kunz B, Raclot C, Paz Montoya J, Abriata LA, Gallagher T, Dal Peraro M, Trono D, D'Angelo G, van der Goot FG. S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity. Dev Cell 2021; 56:2790-2807.e8. [PMID: 34599882 PMCID: PMC8486083 DOI: 10.1016/j.devcel.2021.09.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 12/28/2022]
Abstract
SARS-CoV-2 virions are surrounded by a lipid bilayer that contains membrane proteins such as spike, responsible for target-cell binding and virus fusion. We found that during SARS-CoV-2 infection, spike becomes lipid modified, through the sequential action of the S-acyltransferases ZDHHC20 and 9. Particularly striking is the rapid acylation of spike on 10 cytosolic cysteines within the ER and Golgi. Using a combination of computational, lipidomics, and biochemical approaches, we show that this massive lipidation controls spike biogenesis and degradation, and drives the formation of localized ordered cholesterol and sphingolipid-rich lipid nanodomains in the early Golgi, where viral budding occurs. Finally, S-acylation of spike allows the formation of viruses with enhanced fusion capacity. Our study points toward S-acylating enzymes and lipid biosynthesis enzymes as novel therapeutic anti-viral targets.
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Affiliation(s)
| | - Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Oksana Sergeeva
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Priscilla Turelli
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Béatrice Kunz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Charlène Raclot
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Jonathan Paz Montoya
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Giovanni D'Angelo
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
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12
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Rodríguez FC, Dal Peraro M, Abriata LA. Democratizing interactive, immersive experiences for science education with WebXR. Nat Comput Sci 2021; 1:631-632. [PMID: 38217192 DOI: 10.1038/s43588-021-00142-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Affiliation(s)
- Fabio Cortés Rodríguez
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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13
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Abstract
As most other aspects of life, education was strongly affected by the lockdowns imposed to slow down the spread of the COVID-19 pandemic. Teachers at all levels of education suddenly faced the challenge of adapting their courses to online versions. This posed various problems, from the pedagogical and psychological components of having to teach and learn online to the technical problems of internet connectivity and especially of rethinking hands-on activities. The latter point was especially important for subjects who involve very practical learning, for which teachers had to find out alternative activities that the students could carry out at home. In the subjects dealing with natural sciences, impaired access to instrumentation and reagents was a major limitation, but the community turned out very resourceful. Here I demonstrate this resourcefulness for the case of undergraduate chemistry and biology courses, focusing on how do-it-yourself open technologies, smartphone-based instruments and simulations, at-home chemistry with household reagents, online video material, and introductory programming and bioinformatics, which helped to overcome these difficult times and likely even shape the future of science education.
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Affiliation(s)
- Luciano A Abriata
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Protein Production and Structure Core Facility, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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14
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Chiki A, Zhang Z, Rajasekhar K, Abriata LA, Rostami I, Krapp LF, Boudeffa D, Dal Peraro M, Lashuel HA. Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation. Front Mol Biosci 2021; 8:686086. [PMID: 34381813 PMCID: PMC8352439 DOI: 10.3389/fmolb.2021.686086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/06/2021] [Indexed: 01/24/2023] Open
Abstract
Post-translational modifications (PTMs) within the first 17 amino acids (Nt17) of the Huntingtin protein (Htt) have been shown to inhibit the aggregation and attenuate the toxicity of mutant Htt proteins in vitro and in various models of Huntington’s disease. Here, we expand on these studies by investigating the effect of methionine eight oxidation (oxM8) and its crosstalk with lysine 6 acetylation (AcK6) or threonine 3 phosphorylation (pT3) on the aggregation of mutant Httex1 (mHttex1). We show that M8 oxidation delays but does not inhibit the aggregation and has no effect on the final morphologies of mHttex1aggregates. The presence of both oxM8 and AcK6 resulted in dramatic inhibition of Httex1 fibrillization. Circular dichroism spectroscopy and molecular dynamics simulation studies show that PTMs that lower the mHttex1 aggregation rate (oxM8, AcK6/oxM8, pT3, pT3/oxM8, and pS13) result in increased population of a short N-terminal helix (first eight residues) in Nt17 or decreased abundance of other helical forms, including long helix and short C-terminal helix. PTMs that did not alter the aggregation rate (AcK6) of mHttex1 exhibit a similar distribution of helical conformation as the unmodified peptides. These results show that the relative abundance of N- vs. C-terminal helical conformations and long helices, rather than the overall helicity of Nt17, better explains the effect of different Nt17 PTMs on mHttex1; thus, explaining the lack of correlation between the effect of PTMs on the overall helicity of Nt17 and mHttex1 aggregation in vitro. Taken together, our results provide novel structural insight into the differential effects of single PTMs and crosstalk between different PTMs in regulating mHttex1 aggregation.
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Affiliation(s)
- Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Zhidian Zhang
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Laboratory for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kolla Rajasekhar
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Iman Rostami
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Lucien F Krapp
- Laboratory for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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15
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Louis BBV, Abriata LA. Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures. Mol Biotechnol 2021; 63:863-884. [PMID: 34101125 PMCID: PMC8443528 DOI: 10.1007/s12033-021-00349-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still unsolved even for the relatively simple case of small, soluble, globular, monomeric, two-state-folder proteins. Many articles discuss the limitations of prediction methods and of the datasets used to train them, which result in low reliability for actual applications despite globally capturing trends. Here, we review these and other issues by analyzing one of the most detailed, carefully curated datasets of melting temperature change (ΔTm) upon mutation for proteins with high-resolution structures. After examining the composition of this dataset to discuss imbalances and biases, we inspect several of its entries assisted by an online app for data navigation and structure display and aided by a neural network that predicts ΔTm with accuracy close to that of programs available to this end. We pose that the ΔTm predictions of our network, and also likely those of other programs, account only for a baseline-like general effect of each type of amino acid substitution which then requires substantial corrections to reproduce the actual stability changes. The corrections are very different for each specific case and arise from fine structural details which are not well represented in the dataset and which, despite appearing reasonable upon visual inspection of the structures, are hard to encode and parametrize. Based on these observations, additional analyses, and a review of recent literature, we propose recommendations for developers of stability prediction methods and for efforts aimed at improving the datasets used for training. We leave our interactive interface for analysis available online at http://lucianoabriata.altervista.org/papersdata/proteinstability2021/s1626navigation.html so that users can further explore the dataset and baseline predictions, possibly serving as a tool useful in the context of structural biology and protein biotechnology research and as material for education in protein biophysics.
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Affiliation(s)
- Benjamin B V Louis
- Master of Life Sciences Engineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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16
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Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021; 12:2675. [PMID: 33976148 PMCID: PMC8113477 DOI: 10.1038/s41467-021-22883-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.
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Affiliation(s)
- Corey A Stevens
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabienne Bachtiger
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Xu-Dong Kong
- Laboratory of Therapeutic Proteins and Peptides, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Matthew I Gibson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK.,Warwick Medical School, University of Warwick, Coventry, UK
| | - Harm-Anton Klok
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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17
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Ried MK, Wild R, Zhu J, Pipercevic J, Sturm K, Broger L, Harmel RK, Abriata LA, Hothorn LA, Fiedler D, Hiller S, Hothorn M. Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis. Nat Commun 2021; 12:384. [PMID: 33452263 PMCID: PMC7810988 DOI: 10.1038/s41467-020-20681-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/09/2020] [Indexed: 12/05/2022] Open
Abstract
Phosphorus is an essential nutrient taken up by organisms in the form of inorganic phosphate (Pi). Eukaryotes have evolved sophisticated Pi sensing and signaling cascades, enabling them to stably maintain cellular Pi concentrations. Pi homeostasis is regulated by inositol pyrophosphate signaling molecules (PP-InsPs), which are sensed by SPX domain-containing proteins. In plants, PP-InsP-bound SPX receptors inactivate Myb coiled-coil (MYB-CC) Pi starvation response transcription factors (PHRs) by an unknown mechanism. Here we report that a InsP8–SPX complex targets the plant-unique CC domain of PHRs. Crystal structures of the CC domain reveal an unusual four-stranded anti-parallel arrangement. Interface mutations in the CC domain yield monomeric PHR1, which is no longer able to bind DNA with high affinity. Mutation of conserved basic residues located at the surface of the CC domain disrupt interaction with the SPX receptor in vitro and in planta, resulting in constitutive Pi starvation responses. Together, our findings suggest that InsP8 regulates plant Pi homeostasis by controlling the oligomeric state and hence the promoter binding capability of PHRs via their SPX receptors. Plants regulate phosphate homeostasis via the interaction of PHR transcription factors with SPX receptors bound to inositol pyrophosphate signaling molecules. Here the authors show that inositol pyrophosphate-bound SPX interacts with the coiled-coil domain of PHR, which regulates the oligomerization and activity of the transcription factor.
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Affiliation(s)
- Martina K Ried
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.,Leibniz Institute of Plant Biochemistry, 06120, Halle, Germany
| | - Rebekka Wild
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.,Institut de Biologie Structurale (IBS), 38044, Grenoble, France
| | - Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | | | - Kristina Sturm
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Robert K Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, 12489, Berlin, Germany
| | - Luciano A Abriata
- Protein production and structure Core Facility, EPFL, 1015, Lausanne, Switzerland
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, 30419, Hannover, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, 12489, Berlin, Germany
| | | | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.
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18
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Chiki A, Ricci J, Hegde R, Abriata LA, Reif A, Boudeffa D, Lashuel HA. Site-Specific Phosphorylation of Huntingtin Exon 1 Recombinant Proteins Enabled by the Discovery of Novel Kinases. Chembiochem 2021; 22:217-231. [PMID: 32805086 PMCID: PMC8698011 DOI: 10.1002/cbic.202000508] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Post-translational modifications (PTMs) within the first 17 amino acids (Nt17) of exon 1 of the Huntingtin protein (Httex1) play important roles in modulating its cellular properties and functions in health and disease. In particular, phosphorylation of threonine and serine residues (T3, S13, and/or S16) has been shown to inhibit Htt aggregation in vitro and inclusion formation in cellular and animal models of Huntington's disease (HD). In this paper, we describe a new and simple methodology for producing milligram quantities of highly pure wild-type or mutant Httex1 proteins that are site-specifically phosphorylated at T3 or at both S13 and S16. This advance was enabled by 1) the discovery and validation of novel kinases that efficiently phosphorylate Httex1 at S13 and S16 (TBK1), at T3 (GCK) or T3 and S13 (TNIK and HGK), and 2) the development of an efficient methodology for producing recombinant native Httex1 proteins by using a SUMO-fusion expression and purification strategy.[26] As a proof of concept, we demonstrate how this method can be applied to produce Httex1 proteins that are both site-specifically phosphorylated and fluorescently or isotopically labeled. Together, these advances should increase access to these valuable tools and expand the range of methods and experimental approaches that can be used to elucidate the mechanisms by which phosphorylation influences Httex1 or HTT structure, aggregation, interactome, and function(s) in health and disease.
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Affiliation(s)
- Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Jonathan Ricci
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Ramanath Hegde
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Luciano A. Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular ModelingEcole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB)1015LausanneSwitzerland
| | - Andreas Reif
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
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19
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Abriata LA, Dal Peraro M. State-of-the-art web services for de novo protein structure prediction. Brief Bioinform 2020; 22:5870389. [PMID: 34020540 DOI: 10.1093/bib/bbaa139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent in the last round of the Critical Assessment of Structure Prediction (CASP), which presented several very good models for the hardest targets. Unfortunately, literature reporting on these advances often lacks digests tailored to lay end users; moreover, some of the top-ranking predictors do not provide webservers that can be used by nonexperts. How can then end users benefit from these advances and correctly interpret the predicted models? Here we review the web resources that biologists can use today to take advantage of these state-of-the-art methods in their research, including not only the best de novo modeling servers but also datasets of models precomputed by experts for structurally uncharacterized protein families. We highlight their features, advantages and pitfalls for predicting structures of proteins without clear templates. We present a broad number of applications that span from driving forward biochemical investigations that lack experimental structures to actually assisting experimental structure determination in X-ray diffraction, cryo-EM and other forms of integrative modeling. We also discuss issues that must be considered by users yet still require further developments, such as global and residue-wise model quality estimates and sources of residue coevolution other than monomeric tertiary structure.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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20
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Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science 2020; 368:eaay5051. [PMID: 32409444 PMCID: PMC7391827 DOI: 10.1126/science.aay5051] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/30/2020] [Accepted: 04/08/2020] [Indexed: 12/27/2022]
Abstract
De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a protein design algorithm called TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. In both mice and nonhuman primates, cocktails of three de novo-designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused preexisting antibody responses toward defined neutralization epitopes. Overall, our design approach opens the possibility of targeting specific epitopes for the development of vaccines and therapeutic antibodies and, more generally, will be applicable to the design of de novo proteins displaying complex functional motifs.
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Affiliation(s)
- Fabian Sesterhenn
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Che Yang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Johannes T Cramer
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Xiaolin Wen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Luciano A Abriata
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Iga Kucharska
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Giacomo Castoro
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Sabrina S Vollers
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Elie Dheilly
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Patricia Corthésy
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Sandrine Georgeon
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Mélanie Villard
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | | | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Teresa Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | | | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Sean Ervin
- Wake Forest Baptist Medical Center, Winston Salem, NC 27157, USA
| | | | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - John T Bates
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jean-Philippe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Microbiology and Immunology & Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Theodore Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Institute of Biochemistry, Center of Structural and Cell Biology in Medicine, University of Luebeck, D-23538 Luebeck, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, 30625 Hannover, Germany
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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21
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Kong XD, Moriya J, Carle V, Pojer F, Abriata LA, Deyle K, Heinis C. De novo development of proteolytically resistant therapeutic peptides for oral administration. Nat Biomed Eng 2020; 4:560-571. [DOI: 10.1038/s41551-020-0556-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
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22
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Abstract
Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) have the potential to more broadly explore the conformational landscapes of protein complexes and therefore will enhance our ability to predict the diverse conformations of tertiary and quaternary protein structures that are functionally relevant in physiological conditions.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
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23
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Abriata LA. Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers. PeerJ Comput Sci 2020; 6:e260. [PMID: 33816912 PMCID: PMC7924717 DOI: 10.7717/peerj-cs.260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/22/2020] [Indexed: 06/12/2023]
Abstract
For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, most tools available today for immersive modeling require specialized hardware and software, and are costly and cumbersome to set up. These limitations prevent wide use of immersive technologies in education and research centers in a standardized form, which in turn prevents large-scale testing of the actual effects of such technologies on learning and thinking processes. Here, I discuss building blocks for creating marker-based AR applications that run as web pages on regular computers, and explore how they can be exploited to develop web content for handling virtual molecular systems in commodity AR with no more than a webcam- and internet-enabled computer. Examples span from displaying molecules, electron microscopy maps and molecular orbitals with minimal amounts of HTML code, to incorporation of molecular mechanics, real-time estimation of experimental observables and other interactive resources using JavaScript. These web apps provide virtual alternatives to physical, plastic-made molecular modeling kits, where the computer augments the experience with information about spatial interactions, reactivity, energetics, etc. The ideas and prototypes introduced here should serve as starting points for building active content that everybody can utilize online at minimal cost, providing novel interactive pedagogic material in such an open way that it could enable mass-testing of the effect of immersive technologies on chemistry education.
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Affiliation(s)
- Luciano A. Abriata
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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24
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Abriata LA, Lepore R, Dal Peraro M. About the need to make computational models of biological macromolecules available and discoverable. Bioinformatics 2020; 36:2952-2954. [DOI: 10.1093/bioinformatics/btaa086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/13/2020] [Accepted: 02/06/2020] [Indexed: 12/19/2022] Open
Affiliation(s)
- Luciano A Abriata
- Laboratory for Biomolecular Modeling
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
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25
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Mayorov A, Dal Peraro M, Abriata LA. Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes. Mol Biol Evol 2020; 36:1728-1733. [PMID: 31004173 DOI: 10.1093/molbev/msz096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified the effects of active sites on site-specific constraints for physicochemical traits. We found that conservation gradients respond to constraints for polarity, hydrophobicity, flexibility, rigidity and structure in ways consistent with fold polarity principles; while sites far from active sites seem to experience no physicochemical constraint, rather being highly variable and favoring amino acids of low metabolic cost. Globally, our results highlight that amino acid variation contains finer information about protein structure than usually regarded in evolutionary models, and that this information is retrievable automatically with simple fits. We propose that analyses of the kind presented here incorporated into models of protein evolution should allow for better description of the physical chemistry that underlies molecular evolution.
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Affiliation(s)
- Alexander Mayorov
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Protein Production and Structure Core Facility, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
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26
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Belluzo BS, Abriata LA, Giannini E, Mihovilcevic D, Dal Peraro M, Llarrull LI. An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in β-lactam resistance. Sci Rep 2019; 9:19558. [PMID: 31862951 PMCID: PMC6925264 DOI: 10.1038/s41598-019-55923-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to β-lactam antibiotics, and generally to many other antibacterial agents. Its resistance mechanisms to β-lactam antibiotics are activated only when the bacterium encounters a β-lactam. This activation is regulated by the transmembrane sensor/signal transducer proteins BlaR1 and MecR1. Neither the transmembrane/metalloprotease domain, nor the complete MecR1 and BlaR1 proteins, are isolatable for mechanistic study. Here we propose a model for full-length MecR1 based on homology modeling, residue coevolution data, a new extensive experimental mapping of transmembrane topology, partial structures, molecular simulations, and available NMR data. Our model defines the metalloprotease domain as a hydrophilic transmembrane chamber effectively sealed by the apo-sensor domain. It proposes that the amphipathic helices inserted into the gluzincin domain constitute the route for transmission of the β-lactam-binding event in the extracellular sensor domain, to the intracellular and membrane-embedded zinc-containing active site. From here, we discuss possible routes for subsequent activation of proteolytic action. This study provides the first coherent model of the structure of MecR1, opening routes for future functional investigations on how β-lactam binding culminates in the proteolytic degradation of MecI.
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Affiliation(s)
- Bruno S Belluzo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Estefanía Giannini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Damila Mihovilcevic
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Leticia I Llarrull
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina. .,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000, Rosario, Argentina.
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27
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Morgada MN, Emiliani F, Chacón KN, Álvarez-Paggi D, Murgida DH, Blackburn NJ, Abriata LA, Vila AJ. pH-Induced Binding of the Axial Ligand in an Engineered Cu A Site Favors the π u State. Inorg Chem 2019; 58:15687-15691. [DOI: 10.1021/acs.inorgchem.9b01868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcos N. Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda,
Predio CONICET Rosario, 2000 Rosario, Argentina
| | - Florencia Emiliani
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda,
Predio CONICET Rosario, 2000 Rosario, Argentina
| | - Kelly N. Chacón
- Department of Chemical Physiology and Biochemistry, Oregon Health and Sciences University, Portland, Oregon 97239, United States
| | - Damián Álvarez-Paggi
- INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria C1428EHA, Buenos Aires, Argentina
| | - Daniel H. Murgida
- INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria C1428EHA, Buenos Aires, Argentina
| | - Ninian J. Blackburn
- Department of Chemical Physiology and Biochemistry, Oregon Health and Sciences University, Portland, Oregon 97239, United States
| | - Luciano A. Abriata
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda,
Predio CONICET Rosario, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda,
Predio CONICET Rosario, 2000 Rosario, Argentina
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Abriata LA, Tamò GE, Dal Peraro M. A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments. Proteins 2019; 87:1100-1112. [PMID: 31344267 DOI: 10.1002/prot.25787] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 07/19/2019] [Indexed: 12/22/2022]
Abstract
We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of models for each evaluation unit (EU); (b) ranking of predictors resulting from this evaluation and from global scores; and (c) evaluation of progress, state of the art, and current limitations of protein structure prediction. We witness a sizable improvement in tertiary structure prediction building on the progress observed from CASP11 to CASP12, with (a) top models reaching backbone RMSD <3 å for several EUs of size <150 residues, contributed by many groups; (b) at least one model that roughly captures global topology for all EUs, probably unprecedented in this track of CASP; and (c) even quite good models for full, unsplit targets. Better structure predictions are brought about mainly by improved residue-residue contact predictions, and since this CASP also by distance predictions, achieved through state-of-the-art machine learning methods which also progressed to work with slightly shallower alignments compared to CASP12. As we reach a new realm of tertiary structure prediction quality, new directions are proposed and explored for future CASPs: (a) dropping splitting into EUs, (b) rethinking difficulty metrics probably in terms of contact and distance predictions, (c) assessing also side chains for models of high backbone accuracy, and (d) assessing residue-wise and possibly residue-residue quality estimates.
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Affiliation(s)
- Luciano A Abriata
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Giorgio E Tamò
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matteo Dal Peraro
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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29
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Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA. Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States. mBio 2019; 10:e00405-19. [PMID: 31266860 PMCID: PMC6606795 DOI: 10.1128/mbio.00405-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 01/06/2023] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative, nonfermenting, environmental bacillus that is an important cause of nosocomial infections, primarily associated with the respiratory tract in the immunocompromised population. Aiming to understand the population structure, microbiological characteristics and impact of allelic variation on β-lactamase structure and function, we collected 130 clinical isolates from across the United States. Identification of 90 different sequence types (STs), of which 63 are new allelic combinations, demonstrates the high diversity of this species. The majority of the isolates (45%) belong to genomic group 6. We also report excellent activity of the ceftazidime-avibactam and aztreonam combination, especially against strains recovered from blood and respiratory infections for which the susceptibility is higher than the susceptibility to trimethoprim-sulfamethoxazole, considered the "first-line" antibiotic to treat S. maltophilia Analysis of 73 blaL1 and 116 blaL2 genes identified 35 and 43 novel variants of L1 and L2 β-lactamases, respectively. Investigation of the derived amino acid sequences showed that substitutions are mostly conservative and scattered throughout the protein, preferentially affecting positions that do not compromise enzyme function but that may have an impact on substrate and inhibitor binding. Interestingly, we detected a probable association between a specific type of L1 and L2 and genomic group 6. Taken together, our results provide an overview of the molecular epidemiology of S. maltophilia clinical strains from the United States. In particular, the discovery of new L1 and L2 variants warrants further study to fully understand the relationship between them and the β-lactam resistance phenotype in this pathogen.IMPORTANCE Multiple antibiotic resistance mechanisms, including two β-lactamases, L1, a metallo-β-lactamase, and L2, a class A cephalosporinase, make S. maltophilia naturally multidrug resistant. Thus, infections caused by S. maltophilia pose a big therapeutic challenge. Our study aims to understand the microbiological and molecular characteristics of S. maltophilia isolates recovered from human sources. A highlight of the resistance profile of this collection is the excellent activity of the ceftazidime-avibactam and aztreonam combination. We hope this result prompts controlled and observational studies to add clinical data on the utility and safety of this therapy. We also identify 35 and 43 novel variants of L1 and L2, respectively, some of which harbor novel substitutions that could potentially affect substrate and/or inhibitor binding. We believe our results provide valuable knowledge to understand the epidemiology of this species and to advance mechanism-based inhibitor design to add to the limited arsenal of antibiotics active against this pathogen.
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Affiliation(s)
- Maria F Mojica
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Joseph D Rutter
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Magdalena Taracila
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Krisztina M Papp-Wallace
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Thomas J Walsh
- Transplantation Oncology Infectious Diseases Program, Weill Cornell Medical Center, New York, New York, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Medical Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- GRECC, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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30
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Wang X, Roger M, Clément R, Lecomte S, Biaso F, Abriata LA, Mansuelle P, Mazurenko I, Giudici-Orticoni MT, Lojou E, Ilbert M. Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin. Chem Sci 2018; 9:4879-4891. [PMID: 29910941 PMCID: PMC5982212 DOI: 10.1039/c8sc01615a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 12/15/2022] Open
Abstract
Acidithiobacillus ferrooxidans, a chemolithoautotrophic Gram-negative bacterium, has a remarkable ability to obtain energy from ferrous iron oxidation at pH 2. Several metalloproteins have been described as being involved in this respiratory chain coupling iron oxidation with oxygen reduction. However, their properties and physiological functions remain largely unknown, preventing a clear understanding of the global mechanism. In this work, we focus on two metalloproteins of this respiratory pathway, a diheme cytochrome c4 (Cyt c4) and a green copper protein (AcoP) of unknown function. We first demonstrate the formation of a complex between these two purified proteins, which allows homogeneous intermolecular electron-transfer in solution. We then mimic the physiological interaction between the two partners by replacing one at a time with electrodes displaying different chemical functionalities. From the electrochemical behavior of individual proteins, we show that, while electron transfer on AcoP requires weak electrostatic interaction, electron transfer on Cyt c4 tolerates different charge and hydrophobicity conditions, suggesting a pivotal role of this protein in the metabolic chain. The electrochemical study of the proteins incubated together demonstrates an intermolecular electron transfer involving the protein complex, in which AcoP is reduced through the high potential heme of Cyt c4. Modelling of the electrochemical signals at different scan rates allows us to estimate the rate constant of this intermolecular electron transfer in the range of a few s-1. Possible routes for electron transfer in the acidophilic bacterium are deduced.
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Affiliation(s)
- X Wang
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - M Roger
- School of Life Sciences , University of Dundee , Dundee , DD1 5EH , Scotland , UK
| | - R Clément
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - S Lecomte
- Institute for Chemistry and Biology of Membrane and Nano-objects , Allée Geoffroy St Hilaire , 33600 Pessac , France
| | - F Biaso
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - L A Abriata
- Laboratory for Biomolecular Modeling , École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics , AAB014, Station 19 , 1015 Lausanne , Switzerland
| | - P Mansuelle
- Aix Marseille Univ , CNRS , Institut de Microbiologie de la Méditerranée , FR 3479, Plate-forme Protéomique, Marseille Protéomique (MaP), B.P. 71 , 13402 Marseille Cedex 20 , France
| | - I Mazurenko
- School of Biomedical Sciences , Leeds , LS2 9JT , UK
| | - M T Giudici-Orticoni
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - E Lojou
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - M Ilbert
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
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31
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Bologna NG, Iselin R, Abriata LA, Sarazin A, Pumplin N, Jay F, Grentzinger T, Dal Peraro M, Voinnet O. Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway. Mol Cell 2018; 69:709-719.e5. [PMID: 29398448 DOI: 10.1016/j.molcel.2018.01.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/09/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
Unlike in metazoans, plant microRNAs (miRNAs) undergo stepwise nuclear maturation before engaging cytosolic, sequence-complementary transcripts in association with the silencing effector protein ARGONAUTE1 (AGO1). Since their discovery, how and under which form plant miRNAs translocate to the cytosol has remained unclear, as has their sub-cellular AGO1 loading site(s). Here, we show that the N termini of all plant AGO1s contain a nuclear-localization (NLS) and nuclear-export signal (NES) that, in Arabidopsis thaliana (At), enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(EXPO1)/NES-dependent nuclear export. Nuclear-only AtAGO1 contains the same 2'O-methylated miRNA cohorts as its nucleo-cytosolic counterpart, but it preferentially interacts with the miRNA loading chaperone HSP90. Furthermore, mature miRNA translocation and miRNA-mediated silencing both require AtAGO1 nucleo-cytosolic shuttling. These findings lead us to propose a substantially revised view of the plant miRNA pathway in which miRNAs are matured, methylated, loaded into AGO1 in the nucleus, and exported to the cytosol as AGO1:miRNA complexes in a CRM1(EXPO1)/NES-dependent manner.
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Affiliation(s)
- Nicolas G Bologna
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Raphael Iselin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Alexis Sarazin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Nathan Pumplin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland; Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Florence Jay
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Thomas Grentzinger
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland.
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Völker JM, Dergai M, Abriata LA, Mingard Y, Ysselstein D, Krainc D, Dal Peraro M, Fischer von Mollard G, Fasshauer D, Koliwer J, Schwake M. Functional assays for the assessment of the pathogenicity of variants of GOSR2, an ER-to-Golgi SNARE involved in progressive myoclonus epilepsies. Dis Model Mech 2017; 10:1391-1398. [PMID: 28982678 PMCID: PMC5769602 DOI: 10.1242/dmm.029132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 10/02/2017] [Indexed: 11/20/2022] Open
Abstract
Progressive myoclonus epilepsies (PMEs) are inherited disorders characterized by myoclonus, generalized tonic-clonic seizures, and ataxia. One of the genes that is associated with PME is the ER-to-Golgi Qb-SNARE GOSR2, which forms a SNARE complex with syntaxin-5, Bet1 and Sec22b. Most PME patients are homozygous for a p.Gly144Trp mutation and develop similar clinical presentations. Recently, a patient who was compound heterozygous for p.Gly144Trp and a previously unseen p.Lys164del mutation was identified. Because this patient presented with a milder disease phenotype, we hypothesized that the p.Lys164del mutation may be less severe compared to p.Gly144Trp. To characterize the effect of the p.Gly144Trp and p.Lys164del mutations, both of which are present in the SNARE motif of GOSR2, we examined the corresponding mutations in the yeast ortholog Bos1. Yeasts expressing the orthologous mutants in Bos1 showed impaired growth, suggesting a partial loss of function, which was more severe for the Bos1 p.Gly176Trp mutation. Using anisotropy and gel filtration, we report that Bos1 p.Gly176Trp and p.Arg196del are capable of complex formation, but with partly reduced activity. Molecular dynamics (MD) simulations showed that the hydrophobic core, which triggers SNARE complex formation, is compromised due to the glycine-to-tryptophan substitution in both GOSR2 and Bos1. In contrast, the deletion of residue p.Lys164 (or p.Arg196del in Bos1) interferes with the formation of hydrogen bonds between GOSR2 and syntaxin-5. Despite these perturbations, all SNARE complexes stayed intact during longer simulations. Thus, our data suggest that the milder course of disease in compound heterozygous PME is due to less severe impairment of the SNARE function. Summary: Mutations in the Qb-SNARE GOSR2 cause progressive myoclonus epilepsies. The authors report the effect of two mutations on SNARE function to investigate their correlation with progression and severity of disease.
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Affiliation(s)
- Jörn M Völker
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Mykola Dergai
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Yves Mingard
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland
| | - Daniel Ysselstein
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, 60611 Chicago, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, 60611 Chicago, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | | | - Dirk Fasshauer
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland
| | - Judith Koliwer
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Michael Schwake
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany .,Department of Neurology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, 60611 Chicago, USA
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33
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Abriata LA, Rodrigues JPGLM, Salathé M, Patiny L. Augmenting Research, Education, and Outreach with Client-Side Web Programming. Trends Biotechnol 2017; 36:473-476. [PMID: 29254737 DOI: 10.1016/j.tibtech.2017.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/24/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022]
Abstract
The evolution of computing and web technologies over the past decade has enabled the development of fully fledged scientific applications that run directly on web browsers. Powered by JavaScript, the lingua franca of web programming, these 'web apps' are starting to revolutionize and democratize scientific research, education, and outreach.
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Affiliation(s)
- Luciano A Abriata
- Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
| | - João P G L M Rodrigues
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcel Salathé
- School of Life Sciences, School of Computer and Communication Sciences, EPFL, CH-1015 Lausanne, Switzerland
| | - Luc Patiny
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne CH-1015, Switzerland
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Abstract
This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. Importantly, updates of most of these databases involves steps of curation and error checks based on specific expertise about the subject molecules or interactions, and removal of sequence redundancy, both leading to better data sets for mining studies compared with the full list of raw PDB entries. The article presents the databases in groups such as those aimed to facilitate browsing through PDB entries, their molecules and their general information, those built to link protein structure with sequence and dynamics, those specific for transmembrane proteins, nucleic acids, interactions of biomacromolecules with each other and with small molecules or metal ions, and those concerning specific structural features or specific protein families. A few webservers directly connected to active databases, and a few databases that have been discontinued but would be important to have back, are also briefly commented on. Along the Briefing, sample cases where these databases have been used to aid structural studies or advance our knowledge about biological macromolecules are referenced. A few specific examples are also given where using these databases is easier and more informative than using raw PDB data.
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35
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Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins 2017; 86 Suppl 1:97-112. [DOI: 10.1002/prot.25423] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | - Giorgio E. Tamò
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | | | | | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
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Cirauqui N, Abriata LA, van der Goot FG, Dal Peraro M. Structural, physicochemical and dynamic features conserved within the aerolysin pore-forming toxin family. Sci Rep 2017; 7:13932. [PMID: 29066778 PMCID: PMC5654971 DOI: 10.1038/s41598-017-13714-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/26/2017] [Indexed: 11/10/2022] Open
Abstract
Aerolysin is the founding member of a major class of β-pore-forming toxins (β-PFTs) found throughout all kingdoms of life. PFTs are cytotoxic proteins produced as soluble monomers, which oligomerize at the membrane of target host cells forming pores that may lead to osmotic lysis and cell death. Besides their role in microbial infection, they have become interesting for their potential as biotechnological sensors and delivery systems. Using an approach that integrates bioinformatics with molecular modeling and simulation, we looked for conserved features across this large toxin family. The cell surface-binding domains present high variability within the family to provide membrane receptor specificity. On the contrary, the novel concentric double β-barrel structure found in aerolysin is highly conserved in terms of sequence, structure and conformational dynamics, which likely contribute to preserve a common transition mechanism from the prepore to the mature pore within the family.Our results point to the key role of several amino acids in the conformational changes needed for oligomerization and further pore formation, such as Y221, W227, P248, Q263 and L277, which we propose are involved in the release of the stem loop and the two adjacent β-strands to form the transmembrane β-barrel.
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Affiliation(s)
- Nuria Cirauqui
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Department of Pharmaceutical Biotechnology, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - F Gisou van der Goot
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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Abriata LA, Kinch LN, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics. Proteins 2017; 86 Suppl 1:16-26. [DOI: 10.1002/prot.25403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/03/2017] [Accepted: 10/11/2017] [Indexed: 01/31/2023]
Affiliation(s)
- Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas; Dallas Texas
| | - Giorgio E. Tamò
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | | | | | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
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Timón-Gómez A, Nývltová E, Abriata LA, Vila AJ, Hosler J, Barrientos A. Mitochondrial cytochrome c oxidase biogenesis: Recent developments. Semin Cell Dev Biol 2017; 76:163-178. [PMID: 28870773 DOI: 10.1016/j.semcdb.2017.08.055] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 12/21/2022]
Abstract
Mitochondrial cytochrome c oxidase (COX) is the primary site of cellular oxygen consumption and is essential for aerobic energy generation in the form of ATP. Human COX is a copper-heme A hetero-multimeric complex formed by 3 catalytic core subunits encoded in the mitochondrial DNA and 11 subunits encoded in the nuclear genome. Investigations over the last 50 years have progressively shed light into the sophistication surrounding COX biogenesis and the regulation of this process, disclosing multiple assembly factors, several redox-regulated processes leading to metal co-factor insertion, regulatory mechanisms to couple synthesis of COX subunits to COX assembly, and the incorporation of COX into respiratory supercomplexes. Here, we will critically summarize recent progress and controversies in several key aspects of COX biogenesis: linear versus modular assembly, the coupling of mitochondrial translation to COX assembly and COX assembly into respiratory supercomplexes.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eva Nývltová
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling & Protein Purification and Structure Facility, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Switzerland
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Jonathan Hosler
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS, United States
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States.
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Abriata LA, Spiga E, Peraro MD. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics. Biophys J 2017; 111:743-755. [PMID: 27558718 DOI: 10.1016/j.bpj.2016.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Enrico Spiga
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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40
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Abriata LA, Albanesi D, Dal Peraro M, de Mendoza D. Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor. Acc Chem Res 2017; 50:1359-1366. [PMID: 28475313 DOI: 10.1021/acs.accounts.6b00593] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Histidine kinases (HK) are the sensory proteins of two-component systems, responsible for a large fraction of bacterial responses to stimuli and environmental changes. Prototypical HKs are membrane-bound proteins that phosphorylate cognate response regulator proteins in the cytoplasm upon signal detection in the membrane or periplasm. HKs stand as potential drug targets but also constitute fascinating systems for studying proteins at work, specifically regarding the chemistry and mechanics of signal detection, transduction through the membrane, and regulation of catalytic outputs. In this Account, we focus on Bacillus subtilis DesK, a membrane-bound HK part of a two-component system that maintains appropriate membrane fluidity at low growth temperatures. Unlike most HKs, DesK has no extracytoplasmic signal-sensing domains; instead, sensing is carried out by 10 transmembrane helices (coming from two protomers) arranged in an unknown structure. The fifth transmembrane helix from each protomer connects, without any of the intermediate domains found in other HKs, into the dimerization and histidine phosphotransfer (DHp) domain located in the cytoplasm, which is followed by the ATP-binding domains (ABD). Throughout the years, genetic, biochemical, structural, and computational studies on wild-type, mutant, and truncated versions of DesK allowed us to dissect several aspects of DesK's functioning, pushing forward a more general understanding of its own structure/function relationships as well as those of other HKs. We have shown that the sensing mechanism is rooted in temperature-dependent membrane properties, most likely a combination of thickness, fluidity, and water permeability, and we have proposed possible mechanisms by which DesK senses these properties and transduces the signals. X-ray structures and computational models have revealed structural features of TM and cytoplasmic regions in DesK's kinase- and phosphatase-competent states. Biochemical and genetic experiments and molecular simulations further showed that reversible formation of a two-helix coiled coil in the fifth TM segment and the N-terminus of the cytoplasmic domain is essential for the sensing and signal transduction mechanisms. Together with other structural and functional works, the emerging picture suggests that diverse HKs possess distinct sensing and transduction mechanisms but share as rather general features (i) a symmetric phosphatase state and an asymmetric kinase state and (ii) similar functional outputs on the conserved DHp and ABD domains, achieved through different mechanisms that depend on the nature of the initial signal. We here advance (iii) an important role for TM prolines in transducing the initial signals to the cytoplasmic coiled coils, based on simulations of DesK's TM helices and our previous work on a related HK, PhoQ. Lastly, evidence for DesK, PhoQ, BvgS, and DctB HKs shows that (iv) overall catalytic output is tuned by a delicate balance between hydration potentials, coiled coil stability, and exposure of hydrophobic surface patches at their cytoplasmic coiled coils and at the N-terminal and C-terminal sides of their TM helices. This balance is so delicate that small perturbations, either physiological signals or induced by mutations, lead to large remodeling of the underlying conformational landscape achieving clear-cut changes in catalytic output, mirroring the required response speed of these systems for proper biological function.
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Affiliation(s)
- Luciano A. Abriata
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Daniela Albanesi
- Laboratorio
de Fisiología Microbiana, Instituto de Biología Molecular
y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio
CONICET Rosario, 2000 Rosario, Argentina
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Diego de Mendoza
- Laboratorio
de Fisiología Microbiana, Instituto de Biología Molecular
y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio
CONICET Rosario, 2000 Rosario, Argentina
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41
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Garavaglia BS, Zimaro T, Abriata LA, Ottado J, Gottig N. XacFhaB adhesin, an important Xanthomonas citri ssp. citri virulence factor, is recognized as a pathogen-associated molecular pattern. Mol Plant Pathol 2016; 17:1344-1353. [PMID: 26724481 PMCID: PMC6638363 DOI: 10.1111/mpp.12364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/23/2015] [Accepted: 12/29/2015] [Indexed: 05/24/2023]
Abstract
Adhesion to host tissue is one of the key steps of the bacterial pathogenic process. Xanthomonas citri ssp. citri possesses a non-fimbrial adhesin protein, XacFhaB, required for bacterial attachment, which we have previously demonstrated to be an important virulence factor for the development of citrus canker. XacFhaB is a 4753-residue-long protein with a predicted β-helical fold structure, involved in bacterial aggregation, biofilm formation and adhesion to the host. In this work, to further characterize this protein and considering its large size, XacFhaB was dissected into three regions based on bioinformatic and structural analyses for functional studies. First, the capacity of these protein regions to aggregate bacterial cells was analysed. Two of these regions were able to form bacterial aggregates, with the most amino-terminal region being dispensable for this activity. Moreover, XacFhaB shows features resembling pathogen-associated molecular patterns (PAMPs), which are recognized by plants. As PAMPs activate plant basal immune responses, the role of the three XacFhaB regions as elicitors of these responses was investigated. All adhesin regions were able to induce basal immune responses in host and non-host plants, with a stronger activation by the carboxyl-terminal region. Furthermore, pre-infiltration of citrus leaves with XacFhaB regions impaired X. citri ssp. citri growth, confirming the induction of defence responses and restraint of citrus canker. This work reveals that adhesins from plant pathogens trigger plant defence responses, opening up new pathways for the development of protective strategies for disease control.
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Affiliation(s)
- Betiana S. Garavaglia
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y EsmeraldaRosario 2000Argentina
| | - Tamara Zimaro
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y EsmeraldaRosario 2000Argentina
| | - Luciano A. Abriata
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y EsmeraldaRosario 2000Argentina
- Present address:
Laboratory for Biomolecular Modeling, School of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB)AAB011 Station 191015LausanneSwitzerland
| | - Jorgelina Ottado
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y EsmeraldaRosario 2000Argentina
| | - Natalia Gottig
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y EsmeraldaRosario 2000Argentina
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Abriata LA, Bovigny C, Peraro MD. Erratum to: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. BMC Bioinformatics 2016; 17:439. [PMID: 27799049 PMCID: PMC5087122 DOI: 10.1186/s12859-016-1315-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/24/2022] Open
Affiliation(s)
- Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland.
| | - Christophe Bovigny
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland.,Present address: Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL, Bâtiment Génopode, Lausanne, 1015, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland
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43
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Abriata LA, Bovigny C, Dal Peraro M. Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. BMC Bioinformatics 2016; 17:242. [PMID: 27315797 PMCID: PMC4912743 DOI: 10.1186/s12859-016-1124-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022] Open
Abstract
Background Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting detailed analyses to positions of extremely high or low variability or dubbed important beforehand based on existing knowledge about active sites, interaction surfaces, (de)stabilizing mutations, etc. Results Our new webserver PsychoProt (freely available without registration at http://psychoprot.epfl.ch or at http://lucianoabriata.altervista.org/psychoprot/index.html) helps to detect, quantify, and sequence/structure map the biophysical and biochemical traits that shape amino acid preferences throughout a protein as determined by deep-sequencing of saturated mutational libraries or from large alignments of naturally occurring variants. Discussion We exemplify how PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data. Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory. This and other differences call for caution when extrapolating results from in vitro experiments to natural scenarios in, for example, studies of protein evolution. Conclusion We show through examples how PsychoProt can be a useful tool for the broad communities of structural biology and molecular evolution, particularly for studies about protein modeling, evolution and design. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1124-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland.
| | - Christophe Bovigny
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland.,Present address: Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL, Bâtiment Génopode, Lausanne, 1015, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, AAB014 Station 19, Lausanne, 1015, Switzerland
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Abstract
The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscapes. Conformational dynamics, which is essential for protein function, has received little attention in the context of evolutionary analyses. Here we employ NMR spectroscopy, the chief experimental tool to describe protein dynamics at atomic level in solution at room temperature, to study the intrinsic dynamic features of a metallo- Β: -lactamase enzyme and three variants identified during a directed evolution experiment that led to an expanded substrate profile. We show that conformational dynamics in the catalytically relevant microsecond to millisecond timescale is optimized along the favored evolutionary trajectory. In addition, we observe that the effects of mutations on dynamics are epistatic. Mutation Gly262Ser introduces slow dynamics on several residues that surround the active site when introduced in the wild-type enzyme. Mutation Asn70Ser removes the slow dynamics observed for few residues of the wild-type enzyme, but increases the number of residues that undergo slow dynamics when introduced in the Gly262Ser mutant. These effects on dynamics correlate with the epistatic interaction between these two mutations on the bacterial phenotype. These findings indicate that conformational dynamics is an evolvable trait, and that proteins endowed with more dynamic active sites also display a larger potential for promoting evolution.
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Affiliation(s)
- Mariano M González
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Luciano A Abriata
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Pablo E Tomatis
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Alejandro J Vila
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario, Argentina
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Saita E, Abriata LA, Tsai YT, Trajtenberg F, Lemmin T, Buschiazzo A, Dal Peraro M, de Mendoza D, Albanesi D. A coiled coil switch mediates cold sensing by the thermosensory protein DesK. Mol Microbiol 2015; 98:258-71. [PMID: 26172072 DOI: 10.1111/mmi.13118] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 12/13/2022]
Abstract
The thermosensor histidine kinase DesK from Bacillus subtilis senses changes in membrane fluidity initiating an adaptive response. Structural changes in DesK have been implicated in transmembrane signaling, but direct evidence is still lacking. On the basis of structure-guided mutagenesis, we now propose a mechanism of DesK-mediated signal sensing and transduction. The data indicate that stabilization/destabilization of a 2-helix coiled coil, which connects the transmembrane sensory domain of DesK to its cytosolic catalytic region, is crucial to control its signaling state. Computational modeling and simulations reveal couplings between protein, water and membrane mechanics. We propose that membrane thickening is the main driving force for signal sensing and that it acts by inducing helix stretching and rotation prompting an asymmetric kinase-competent state. Overall, the known structural changes of the sensor kinase, as well as further dynamic rearrangements that we now predict, consistently link structure determinants to activity modulation.
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Affiliation(s)
- Emilio Saita
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, 2000, Rosario, Argentina
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics (SIB), AAB011 Station 19, 1015, Lausanne, Switzerland
| | - Yi Ting Tsai
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, 2000, Rosario, Argentina
| | - Felipe Trajtenberg
- Institut Pasteur de Montevideo, Unit of Protein Crystallography, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Thomas Lemmin
- Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics (SIB), AAB011 Station 19, 1015, Lausanne, Switzerland
| | - Alejandro Buschiazzo
- Institut Pasteur de Montevideo, Unit of Protein Crystallography, Mataojo 2020, Montevideo, 11400, Uruguay.,Département de Biologie Structurale et Chimie, Institut Pasteur, 25 rue du Dr. Roux, Paris, 75015, France
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics (SIB), AAB011 Station 19, 1015, Lausanne, Switzerland
| | - Diego de Mendoza
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, 2000, Rosario, Argentina
| | - Daniela Albanesi
- Laboratorio de Fisiología Microbiana, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, 2000, Rosario, Argentina
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Zitare U, Alvarez-Paggi D, Morgada MN, Abriata LA, Vila AJ, Murgida DH. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in CuASites of Cytochrome cOxidase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zitare U, Alvarez-Paggi D, Morgada MN, Abriata LA, Vila AJ, Murgida DH. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase. Angew Chem Int Ed Engl 2015; 54:9555-9. [PMID: 26118421 DOI: 10.1002/anie.201504188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 11/06/2022]
Abstract
The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics.
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Affiliation(s)
- Ulises Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina)
| | - Damián Alvarez-Paggi
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina)
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Luciano A Abriata
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina).
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Tamò GE, Abriata LA, Dal Peraro M. The importance of dynamics in integrative modeling of supramolecular assemblies. Curr Opin Struct Biol 2015; 31:28-34. [PMID: 25795087 DOI: 10.1016/j.sbi.2015.02.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 11/16/2022]
Abstract
Revealing the atomistic architecture of supramolecular complexes is a fundamental step toward a deeper understanding of cellular functioning. To date, this formidable task is facilitated by an emerging array of integrative modeling approaches that combine experimental data from different sources. One major challenge these methods have to face is the treatment of the dynamic rearrangements of the individual subunits upon assembly. While this flexibility can be sampled at different levels, integrating native dynamic determinants with available experimental inputs can provide an effective way to reveal the molecular recognition mechanisms at the basis of supramolecular assembly.
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Affiliation(s)
- Giorgio E Tamò
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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Abriata LA, Pontel LB, Vila AJ, Dal Peraro M, Soncini FC. A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP. J Inorg Biochem 2014; 140:199-201. [PMID: 25151035 DOI: 10.1016/j.jinorgbio.2014.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 11/27/2022]
Abstract
CueP confers bacterial copper resistance in the periplasm, particularly under anaerobic conditions, through an unknown mechanism. The only available structure and limited solution data suggest that CueP forms noncovalent dimers in solution, whereas sequence conservation suggests important roles for three cysteines and two histidines as copper ligands. Here we report evidence of a dimerization equilibrium mediated by a newly identified interface of functional relevance, which occludes internal copper sites and disulfide bonds but allows for intra- and interchain disulfide bonding, an extensive disulfide relay, and interfacial copper sites. Our results suggest a role for CueP linking redox-state sensing and copper detoxification.
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Affiliation(s)
- Luciano A Abriata
- Laboratory of Biomolecular Modeling, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Lucas B Pontel
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, UNR), 2000 Rosario, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, UNR), 2000 Rosario, Argentina
| | - Matteo Dal Peraro
- Laboratory of Biomolecular Modeling, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, UNR), 2000 Rosario, Argentina.
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50
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Spiga E, Abriata LA, Piazza F, Dal Peraro M. Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics. J Phys Chem B 2014; 118:5310-21. [PMID: 24773474 DOI: 10.1021/jp4126705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomistic level. We observe that the protein acts as a seed that speeds up the natural propensity of glucose to cluster at high concentration; the sugar molecules thus aggregate around the protein trapping it inside a dynamic cage. This process extensively dehydrates the protein surface, restricts the motions of the remaining water molecules, and drags the large-scale, collective motions of protein atoms slowing down the rate of exploration of the conformational space despite only a slight dampening of fast, local dynamics. We discuss how these effects could be relevant to the function of sugars as preservation agents in biological materials, and how crowding by small sticky molecules could modulate proteins across different reaction coordinates inside the cellular cytosol.
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Affiliation(s)
- Enrico Spiga
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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