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Benning FMC, Jenni S, Garcia CY, Nguyen TH, Zhang X, Chao LH. Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. Nat Commun 2024; 15:250. [PMID: 38177118 PMCID: PMC10767040 DOI: 10.1038/s41467-023-44596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We use electron cryomicroscopy to determine a 3.2 Å helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a distinct protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism shows that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
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Affiliation(s)
- Friederike M C Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Coby Y Garcia
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard College, Cambridge, MA, 02138, USA
| | - Tran H Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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Benning FMC, Jenni S, Garcia CY, Nguyen TH, Zhang X, Chao LH. Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545104. [PMID: 37398449 PMCID: PMC10312762 DOI: 10.1101/2023.06.15.545104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We determined a 3.2 Å electron cryomicroscopy helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a unique protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism revealed that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
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Affiliation(s)
- Friederike M. C. Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Coby Y. Garcia
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard College, Cambridge, MA 02138, USA
| | - Tran H. Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luke H. Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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Li X, Buda F, de Groot HJ, Sevink GJA. The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes. iScience 2022; 25:103618. [PMID: 35005556 PMCID: PMC8719020 DOI: 10.1016/j.isci.2021.103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution. We find that both the optical and the mechanical behavior are strongly dependent on chirality. The optical-chirality relation enables a direct interpretation of experimental spectra in terms of overall tube chirality. The mechanical response shows that the overall chirality regulates the hardness of the tube and provides a new characteristic for relating chlorosomes to distinct chirality. Our protocol also applies to other TMA systems and will inspire other systematic studies beyond lattice models. Classifies chlorosomes in terms of a tubular plastic crystal phase Clarifies the unique strategy of chlorosomes for harvesting and transporting energy Presents a protocol for building atom-resolved helical tube structures Maps tube chirality directly to measurable optical and mechanical responses
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Affiliation(s)
- Xinmeng Li
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, P.O.Box 1033, Blindern, Oslo, 0315 Oslo, Norway
- Corresponding author
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - Huub J.M. de Groot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - G. J. Agur Sevink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Corresponding author
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Principles and characteristics of biological assemblies in experimentally determined protein structures. Curr Opin Struct Biol 2019; 55:34-49. [PMID: 30965224 DOI: 10.1016/j.sbi.2019.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
More than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.
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Monet G, Amara MS, Rouzière S, Paineau E, Chai Z, Elliott JD, Poli E, Liu LM, Teobaldi G, Launois P. Structural resolution of inorganic nanotubes with complex stoichiometry. Nat Commun 2018; 9:2033. [PMID: 29789570 PMCID: PMC5964105 DOI: 10.1038/s41467-018-04360-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Determination of the atomic structure of inorganic single-walled nanotubes with complex stoichiometry remains elusive due to the too many atomic coordinates to be fitted with respect to X-ray diffractograms inherently exhibiting rather broad features. Here we introduce a methodology to reduce the number of fitted variables and enable resolution of the atomic structure for inorganic nanotubes with complex stoichiometry. We apply it to recently synthesized methylated aluminosilicate and aluminogermanate imogolite nanotubes of nominal composition (OH)3Al2O3Si(Ge)CH3. Fitting of X-ray scattering diagrams, supported by Density Functional Theory simulations, reveals an unexpected rolling mode for these systems. The transferability of the approach opens up for improved understanding of structure–property relationships of inorganic nanotubes to the benefit of fundamental and applicative research in these systems. Structural determination of inorganic nanotubes has lagged far behind that of their carbon-based counterparts. Here, the authors present a transferable methodology, combining wide angle X-ray scattering and computation, to quantitatively resolve the atomic structure of inorganic nanotubes with complex stoichiometry.
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Affiliation(s)
- Geoffrey Monet
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud, Université Paris Saclay, 91405, Orsay Cedex, France
| | - Mohamed S Amara
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud, Université Paris Saclay, 91405, Orsay Cedex, France
| | - Stéphan Rouzière
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud, Université Paris Saclay, 91405, Orsay Cedex, France
| | - Erwan Paineau
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud, Université Paris Saclay, 91405, Orsay Cedex, France
| | - Ziwei Chai
- Beijing Computational Science Research Centre, 100193, Beijing, China
| | - Joshua D Elliott
- Stephenson Institute for Renewable Energy and Department of Chemistry, The University of Liverpool, Liverpool, L69 3BX, UK.,Dipartimento di Fisica e Astronomia "Galileo Galilei", Università degli Studi di Padova, I-35131, Padova, Italy
| | - Emiliano Poli
- Stephenson Institute for Renewable Energy and Department of Chemistry, The University of Liverpool, Liverpool, L69 3BX, UK.,The Abdus Salam International Centre for Theoretical Physics, 34151, Trieste, Italy
| | - Li-Min Liu
- Beijing Computational Science Research Centre, 100193, Beijing, China.,School of Physics, Beihang University, 100191, Beijing, China
| | - Gilberto Teobaldi
- Beijing Computational Science Research Centre, 100193, Beijing, China. .,Stephenson Institute for Renewable Energy and Department of Chemistry, The University of Liverpool, Liverpool, L69 3BX, UK.
| | - Pascale Launois
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud, Université Paris Saclay, 91405, Orsay Cedex, France.
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In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature. Sci Rep 2017; 7:2913. [PMID: 28588198 PMCID: PMC5460288 DOI: 10.1038/s41598-017-02060-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
During a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
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