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Kraj P, Hewagama ND, Douglas T. Diffusion and molecular partitioning in hierarchically complex virus-like particles. Virology 2023; 580:50-60. [PMID: 36764014 DOI: 10.1016/j.virol.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Viruses are diverse infectious agents found in virtually every type of natural environment. Due to the range of conditions in which viruses have evolved, they exhibit a wide range of structure and function which has been exploited for biotechnology. The self-assembly process of virus-like particles (VLPs), derived from structural virus components, allows for the assembly of a hierarchy of materials. Because VLPs are robust in both their assembly and the final product, functionality can be incorporated through design of their building blocks or chemical modification after their synthesis and assembly. In particular, encapsulation of active enzymes inside VLP results in macromolecular concentration approximating that of cells, introducing excluded volume effects on encapsulated cargo which are not present in traditional experiments done on dilute proteins. This work reviews the hierarchical assembly of VLPs, experiments investigating diffusion in VLP systems, and methods for partitioning of chemical species in VLPs as functional biomaterials.
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Affiliation(s)
- Pawel Kraj
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA.
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2
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Essus VA, Souza Júnior GSE, Nunes GHP, Oliveira JDS, de Faria BM, Romão LF, Cortines JR. Bacteriophage P22 Capsid as a Pluripotent Nanotechnology Tool. Viruses 2023; 15:516. [PMID: 36851730 PMCID: PMC9962691 DOI: 10.3390/v15020516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
The Salmonella enterica bacteriophage P22 is one of the most promising models for the development of virus-like particle (VLP) nanocages. It possesses an icosahedral T = 7 capsid, assembled by the combination of two structural proteins: the coat protein (gp5) and the scaffold protein (gp8). The P22 capsid has the remarkable capability of undergoing structural transition into three morphologies with differing diameters and wall-pore sizes. These varied morphologies can be explored for the design of nanoplatforms, such as for the development of cargo internalization strategies. The capsid proteic nature allows for the extensive modification of its structure, enabling the addition of non-native structures to alter the VLP properties or confer them to diverse ends. Various molecules were added to the P22 VLP through genetic, chemical, and other means to both the capsid and the scaffold protein, permitting the encapsulation or the presentation of cargo. This allows the particle to be exploited for numerous purposes-for example, as a nanocarrier, nanoreactor, and vaccine model, among other applications. Therefore, the present review intends to give an overview of the literature on this amazing particle.
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Affiliation(s)
- Victor Alejandro Essus
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Getúlio Silva e Souza Júnior
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Gabriel Henrique Pereira Nunes
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Juliana dos Santos Oliveira
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Bruna Mafra de Faria
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bl. F026, Rio de Janeiro 21941-590, Brazil
| | - Luciana Ferreira Romão
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bl. F026, Rio de Janeiro 21941-590, Brazil
| | - Juliana Reis Cortines
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
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3
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Strobl K, Selivanovitch E, Ibáñez-Freire P, Moreno-Madrid F, Schaap IAT, Delgado-Buscalioni R, Douglas T, de Pablo PJ. Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200059. [PMID: 35718881 PMCID: PMC9528512 DOI: 10.1002/smll.202200059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.
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Affiliation(s)
- Klara Strobl
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Pablo Ibáñez-Freire
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Francisco Moreno-Madrid
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Rafael Delgado-Buscalioni
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Pedro J de Pablo
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
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Asija K, Teschke CM. Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein. Virology 2019; 534:45-53. [PMID: 31176063 PMCID: PMC6614003 DOI: 10.1016/j.virol.2019.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/27/2019] [Accepted: 05/31/2019] [Indexed: 01/14/2023]
Abstract
Tailed dsDNA bacteriophages and herpesviruses form capsids using coat proteins that have the HK97 fold. In these viruses, the coat proteins first assemble into procapsids, which subsequently mature during DNA packaging. Generally interactions between the coat protein E-loop of one subunit and the P-domain of an adjacent subunit help stabilize both capsomers and capsids. Based on a recent 3.3 Å cryo-EM structure of the bacteriophage P22 virion, E-loop amino acids E52, E59 and E72 were suggested to stabilize the capsid through intra-capsomer salt bridges with the P-domain residues R102, R109 and K118. The glutamic acid residues were each mutated to alanine to test this hypothesis. The substitutions resulted in a WT phenotype and did not destabilize capsids; rather, the alanine substituted coat proteins increased the stability of procapsids and virions. These results indicate that different types of interactions must be used between the E-loop and P-domain to stabilize phage P22 procapsids and virions.
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Affiliation(s)
- Kunica Asija
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Department of Chemistry, University of Connecticut, Storrs, CT, USA.
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5
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Virus capsid assembly across different length scales inspire the development of virus-based biomaterials. Curr Opin Virol 2019; 36:38-46. [PMID: 31071601 DOI: 10.1016/j.coviro.2019.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/12/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
In biology, there are an abundant number of self-assembled structures organized according to hierarchical levels of complexity. In some examples, the assemblies formed at each level exhibit unique properties and behaviors not present in individual components. Viruses are an example of such where first individual subunits come together to form a capsid structure, some utilizing a scaffolding protein to template or catalyze the capsid formation. Increasing the level of complexity, the viral capsids can then be used as building blocks of higher-level assemblies. This has inspired scientists to design and construct virus capsid-based functional nano-materials. This review provides some insight into the assembly of virus capsids across several length scales, and certain properties that arise at different levels, providing examples found in naturally occurring systems and those that are synthetically designed.
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Architect of Virus Assembly: the Portal Protein Nucleates Procapsid Assembly in Bacteriophage P22. J Virol 2019; 93:JVI.00187-19. [PMID: 30787152 DOI: 10.1128/jvi.00187-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022] Open
Abstract
Tailed double-stranded DNA (dsDNA) bacteriophages, herpesviruses, and adenoviruses package their genetic material into a precursor capsid through a dodecameric ring complex called the portal protein, which is located at a unique 5-fold vertex. In several phages and viruses, including T4, Φ29, and herpes simplex virus 1 (HSV-1), the portal forms a nucleation complex with scaffolding proteins (SPs) to initiate procapsid (PC) assembly, thereby ensuring incorporation of only one portal ring per capsid. However, for bacteriophage P22, the role of its portal protein in initiation of procapsid assembly is unclear. We have developed an in vitro P22 assembly assay where portal protein is coassembled into procapsid-like particles (PLPs). Scaffolding protein also catalyzes oligomerization of monomeric portal protein into dodecameric rings, possibly forming a scaffolding protein-portal protein nucleation complex that results in one portal ring per P22 procapsid. Here, we present evidence substantiating that the P22 portal protein, similarly to those of other dsDNA viruses, can act as an assembly nucleator. The presence of the P22 portal protein is shown to increase the rate of particle assembly and contribute to proper morphology of the assembled particles. Our results highlight a key function of portal protein as an assembly initiator, a feature that is likely conserved among these classes of dsDNA viruses.IMPORTANCE The existence of a single portal ring is essential to the formation of infectious virions in the tailed double-stranded DNA (dsDNA) phages, herpesviruses, and adenoviruses and, as such, is a viable antiviral therapeutic target. How only one portal is selectively incorporated at a unique vertex is unclear. In many dsDNA viruses and phages, the portal protein acts as an assembly nucleator. However, early work on phage P22 assembly in vivo indicated that the portal protein did not function as a nucleator for procapsid (PC) assembly, leading to the suggestion that P22 uses a unique mechanism for portal incorporation. Here, we show that portal protein nucleates assembly of P22 procapsid-like particles (PLPs). Addition of portal rings to an assembly reaction increases the rate of formation and yield of particles and corrects improper particle morphology. Our data suggest that procapsid assembly may universally initiate with a nucleation complex composed minimally of portal and scaffolding proteins (SPs).
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Selivanovitch E, Koliyatt R, Douglas T. Chemically Induced Morphogenesis of P22 Virus-like Particles by the Surfactant Sodium Dodecyl Sulfate. Biomacromolecules 2018; 20:389-400. [PMID: 30462501 DOI: 10.1021/acs.biomac.8b01357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the infectious P22 bacteriophage, the packaging of DNA into the initially formed procapsid triggers a remarkable morphological transformation where the capsid expands from 58 to 62 nm. Along with the increase in size, this maturation also provides greater stability to the capsid and initiates the release of the scaffolding protein (SP). (2,4) In the P22 virus-like particle (VLP), this transformation can be mimicked in vitro by heating the procapsid particles to 65 °C or by treatment with sodium dodecyl sulfate (SDS). (5,6) Heating the P22 particles at 65 °C for 20 min is well established to trigger the transformation of P22 to the expanded (EX) P22 VLP but does not always result in a fully expanded population. Incubation with SDS resulted in a >80% expanded population for all P22 variants used in this work. This study elucidates the importance of the stoichiometric ratio between P22 subunits and SDS, the charge of the headgroup, and length of the carbon chain for the transformation. We propose a mechanism by which the expansion takes place, where both the negatively charged sulfate group and hydrophobic tail interact with the coat protein (CP) monomers within the capsid shell in a process that is facilitated by an internal osmotic pressure generated by an encapsulated macromolecular cargo.
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Affiliation(s)
| | - Ranjit Koliyatt
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Trevor Douglas
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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8
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Fonseca P, Romano F, Schreck JS, Ouldridge TE, Doye JPK, Louis AA. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J Chem Phys 2018; 148:134910. [PMID: 29626893 DOI: 10.1063/1.5019344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
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Affiliation(s)
- Pedro Fonseca
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, USA
| | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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Aoki E, Sato D, Fujiwara K, Ikeguchi M. Electrostatic Repulsion between Unique Arginine Residues Is Essential for the Efficient in Vitro Assembly of the Transmembrane Domain of a Trimeric Autotransporter. Biochemistry 2017; 56:2139-2148. [PMID: 28357859 DOI: 10.1021/acs.biochem.6b01130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Haemophilus influenzae adhesin (Hia) belongs to the trimeric autotransporter family and mediates the adherence of these bacteria to the epithelial cells of host organisms. Hia contains a passenger and a transmembrane domain. The transmembrane domain forms a 12-stranded β-barrel in which four strands are provided by each subunit. The β-barrel has a pore that is traversed by three α-helices. This domain has a unique arginine cluster, in which the side chains of the three arginine residues located at position 1077 (Arg1077) protrude into the pore of the β-barrel. This arrangement seems to be unfavorable for assembly, because of repulsion between the positive charges. In this study, we investigated the in vitro assembly of the Hia transmembrane minimum domain (mHiaTD) and found that the dissociated mHiaTD reassembled in detergent solution. To investigate the role of Arg1077 in trimer assembly, we generated mutant proteins in which Arg1077 was replaced with methionine or lysine. The reassembly kinetics of the mutants was compared with that of the wild-type protein. The methionine mutant showed misassembly, whereas the lysine mutant showed reversible assembly, similar to that observed for the wild-type protein. These results show that electrostatic repulsion between the positive charges of Arg1077 is important for preventing the formation of misassembled oligomers by the mHiaTD in vitro.
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Affiliation(s)
- Eriko Aoki
- Department of Bioinformatics, Soka University , 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Daisuke Sato
- Department of Bioinformatics, Soka University , 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kazuo Fujiwara
- Department of Bioinformatics, Soka University , 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University , 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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Medrano M, Fuertes MÁ, Valbuena A, Carrillo PJP, Rodríguez-Huete A, Mateu MG. Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid. J Am Chem Soc 2016; 138:15385-15396. [PMID: 27933931 DOI: 10.1021/jacs.6b07663] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.
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Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Miguel Ángel Fuertes
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Pablo J P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
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Scibilia S, Lentini G, Fazio E, Franco D, Neri F, Mezzasalma AM, Guglielmino SPP. Self-assembly of silver nanoparticles and bacteriophage. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Wang C, Sauvageau D, Elias A. Immobilization of Active Bacteriophages on Polyhydroxyalkanoate Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:1128-38. [PMID: 26741170 DOI: 10.1021/acsami.5b08664] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A rapid, efficient technique for the attachment of bacteriophages (phages) onto polyhydroxyalkanoate (PHA) surfaces has been developed and compared to three reported methods for phage immobilization. Polymer surfaces were modified to facilitate phage attachment using (1) plasma treatment alone, (2) plasma treatment followed by activation by 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide hydrochloride (EDC) and N-hydroxysulfosuccinimide (sulfo-NHS), (3) plasma-initiated acrylic acid grafting, or (4) plasma-initiated acrylic acid grafting with activation by EDC and sulfo-NHS. The impact of each method on the surface chemistry of PHA was investigated using contact angle analysis and X-ray photoelectron spectroscopy. Each of the four treatments was shown to result in both increased hydrophilicity and in the modification of the surface functional groups. Modified surfaces were immersed in suspensions of phage T4 for immobilization. The highest level of phage binding was observed for the surfaces modified by plasma treatment alone. The change in chemical bond states observed for surfaces that underwent plasma treatment is suspected to be the cause of the increased binding of active phages. Plasma-treated surfaces were further analyzed through phage-staining and fluorescence microscopy to assess the surface density of immobilized phages and their capacity to capture hosts. The infective capability of attached phages was confirmed by exposing the phage-immobilized surfaces to the host bacteria Escherichia coli in both plaque and infection dynamic assays. Plasma-treated surfaces with immobilized phages displayed higher infectivity than surfaces treated with other methods; in fact, the equivalent initial multiplicity of infection was 2 orders of magnitude greater than with other methods. Control samples - prepared by immersing polymer surfaces in phage suspensions (without prior plasma treatment) - did not show any bacterial growth inhibition, suggesting they did not bind phages from the suspension.
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Affiliation(s)
- Chanchan Wang
- Department of Chemical and Material Engineering, University of Alberta , 9211 116 Street NW, Edmonton, Alberta T6G 1H9, Canada
| | - Dominic Sauvageau
- Department of Chemical and Material Engineering, University of Alberta , 9211 116 Street NW, Edmonton, Alberta T6G 1H9, Canada
| | - Anastasia Elias
- Department of Chemical and Material Engineering, University of Alberta , 9211 116 Street NW, Edmonton, Alberta T6G 1H9, Canada
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13
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Sato D, Takebe S, Kurobe A, Ohtomo H, Fujiwara K, Ikeguchi M. Electrostatic Repulsion during Ferritin Assembly and Its Screening by Ions. Biochemistry 2016; 55:482-8. [DOI: 10.1021/acs.biochem.5b01197] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Daisuke Sato
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Satsuki Takebe
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Atsushi Kurobe
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Hideaki Ohtomo
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kazuo Fujiwara
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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14
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Suhanovsky MM, Teschke CM. Nature's favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold. Virology 2015; 479-480:487-97. [PMID: 25864106 PMCID: PMC4424165 DOI: 10.1016/j.virol.2015.02.055] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 01/08/2023]
Abstract
For many (if not all) bacterial and archaeal tailed viruses and eukaryotic Herpesvirdae the HK97-fold serves as the major architectural element in icosahedral capsid formation while still enabling the conformational flexibility required during assembly and maturation. Auxiliary proteins or Δ-domains strictly control assembly of multiple, identical, HK97-like subunits into procapsids with specific icosahedral symmetries, rather than aberrant non-icosahedral structures. Procapsids are precursor structures that mature into capsids in a process involving release of auxiliary proteins (or cleavage of Δ-domains), dsDNA packaging, and conformational rearrangement of the HK97-like subunits. Some coat proteins built on the ubiquitous HK97-fold also have accessory domains or loops that impart specific functions, such as increased monomer, procapsid, or capsid stability. In this review, we analyze the numerous HK97-like coat protein structures that are emerging in the literature (over 40 at time of writing) by comparing their topology, additional domains, and their assembly and misassembly reactions.
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Affiliation(s)
- Margaret M Suhanovsky
- Department of Molecular and Cell Biology, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA.
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA; Department of Chemistry, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA.
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15
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Switt AIM, Sulakvelidze A, Wiedmann M, Kropinski AM, Wishart DS, Poppe C, Liang Y. Salmonella phages and prophages: genomics, taxonomy, and applied aspects. Methods Mol Biol 2015; 1225:237-87. [PMID: 25253259 DOI: 10.1007/978-1-4939-1625-2_15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.
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Affiliation(s)
- Andrea I Moreno Switt
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Escuela de Medicina Veterinaria, Republica 440, 8370251, Santiago, Chile
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16
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Electrostatic interactions drive the self-assembly and the transcription activity of the Pseudomonas phage ϕ6 procapsid. J Virol 2014; 88:7112-6. [PMID: 24719418 DOI: 10.1128/jvi.00467-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Assembly of an empty procapsid is a crucial step in the formation of many complex viruses. Here, we used the self-assembly system of the double-stranded RNA bacteriophage ϕ6 to study the role of electrostatic interactions in a scaffolding-independent procapsid assembly pathway. We demonstrate that ϕ6 procapsid assembly is sensitive to salt at both the nucleation and postnucleation steps. Furthermore, we observed that the salt sensitivity of ϕ6 procapsid-directed transcription is reversible.
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17
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Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein. J Virol 2014; 88:5287-97. [PMID: 24600011 DOI: 10.1128/jvi.00036-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Icosahedral virus assembly requires a series of concerted and highly specific protein-protein interactions to produce a proper capsid. In bacteriophage P22, only coat protein (gp5) and scaffolding protein (gp8) are needed to assemble a procapsid-like particle, both in vivo and in vitro. In scaffolding protein's coat binding domain, residue R293 is required for procapsid assembly, while residue K296 is important but not essential. Here, we investigate the interaction of scaffolding protein with acidic residues in the N-arm of coat protein, since this interaction has been shown to be electrostatic. Through site-directed mutagenesis of genes 5 and 8, we show that changing coat protein N-arm residue 14 from aspartic acid to alanine causes a lethal phenotype. Coat protein residue D14 is shown by cross-linking to interact with scaffolding protein residue R293 and, thus, is intimately involved in proper procapsid assembly. To a lesser extent, coat protein N-arm residue E18 is also implicated in the interaction with scaffolding protein and is involved in capsid size determination, since a cysteine mutation at this site generated petite capsids. The final acidic residue in the N-arm that was tested, E15, is shown to only weakly interact with scaffolding protein's coat binding domain. This work supports growing evidence that surface charge density may be the driving force of virus capsid protein interactions. IMPORTANCE Bacteriophage P22 infects Salmonella enterica serovar Typhimurium and is a model for icosahedral viral capsid assembly. In this system, coat protein interacts with an internal scaffolding protein, triggering the assembly of an intermediate called a procapsid. Previously, we determined that there is a single amino acid in scaffolding protein required for P22 procapsid assembly, although others modulate affinity. Here, we identify partners in coat protein. We show experimentally that relatively weak interactions between coat and scaffolding proteins are capable of driving correctly shaped and sized procapsids and that the lack of these proper protein-protein interfaces leads to aberrant structures. The present work represents an important contribution supporting the hypothesis that virus capsid assembly is governed by seemingly simple interactions. The highly specific nature of the subunit interfaces suggests that these could be good targets for antivirals.
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18
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Ouldridge TE. Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble. J Chem Phys 2013; 137:144105. [PMID: 23061837 DOI: 10.1063/1.4757267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this paper, we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling systems of characteristic finite size. In particular, schemes for extrapolating the results of simulations of a single self-assembling object to the bulk limit are established in three cases: for assembly involving multiple particle species, for systems with one species localized in space and for simulations in the grand canonical ensemble. Furthermore, methodologies are introduced for evaluating the accuracy of these extrapolations. Example systems demonstrate that differences in cluster concentrations between simulations of a single self-assembling structure and bulk studies of the same model under identical conditions can be large, and that convergence on bulk results as system size is increased can be slow and non-trivial.
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Affiliation(s)
- Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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19
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Effects of an early conformational switch defect during ϕX174 morphogenesis are belatedly manifested late in the assembly pathway. J Virol 2012; 87:2518-25. [PMID: 23255785 DOI: 10.1128/jvi.02839-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
C-terminal, aromatic amino acids in the ϕX174 internal scaffolding protein B mediate conformational switches in the viral coat protein. These switches direct the coat protein through early assembly. In addition to the aromatic amino acids, two acidic residues, D111 and E113, form salt bridges with basic, coat protein side chains. Although salt bridge formation did not appear to be critical for assembly, the substitution of an aromatic amino acid for D111 produced a lethal phenotype. This side chain is uniquely oriented toward the center of the coat-scaffolding binding pocket, which is heavily dominated by aromatic ring-ring interactions. Thus, the D111Y substitution may restructure pocket contacts. Previously characterized B(-) mutants blocked assembly before procapsid formation. However, the D111Y mutant produced an assembled particle, which contained the structural and external scaffolding proteins but lacked protein B and DNA. A suppressor within the external scaffolding protein, which mediates the later stages of particle morphogenesis, restored viability. The unique formation of a postprocapsid particle and the novel suppressor may be indicative of a novel B protein function. However, genetic data suggest that the particle represents the delayed manifestation of an early assembly error. This seemingly late-acting defect was rescued by previously characterized suppressors of early, preprocapsid, B(-) assembly mutations, which act on the level of coat protein flexibility. Likewise, the newly isolated suppressor in the external scaffolding protein also exhibited a global suppressing phenotype. Thus, the off-pathway product isolated from infected cells may not accurately reflect the temporal nature of the initial defect.
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20
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Padilla-Meier GP, Gilcrease EB, Weigele PR, Cortines JR, Siegel M, Leavitt JC, Teschke CM, Casjens SR. Unraveling the role of the C-terminal helix turn helix of the coat-binding domain of bacteriophage P22 scaffolding protein. J Biol Chem 2012; 287:33766-80. [PMID: 22879595 DOI: 10.1074/jbc.m112.393132] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction.
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Affiliation(s)
- G Pauline Padilla-Meier
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
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21
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Conformational switch-defective X174 internal scaffolding proteins kinetically trap assembly intermediates before procapsid formation. J Virol 2012; 86:9911-8. [PMID: 22761377 DOI: 10.1128/jvi.01120-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conformational switching is an overarching paradigm in which to describe scaffolding protein-mediated virus assembly. However, rapid morphogenesis with small assembly subunits hinders the isolation of early morphogenetic intermediates in most model systems. Consequently, conformational switches are often defined by comparing the structures of virions, procapsids and aberrantly assembled particles. In contrast, X174 morphogenesis proceeds through at least three preprocapsid intermediates, which can be biochemically isolated. This affords a detailed analysis of early morphogenesis and internal scaffolding protein function. Amino acid substitutions were generated for the six C-terminal, aromatic amino acids that mediate most coat-internal scaffolding protein contacts. The biochemical characterization of mutant assembly pathways revealed two classes of molecular defects, protein binding and conformational switching, a novel phenotype. The conformational switch mutations kinetically trapped assembly intermediates before procapsid formation. Although mutations trapped different particles, they shared common second-site suppressors located in the viral coat protein. This suggests a fluid assembly pathway, one in which the scaffolding protein induces a single, coat protein conformational switch and not a series of sequential reactions. In this model, an incomplete or improper switch would kinetically trap intermediates.
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22
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Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM. Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 2012; 33:5628-37. [PMID: 22575828 DOI: 10.1016/j.biomaterials.2012.04.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 04/08/2012] [Indexed: 01/18/2023]
Abstract
A stepwise addition protocol was developed to display cargo using bacteriophage P22 capsids and the phage decoration (Dec) protein. Three-dimensional image reconstructions of frozen-hydrated samples of P22 particles with nanogold-labeled Dec bound to them revealed the locations of the N- and C-termini of Dec. Each terminus is readily accessible for molecular display through affinity tags such as nickel-nitrilotriacetic acid, providing a total of 240 cargo-binding sites. Dec was shown by circular dichroism to be a β-sheet rich protein, and fluorescence anisotropy binding experiments demonstrated that Dec binds to P22 heads with high (~110 nm) affinity. Dec also binds to P22 nanotubes, which are helically symmetric assemblies that form when the P22 coat protein contains the F170A amino acid substitution. Several classes of tubes with Dec bound to them were visualized by cryo-electron microscopy and their three-dimensional structures were determined by helical reconstruction methods. In all instances, Dec trimers bound to P22 capsids and nanotubes at positions where three neighboring capsomers (oligomers of six coat protein subunits) lie in close proximity to one another. Stable interactions between Dec and P22 allow for the development of robust, nanoscale size, display vehicles.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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23
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Zlotnick A, Suhanovsky MM, Teschke CM. The energetic contributions of scaffolding and coat proteins to the assembly of bacteriophage procapsids. Virology 2012; 428:64-9. [PMID: 22520942 DOI: 10.1016/j.virol.2012.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/18/2012] [Accepted: 03/29/2012] [Indexed: 01/17/2023]
Abstract
In vitro assembly of bacteriophage P22 procapsids requires coat protein and sub-stoichiometric concentrations of the internal scaffolding protein. If there is no scaffolding protein, coat protein assembles aberrantly, but only at higher concentrations. Too much scaffolding protein results in partial procapsids. By treating the procapsid as a lattice that can bind and be stabilized by scaffolding protein we dissect procapsid assembly as a function of protein concentration and scaffolding/coat protein ratio. We observe that (i) the coat-coat association is weaker for procapsids than for aberrant polymer formation, (ii) scaffolding protein makes a small but sufficient contribution to stability to favor the procapsid form, and (iii) there are multiple classes of scaffolding protein binding sites. This approach should be applicable to other heterogeneous virus assembly reactions and will facilitate our ability to manipulate such in vitro reactions to probe assembly, and for development of nanoparticles.
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Affiliation(s)
- Adam Zlotnick
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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24
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Building the Machines: Scaffolding Protein Functions During Bacteriophage Morphogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:325-50. [DOI: 10.1007/978-1-4614-0980-9_14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Cortines JR, Weigele PR, Gilcrease EB, Casjens SR, Teschke CM. Decoding bacteriophage P22 assembly: identification of two charged residues in scaffolding protein responsible for coat protein interaction. Virology 2011; 421:1-11. [PMID: 21974803 DOI: 10.1016/j.virol.2011.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/15/2011] [Accepted: 09/08/2011] [Indexed: 11/17/2022]
Abstract
Proper assembly of viruses must occur through specific interactions between capsid proteins. Many double-stranded DNA viruses and bacteriophages require internal scaffolding proteins to assemble their coat proteins into icosahedral capsids. The 303 amino acid bacteriophage P22 scaffolding protein is mostly helical, and its C-terminal helix-turn-helix (HTH) domain binds to the coat protein during virion assembly, directing the formation of an intermediate structure called the procapsid. The interaction between coat and scaffolding protein HTH domain is electrostatic, but the amino acids that form the protein-protein interface have yet to be described. In the present study, we used alanine scanning mutagenesis of charged surface residues of the C-terminal HTH domain of scaffolding protein. We have determined that P22 scaffolding protein residues R293 and K296 are crucial for binding to coat protein and that the neighboring charges are not essential but do modulate the affinity between the two proteins.
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Affiliation(s)
- Juliana R Cortines
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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26
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Medina EM, Andrews BT, Nakatani E, Catalano CE. The bacteriophage lambda gpNu3 scaffolding protein is an intrinsically disordered and biologically functional procapsid assembly catalyst. J Mol Biol 2011; 412:723-36. [PMID: 21821043 PMCID: PMC3247018 DOI: 10.1016/j.jmb.2011.07.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 07/19/2011] [Accepted: 07/21/2011] [Indexed: 10/17/2022]
Abstract
Procapsid assembly is a process whereby hundreds of copies of a major capsid protein assemble into an icosahedral protein shell into which the viral genome is packaged. The essential features of procapsid assembly are conserved in both eukaryotic and prokaryotic complex double-stranded DNA viruses. Typically, a portal protein nucleates the co-polymerization of an internal scaffolding protein and the major capsid protein into an icosahedral capsid shell. The scaffolding proteins are essential to procapsid assembly. Here, we describe the solution-based biophysical and functional characterization of the bacteriophage lambda (λ) scaffolding protein gpNu3. The purified protein possesses significant α-helical structure and appears to be partially disordered. Thermally induced denaturation studies indicate that secondary structures are lost in a cooperative, apparent two-state transition (T(m)=40.6±0.3 °C) and that unfolding is, at least in part, reversible. Analysis of the purified protein by size-exclusion chromatography suggests that gpNu3 is highly asymmetric, which contributes to an abnormally large Stokes radius. The size-exclusion chromatography data further indicate that the protein self-associates in a concentration-dependent manner. This was confirmed by analytical ultracentrifugation studies, which reveal a monomer-dimer equilibrium (K(d,app)~50 μM) and an asymmetric protein structure at biologically relevant concentrations. Purified gpNu3 promotes the polymerization of gpE, the λ major capsid protein, into virus-like particles that possess a native-like procapsid morphology. The relevance of this work with respect to procapsid assembly in the complex double-stranded DNA viruses is discussed.
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Affiliation(s)
| | | | - Eri Nakatani
- Department of Medicinal Chemistry, University of Washington, H172 Health Science Building, Seattle, WA 98195, USA
| | - Carlos Enrique Catalano
- Department of Medicinal Chemistry, University of Washington, H172 Health Science Building, Seattle, WA 98195, USA
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27
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Cherwa JE, Organtini LJ, Ashley RE, Hafenstein SL, Fane BA. In VITRO ASSEMBLY of the øX174 procapsid from external scaffolding protein oligomers and early pentameric assembly intermediates. J Mol Biol 2011; 412:387-96. [PMID: 21840317 DOI: 10.1016/j.jmb.2011.07.070] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/29/2011] [Accepted: 07/31/2011] [Indexed: 11/28/2022]
Abstract
Bacteriophage øX174 morphogenesis requires two scaffolding proteins: an internal species, similar to those employed in other viral systems, and an external species, which is more typically associated with satellite viruses. The current model of øX174 assembly is based on structural and in vivo data. During morphogenesis, 240 copies of the external scaffolding protein mediate the association of 12 pentameric particles into procapsids. The hypothesized pentameric intermediate, the 12S⁎ particle, contains 16 proteins: 5 copies each of the coat, spike and internal scaffolding proteins and 1 copy of the DNA pilot protein. Assembly naïve 12S⁎ particles and external scaffolding oligomers, most likely tetramers, formed procapsid-like particles in vitro, suggesting that the 12S⁎ particle is a bona fide assembly intermediate and validating the current model of procapsid morphogenesis. The in vitro system required a crowding agent, was influenced by the ratio of the reactants and was most likely driven by hydrophobic forces. While the system reported here shared some characteristics with other in vitro internal scaffolding protein-mediated systems, it displayed unique features. These features most likely reflect external scaffolding protein-mediated morphogenesis and the øX174 procapsid structure, in which external scaffolding-scaffolding protein interactions, as opposed to coat-coat protein interactions between pentamers, constitute the primary lattice-forming contacts.
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Affiliation(s)
- James E Cherwa
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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28
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Padilla-Meier GP, Teschke CM. Conformational changes in bacteriophage P22 scaffolding protein induced by interaction with coat protein. J Mol Biol 2011; 410:226-40. [PMID: 21605566 DOI: 10.1016/j.jmb.2011.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/28/2011] [Accepted: 05/05/2011] [Indexed: 11/25/2022]
Abstract
Many prokaryotic and eukaryotic double-stranded DNA viruses use a scaffolding protein to assemble their capsid. Assembly of the double-stranded DNA bacteriophage P22 procapsids requires the interaction of 415 molecules of coat protein and 60-300 molecules of scaffolding protein. Although the 303-amino-acid scaffolding protein is essential for proper assembly of procapsids, little is known about its structure beyond an NMR structure of the extreme C-terminus, which is known to interact with coat protein. Deletion mutagenesis indicates that other regions of scaffolding protein are involved in interactions with coat protein and other capsid proteins. Single-cysteine and double-cysteine variants of scaffolding protein were generated for use in fluorescence resonance energy transfer and cross-linking experiments designed to probe the conformation of scaffolding protein in solution and within procapsids. We showed that the N-terminus and the C-terminus are proximate in solution, and that the middle of the protein is near the N-terminus but not accessible to the C-terminus. In procapsids, the N-terminus was no longer accessible to the C-terminus, indicating that there is a conformational change in scaffolding protein upon assembly. In addition, our data are consistent with a model where scaffolding protein dimers are positioned parallel with one another with the associated C-termini.
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29
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Zlotnick A, Mukhopadhyay S. Virus assembly, allostery and antivirals. Trends Microbiol 2010; 19:14-23. [PMID: 21163649 PMCID: PMC3026312 DOI: 10.1016/j.tim.2010.11.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/29/2010] [Accepted: 11/09/2010] [Indexed: 12/13/2022]
Abstract
Assembly of virus capsids and surface proteins must be regulated to ensure that the resulting complex is an infectious virion. In this review, we examine assembly of virus capsids, focusing on hepatitis B virus and bacteriophage MS2, and formation of glycoproteins in the alphaviruses. These systems are structurally and biochemically well-characterized and are simplest-case paradigms of self-assembly. Published data suggest that capsid and glycoprotein assembly is subject to allosteric regulation, that is regulation at the level of conformational change. The hypothesis that allostery is a common theme in viruses suggests that deregulation of capsid and glycoprotein assembly by small molecule effectors will be an attractive antiviral strategy, as has been demonstrated with hepatitis B virus.
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Affiliation(s)
- Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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30
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Parent KN, Sinkovits RS, Suhanovsky MM, Teschke CM, Egelman EH, Baker TS. Cryo-reconstructions of P22 polyheads suggest that phage assembly is nucleated by trimeric interactions among coat proteins. Phys Biol 2010; 7:045004. [PMID: 21149969 PMCID: PMC3202341 DOI: 10.1088/1478-3975/7/4/045004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacteriophage P22 forms an isometric capsid during normal assembly, yet when the coat protein (CP) is altered at a single site, helical structures (polyheads) also form. The structures of three distinct polyheads obtained from F170L and F170A variants were determined by cryo-reconstruction methods. An understanding of the structures of aberrant assemblies such as polyheads helps to explain how amino acid substitutions affect the CP, and these results can now be put into the context of CP pseudo-atomic models. F170L CP forms two types of polyhead and each has the CP organized as hexons (oligomers of six CPs). These hexons have a skewed structure similar to that in procapsids (precursor capsids formed prior to dsDNA packaging), yet their organization differs completely in polyheads and procapsids. F170A CP forms only one type of polyhead, and though this has hexons organized similarly to hexons in F170L polyheads, the hexons are isometric structures like those found in mature virions. The hexon organization in all three polyheads suggests that nucleation of procapsid assembly occurs via a trimer of CP monomers, and this drives formation of a T = 7, isometric particle. These variants also form procapsids, but they mature quite differently: F170A expands spontaneously at room temperature, whereas F170L requires more energy. The P22 CP structure along with scaffolding protein interactions appear to dictate curvature and geometry in assembled structures and residue 170 significantly influences both assembly and maturation.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Robert S Sinkovits
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Edward H Egelman
- Department of Biochemistry and Molecular University of Genetics, University of Virginia, Charlottesville, VA, USA
| | - Timothy S Baker
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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31
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Affiliation(s)
- Adam Zlotnick
- Department of Biology, Indiana University Bloomington IN 47405 USA
| | - Bentley A. Fane
- Division of Plant Pathology and Microbiology, Department of Plant Sciences and The BIO5 Institute, University of Arizona Tucson AZ 85721 USA
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32
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Suhanovsky MM, Parent KN, Dunn SE, Baker TS, Teschke CM. Determinants of bacteriophage P22 polyhead formation: the role of coat protein flexibility in conformational switching. Mol Microbiol 2010; 77:1568-82. [PMID: 20659287 DOI: 10.1111/j.1365-2958.2010.07311.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated determinants of polyhead formation in bacteriophage P22 in order to understand the molecular mechanism by which coat protein assembly goes astray. Polyhead assembly is caused by amino acid substitutions in coat protein at position 170, which is located in the β-hinge. In vivo scaffolding protein does not correct polyhead assembly by F170A or F170K coat proteins, but does for F170L. All F170 variants bind scaffolding protein more weakly than wild-type as observed by affinity chromatography with scaffolding protein-agarose and scaffolding protein shell re-entry experiments. Electron cryo-microscopy and three-dimensional image reconstructions of F170A and F170K empty procapsid shells showed that there is a decreased flexibility of the coat subunits relative to wild-type. This was confirmed by limited proteolysis and protein sequencing, which showed increased protection of the A-domain. Our data support the conclusion that the decrease in flexibility of the A-domain leads to crowding of the subunits at the centre of the pentons, thereby favouring the hexon configuration during assembly. Thus, correct coat protein interactions with scaffolding protein and maintenance of sufficient coat protein flexibility are crucial for proper P22 assembly. The coat protein β-hinge region is the major determinant for both features.
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Affiliation(s)
- Margaret M Suhanovsky
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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33
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Teixeira LM, Strickland A, Mark SS, Bergkvist M, Sierra-Sastre Y, Batt CA. Entropically driven self-assembly of Lysinibacillus sphaericus S-layer proteins analyzed under various environmental conditions. Macromol Biosci 2010; 10:147-55. [PMID: 19637150 DOI: 10.1002/mabi.200900175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
S-Layer proteins are an example of bionanostructures that can be exploited in nanofabrication. In addition to their ordered structure, the ability to self-assembly is a key feature that makes them a promising technological tool. Here, in vitro self-assembly kinetics of SpbA was investigated, and found that it occurs at a rate that is dependent on temperature, its concentration, and the concentration of calcium ions and sodium chloride. The activation enthalpy (120.81 kJ . mol(-1)) and entropy (129.34 J . mol(-1) . K(-1)) obtained infers that the incorporation of monomers incurs in a net loss of hydrophobic surface. By understanding how the protein monomers drive the self-assembly at different conditions, the rational optimization of this process was feasible.
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Hagan MF, Elrad OM. Understanding the concentration dependence of viral capsid assembly kinetics--the origin of the lag time and identifying the critical nucleus size. Biophys J 2010; 98:1065-74. [PMID: 20303864 DOI: 10.1016/j.bpj.2009.11.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 10/19/2022] Open
Abstract
The kinetics for the assembly of viral proteins into a population of capsids can be measured in vitro with size exclusion chromatography or dynamic light scattering, but extracting mechanistic information from these studies is challenging. For example, it is not straightforward to determine the critical nucleus size or the elongation time (the time required for a nucleus to grow to completion). In this work, we study theoretical and computational models for capsid assembly to show that the critical nucleus size can be determined from the concentration dependence of the assembly half-life and that the elongation time is revealed by the length of the lag phase. Furthermore, we find that the system becomes kinetically trapped when nucleation becomes fast compared to elongation. Implications of this constraint for determining elongation mechanisms from experimental assembly data are discussed.
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Affiliation(s)
- Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts, USA.
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35
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Ouldridge TE, Louis AA, Doye JPK. Extracting bulk properties of self-assembling systems from small simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:104102. [PMID: 21389436 DOI: 10.1088/0953-8984/22/10/104102] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For systems that self-assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems can lead to significant finite-size effects due to the suppression of concentration fluctuations. We introduce methods for estimating the bulk yields from simulations of small systems and for following the convergence of yields with system size, under the assumptions that the various species behave ideally.
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Affiliation(s)
- Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
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36
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Saugar I, Irigoyen N, Luque D, Carrascosa JL, Rodríguez JF, Castón JR. Electrostatic interactions between capsid and scaffolding proteins mediate the structural polymorphism of a double-stranded RNA virus. J Biol Chem 2009; 285:3643-3650. [PMID: 19933276 DOI: 10.1074/jbc.m109.075994] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Capsid proteins that adopt distinct conformations constitute a paradigm of the structural polymorphism of macromolecular assemblies. We show the molecular basis of the flexibility mechanism of VP2, the capsid protein of the double-stranded RNA virus infectious bursal disease virus. The initial assembly, a procapsid-like structure, is built by the protein precursor pVP2 and requires VP3, the other infectious bursal disease virus major structural protein, which acts as a scaffold. The pVP2 C-terminal region, which is proteolyzed during virus maturation, contains an amphipathic alpha-helix that acts as a molecular switch. In the absence of VP3, efficient virus-like particle assembly occurs when the structural unit is a VP2-based chimeric protein with an N-terminal-fused His(6) tag. The His tag has a positively charged N terminus and a negatively charged C terminus, both important for virion-like structure assembly. The charge distributions of the VP3 C terminus and His tag are similar. We tested whether the His tag emulates the role of VP3 and found that the presence of a VP3 C-terminal peptide in VP2-based chimeric proteins resulted in the assembly of virus-like particles. We analyzed the electrostatic interactions between these two charged morphogenetic peptides, in which a single residue was mutated to impede the predicted interaction, followed by a compensatory double mutation to rescue electrostatic interactions. The effects of these mutations were monitored by following the virus-like and/or virus-related assemblies. Our results suggest that the basic face of the pVP2 amphipathic alpha-helix interacts with the acidic region of the VP3 C terminus and that this interaction is essential for VP2 acquisition of competent conformations for capsid assembly.
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Affiliation(s)
- Irene Saugar
- From the Departments of Structure of Macromolecules, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain
| | - Nerea Irigoyen
- Molecular and Cellular Biology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain
| | - Daniel Luque
- From the Departments of Structure of Macromolecules, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain
| | - José L Carrascosa
- From the Departments of Structure of Macromolecules, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain
| | - José F Rodríguez
- Molecular and Cellular Biology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain
| | - José R Castón
- From the Departments of Structure of Macromolecules, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Cantoblanco, 28049 Madrid, Spain.
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37
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Wilber AW, Doye JPK, Louis AA, Lewis ACF. Monodisperse self-assembly in a model with protein-like interactions. J Chem Phys 2009; 131:175102. [DOI: 10.1063/1.3243581] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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38
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Tuma R, Tsuruta H, French KH, Prevelige PE. Detection of intermediates and kinetic control during assembly of bacteriophage P22 procapsid. J Mol Biol 2008; 381:1395-406. [PMID: 18582476 DOI: 10.1016/j.jmb.2008.06.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 06/04/2008] [Accepted: 06/10/2008] [Indexed: 11/17/2022]
Abstract
Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter approximately 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibrium (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.
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Affiliation(s)
- Roman Tuma
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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39
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Purdy JG, Flanagan JM, Ropson IJ, Rennoll-Bankert KE, Craven RC. Critical role of conserved hydrophobic residues within the major homology region in mature retroviral capsid assembly. J Virol 2008; 82:5951-61. [PMID: 18400856 PMCID: PMC2395126 DOI: 10.1128/jvi.00214-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 03/28/2008] [Indexed: 12/26/2022] Open
Abstract
During retroviral maturation, the CA protein undergoes dramatic structural changes and establishes unique intermolecular interfaces in the mature capsid shell that are different from those that existed in the immature precursor. The most conserved region of CA, the major homology region (MHR), has been implicated in both immature and mature assembly, although the precise contribution of the MHR residues to each event has been largely undefined. To test the roles of specific MHR residues in mature capsid assembly, an in vitro system was developed that allowed for the first-time formation of Rous sarcoma virus CA into structures resembling authentic capsids. The ability of CA to assemble organized structures was destroyed by substitutions of two conserved hydrophobic MHR residues and restored by second-site suppressors, demonstrating that these MHR residues are required for the proper assembly of mature capsids in addition to any role that these amino acids may play in immature particle assembly. The defect caused by the MHR mutations was identified as an early step in the capsid assembly process. The results provide strong evidence for a model in which the hydrophobic residues of the MHR control a conformational reorganization of CA that is needed to initiate capsid assembly and suggest that the formation of an interdomain interaction occurs early during maturation.
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Affiliation(s)
- John G Purdy
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
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40
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Wilber AW, Doye JPK, Louis AA, Noya EG, Miller MA, Wong P. Reversible self-assembly of patchy particles into monodisperse icosahedral clusters. J Chem Phys 2007; 127:085106. [PMID: 17764305 DOI: 10.1063/1.2759922] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We systematically study the design of simple patchy sphere models that reversibly self-assemble into monodisperse icosahedral clusters. We find that the optimal patch width is a compromise between structural specificity (the patches must be narrow enough to energetically select the desired clusters) and kinetic accessibility (they must be sufficiently wide to avoid kinetic traps). Similarly, for good yields the temperature must be low enough for the clusters to be thermodynamically stable, but the clusters must also have enough thermal energy to allow incorrectly formed bonds to be broken. Ordered clusters can form through a number of different dynamic pathways, including direct nucleation and indirect pathways involving large disordered intermediates. The latter pathway is related to a reentrant liquid-to-gas transition that occurs for intermediate patch widths upon lowering the temperature. We also find that the assembly process is robust to inaccurate patch placement up to a certain threshold and that it is possible to replace the five discrete patches with a single ring patch with no significant loss in yield.
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Affiliation(s)
- Alex W Wilber
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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41
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Zhang T, Kim WT, Schwartz R. Investigating Scaling Effects on Virus Capsid-Like Self-Assembly Using Discrete Event Simulations. IEEE Trans Nanobioscience 2007; 6:235-41. [DOI: 10.1109/tnb.2007.903484] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Parent KN, Suhanovsky MM, Teschke CM. Polyhead formation in phage P22 pinpoints a region in coat protein required for conformational switching. Mol Microbiol 2007; 65:1300-10. [PMID: 17680786 PMCID: PMC3215258 DOI: 10.1111/j.1365-2958.2007.05868.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eighteen single amino acid substitutions in phage P22 coat protein cause temperature-sensitive folding defects (tsf). Three intragenic global suppressor (su) substitutions (D163G, T166I and F170L), localized to a flexible loop, rescue the folding of several tsf coat proteins. Here we investigate the su substitutions in the absence of the original tsf substitutions. None of the su variant coat proteins displayed protein folding defects. Individual su substitutions had little effect on phage production in vivo; yet double and triple combinations resulted in a cold-sensitive (cs) phenotype, consistent with a defect in assembly. During virus assembly and maturation, conformational switching of capsid subunits is required when chemically identical capsid subunits form an icosahedron. Analysis of double- and triple-su phage-infected cell lysates by negative-stain electron microscopy reveals an increase in aberrant structures at the cs temperature. In vitro assembly of F170L coat protein causes production of polyheads, never seen before in phage P22. Purified procapsids composed of all of the su coat proteins showed defects in expansion, which mimics maturation in vitro. Our results suggest that a previously identified surface-exposed loop in coat protein is critical in conformational switching of subunits during both procapsid assembly and maturation.
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43
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Parent KN, Teschke CM. GroEL/S substrate specificity based on substrate unfolding propensity. Cell Stress Chaperones 2007; 12:20-32. [PMID: 17441504 PMCID: PMC1852890 DOI: 10.1379/csc-219r.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Phage P22 wild-type (WT) coat protein does not require GroEL/S to fold but temperature-sensitive-folding (tsf) coat proteins need the chaperone complex for correct folding. WT coat protein and all variants absolutely require P22 scaffolding protein, an assembly chaperone, to assemble into precursor structures termed procapsids. Previously, we showed that a global suppressor (su) substitution, T1661, which rescues several tsf coat protein variants, functioned by inducing GroEL/S. This led to an increased formation of tsf:T1661 coat protein:GroEL complexes compared with the tsf parents. The increased concentration of complexes resulted in more assembly-competent coat proteins because of a shift in the chaperone-driven kinetic partitioning between aggregation-prone intermediates toward correct folding and assembly. We have now investigated the folding and assembly of coat protein variants that carry a different global su substitution, F170L. By monitoring levels of phage production in the presence of a dysfunctional GroEL we found that tsf:F170L proteins demonstrate a less stringent requirement for GroEL. Tsf:F170L proteins also did not cause induction of the chaperones. Circular dichroism and tryptophan fluorescence indicate that the native state of the tsf: F170L coat proteins is restored to WT-like values. In addition, native acrylamide gel electrophoresis shows a stabilized native state for tsf:F170L coat proteins. The F170L su substitution also increases procapsid production compared with their tsf parents. We propose that the F170L su substitution has a decreased requirement for the chaperones GroEL and GroES as a result of restoring the tsf coat proteins to a WT-like state. Our data also suggest that GroEL/S can be induced by increasing the population of unfolding intermediates.
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Affiliation(s)
- Kristin N Parent
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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44
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Kropinski AM, Sulakvelidze A, Konczy P, Poppe C. Salmonella phages and prophages--genomics and practical aspects. Methods Mol Biol 2007; 394:133-75. [PMID: 18363236 DOI: 10.1007/978-1-59745-512-1_9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host genome sequencing projects. Phylogenetic analysis of the sequenced phages, based on related protein content using CoreGenes, reveals that these viruses fall into five groupings (P27-like, P2-like, lambdoid, P22-like, and T7-like) and three outliers (epsilon15, KS7, and Felix O1). The P27 group is only represented by ST64B; the P2 group contains Fels-2, SopEphi, and PSP3; the lambdoid Salmonella phages include Gifsy-1, Gifsy-2, and Fels-1. The P22-like viruses include epsilon34, ES18, P22, ST104, and ST64T. The only member of the T7-like group is SP6. The properties of each of these phages are discussed, along with their role as agents of genetic exchange and as therapeutic agents and their involvement in phage typing.
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Affiliation(s)
- Andrew M Kropinski
- Host and Pathogen Determinants, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario
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45
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Zlotnick A. Distinguishing reversible from irreversible virus capsid assembly. J Mol Biol 2006; 366:14-8. [PMID: 17157314 PMCID: PMC1941720 DOI: 10.1016/j.jmb.2006.11.034] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/07/2006] [Accepted: 11/08/2006] [Indexed: 11/17/2022]
Abstract
Capsids of spherical viruses may be constructed from hundreds or thousands of copies of the major capsid protein(s). These assembly reactions are poorly understood. Here we consider the predicted behavior for assembly where the component reactions have weak association energy and are reversible and compare them to essentially irreversible reactions. The comparisons are based on mass action calculations and the behavior predicted from kinetic simulations where assembly is described as a cascade of low order reactions. Reversible reactions are characterized by a pseudo-critical concentration, whereas irreversible reactions consume all free subunits. Irreversible reactions are more susceptible to kinetic traps comprised of numerous small intermediates. In the case where only the ultimate step is irreversible, very low concentrations of intermediates slow the completion of the reaction so that overall it closely matches the predictions for the reversible reactions that make up the majority of the cascade. Data in the literature strongly support the hypothesis that most viruses are held together by many weak interactions.
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Affiliation(s)
- Adam Zlotnick
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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46
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Parent KN, Suhanovsky MM, Teschke CM. Phage P22 procapsids equilibrate with free coat protein subunits. J Mol Biol 2006; 365:513-22. [PMID: 17067636 PMCID: PMC2790821 DOI: 10.1016/j.jmb.2006.09.088] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 09/25/2006] [Accepted: 09/27/2006] [Indexed: 11/18/2022]
Abstract
Assembly of bacteriophage P22 procapsids has long served as a model for assembly of spherical viruses. Historically, assembly of viruses has been viewed as a non-equilibrium process. Recently alternative models have been developed that treat spherical virus assembly as an equilibrium process. Here we have investigated whether P22 procapsid assembly reactions achieve equilibrium or are irreversibly trapped. To assemble a procapsid-like particle in vitro, pure coat protein monomers are mixed with scaffolding protein. We show that free subunits can exchange with assembled structures, indicating that assembly is a reversible, equilibrium process. When empty procapsid shells (procapsids with the scaffolding protein stripped out) were diluted so that the concentration was below the dissociation constant ( approximately 5 microM) for coat protein monomers, free monomers were detected. The released monomers were assembly-competent; when NaCl was added to metastable partial capsids that were aged for an extended period, the released coat subunits were able to rapidly re-distribute from the partial capsids and form whole procapsids. Lastly, radioactive monomeric coat subunits were able to exchange with the subunits from empty procapsid shells. The data presented illustrate that coat protein monomers are able to dissociate from procapsids in an active state, that assembly of procapsids is consistent with reactions at equilibrium and that the reaction follows the law of mass action.
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Affiliation(s)
- Kristin N Parent
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, CT 06269-3125, USA
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47
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Parent KN, Zlotnick A, Teschke CM. Quantitative Analysis of Multi-component Spherical Virus Assembly: Scaffolding Protein Contributes to the Global Stability of Phage P22 Procapsids. J Mol Biol 2006; 359:1097-106. [PMID: 16697406 DOI: 10.1016/j.jmb.2006.03.068] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 03/10/2006] [Accepted: 03/31/2006] [Indexed: 02/02/2023]
Abstract
Assembly of the hundreds of subunits required to form an icosahedral virus must proceed with exquisite fidelity, and is a paradigm for the self-organization of complex macromolecular structures. However, the mechanism for capsid assembly is not completely understood for any virus. Here we have investigated the in vitro assembly of phage P22 procapsids using a quantitative model specifically developed to analyze assembly of spherical viruses. Phage P22 procapsids are the product of the co-assembly of 420 molecules of coat protein and approximately 100-300 molecules of scaffolding protein. Scaffolding protein serves as an assembly chaperone and is not part of the final mature capsid, but is essential for proper procapsid assembly. Here we show that scaffolding protein also affects the thermodynamics of assembly, and for the first time this quantitative analysis has been performed on a virus composed of more than one type of protein subunit. Purified coat and scaffolding proteins were mixed in varying ratios in vitro to form procapsids. The reactions were allowed to reach equilibrium and the proportion of the input protein assembled into procapsids or remaining as free subunits was determined by size exclusion chromatography and SDS-PAGE. The results were used to calculate the free energy contributions for individual coat and scaffolding proteins. Each coat protein subunit was found to contribute -7.2(+/-0.1)kcal/mol and each scaffolding protein -6.1(+/-0.2)kcal/mol to the stability of the procapsid. Because each protein interacts with two or more neighbors, the pair-wise energies are even less. The weak protein interactions observed in the assembly of procapsids are likely important in the control of nucleation, since an increase in affinity between coat and scaffolding proteins can lead to kinetic traps caused by the formation of too many nuclei. In addition, we find that adjusting the molar ratio of scaffolding to coat protein can alter the assembly product. When the scaffolding protein concentration is low relative to coat protein, there is a correspondingly low yield of proper procapsids. When the relative concentration is very high, too many nuclei form, leading to kinetically trapped assembly intermediates.
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Affiliation(s)
- Kristin N Parent
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
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48
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Zhang T, Schwartz R. Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics. Biophys J 2005; 90:57-64. [PMID: 16214864 PMCID: PMC1367037 DOI: 10.1529/biophysj.105.072207] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The process by which hundreds of identical capsid proteins self-assemble into icosahedral structures is complex and poorly understood. Establishing constraints on the assembly pathways is crucial to building reliable theoretical models. For example, it is currently an open question to what degree overall assembly kinetics are dominated by one or a few most efficient pathways versus the enormous number theoretically possible. The importance of this question, however, is often overlooked due to the difficulties of addressing it in either theoretical or experimental practice. We apply a computer model based on a discrete-event simulation method to evaluate the contributions of nondominant pathways to overall assembly kinetics. This is accomplished by comparing two possible assembly models: one allowing growth to proceed only by the accretion of individual assembly subunits and the other allowing the binding of sterically compatible assembly intermediates any sizes. Simulations show that the two models perform almost identically under low binding rate conditions, where growth is strongly nucleation-limited, but sharply diverge under conditions of higher association rates or coat protein concentrations. The results suggest the importance of identifying the actual binding pattern if one is to build reliable models of capsid assembly or other complex self-assembly processes.
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Affiliation(s)
- Tiequan Zhang
- Department of Biological Sciences and Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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