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Haque F, Zhang H, Wang S, Chang CL, Savran C, Guo P. Methods for Single-Molecule Sensing and Detection Using Bacteriophage Phi29 DNA Packaging Motor. Methods Mol Biol 2018; 1805:423-450. [PMID: 29971730 DOI: 10.1007/978-1-4939-8556-2_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacteriophage phi29 DNA packaging motor consists of a dodecameric portal channel protein complex termed connector that allows transportation of genomic dsDNA and a hexameric packaging RNA (pRNA) ring to gear the motor. The elegant design of the portal protein has facilitated its applications for real-time single-molecule detection of biopolymers and chemicals with high sensitivity and selectivity. The robust self-assembly property of the pRNA has enabled biophysical studies of the motor complex to determine the stoichiometry and structure/folding of the pRNA at single-molecule level. This chapter focuses on biophysical and analytical methods for studying the phi29 motor components at the single-molecule level, such as single channel conductance assays of membrane-embedded connectors; single molecule photobleaching (SMPB) assay for determining the stoichiometry of phi29 motor components; fluorescence resonance energy transfer (FRET) assay for determining the structure and folding of pRNA; atomic force microscopy (AFM) for imaging pRNA nanoparticles of various size, shape, and stoichiometry; and bright-field microscopy with magnetomechanical system for direct visualization of viral DNA packaging process. The phi29 system with explicit engineering capability has incredible potentials for diverse applications in nanotechnology and nanomedicine including, but not limited to, DNA sequencing, drug delivery to diseased cells, environmental surveillance, and early disease diagnosis.
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Affiliation(s)
- Farzin Haque
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Chun-Li Chang
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Cagri Savran
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA. .,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA. .,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA. .,Markey Cancer Center, University of Kentucky, Lexington, KY, USA. .,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA. .,Sylvan G. Frank Endowed Chair in Pharmaceutics and Drug Delivery, The Ohio State University, Columbus, OH, USA.
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2
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Moleiro L, Mell M, Bocanegra R, López-Montero I, Fouquet P, Hellweg T, Carrascosa J, Monroy F. Permeability modes in fluctuating lipid membranes with DNA-translocating pores. Adv Colloid Interface Sci 2017; 247:543-554. [PMID: 28735883 DOI: 10.1016/j.cis.2017.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 10/19/2022]
Abstract
Membrane pores can significantly alter not only the permeation dynamics of biological membranes but also their elasticity. Large membrane pores able to transport macromolecular contents represent an interesting model to test theoretical predictions that assign active-like (non-equilibrium) behavior to the permeability contributions to the enhanced membrane fluctuations existing in permeable membranes [Maneville et al. Phys. Rev. Lett. 82, 4356 (1999)]. Such high-amplitude active contributions arise from the forced transport of solvent and solutes through the open pores, which becomes even dominant at large permeability. In this paper, we present a detailed experimental analysis of the active shape fluctuations that appear in highly permeable lipid vesicles with large macromolecular pores inserted in the lipid membrane, which are a consequence of transport permeability events occurred in an osmotic gradient. The experimental results are found in quantitative agreement with theory, showing a remarkable dependence with the density of membrane pores and giving account of mechanical compliances and permeability rates that are compatible with the large size of the membrane pore considered. The presence of individual permeation events has been detected in the fluctuation time-series, from which a stochastic distribution of the permeation events compatible with a shot-noise has been deduced. The non-equilibrium character of the membrane fluctuations in a permeation field, even if the membrane pores are mere passive transporters, is clearly demonstrated. Finally, a bio-nano-technology outlook of the proposed synthetic concept is given on the context of prospective uses as active membrane DNA-pores exploitable in gen-delivery applications based on lipid vesicles.
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3
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Haque F, Wang S, Stites C, Chen L, Wang C, Guo P. Single pore translocation of folded, double-stranded, and tetra-stranded DNA through channel of bacteriophage phi29 DNA packaging motor. Biomaterials 2015; 53:744-52. [PMID: 25890769 DOI: 10.1016/j.biomaterials.2015.02.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/22/2015] [Accepted: 02/24/2015] [Indexed: 12/11/2022]
Abstract
The elegant architecture of the channel of bacteriophage phi29 DNA packaging motor has inspired the development of biomimetics for biophysical and nanobiomedical applications. The reengineered channel inserted into a lipid membrane exhibits robust electrophysiological properties ideal for precise sensing and fingerprinting of dsDNA at the single-molecule level. Herein, we used single channel conduction assays to quantitatively evaluate the translocation dynamics of dsDNA as a function of the length and conformation of dsDNA. We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process. A ∼35-fold slower speed of translocation per base-pair was observed for long dsDNA, a significant contrast to the speed of dsDNA crossing synthetic pores. It was found that the channel could translocate both dsDNA with ∼32% of channel current blockage and with ∼64% for tetra-stranded DNA (two parallel dsDNA). The calculation of both cross-sectional areas of the dsDNA and tetra-stranded DNA suggested that the blockage was purely proportional to the physical space of the channel lumen and the size of the DNA substrate. Folded dsDNA configuration was clearly reflected in their characteristic current signatures. The finding of translocation of tetra-stranded DNA with 64% blockage is in consent with the recently elucidated mechanism of viral DNA packaging via a revolution mode that requires a channel larger than the dsDNA diameter of 2 nm to provide room for viral DNA revolving without rotation. The understanding of the dynamics of dsDNA translocation in the phi29 system will enable us to design more sophisticated single pore DNA translocation devices for future applications in nanotechnology and personal medicine.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Chris Stites
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Li Chen
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Biostatistics, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Biostatistics, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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4
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Wang S, Haque F, Rychahou PG, Evers BM, Guo P. Engineered nanopore of Phi29 DNA-packaging motor for real-time detection of single colon cancer specific antibody in serum. ACS NANO 2013; 7:9814-22. [PMID: 24152066 PMCID: PMC3915501 DOI: 10.1021/nn404435v] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The ingenious design of the bacterial virus phi29 DNA packaging nanomotor with an elegant and elaborate channel has inspired its application for single molecule detection of antigen/antibody interactions. The hub of this bacterial virus nanomotor is a truncated cone-shaped connector consisting of 12 protein subunits. These subunits form a ring with a central 3.6-nm channel acting as a path for dsDNA to enter during packaging and to exit during infection. The connector has been inserted into a lipid bilayer. Herein, we reengineered an Epithelial Cell Adhesion Molecule (EpCAM) peptide into the C-terminal of nanopore as a probe to specifically detect EpCAM antibody (Ab) in nanomolar concentration at the single molecule level. The binding of Abs sequentially to each peptide probe induced stepwise blocks in current. The distinctive current signatures enabled us to analyze the docking and undocking kinetics of Ab-probe interactions and determine the Kd. The signal of EpCAM antibody can be discriminated from the background events in the presence of nonspecific antibody or serum. Our results demonstrate the feasibility of generating a highly sensitive platform for detecting antibodies at extremely low concentrations in the presence of contaminants.
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Affiliation(s)
- Shaoying Wang
- Nanobiotechnology Center, ‡Department of Pharmaceutical Sciences, College of Pharmacy, and §Markey Cancer Center, University of Kentucky , Lexington, Kentucky 40536, United States
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5
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Geng J, Wang S, Fang H, Guo P. Channel size conversion of Phi29 DNA-packaging nanomotor for discrimination of single- and double-stranded nucleic acids. ACS NANO 2013; 7:3315-23. [PMID: 23488809 PMCID: PMC3663147 DOI: 10.1021/nn400020z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanopores have been utilized to detect the conformation and dynamics of polymers, including DNA and RNA. Biological pores are extremely reproducible at the atomic level with uniform channel sizes. The channel of the bacterial virus phi29 DNA-packaging motor is a natural conduit for the transportation of double-stranded DNA (dsDNA) and has the largest diameter among the well-studied biological channels. The larger channel facilitates translocation of dsDNA and offers more space for further channel modification and conjugation. Interestingly, the relatively large wild-type channel, which translocates dsDNA, cannot detect single-stranded nucleic acids (ssDNA or ssRNA) under the current experimental conditions. Herein, we reengineered this motor channel by removing the internal loop segment of the channel. The modification resulted in two classes of channels. One class was the same size as the wild-type channel, while the other class had a cross-sectional area about 60% of the wild-type. This smaller channel was able to detect the real-time translocation of single-stranded nucleic acids at single-molecule level. While the wild-type connector exhibited a one-way traffic property with respect to dsDNA translocation, the loop-deleted connector was able to translocate ssDNA and ssRNA with equal competencies from both termini. This finding of size alterations in reengineered motor channels expands the potential application of the phi29 DNA-packaging motor in nanomedicine, nanobiotechnology, and high-throughput single-pore DNA sequencing.
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Affiliation(s)
- Jia Geng
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Huaming Fang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536, USA
- Address correspondence to: Peixuan Guo, University of Kentucky, Department of Pharmaceutical Sciences, 789 S. Limestone Avenue, Room # 565, Lexington, KY, USA 40536-0596, , Phone:859-218-0128, Fax:859-257-1307
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6
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Shim JS, Geng J, Ahn CH, Guo P. Formation of lipid bilayers inside microfluidic channel array for monitoring membrane-embedded nanopores of phi29 DNA packaging nanomotor. Biomed Microdevices 2013; 14:921-8. [PMID: 22773160 DOI: 10.1007/s10544-012-9671-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An efficient method to form lipid bilayers inside an array of microfluidic channels has been developed and applied to monitor the membrane-embedded phi29 DNA packaging motor with an electrochemical characterization on a lab-on-a-chip (LOC) platform. A push-pull junction capturing approach was applied to confine a small amount of the lipid solution inside a microchannel. The selective permeability between solvents and water in PDMS was utilized to extract the solvent from the lipid solution, resulting in a self-formation of the lipid bilayer in the microchannel array. Each microchannel was independently connected to a silver/silver chloride (Ag/AgCl) electrode array, leading to a high-throughput monitoring of the nanopore insertion in the formed lipid bilayers. The formation of multiple lipid bilayers inside an array of microchannels and the simultaneous electrical and optical monitoring of multiple bilayer provides an efficient LOC platform for the further development of single phi29 motor pore sensing and high throughput single pore dsDNA sequencing.
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Affiliation(s)
- Joon S Shim
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
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7
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Incorporation of a viral DNA-packaging motor channel in lipid bilayers for real-time, single-molecule sensing of chemicals and double-stranded DNA. Nat Protoc 2013; 8:373-92. [PMID: 23348364 DOI: 10.1038/nprot.2013.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over the past decade, nanopores have rapidly emerged as stochastic biosensors. This protocol describes the cloning, expression and purification of the channel of the bacteriophage phi29 DNA-packaging nanomotor and its subsequent incorporation into lipid membranes for single-pore sensing of double-stranded DNA (dsDNA) and chemicals. The membrane-embedded phi29 nanochannel remains functional and structurally intact under a range of conditions. When ions and macromolecules translocate through this nanochannel, reliable fingerprint changes in conductance are observed. Compared with other well-studied biological pores, the phi29 nanochannel has a larger cross-sectional area, which enables the translocation of dsDNA. Furthermore, specific amino acids can be introduced by site-directed mutagenesis within the large cavity of the channel to conjugate receptors that are able to bind specific ligands or analytes for desired applications. The lipid membrane-embedded nanochannel system has immense potential nanotechnological and biomedical applications in bioreactors, environmental sensing, drug monitoring, controlled drug delivery, early disease diagnosis and high-throughput DNA sequencing. The total time required for completing one round of this protocol is around 1 month.
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8
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Moleiro LH, López-Montero I, Márquez I, Moreno S, Vélez M, Carrascosa JL, Monroy F. Efficient orthogonal integration of the bacteriophage ϕ29 DNA-portal connector protein in engineered lipid bilayers. ACS Synth Biol 2012; 1:414-24. [PMID: 23651339 DOI: 10.1021/sb3000063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The portal connector of bacteriophage viruses constitutes a robust molecular machine for DNA translocation. In this paper we propose an optimized reconstitution method for efficient orthogonal integration of native viral connectors into lipid bilayers, particularly of giant unilamellar vesicles. Our nanoengineering plan considers the hydrophilic connector protein of the bacteriophage virus ϕ29 integrated into a specifically engineered bilayer made of "hydrophylized" lipids. From the precise knowledge of the connector structure, the membrane chemistry was designed by tuning reactivity in the bilayer using specific functional lipids. We show details on the reconstitution methods and experimental evidence about the integration of the portal protein in the engineered membrane. The proposed route provides an efficient method for orthogonal integration of native viral connectors into lipid bilayers in conditions adequate for functional DNA translocation. This concept could be potentially exploited in advanced nanotechnological realizations, particularly for the integration of these powerful machines into giant lipid vesicles with the aim of building a cargo-device useful for gene delivery applications.
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Affiliation(s)
- Lara H. Moleiro
- Departamento de Química
Física I, Universidad Complutense, 28040 Madrid, Spain
| | - Iván López-Montero
- Departamento de Química
Física I, Universidad Complutense, 28040 Madrid, Spain
| | - Ileana Márquez
- Instituto de Catálisis
y Petroleoquímica, CSIC, Marie Curie
2, Cantoblanco, 28049 Madrid, Spain
| | - Sonia Moreno
- Centro Nacional de Biotecnología, CSIC, c/Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Marisela Vélez
- Instituto de Catálisis
y Petroleoquímica, CSIC, Marie Curie
2, Cantoblanco, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia),
Cantoblanco, 28049 Madrid, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología, CSIC, c/Darwin 3, Cantoblanco, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia),
Cantoblanco, 28049 Madrid, Spain
| | - Francisco Monroy
- Departamento de Química
Física I, Universidad Complutense, 28040 Madrid, Spain
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9
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Haque F, Lunn J, Fang H, Smithrud D, Guo P. Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor. ACS NANO 2012; 6:3251-3261. [PMID: 22458779 PMCID: PMC3337346 DOI: 10.1021/nn3001615] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This article reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of 12 protein subunits encircled into a 3.6 nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Da), thymine (167 Da), and benzene (105 Da) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete stepwise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
| | - Jennifer Lunn
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45267
| | - Huaming Fang
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
| | - David Smithrud
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45267
| | - Peixuan Guo
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536
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10
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Geng J, Fang H, Haque F, Zhang L, Guo P. Three reversible and controllable discrete steps of channel gating of a viral DNA packaging motor. Biomaterials 2011; 32:8234-42. [PMID: 21807410 DOI: 10.1016/j.biomaterials.2011.07.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/11/2011] [Indexed: 01/06/2023]
Abstract
The channel of the viral DNA packaging motor allows dsDNA to enter the protein procapsid shell during maturation and to exit during infection. We recently showed that the bacteriophage phi29 DNA packaging motor exercises a one-way traffic property using a channel as a valve for dsDNA translocation. This raises a question of how dsDNA is ejected during infection if the channel only allows the dsDNA to travel inward. We proposed that DNA forward or reverse travel is controlled by conformational changes of the channel. Here we reported our direct observation that the channel indeed exercises conformational changes by single channel recording at a single-molecule level. The changes were induced by high electrical voltage, or by affinity binding to the C-terminal wider end located within the capsid. Novel enough, the conformational change of the purified connector channel exhibited three discrete gating steps, with a size reduction of 32% for each step. We investigated the role of the terminal and internal loop of the channel in gating by different mutants. The step-wise conformational change of the channel was also reversible and controllable, making it an ideal nano-valve for constructing a nanomachine with potential applications in nanobiotechnology and nanomedicine.
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Affiliation(s)
- Jia Geng
- Nanobiomedical Center, SEEBME, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45267, USA
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11
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Jing P, Haque F, Vonderheide AP, Montemagno C, Guo P. Robust properties of membrane-embedded connector channel of bacterial virus phi29 DNA packaging motor. MOLECULAR BIOSYSTEMS 2010; 6:1844-52. [PMID: 20523933 DOI: 10.1039/c003010d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biological systems contain highly-ordered macromolecular structures with diverse functions, inspiring their utilization in nanotechnology. A motor allows linear dsDNA viruses to package their genome into a preformed procapsid. The central component of the motor is the portal connector that acts as a pathway for the translocation of dsDNA. The elegant design of the connector and its channel motivates its application as an artificial nanopore (Nature Nanotechnology, 4, 765-772). Herein, we demonstrate the robust characteristics of the connector of the bacteriophage phi29 DNA packaging motor by single pore electrophysiological assays. The conductance of each pore is almost identical and is perfectly linear with respect to the applied voltage. Numerous transient current blockade events induced by dsDNA are consistent with the dimensions of the channel and dsDNA. Furthermore, the connector channel is stable under a wide range of experimental conditions including high salt and pH 2-12. The robust properties of the connector nanopore made it possible to develop a simple reproducible approach for connector quantification. The precise number of connectors in each sheet of the membrane was simply derived from the slopes of the plot of voltage against current. Such quantifications led to a reliable real time counting of DNA passing through the channel. The fingerprint of DNA translocation in this system has provided a new tool for future biophysical and physicochemical characterizations of DNA transportation, motion, and packaging.
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Affiliation(s)
- Peng Jing
- Department of Biomedical Engineering, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
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12
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Wendell D, Jing P, Geng J, Subramaniam V, Lee TJ, Montemagno C, Guo P. Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores. NATURE NANOTECHNOLOGY 2009; 4:765-72. [PMID: 19893523 PMCID: PMC2777743 DOI: 10.1038/nnano.2009.259] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 08/04/2009] [Indexed: 05/18/2023]
Abstract
Biological pores have been used to study the transport of DNA and other molecules, but most pores have channels that allow only the movement of small molecules and single-stranded DNA and RNA. The bacteriophage phi29 DNA-packaging motor, which allows double-stranded DNA to enter the virus during maturation and exit during an infection, contains a connector protein with a channel that is between 3.6 and 6 nm wide. Here we show that a modified version of this connector protein, when reconstituted into liposomes and inserted into planar lipid bilayers, allows the translocation of double-stranded DNA. The measured conductance of a single connector channel was 4.8 nS in 1 M KCl. This engineered and membrane-adapted phage connector is expected to have applications in microelectromechanical sensing, microreactors, gene delivery, drug loading and DNA sequencing.
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Affiliation(s)
| | | | | | | | | | | | - Peixuan Guo
- Address correspondence to: Peixuan Guo, Vontz Center for Molecular Studies Rm 1301, 3125 Eden Ave., Cincinnati, OH 45267-0508, Phone: (513)558-0024 (Lab), (513)558-0041 (Office), FAX: (513)558-0024,
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13
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Kang S, Poliakov A, Sexton J, Renfrow MB, Prevelige PE. Probing conserved helical modules of portal complexes by mass spectrometry-based hydrogen/deuterium exchange. J Mol Biol 2008; 381:772-84. [PMID: 18621389 DOI: 10.1016/j.jmb.2008.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 11/18/2022]
Abstract
The Double-stranded DNA bacteriophage P22 has a ring-shaped dodecameric complex composed of the 84 kDa portal protein subunit that forms the central channel of the phage DNA packaging motor. The overall morphology of the P22 portal complex is similar to that of the portal complexes of Phi29, SPP1, T3, T7 phages and herpes simplex virus. Secondary structure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal complexes suggested that the P22 portal protein complex shares conserved helical modules that were found in the dodecameric interfaces of the Phi29 portal complex. To identify the amino acids involved in intersubunit contacts in the P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deuterium exchange analysis of monomeric and in vitro assembled portal proteins of P22 and the dodecameric Phi29 portal. Hydrogen/deuterium exchange experiments provided evidence of intersubunit interactions in the P22 portal complex similar to those in the Phi29 portal that map to the regions predicted to be conserved helical modules.
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Affiliation(s)
- Sebyung Kang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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Poliakov A, van Duijn E, Lander G, Fu CY, Johnson JE, Prevelige PE, Heck AJR. Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the heterogeneity of bacteriophage portal assemblies. J Struct Biol 2007; 157:371-83. [PMID: 17064935 DOI: 10.1016/j.jsb.2006.09.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 09/08/2006] [Accepted: 09/08/2006] [Indexed: 11/23/2022]
Abstract
The success of electron-cryo microscopy (cryo-EM) and image reconstruction of cyclic oligomers, such as the viral and bacteriophage portals, depends on the accurate knowledge of their order of symmetry. A number of statistical methods of image analysis address this problem, but often do not provide unambiguous results. Direct measurement of the oligomeric state of multisubunit protein assemblies is difficult when the number of subunits is large and one subunit renders only a small increment to the full size of the oligomer. Moreover, when mixtures of different stochiometries are present techniques such as analytical centrifugation or size-exclusion chromatography are also less helpful. Here, we use electrospray ionization mass spectrometry to directly determine the oligomeric states of the in vitro assembled portal oligomers of the phages P22, Phi-29 and SPP1, which range in mass from 430 kDa to about 1 million Da. Our data unambiguously reveal that the oligomeric states of Phi-29 and SPP1 portals were 12 and 13, respectively, in good agreement with crystallographic and electron microscopy data. However, in vitro assembled P22 portals were a mixture of 11- and 12-mer species in an approximate ratio of 2:1, respectively. A subsequent reference-free alignment of electron microscopy images of the P22 portal confirmed this mixture of oligomeric states. We conclude that macromolecular mass spectrometry is a valuable tool in structural biology that can aide in the determination of oligomeric states and symmetry of assemblies, providing a good starting point for improved image analysis of cryo-EM data.
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Affiliation(s)
- Anton Poliakov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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15
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Xiao F, Moll WD, Guo S, Guo P. Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacteriophage phi29. Nucleic Acids Res 2005; 33:2640-9. [PMID: 15886394 PMCID: PMC1092275 DOI: 10.1093/nar/gki554] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
During assembly, bacterial virus phi29 utilizes a motor to insert genomic DNA into a preformed protein shell called the procapsid. The motor contains one twelve-subunit connector with a 3.6 nm central channel for DNA transportation, six viral-encoded RNA (packaging RNA or pRNA) and a protein, gp16, with unknown stoichiometry. Recent DNA-packaging models proposed that the 5-fold procapsid vertexes and 12-fold connector (or the hexameric pRNA ring) represented a symmetry mismatch enabling production of a force to drive a rotation motor to translocate and compress DNA. There was a discrepancy regarding the location of the foothold for the pRNA. One model [C. Chen and P. Guo (1997) J. Virol., 71, 3864–3871] suggested that the foothold for pRNA was the connector and that the pRNA–connector complex was part of the rotor. However, one other model suggested that the foothold for pRNA was the 5-fold vertex of the capsid protein and that pRNA was the stator. To elucidate the mechanism of phi29 DNA packaging, it is critical to confirm whether pRNA binds to the 5-fold vertex of the capsid protein or to the 12-fold symmetrical connector. Here, we used both purified connector and purified procapsid for binding studies with in vitro transcribed pRNA. Specific binding of pRNA to the connector in the procapsid was found by photoaffinity crosslinking. Removal of the N-terminal 14 amino acids of the gp10 protein by proteolytic cleavage resulted in undetectable binding of pRNA to either the connector or the procapsid, as investigated by agarose gel electrophoresis, SDS–PAGE, sucrose gradient sedimentation and N-terminal peptide sequencing. It is therefore concluded that pRNA bound to the 12-fold symmetrical connector to form a pRNA–connector complex and that the foothold for pRNA is the connector but not the capsid protein.
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Affiliation(s)
| | | | | | - Peixuan Guo
- To whom correspondence should be addressed. Tel: +1 765 494 7561; Fax: +1 765 496 1795;
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16
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Ibarra B, Valpuesta JM, Carrascosa JL. Purification and functional characterization of p16, the ATPase of the bacteriophage Phi29 packaging machinery. Nucleic Acids Res 2001; 29:4264-73. [PMID: 11691914 PMCID: PMC60195 DOI: 10.1093/nar/29.21.4264] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteriophage Phi29 codes for a protein (p16) that is required for viral DNA packaging both in vivo and in vitro. Co-expression of p16 with the chaperonins GroEL and GroES has allowed its purification in a soluble form. Purified p16 shows a weak ATPase activity that is stimulated by either DNA or RNA, irrespective of the presence of any other viral component. The stimulation of ATPase activity of p16, although induced under packaging conditions, is not dependent of the actual DNA packaging and in this respect the Phi29 enzyme is similar to other viral terminases. Protein p16 competes with DNA and RNA in the interaction with the viral prohead, which occurs through the N-terminal region of the connector protein (p10). In fact, p16 interacts in a nucleotide-dependent fashion with the viral Phi29-encoded RNA (pRNA) involved in DNA packaging, and this binding can be competed with DNA. Our results are consistent with a model for DNA translocation in which p16, bound and organized around the connector, acts as a power stroke to pump the DNA into the prohead, using the hydrolysis of ATP as an energy source.
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Affiliation(s)
- B Ibarra
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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17
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Valle M, Muñoz M, Kremer L, Valpuesta JM, Martínez-A C, Carrascosa JL, Albar JP. Selection of antibody probes to correlate protein sequence domains with their structural distribution. Protein Sci 1999; 8:883-9. [PMID: 10211834 PMCID: PMC2144296 DOI: 10.1110/ps.8.4.883] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We propose a new approach that permits correlation of specific domains defined by their primary sequence with their location in the structure of complex macromolecular aggregates. It is based on the combination of well-established structural analysis methods that incorporate the use of overlapping peptides on cellulose membranes for the isolation and purification of specific antibodies from a polyclonal antiserum. Monospecific antibodies to the connector protein of bacteriophage phi29 were isolated from polyclonal antisera using a new development of the spotscan method. These antibodies can be purified in quantities that allow antigenicity testing in enzyme-linked immunosorbent assays, Western blotting and immunoprecipitations, demonstrating the specificity of this isolation procedure. This approach has allowed us to generate direct antibody probes for immunoelectron microscopy mapping of different connector protein domains in a low resolution three-dimensional epitope map.
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Affiliation(s)
- M Valle
- Department of Macromolecular Structure, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, Spain
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18
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Valpuesta JM, Fernández JJ, Carazo JM, Carrascosa JL. The three-dimensional structure of a DNA translocating machine at 10 A resolution. Structure 1999; 7:289-96. [PMID: 10368298 DOI: 10.1016/s0969-2126(99)80039-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Head-tail connectors are viral substructures that are very important in the viral morphogenetic cycle, having roles in the formation of the precursor capsid (prohead), DNA packaging, tail binding to the mature head and in the infection process. Structural information on the connector would, therefore, help us to understand how this structure is related to a multiplicity of functions. RESULTS Recombinant bacteriophage phi29 connectors have been crystallized in two-dimensional aggregates. An average projection image and a three-dimensional map have been obtained at 8 A and 10 A resolution, respectively, from untilted and tilted images of vitrified specimens of the two-dimensional crystals. The average projection image reveals a central mass surrounding a channel with 12 appendages protruding from the central mass. The three-dimensional map reveals a wide domain surrounded by 12 appendages that interact with the prohead vertex, and a narrow domain that interacts with the bacteriophage tail. At the junction of the two domains, 12 smaller appendages are visualized. A channel runs along the axis of the connector structure and is sufficiently wide to allow a double-stranded DNA molecule to pass through. CONCLUSIONS The propeller-like structure of the phi29 connector strengthens the notion of the connector rotating during DNA packaging. The groove formed by the two lanes of large and small appendages may act as a rail to prevent the liberation of the connector from the prohead vertex during rotation.
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Affiliation(s)
- J M Valpuesta
- Centro Nacional de Biotecnología CSIC, Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
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19
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Guasch A, Parrága A, Pous J, Valpuesta JM, Carrascosa JL, Coll M. Purification, crystallization and preliminary X-ray diffraction studies of the bacteriophage phi29 connector particle. FEBS Lett 1998; 430:283-7. [PMID: 9688556 DOI: 10.1016/s0014-5793(98)00672-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The connector or portal particle from double-stranded DNA bacteriophage phi29 has been crystallized. This structure, which connects the head of the virus with the tail and plays a central role in prohead assembly and DNA packaging and translocation, is formed by 12 subunits of the p10 protein and has a molecular weight of 430 kDa. The connector structure was proteolysed with endoproteinase Glu-C from Staphylococcus aureus V8, which removes 13 and 18 amino acids from the amino- and carboxy-terminal regions of the p10 protein, respectively. Two crystal forms were grown from drops containing an alcohol solution and paraffin oil. Crystals of form I are monoclinic, space group C2 with cell dimensions a = 416.86 A, b = 227.62 A, c = 236.68 A and beta = 96.3 degrees and contain four connector particles per asymmetric unit. Crystals of form II are tetragonal, space group P4(2)2(1)2 with cell dimensions a = b = 170.2 A, c = 156.9 A and contain half a particle per asymmetric unit. X-ray diffraction data from both native crystal forms have been collected to 6.0 and 3.2 A respectively, using synchrotron radiation. Crystals of form II are likely to have the same packing arrangement as the two-dimensional crystals analyzed previously by electron microscopy.
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Affiliation(s)
- A Guasch
- Departament de Biologia Molecular i Cel.lular, Centre d'Investigació i Desenvolupament, CSIC, Barcelona, Spain
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20
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Guo P, Zhang C, Chen C, Garver K, Trottier M. Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 1998; 2:149-55. [PMID: 9702202 DOI: 10.1016/s1097-2765(00)80124-0] [Citation(s) in RCA: 277] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ds-DNA viruses package their DNA into a preformed protein shell (procapsid) during maturation. Bacteriophage phi29 requires an RNA (pRNA) to package its genomic DNA into the procapsid. We report here that the pRNA upper and lower loops are involved in RNA/RNA interactions. Mutation in only one loop results in inactive pRNAs. However, mixing of two, three and six inactive mutant pRNAs restores DNA packaging activity as long as an interlocking hexameric ring can be predicted to form by base pairing of the mutated loops in separate RNA molecules. The stoichiometry of pRNA for the packaging of one viral DNA genome is six. Homogeneous pRNA purified from a single band in denaturing gels showed six bands when rerun in native gels. These results suggest that six pRNAs form a hexameric ring by the intermolecular interaction of two RNA loops to serve as part of the DNA transportation machinery.
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Affiliation(s)
- P Guo
- Department of Pathobiology, Purdue Biochemistry and Molecular Biology Program, Purdue University, West Lafayette, Indiana 47907, USA.
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21
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Rishovd S, Holzenburg A, Johansen BV, Lindqvist BH. Bacteriophage P2 and P4 morphogenesis: structure and function of the connector. Virology 1998; 245:11-7. [PMID: 9614863 DOI: 10.1006/viro.1998.9153] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The connector, the structure located between the bacteriophage capsid and tail, is interesting from several points of view. The connector is in many cases involved in the initiation of the capsid assembly process, functions as a gate for DNA transport in and out of the capsid, and is, as implied by the name, the structure connecting a tail to the capsid. Occupying a position on a 5-fold axis in the capsid and connected to a coaxial 6-fold tail, it mediates a symmetry mismatch between the two. To understand how the connector is capable of all these interactions its structure needs to be worked out. We have focused on the bacteriophage P2/P4 connector, and here we report an image reconstruction based on 2D crystalline layers of connector protein expressed from a plasmid in the absence of other phage proteins. The overall design of the connector complies well with that of other phage connectors, being a toroid structure having a conspicuous central channel. Our data suggests a 12-fold symmetry, i.e., 12 protrusions emerge from the more compact central part of the structure. However, rotational analysis of single particles suggests that there are both 12- and 13-mers present in the crude sample. The connectors used in this image reconstruction work differ from connectors in virions by having retained the amino-terminal 26 amino acids normally cleaved off during the morphogenetic process. We have used different late gene mutants to demonstrate that this processing occurs during DNA packaging, since only mutants in gene P, coding for the large terminase subunit, accumulate uncleaved connector protein. The suggestion that the cleavage might be intimately involved in the DNA packaging process is substantiated by the fact that the fragment cleaved off is highly basic and is homologous to known DNA binding sequences.
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Affiliation(s)
- S Rishovd
- Institute of Biology, University of Oslo, Norway
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22
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Müller DJ, Amrein M, Engel A. Adsorption of biological molecules to a solid support for scanning probe microscopy. J Struct Biol 1997; 119:172-88. [PMID: 9245758 DOI: 10.1006/jsbi.1997.3875] [Citation(s) in RCA: 244] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Scanning probe microscopes are now established tools to study the surface structure of biological macromolecules under physiological conditions. Sample preparation methods for this microscopy all have the objective to attach the specimen firmly to a support. Here we analyse the commonly used method of adsorbing biological specimens to freshly cleaved mica. This is facilitated by adjusting the electrolyte concentration and the pH of the buffer solution. Native macromolecular systems absorbed to mica in this way can be reproducibly imaged at submolecular resolution.
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Affiliation(s)
- D J Müller
- M.E. Müller-Institute for Microscopy, University of Basel, Switzerland
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23
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Müller DJ, Engel A, Carrascosa JL, Vélez M. The bacteriophage phi29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution. EMBO J 1997; 16:2547-53. [PMID: 9184202 PMCID: PMC1169866 DOI: 10.1093/emboj/16.10.2547] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The surfaces of two- and three-dimensional phi29 connector crystals were imaged in buffer solution by atomic force microscopy (AFM). Both topographies show a rectangular unit cell with dimensions of 16.5 nm x 16.5 nm. High resolution images of connectors from the two-dimensional crystal surface show two connectors per unit cell confirming the p42(1)2 symmetry. The height of the connector was estimated to be at least 7.6 nm, a value close to that found in previous studies using different techniques. The 12 subunits of the wide connector domain were clearly resolved and showed a right-handed vorticity. The channel running along the connector had a diameter of 3.7 nm in the wide domain, while it was 1.7 nm in the narrow domain end, thus suggesting a tronco-conical channel shape. Moreover, the narrow connector end appears to be rather flexible. When the force applied to the stylus was between 50 and 100 pN, the connector end was fully extended. At forces of approximately 150 pN, these ends were pushed towards the crystal surface. The complementation of the AFM data with the three-dimensional reconstruction obtained from electron microscopy not only confirmed the model proposed, but also offers new insights that may help to explain the role of the connector in DNA packing.
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Affiliation(s)
- D J Müller
- M.E. Müller-Institute for Microscopic Structural Biology, Biozentrum, University of Basel, Switzerland
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24
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Abstract
The mechanism of viral capsid assembly is an intriguing problem because of its fundamental importance to research on synthetic viral particle vaccines, gene delivery systems, antiviral drugs, chimeric viruses displaying antigens or ligands, and the study of macromolecular interactions. The genes coding for the scaffolding (gp7), capsid (gp8), and portal vertex (gp10) proteins of the procapsid of bacteriophage phi 29 of Bacillus subtilis were expressed in Escherichia coli individually or in combination to study the mechanism of phi 29 procapsid assembly. When expressed alone, gp7 existed as a soluble monomer, gp8 aggregated into inclusion bodies, and gp10 formed the portal vertex. Circular dichroisin spectrum analysis indicated that gp7 is mainly composed of alpha helices. When two of the proteins were coexpressed, gp7 and gp8 assembled into procapsid-like particles with variable sizes and shapes, gp7 and gp10 formed unstable complexes, and gp8 and gp10 did not interact. These results suggested that gp7 served as a bridge for gp8 and gp10. When gp7, gp8, and gp10 were coexpressed, active procapsids were produced. Complementation of extracts containing one or two structural components could not produce active procapsids, indicating that no stable intermediates were formed. A dimeric gp7 concatemer promoted the solubility of gp8 but was inactive in the assembly of procapsid or procapsid-like particles. Mutation at the C terminus of gp7 prevented it from interacting with gp8, indicating that this part of gp7 may be important for interaction with gp8. Coexpression of the portal protein (gp20) of phage T4 with phi 29 gp7 and gp8 revealed the lack of interaction between T4 gp20 and phi 29 gp7 and/or gp8. Perturbing the ratio of the three structural proteins by duplicating one or another gene did not reduce the yield of potentially infectious particles. Changing of the order of gene arrangement in plasmids did not affect the formation of active procapsids significantly. These results indicate that phi 29 procapsid assembly deviated from the single-assembly pathway and that coexistence of all three components with a threshold concentration was required for procapsid assembly. The trimolecular interaction was so rapid that no true intermediates could be isolated. This finding is in accord with the result of capsid assembly obtained by the equilibrium model proposed by A. Zlotnick (J. Mol. Biol. 241:59-67, 1994).
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Affiliation(s)
- C S Lee
- Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
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25
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Urbaneja MA, Rivas S, Carrascosa JL, Valpuesta JM. An intrinsic-tryptophan-fluorescence study of phage phi 29 connector/nucleic acid interactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 225:747-53. [PMID: 7957190 DOI: 10.1111/j.1432-1033.1994.00747.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The protein p10 of bacteriophage phi 29 assembled into connectors exhibit an intrinsic fluorescence with an emission peak centered at 335 nm, which suggests a hydrophobic environment of the three tryptohan residues that the protein contains. Upon incubation with linear DNA (but not with circular DNA), a decrease in the connector intrinsic fluorescence is measured which does not show any sequence specificity. The decrease in fluorescence is not observed when DNA is incubated with proteolyzed connectors, which lack the DNA-binding domain, suggesting that the fluorescence quenching is related to the binding of DNA to the phi 29 connectors. Acrylamide quenching studies reveal a higher accessibility of tryptophan residues to the quencher when the connector is bound to DNA. Protein denaturation by guanidine hydrochloride occurs at lower denaturant concentrations in the presence of linear DNA (but not circular DNA) than in its absence, suggesting a conformational change of phi 29 connector upon binding to linear DNA. This hypothesis is supported by the fact that the proteolyzed connectors, which do not bind DNA, are denatured at the same denaturant concentration, regardless of the presence of DNA. phi 29 connectors also bind RNA, but this interaction does not exert any effect on acrylamide quenching or guanidine hydrochloride denaturation. This result, together with that showing that proteolyzed connectors are able to interact with RNA, reinforces the idea that phi 29 connectors have two independent domains for interaction with DNA and RNA.
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Affiliation(s)
- M A Urbaneja
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad del País Vasco, Bilbao, Spain
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26
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Tsuprun V, Anderson D, Egelman EH. The bacteriophage phi 29 head-tail connector shows 13-fold symmetry in both hexagonally packed arrays and as single particles. Biophys J 1994; 66:2139-50. [PMID: 8075347 PMCID: PMC1275939 DOI: 10.1016/s0006-3495(94)81009-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The symmetry of the phi 29 head-tail connector is controversial: several studies of two-dimensional arrays of the connector have found a 12-fold symmetry, while a recent study of isolated particles has found a 13-fold symmetry. To investigate whether a polymorphism of the structure might explain these different results, electron microscopy and image analysis were used to study both isolated connectors and particles in hexagonally packed arrays. The hexagonally packed arrays have a P1 symmetry, and the connectors displayed 13 subunits both in the arrays and as isolated single particles. While we do not observe a polymorphism between connectors in two-dimensional arrays and as isolated particles, data show that the connectors can exist with either 12 or 13 subunits. A three-dimensional reconstruction of our 13-fold connector was generated by combining an averaged side-view projection with the known symmetry. The structure of rosettes of the connectors formed in the presence of phi 29 prohead RNA (pRNA) was also examined. These rosettes contain five connectors arranged about a single connector in the center, and this arrangement may reflect an essential role of the pRNA in mediating a symmetry mismatch between either a 12- or 13-fold symmetric connector and a putative fivefold symmetric prohead portal vertex into which the connector fits.
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Affiliation(s)
- V Tsuprun
- Department of Cell Biology and Neuroanatomy, University of Minnesota Medical School, Minneapolis 55455-0303
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27
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Valpuesta JM, Carrascosa JL. Structure of viral connectors and their function in bacteriophage assembly and DNA packaging. Q Rev Biophys 1994; 27:107-155. [PMID: 7984775 DOI: 10.1017/s0033583500004510] [Citation(s) in RCA: 142] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The viruses have been an attractive model for the study of basic mechanisms of protein/protein and protein/nucleic acid interactions involved in the assembly of macromolecular aggregates. This has been due primarily to their relative genetic simplicity as compared to their structural and functional complexity. Although most of the initial studies were carried out on bacterial and plant viruses, increasing data has also been accumulated from animal viruses, which has led to an understanding of some basic principles, as well as to many specific strategies in every system. The study of virus assembly has been a source of ideas that underlie our present knowledge of the organization of biological systems. It has also provided, since the production of bacteriophage mutants which have allowed the study of assembly intermediates, the first system in which the genetic studies played a dominant role. The increasing volume of data over the last years has revealed how the structural components can interact sequentially through an ordered pathway to yield macromolecular assemblies that satisfy the demands of stability required for a successful transfer of genetic information from host to host.
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Affiliation(s)
- J M Valpuesta
- Centro Nacional de Biotecnología, CSIC, Universidad Autónoma de Madrid, Cantoblanco, Spain
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28
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Donate L, Valpuesta J, Mier C, Rojo F, Carrascosa J. Characterization of an RNA-binding domain in the bacteriophage phi 29 connector. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80714-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Valpuesta JM, Serrano M, Donate LE, Herranz L, Carrascosa JL. DNA conformational change induced by the bacteriophage phi 29 connector. Nucleic Acids Res 1992; 20:5549-54. [PMID: 1454519 PMCID: PMC334385 DOI: 10.1093/nar/20.21.5549] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Translocation of viral DNA inwards and outwards of the capsid of double-stranded DNA bacteriophages occurs through the connector, a key viral structure that is known to interact with DNA. It is shown here that phage phi 29 connector binds both linear and circular double-stranded DNA. However, DNA-mediated protection of phi 29 connectors against Staphylococcus aureus endoprotease V8 digestion suggests that binding to linear DNA is more stable than to circular DNA. Endoprotease V8-protection assays also suggest that the length of the linear DNA required to produce a stable phi 29 connector-DNA interaction is, at least, twice longer than the phi 29 connector channel. This result is confirmed by experiments of phi 29 connector-protection of DNA against DNase I digestion. Furthermore, DNA circularization assays indicate that phi 29 connectors restrain negative supercoiling when bound to linear DNA. This DNA conformational change is not observed upon binding to circular DNA and it could reflect the existence of some left-handed DNA coiling or DNA untwisting inside of the phi 29 connector channel.
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Affiliation(s)
- J M Valpuesta
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma de Madrid, Spain
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30
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Turnquist S, Simon M, Egelman E, Anderson D. Supercoiled DNA wraps around the bacteriophage phi 29 head-tail connector. Proc Natl Acad Sci U S A 1992; 89:10479-83. [PMID: 1438237 PMCID: PMC50362 DOI: 10.1073/pnas.89.21.10479] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Supercoiled pBR322 DNA wraps around the outside of the isolated Bacillus subtilis bacteriophage phi 29 head-tail connector, the crux of the DNA packaging machine of the viral precursor capsid or prohead. The contour length of the supercoiled DNA, determined by EM, decreased by approximately 180 base pairs for each connector bound. Mass and radial density determinations by scanning transmission EM showed that the increased mass of the connector-DNA complex relative to the connector alone was equivalent to approximately 170 base pairs of DNA and was located around the outside of the connector. Topoisomerase I treatment of the complexes followed by deproteinization suggested that supercoils were restrained by the connectors. Connectors bound linear and open-circular plasmid DNAs inefficiently but were not wrapped by these DNAs. The wrapping of supercoiled DNA around the isolated phi 29 connector is hypothesized to reflect the initiation phase of the normal process of DNA packaging. Packaging substrates would be supercoiled, wrapped by the connector, linearized, and translocated by rotation of the connector relative to the viral capsid with the aid of ATP hydrolysis.
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Affiliation(s)
- S Turnquist
- Department of Microbiology, University of Minnesota, Minneapolis 55455
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31
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Donate L, Valpuesta J, Rocher A, Méndez E, Rojo F, Salas M, Carrascosa J. Role of the amino-terminal domain of bacteriophage phi 29 connector in DNA binding and packaging. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50106-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Guo PX, Erickson S, Xu W, Olson N, Baker TS, Anderson D. Regulation of the phage phi 29 prohead shape and size by the portal vertex. Virology 1991; 183:366-73. [PMID: 1905079 PMCID: PMC4167689 DOI: 10.1016/0042-6822(91)90149-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriophage phi 29 of Bacillus subtilis packages its double-stranded DNA into a preformed prohead during morphogenesis. The prohead is composed of the scaffold protein gp7, the capsid protein pg8, the portal protein gp10, and the dispensable head fiber protein gp8.5. Our objective was to elucidate the phi 29 prohead assembly pathway and to define the factors that determine prohead shape and size. The structural genes of the phi 29 prohead were cloned and expressed in Escherichia coli individually or in combination to study form determination. The scaffold protein was purified from E. coli as a soluble monomer. In vivo and in vitro studies showed that the scaffolding protein interacted with both the portal vertex and capsid proteins. When the scaffold protein interacted only with the capsid protein in vivo, particles were formed with variable size and shape. However, in the presence of the portal vertex protein, particles with uniform size and shape were produced in vivo. SDS-PAGE analysis showed that the latter particles contained the proteins of the scaffold, capsid, head fiber, and portal vertex. These results suggest that the scaffolding protein serves as the linkage between the portal vertex and the capsid proteins, and that the portal vertex plays a crucial role in regulating the size and shape of the prohead.
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Affiliation(s)
- P X Guo
- Department of Veterinary Pathobiology, Purdue University, West Lafayette, Indiana 47907
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33
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Donate LE, Carrascosa JL. Characterization of a versatile in vitro DNA-packaging system based on hybrid lambda/phi 29 proheads. Virology 1991; 182:534-44. [PMID: 1827226 DOI: 10.1016/0042-6822(91)90594-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have studied the assembly of bacteriophage lambda head proteins on the phage phi 29 connector to produce in vitro chimeric proheads, whose ability to package different types of DNA depends on the physical integrity of the phi 29 connector. Terminal protein-free phi 29 as well as nonviral DNAs have been shown to be efficiently packaged by this hybrid system. An RNA, that can be provided by any of the extracts used in the complementation mixture, was required for DNA packaging, both by the hybrid system as well as by the homologous lambda system. The DNA-packaging activity of RNase-treated proheads can be restored by adding a mixture of ribosomal RNAs. There is also a requirement for a minimal length of DNA to be stably packaged. The packaging protein p16 of phi 29 can replace the lambda terminase complex in the in vitro packaging system, both with the chimeric as well as genuine lambda proheads.
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Affiliation(s)
- L E Donate
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
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34
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Wilkinson DL, Harrison RG. Predicting the Solubility of Recombinant Proteins in Escherichia coli. Nat Biotechnol 1991; 9:443-8. [PMID: 1367308 DOI: 10.1038/nbt0591-443] [Citation(s) in RCA: 177] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have studied the cause of inclusion body formation in Escherichia coli grown at 37 degrees C using statistical analysis of the composition of 81 proteins that do and do not form inclusion bodies. Six composition derived parameters were used. In declining order of their correlation with inclusion body formation, the parameters are charge average, turn forming residue fraction, cysteine fraction, proline fraction, hydrophilicity, and total number of residues. The correlation with inclusion body formation is strong for the first two parameters but weak for the last four. This correlation can be used to predict the probability that a protein will form inclusion bodies using only the protein's amino acid composition as the basis for the prediction.
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Affiliation(s)
- D L Wilkinson
- School of Chemical Engineering and Material Science, University of Oklahoma, Norman 73019
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Abstract
Proheads of bacteriophage lambda which carry the connector of phage phi 29 instead of that of lambda have been produced in vitro. These hybrid proheads have a structure similar to that of normal lambda proheads. Furthermore, the chimeric proheads can package both lambda and phi 29 DNA. These data show that the connector domains involved in both head assembly and DNA packaging are functionally similar. The DNA-containing lambda-phi 29 proheads can be complemented in vitro with phi 29 tails to yield infective particles capable of DNA transfer.
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Affiliation(s)
- L E Donate
- Centro de Biología Molecular (CSIC-UAM), Facultad de Ciencias, Universidad Autónoma, Madrid, Spain
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Herranz L, Bordas J, Towns-Andrews E, Mendez E, Usobiaga P, Carrascosa JL. Conformational changes in bacteriophage phi 29 connector prevents DNA-binding activity. J Mol Biol 1990; 213:263-73. [PMID: 2342107 DOI: 10.1016/s0022-2836(05)80189-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In vitro DNA packaging activity in a defined system derived from bacteriophage phi 29 depends upon the chemical integrity of the connector protein p10. Proteolytic cleavage of p10 rendered the proheads inactive for DNA packaging. A similar treatment on isolated connectors abolished the DNA-binding activity of the native p10, but the general shape and size of the connector was not changed as revealed by electron microscopy. Analytical ultracentrifugation showed that the proteolyzed connectors had a smaller sedimentation coefficient, while amino acid analysis after dialysis of the proteolyzed p10 confirmed the loss of 16 and 19 amino acids from the amino and carboxy termini, respectively. Low angle X-ray scattering revealed that proteolysis was followed by a small decrease in the radius of gyration and a reorganization of the distal domain of the cylindrical inner part of the connector. Characterization of the cleavage sites in the primary sequence allowed us to propose the location of the DNA-binding domain in the connector model.
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Affiliation(s)
- L Herranz
- Centro de Biología Molecular (CSIC-U AM) Universidad Autónoma de Madrid, Spain
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37
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Guo PX, Bailey S, Bodley JW, Anderson D. Characterization of the small RNA of the bacteriophage phi 29 DNA packaging machine. Nucleic Acids Res 1987; 15:7081-90. [PMID: 3116499 PMCID: PMC306194 DOI: 10.1093/nar/15.17.7081] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The prohead connector of the bacteriophage luminal diameter 29 DNA packaging machine was reconstructed with the small RNA that regulates DNA packaging in vitro. The complete sequence of the 120 nucleotide RNA proved its origination from the promoter PE1(A1) of the left early region of phi 29 DNA, the end packaged first during assembly. The prohead RNA was clearly distinct from eubacterial 5S rRNA in sequence and composition.
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Affiliation(s)
- P X Guo
- Department of Microbiology/Dentistry, University of Minnesota, Minneapolis 55455
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38
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Carazo JM, Donate LE, Herranz L, Secilla JP, Carrascosa JL. Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution. J Mol Biol 1986; 192:853-67. [PMID: 3586012 DOI: 10.1016/0022-2836(86)90033-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The three-dimensional reconstruction of the connector of bacteriophage phi 29 has been obtained from tilt series of negatively stained tetragonal ordered aggregates under low-dose conditions and up to a resolution of (1/1.8) nm-1. These connectors are built up as dodecamers of only one structural polypeptide (p10). Two connectors form the crystal unit cell, each one facing in the opposite direction with respect to the plane of the crystal and partially overlapping. The main features of the two connectors that build the unit cell were essentially the same, although they were negatively stained in slightly different ways, probably due to their situations with respect to the carbon-coated support grid. The main features of the phi 29 connector structure revealed by this three-dimensional reconstruction are: the existence of two clearly defined domains, one with a diameter of around 14 nm and the other narrower (diameter approximately equal to 7.5 nm); an inner hole running all along the structure (around 7 to 8 nm in height) with a cylindrical profile and an average diameter of 4 nm; a general 6-fold symmetry along the whole structure and a 12-fold one in the wider domain; a clockwise twist of the more contrasted regions of both domains from the narrower towards the wider domain (the direction of DNA encapsidation). These features are compatible with an active role for the connector in the process of DNA packaging.
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Herranz L, Salas M, Carrascosa JL. Interaction of the bacteriophage phi 29 connector protein with the viral DNA. Virology 1986; 155:289-92. [PMID: 3095983 DOI: 10.1016/0042-6822(86)90191-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The protein that forms the connector of phage phi 29, p10, binds to DNA. Apparently, p10 binding is not sequence specific. Nevertheless, the presence of the terminal protein (p3) covalently attached to the ends of phi 29 DNA produces a significant increase of p10 molecules bound to the DNA ends, thus suggesting a terminal protein-mediated recognition of DNA ends by the phage connector. As the p3-DNA complex is the substrate for phage phi 29 DNA packaging, these results may reflect a direct implication of the phage connector in the packaging process.
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40
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Baró AM, Miranda R, Alamán J, García N, Binnig G, Rohrer H, Gerber C, Carrascosa JL. Determination of surface topography of biological specimens at high resolution by scanning tunnelling microscopy. Nature 1985; 315:253-4. [PMID: 4000254 DOI: 10.1038/315253a0] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although techniques are available for the determination of the three-dimensional structure of biological specimens, for example scanning electron microscopy, they all have some serious drawback, such as low resolution, the requirement for crystals or for the sample to be analysed in a high vacuum. In an attempt to develop a technique for high-resolution three-dimensional structure analysis of non-crystalline biological material, we have tested the applicability of scanning tunnelling microscopy (STM), a method that has been used successfully in the analysis of metal and semiconductor surface structures. We report here that scanning tunnelling electron microscopy can be used to determine the surface topography of biological specimens at atmospheric pressure and room temperature, giving a vertical resolution of the order of 1 A. Our results show that quantum mechanical tunnelling of electrons through biological material is possible provided that the specimen is deposited on a conducting surface.
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Carrascosa JL, Carazo JM, Ibañez C, Santisteban A. Structure of phage phi 29 connector protein assembled in vivo. Virology 1985; 141:190-200. [PMID: 3936270 DOI: 10.1016/0042-6822(85)90251-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The protein p10 that forms the connector of phage phi 29, has been produced in Escherichia coli harboring a plasmid that carried the gene coding for this protein. The connector protein is assembled in a 13.4-S oligomer that has an apparent molecular weight of 460,000, suggesting that it is a dodecamer. The purified oligomers have been studied by electron microscopy of the isolated particles as well as by image-processing techniques (Fourier and rotational filtering) of artificially induced two-dimensional aggregates. The results show that the purified p10 is assembled in a circular structure with a hole in its center and 12 morphological units in the periphery. Both the morphology and the dimensions of this p10 oligomer are very similar to those of the upper neck collar extracted from phi 29 viral particles. The results strongly suggest the close relationship between the p10 oligomers assembled in E. coli and the ones produced in phi 29 infected Bacillis subtilis.
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42
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García JA, Méndez E, Salas M. Cloning, nucleotide sequence and high level expression of the gene coding for the connector protein of Bacillus subtilis phage phi 29. Gene 1984; 30:87-98. [PMID: 6096227 DOI: 10.1016/0378-1119(84)90108-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The phi 29 DNA restriction fragment HindIII-D, shown to contain gene 10 coding for the connector protein, has been cloned in plasmid pPLc28 under the control of the pL promoter of phage lambda. After heat induction to inactivate the lambda repressor, a protein with the electrophoretic mobility of the connector protein p10 was synthesized, accounting for about 30% of the total Escherichia coli protein after 3 h of induction. The 2205 nucleotide-long sequence of the cloned HindIII-D fragment has been determined. The sequenced region has an ORF coding for a protein of Mr 35881 that was shown to correspond to the connector protein by determination of the amino-terminal sequence of purified protein p10. Features of the nucleotide sequence and the amino acid sequence of protein p10 are discussed.
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