Three-step channel conformational changes common to DNA packaging motors of bacterial viruses T3, T4, SPP1, and Phi29

Wang, Shaoying; Ji, Zhouxiang; Yan, Erfu; Haque, Farzin; Guo, Peixuan

doi:10.1016/j.virol.2016.04.015

Cited by 21 publications

(20 citation statements)

References 42 publications

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“…2c). At voltages greater than ±100 mV, SPP1 connector displayed discrete stepwise gating of the channel [37]. …”

Section: Resultsmentioning

confidence: 99%

“…In search for alternative larger sized channels, we previously developed membrane-embedded phi29 motor channels[27–29] for single molecule sensing of nucleic acids[27,28,30–33], chemicals[34], peptides[35] or binding assays of antibody based on channel conformational change[30,36]. Herein, we utilized our recently developed membrane-embedded SPP1 motor channel[37,38] for quantifying the translocation and dynamics of peptide oligomeric states at single molecule level.…”

Section: Introductionmentioning

confidence: 99%

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Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states

et al. 2017

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Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the pass of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures. Utilizing single channel conduction assay and optical single molecule imaging, we observed translocation of peptides and quantitatively analyzed the dynamics of peptide oligomeric states in real-time at single molecule level. The oxidative and the reduced states of peptides were clearly differentiated based on their characteristic electronic signatures. A similar Gibbs free energy (ΔG0) was obtained when different concentrations of substrates were applied, suggesting that the use of SPP1 nanopore for real-time quantification of peptide oligomeric states is feasible. With the intrinsic nature of size and conjugation amenability, the SPP1 nanopore has the potential for development into a tool for the quantification of peptide and protein structures in real time.

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“…2c). At voltages greater than ±100 mV, SPP1 connector displayed discrete stepwise gating of the channel [37]. …”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states

et al. 2017

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“…The expression and purification of C-His SPP1 gp6 [25] and phi29 gp10 connector has been described previously [8; 28]. …”

Section: Methodsmentioning

confidence: 99%

“…1). We have previously reengineered the connector at the C-terminal end to introduce a 6×His-tag, purified the connector, and inserted it in planar lipid bilayer to serve as a membrane-embedded nanopore [25]. …”

Section: Introductionmentioning

confidence: 99%

Oriented single directional insertion of nanochannel of bacteriophage SPP1 DNA packaging motor into lipid bilayer via polar hydrophobicity

Zhou

Wang

et al. 2016

Biomaterials

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Insertion of biological nanopore into artificial membrane is of fundamental importance in nanotechnology. Many applications require control and knowledge of channel orientation. In this work, the insertion orientation of the bacteriophage SPP1 and phi29 DNA packaging motor into lipid membranes was investigated. Single molecule electrophysiological assays and Ni-NTA-nanogold binding assays revealed that both SPP1 and phi29 motor channels exhibited a one-way traffic property for TAT peptide translocation from N- to C-termini of the protein channels. SPP1 motor channels preferentially inserts into liposomes with their C-terminal wider region facing inward. Changing the hydrophobicity of the N- or C-termini of phi29 connector alters the insertion orientation, suggesting that the hydrophobicity and hydrophilicity of the termini of the protein channel governs the orientation of the insertion into lipid membrane. It is proposed that the specificity in motor channel orientation is a result of the hydrophilic/hydrophobic interaction at the air/water interface when the protein channels are incorporating into liposome membranes.

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“…[30–36] In dsDNA animal or bacterial viruses such as Phi29, SPP1, T3, T4, T5, and T7, their genome enters and exits the bacteriophage capsid during replication and infection, respectively, through a portal protein channel called the connector. [37–43] Bacteriophage T7 belongs to the Podoviridae family, which infects Escherichia coli ( E.coli ). Data from cryo-electron microscopy reveals that the T7 connector is composed of twelve subunits encoded by gene 8 (gp8) with a molecular weight of 59 k Da.…”

Section: Introductionmentioning

confidence: 99%

Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference

Kang

Wang

et al. 2018

Biomaterials

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Detection, differentiation, mapping, and sequencing of proteins are important in proteomics for the assessment of cell development such as protein methylation or phosphorylation as well as the diagnosis of diseases including metabolic disorder, mental illness, immunological ailments, and malignant cancers. Nanopore technology has demonstrated the potential for the sequencing or sensing of DNA, RNA, chemicals, or other macromolecules. Due to the diversity of protein in shape, structure and charge and the composition versatility of 20 amino acids, the sequencing of proteins remains challenging. Herein, we report the application of the channel of bacteriophage T7 DNA packaging motor for the differentiation of an assortment of peptides of a single amino acid difference. Explicit fingerprints or signatures were obtained based on current blockage and dwell time of individual peptide. Data from the clear mapping of small proteins after protease digestion suggests the potential of using T7 motor channel for proteomics including protein sequencing.

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Three-step channel conformational changes common to DNA packaging motors of bacterial viruses T3, T4, SPP1, and Phi29

Cited by 21 publications

References 42 publications

Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states

Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states

Oriented single directional insertion of nanochannel of bacteriophage SPP1 DNA packaging motor into lipid bilayer via polar hydrophobicity

Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference

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