Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides

Sekiya, Yusuke; Sakashita, Shungo; Shimizu, Keisuke; Usui, Kenji; Kawano, Ryuji

doi:10.1039/c8an00243f

“…The difficulty of conventional methods in structural characterization of short transmembrane peptides has recently led to the development of the channel current method [ 272 , 273 ]. The approach uses a droplet contact method to form a stable planar bilayer lipid membrane (pBLM) through which current passes.…”

Section: Emerging Approachesmentioning

confidence: 99%

“…By interpreting the current signals, it is possible to categorize peptides based on their possible translocation mechanisms such as barrel-stave, toroidal pore, and penetration models. Further analysis using three parameters, namely the current amplitude, the duration time, and the time between spike signals, gives information on the size of the defect in the membrane, duration of the defect formation, and event frequency of the penetration [ 272 ].…”

Section: Emerging Approachesmentioning

confidence: 99%

Membrane Active Peptides and Their Biophysical Characterization

Avcı

¹

,

Akbulut

²

,

Özkırımlı

³

2018

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In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.

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“…We have previously proposed current signal classification for several different signal shapes, and assigned these to various pore-forming models of α-helical peptides. [50][51][52] In this study, we also classified these signals into four types of current signals: step, square-top, multi-level, and erratic. The definition of signal classification is described in Fig.…”

Section: Confirmation Of Pore Formation Using Channel Current Measurementioning

confidence: 99%

“…54 We have also proposed the assignment of current signals to these models in planar lipid bilayer experiments. 52 Although there are few studies on the pore-formation of β-sheet peptides, it has been reported that the β-sheet peptides also construct barrel-stave and toroidal pores. 55 Our electrophysiological measurements herein also presented the step and multi-level signals, analogous to those previously assigned to the barrel-stave and the toroidal models.…”

Section: ) Incubation Of Sv28 Monomers To Form Oligomer Structures Wmentioning

confidence: 99%

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

Shimizu¹,

Mijiddorj²,

Yoshida³

et al. 2020

Preprint

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The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

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“…We have previously proposed current signal classification for several different signal shapes, and assigned these to various pore-forming models of α-helical peptides. 50,51,52 In this study, we also classified these signals into four types of current signals: step, square-top ( Fig. 3c), multi-level, and erratic (Fig.…”

Section: Confirmation Of Pore Formation Using Channel Current Measurementioning

confidence: 99%

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

Shimizu¹,

Mijiddorj²,

Yoshida³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

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Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides

Cited by 31 publications

References 33 publications

Membrane Active Peptides and Their Biophysical Characterization

Membrane Active Peptides and Their Biophysical Characterization

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

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