☆ 4.8 Article

Cell-Free Expression of De Novo Designed Peptides That Form fl-Barrel Nanopores

ACS NANO (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Nanoscience & Nanotechnology

De novo design of a nanopore for single-molecule detection that incorporates a β-hairpin peptide

Keisuke Shimizu et al.

Summary: A de novo designed peptide with a beta-hairpin structure is able to assemble into beta-barrelled nanopores for single-molecule detection of polynucleotides and polypeptide chains. By manipulating amino acid sequences, artificial proteins and peptides with desired functionality can be developed. Redesigning the peptide to create monodisperse pores allows for detection of single polypeptide chains, showing potential for creating artificial nanopores adjustable to target molecules.

NATURE NANOTECHNOLOGY (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Formation and function of OmpG or OmpA-incorporated liposomes using an in vitro translation system

Koki Kamiya

Summary: This study investigates the incorporation of OmpG protein into purified nano-sized liposomes with various lipid compositions using in vitro translation. The results show that liposomes prepared with E. coli lipid extract had the highest amount of OmpG incorporated.

SCIENTIFIC REPORTS (2022)

添加到收藏夹

Article Biochemical Research Methods

Single polypeptide detection using a translocon EXP2 nanopore

Mitsuki Miyagi et al.

Summary: The EXP2 nanopore has been shown to detect poly-L-lysine with single-molecule sensitivity and sufficient resolution to differentiate between two individual PLLs of different molecular weights. Exploring biological nanopores suitable for peptide sensing is key to achieving amino acid sequence determination.

PROTEOMICS (2022)

添加到收藏夹

Article Chemistry, Multidisciplinary

Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

Nanami Takeuchi et al.

Summary: This study presents a method for detection miRNA expression patterns using nanopore-based DNA computing technology. The system successfully recognized and detected miRNA patterns from plasma samples of bile duct cancer patients, offering a simple and label-free approach to cancer diagnosis. The method also improved the limit of detection for miRNA complexes compared to previous analytical platforms.

JACS AU (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Multiple rereads of single proteins at single-amino acid resolution using nanopores

Henry Brinkerhoff et al.

Summary: This study presents a nanopore-based single-molecule peptide reader capable of identifying single amino acid substitutions within individual peptides with high accuracy. By pulling a DNA-peptide conjugate through a biological nanopore and reading the ion current signal, discrimination of single amino acid substitutions in single reads was achieved. The ability to obtain numerous independent reads of the same molecule and achieve a low error rate in amino acid variant identification signifies a promising advancement towards single-molecule protein fingerprinting and analysis technology.

SCIENCE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

De novo design of transmembrane β barrels

Anastassia A. Vorobieva et al.

Summary: Through computational design, researchers successfully developed novel TMBs with no homology to known TMBs, which can reversibly insert and fold into synthetic lipid membranes, and exhibit experimental structures highly similar to computational models. This advancement is expected to facilitate the custom design of pores for various applications.

SCIENCE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Protein identification by nanopore peptide profiling

Florian Leonardus Rudolfus Lucas et al.

Summary: Nanopores can be used for protein identification by measuring peptide spectra produced from hydrolyzed proteins. The spectra from nanopore experiments and mass spectrometry share similar profiles, enabling protein fingerprinting. This approach is quantitative, showing the potential of a low-cost, portable nanopore-based analyzer for protein identification.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Constructing ion channels from water-soluble α-helical barrels

Alistair J. Scott et al.

Summary: The design of peptides that assemble in membranes to form functional ion channels is challenging. By using rational de novo design to generate water-soluble alpha-helical barrels with polar interiors and modifying the sequences to facilitate their insertion into lipid bilayers, stable membrane-spanning cation-selective channels have been successfully designed. Insights from the structures of these peptides have been used to achieve this result.

NATURE CHEMISTRY (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore

Shuanghong Yan et al.

Summary: Proteins exhibit diverse functions due to their variable amino acid sequences, but current technology for direct protein sequence analysis remains inadequate. The development of nanopore sequencing has sparked efforts to sequence peptides in a similar manner, successfully achieving direct observation of peptide's ratcheting motion and showing potential for peptide fingerprinting.

NANO LETTERS (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A

Yuqin Wang et al.

Summary: The folding of RNA plays important roles in the regulation of biological activities, but high-resolution observation of their structures remains challenging. A sensing mode called nanopore trapping/translocation can distinguish different types of RNA, and a custom machine learning algorithm has been developed for accurate automatic classification. tRNAs exhibit highly distinguishable sensing features and show a high structural conservation across different species when measured using this strategy.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Review Multidisciplinary Sciences

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

Keisuke Motone et al.

Summary: Proteins are essential for life's functions, and comprehensive proteome analysis technologies are crucial for understanding the principles of biological systems. Current proteomics techniques have limitations in sensitivity and throughput, but nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. The challenge lies in controlling protein/peptide translocation through the nanopore sensor for processive strand analysis.

ISCIENCE (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Nanopore decoding for a Hamiltonian path problem

Sotaro Takiguchi et al.

Summary: DNA computing is attractive for solving mathematical problems due to its massive parallelism and low energy consumption, but decoding the output information to a human-recognizable signal is usually time-consuming. This study demonstrates rapid decoding of DNA-computed output using nanopore technology, showing the feasibility of nanopore measurement as a rapid and label-free decoding method for mathematical DNA computation.

NANOSCALE (2021)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

Hadjer Ouldali et al.

NATURE BIOTECHNOLOGY (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

DNA nanotechnology assisted nanopore-based analysis

Taoli Ding et al.

NUCLEIC ACIDS RESEARCH (2020)

添加到收藏夹

Article Chemistry, Physical

Recognition of Single-Point Mutation Using a Biological Nanopore

Ping Liu et al.

SMALL METHODS (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Computational design of transmembrane pores

Chunfu Xu et al.

NATURE (2020)

添加到收藏夹

Review Chemistry, Multidisciplinary

Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge

Yi-Lun Ying et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

添加到收藏夹

Article Nanoscience & Nanotechnology

Electrophysiological Analysis of Membrane Disruption by Bombinin and Its Isomer Using the Lipid Bilayer System

Yusuke Sekiya et al.

ACS APPLIED BIO MATERIALS (2019)

添加到收藏夹

Article Chemistry, Analytical

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

Yusuke Sekiya et al.

ANALYST (2018)

添加到收藏夹

Article Chemistry, Multidisciplinary

Mechanism of OmpG pH-Dependent Gating from Loop Ensemble and Single Channel Studies

Alan Perez-Rathke et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

添加到收藏夹

Review Biochemical Research Methods

Nanopore Decoding of Oligonucleotides in DNA Computing

Ryuji Kawano

BIOTECHNOLOGY JOURNAL (2018)

添加到收藏夹

Review Nanoscience & Nanotechnology

Paving the way to single-molecule protein sequencing

Laura Restrepo-Perez et al.

NATURE NANOTECHNOLOGY (2018)

添加到收藏夹

Review Chemistry, Multidisciplinary

Single-molecule protein sensing in a nanopore: a tutorial

Nitinun Varongchayakul et al.

CHEMICAL SOCIETY REVIEWS (2018)

添加到收藏夹

Article Biochemical Research Methods

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

添加到收藏夹

Review Nanoscience & Nanotechnology

Building membrane nanopores

Stefan Howorka

NATURE NANOTECHNOLOGY (2017)

添加到收藏夹

Article Biology

Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport

Nathan H. Joh et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

添加到收藏夹

Article Biochemical Research Methods

Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System

Masayuki Ohara et al.

ACS SYNTHETIC BIOLOGY (2017)

添加到收藏夹

Article Chemistry, Analytical

Analysis of Pore Formation and Protein Translocation Using Large Biological Nanopores

Hirokazu Watanabe et al.

ANALYTICAL CHEMISTRY (2017)

添加到收藏夹

Article Chemistry, Analytical

Amplification and Quantification of an Antisense Oligonucleotide from Target microRNA Using Programmable DNA and a Biological Nanopore

Moe Hiratani et al.

ANALYTICAL CHEMISTRY (2017)

添加到收藏夹

Article Nanoscience & Nanotechnology

Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

Chan Cao et al.

Nature Nanotechnology (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Miten Jain et al.

GENOME BIOLOGY (2016)

添加到收藏夹

Article Chemistry, Multidisciplinary

High-Resolution Size-Discrimination of Single Nonionic Synthetic Polymers with a Highly Charged Biological Nanopore

Gerhard Baaken et al.

ACS NANO (2015)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system

Yasuaki Kazuta et al.

JOURNAL OF BIOSCIENCE AND BIOENGINEERING (2014)

添加到收藏夹

Article Chemistry, Multidisciplinary

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

Emilia L. Wu et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)

添加到收藏夹

Article Statistics & Probability

The exact bootstrap method shown on the example of the mean and variance estimation

Joanna Kisielinska

COMPUTATIONAL STATISTICS (2013)

添加到收藏夹

Review Biochemical Research Methods

Recent trends in nanopores for biotechnology

Daniel H. Stoloff et al.

CURRENT OPINION IN BIOTECHNOLOGY (2013)

添加到收藏夹

Article Biochemistry & Molecular Biology

Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm

Nicholas J. Anthis et al.

PROTEIN SCIENCE (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Automated Parallel Recordings of Topologically Identified Single Ion Channels

Ryuji Kawano et al.

SCIENTIFIC REPORTS (2013)

添加到收藏夹

Article Chemistry, Analytical

Thermal Unfolding of Proteins Probed at the Single Molecule Level Using Nanopores

Linda Payet et al.

ANALYTICAL CHEMISTRY (2012)

添加到收藏夹

Review Chemistry, Multidisciplinary

Disease Detection and Management via Single Nanopore-Based Sensors

Joseph E. Reiner et al.

CHEMICAL REVIEWS (2012)

添加到收藏夹

Article Biochemistry & Molecular Biology

alpha-Hemolysin pore formation into a supported phospholipid bilayer using cell-free expression

Jerome Chalmeau et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2011)

添加到收藏夹

Article Multidisciplinary Sciences

Nanopore DNA sequencing with MspA

Ian M. Derrington et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

添加到收藏夹

Article Chemistry, Multidisciplinary

Nanopore analysis of a small 86-residue protein

Radu Stefureac et al.

SMALL (2008)

添加到收藏夹

Article Chemistry, Multidisciplinary

Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins

Heedeok Hong et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

添加到收藏夹

Article Chemistry, Physical

Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations

Carl P. Goodrich et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Optimization of protein fusion partner length for maximizing in vitro translation of peptides

Christopher R. Loose et al.

BIOTECHNOLOGY PROGRESS (2007)

添加到收藏夹

Article Biochemistry & Molecular Biology

Transport of α-helical peptides through α-hemolysin and aerolysin pores

Radu Stefureac et al.

BIOCHEMISTRY (2006)

添加到收藏夹

Article Biochemical Research Methods

Enhanced recognition of protein transmembrane domains with prediction-based structural profiles

BQ Cao et al.

BIOINFORMATICS (2006)

添加到收藏夹

Review Chemistry, Multidisciplinary

GROMACS: Fast, flexible, and free

D Van der Spoel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

添加到收藏夹

Article Biophysics

Interactions of peptides with a protein pore

L Movileanu et al.

BIOPHYSICAL JOURNAL (2005)

添加到收藏夹

Article Chemistry, Multidisciplinary

Novel and efficient synthesis of difficult sequence-containing peptides through O-N intramolecular acyl migration reaction of O-acyl E isopeptides

Y Sohma et al.

CHEMICAL COMMUNICATIONS (2004)

添加到收藏夹

Article Chemistry, Multidisciplinary

Structure of peptides investigated by nanopore analysis

TC Sutherland et al.

NANO LETTERS (2004)

添加到收藏夹

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

添加到收藏夹

Review Chemistry, Multidisciplinary

Characterization of nucleic acids by nanopore analysis

DW Deamer et al.

ACCOUNTS OF CHEMICAL RESEARCH (2002)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Cell-free translation reconstituted with purified components

Y Shimizu et al.

NATURE BIOTECHNOLOGY (2001)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.