Literature DB >> 34099939

The emerging landscape of single-molecule protein sequencing technologies.

Javier Antonio Alfaro1, Peggy Bohländer2, Mingjie Dai3,4, Mike Filius5, Cecil J Howard6, Xander F van Kooten7, Shilo Ohayon7, Adam Pomorski5, Sonja Schmid8, Amit Meller9,10, Chirlmin Joo11, Aleksei Aksimentiev12, Eric V Anslyn6, Georges Bedran13, Chan Cao14, Mauro Chinappi15, Etienne Coyaud16, Cees Dekker5, Gunnar Dittmar17,18, Nicholas Drachman19, Rienk Eelkema2, David Goodlett13,20, Sébastien Hentz21, Umesh Kalathiya13, Neil L Kelleher22, Ryan T Kelly23, Zvi Kelman24,25, Sung Hyun Kim5, Bernhard Kuster26,27, David Rodriguez-Larrea28, Stuart Lindsay29, Giovanni Maglia30, Edward M Marcotte31, John P Marino24, Christophe Masselon32, Michael Mayer33, Patroklos Samaras26, Kumar Sarthak12, Lusia Sepiashvili34, Derek Stein19, Meni Wanunu35,36, Mathias Wilhelm26, Peng Yin3,4.   

Abstract

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

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Year:  2021        PMID: 34099939      PMCID: PMC8223677          DOI: 10.1038/s41592-021-01143-1

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   47.990


  123 in total

Review 1.  Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection.

Authors:  Joshua D Spitzberg; Adam Zrehen; Xander F van Kooten; Amit Meller
Journal:  Adv Mater       Date:  2019-04-03       Impact factor: 30.849

Review 2.  Targeting the N terminus for site-selective protein modification.

Authors:  Christian B Rosen; Matthew B Francis
Journal:  Nat Chem Biol       Date:  2017-06-20       Impact factor: 15.040

3.  Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation.

Authors:  Shang Jia; Dan He; Christopher J Chang
Journal:  J Am Chem Soc       Date:  2019-04-24       Impact factor: 15.419

4.  Tyrosine bioconjugation through aqueous ene-type reactions: a click-like reaction for tyrosine.

Authors:  Hitoshi Ban; Julia Gavrilyuk; Carlos F Barbas
Journal:  J Am Chem Soc       Date:  2010-02-10       Impact factor: 15.419

Review 5.  Metabolic glycoengineering: sialic acid and beyond.

Authors:  Jian Du; M Adam Meledeo; Zhiyun Wang; Hargun S Khanna; Venkata D P Paruchuri; Kevin J Yarema
Journal:  Glycobiology       Date:  2009-08-12       Impact factor: 4.313

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

Authors:  Hadjer Ouldali; Kumar Sarthak; Tobias Ensslen; Fabien Piguet; Philippe Manivet; Juan Pelta; Jan C Behrends; Aleksei Aksimentiev; Abdelghani Oukhaled
Journal:  Nat Biotechnol       Date:  2019-12-16       Impact factor: 54.908

7.  Controlling protein translocation through nanopores with bio-inspired fluid walls.

Authors:  Erik C Yusko; Jay M Johnson; Sheereen Majd; Panchika Prangkio; Ryan C Rollings; Jiali Li; Jerry Yang; Michael Mayer
Journal:  Nat Nanotechnol       Date:  2011-02-20       Impact factor: 39.213

8.  Programmable autonomous synthesis of single-stranded DNA.

Authors:  Jocelyn Y Kishi; Thomas E Schaus; Nikhil Gopalkrishnan; Feng Xuan; Peng Yin
Journal:  Nat Chem       Date:  2017-11-06       Impact factor: 24.427

9.  MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

Authors:  Andy T Kong; Felipe V Leprevost; Dmitry M Avtonomov; Dattatreya Mellacheruvu; Alexey I Nesvizhskii
Journal:  Nat Methods       Date:  2017-04-10       Impact factor: 28.547

10.  Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores.

Authors:  Gang Huang; Kherim Willems; Mart Bartelds; Pol van Dorpe; Misha Soskine; Giovanni Maglia
Journal:  Nano Lett       Date:  2020-04-13       Impact factor: 11.189

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  32 in total

1.  Modifying the pH sensitivity of OmpG nanopore for improved detection at acidic pH.

Authors:  Monifa A V Fahie; Fanjun Li; Carolyn Palmer; Connie Yoon; Min Chen
Journal:  Biophys J       Date:  2022-02-05       Impact factor: 4.033

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

Authors:  Henry Brinkerhoff; Albert S W Kang; Jingqian Liu; Aleksei Aksimentiev; Cees Dekker
Journal:  Science       Date:  2021-11-04       Impact factor: 47.728

3.  Photoredox-Catalyzed Decarboxylative C-Terminal Differentiation for Bulk- and Single-Molecule Proteomics.

Authors:  Le Zhang; Brendan M Floyd; Maheshwerreddy Chilamari; James Mapes; Jagannath Swaminathan; Steven Bloom; Edward M Marcotte; Eric V Anslyn
Journal:  ACS Chem Biol       Date:  2021-11-04       Impact factor: 5.100

4.  Single-File Translocation Dynamics of SDS-Denatured, Whole Proteins through Sub-5 nm Solid-State Nanopores.

Authors:  Neeraj Soni; Noam Freundlich; Shilo Ohayon; Diana Huttner; Amit Meller
Journal:  ACS Nano       Date:  2022-07-03       Impact factor: 18.027

5.  Utility of tissue-specific gene expression scores for gene prioritization in Mendelian diseases.

Authors:  Daiki Kato; Satomi Mitsuhashi; Fuyuki Miya; Shinji Saitoh; Nobuhiko Okamoto; Tatsuhiko Tsunoda; Yuta Kochi
Journal:  J Hum Genet       Date:  2022-08-09       Impact factor: 3.755

Review 6.  Localized Nanopore Fabrication via Controlled Breakdown.

Authors:  Cuifeng Ying; Tianji Ma; Lei Xu; Mohsen Rahmani
Journal:  Nanomaterials (Basel)       Date:  2022-07-12       Impact factor: 5.719

7.  Progress and Challenges in Studying the Ecophysiology of Archaea.

Authors:  Panagiotis S Adam; Till L V Bornemann; Alexander J Probst
Journal:  Methods Mol Biol       Date:  2022

Review 8.  A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices.

Authors:  Mahmudur Rahman; Kazi Rafiqul Islam; Md Rashedul Islam; Md Jahirul Islam; Md Rejvi Kaysir; Masuma Akter; Md Arifur Rahman; S M Mahfuz Alam
Journal:  Micromachines (Basel)       Date:  2022-06-18       Impact factor: 3.523

9.  Counting protein molecules for single-cell proteomics.

Authors:  Nikolai Slavov
Journal:  Cell       Date:  2022-01-20       Impact factor: 41.582

Review 10.  Multi-resolution simulation of DNA transport through large synthetic nanostructures.

Authors:  Adnan Choudhary; Christopher Maffeo; Aleksei Aksimentiev
Journal:  Phys Chem Chem Phys       Date:  2022-02-02       Impact factor: 3.676

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