Nanopore-based technologies beyond DNA sequencing

YL Ying, ZL Hu, S Zhang, Y Qing, A Fragasso… - Nature …, 2022 - nature.com
Inspired by the biological processes of molecular recognition and transportation across
membranes, nanopore techniques have evolved in recent decades as ultrasensitive …

Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D Jin, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …

ColabFold: making protein folding accessible to all

M Mirdita, K Schütze, Y Moriwaki, L Heo… - Nature …, 2022 - nature.com
ColabFold offers accelerated prediction of protein structures and complexes by combining
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …

A brief history of de novo protein design: minimal, rational, and computational

DN Woolfson - Journal of Molecular Biology, 2021 - Elsevier
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the
primary motivation for de novo protein design was to test our understanding of the …

Native mass spectrometry: recent progress and remaining challenges

KR Karch, DT Snyder, SR Harvey… - Annual review of …, 2022 - annualreviews.org
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure
and function of macromolecules and their complexes in the gas phase. In this review, we …

De novo metalloprotein design

MJ Chalkley, SI Mann, WF DeGrado - Nature Reviews Chemistry, 2022 - nature.com
Natural metalloproteins perform many functions—ranging from sensing to electron transfer
and catalysis—in which the position and property of each ligand and metal are dictated by …

Engineering biological nanopore approaches toward protein sequencing

X Wei, T Penkauskas, JE Reiner, C Kennard… - ACS …, 2023 - ACS Publications
Biotechnological innovations have vastly improved the capacity to perform large-scale
protein studies, while the methods we have for identifying and quantifying individual proteins …

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

K Shimizu, B Mijiddorj, M Usami, I Mizoguchi… - Nature …, 2022 - nature.com
The amino-acid sequence of a protein encodes information on its three-dimensional
structure and specific functionality. De novo design has emerged as a method to manipulate …

Building enzymes through design and evolution

EJ Hossack, FJ Hardy, AP Green - ACS Catalysis, 2023 - ACS Publications
Designing efficient enzymes is a formidable challenge at the forefront of modern
biocatalysis. Here, we review recent developments in the field and illustrate how the …

Easy and accurate protein structure prediction using ColabFold

G Kim, S Lee, E Levy Karin, H Kim, Y Moriwaki… - Nature …, 2024 - nature.com
Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological
questions, by using predicted protein structures of single monomers or full complexes, a …