Site-specific dual encoding and labeling of proteins via genetic code expansion

RM Bednar, PA Karplus, RA Mehl - Cell chemical biology, 2023 - cell.com
The ability to selectively modify proteins at two or more defined locations opens new
avenues for manipulating, engineering, and studying living systems. As a chemical biology …

Nanopores: a versatile tool to study protein dynamics

S Schmid, C Dekker - Essays in biochemistry, 2021 - portlandpress.com
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular
functions from DNA replication and general biosynthesis to metabolic signaling and …

Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method

T Włodarski, JO Streit, A Mitropoulou, LD Cabrita… - Scientific Reports, 2024 - nature.com
Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the
determination of structures of complex biological molecules. The accurate characterisation …

Fluorescence nanoscopy at the sub-10 nm scale

LA Masullo, AM Szalai, LF Lopez, FD Stefani - Biophysical Reviews, 2021 - Springer
Fluorescence nanoscopy represented a breakthrough for the life sciences as it delivers 20–
30 nm resolution using far-field fluorescence microscopes. This resolution limit is not …

[HTML][HTML] Stability of ligand-induced protein conformation influences affinity in maltose-binding protein

M van den Noort, M de Boer, B Poolman - Journal of molecular biology, 2021 - Elsevier
Our understanding of what determines ligand affinity of proteins is poor, even with high-
resolution structures available. Both the non-covalent ligand–protein interactions and the …

Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

JC Sanders, ED Holmstrom - Essays in biochemistry, 2021 - portlandpress.com
The conformations of biological macromolecules are intimately related to their cellular
functions. Conveniently, the well-characterized dipole–dipole distance-dependence of …

Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments

PD Harris, E Lerner - Biophysical reports, 2022 - cell.com
Single-molecule spectroscopy has revolutionized molecular biophysics and provided means
to probe how structural moieties within biomolecules spatially reorganize at different …

Evidence for a compact σ70 conformation in vitro and in vivo

K Joron, J Zamel, N Kalisman, E Lerner - Iscience, 2024 - cell.com
The initiation of transcription in Escherichia coli (E. coli) is facilitated by promoter specificity
factors, also known as σ factors, which may bind a promoter only as part of a complex with …

Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ

E Ploetz, GK Schuurman-Wolters, N Zijlstra… - Open …, 2021 - royalsocietypublishing.org
The ATP-binding cassette transporter GlnPQ is an essential uptake system that transports
glutamine, glutamic acid and asparagine in Gram-positive bacteria. It features two extra …

From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

PO Heidarsson, C Cecconi - Essays in Biochemistry, 2021 - portlandpress.com
Single-molecule manipulation with optical tweezers has uncovered macromolecular
behaviour hidden to other experimental techniques. Recent instrumental improvements …