Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer
BACKGROUND Biomolecular mechanisms are typically inferred from static structural
“snapshots” obtained by x-ray crystallography, nuclear magnetic resonance (NMR) …
“snapshots” obtained by x-ray crystallography, nuclear magnetic resonance (NMR) …
Rationally engineered nucleic acid architectures for biosensing applications
Development of biosensing platforms plays a key role in research settings for identification
of biomarkers and in clinical applications for diagnostics. Biosensors based on nucleic acids …
of biomarkers and in clinical applications for diagnostics. Biosensors based on nucleic acids …
Quantitative mass imaging of single biological macromolecules
G Young, N Hundt, D Cole, A Fineberg, J Andrecka… - Science, 2018 - science.org
The cellular processes underpinning life are orchestrated by proteins and their interactions.
The associated structural and dynamic heterogeneity, despite being key to function, poses a …
The associated structural and dynamic heterogeneity, despite being key to function, poses a …
Single-molecule plasmon sensing: current status and future prospects
AB Taylor, P Zijlstra - ACS sensors, 2017 - ACS Publications
Single-molecule detection has long relied on fluorescent labeling with high quantum-yield
fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing …
fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing …
Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation
Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the
nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid–liquid …
nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid–liquid …
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …
demonstrated in a large number of applications, limitations in the model with respect to the …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Non-Markovian modeling of protein folding
C Ayaz, L Tepper, FN Brünig… - Proceedings of the …, 2021 - National Acad Sciences
We extract the folding free energy landscape and the time-dependent friction function, the
two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular …
two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular …
Nanopore-based measurements of protein size, fluctuations, and conformational changes
P Waduge, R Hu, P Bandarkar, H Yamazaki… - ACS …, 2017 - ACS Publications
Proteins are structurally dynamic macromolecules, and it is challenging to quantify the
conformational properties of their native state in solution. Nanopores can be efficient tools to …
conformational properties of their native state in solution. Nanopores can be efficient tools to …