Probing microscopic conformational dynamics in folding reactions by measuring transition paths
NQ Hoffer, MT Woodside - Current Opinion in Chemical Biology, 2019 - Elsevier
Transition paths comprise those parts of a folding trajectory where the molecule passes
through the high-energy transition states separating folded and unfolded conformations. The …
through the high-energy transition states separating folded and unfolded conformations. The …
Lessons about protein folding and binding from archetypal folds
Conspectus The function of proteins as biological nanomachines relies on their ability to fold
into complex 3D structures, bind selectively to partners, and undergo conformational …
into complex 3D structures, bind selectively to partners, and undergo conformational …
Robust membrane protein tweezers reveal the folding speed limit of helical membrane proteins
S Kim, D Lee, WCB Wijesinghe, D Min - Elife, 2023 - elifesciences.org
Single-molecule tweezers, such as magnetic tweezers, are powerful tools for probing nm-
scale structural changes in single membrane proteins under force. However, the weak …
scale structural changes in single membrane proteins under force. However, the weak …
Direct observation of single-protein transition state passage by nanopore ionic current jumps
Conformational transitions of proteins are governed by chemical kinetics, often toggled by
passage through an activated state separating two conformational ensembles. The passage …
passage through an activated state separating two conformational ensembles. The passage …
Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification
C Scaletti, PPS Russell, KJ Hebel… - Proceedings of the …, 2024 - National Acad Sciences
Protein–protein and protein–water hydrogen bonding interactions play essential roles in the
way a protein passes through the transition state during folding or unfolding, but the large …
way a protein passes through the transition state during folding or unfolding, but the large …
Topological bio-scaling analysis as a universal measure of protein folding
S Shityakov, EV Skorb… - Royal Society Open …, 2022 - royalsocietypublishing.org
Scaling relationships for polymeric molecules establish power law dependencies between
the number of molecular segments and linear dimensions, such as the radius of gyration …
the number of molecular segments and linear dimensions, such as the radius of gyration …
[HTML][HTML] Phage display identification of nanomolar ligands for human NEDD4-WW3: Energetic and dynamic implications for the development of broad-spectrum …
The recognition of PPxY viral Late domains by the third WW domain of the human HECT-E3
ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses …
ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses …
Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase
The way in which multidomain proteins fold has been a puzzling question for decades. Until
now, the mechanisms and functions of domain interactions involved in multidomain protein …
now, the mechanisms and functions of domain interactions involved in multidomain protein …
Rational design of protein-specific folding modifiers
Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living
organism and the pharmaceutical industry, respectively. Here we propose a design principle …
organism and the pharmaceutical industry, respectively. Here we propose a design principle …
Protein folding dynamics as diffusion on a free energy surface: rate equation terms, transition paths, and analysis of single-molecule photon trajectories
The rates of protein (un) folding are often described as diffusion on the projection of a
hyperdimensional energy landscape onto a few (ideally one) order parameters. Testing …
hyperdimensional energy landscape onto a few (ideally one) order parameters. Testing …