Advances in free-energy-based simulations of protein folding and ligand binding
Highlights•Molecular dynamics is reaching longer timescales faster than Moore's law's
rate.•Improved sampling algorithms, force fields and computers drive advances.•At current …
rate.•Improved sampling algorithms, force fields and computers drive advances.•At current …
Limited cooperativity in protein folding
Theory and simulations predict that the structural concert of protein folding reactions is
relatively low. Experimentally, folding cooperativity has been difficult to study, but in recent …
relatively low. Experimentally, folding cooperativity has been difficult to study, but in recent …
Fluorescence-detected mid-infrared photothermal microscopy
We demonstrate instrumentation and methods to enable fluorescence-detected
photothermal infrared (F-PTIR) microscopy and then demonstrate the utility of F-PTIR to …
photothermal infrared (F-PTIR) microscopy and then demonstrate the utility of F-PTIR to …
Threading single proteins through pores to compare their energy landscapes
Translocation of proteins is correlated with structural fluctuations that access conformational
states higher in free energy than the folded state. We use electric fields at the solid-state …
states higher in free energy than the folded state. We use electric fields at the solid-state …
In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non‐native interactions
We examine the influence of cellular interactions in all‐atom models of a section of the
Homo sapiens cytoplasm on the early folding events of the three‐helix bundle protein B …
Homo sapiens cytoplasm on the early folding events of the three‐helix bundle protein B …
Disulfide bonds in protein folding and stability
MJ Feige, I Braakman, LM Hendershot - 2018 - books.rsc.org
Disulfide Bonds in Protein Folding and Stability | Oxidative Folding of Proteins: Basic
Principles, Cellular Regulation and Engineering | Books Gateway | Royal Society of Chemistry …
Principles, Cellular Regulation and Engineering | Books Gateway | Royal Society of Chemistry …
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 …
Molecular mechanism behind the fast folding/unfolding transitions of villin headpiece subdomain: Hierarchy and heterogeneity
T Mori, S Saito - The Journal of Physical Chemistry B, 2016 - ACS Publications
Proteins involve motions over a wide range of spatial and temporal scales. While the large
conformational changes, such as folding and functioning, are slow and appear to occur in a …
conformational changes, such as folding and functioning, are slow and appear to occur in a …
A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy
For small molecule reaction kinetics, computed reaction coordinates often mimic
experimentally measured observables quite accurately. Although nowadays simulated and …
experimentally measured observables quite accurately. Although nowadays simulated and …
Unravelling the intricacy of the crowded environment through tryptophan quenching in lysozyme
P Singh, PK Chowdhury - The Journal of Physical Chemistry B, 2017 - ACS Publications
Global conformational modulation of proteins in the presence of crowding agents is well-
known. In this work, using the intrinsic tryptophan (Trp) residues of lysozyme, we have …
known. In this work, using the intrinsic tryptophan (Trp) residues of lysozyme, we have …