Advances in free-energy-based simulations of protein folding and ligand binding

A Perez, JA Morrone, C Simmerling, KA Dill - Current opinion in structural …, 2016 - Elsevier
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 …

Limited cooperativity in protein folding

V Munoz, LA Campos, M Sadqi - Current Opinion in Structural Biology, 2016 - Elsevier
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 …

Fluorescence-detected mid-infrared photothermal microscopy

M Li, A Razumtcev, R Yang, Y Liu, J Rong… - Journal of the …, 2021 - ACS Publications
We demonstrate instrumentation and methods to enable fluorescence-detected
photothermal infrared (F-PTIR) microscopy and then demonstrate the utility of F-PTIR to …

Threading single proteins through pores to compare their energy landscapes

P Tripathi, A Firouzbakht… - Proceedings of the …, 2022 - National Acad Sciences
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 …

In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non‐native interactions

PPS Russell, MM Rickard, M Boob, M Gruebele… - Protein …, 2023 - Wiley Online Library
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 …

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 …

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 …

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 …

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy

CM Davis, L Zanetti-Polzi, M Gruebele, A Amadei… - Chemical …, 2018 - pubs.rsc.org
For small molecule reaction kinetics, computed reaction coordinates often mimic
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 …