Chemical exchange in biomacromolecules: past, present, and future

AG Palmer III - Journal of magnetic resonance, 2014 - Elsevier
The perspective reviews quantitative investigations of chemical exchange phenomena in
proteins and other biological macromolecules using NMR spectroscopy, particularly …

Biophysics of chromatin dynamics

B Fierz, MG Poirier - Annual review of biophysics, 2019 - annualreviews.org
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate
DNA processes, including transcription, replication, and repair. Conformational dynamics …

Structure of SARS-CoV-2 M protein in lipid nanodiscs

KA Dolan, M Dutta, DM Kern, A Kotecha, GA Voth… - Elife, 2022 - elifesciences.org
SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope
(E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by …

Routine access to millisecond time scale events with accelerated molecular dynamics

LCT Pierce, R Salomon-Ferrer… - Journal of chemical …, 2012 - ACS Publications
In this work, we critically assess the ability of the all-atom enhanced sampling method
accelerated molecular dynamics (aMD) to investigate conformational changes in proteins …

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

A Sekhar, LE Kay - Proceedings of the National Academy of …, 2013 - National Acad Sciences
The importance of dynamics to biomolecular function is becoming increasingly clear. A
description of the structure–function relationship must, therefore, include the role of motion …

How to learn from inconsistencies: Integrating molecular simulations with experimental data

S Orioli, AH Larsen, S Bottaro… - Progress in Molecular …, 2020 - Elsevier
Molecular simulations and biophysical experiments can be used to provide independent
and complementary insights into the molecular origin of biological processes. A particularly …

Picosecond to millisecond structural dynamics in human ubiquitin

K Lindorff-Larsen, P Maragakis, S Piana… - The Journal of …, 2016 - ACS Publications
Human ubiquitin has been extensively characterized using a variety of experimental and
computational methods and has become an important model for studying protein dynamics …

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

AT Fenley, HS Muddana… - Proceedings of the …, 2012 - National Acad Sciences
Molecular dynamics simulations of unprecedented duration now can provide new insights
into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the …

[HTML][HTML] Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

WLM Alencar, T da Silva Arouche, AFG Neto… - Scientific Reports, 2022 - nature.com
The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its
high rate of contamination, propagation capacity, and lethality rate. In this work, we …

[HTML][HTML] Slow conformational exchange and overall rocking motion in ubiquitin protein crystals

V Kurauskas, SA Izmailov, ON Rogacheva… - Nature …, 2017 - nature.com
Proteins perform their functions in solution but their structures are most frequently studied
inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using …