Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL ** of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
AD Garst, MC Bassalo, G Pines, SA Lynch… - Nature …, 2017 - nature.com
Improvements in DNA synthesis and sequencing have underpinned comprehensive
assessment of gene function in bacteria and eukaryotes. Genome-wide analyses require …

Structure determination of high-energy states in a dynamic protein ensemble

JB Stiller, R Otten, D Häussinger, PS Rieder… - Nature, 2022 - nature.com
Macromolecular function frequently requires that proteins change conformation into high-
energy states,,–. However, methods for solving the structures of these functionally essential …

Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch

A Bah, RM Vernon, Z Siddiqui, M Krzeminski… - Nature, 2015 - nature.com
Intrinsically disordered proteins play important roles in cell signalling, transcription,
translation and cell cycle regulation,. Although they lack stable tertiary structure, many …

Ratcheting synthesis

S Borsley, JM Gallagher, DA Leigh… - Nature Reviews …, 2024 - nature.com
Synthetic chemistry has traditionally relied on reactions between reactants of high chemical
potential and transformations that proceed energetically downhill to either a global or local …

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism

JB Greisman, KM Dalton, DE Brookner… - Proceedings of the …, 2024 - pnas.org
Enzymes catalyze biochemical reactions through precise positioning of substrates,
cofactors, and amino acids to modulate the transition-state free energy. However, the role of …

The role of dynamic conformational ensembles in biomolecular recognition

DD Boehr, R Nussinov, PE Wright - Nature chemical biology, 2009 - nature.com
Molecular recognition is central to all biological processes. For the past 50 years,
Koshland's' induced fit'hypothesis has been the textbook explanation for molecular …

An introduction to NMR-based approaches for measuring protein dynamics

IR Kleckner, MP Foster - Biochimica et Biophysica Acta (BBA)-Proteins and …, 2011 - Elsevier
Proteins are inherently flexible at ambient temperature. At equilibrium, they are
characterized by a set of conformations that undergo continuous exchange within a …

Parallel molecular mechanisms for enzyme temperature adaptation

MM Pinney, DA Mokhtari, E Akiva, F Yabukarski… - Science, 2021 - science.org
INTRODUCTION Over billions of years, organisms and their enzymes have been evolving
and adapting in response to selection pressures from their environments. In particular …