NMR-based methods for protein analysis

Y Hu, K Cheng, L He, X Zhang, B Jiang… - Analytical …, 2021‏ - ACS Publications
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for
analyzing protein structure, interaction, and dynamics at atomic resolution and in various …

Predicting binding free energies: frontiers and benchmarks

DL Mobley, MK Gilson - Annual review of biophysics, 2017‏ - annualreviews.org
Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

Conformational states dynamically populated by a kinase determine its function

T **e, T Saleh, P Rossi, CG Kalodimos - Science, 2020‏ - science.org
INTRODUCTION Protein kinases mediate many cell signaling processes. Central to their
physiological function is the regulation of their binding and enzymatic activities, which is …

NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function

TR Alderson, LE Kay - Cell, 2021‏ - cell.com
Biomolecules are in constant motion. To understand how they function, and why
malfunctions can cause disease, it is necessary to describe their three-dimensional …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W **, R Nussinov, B Ma - Chemical reviews, 2016‏ - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015‏ - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Protein activity regulation by conformational entropy

SR Tzeng, CG Kalodimos - Nature, 2012‏ - nature.com
How the interplay between protein structure and internal dynamics regulates protein function
is poorly understood. Often, ligand binding, post-translational modifications and mutations …

Studying “invisible” excited protein states in slow exchange with a major state conformation

P Vallurupalli, G Bouvignies, LE Kay - Journal of the American …, 2012‏ - ACS Publications
Ever since its initial development, solution NMR spectroscopy has been used as a tool to
study conformational exchange. Although many systems are amenable to relaxation …

An NMR view of protein dynamics in health and disease

A Sekhar, LE Kay - Annual review of biophysics, 2019‏ - annualreviews.org
Biological molecules are often highly dynamic, and this flexibility can be critical for function.
The large range of sampled timescales and the fact that many of the conformers that are …

Integrative, dynamic structural biology at atomic resolution—it's about time

H Van Den Bedem, JS Fraser - Nature methods, 2015‏ - nature.com
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …