Paramagnetic chemical probes for studying biological macromolecules

Q Miao, C Nitsche, H Orton, M Overhand… - Chemical …, 2022 - ACS Publications
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR)
and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent …

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 …

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

J Huang, AD MacKerell Jr - Journal of computational chemistry, 2013 - Wiley Online Library
Protein structure and dynamics can be characterized on the atomistic level with both nuclear
magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here …

Population shuffling of protein conformations

CA Smith, D Ban, S Pratihar, K Giller… - Angewandte Chemie …, 2015 - Wiley Online Library
Motions play a vital role in the functions of many proteins. Discrete conformational transitions
to excited states, happening on timescales of hundreds of microseconds, have been …

How much entropy is contained in NMR relaxation parameters?

F Hoffmann, FAA Mulder… - The Journal of Physical …, 2021 - ACS Publications
Solution-state NMR relaxation experiments are the cornerstone to study internal protein
dynamics at an atomic resolution on time scales that are faster than the overall rotational …

Time-resolved protein side-chain motions unraveled by high-resolution relaxometry and molecular dynamics simulations

SF Cousin, P Kadeřávek, N Bolik-Coulon… - Journal of the …, 2018 - ACS Publications
Motions of proteins are essential for the performance of their functions. Aliphatic protein side
chains and their motions play critical roles in protein interactions: for recognition and binding …

Observation of sub-microsecond protein methyl-side chain dynamics by nanoparticle-assisted NMR spin relaxation

X Xiang, AL Hansen, L Yu, G Jameson… - Journal of the …, 2021 - ACS Publications
Amino-acid side-chain properties in proteins are key determinants of protein function. NMR
spin relaxation of side chains is an important source of information about local protein …

Structure-based prediction of methyl chemical shifts in proteins

AB Sahakyan, WF Vranken, A Cavalli… - Journal of biomolecular …, 2011 - Springer
Protein methyl groups have recently been the subject of much attention in NMR
spectroscopy because of the opportunities that they provide to obtain information about the …

Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone

KH DuBay, JP Bothma, PL Geissler - PLoS computational biology, 2011 - journals.plos.org
Allosteric regulation is a key component of cellular communication, but the way in which
information is passed from one site to another within a folded protein is not often clear. While …

Applications of NMR and computational methodologies to study protein dynamics

C Narayanan, K Bafna, LD Roux, PK Agarwal… - Archives of biochemistry …, 2017 - Elsevier
Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in
biological events such as allostery, cell signaling, and enzyme catalysis. Over the years …