Structural dynamics of bio-macromolecules by NMR: The slowly relaxing local structure approach

E Meirovitch, YE Shapiro, A Polimeno… - Progress in nuclear …, 2010 - Elsevier
Protein dynamics by NMR has been reviewed extensively in recent years [1–10]. These
surveys show decisively that information on structure should be complemented by …

Entropy in molecular recognition by proteins

JA Caro, KW Harpole, V Kasinath… - Proceedings of the …, 2017 - National Acad Sciences
Molecular recognition by proteins is fundamental to molecular biology. Dissection of the
thermodynamic energy terms governing protein–ligand interactions has proven difficult, with …

On the molecular origin of the cooperative coil-to-globule transition of poly (N-isopropylacrylamide) in water

L Tavagnacco, E Zaccarelli, E Chiessi - Physical Chemistry Chemical …, 2018 - pubs.rsc.org
By means of atomistic molecular dynamics simulations we investigate the behaviour of poly
(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower …

How to strike a conformational balance in protein force fields for molecular dynamics simulations?

W Kang, F Jiang, YD Wu - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
Molecular dynamics (MD) simulation is a powerful tool for exploring the conformational
energy landscape of proteins, and the reliability of MD results is crucially dependent on the …

Modulation of Rotational Dynamics in Halogen-Bonded Cocrystalline Solids

SS Gunaga, DL Bryce - Journal of the American Chemical Society, 2023 - ACS Publications
Dynamic processes are responsible for the functionality of a range of materials,
biomolecules, and catalysts. We report a detailed systematic study of the modulation of …

Peptide and protein dynamics and low-temperature/DNP magic angle spinning NMR

QZ Ni, E Markhasin, TV Can, B Corzilius… - The Journal of …, 2017 - ACS Publications
In DNP MAS NMR experiments at∼ 80–110 K, the structurally important− 13CH3 and−
15NH3+ signals in MAS spectra of biological samples disappear due to the interference of …

Observing the overall rocking motion of a protein in a crystal

P Ma, Y Xue, N Coquelle, JD Haller, T Yuwen… - Nature …, 2015 - nature.com
The large majority of three-dimensional structures of biological macromolecules have been
determined by X-ray diffraction of crystalline samples. High-resolution structure …

Protein side-chain dynamics as observed by solution-and solid-state NMR spectroscopy: a similarity revealed

V Agarwal, Y Xue, B Reif… - Journal of the American …, 2008 - ACS Publications
In this paper, we seek to compare the internal dynamics of a small globular protein, SH3
domain from α-spectrin, in solution and in a crystalline state. The comparison involves side …

Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H−15N NMR Spectroscopy

A Esadze, DW Li, T Wang… - Journal of the …, 2011 - ACS Publications
Despite their importance in macromolecular interactions and functions, the dynamics of
lysine side-chain amino groups in proteins are not well understood. In this study, we have …

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 …