Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

C Selvaraj, O Rudhra, AS Alothaim, M Alkhanani… - Advances in Protein …, 2022 - Elsevier
Enzymes, which are biological molecules, are constructed from polypeptide chains, and
these molecules are activated through reaction mechanisms. It is the role of enzymes to …

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 …

ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy

C Olivieri, GC Li, Y Wang, M VS, C Walker, J Kim… - Science …, 2022 - science.org
ATP-competitive inhibitors are currently the largest class of clinically approved drugs for
protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic …

Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers

S Bhattacharya, KM Varney, T Dahmane… - Journal of Biomolecular …, 2024 - Springer
Deuterium (2H) spin relaxation of 13CH2D methyl groups has been widely applied to
investigate picosecond-to-nanosecond conformational dynamics in proteins by solution …

Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics

V Kharchenko, M Nowakowski, M Jaremko… - Journal of Biomolecular …, 2020 - Springer
Intramolecular motions in proteins are one of the important factors that determine their
biological activity and interactions with molecules of biological importance. Magnetic …

RING NMR dynamics: software for analysis of multiple NMR relaxation experiments

MA Beckwith, T Erazo-Colon, BA Johnson - Journal of Biomolecular NMR, 2021 - Springer
Molecular motions are fundamental to the existence of life, and NMR spectroscopy remains
one of the most useful and powerful methods to measure their rates and molecular …

Protein conformational entropy is not slaved to water

BS Marques, MA Stetz, C Jorge, KG Valentine… - Scientific reports, 2020 - nature.com
Conformational entropy can be an important element of the thermodynamics of protein
functions such as the binding of ligands. The observed role for conformational entropy in …

Uremic Toxin-Induced Exosome-like Extracellular Vesicles Contain Enhanced Levels of Sulfated Glycosaminoglycans which Facilitate the Interaction with Very Small …

C Freise, A Zappe, N Löwa, J Schnorr, K Pagel… - International Journal of …, 2023 - mdpi.com
Uremic toxins exert pathophysiological effects on cells and tissues, such as the generation
of a pro-calcifying subtype of exosome-like extracellular vesicles (EVs) in vascular cells …

Detection of molecular transitions with nitrogen-vacancy centers and electron-spin labels

C Munuera-Javaloy, R Puebla, B D'Anjou… - npj Quantum …, 2022 - nature.com
We present a protocol that detects molecular conformational changes with two nitroxide
electron-spin labels and a nitrogen-vacancy (NV) center in diamond. More specifically, we …

The native state conformational heterogeneity in the energy landscape of protein folding

P Mishra, SK Jha - Biophysical Chemistry, 2022 - Elsevier
The native structure of proteins is central to various functions performed by cells. A vital part
of the structure-function paradigm of proteins is their inherent flexibility and dynamics. The …