[HTML][HTML] Structure-guided metagenome mining to tap microbial functional diversity

SL Robinson - Current Opinion in Microbiology, 2023 - Elsevier
Scientists now have access to millions of accurate three-dimensional (3D) models of protein
structures. How do we leverage 3D structural models to learn about microbial functions …

Liquid–liquid phase separation modifies the dynamic properties of intrinsically disordered proteins

S Guseva, V Schnapka, W Adamski… - Journal of the …, 2023 - ACS Publications
Liquid–liquid phase separation of flexible biomolecules has been identified as a ubiquitous
phenomenon underlying the formation of membraneless organelles that harbor a multitude …

Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

G Widmalm - JACS Au, 2024 - ACS Publications
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are
ubiquitous in nature, and their structures range from linear assemblies to highly branched …

Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro

T Agback, D Lesovoy, X Han, A Lomzov, R Sun… - Communications …, 2023 - nature.com
The dengue protease NS2B/NS3pro has been reported to adopt either an 'open'or a
'closed'conformation. We have developed a conformational filter that combines NMR with …

Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy

MM Islam, SU Nawagamuwage… - Journal of the …, 2023 - ACS Publications
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic
interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an …

Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center

L Querci, D Grifagni, IB Trindade, JM Silva… - Journal of Biomolecular …, 2023 - Springer
The robustness of NMR coherence transfer in proximity of a paramagnetic center depends
on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins …

Parsing dynamics of protein backbone NH and side-chain methyl groups using molecular dynamics simulations

NE Banayan, A Hsu, JF Hunt… - Journal of Chemical …, 2024 - ACS Publications
Experimental NMR spectroscopy and theoretical molecular dynamics (MD) simulations
provide complementary insights into protein conformational dynamics and hence into …

Fitting force field parameters to NMR relaxation data

F Kümmerer, S Orioli… - Journal of Chemical …, 2023 - ACS Publications
We present an approach to optimize force field parameters using time-dependent data from
NMR relaxation experiments. To do so, we scan parameters in the dihedral angle potential …

[HTML][HTML] Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin

C Champion, M Lehner, AA Smith, F Ferrage… - The Journal of …, 2024 - pubs.aip.org
Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of
molecular systems in the picosecond to millisecond timescales. As these methods cannot …

Probing methyl group dynamics in proteins by NMR cross-correlated dipolar relaxation and molecular dynamics simulations

AAAI Ali, F Hoffmann, LV Schäfer… - Journal of Chemical …, 2022 - ACS Publications
Nuclear magnetic resonance (NMR) spin relaxation is the most informative approach to
experimentally probe the internal dynamics of proteins on the picosecond to nanosecond …