Resolution in cryogenic solid state NMR: Challenges and solutions

IV Sergeyev, K Fritzsching, R Rogawski… - Protein …, 2024 - Wiley Online Library
NMR at cryogenic temperatures has the potential to provide rich site‐specific details
regarding biopolymer structure, function, and mechanistic intermediates. Broad spectral …

TUPÃ: Electric field analyses for molecular simulations

MD Polêto, JA Lemkul - Journal of computational chemistry, 2022 - Wiley Online Library
We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in
molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in …

Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics

X Yi, L Zhang, RA Friesner… - The journal of physical …, 2024 - ACS Publications
NMR chemical shifts provide a sensitive probe of protein structure and dynamics but remain
challenging to predict and interpret. We examine the effect of protein conformational …

Conformational ensemble of the NSP1 CTD in SARS-CoV-2: Perspectives from the free energy landscape

P Dutta, A Kshirsagar, P Bibekar, N Sengupta - Biophysical Journal, 2023 - cell.com
Abstract The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-
associated coronavirus 2 plays a crucial role in the translational shutdown and immune …

High-resolution magic angle spinning NMR of KcsA in liposomes: the highly mobile C-terminus

GS Howarth, AE McDermott - Biomolecules, 2022 - mdpi.com
The structure of the transmembrane domain of the pH-activated bacterial potassium channel
KcsA has been extensively characterized, yet little information is available on the structure of …

Free energy landscapes of KcsA inactivation

S Pérez-Conesa, L Delemotte - bioRxiv, 2023 - biorxiv.org
The bacterial ion channel KcsA has become a useful model of complex K+-ion channels
thanks to its single pore domain structure whose sequence shares many similarities with …

Full opening of helix bundle crossing does not lead to NaK channel activation

V Kurauskas, M Tonelli… - Journal of General …, 2022 - rupress.org
A critical part of ion channel function is the ability to open and close in response to stimuli
and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels …

Mechanistic Studies of Membrane Proteins Using Integrated Solid-state NMR and Computational Approaches

H SAWCZYC, A LANGE - Integrated Structural Biology, 2023 - books.google.com
Proteins are a major constituent of cellular membranes, with an average plasma membrane
being approximately 50% membrane proteins by mass. 1 In addition to their large number …

In-cell Structural Biology Through the Integration of Solution NMR Spectroscopy and Computational Science

Y Ito, T Ikeya, K Inomata - 2023 - books.rsc.org
The intracellular environment is highly crowded (molecular crowding) and differs
significantly from the environment in dilute solutions that we usually use in biochemical …

LEGOLAS: a Machine Learning method for rapid and accurate predictions of protein NMR chemical shifts.

M Darrows, D Kodituwakku, J Xue, I Pickering, N Terrel… - 2025 - chemrxiv.org
This work introduces LEGOLAS, a fully open source TorchANI-based neural network model
designed to predict NMR chemical shifts for protein backbone atoms. LEGOLAS has been …