Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

AJ Dominic III, S Cao, A Montoya-Castillo… - Journal of the …, 2023 - ACS Publications
Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …

An efficient path classification algorithm based on variational autoencoder to identify metastable path channels for complex conformational changes

Y Qiu, MS O'Connor, M Xue, B Liu… - Journal of chemical …, 2023 - ACS Publications
Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …

Kinetic network models to study molecular self-assembly in the wake of machine learning

B Liu, Y Qiu, EC Goonetilleke, X Huang - MRS Bulletin, 2022 - Springer
Self-assembly provides a powerful tool to fabricate advanced materials through the bottom-
up approach. Understanding the kinetics of self-assembly would thus greatly help achieve …

Integrating Hydrogen Deuterium Exchange–Mass Spectrometry with Molecular Simulations Enables Quantification of the Conformational Populations of the Sugar …

R Jia, RT Bradshaw, V Calvaresi… - Journal of the American …, 2023 - ACS Publications
A yet unresolved challenge in structural biology is to quantify the conformational states of
proteins underpinning function. This challenge is particularly acute for membrane proteins …

Computational modeling of molecular structures guided by hydrogen-exchange data

D Devaurs, DA Antunes, AJ Borysik - Journal of the American …, 2022 - ACS Publications
Data produced by hydrogen-exchange monitoring experiments have been used in structural
studies of molecules for several decades. Despite uncertainties about the structural …

Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes

Y Wu, S Cao, Y Qiu, X Huang - The Journal of Chemical Physics, 2024 - pubs.aip.org
Protein conformational changes play crucial roles in their biological functions. In recent
years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) …

Hydrogen/Deuterium Exchange Mass Spectrometry: Fundamentals, Limitations, and Opportunities

L Konermann, PM Scrosati - Molecular & Cellular Proteomics, 2024 - mcponline.org
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) probes dynamic motions of
proteins by monitoring the kinetics of backbone amide deuteration. Dynamic regions exhibit …

Interpretation of HDX data by maximum-entropy reweighting of simulated structural ensembles

RT Bradshaw, F Marinelli, JD Faraldo-Gómez… - Biophysical …, 2020 - cell.com
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely
applied biophysical technique that probes the structure and dynamics of biomolecules …

Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR

TT Nguyen, DR Marzolf, JT Seffernick, S Heinze… - Structure, 2022 - cell.com
Hydrogen-deuterium exchange (HDX) measured by nuclear magnetic resonance (NMR)
provides structural information for proteins relating to solvent accessibility and flexibility …

HDX-MS and MD simulations provide evidence for stabilization of the IgG1—FcγRIa (CD64a) immune complex through intermolecular glycoprotein bonds

KW Anderson, C Bergonzo, K Scott… - Journal of molecular …, 2022 - Elsevier
Previous reports present different models for the stabilization of the Fc—FcγRI immune
complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic …