Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently
Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
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
Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …
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
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 …
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 …
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 …
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
Protein conformational changes play crucial roles in their biological functions. In recent
years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) …
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 …
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 …
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 …
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 …
complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic …