B. Strodel

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations

This study uses QM/MM simulations to analyze PET degradation mechanisms in PET hydrolases, revealing conformational changes and the impact of QM methods on reaction pathways.

From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets

The paper uses molecular dynamics simulations to uncover the binding pathway of PET hydrolases into PET material and identifies key residues affecting PET entry.

Insulin Amyloid Morphology is Encoded in H-bonds and Electrostatics Interactions Ruling Protein Phase Separation

The paper investigates how anion-protein interactions influence insulin phase separation and amyloid formation through H-bonds and electrostatics, revealing alternative pathways to fibril formation.

Allosteric communication induced by GTP binding sets off a closed-to-open transition in a bacterial dynamin-like protein

The paper uses molecular dynamics simulations to show GTP binding triggers a closed-to-open conformational change in a bacterial dynamin-like protein through an allosteric network.

Integrative modeling of guanylate binding protein dimers

The paper models dimer structures of GBP proteins using integrative methods, revealing structural differences that explain functional divergence.

Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2

This study investigates the molecular mechanisms of murine GBP2, revealing its lipid-binding affinity and dynamic behavior on membranes, which may contribute to membrane destruction.

Structural dissection of the first events following membrane binding of the islet amyloid polypeptide

This study investigates the early molecular events of IAPP binding to lipid membranes using spectroscopy, microscopy, and simulations, revealing how residue 18 affects structure and aggregation.

Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane

This study uses molecular dynamics simulations to show that Aβ42 dimers form β-sheets in solution but not at neuronal membranes, with GM1 gangliosides inhibiting ordered oligomer formation.

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations

This study evaluates new force fields for simulating amyloid-beta peptide aggregation, finding that force field choice significantly affects aggregation pathways and that CHARMM36m performs best.

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

This study uses 30-microsecond MD simulations with seven force fields to analyze the thermodynamics and kinetics of Aβ40, identifying suitable force fields and equilibrium times.

Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks

The paper provides protocols for setting up and analyzing molecular dynamics simulations of peptide aggregation using GROMACS, including tools for determining oligomer size and deriving Markov state models and transition networks.

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

This study uses multi-resolution simulations to reveal large-scale motions in hGBP1, providing insights into its dynamics and dimerization mechanism.

A structural and kinetic link between membrane association and amyloid fibril formation of α-Synuclein

This study investigates how α-Synuclein interacts with membrane surfaces and how these interactions influence its aggregation into amyloid fibrils.