Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations

2018/01/01 by Carolin König, Robin Skånberg, Ingrid Hotz +3 · 28 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Medicine · Neuroscience · Physics and Astronomy · #Alzheimer's disease research and treatments #Amyloid (mycology) #Amyloid β #Biology #Biophysics #Chemistry #Computational Drug Discovery Methods #Computational chemistry #Conjugated system #Functional Brain Connectivity Studies #Luminescence #Materials science #Medicine #Molecular dynamics #Nanotechnology #Optoelectronics #Organic chemistry #Pathology #Polymer #physics.bio-ph #physics.chem-ph #q-bio.BM

paper · pdf · doi:10.1039/c8cc00105g

published in Chemical Communications 54(24), 3030-3033 (Royal Society of Chemistry) · not peer-reviewed pre-print

openalex publication_date 2018/01/01 · arxiv created 2018/08/22 · arxiv updated 2018/08/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

due to the interactions between the anionic carboxyl groups of the probe and the cationic ε-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

Citations

• GROMACS: A message-passing parallel molecular dynamics implementation
• A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
• GROMACS 3.0: a package for molecular simulation and trajectory analysis
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
• Protein Misfolding, Functional Amyloid, and Human Disease
• GROMACS: Fast, flexible, and free