2024/05/07 by Liam Haas‐Neill, Khalil Joron, Eitan Lerner +1 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Cellular transport and secretion #Protein Structure and Dynamics #Biotin and Related Studies
paper · pdf · doi:10.1101/2024.05.07.592799
openalex publication_date 2024/05/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/14
Abstract The dense cellular environment influences bio-macromolecular structure, dynamics, interactions and function. Despite advancements in understanding protein-crowder interactions, predicting their precise effects on protein structure and function remains challenging. Here, we elucidate the effects of PEG-induced crowding on the fluorescent protein mCherry using molecular dynamics simulations and fluorescence-based experiments. We identify and characterize specific PEG-induced structural and dynamical changes in mCherry. Importantly, we find interactions in which PEG molecules wrap around specific surface-exposed residues in a binding mode previously observed in protein crystal structures. Fluorescence correlation spectroscopy experiments capture PEG-induced changes, including aggregation, suggesting a potential role for the specific PEG-mCherry interactions identified in simulations. Additionally, mCherry fluorescence lifetimes are influenced by PEG and not by the bulkier crowder dextran or by another linear polymer, polyvinyl alcohol, highlighting the importance of crowder-protein soft interactions. This work augments our understanding of macromolecular crowding effects on protein structure and dynamics.