| Autor: |
Mathur A; Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany., Ghosh R; Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.; Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States., Nunes-Alves A; Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany. |
| Jazyk: |
angličtina |
| Zdroj: |
Journal of chemical information and modeling [J Chem Inf Model] 2024 Dec 23; Vol. 64 (24), pp. 9063-9081. Date of Electronic Publication: 2024 Dec 11. |
| DOI: |
10.1021/acs.jcim.4c01520 |
| Abstrakt: |
Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone. In this review, we focus on the various physics-based and data-driven computational methods developed in the past few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules to the entire cellular cytoplasm. We further discuss the effects of macromolecular crowding on different phenomena, such as diffusion, protein-ligand binding, and mechanical and viscoelastic properties, such as surface tension of condensates. Finally, we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model cellular environments by reproducing in vivo conditions as accurately as possible. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
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