Introduction of phosphorylated residues into the UNRES coarse-grained model: toward modeling of signaling processes
Adam Sieradzan , Małgorzata Bogunia , Paulina Mech , Robert Ganzynkowicz , Artur Giełdoń , Józef Adam Liwo , Mariusz Makowski
AbstractPhosphorylated proteins take part in many signaling pathways and play a key role in homeostasis regulation. The all-atom force fields enable us to study the systems containing phosphorylated proteins, but they are limited to short time scales. In this paper, we report the extension of the physics-based coarse-grained UNRES force field to treat systems with phosphorylated amino-acid residues. To derive the respective potentials, appropriate physics-based analytical expressions were fitted to the potentials of mean force of systems modeling phosphorylated amino-acid residues computed in our previous work and implemented in UNRES. The extended UNRES performed well in ab initio simulations of two miniproteins containing phosphorylated residues, strongly suggesting that realistic large-scale simulations of processes involving phosphorylated proteins, especially signaling processes, are now possible.
|Journal series||Journal of Physical Chemistry B, ISSN 1520-6106, (N/A 140 pkt)|
|Publication size in sheets||0.5|
|ASJC Classification||; ;|
|Score||= 140.0, 29-05-2020, ArticleFromJournal|
|Publication indicators||= 1; = 1; : 2018 = 0.965; : 2018 = 2.923 (2) - 2018=2.996 (5)|
|Citation count*||1 (2020-05-30)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.