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

Abstract

Phosphorylated 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.
Author Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Małgorzata Bogunia (FCh / KChBionieorg. / LII)
Małgorzata Bogunia ,,
- Laboratory of Intermolecular Interactions
, Paulina Mech (FCh / KChBionieorg. / LII)
Paulina Mech,,
- Laboratory of Intermolecular Interactions
, Robert Ganzynkowicz (FCh / DTCh / LMM)
Robert Ganzynkowicz,,
- Laboratory of Molecular Modeling
, Artur Giełdoń (FCh / DTCh / LSP)
Artur Giełdoń,,
- Laboratory of Simulation of Polymers
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
, Mariusz Makowski (FCh / KChBionieorg. / LII)
Mariusz Makowski,,
- Laboratory of Intermolecular Interactions
Journal seriesJournal of Physical Chemistry B, ISSN 1520-6106, (A 30 pkt)
Issue year2019
Vol123
No27
Pages5721-5729
Publication size in sheets0.5
ASJC Classification2505 Materials Chemistry; 2508 Surfaces, Coatings and Films; 1606 Physical and Theoretical Chemistry
DOIDOI:10.1021/acs.jpcb.9b03799
URL https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03799
Languageen angielski
Score (nominal)30
ScoreMinisterial score = 30.0, 24-07-2019, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2017 = 1.015; WoS Impact Factor: 2017 = 3.146 (2) - 2017=3.101 (5)
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