Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins

Journal article

A. Lipska, Anna Antoniak, P. Wesołowski, Alan Warszawski, S. Samsonov, A. Sieradzan
Journal of Molecular Modeling, 2021

Cite

APA Click to copy
Lipska, A., Antoniak, A., Wesołowski, P., Warszawski, A., Samsonov, S., & Sieradzan, A. (2021). Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. Journal of Molecular Modeling.

Chicago/Turabian Click to copy
Lipska, A., Anna Antoniak, P. Wesołowski, Alan Warszawski, S. Samsonov, and A. Sieradzan. “Coarse-Grained Modeling of the Calcium, Sodium, Magnesium and Potassium Cations Interacting with Proteins.” Journal of Molecular Modeling (2021).

MLA Click to copy
Lipska, A., et al. “Coarse-Grained Modeling of the Calcium, Sodium, Magnesium and Potassium Cations Interacting with Proteins.” Journal of Molecular Modeling, 2021.

BibTeX Click to copy

@article{a2021a,
  title = {Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins},
  year = {2021},
  journal = {Journal of Molecular Modeling},
  author = {Lipska, A. and Antoniak, Anna and Wesołowski, P. and Warszawski, Alan and Samsonov, S. and Sieradzan, A.}
}

Abstract

Metal ions play important biological roles, e.g., activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e., calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.