Protocol for Simulations of PEGylated Proteins with Martini 3

Book chapter

Protocol

Proteins

Polymers

Author

Fabian Grünewald, Peter C Kroon, Paulo CT Souza, Siewert J Marrink

Doi

https://doi.org/10.1007/978-1-0716-0892-0_18

Citation (APA 7)

Grünewald, F., Kroon, P. C., Souza, P. C., & Marrink, S. J. (2021). Protocol for simulations of PEGylated proteins with martini 3. Structural Genomics: General Applications, 315-335.

Abstract

Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.