Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Bogdan Barz, Jennifer Loschwitz and Birgit Strodel

PLOS Computational Biology, 2019, vol. 15, issue 10, 1-29

Abstract: Guanylate binding proteins (GBPs) belong to the dynamin-related superfamily and exhibit various functions in the fight against infections. The functions of the human guanylate binding protein 1 (hGBP1) are tightly coupled to GTP hydrolysis and dimerization. Despite known crystal structures of the hGBP1 monomer and GTPase domain dimer, little is known about the dynamics of hGBP1. To gain a mechanistic understanding of hGBP1, we performed sub-millisecond multi-resolution molecular dynamics simulations of both the hGBP1 monomer and dimer. We found that hGBP1 is a highly flexible protein that undergoes a hinge motion similar to the movements observed for other dynamin-like proteins. Another large-scale motion was observed for the C-terminal helix α13, providing a molecular view for the α13–α13 distances previously reported for the hGBP1 dimer. Most of the loops of the GTPase domain were found to be flexible, revealing why GTP binding is needed for hGBP1 dimerization to occur.Author summary: Guanylate binding proteins are key fighters against microbial and viral pathogens. In the human body there are seven types of such proteins, among which is the guanylate binding protein 1 (hGBP1). This protein is able to perform its function only once it is activated by binding and converting guanosine triphosphat (GTP) to guanosine diphosphat and guanosine monophosphat via hydrolysis. In concert with the conversion of GTP the dimerization of hGBP1 occurs, which can further interact with the lipid membrane of the pathogen and disrupt it. While the crystal structure of the protein is known, the activation and dimerization steps are not well understood at molecular level as studying them experimentally is difficult. An alternative approach is given by molecular simulations, allowing us to elucidate the protein dynamics closely connected to these steps. From our simulations applied to both the hGBP1 monomer and dimer we identified large-scale motions taking place in hGBP1 that had not been reported before. We discuss the relevance of these motions in terms of their biological function, such as possible membrane damage caused by one of the motions or locking the protein in the dimer state.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1007193

DOI: 10.1371/journal.pcbi.1007193

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