Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein

0556414 - BTÚ 2022 RIV US eng J - Journal Article
Aliakbar Tehrani, Zahra - Rulíšek, Lubomír - Černý, Jiří
Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein.
Journal of Biomolecular Structure & Dynamics. JUN 2021, JUN 2021 (2021), č. článku 2021-07-12. ISSN 0739-1102
R&D Projects: GA MŠMT(CZ) EF16_013/0001777; GA MŠMT(CZ) ED1.1.00/02.0109; GA MŠMT(CZ) LM2018131; GA MŠMT(CZ) EF16_013/0001776; GA ČR(CZ) GA20-08772S
Research Infrastructure: CESNET II - 90042
Institutional support: RVO:86652036 ; RVO:61388963
Keywords : NETWORK ANALYSIS * INTERFERON GENES * LIGAND * RECOGNITION
OECD category: Biochemistry and molecular biology
Impact factor: 5.235, year: 2021
Method of publishing: Limited access
https://www.tandfonline.com/doi/full/10.1080/07391102.2021.1942213

Human stimulator of interferon genes (hSTING) is a signaling adaptor protein that triggers innate immune system by response to cytosolic DNA and second messenger cyclic dinucleotides (CDNs). Natural CDNs contain purine nucleobase with different phosphodiester linkage types (3 '-3 ', 2 '-2 ' or mixed 2 '-3 '-linkages) and exhibit different binding affinity towards hSTING, ranging from micromolar to nanomolar. High-affinity CDNs are considered as suitable candidates for treatment of chronic hepatitis B and cancer. We have used molecular dynamics simulations to investigate dynamical aspects of binding of natural CDNs (specifically, 2'-2'-cGAMP, 2'-3'-cGAMP, 3'-3'-cGAMP, 3'-3'-c-di-AMP, and 3'-3'-c-di-GMP) with hSTING(wt) protein. Our results revealed that CDN/hSTING(wt) interactions are controlled by the balance between fluctuations (conformational changes) in the CDN ligand and the protein dynamics. Binding of different CDNs induces different degrees of conformational/dynamics changes in hSTING(wt) ligand binding cavity, especially in alpha(1)-helices, the so-called lid region and alpha(2)-tails. The ligand residence time in hSTING(wt) protein pocket depends on different contribution of R232 and R238 residues interacting with oxygen atoms of phosphodiester groups in ligand, water distribution around interacting charged centers (in protein residues and ligand) and structural stability of closed conformation state of hSTING(wt) protein. These findings may perhaps guide design of new compounds modulating hSTING activity. Communicated by Ramaswamy H. Sarma
Permanent Link: http://hdl.handle.net/11104/0330635