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bioRxiv · 10.1101/2023.08.17.553662

Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations

Dogan, B.·Durdagi, S.
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Abstract

CCR5 is one of the co-receptors for HIV-1 entry into host cells and is class A GPCR. This receptor has vital roles in the immune system and is involved in the pathogenesis of different diseases. Various studies were conducted to understand its activation mechanism including structural studies in which inactive and active states of the receptor were determined in complex with various binding partners. These determined structures provided opportunities to perform molecular dynamics simulations (MD) and analyze conformational changes observed in protein structures. The atomic level dynamical studies allow us to explore the effects of ionizable residues in the receptor. Here, our aim was to investigate the changes observed in the conformation of CCR5 when it is in complex with inhibitor maraviroc (MRV), an approved anti-HIV drug or HIV-1 envelope protein GP120 in comparison to when the receptor was in apo form. In our simulations, we considered both ionized and protonated states of ionizable binding site residue GLU2837.39 in CCR5 as the protonation state of this residue was considered ambiguously in previous studies. Our simulation results suggested that in fact, the change in the protonation state of GLU2837.39 caused interaction profiles to be different between CCR5 and its binding partners, GP120 or MRV. We observed that when the protonated state of GLU2837.39 was considered in complex with envelope protein GP120, there were substantial structural changes in CCR5 indicating it adopts more of an active-like conformation. On the other hand, CCR5 when it was in complex with MRV always adopted inactive conformation regardless of the protonation state. Hence, CCR5 coreceptor displays conformational heterogeneity not only based on its binding partner but also on the state of the protonation state of a binding site residue GLU2837.39. This outcome is also in accordance with some studies showing that GP120 binding could activate signaling pathways. Additionally, this outcome could also have critical implications for the discovery of novel CCR5 inhibitors to be used as anti-HIV drugs by in silico methods such as molecular docking since consideration of the protonated state of GLU2837.39 could be required.

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Dogan, B., Durdagi, S.. 2023-08-18. Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations. https://doi.org/10.1101/2023.08.17.553662

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