Molecular dynamic simulations of CCR5 bound to different viral gp120 variants
This example described two simulations produced by all-atom classical molecular dynamic of a human chemokine type 5 receptor (CCR5), a HIV-1 glycoprotein 120 (gp120) and a human cluster of differentiation 4 (CD4) complex. The only difference between the two simulations is the amino acid sequence of gp120. The first complex has the #25 gp120 variant and the second has the #34 gp120 variant. A third entry described a single structure of an unliganded CCR5.
For more details about these systems, please refer to the following articles:
- Colin et al. CCR5 structural plasticity shapes HIV-1 phenotypic properties. PLOS Pathog. 2018, 14, e1007432. DOI: 10.1371/journal.ppat.1007432
- Jacquemard et al. Modeling of CCR5 Recognition by HIV-1 gp120: How the Viral Protein Exploits the Conformational Plasticity of the Coreceptor. Viruses. 2021, 13, 1395. DOI: 10.3390/v13071395
Cristallographic structures of P2X receptor
This example described 27 structures of ligand-gated P2X receptor from the Protein Data Bank.