Binding of histamine to the H1 receptor-a molecular dynamics study.

Binding of histamine to the G-protein coupled histamine H ₁ receptor plays an important role in the context of allergic reactions; however, no crystal structure of the resulting complex is available yet. To deduce the histamine binding site, we performed unbiased molecular dynamics (MD) simulations on a microsecond time scale, which allowed to monitor one binding event, in which particularly the residues of the extracellular loop 2 were involved in the initial recognition process. The final histamine binding pose in the orthosteric pocket is characterized by interactions with Asp107 ^3.32 , Tyr108 ^3.33 , Thr194 ^5.43 , Asn198 ^5.46 , Trp428 ^6.48 , Tyr431 ^6.51 , Phe432 ^6.52 , and Phe435 ^6.55 , which is in agreement with existing mutational data. The conformational stability of the obtained complex structure was subsequently confirmed in 2 μs equilibrium MD simulations, and a metadynamics simulation proved that the detected binding site represents an energy minimum. A complementary investigation of a D107A mutant, which has experimentally been shown to abolish ligand binding, revealed that this exchange results in a significantly weaker interaction and enhanced ligand dynamics. This finding underlines the importance of the electrostatic interaction between the histamine ammonium group and the side chain of Asp107 ^3.32 for histamine binding.