Theoretical study of the human bradykinin-bradykinin B2 receptor complex.
The interaction of bradykinin (BK) with the bradykinin B2 receptor (B2R) was analyzed by using molecular modeling (MM) and molecular dynamics (MD) simulations. A homology model for B2R has been generated and the recently determined receptor-bound solid-state NMR spectroscopic structure of BK (Lopez et al., Angew. Chem. 2008, 120, 1692-1695; Angew. Chem. Int. Ed. 2008, 47, 1668-1671) has been modeled into the binding pocket of the receptor to probe the putative ligand-receptor interface. The experimental hormone structure fitted well into the binding pocket of the receptor model and remained stable during the MD simulation. We propose a parallel orientation of the side chains for Arg1 and Arg9 in BK that is bound to B2R. The MD simulation study also allows the conformational changes that lead to the activated form of B2R to be analyzed. The hydrogen bond between N140 (3.35) and W283 (6.48) is the key interaction that keeps the receptor in its inactive form. This hydrogen bond is broken during the MD simulation due to rotation of transmembrane helix 3 (TM3) and is replaced by a new hydrogen bond between W283 (6.48) and N324 (7.45). We propose that this interaction is specific for the activated form of the bradykinin B2 receptor. Additionally, we compared and discussed our putative model in the context of the structural model of the partially activated rhodopsin (Rh*) and with the known biochemical and structural data.
Gieldon
Artur
A
Johann Wolfgang Goethe-Universität, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Frankfurt Germany.
Lopez
Jakob J
JJ
Glaubitz
Clemens
C
Schwalbe
Harald
H
D001665:Binding Sites; D001669:Biochemical Phenomena; D003198:Computer Simulation; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D043782:Receptor, Bradykinin B2 / Q000737:chemistry* / Q000378:metabolism*
D008024:Ligands; D043782:Receptor, Bradykinin B2