Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors.
G protein coupled receptors (GPCRs) are a large family of integral membrane proteins involved in signal transduction pathways, making them appealing drug targets for a wide spectrum of diseases. The recently crystallized structures of two engineered adrenergic receptors have opened new avenues for the understanding of the molecular mechanisms of action of GPCRs. Taking the two crystal structures as a starting point, we carried out submicrosecond molecular dynamics simulations of wild-type beta(1) and beta(2) adrenergic receptors in a lipid bilayer under physiological conditions. These simulations give access to structural and dynamic properties of the receptors in pseudo in vivo conditions. For both systems the overall fold properties of the transmembrane region as well as the binding pocket remain close to the crystal structure of the engineered systems, thus suggesting that the ligand binding mode is not affected by the introduced modifications. Both simulations indicate the presence of one or two internal water molecules absent in both crystal structures and essential for the stabilization of the binding pocket at the interface between transmembrane helices III, IV, and V. The different interactions arising from the substitution of Tyr308 in beta(2)AR into Phe325 in beta(1)AR induce different conformations of the homologous Asn(6.55) inside the binding pockets of the two receptors, suggesting a possible origin of receptor specificity in agonist binding. The equilibrated structures of both receptors recover all of the previously suggested features of inactive GPCRs including formation of a salt bridge between the cytoplasmatic moieties of helices III and VI ("ionic lock") that is absent in the crystal structures.
Vanni
Stefano
S
Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology, EPFL, CH-1015 Lausanne, Switzerland.
Neri
Marilisa
M
Tavernelli
Ivano
I
Rothlisberger
Ursula
U
D000818:Animals; D001120:Arginine / Q000737:chemistry / Q000235:genetics; D018360:Crystallography, X-Ray; D003593:Cytoplasm / Q000737:chemistry / Q000378:metabolism; D018698:Glutamic Acid / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007477:Ions / Q000737:chemistry*; D008024:Ligands; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding / Q000235:genetics; D015202:Protein Engineering; D017510:Protein Folding; D017433:Protein Structure, Secondary / Q000235:genetics; D018342:Receptors, Adrenergic, beta-1 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D014422:Turkeys
D007477:Ions; D008024:Ligands; D008051:Lipid Bilayers; D018342:Receptors, Adrenergic, beta-1; D018698:Glutamic Acid; D001120:Arginine