Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. Export

@article{citeulike:4469770, abstract = {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 beta1 and beta2 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 beta2AR into Phe325 in beta1AR 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 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.}, author = {Vanni, Stefano and Neri, Marilisa and Tavernelli, Ivano and Rothlisberger, Ursula}, citeulike-article-id = {4469770}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/bi900299f}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/bi900299f}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19378975}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19378975}, day = {20}, doi = {10.1021/bi900299f}, issn = {1520-4995}, journal = {Biochemistry}, keywords = {activation, b2ar, dry, dynamics, flexibility, ionic, lock, md, protonation, solvation, switch, tm3, tm6, water}, month = {April}, posted-at = {2009-05-06 09:56:27}, priority = {2}, title = {Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors.}, url = {http://dx.doi.org/10.1021/bi900299f}, year = {2009} }

TY - JOUR ID - citeulike:4469770 L3 - citeulike-article-id:4469770 N2 - 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 beta1 and beta2 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 beta2AR into Phe325 in beta1AR 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 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. JF - Biochemistry SN - 1520-4995 TI - Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. KW - activation KW - b2ar KW - dry KW - dynamics KW - flexibility KW - ionic KW - lock KW - md KW - protonation KW - solvation KW - switch KW - tm3 KW - tm6 KW - water AU - Vanni, Stefano AU - Neri, Marilisa AU - Tavernelli, Ivano AU - Rothlisberger, Ursula PY - 2009/04/20/ UR - http://dx.doi.org/10.1021/bi900299f ER -