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Ncomms5733.Pdf ARTICLE Received 14 May 2014 | Accepted 17 Jul 2014 | Published 9 Sep 2014 DOI: 10.1038/ncomms5733 Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway Shuguang Yuan1,w, Slawomir Filipek2, Krzysztof Palczewski3 & Horst Vogel1 Recent crystal structures of G-protein-coupled receptors (GPCRs) have revealed ordered internal water molecules, raising questions about the functional role of those waters for receptor activation that could not be answered by the static structures. Here, we used molecular dynamics simulations to monitor—at atomic and high temporal resolution— conformational changes of central importance for the activation of three prototypical GPCRs with known crystal structures: the adenosine A2A receptor, the b2-adrenergic receptor and rhodopsin. Our simulations reveal that a hydrophobic layer of amino acid residues next to the characteristic NPxxY motif forms a gate that opens to form a continuous water channel only upon receptor activation. The highly conserved tyrosine residue Y7.53 undergoes transitions between three distinct conformations representative of inactive, G-protein activated and GPCR metastates. Additional analysis of the available GPCR crystal structures reveals general principles governing the functional roles of internal waters in GPCRs. 1 Laboratory of Physical Chemistry of Polymers and Membranes, E´cole Polytechnique Fe´de´rale de Lausanne, 1015 Lausanne, Switzerland. 2 Laboratory of Biomodeling, Faculty of Chemistry & Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland. 3 Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA. w Present address: Actelion Pharmaceuticals Ltd, 4123 Basel, Switzerland. Correspondence and requests for materials should be addressed to S.Y. (email: [email protected]) or to H.V. (email: horst.vogel@epfl.ch). NATURE COMMUNICATIONS | 5:4733 | DOI: 10.1038/ncomms5733 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5733 nternal water molecules are essential for the function of many molecules couple to the protein structure and thereby affect membrane proteins such as channel and transport proteins1. GPCR activation at the atomic level cannot be solved by static IFor G-protein-coupled receptors (GPCRs), which form the X-ray structures. Alternatively, molecular dynamics (MD) largest class of membrane proteins transmitting extracellular simulations can resolve atomic details of structural transitions signals across the plasma membrane, internal water molecules of receptors and their internal waters, which are experimentally have been proposed to play an important role for receptor not accessible8–11. Here, by using a total of 32-ms all-atom MD activation but mechanistic models remain speculative2. Previous simulations, we studied with high spatial and temporal resolution studies revealed that water molecules from the cytoplasmic region important steps during the activation of three different receptors of rhodopsin (Rho) are involved in the hydrolytic release of from class A GPCRs to elucidate how water molecules enter the retinal upon Rho activation by light3,4. Crystal structures of Rho inner space of a receptor, couple to and influence this protein’s 7 and the beta-2 adrenergic receptor (b2AR) revealed further structural transitions. Contrary to Liu et al. , our simulations details. Distinct conformational changes occur during activation revealed that in the inactivated state of the A2AR the internal of these receptors, including reorganizations of inner protein water pathway is interrupted by a gate of hydrophobic amino hydrogen bonding networks, which could be in contact with acids, which upon receptor activation evoke conformational internal waters5,6. An important step forward came from the changes opening a continuous internal water channel. By recent high-resolution crystal structures of the A2A adenosine analyzing all presently available GPCR crystal structures we receptor (A2AR) and the delta opioid receptor (dOR), which were able to identify common functional roles of internal waters revealed internal ordered water molecules that could be crucial within the members of class A GPCRs. for GPCR activation7,8. On the basis of their crystal structures, 7 Liu et al. proposed that the A2AR in the non-activated state contains a nearly continuous internal water channel, which is Results disrupted in the activated receptor. However, this detailed Hydrophobic layers of amino acid residues in the A2AR.We suggestion on the extension of the internal water channel is not started our MD investigations from the 1.8-Å resolution A2AR conclusive for several reasons: (1) As is shown in this article, the (PDB 4EIY) crystal structure7, which shows a comprehensive A2A receptor’s internal water molecules are quite mobile, which network of 57 solvent molecules inside the receptor together exclude determination of their precise spatial localization within with a sodium ion at the allosteric site. According to the the protein’s structural framework. (2) To calculate the receptor’s crystallographic b-factors (Fig. 1a) many of the receptor’s intrinsic water pathway, Liu et al.7 increased the radius of water intrinsic water molecules are mobile, a property further molecules and connected all water molecules with each other manifested by the poor electron density map in several regions because it is not possible to distinguish between a continuous and of the receptor, especially those close to Y2887.53 in the NPxxY a discontinuous water channel from crystal structures. motif and D522.50 at the allosteric site. Meanwhile, another 1.8-Å However, it is important to know the exact spatiotemporal resolution GPCR crystal structure, that of the DOR (PDB 4N6H), 12 distribution of water inside of GPCRs and their contact sites with was released . This also contains internal waters just as the A2AR the receptor’s polypeptide backbone and side chains to finally does (Fig. 1b). understand the relationship of an internal water channel to the To reveal how water molecules located inside the receptor are receptor’s function. Internal waters can strongly interfere with distributed spatially and temporally and how they couple to the internal hydrogen bonding networks of a protein’s backbone and protein’s structural fluctuations during GPCR activation, we side chains, thereby strongly influencing its conformational and performed all-atom long-timescale MD simulations starting from structural changes. Notably, the details of how the intrinsic water particular crystal structures of the A2AR: (a) ZMA antagonist ab TM2 TM2 TM3 TM1 8Å TM1 TM4 TM7 TM4 W2 TM7 6Å W2 TM3 D952.50 TM5 D522.50 TM5 W1 W1 Y1975.58 Y3187.53 Y288 7.53 14Å 8Å H8 H8 b-factors 15 35 55 Figure 1 | Water molecules and hydrophobic layers of amino acid residues in the crystal structures of adrenergic and opioid receptors. (a) A2AR (PDB 4EIY) and (b) dOR (PDB 4N6H). The precision of defining the position of individual water molecules (depicted as coloured spheres) is given by the crystallographic b-factors (see colour code). A crystallographic electron density map of water molecules at 1.5s level is pictured with COOT software56. 2FO-FC map is in blue grid and FO-FC map is in red grid. 2 NATURE COMMUNICATIONS | 5:4733 | DOI: 10.1038/ncomms5733 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5733 ARTICLE I bound to A2AR (ZMA/A2AR) representing an inactivated GPCR, For the activated GPCR in the NECA/A2AR complex, many I I (b) agonist NECA docked to inactive A2AR (NECA/A2AR )as more water molecules were located inside the receptor (Fig. 2b) II II well as activated A2AR crystal structures (NECA/A2AR ) than for the inactive GPCR in the ZMA/A2AR complex. In ZMA/ representing a GPCR in the meta state between a inactivated A2AR, water molecules from the bulk directly accessed HL1, I and activated receptor, and (c) NECA bound to A2AR in presence and in NECA/A2AR , the NECA agonist was connected to the of a C-terminal helix fragment of the Gs protein a-subunit (Ga)at NPxxY motif through a network of continuous water molecules the cytoplasmic side (NECA/A2AR/Ga) representing an activated involving a sodium ion inside the receptor. In addition, the GPCR/G-protein complex7. Two parallel MD simulations of conformation of Y2887.53 underwent a single flip-transition 1.6 ms duration were performed for each of the above-mentioned during MD simulations in the time range of 0.3–0.6 ms (Fig. 3c,d). I cases (Supplementary Table 1). Superposing the final structure of NECA/A2AR from MD Although many water molecules were found inside the receptor simulations (after a residue flip) with the NECA/A2AR crystal 12 7.53 during our MD simulations in the case of ZMA/A2AR, two structure , we found that the residue Y288 adopted identical distinct water-free layers of hydrophobic amino acid side chains conformations (Supplementary Fig. 1a). Moreover, the HL2 were resolved based on water density maps (Fig. 2a). These were observed in the ZMA/A2AR complex was retained in the NECA/ I also revealed from the water molecule distribution in the crystal A2AR complex, but the thickness was reduced to B10 Å structure (Fig. 1a). The first hydrophobic layer (HL1) was located (Fig. 2b). The HL2 was also observed within two independent between the orthosteric and the allosteric sites, and had a additional 1.6 ms MD simulations, starting from the NECA/ B II 13 thickness of 7 Å (Fig. 2a). Interestingly, water molecules from A2AR structure (Fig. 2c). the bulk next to the bound agonist NECA only rarely diffused Notably, during a simulation of the NECA/A2AR/Ga complex into the deep pocket of the receptor. The second hydrophobic with Ga present at the cytoplasmic G-protein-binding site, both layer (HL2) of B12 Å thickness was located close to the highly HLs were no longer detected in the receptor. Instead, a conserved NPxxY motif in TM7.
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