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Computational Study on the Different Ligands Induced Conformation Change of β2 Adrenergic Receptor-Gs Protein Complex

β2 adrenergic receptor (β2AR) regulated many key physiological processes by activation of a heterotrimeric GTP binding protein (Gs protein). This process could be modulated by different types of ligands. But the details about this modulation process were still not depicted. Here, we performed molecular dynamics (MD) simulations on the structures of β2AR-Gs protein in complex with different types of ligands. The simulation results demonstrated that the agonist BI-167107 could form hydrogen bonds with Ser2035.42, Ser2075.46 and Asn2936.55 more than the inverse agonist ICI 118,551. The different binding modes of ligands further affected the conformation of β2AR. The energy landscape profiled the energy contour map of the stable and dissociated conformation of Gαs and Gβγ when different types of ligands bound to β2AR. It also showed the minimum energy pathway about the conformational change of Gαs and Gβγ along the reaction coordinates. By using interactive essential dynamics analysis, we found that Gαs and Gβγ domain of Gs protein had the tendency to separate when the inverse agonist ICI 118,551 bound to β2AR. The α5-helix had a relatively quick movement with respect to transmembrane segments of β2AR when the inverse agonist ICI 118,551 bound to β2AR. Besides, the analysis of the centroid distance of Gαs and Gβγ showed that the Gαs was separated from Gβγ during the MD simulations. Our results not only could provide details about the different types of ligands that induced conformational change of β2AR and Gs protein, but also supplied more information for different efficacies of drug design of β2AR.


Introduction
The b 2 adrenergic receptor (b 2 AR) belonged to class A G protein-coupled receptors (GPCRs) [1] and regulated many key physiologically processes such as smooth muscle relaxation in the airways and the vasculature [2][3][4][5][6][7]. During the past years, much progress had been made in the determination of the crystal structure of b 2 AR with different types of ligands. The crystal structure of b 2 AR in complex with the inverse agonist carazolol was determined in 2007. It revealed the inactive conformation of b 2 AR [8]. The neutral antagonist alprenolol bound to b 2 AR structure was reported in 2010. This work showed that the antagonist could block agonist signal but maintain basal signal [9]. The irreversible agonist-b 2 AR complex was reported in 2011. This agonist was irreversible because it was covalently tethered to a specific site of b 2 AR [10]. At the same time, a reversible agonistb 2 AR in complex with the camelid antibody fragment that exhibited G protein-like behavior was obtained by X-ray crystallography [11]. Besides, Rasmussen et al. reported the crystal structure of agonist-occupied b 2 AR and nucleotide-free Gs heterotrimer (a, b and c). This work gave a model system for understanding the detailed mechanism about the activation of Gs and also for understanding the ligands induced conformation change of b 2 adrenergic receptor-Gs (b 2 AR-Gs) protein complex [12]. The analysis of b 2 AR-Gs complex could provide some information about the essential mechanism of structural events linking GPCR-Gs protein complex formation by using peptide amide hydrogen-deuterium exchange mass spectrometry [13]. Engineering and characterization of b 2 AR-based on ion-channel coupled receptors gave new insights into the conformational dynamics of b 2 AR [14]. All these studies also indicated that it was difficult to obtain the crystal structure of the agonist-bound to active conformation of b 2 AR if the G protein did not bind to b 2 AR.
Even though the active conformation of b 2 AR-Gs have been resolved, it was still difficult to obtain the detailed information about the dynamic process of inactive or active state of b 2 AR-Gs from real experiments. Compared with experimental study, all atoms molecular dynamics simulations [15][16][17][18][19][20] and coarsegrained molecular dynamics simulations [21,22] methods could provide much more dynamic information at the atomic level about the activation or inactivation mechanism of b 2 AR. Other computational methods such as molecular docking and conformational analysis [23][24][25][26][27] were also successfully used to study the function and activation mechanism as well as to discovery the small molecular ligands of b 2 AR on basis of the crystal structures.
The MD simulations of agonist-b 2 AR complex showed that agonist, inverse agonist and antagonist had different interaction modes with the active sites of b 2 AR. The main reason was that the waters in the cavity of b 2 AR had different contribution to the stabilization of the interaction network [20]. The atomic level description illuminated that drug must cross two energetic barriers to get into the active site of b 2 AR. The first barrier was mainly due to hydrophobic interaction. The second energetic barrier was due to dehydration and allosteric receptor when the drug moved into the binding pocket [28]. In addition, Dror et al. proposed that the agonist-b 2 AR could transform momentarily from active to the inactive conformation based on the results of MD simulations. This study also showed b 2 AR had an intermediate state. The conformation of b 2 AR would be induced to active or inactive state if agonist or inverse agonist bound to the cavity of receptor [29]. Provasi et al. performed free energy calculation on the crystal structure of b 2 AR with different ligands (either inverse agonists, neural antagonists, or agonists). The simulation results suggested that different type ligands had different free energy landscape. Especially, the agonist had opposite energy barrier to the inverse agonist. And there was nearly no energy barrier when b 2 AR had no ligands in the cavity [30]. Goetz et al. studied the interaction between C-terminal end of Gas and b 2 AR by performing MD simulations [31]. Feng et al. carried out 20 ns MD simulations on agonist-bound part of b 2 AR without Gbc domain to investigate the activation mechanism of b 2 AR [32].
Despite these recent remarkable advances in b 2 AR structure determination and molecular dynamics simulation, the detailed mechanism by which different types of ligands induced dynamic conformational changes of b 2 AR and Gs protein during the modulated process was still not reported. Most of the reported works mainly focused on the complex of b 2 AR and ligands. In order to understand the modulation of Gs by b 2 AR, it was more reliable to perform MD simulation based on the crystal structure of b 2 AR-Gs complex. The following important questions still need to be answered, such as: what is the difference of binding mode between b 2 AR and different kinds of ligands? which kind of ligand could induce Gas to separate from Gbc? How did the inactive conformation of b 2 AR interact with Gs protein?
In order to further explore how different types of ligands affected the behavior of Gas and Gbc in the b 2 AR-Gs complex. We performed a total of 800 ns MD simulations on the complex of b 2 AR-Gs bound to agonist (BI-167107), antagonist (alprenolol), inverse agonist (ICI 118,551) and their unliganded form with explicit solvent and lipids at constant pressure and constant temperature. The graphics processing unit (GPU) computer was used to accelerate the MD simulations. The analysis of energy landscape was performed to illustrate the minimum energy pathway of the conformational change of Gas and Gbc along the reaction coordinates when ICI 118,551 bound to b 2 AR. Furthermore, we used interactive essential dynamics (IED) [33] to identify the dissociation of Gas and Gbc by analyzing the MD simulated trajectory. Our simulated results showed that Gas was separated from the Gbc when the ICI 118,551 bound to active sites of b 2 AR. Besides, the a5-helix had fast motion relative to TM3, TM5, TM6, TM7 of b 2 AR if the ICI 118,551 bound to b 2 AR. Our results could also provide the information about the inactivation and activation mechanism of Gs protein induced by different types of ligands.

Structure of b 2 AR-Gs Complex
The structure of b 2 AR-Gs with explicit waters and lipids was shown as in Figure 1. The thickness for membrane location was about 3061.0 Å , which was calculated by OPM database [34]. The main part of b 2 AR-Gs consisted of b 2 AR, Gas and Gbc. The loop between TM5 and TM6 was modeled on basis of the crystal structure of b 2 AR-Gs. TM3, TM5, TM6 and TM7 (TM3,5,6,7) were shown in the origin part of b 2 AR-Gs. The black part was a5helix. The residues of the active site in the pocket of b 2 AR include Asp113 3.32 , Ser203 5.42 , Ser207 5.46 , Asn293 6.5 , Tyr308 7.35 and Asn312 7.39 (see Figure 2A). The space surrounded by these sites was the volume of b 2 AR. The crystal structure of b 2 AR-Gs in complex with the agonist (BI-167107) was used in our simulations In order to get b 2 AR-Gs in complex with different kinds of ligands, the inverse agonist (ICI 118,551) and antagonist (alprenolol) were docked into the pocket of b 2 AR-Gs. The 200 ns MD simulations were performed for b 2 AR-Gs in complex with different ligands on a workstation equipped with four pieces of graphics processing unit (GPU) and two processors with six cores (see Figure S1).

Ligands Bound to Different Sites of b 2 AR
After 200 ns MD simulations, the analysis of hydrogen bonds occupancy showed that inverse agonist (ICI 118,551), antagonist (alprenolol) and agonist (BI-167107) could form hydrogen bonds with different sites of b 2 AR-Gs ( Figure 3A and 3B). We also obtained the hydrogen bond interaction between b 2 AR and different ligands (see Figure 2B, 2C and 2D) from the MD simulation trajectory at the same time. ICI 118,551 only had two stable hydrogen bonds with Asp113 3.32 and Asn312 7.39 ( Figure 2D and Figure 3A). In comparison, BI-167107 had another three stable hydrogen bonds with Ser203 5.42 , Ser207 5.46 and Asn293 6.55 besides Asp113 3.32 and Asn312 7.39 ( Figure 3A, 3B and Figure 2C). Alprenolol had a similar binding mode with ICI 118,551 except lower hydrogen bonds occupancy on Tyr308 7.35 ( Figure 3A, 3B and Figure 2B). The number of hydrogen bonds also showed BI-167107 could form more hydrogen bonds than alprenolol and ICI 118,551 along the simulation time ( Figure 3C). The main reason was that BI-167107 had more oxygen and hydroxyl groups than Alprenolol and ICI 118,551 as shown in the black oval of Figure 4, so BI-167107 could be easy to form another three hydrogen bonds with Ser203 5.42 , Ser207 5.46 and Asn293 6.55 (see Figure 2C). The results showed that inverse agonist had different binding modes with agonist and antagonist.
In order to measure the pocket change of b 2 AR during the simulations, the pocket detection plugin of VMD [35,36] was used to calculate the lignad-bound pocket volume versus simulation time ( Figure 1 and Figure 3D). The value of the pocket volume of unliganded complex showed that this conformation of b 2 AR was in the intermediate state. The pocket volume would become larger when the inverse agonist ICI 118,551 bound to the pocket of b 2 AR, while the pocket volume would shrink when the agonist BI-167107 or antagonist alprenolol bound to b 2 AR. These results indicated different ligands could adjust the pocket space size of the b 2 AR though different binding modes of b 2 AR. The changes of pocket volume size would further affect the conformation of b 2 AR.

Conformation CHANGE of b 2 AR Induced by Different Ligands
In order to study conformational change of b 2 AR induced by different ligands, the root mean square deviation (RMSD) of the backbone atoms of b 2 AR was measured versus simulation time ( Figure 5A). The b 2 AR in complex with ICI 118,551 reached equilibrium phase after 5 ns MD simulations (see Figure S2). The RMSD of b 2 AR-ICI 118,551 still maintained about 2.7 Å until 26 ns MD simulations ( Figure 5A). By comparison with the RMSD of b 2 AR-BI-167107, we could see that b 2 AR-ICI 118,551 was still in active conformation. After 26 ns, the conformation of b 2 AR was changed into another state. In order to make sure the conformational feature of b 2 AR, FATCAT rigid algorithm [37] was used to calculate the RMSD with respect to the crystal structure of inverse agonist ICI 118,551-bound b 2 AR (PDB code: 3NY8) (see Table S1). The RMSD values in the Table S1 indicated the simulated conformation was closer to the inactive conformation, while the increased value of RMSD after about 26 ns suggested that simulated structures had different conformation with the agonistbound b 2 AR (see Figure 5A). The b 2 AR-alprenolol and unliganded form of b 2 AR had similar RMSD with b 2 AR-BI-167107. It suggested that b 2 AR did not change its active state if alprenolol, BI-167107 or no ligand bound to b 2 AR. The active and inactive state of b 2 AR could be identified by some reported sites (Ile121 3.40 / Phe282 6.44 , NPxxY region: Asn322 7.49 -Tyr326 7.53 and Asp192 5.31 / Lys305 7.32 ) [9,29]. These sites could be used to distinguish the active and inactive conformation of b 2 AR.     Figure 5C showed the RMSD of the backbone atoms of NPxxY motif which could distinguish different states of b 2 AR. The RMSD of NPxxY region of b 2 AR-unligand was close to the level of b 2 AR-BI-167107 after about 148 ns MD simulations (see Figure 5C). The data also showed that b 2 AR-alprenolol had different RMSD of NPxxY region with unliganded, BI-167107 and ICI 118,551bound b 2 AR. The possible reason was that the conserved NPxxY region could discern diverse conformations of b 2 AR when different types of ligands bound to b 2 AR. Figure 5D described the distance of Ca carbons of Asp192 5.31 and Lys305 7.32 versus MD simulation time. The distance divided the conformation of b 2 AR into the inactive part and active part because Asp192 5.31 and Lys305 7.32 only represented part of extracellular surface of b 2 AR. ICI 118,551 and unligand belonged to inactive part while alprenolol and BI-167107 played an active role.
All these results corresponded to distinct functional behavior of different types of ligands. The inverse agonist ICI 118,551 could block the activating signaling. In contrast, unliganded and alprenolol-bound b 2 AR could maintain the basal activity signaling. BI-167107 could enhance the active signaling of b 2 AR [9].

Energy Landscape of Gas and Gbc
The above simulated results showed that different types of ligands could regulate the diverse states of b 2 AR. Besides, Gas and Gbc had shown some interesting conformations when BI-167107, alprenolol, ICI 118,551 or no ligand bound to the active sites of b 2 AR. Our molecular dynamics simulations trajectory of b 2 AR-Gs contained a wide range of conformational spaces. Therefore, abundant information was supplied for the energy landscape analysis of the conformations of Gas and Gbc. Two major motions represented the conformations of Gas and Gbc: one was the centroid distance of Gas and Gbc, the other was the RMSD of Gas and Gbc. Figure 6 illustrated the energy landscape of Gas and Gbc corresponding to two reaction coordinates. This energy landscape contained one major deep well when the BI-167107, alprenolol or no ligand bound to b 2 AR (see Figure 6A, 6B and 6C). This energy part represented the stable structure of Gas and Gbc which was not separated from each other. However, the energy landscape consisted of three main deep wells when the ICI 118,551 combined with b 2 AR. The white points depicted the minimum energy pathway. It was mainly relevant to the stable conformation of Gas and Gbc (0,43 ns) before the first deep well. Along with the change of simulated time, the Gas and Gbc complex passed over an energy barrier of ,2.0 kcal/mol. At the same time, the stable conformation of Gas and Gbc became to dissociated state. It only need overcome the energy barrier of ,0.5 kcal/mol for each neighboring deep well. These three deep wells represented the dissociated conformation of Gas and Gbc (see Figure 6D). In additions, Figure 6D showed the lowest energy barrier of ,1.5 kcal/mol in the deep well, while Figure 6A, 6B, 6C showed the lowest energy barrier of deep well was ,0.5 kcal/mol. It further indicated the domain of Gas and Gbc was not stable when ICI 118,551 bound to b 2 AR.

Gas is Separated from Gbc
After analysis of the energy landscape of Gas and Gbc, it is interesting to study the movement of Gas and Gbc. The motions of Gas and Gbc were analyzed by interactive essential dynamics (IED) analysis [33]. The two principal components of motions revealed the movements of TM5, TM6 and Gas and Gbc (Figure 7). The Gas did not move away from Gbc when BI-167107 and alprenolol bound to b 2 AR ( Figure 7A and 7B). The Gas and Gbc domain was also not dissociated when there was no ligand on the b 2 AR ( Figure 7D). In this case, TM5 and TM6 had almost no relative motion. In comparison, the Gas domain was separated from Gbc domain when ICI 118,551 bound to b 2 AR. At the same time, TM5 and TM6 had the open tendency with respect to Gbc domain ( Figure 7C).
The a5-helix had been reported to play an important role on the interaction between b 2 AR and Gs protein [12,13,32]. The sketch of the structure of a5-helix and TM3,5,6,7 was shown in Figure 1. The centroid distance between a5-helix and TM3,5,6,7 was measured over the simulation time. As shown in black oval of Figure 8A, the centroid distance between a5-helix and TM3,5,6,7 was dropped sharply when ICI 118,551 bound to the pocket of b 2 AR. It indicated that a5-helix moved quickly relative to TM3,5,6,7. After about 43 ns MD simulations, the centroid distance became longer when BI-167107, alprenolol or no ligands was in the active pocket of b 2 AR, while the distance was shorter when ICI 118,551 bound to b 2 AR. We also analyzed the RMSD of the backbone atoms of a5-helix and TM3,5,6,7 (see Figure S3). It could be seen that both of the studied systems reached equilibrium in 200 ns. The b 2 AR-ICI 118,551 system had larger RMSD value of a5-helix and TM3,5,6,7 than the b 2 AR bound to alprenolol and BI-167107. It also suggested that the conformation of a5-helix and TM3,5,6,7 had a larger structural fluctuation when ICI 118,551 combined with b 2 AR. Besides, we also calculated the centroid distance of Gas and Gbc domain ( Figure 8B). The centroid distance of Gas and Gbc domain kept in about 37 Å when alprenolol, BI-167107 or no ligand bound to b 2 AR. In contrast, Gas and Gbc domain was separated obviously from each other after 43 ns MD simulations when ICI 118,551 bound to the pocket of b 2 AR. Movie S1 gave a detailed animation about the separation or association of Gas and Gbc induced by different ligands. This dissociation was almost accompanied with the relative movement of a5-helix. When the relative motion of a5-helix stopped at about 43 ns, the Gas and Gbc were separated from each other (see Figure 8A and 8B). At the same time, we could see the RMSD of b 2 AR changed after about 26 ns ( Figure 5A). After another 17 ns, Gas moved away from Gbc. It suggested the inverse agonist ICI 118,551 induced the separation of Gas and Gbc though changing the conformation of b 2 AR.
The above results indicated that different kinds of ligands could induce the different behaviors of Gas and Gbc through changing the conformation of b 2 AR. The Gas and Gbc domain were not stable when ICI 118,551 bound to b 2 AR. In contrast, Gas and Gbc domain would keep the stable distance if BI-167107, alprenolol or no ligand bound to b 2 AR [9].

Conclusions
In this study, we focused on the binding mode between b 2 AR and different ligands and the conformational states of b 2 AR in complex with Gas and Gbc domain. The hydrogen bonds occupancy showed that Alprenolol, BI-167107 and ICI 118,551 in the pocket of b 2 AR formed different number of hydrogen bonds with the binding site of b 2 AR. These different binding modes would affect the pocket volume size of b 2 AR. The changes of pocket space further affected the conformation of b 2 AR. The results of RMSD indicated that ICI 118,551 could induce b 2 AR to change from active conformation to inactive state. The other ligands were inclined to keep b 2 AR active. Specially, the energy landscape showed three main deep wells when the ICI 118,551 bound with b 2 AR. It suggested ICI 118,55 could induced the conformational change of Gas and Gbc. The analysis of IED and centroid distance further illustrated the inactive conformation of b 2 AR induced by ICI 118,551 could lead to the dissociation of Gas and Gbc. In comparison, the Gas and Gbc would maintain the relative stable distance if there was alprenolol, BI-167107 or no ligand in the active site of b 2 AR ( Figure 8C). In total, our MD simulations and energy landscape results demonstrated that different ligands-bound b 2 AR induced the dissociation of downstream Gas and Gbc. These results not only depicted the detail dissociation mechanism of Gas and Gbc domain which was adjusted indirectly by different ligands, but also could give more clues for the design of potential ligands with different modulating functions.

Protein Structures Preparation
The agonist-bound model of b 2 AR was prepared beginning from the crystal structure (PDB ID: 3SN6) [12] by removing T4 lysozyme and nanobody (Nb35). Because TM5 and TM6 played an important role in the interaction between b 2 AR and Gs, the missing intracellular loop 3 was added by using the loop model algorithm of MODELLER [38] (see Protocol S1). The neutral antagonist (alprenolol) was extracted from the model (PDB ID: 3NYA) [39]. The inverse agonist (ICI 118,551) was obtained from the crystal structure (PDB ID: 3NY8) [39]. In order to obtain the protein-ligand complex, the inverse agonist and neutral antagonist were docked into the pocket of b 2 AR using AutoDock Vina program [40]. The docking complexes were then used as the starting models for membrane location. The model of b 2 AR-Gs was embedded into an explicit 1-palmitoyl-2-oleoyl-sn-glycero-3phosphocholine (POPC) by using VMD program [36]. The orientation of membrane was described in Protocol S1 and Figure 1. The length and width of lipid box was 120 Å 6 120 Å . The TIP3P water model [41] was used to build the water box which dimensions were 120 Å 6 120 Å 6 150 Å . Seven sodium ions were added to neutralize the system which contained about 200,010 atoms per periodic cell. The CHARMM force field parameterizations of BI-167107, alprenolol and ICI 118,551 were developed by using VMD Paratool Plugin v1.2 [42] and Gaussian 98 Revision A.9 [43]: The RHF/6-31G* model was used with tight SCF convergence criteria for geometry optimization calculation. The single point calculation was computed at the theory of RHF/6-31G* level with tight SCF convergence criteria.

Molecular Dynamics Simulations
The b 2 AR-Gs in complex with alprenolol, BI-167107, ICI 118,551 or without ligand were built with explicit lipids and water, respectively. In order to equilibrate these four systems, firstly, each system was fixed except lipid tail for minimizing 100 ps and equilibrating 1000 ps under constant temperature (300 K) and constant pressure (1 bar). Secondly, each system was minimized for 500 ps and equilibrated for 0.5 ns with protein and ligand constrained. Then, 5 ns equilibrated simulations were performed without any constraint. At last, a total of 200 ns MD simulations were performed on the each system under a constant temperature of 300 k and a constant pressure of 1 bar.
Our MD simulations were performed with time step of 2 fs in explicit water and periodically infinite lipid through using NAMD package (version 2.9b3) [44] with CHARMM27 force field [45]. The minimization was based on a conjugate gradient method. The particle-mesh Ewald (PME) [46] method was used to calculate electrostatics with a 12 Å nonbonded cutoff. Langevin piston and Langevin barostat methods were employed for the temperature and pressure respectively [47]. The frames were saved every 20.0 ps during the MD simulations.
All MD simulations were performed on the GPU workstation. In order to get the highest efficiency of GPU, the speed test of GPU workstation was carried out with different collocations of Cores and GPU (see Figure S1).The speed test results proved that running on 12 cores of an array of two 2.66-GHz Intel Xeon 5650 processors and 4 pieces of NVDIA Tesla C 2050 graphics card could get the highest speed. The wall clock time was about 3.46 ns per day.

Hydrogen Bonds and Volume Calculation
In the statistical analysis of the hydrogen bonds occupancy, the distance and angle between the acceptor and donor atoms were set less than 3.5 Å and 35u, respectively [48,49]. The polyhedral volumetric model of the pocket detection plugin of VMD [35,36] was used to find the pocket volume of b 2 AR.

Interactive Essential Dynamics Analysis
For the interactive essential dynamics (IED) analysis [33], the complex were split into three parts: b 2 AR, Gas and Gbc. 25 eigenvectors were generated for each part on the basis of trajectory file, then 25 projections were obtained from eigenvectors. The IED was calculated by equation 1: z i~ai1 x 1 za i2 x 2 z:::za im x m ð1Þ Where z i represented the ith principal component. a im was weight coefficient. x m represented the position. The first two components could represent the main motions of protein. More details about IED method were described in the Text S1. Trajectory analysis was carried out using AmberTools12 and VMD [36,50].

Energy Landscape Analysis
The energy landscape of the conformational change of protein complex could be estimated by an appropriate conformation sampling method. In order to get the a two dimensional (2D) energy landscape map, the centroid distance between Gas and Gbc, which mainly represented the motion, and the RMSD of Gas and Gbc, which corresponded the conformational fluctuation, were chosen as the reaction coordinates. The energy landscape could be calculated along these two reaction coordinates as equation 2 [51][52][53][54] shown: DG(p 1 ,p 2 )~{k B T ln r(p 1 ,p 2 ) ð2Þ Where k B represented the Boltzmann constant, T was the simulated temperature, and r(p 1 ,p 2 ) represented the normalized joint probability distribution.  Text S1 Interactive Essential Dynamics.

(DOC)
Movie S1 Animation about the separation or association of Gas and Gbc induced by different ligands. (AVI)