Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling

Abstract

Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

New Insights into the Stereochemical Requirements of the Bombesin BB1 Receptor Antagonists Binding

“…Figure 3 shows the evolution of the root-mean-square-deviation (rmsd) computed using the Cα of the BB1 receptor structure along the MD trajectory. A can be seen, it required more than 100 ns for the structure to have the structure equilibrated as had been observed previously with other MD simulations of GPCRs [ 28 ]. The procedure permitted the construction of a final model of the BB1 receptor that was generated as the average structure obtained using the last 100 ns of the molecular dynamics trajectory.…”

“…A crude model of the human bombesin BB1 receptor was constructed by homology modeling using the rat neurotensin receptor NTS1 (PDB entry: 4GRV) as a template [ 41 ]. The template was selected for being one of the few receptors with a known crystallography structure located in the same branch of bombesin in the GPCRs phylogenetic tree [ 28 , 42 ]. Since the 4GRV structure corresponds to a fusion protein of NTS1 and the T4 Lysozyme, the template structure was edited by removing the coordinates of the latter and joining the segments of the ECL3 left at both sides.…”

“…Refinement of the receptor was carried out using molecular dynamics with a ligand bound in the orthosteric site. The presence of a ligand provides a more efficient refinement of the constructed model [ 28 ]. Accordingly, the antagonist PD176252 ( Figure 1 ) [ 17 ] was docked in different conformations into the orthosteric site of the crude model using the GLIDE software (version 6.7) [ 29 ].…”

Binding Mode Exploration of B1 Receptor Antagonists’ by the Use of Molecular Dynamics and Docking Simulation—How Different Target Engagement Can Determine Different Biological Effects

“…Our receptor/ligand recognition studies were based on a high-quality homology model of the B1 receptor generated with Iterative Threading ASSEmbly Refinement (I-TASSER), refined with the Maestro Macromodel and then energetically minimized by molecular dynamics (MD) simulations of the receptor in the membrane [ 21 ]. The MD calculation was evaluated monitoring the Root mean square deviation (RMSD) values, computed on backbone atoms and the total energy of the system ( Figure S2, Supplementary Materials ).…”

Molecular Features of Non-Selective Small Molecule Antagonists of the Bradykinin Receptors

“…Initial crude models of the receptors were constructed by threading the sequences of the B1 and B2 receptors onto the backbone of the template following the sequence alignment and subsequently validated using the Modeller 9 version 8 (9v8) software [48]. Next, models were refined using molecular dynamics simulations using a system consisting of each of the respective receptors embedded in a lipid bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids and water molecules, using GROMACS 4.6 package [49] as described elsewhere [50]. B1 and B2 small molecule pharmacophores were defined after docking studies of diverse non-peptide selective ligands to each of the two receptors [32,33].…”