Computational protocol: The Role of Water in Activation Mechanism of Human N-Formyl Peptide Receptor 1 (FPR1) Based on Molecular Dynamics Simulations

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Protocol publication

[…] The homology models of FPR1 were obtained by Modeller 9v8 using the crystal structure of chemokine receptor type 4 (CXCR4, PDB id 3OE0) which shares the highest homology (31.0% identity, 53.8% similarity) with FPR1 according to Discovery Studio Visualizer . Since the region corresponding to helix H8 at cytoplasmic side of CXCR4 is unfolded in the crystal, the crystal structure of human β2-adrenergic receptor (PDB id 2RH1) was used as the second template for the H8 regions of FPR1. The sequence alignments (Figure S5 in ) were performed automatically in MUSCLE and adjusted manually in Discovery Studio Visualizer for proper aligning of conserved motifs and disulfide bridge. The 1500 models of initial FPR1 receptor were generated in Modeller with fully annealed protocol, and the optimal model was chosen according to DOPE (Discrete Optimized Protein Energy) score . Low homology regions of loops between transmembrane helices were constructed with loop refinement protocol in Modeller and the lowest DOPE score model from 1000 generated models was selected for further study. To obtain the proper orientation of the receptor in the membrane the refined model of FPR1 was aligned with CXCR4 crystal structure (PDB id 3OE0) taken from OPM (Orientations of Proteins in Membranes) database . The hydrogen atoms were added to the FPR1 structure according to the physiology pH environment. To remove unfavorable steric contacts and to release strain among amino acid residues the model was submitted to Prime (Schrödinger 2011 suite) for backbone-constrained truncated-Newton minimization refinement, using the OPLS_2005 force field and implicit membrane model. [...] To obtain the non-standard residues (-CHO and tBoc-) the force field parameters for MD simulation, the partial atomic charges for the ligands were obtained in GAUSSIAN 09 program via obtained Hartree-Fock 6–31G* electrostatic potential (ESP) and then using the fitting procedure performed by the R.E.D. tool . The membranous system was built and equilibrated as mentioned above. Nine 100 ns MD simulations with 1.0 kcal mol−1 Å−2 harmonic restraints on backbone of TM regions were conducted employing CHARMM36 full-atom force field . Three simulations for Apo-FPR1 as well as three simulations per each of its complexes with agonist fMLF and antagonist tBocMLF. Using harmonic restraints restricts sampling to the neighborhood of the initial model and prevents deterioration of the homology model which is a result of insufficient accuracy of current force fields . Data analysis was done using Desmond utilities and the molecular figures were made in VMD and Pymol . […]

Pipeline specifications

Software tools VMD, PyMOL
Application Protein structure analysis
Organisms Homo sapiens
Diseases Genetic Diseases, Inborn
Chemicals Hydrogen, Rhodopsin