Protocol of computational modeling of Aβ₄₂ and α_2AAR

Dr. Sixue Zhang, Chemistry Department, Drug Discovery Division, Southern Research, USA

Use Schrödinger Small Molecule Drug Discovery Suite (Schrödinger LLC, New York, NY) for homology model building as well as docking of Aβ₄₂ and α_2AAR.

Building homology model of α_2AAR

Download the sequence of human α_2AAR from UniProt database (https://www.uniprot.org/) with UniProt ID P08913.

Download the crystal structure of human adrenergic receptor β₂ from PDB database (https://www.rcsb.org/) with PDB ID 3PDS.

Use Schrödinger Maestro to delete irrelevant parts in the β₂AR crystal structure and only retain residue 29 to 342.

Follow the default Schrödinger homology model building procedures, use α_2AAR sequence as the inquiry sequence and β₂AR residue 29 to 342 as the template to build the human α_2AAR homology model.

Building homology model of Aβ₄₂ pentamer

Download the NMR structure of Aβ₄₂ from PDB database with PDB ID 1Z0Q.

Choose the first NMR entry as the 3D structure of Aβ₄₂ for subsequent procedures

Use Schrödinger Protein Preparation Wizard to prepare the raw structure, minimize hydrogen atoms only

Use the dimer option in Schrödinger PIPER module to dock two prepared Aβ₄₂ monomers to make a dimer. Criterion for choosing the best dimer conformation: residues 39 to 42 from each monomer must be in contact with each other.

Use the trimer option in Schrödinger PIPER module to dock three prepared Aβ₄₂ monomers to make a trimer. Criterion for choosing the best trimer conformation: residues 39 to 42 from each monomer must be in contact with each other.

Use the receptor/ligand option in Schrödinger PIPER module to dock the previously generated dimer (as the ligand) to the trimer (as the receptor) to make the pentamer, use the characters of Aβ₄₂ pentamer described in the literature (Tran, L.; et. al. Sci. Rep. 2016, 6: 21429) as guidelines to choose the best generated pentamer conformation. Namely, residues 39 to 42 from each monomer form a hydrophobic core, overall shape is disc-like, and the angles between each of the five arms are relatively even.

Docking Aβ₄₂ onto α_2AAR

Use the receptor/ligand option in Schrödinger PIPER module to dock previously generated Aβ₄₂ pentamer (as the ligand) to α_2AAR homology model (as the receptor). Choose type “repulsion” as the constraint for the residues of α_2AAR in the transmembrane region and intracellular region to ensure Aβ₄₂ pentamer is only docked to the extracellular region of α_2AAR. Criterion for choosing the best docked complex conformation: no part of Aβ₄₂ pentamer intrudes into the transmembrane region.

Use Schrödinger Prime to perform a geometry optimization on the residues within the contact region between Aβ₄₂ and α_2AAR to eliminate any atom clash.

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