Computational protocol: The low binding affinity of D-serine at the ionotropic glutamate receptor GluD2 can be attributed to the hinge region

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Protocol publication

[…] The Schrödinger Software Release 2013–2 (Schrödinger, LLC, New York, 2013) and the Protein Preparation Wizard 2013-2 (Epik version 2.4, Impact version 5.9, Prime version 3.2, Schrödinger, LLC, New York, 2013) were used to prepare protein structures for the MD simulations. All crystallographic waters were kept during the preprocessing step. Missing side chains were added, selenomethionine converted to methionine and buffer molecules deleted. The hydrogen bond assignment was done using default settings. The tleap program of the Amber 12 package (Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Götz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko Gusarov TS, Kovalenko A & Kollman PA (2012), AMBER 12, University of California, San Francisco) was used to create prmtop and prmcrd, topology and coordinate files of the proteins, respectively, with the ff99SB force field. The proteins were neutralised with counter ions. The tool ACPYPE was used to convert prmtop and prmcrd to GROMACS format, and GROMACS 5.0.2 was used for periodic box generation, solvation, equilibration and MD simulations (Abraham MJ, van der Spoel D, Lindahl E & Hess B (2014) The GROMACS development team, GROMACS User Manual Version 5.0.2). All protein structures were solvated in a truncated octahedron box with TIP3P water. Equilibration of the systems included minimisation of the solvent, gradual heating from 0 to 300 K in the NVT ensemble and 1 ns simulation at 300 K and 1.01325 bar in the NPT ensemble. Finally, production MD runs of 100 ns were carried out. The MD simulations were analysed with VMD 1.9.1. […]

Pipeline specifications

Software tools Protein Preparation Wizard, GROMACS, VMD
Applications Drug design, Protein structure analysis
Organisms Homo sapiens
Chemicals Glycine, Glutamic Acid