In silico mutation of cysteine residues in the ligand-binding domain of an N-methyl-D-aspartate receptor.
Kaye SL., Sansom MSP., Biggin PC.
The precise nature of redox modulation of N-methyl-d-aspartate (NMDA) receptors is still unclear, although it is thought to be related to the formation and breaking of disulfide bonds. Recent structural data demonstrated the way in which disulfide bonds in the ligand-binding core of the NR1 subunit are arranged. However, the structures were not able to reconcile existing experimental data that examined the effects of mutating these cysteine residues. We have used molecular dynamics (MD) simulations of a series of in silico mutations to try and address this in terms of the current structure of the NR1 ligand-binding domain. A double mutation that removes the disulfide bridge between C744 and C798 gives rise to greater interlobe mobility which was predicted from the crystal structure information but, unexpectedly, also appears to predispose the receptor toward greater flexibility in the hinge region. Removal of the disulfide bond between C454 and C420 did not show any appreciable difference from the "wild-type" simulation, suggesting that removal of this would not change receptor properties, which is in agreement with experimental findings. Furthermore, the position of the C454 side chain could be characterized into discrete rotamers, which may reflect the observation of alternative density in the crystal structure for this residue. Simulations in which two of the disulfide bonds are removed via mutations to alanine (C420A and C436A) resulted in a tendency of the protein to adopt a partially closed conformation.