Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors

Abstract

N-methyl-D-aspartate receptors (NMDARs)-i.e., transmembrane proteins expressed in neurons-play a central role in the molecular mechanisms of learning and memory formation. It is unclear how the known atomic structures of NMDARs determined by x-ray crystallography and electron cryomicroscopy (18 published Protein Data Bank entries) relate to the functional states of NMDARs inferred from electrophysiological recordings (multiple closed, open, preopen, etc. states). We address this problem by using molecular dynamics simulations at atomic resolution, a method successfully applied in the past to much smaller biomolecules. Our simulations predict that several conformations of NMDARs with experimentally determined geometries, including four "nonactive" electron cryomicroscopy structures, rapidly interconvert on submicrosecond timescales and therefore may correspond to the same functional state of the receptor (specifically, one of the closed states). This conclusion is not trivial because these conformational transitions involve changes in certain interatomic distances as large as tens of Å. The simulations also predict differences in the conformational dynamics of the apo and holo (i.e., agonist and coagonist bound) forms of the receptor on the microsecond timescale. To our knowledge, five new conformations of NMDARs, with geometries joining various features from different known experimental structures, are also predicted by the model. The main limitation of this work stems from its limited sampling (30 μs of aggregate length of molecular dynamics trajectories). Though this level significantly exceeds the sampling in previous simulations of parts of NMDARs, it is still much lower than the sampling recently achieved for smaller biomolecules (up to a few milliseconds), thus precluding, in particular, the observation of transitions between different functional states of NMDARs. Despite this limitation, such computational predictions may guide further experimental studies on the structure, dynamics, and function of NMDARs, for example by suggesting optimal locations of spectroscopic probes. Overall, atomic resolution simulations provide, to our knowledge, a novel perspective on the structure and dynamics of NMDARs, complementing information obtained by experimental methods.

Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling

“…A direct analysis of full-length NMDARs, with dozens of N-glycans on them, goes beyond the current abilities of the computational approach proposed in this paper, due to complexity of the NMDAR. Computer simulations may provide an insight into the structure and dynamics of N-glycans in full-length NMDARs in the future; as for now, the largest set of simulations of NMDARs has a significantly lower aggregate temporal sampling in comparison to the aggregate sampling of the GluN1 LBD reported here (Sinitskiy and Pande, 2018).…”

Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

“…This may provide an explanation for some of the clinical observations [ 2 ]. In future studies, simulation of the full-length receptor similar to those performed by Černý et al [ 30 ] and Sinitskiy and Pande [ 32 ], as well as experimental determination of the mutated S688Y receptor structure would also be welcome, as would other mutant NMDAR structures, to assist the study of the available ligand binding modes, and ultimately the design of agents that can modulate the activity of mutant receptors to aid personalized treatments.…”

“…However, dysfunction of the NMDAR has been associated with complex, multifactorial conditions such as schizophrenia [ 23 , 24 , 25 , 26 ] and Alzheimer’s disease [ 27 , 28 ]. There have been several studies conducted which utilize molecular dynamics simulations to study the function and effects of the NMDAR [ 29 , 30 , 31 , 32 , 33 ].…”