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Computational Neuroscience and Compartmental Modeling
Published in Bahman Zohuri, Patrick J. McDaniel, Electrical Brain Stimulation for the Treatment of Neurological Disorders, 2019
Bahman Zohuri, Patrick J. McDaniel
Note that, the N-methyl-D-aspartate receptor (also known as the NMDA receptor or NMDAR), is a glutamate receptor and ion channel protein found in nerve cells. The NMDA receptor is one of three types of ionotropic glutamate receptors, the others being the AMPA and kainate receptors. It is activated when glutamate and glycine (or D-serine) bind to it, and when activated it allows positively charged ions to flow through the cell membrane.99 The NMDA receptor is very important for controlling synaptic plasticity and memory function.100
Organic Chemicals
Published in William J. Rea, Kalpana D. Patel, Reversibility of Chronic Disease and Hypersensitivity, Volume 4, 2017
William J. Rea, Kalpana D. Patel
Calcium flux through the NMDA receptor and cell membrane is thought to be critical in synaptic plasticity, a cellular mechanism for learning and memory deficiency is observed in many cases of chemical sensitivity. The NMDA receptor is distinct in two ways: first, it is both ligand gated and voltage dependent; second, it requires coactivation by two ligands: glutamate and either d-serine or glycine22 transcripts and differential expression of the NR2 subunits.
Clinical Effects of Pollution
Published in William J. Rea, Kalpana D. Patel, Reversibility of Chronic Disease and Hypersensitivity, Volume 5, 2017
William J. Rea, Kalpana D. Patel
Known NMDA receptor agonists of the NMA receptors are (1) NMDA, (2) 3,5-dibromo-l-phenylalanine,136 and (3) GLYX-13. The NMDA receptors are modulated by a number of endogenous and exogenous compounds and play a key role in a wide range of physiological (e.g., memory) and pathological processes (e.g., excitotoxicity).
Three-stage multiscale modelling of the NMDA neuroreceptor
Published in Molecular Physics, 2021
Francesco Di Palma, Sauro Succi, Fabio Sterpone, Marco Lauricella, Franck Pérot, Simone Melchionna
Such achievements unquestionably push the frontiers of simulation further ahead and pave the way to disruptive progress in many areas of biology and medicine. In particular, the possibility of simulating large systems is key to neuroscience, where the response of neuroreceptors to binding with natural or synthetic ligands can reveal the allosteric transitions in the membrane protein and how the channel pore function, with the modulation of the ionic passage. NMDA receptors, in particular, play a critical role in brain development and function, including learning and memory formation [4,5]. Dysfunctional NMDA is involved in various neurological disorders, such as Alzheimer's disease, depression, stroke, epilepsy and schizophrenia. Therefore, the computational capability to tackle large-scale protein transitions and ion passage has major potential to study many neurological diseases and design new drugs through medicinal chemistry methods. Some initial studies have indeed tackled the study of NMDA by a brute force MD simulations that, while showing some degree of success, have also highlighted the difficulty of covering the complete times scale of the allosteric and functional response [3,6–8].
Physiological and pathophysiological implications of hydrogen sulfide: a persuasion to change the fate of the dangerous molecule
Published in Journal of the Chinese Advanced Materials Society, 2018
Jan Mohammad Mir, Ram Charitra Maurya
The interaction of H2S and NMDA receptors has the potential to affect other neuronal activities, such as epilepsy, neuropathic pain, stroke, and PDs. Prolonged activation of NMDA receptors causes calcium overload in cells and eventually leads to cell death. It has been reported that the blockade of NMDA receptors inhibits H2S-induced cell death in neurons.[126] H2S may promote excitation and regulate survival/death decisions of neurons. NMDA receptors have important roles in conditions such as stroke, neuropathic pain, epilepsy, and PD.[127]
Ethanol-induced conformational fluctuations of NMDA receptors
Published in Molecular Physics, 2019
Hamid R. Noori, Christian Mücksch, Herbert M. Urbassek
Alcohol intake induces a multi-scale spectrum of spatiotemporal effects, the underlying neurobiology and physiology of which are not yet completely understood. Among a variety of proteins as primary sites of action of ethanol in the central nervous system, the ionotropic glutamatergic N-methyl-d-aspartate (NMDA) receptor represents the most prominent target [1–4]. At concentrations of 5–50 mM that also produce intoxication, ethanol has been shown to inhibit the NMDA-activated ion current in a non-competitive manner [5–10] but also the NMDA-induced calcium influx, long-term potentiation and transmitter release [11–14]. The NMDA receptor is a ligand- and voltage-gated ion channel that is in general an assembly of GluN1, GluN2 (A–D) and GluN3 subunits forming heterodimers with the two-fold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD) and a transmembrane domain (TMD). The ion channel activates upon concurrent binding of glycine or d-serine and glutamate at the LBDs of GluN1 and GluN2 subunits, respectively [15] and relief of magnesium blockade of the channel pore by membrane depolarisation. A number of studies have focused on the identification of the molecular locus of alcohol action on NMDA receptors, particularly within the membrane-associated (M) domains of GluN1 and GluN2 subunits. Thereby, substitutions of phenylalanine (F637 and F639) at M3 of GluN1 subunit [16–18] as well as tyrosine T822, methionine M823 and alanine A825 of the GluN2 subunit [19,20] have been shown to influence the sensitivity of NMDA receptor to ethanol. Due to the high conservation level of the M-domains between GluN1 and GluN2 subunits, it is safe to assume that these sites correspond to ethanol sensitive amino acids in the other subunit. Despite the value of these investigations, their search strategies have been hypothesis-driven and site directed as a precise description of the complete structure of NMDA receptor including the M-domains was not available until recently [21,22]. Furthermore, the relationship between the ethanol interaction and the conformational dynamics of the receptor [23,24] is still missing.