Conformational spread and dynamics in allostery of NMDA receptors

Durham, Ryan J.; Paudyal, Nabina; Carrillo, Elisa; Bhatia, Nidhi Kaur; MacLean, David M.; Berka, Vladimír; Dolino, Drew M.; Gorfe, Alemayehu A.; Jayaraman, Vasanthi

doi:10.1073/pnas.1910950117

Cited by 34 publications

(39 citation statements)

References 55 publications

(68 reference statements)

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“…This coupling is mediated in a large part by a GluN2 LBD surface loop (Fig. 5D; Regalado et al 2001;Durham et al 2020), which protrudes at the interface between the two constitutive GluN1-GluN2 LBD heterodimers (Karakas & Furukawa, 2014;Lee et al 2014). Comprising 30-40 residues, this loop contains several β-sheets tightly maintained by a pool of highly conserved cysteine residues engaged into disulfide bonds.…”

Section: Figure 5 Domain Evolution Shapes Nmdar Propertiesmentioning

confidence: 99%

Architecture and function of NMDA receptors: an evolutionary perspective

Stroebel

Paoletti

2020

The Journal of Physiology

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Ionotropic glutamate receptors (iGluRs) are a major class of ligand‐gated ion channels that are widespread in the living kingdom. Their critical role in excitatory neurotransmission and brain function of arthropods and vertebrates has made them a compelling subject of interest for neurophysiologists and pharmacologists. This is particularly true for NMDA receptor (NMDARs), a subclass of iGluRs that act as central drivers of synaptic plasticity in the CNS. How and when the unique properties of NMDARs arose during evolution, and how they relate to the evolution of the nervous system, remain open questions. Recent years have witnessed a boom in both genomic and structural data, such that it is now possible to analyse the evolution of iGluR genes on an unprecedented scale and within a solid molecular framework. In this review, combining insights from phylogeny, atomic structure and physiological and mechanistic data, we discuss how evolution of NMDAR motifs and sequences shaped their architecture and functionalities. We trace differences and commonalities between NMDARs and other iGluRs, emphasizing a few distinctive properties of the former regarding ligand binding and gating, permeation, allosteric modulation and intracellular signalling. Finally, we speculate on how specific molecular properties of iGuRs arose to supply new functions to the evolving structure of the nervous system, from early metazoan to present mammals.

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Section: Figure 5 Domain Evolution Shapes Nmdar Propertiesmentioning

confidence: 99%

Architecture and function of NMDA receptors: an evolutionary perspective

Stroebel

Paoletti

2020

The Journal of Physiology

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“…Transfections were performed the day before the smFRET experiment using JetPRIME transfection reagent (polyplus). On the day of experiment, i.e., 24 h post-transfection, the cells were labeled with donor and acceptor fluorophore and the sample was prepared as described previously ( Dolino et al, 2017 ; Litwin et al, 2019 ; Durham et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…For smFRET slide preparation, we used the same protocol as described previously ( Durham et al, 2020 ). To selectively pull down the NMDA receptors onto the slide, we used biotinylated anti-mouse antibody bound to the streptavidin-coated slide followed by anti-NMDAR1 antibody (ab64572, Abcam).…”

Section: Methodsmentioning

confidence: 99%

A de novo GRIN1 Variant Associated With Myoclonus and Developmental Delay: From Molecular Mechanism to Rescue Pharmacology

et al. 2021

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N-Methyl-D-aspartate receptors (NMDARs) are highly expressed in brain and play important roles in neurodevelopment and various neuropathologic conditions. Here, we describe a new phenotype in an individual associated with a novel de novo deleterious variant in GRIN1 (c.1595C>A, p.Pro532His). The clinical phenotype is characterized with developmental encephalopathy, striking stimulus-sensitive myoclonus, and frontal lobe and frontal white matter hypoplasia, with no apparent seizures detected. NMDARs that contained the P532H within the glycine-binding domain of GluN1 with either the GluN2A or GluN2B subunits were evaluated for changes in their pharmacological and biophysical properties, which surprisingly revealed only modest changes in glycine potency but a significant decrease in glutamate potency, an increase in sensitivity to endogenous zinc inhibition, a decrease in response to maximally effective concentrations of agonists, a shortened synaptic-like response time course, a decreased channel open probability, and a reduced receptor cell surface expression. Molecule dynamics simulations suggested that the variant can lead to additional interactions across the dimer interface in the agonist-binding domains, resulting in a more open GluN2 agonist-binding domain cleft, which was also confirmed by single-molecule fluorescence resonance energy transfer measurements. Based on the functional deficits identified, several positive modulators were evaluated to explore potential rescue pharmacology.

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“…Experimental methods concerning smFRET slide preparation, data collection, and data analysis are as previously described (Durham et al, 2020). In brief, glass coverslips were used to immobilize sample molecules for smFRET measurements.…”

Section: Slide Preparationmentioning

confidence: 99%

“…Spectroscopic approaches are powerful tools for monitoring protein conformational dynamics that are not captured in static structures (Elvington and Maduke, 2008;McHaourab et al, 2011;Sekhar and Kay, 2019;Sahu and Lorigan, 2020). Single-molecule Förster resonance energy transfer (smFRET) has emerged as an important player in the spectroscopic toolbox, as a method that can monitor conformational transitions in real time (Zhao et al, 2010;Landes et al, 2011;Akyuz et al, 2015;Dolino et al, 2015;Vafabakhsh et al, 2015;Juette et al, 2016;Dyla et al, 2017;Han et al, 2017;Lerner et al, 2018;Ren et al, 2018;Wang et al, 2018;de Boer et al, 2019;MacLean et al, 2019;Mazal and Haran, 2019;Zhu et al, 2019;Carrillo et al, 2020;Durham et al, 2020). In addition, the single-molecule approach confers flexibility in labeling strategies, allowing labeling at multiple sites without concerns of sample heterogeneity, which can thwart ensemble-spectroscopic measurements.…”

Section: Introductionmentioning

confidence: 99%

Single-molecule FRET monitors CLC transporter conformation and subunit independence

Cheng

Krishnamoorti

Berka

et al. 2020

Preprint

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CLC transporters catalyze the exchange of chloride ions for protons across cellular membranes. As secondary active transporters, CLCs must alternately allow ion permeation to the extracellular and intracellular sides of the membrane, adopting outward-facing and inward-facing conformational states. Here, we use single-molecule Forster resonance energy transfer (smFRET) to monitor the conformational state of CLC-ec1, an E. coli homolog for which high-resolution structures of occluded and outward-facing states are known. Since each subunit within the CLC homodimer contains its own transport pathways for chloride and protons, we developed a labeling strategy to follow conformational change within a subunit, without crosstalk from the second subunit of the dimer. Using this strategy, we evaluated smFRET efficiencies for labels positioned on the extracellular side of the protein, to monitor the status of the outer permeation pathway. When [H+] is increased to enrich the outward-facing state, the smFRET efficiencies for this pair decrease. In a triple-mutant CLC-ec1 that mimics the protonated state of the protein and is known to favor the outward-facing conformation, the lower smFRET efficiency is observed at both low and high [H+]. These results confirm that the smFRET assay is following the transition to the outward-facing state and demonstrate the feasibility of using smFRET to monitor the relatively small (~1 Angstrom) motions involved in CLC transporter conformational change. Using the smFRET assay, we show that the conformation of the partner subunit does not influence the conformation of the subunit being monitored by smFRET, thus providing evidence for the independence of the two subunits in the transport process.

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Conformational spread and dynamics in allostery of NMDA receptors

Cited by 34 publications

References 55 publications

Architecture and function of NMDA receptors: an evolutionary perspective

Architecture and function of NMDA receptors: an evolutionary perspective

A de novo GRIN1 Variant Associated With Myoclonus and Developmental Delay: From Molecular Mechanism to Rescue Pharmacology

Single-molecule FRET monitors CLC transporter conformation and subunit independence

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