30 research outputs found
Can Activation and Desensitization Properties of iGluRs Be Predicted and Understood by Studying the LBD Dimer Dynamics?
Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors
The stability of
protein–protein interfaces can be essential
for protein function. For ionotropic glutamate receptors, a family
of ligand-gated ion channels vital for normal function of the central
nervous system, such an interface exists between the extracellular
ligand binding domains (LBDs). In the full-length protein, the LBDs
are arranged as a dimer of dimers. Agonist binding to the LBDs opens
the ion channel, and briefly after activation the receptor desensitizes.
Several residues at the LBD dimer interface are known to modulate
desensitization, and conformational changes around these residues
are believed to be involved in the state transition. The general hypothesis
is that the interface is disrupted upon desensitization, and structural
evidence suggests that the disruption might be substantial. However,
when cross-linking the central part of this interface, functional
data suggest that the receptor can still undergo desensitization,
contradicting the hypothesis of major interface disruption. Here,
we illustrate how opening the dimer interface using steered molecular
dynamics (SMD) simulations, and analyzing the work values required,
provides a quantitative measure for interface stability. For one subtype
of glutamate receptors, which is regulated by ion binding to the dimer
interface, we show that opening the interface without ions bound requires
less work than with ions present, suggesting that ion binding indeed
stabilizes the interface. Likewise, for interface mutants with longer-lived
active states, the interface is more stable, while the work required
to open the interface is reduced for less active mutants. Moreover,
a cross-linked mutant can still undergo initial interface opening
motions similar to the native receptor and at similar energetic cost.
Thus, our results support that interface opening is involved in desensitization.
Furthermore, they provide reconciliation of apparently opposing data
and demonstrate that SMD simulations can give relevant biological
insight into longer time scale processes without the need for expensive
calculations
Can Activation and Desensitization Properties of iGluRs Be Predicted and Understood by Studying the LBD Dimer Dynamics?
Regulatory Ions Bound at the iGluR Ligand Binding Domain Dimer Interface - A Shared Property of GluK2 and AvGluR1?
Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes
SummaryNeurotransmitter-gated ion channels adopt different gating modes to fine-tune signaling at central synapses. At glutamatergic synapses, high and low activity of AMPA receptors (AMPARs) is observed when pore-forming subunits coassemble with or without auxiliary subunits, respectively. Whether a common structural pathway accounts for these different gating modes is unclear. Here, we identify two structural motifs that determine the time course of AMPAR channel activation. A network of electrostatic interactions at the apex of the AMPAR ligand-binding domain (LBD) is essential for gating by pore-forming subunits, whereas a conserved motif on the lower, D2 lobe of the LBD prolongs channel activity when auxiliary subunits are present. Accordingly, channel activity is almost entirely abolished by elimination of the electrostatic network but restored via auxiliary protein interactions at the D2 lobe. In summary, we propose that activation of native AMPAR complexes is coordinated by distinct structural pathways, favored by the association/dissociation of auxiliary subunits
A dynamically interacting flexible loop assists oligomerisation of the Caenorhabditis elegans centriolar protein SAS-6
Abstract Centrioles are conserved organelles fundamental for the organisation of microtubules in animal cells. Oligomerisation of the spindle assembly abnormal protein 6 (SAS-6) is an essential step in the centriole assembly process and may act as trigger for the formation of these organelles. SAS-6 oligomerisation is driven by two independent interfaces, comprising an extended coiled coil and a dimeric N-terminal globular domain. However, how SAS-6 oligomerisation is controlled remains unclear. Here, we show that in the Caenorhabditis elegans SAS-6, a segment of the N-terminal globular domain, unresolved in crystallographic structures, comprises a flexible loop that assists SAS-6 oligomerisation. Atomistic molecular dynamics simulations and nuclear magnetic resonance experiments suggest that transient interactions of this loop across the N-terminal dimerisation interface stabilise the SAS-6 oligomer. We discuss the possibilities presented by such flexible SAS-6 segments for the control of centriole formation