Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe

doi:10.1074/jbc.m115.651877

Cited by 24 publications

(99 citation statements)

References 62 publications

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“…Collective motions between −0.25 and 0.25 were not considered significant (Fig. white) . For CheY, the middle and upper right areas show positively correlated motions between residues 80–89 and 101–110 (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Protein dynamics are intimately involved in enzyme activity and catalysis. Previous work has speculated that areas undergoing collective motions within proteins are likely distinct subdomains of functionally related residues . To identify these regions, with the notion that they may prove relevant to the phosphorylated state and protein function, we generated dynamical cross‐correlation maps (DCCM) for all five rec domains .…”

Section: Resultsmentioning

confidence: 99%

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Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two‐component signaling systems

Foster

West

2016

Proteins

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Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two‐component signaling systems

Foster

West

2016

Proteins

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“…The β‐subdomain, which remains largely invariant across the thermodynamic cycle, is denoted as ‘β’, and the most populated in/out topologies for the N3A motif in each state are shown. Figure (A–D) reproduced from reference , while figure (E–H) reproduced from reference .…”

Section: A Model For the Apo Human Hcn4 Structure And For The Camp‐dementioning

confidence: 92%

The structure of the apo cAMP‐binding domain of HCN4 – a stepping stone toward understanding the cAMP‐dependent modulation of the hyperpolarization‐activated cyclic‐nucleotide‐gated ion channels

2018

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The hyperpolarization-activated cyclic-nucleotide-gated (HCN) ion channels control nerve impulse transmission and cardiac pacemaker activity. The modulation by cAMP is critical for the regulatory function of HCN in both neurons and cardiomyocytes, but the underlying mechanism is not fully understood. Here, we show how the structure of the apo cAMPbinding domain of the HCN4 isoform has contributed to a model for the cAMP-dependent modulation of the HCN ion-channel. This model recapitulates the structural and dynamical changes that occur along the thermodynamic cycle arising from the coupling of cAMP-binding and HCN self-association equilibria. The proposed model addresses some of the questions previously open about the auto-inhibition of HCN and its cAMP-induced activation, while opening new opportunities for selectively targeting HCN through allosteric ligands. A remaining challenge is the investigation of HCN dimers and their regulatory role. Overcoming this challenge will require the integration of crystallography, cryo electron microscopy, NMR, electrophysiology and simulations.

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“…It is still not clear how the S672R mutation perturbs the apo-CBD, and in general the CBD dynamics, which has been recognized as a key determinant of the auto-inhibitory CBD function in HCN gating and in other cAMP-dependent systems (9,13,(21)(22)(23)(24)(25)(26)(27)(28)(29). One of the aspects of CBD dynamics that is most relevant for auto-inhibition is the equilibrium between inactive and active conformations (Fig.…”

mentioning

confidence: 99%

“…This is because the cAMP-driven lid closure is coupled to conformational changes in the N-terminal ␣-subdomain (N3A) (Fig. 1B), which controls the IR tetramerization by removing steric clashes between the C-linker and the rigid ␤-subdomain of the apo-CBD (8,9,12,13). In the absence of the steric clashes aris-ing from the apo-CBD, the C-linker forms a stable IR tetramer, and the tonic HCN auto-inhibition is removed (9).…”

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confidence: 99%

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

Boulton¹,

Akimoto

Akbarizadeh

et al. 2017

Journal of Biological Chemistry

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Edited by Norma AllewellThe hyperpolarization-activated and cyclic nucleotide-modulated ion channel (HCN) drives the pacemaker activity in the heart, and its malfunction can result in heart disorders. One such disorder, familial sinus bradycardia, is caused by the S672R mutation in HCN, whose electrophysiological phenotypes include a negative shift in the channel activation voltage and an accelerated HCN deactivation. The outcomes of these changes are abnormally low resting heart rates. However, the molecular mechanism underlying these electrophysiological changes is currently not fully understood. Crystallographic investigations indicate that the S672R mutation causes limited changes in the structure of the HCN intracellular gating tetramer, but its effects on protein dynamics are unknown. Here, we utilize comparative S672R versus WT NMR analyses to show that the S672R mutation results in extensive perturbations of the dynamics in both apo-and holo-forms of the HCN4 isoform, reflecting how S672R remodels the free energy landscape for the modulation of HCN4 by cAMP, i.e. the primary cyclic nucleotide modulator of HCN channels. We show that the S672R mutation results in a constitutive shift of the dynamic auto-inhibitory equilibrium toward inactive states of HCN4 and broadens the free-energy well of the apo-form, enhancing the millisecond to microsecond dynamics of the holo-form at sites critical for gating cAMP binding. These S672R-induced variations in dynamics provide a molecular basis for the electrophysiological phenotypes of this mutation and demonstrate that the pathogenic effects of the S672R mutation can be rationalized primarily in terms of modulations of protein dynamics.

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Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels

Cited by 24 publications

References 62 publications

Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two‐component signaling systems

Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two‐component signaling systems

The structure of the apo cAMP‐binding domain of HCN4 – a stepping stone toward understanding the cAMP‐dependent modulation of the hyperpolarization‐activated cyclic‐nucleotide‐gated ion channels

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

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