Voltage-Gated Sodium Channels

Ma, Kasimova; Granata, Daniele; Carnevale, Vincenzo

doi:10.1016/bs.ctm.2016.05.002

Cited by 21 publications

(8 citation statements)

References 95 publications

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“…Recent structural analysis, simulation/modeling, and experimental studies of both eukaryotic and prokaryotic Nav channels provide a rich background for interpretation of our data (see [9]), and for guided speculation about underlying molecular bases of our observations. Molecular simulations have been reviewed in a variety of functional and evolutionary issues [33,34,35,36,37,38]. Other discussions deal with modulation, and potential roles of tissue- or organ-specific Nav channel gating [39,40,41,42,43,44].…”

Section: Discussionmentioning

confidence: 99%

Extremely Potent Block of Bacterial Voltage-Gated Sodium Channels by µ-Conotoxin PIIIA

et al. 2019

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µ-Conotoxin PIIIA, in the sub-picomolar, range inhibits the archetypal bacterial sodium channel NaChBac (NavBh) in a voltage- and use-dependent manner. Peptide µ-conotoxins were first recognized as potent components of the venoms of fish-hunting cone snails that selectively inhibit voltage-gated skeletal muscle sodium channels, thus preventing muscle contraction. Intriguingly, computer simulations predicted that PIIIA binds to prokaryotic channel NavAb with much higher affinity than to fish (and other vertebrates) skeletal muscle sodium channel (Nav 1.4). Here, using whole-cell voltage clamp, we demonstrate that PIIIA inhibits NavBac mediated currents even more potently than predicted. From concentration-response data, with [PIIIA] varying more than 6 orders of magnitude (10−12 to 10−5 M), we estimated an IC50 = ~5 pM, maximal block of 0.95 and a Hill coefficient of 0.81 for the inhibition of peak currents. Inhibition was stronger at depolarized holding potentials and was modulated by the frequency and duration of the stimulation pulses. An important feature of the PIIIA action was acceleration of macroscopic inactivation. Docking of PIIIA in a NaChBac (NavBh) model revealed two interconvertible binding modes. In one mode, PIIIA sterically and electrostatically blocks the permeation pathway. In a second mode, apparent stabilization of the inactivated state was achieved by PIIIA binding between P2 helices and trans-membrane S5s from adjacent channel subunits, partially occluding the outer pore. Together, our experimental and computational results suggest that, besides blocking the channel-mediated currents by directly occluding the conducting pathway, PIIIA may also change the relative populations of conducting (activated) and non-conducting (inactivated) states.

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Section: Discussionmentioning

confidence: 99%

Extremely Potent Block of Bacterial Voltage-Gated Sodium Channels by µ-Conotoxin PIIIA

et al. 2019

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“…With reference to PIPC1 and PIPC2, such a rearrangement of M953 abolished interaction with the fluorophenyl in PIPC1 or the phenyl moiety in PIPC2. In other TRP channels, like TRPV1, an asparagine residue (N676) was shown to rotate toward the pore or to point far away from it (38, 39) as a consequence of the rearrangement in the conserved π-bulge. When N676 faced the lumen in the TM pore (open, conductive state), the channel became fully hydrated.…”

Section: Resultsmentioning

confidence: 99%

“…6 B and D ). Accordingly, N954, a conserved asparagine residue, known in other TRPs to be responsible for pore hydration (38, 39) in conductive channels, faces the pore lumen only in the open TRPA1 state. It is noteworthy that M953 stabilizes the most potent PIPCs by interacting with the fluorophenyl group, a moiety critical for potency.…”

Section: Discussionmentioning

confidence: 99%

TRPA1 modulation by piperidine carboxamides suggests an evolutionarily conserved binding site and gating mechanism

Chernov-Rogan¹,

Gianti

Liu³

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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The transient receptor potential ankyrin 1 (TRPA1) channel functions as an irritant sensor and is a therapeutic target for treating pain, itch, and respiratory diseases. As a ligand-gated channel, TRPA1 can be activated by electrophilic compounds such as allyl isothiocyanate (AITC) through covalent modification or activated by noncovalent agonists through ligand binding. However, how covalent modification leads to channel opening and, importantly, how noncovalent binding activates TRPA1 are not well-understood. Here we report a class of piperidine carboxamides (PIPCs) as potent, noncovalent agonists of human TRPA1. Based on their species-specific effects on human and rat channels, we identified residues critical for channel activation; we then generated binding modes for TRPA1–PIPC interactions using structural modeling, molecular docking, and mutational analysis. We show that PIPCs bind to a hydrophobic site located at the interface of the pore helix 1 (PH1) and S5 and S6 transmembrane segments. Interestingly, this binding site overlaps with that of known allosteric modulators, such as A-967079 and propofol. Similar binding sites, involving π-helix rearrangements on S6, have been recently reported for other TRP channels, suggesting an evolutionarily conserved mechanism. Finally, we show that for PIPC analogs, predictions from computational modeling are consistent with experimental structure–activity studies, thereby suggesting strategies for rational drug design.

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“…For constructing the MSA for adenylate kinase we use the same approach described in [43]. Finally, the three ion-channel MSAs were the same produced and analyzed in [72].…”

Section: The Datasetmentioning

confidence: 99%

“…We analyzed the MSAs for the three families based on a pool of ∼ 800 sequences, each with 200 positions [72] from which we omitted the highly gapped regions of the alignments (typically occurring in loops between the six trans-membrane helices). Although the dataset that we used is the most comprehensive available at the moment, its size is clearly limited by comparison to the much better populated cases discussed in the previous sections, showing a pretty low ∆C (see Fig.…”

Section: Correlation With Dynamical Domainsmentioning

confidence: 99%

From Sequence to Function: Coevolving Amino Acids Encode Structural and Functional Domains

Granata¹,

Ponzoni

Micheletti

et al. 2017

Preprint

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Amino acids interactions within protein families are so optimized that the sole analysis of evolutionary co-mutations can identify pairs of contacting residues. It is also known that evolution conserves functional dynamics, i.e., the concerted motion or displacement of large protein regions or domains. Is it, therefore, possible to use a pure sequence-based analysis to identify these dynamical domains? To address this question, we introduce here a general co-evolutionary coupling analysis strategy and apply it to a curated sequence database of hundreds of protein families. For most families, the sequence-based method partitions amino acids into few clusters. When viewed in the context of the native structure, these clusters have the signature characteristics of viable protein domains: they are spatially separated but individually compact. They have a direct functional bearings too, as shown for various reference cases. We conclude that even large-scale structural and functionally-related properties can be recovered from inference methods applied to evolutionaryrelated sequences. The method introduced here is available as a software package and web server (http://spectrus.sissa.it/spectrus-evo_webserver).

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Voltage-Gated Sodium Channels

Cited by 21 publications

References 95 publications

Extremely Potent Block of Bacterial Voltage-Gated Sodium Channels by µ-Conotoxin PIIIA

Extremely Potent Block of Bacterial Voltage-Gated Sodium Channels by µ-Conotoxin PIIIA

TRPA1 modulation by piperidine carboxamides suggests an evolutionarily conserved binding site and gating mechanism

From Sequence to Function: Coevolving Amino Acids Encode Structural and Functional Domains

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