scholarly journals A pharmacological master key mechanism that unlocks the selectivity filter gate in K+channels

Science ◽  
2019 ◽  
Vol 363 (6429) ◽  
pp. 875-880 ◽  
Author(s):  
Marcus Schewe ◽  
Han Sun ◽  
Ümit Mert ◽  
Alexandra Mackenzie ◽  
Ashley C. W. Pike ◽  
...  
Keyword(s):  
Selectivity Filter ◽  
Rational Drug Design ◽  
Related Gene ◽  
K Channels ◽  
X Ray ◽  
Voltage Gated ◽  
X Ray Crystallography ◽  
Rational Drug ◽  
Dynamics Simulations ◽  
Pore Domain

Potassium (K+) channels have been evolutionarily tuned for activation by diverse biological stimuli, and pharmacological activation is thought to target these specific gating mechanisms. Here we report a class of negatively charged activators (NCAs) that bypass the specific mechanisms but act as master keys to open K+channels gated at their selectivity filter (SF), including many two-pore domain K+(K2P) channels, voltage-gated hERG (human ether-à-go-go–related gene) channels and calcium (Ca2+)–activated big-conductance potassium (BK)–type channels. Functional analysis, x-ray crystallography, and molecular dynamics simulations revealed that the NCAs bind to similar sites below the SF, increase pore and SF K+occupancy, and open the filter gate. These results uncover an unrecognized polypharmacology among K+channel activators and highlight a filter gating machinery that is conserved across different families of K+channels with implications for rational drug design.

REFINEMENT OF NMR-DETERMINED PROTEIN STRUCTURES WITH DATABASE DERIVED DISTANCE CONSTRAINTS

2005 ◽  
Vol 03 (06) ◽  
pp. 1315-1329 ◽  
Author(s):  
FENG CUI ◽  
ROBERT JERNIGAN ◽  
ZHIJUN WU
Keyword(s):  
Protein Structures ◽  
Rational Drug Design ◽  
Resonance Spectroscopy ◽  
Distance Constraints ◽  
X Ray ◽  
X Ray Crystallography ◽  
Nmr Structures ◽  
High Quality Protein ◽  
Rational Drug ◽  
Distance Data

The protein structures determined by NMR (Nuclear Magnetic Resonance Spectroscopy) are not as detailed and accurate as those by X-ray crystallography and are often underdetermined due to the inadequate distance data available from NMR experiments. The uses of NMR-determined structures in such important applications as homology modeling and rational drug design have thus been severely limited. Here we show that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures. We show through a survey on 462 NMR structures that, in fact, many inter-atomic distances in these structures deviate considerably from their database distributions and based on the refinement results on 10 selected NMR structures that these structures can actually be improved significantly when a selected set of distances are constrained within their high probability ranges in their database distributions.

scholarly journals Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel

2021 ◽  
Vol 153 (9) ◽  
Author(s):  
Jing Li ◽  
Rong Shen ◽  
Ahmed Rohaim ◽  
Ramon Mendoza Uriarte ◽  
Mikolai Fajer ◽  
...  
Keyword(s):  
Potassium Channel ◽  
Computational Study ◽  
Homology Model ◽  
Selectivity Filter ◽  
K Channels ◽  
Activation Gate ◽  
Voltage Dependent ◽  
Signature Sequence ◽  
Dynamics Simulations ◽  
Pore Domain

C-type inactivation is a time-dependent process of great physiological significance that is observed in a large class of K+ channels. Experimental and computational studies of the pH-activated KcsA channel show that the functional C-type inactivated state, for this channel, is associated with a structural constriction of the selectivity filter at the level of the central glycine residue in the signature sequence, TTV(G)YGD. The structural constriction is allosterically promoted by the wide opening of the intracellular activation gate. However, whether this is a universal mechanism for C-type inactivation has not been established with certainty because similar constricted structures have not been observed for other K+ channels. Seeking to ascertain the general plausibility of the constricted filter conformation, molecular dynamics simulations of a homology model of the pore domain of the voltage-gated potassium channel Shaker were performed. Simulations performed with an open intracellular gate spontaneously resulted in a stable constricted-like filter conformation, providing a plausible nonconductive state responsible for C-type inactivation in the Shaker channel. While there are broad similarities with the constricted structure of KcsA, the hypothetical constricted-like conformation of Shaker also displays some subtle differences. Interestingly, those are recapitulated by the Shaker-like E71V KcsA mutant, suggesting that the residue at this position along the pore helix plays a pivotal role in determining the C-type inactivation behavior. Free energy landscape calculations show that the conductive-to-constricted transition in Shaker is allosterically controlled by the degree of opening of the intracellular activation gate, as observed with the KcsA channel. The behavior of the classic inactivating W434F Shaker mutant is also characterized from a 10-μs MD simulation, revealing that the selectivity filter spontaneously adopts a nonconductive conformation that is constricted at the level of the second glycine in the signature sequence, TTVGY(G)D.

Comparisons of voltage-gated sodium channel structures with open and closed gates and implications for state-dependent drug design

2018 ◽  
Vol 46 (6) ◽  
pp. 1567-1575 ◽  
Author(s):  
Giulia Montini ◽  
Jennifer Booker ◽  
Altin Sula ◽  
B.A. Wallace
Keyword(s):  
Drug Design ◽  
Sodium Channels ◽  
Rational Drug Design ◽  
Voltage Gated ◽  
Voltage Gated Sodium Channels ◽  
State Dependent ◽  
Rational Drug ◽  
Sequence Homologies ◽  
Arcobacter Butzleri ◽  
Functional Consequences

Voltage-gated sodium channels (Navs) are responsible for the initiation of the action potential in excitable cells. Several prokaryotic sodium channels, most notably NavMs from Magnetococcus marinus and NavAb from Arcobacter butzleri, have been shown to be good models for human sodium channels based on their sequence homologies and high levels of functional similarities, including ion flux, and functional consequences of critical mutations. The complete full-length crystal structures of these prokaryotic sodium channels captured in different functional states have now revealed the molecular natures of changes associated with the gating process. These include the structures of the intracellular gate, the selectivity filter, the voltage sensors, the intra-membrane fenestrations, and the transmembrane (TM) pore. Here we have identified for the first time how changes in the fenestrations in the hydrophobic TM region associated with the opening of the intracellular gate could modulate the state-dependent ingress and binding of drugs in the TM cavity, in a way that could be exploited for rational drug design.

Uterine Excitability and Ion Channels and Their Changes with Gestation and Hormonal Environment

2020 ◽  
Vol 83 (1) ◽  
Author(s):  
Susan Wray ◽  
Sarah Arrowsmith
Keyword(s):  
Ion Channels ◽  
Inward Rectifier ◽  
Cation Channels ◽  
Annual Review ◽  
Publication Date ◽  
K Channels ◽  
Voltage Gated ◽  
New Findings ◽  
Voltage Dependent ◽  
Pore Domain

We address advances in the understanding of myometrial physiology, focusing on excitation and the effects of gestation on ion channels and their relevance to labor. This review moves through pioneering studies to exciting new findings. We begin with the myometrium and its myocytes and describe how excitation might initiate and spread in this myogenic smooth muscle. We then review each of the ion channels in the myometrium: L- and T-type Ca2+ channels, KATP (Kir6) channels, voltage-dependent K channels (Kv4, Kv7, and Kv11), twin-pore domain K channels (TASK, TREK), inward rectifier Kir7.1, Ca2+-activated K+ channels with large (KCNMA1, Slo1), small (KCNN1–3), and intermediate (KCNN4) conductance, Na-activated K channels (Slo2), voltage-gated (SCN) Na+ and Na+ leak channels, nonselective (NALCN) channels, the Na K-ATPase, and hyperpolarization-activated cation channels. We finish by assessing how three key hormones— oxytocin, estrogen, and progesterone—modulate and integrate excitability throughout gestation. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Mutations reveal voltage gating of CNGA1 channels in saturating cGMP

2009 ◽  
Vol 134 (2) ◽  
pp. 151-164 ◽  
Author(s):  
Juan Ramón Martínez-François ◽  
Yanping Xu ◽  
Zhe Lu
Keyword(s):  
Ion Selectivity ◽  
Selectivity Filter ◽  
Open Probability ◽  
K Channels ◽  
Voltage Gated ◽  
Open Conformation ◽  
Voltage Dependent ◽  
Pore Opening ◽  
Low Probability ◽  
Inherent Voltage

Activity of cyclic nucleotide–gated (CNG) cation channels underlies signal transduction in vertebrate visual receptors. These highly specialized receptor channels open when they bind cyclic GMP (cGMP). Here, we find that certain mutations restricted to the region around the ion selectivity filter render the channels essentially fully voltage gated, in such a manner that the channels remain mostly closed at physiological voltages, even in the presence of saturating concentrations of cGMP. This voltage-dependent gating resembles the selectivity filter-based mechanism seen in KcsA K+ channels, not the S4-based mechanism of voltage-gated K+ channels. Mutations that render CNG channels gated by voltage loosen the attachment of the selectivity filter to its surrounding structure, thereby shifting the channel's gating equilibrium toward closed conformations. Significant pore opening in mutant channels occurs only when positive voltages drive the pore from a low-probability open conformation toward a second open conformation to increase the channels' open probability. Thus, the structure surrounding the selectivity filter has evolved to (nearly completely) suppress the expression of inherent voltage-dependent gating of CNGA1, ensuring that the binding of cGMP by itself suffices to open the channels at physiological voltages.

scholarly journals Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations

Biochemistry ◽  
2016 ◽  
Vol 55 (26) ◽  
pp. 3692-3701 ◽  
Author(s):  
Boon Chong Goh ◽  
Huixing Wu ◽  
Michael J. Rynkiewicz ◽  
Klaus Schulten ◽  
Barbara A. Seaton ◽  
...  
Keyword(s):  
Binding Sites ◽  
Lung Surfactant ◽  
Protein A ◽  
Surfactant Protein ◽  
Lipid Binding ◽  
Surfactant Protein A ◽  
X Ray ◽  
X Ray Crystallography ◽  
Lung Surfactant Protein ◽  
Dynamics Simulations

scholarly journals Mechanism of activation at the selectivity filter of the KcsA K+ channel

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Florian T Heer ◽  
David J Posson ◽  
Wojciech Wojtas-Niziurski ◽  
Crina M Nimigean ◽  
Simon Bernèche
Keyword(s):  
Conformational Changes ◽  
Selectivity Filter ◽  
K Channel ◽  
Ion Permeation ◽  
K Channels ◽  
Narrow Region ◽  
Gating Mechanism ◽  
Structural Fluctuations ◽  
Extracellular Side ◽  
Dynamics Simulations

Potassium channels are opened by ligands and/or membrane potential. In voltage-gated K+ channels and the prokaryotic KcsA channel, conduction is believed to result from opening of an intracellular constriction that prevents ion entry into the pore. On the other hand, numerous ligand-gated K+ channels lack such gate, suggesting that they may be activated by a change within the selectivity filter, a narrow region at the extracellular side of the pore. Using molecular dynamics simulations and electrophysiology measurements, we show that ligand-induced conformational changes in the KcsA channel removes steric restraints at the selectivity filter, thus resulting in structural fluctuations, reduced K+ affinity, and increased ion permeation. Such activation of the selectivity filter may be a universal gating mechanism within K+ channels. The occlusion of the pore at the level of the intracellular gate appears to be secondary.

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