Structure-function studies on the voltage-gated sodium channel

Leveraging a meta-learning approach to advance the accuracy of Nav blocking peptides prediction

The voltage-gated sodium (Nav) channel is a crucial molecular component responsible for initiating and propagating action potentials. While the α subunit, forming the channel pore, plays a central role in this function, the complete physiological function of Nav channels relies on crucial interactions between the α subunit and auxiliary proteins, known as protein-protein interactions (PPI). Nav blocking peptides (NaBPs) have been recognized as a promising and alternative therapeutic agent for pain and itch. Although traditional experimental methods can precisely determine the effect and activity of NaBPs, they remain time-consuming and costly. Hence, machine learning (ML)-based methods that are capable of accurately contributing in silico prediction of NaBPs are highly desirable. In this study, we develop an innovative meta-learning-based NaBP prediction method (MetaNaBP). MetaNaBP generates new feature representations by employing a wide range of sequence-based feature descriptors that cover multiple perspectives, in combination with powerful ML algorithms. Then, these feature representations were optimized to identify informative features using a two-step feature selection method. Finally, the selected informative features were applied to develop the final meta-predictor. To the best of our knowledge, MetaNaBP is the first meta-predictor for NaBP prediction. Experimental results demonstrated that MetaNaBP achieved an accuracy of 0.948 and a Matthews correlation coefficient of 0.898 over the independent test dataset, which were 5.79% and 11.76% higher than the existing method. In addition, the discriminative power of our feature representations surpassed that of conventional feature descriptors over both the training and independent test datasets. We anticipate that MetaNaBP will be exploited for the large-scale prediction and analysis of NaBPs to narrow down the potential NaBPs.

The voltage-gated sodium channel Nav1.7 associated with endometrial cancer

Background: Endometrial cancer is the most common gynecologic malignancy in women in the developed countries. Despite recent progress in functional characterization of voltage-gated sodium channel (Na_v) in multiple cancers, very little was known about the expression of Na_v in human endometrial cancer. The present study sought to determine the role of Na_v and molecular nature of this channel in the endometrial cancer.

Methods: PCR approach was introduced to determine expression level of Na_v subunits in endometrial cancer specimens. Pharmacological agents were used to investigate Na_v function in endometrial cancer cells. Flow cytometry were used to test cancer apoptosis, and invasion assays were applied to test tumor metastasis.

Results: Transcriptional levels of the all Na_v α and β subunits were determined by real time-PCR in endometrial cancer with pair tissues of carcinoma and adjacent nonneoplastic tissue, Na_v1.7 was the most highly expressed Na_v subtype in endometrial cancer tissues. Na_v1.7 level was closely associated with tumor size, local lymph node metastasis, and 5-year and 10-year survival ratio. Inhibition of this channel by Na_v1.7 blocker PF-05089771, promoted cancer apoptosis and attenuated cancer cell invasion.

Conclusion: These results establish a relationship between voltage-gated sodium channel protein and endometrial cancer, and suggest that Na_v1.7 is a potential prognostic biomarker and could serve as a novel therapeutic target for endometrial cancer.

Neurobiology and therapeutic utility of neurotoxins targeting postsynaptic mechanisms of neuromuscular transmission

The neuromuscular junction (NMJ) is the principal site for the translation of motor neurochemical signals to muscle activity. Therefore, the release and sensing machinery of acetylcholine (ACh) along with muscle contraction are two of the main targets of natural toxins and pathogens, causing paralysis. Given pharmacology and medical advances, the active ingredients of toxins that target postsynaptic mechanisms have become of major interest, showing promise as drug leads. Herein, we review key facets of prevalent toxins modulating the mechanisms of ACh sensing and generation of the postsynaptic response, with muscle contraction. We consider the correlation between their outstanding selectivity and potency plus effects on motor function, and discuss emerging data advocating their usage for the development of therapies alleviating neuromuscular dysfunction.

Three-dimensional Modelling of the Voltage-gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites

Background:

The eukaryotic voltage-gated sodium channel(e-Nav) is a large asymmetric transmembrane protein with important functions concerning neurological function. No structure has been resolved at high resolution for this protein.

Methods:

A homology model of the transmembrane and extracellular regions of an Anopheles gambiae para-like channel with emphasis on the pore entrance has been constructed, based upon the templates provided by a prokaryotic sodium channel and a potassium two-pore channel. The latter provides a template for the extracellular regions, which are located above the entrance to the pore, which is likely to open at a side of a dome formed by these loops.

Results:

A model created with this arrangement shows a structure similar to low-resolution cryo-electron microscope images of a related structure. The pore entrance also shows favorable electrostatic interface.

Conclusion:

Residues responsible for the negative charge around the pore have been traced in phylogeny to highlight their importance. This model is intended for the study of pore-blocking toxins..

Diffusion coefficient in biomembrane critical pores

Diffusion is fundamental to the random movement of solutes in solution throughout biological systems. Theoretical studies of diffusing solutes across cell membranes confined in a microscopic size of pores have been an interesting subject in life and medical sciences. When a solute is confined in a critical area of membrane pores, which shows a quite different behavior compared to the homogeneous-bulk fluid whose transport is isotropic in all directions. This property has novel features, which are of considerable physiological interest.

In silico docking reveals possible Riluzole binding sites on Nav1.6 sodium channel: implications for amyotrophic lateral sclerosis therapy

Amyotrophic lateral sclerosis (ALS) is a common neurodegenerative disorder characterized mainly by a progressive loss of motor neurons. Glutamate excitotoxicity is likely the main cause of neuronal death, and Riluzole interferes with glutamate-mediated transmission. Thus, in such independent pathway, these effects may be partly due to inactivation of voltage-dependent sodium channels. Here we predict the structural model of the interaction and report the possible binding sites of Riluzole on Nav1.6 channel. The docked complexes were subjected to minimization and we further investigated the key interacting residues, binding free energies, pairing bridge determination, folding pattern, hydrogen bounding formation, hydrophobic contacts and flexibilities. Our results demonstrate that Riluzole interacts with the Nav1.6 channel, more specifically in the key residues TYR 1787, LEU 1843 and GLN 1799, suggesting possible cellular implications driven by these amino acids on Riluzole-Nav1.6 interaction, which may serve as an important output for a more specific and experimental drug design therapy against ALS.

Fluorescent saxitoxins for live cell imaging of single voltage-gated sodium ion channels beyond the optical diffraction limit

A desire to better understand the role of voltage-gated sodium channels (Na(V)s) in signal conduction and their dysregulation in specific disease states motivates the development of high precision tools for their study. Nature has evolved a collection of small molecule agents, including the shellfish poison (+)-saxitoxin, that bind to the extracellular pore of select Na(V) isoforms. As described in this report, de novo chemical synthesis has enabled the preparation of fluorescently labeled derivatives of (+)-saxitoxin, STX-Cy5, and STX-DCDHF, which display reversible binding to Na(V)s in live cells. Electrophysiology and confocal fluorescence microscopy studies confirm that these STX-based dyes function as potent and selective Na(V) labels. The utility of these probes is underscored in single-molecule and super-resolution imaging experiments, which reveal Na(V) distributions well beyond the optical diffraction limit in subcellular features such as neuritic spines and filopodia.

Pain disorders and erythromelalgia caused by voltage-gated sodium channel mutations

Voltage-gated sodium channels play a pivotal role in pain transmission. They are widely expressed in nociceptive neurons, and participate in the generation of action potentials. Alteration in ionic conduction of these channels causes abnormal electrical firing, thus renders neurons hyperexcitable. So far, mutations in the Na(v)1.7 sodium channel, which is expressed in the dorsal root ganglia cells and sympathetic neurons, have been described to cause perturbations in pain sensation. Until recently, gain-of-function Na(v)1.7 mutations were known to cause two neuropathic pain syndromes: inherited erythromelalgia and paroxysmal extreme pain syndrome. These syndromes are inherited in a dominant trait; they usually begin in childhood or infancy, and are characterized by attacks of severe neuropathic pain accompanied with autonomic symptoms. Recently, small fiber neuropathy and chronic nonparoxysmal pain have been described in patients harboring gain-of-function mutations in Na(v)1.7 channel. Loss-of-function mutations in Na(v)1.7 are extremely rare, and invariably cause congenital inability to perceive pain.

Techniques for recording reconstituted ion channels

This review describes and discusses techniques useful for monitoring the activity of protein ion channels in vitro. In the first section the biological importance and the classification of ion channels are outlined in order to justify the strong motivation for dealing with this important class of membrane proteins. The expression, reconstitution and integration of recombinant proteins into lipid bilayers are crucial steps to obtain consistent data when working with ion channels. In the second section recording techniques used in research are presented. Since this review focuses on analytical systems bearing reconstituted ion channels the industrial most important patch-clamp techniques of cells are only briefly mentioned. In section three, artificial systems developed in the last decades are described while the emerging technologies using nanostructured supports or microfluidic systems are presented in section four. Finally, the remaining challenges of membrane protein analysis and its potential applications are briefly outlined.