scholarly journals Naked mole-rat acid-sensing ion channel 3 forms nonfunctional homomers, but functional heteromers

2017 ◽  
Author(s):  
Laura-Nadine Schuhmacher ◽  
Gerard Callejo ◽  
Shyam Srivats ◽  
Ewan St. John Smith
Keyword(s):  
Carbon Dioxide ◽  
Ion Channels ◽  
Ion Channel ◽  
Drg Neurons ◽  
Whole Cell Patch Clamp ◽  
Mole Rat ◽  
Wide Range ◽  
Naked Mole Rat ◽  
Patch Clamp Electrophysiology ◽  
Carbon Dioxide Levels

ABSTRACTAcid-sensing ion channels (ASICs) form both homotrimeric and heterotrimeric ion channels that are activated by extracellular protons and are involved in a wide range of physiological and pathophysiological processes, including pain and anxiety. ASIC proteins can form both homotrimeric and heterotrimeric ion channels. The ASIC3 subunit has been shown to be of particular importance in the peripheral nervous system with pharmacological and genetic manipulations demonstrating a role in pain. Naked mole-rats, despite having functional ASICs, are insensitive to acid as a noxious stimulus and show diminished avoidance of acidic fumes, ammonia and carbon dioxide. Here we cloned naked mole-rat ASIC3 (nmrASIC3) and used a cell surface biotinylation assay to demonstrate that it traffics to the plasma membrane, but using whole-cell patch-clamp electrophysiology we observed that nmrASIC3 is insensitive to both protons and the non-proton ASIC3 agonist 2-Guanidine-4-methylquinazoline (GMQ). However, in line with previous reports of ASIC3 mRNA expression in dorsal root ganglia (DRG) neurons, we found that the ASIC3 antagonist APETx2 reversibly inhibits ASIC-like currents in naked mole-rat DRG neurons. We further show that like the proton-insensitive ASIC2b and ASIC4, nmrASIC3 forms functional, proton sensitive heteromers with other ASIC subunits. An amino acid alignment of ASIC3s between 9 relevant rodent species and human identified unique sequence differences that might underlie the proton insensitivity of nmrASIC3. However, introducing nmrASIC3 differences into rat ASIC3 (rASIC3) produced only minor differences in channel function, and replacing nmrASIC3 sequence with that of rASIC3 did not produce a proton-sensitive ion channel. Our observation that nmrASIC3 forms nonfunctional homomers may reflect a further adaptation of the naked mole-rat to living in an environment with high-carbon dioxide levels.

scholarly journals Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

2020 ◽  
Vol 55 (S3) ◽  
pp. 14-45
Keyword(s):  
Artificial Intelligence ◽  
Molecular Dynamics ◽  
Ion Channels ◽  
Ion Channel ◽  
Computational Methods ◽  
Homology Modelling ◽  
Channel Structure ◽  
Learning Approaches ◽  
Qsar Analysis ◽  
Wide Range

Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods have evolved into important and invaluable approaches for studying ion channels and their functions. This is mainly due to their demanding mechanism of action where a static picture of an ion channel structure is often insufficient to fully understand the underlying mechanism. Therefore, the use of computational methods is as important as chemical-biological based experimental methods for a better understanding of ion channels. This review provides an overview on a variety of computational methods and software specific to the field of ion-channels. Artificial intelligence (or more precisely machine learning) approaches are applied for the sequence-based prediction of ion channel family, or topology of the transmembrane region. In case sufficient data on ion channel modulators is available, these methods can also be applied for quantitative structureactivity relationship (QSAR) analysis. Molecular dynamics (MD) simulations combined with computational molecular design methods such as docking can be used for analysing the function of ion channels including ion conductance, different conformational states, binding sites and ligand interactions, and the influence of mutations on their function. In the absence of a three-dimensional protein structure, homology modelling can be applied to create a model of your ion channel structure of interest. Besides highlighting a wide range of successful applications, we will also provide a basic introduction to the most important computational methods and discuss best practices to get a rough idea of possible applications and risks.

scholarly journals Naked mole-rat acid-sensing ion channel 3 forms nonfunctional homomers, but functional heteromers

2017 ◽  
Vol 293 (5) ◽  
pp. 1756-1766 ◽  
Author(s):  
Laura-Nadine Schuhmacher ◽  
Gerard Callejo ◽  
Shyam Srivats ◽  
Ewan St. John Smith
Keyword(s):  
Ion Channel ◽  
Mole Rat ◽  
Naked Mole Rat

scholarly journals Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses

2020 ◽  
Author(s):  
Yongjun Tan ◽  
Theresa Schneider ◽  
Prakash K. Shukla ◽  
Mahesh B. Chandrasekharan ◽  
L Aravind ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
M Protein ◽  
Homology Detection ◽  
Virion Assembly ◽  
Host Molecules ◽  
Wide Range ◽  
M Proteins ◽  
Immune Attack ◽  
Selection For

ABSTRACTThe new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack.IMPORTANCECoronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.

scholarly journals Unification and extensive diversification of M/ORF3-related ion channel proteins in coronaviruses and other nidoviruses

2021 ◽  
Author(s):  
Yongjun Tan ◽  
Theresa Schneider ◽  
Prakash K Shukla ◽  
Mahesh B Chandrasekharan ◽  
L Aravind ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
M Protein ◽  
Detection Methods ◽  
Homology Detection ◽  
Virion Assembly ◽  
Wide Range ◽  
M Proteins ◽  
Slow Evolution ◽  
Membrane Budding

Abstract The coronavirus, SARS-CoV-2, responsible for the ongoing COVID-19 pandemic, has emphasized the need for a better understanding of the evolution of virus-host interactions. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) implicated in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. We present computational evidence that these viral families might utilize specific conserved polar residues to constitute an aqueous pore within the membrane-spanning region. We reconstruct an evolutionary history of these families and objectively establish the common origin of the M proteins of CoVs and Toroviruses. We also show that the divergent ORF3 clade (ORF3a/ORF3b/ORF3c/ORF5 families) represents a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a hypothesis for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly and membrane budding. We show that M and ORF3 are under different evolutionary pressures; in contrast to the slow evolution of M as core structural component, the ORF3 clade is under selection for diversification, which suggests it might act at the interface with host molecules and/or immune attack.

scholarly journals Heterozygous variants in the mechanosensitive ion channelTMEM63Aresult in transient hypomyelination during infancy

2019 ◽  
Author(s):  
Huifang Yan ◽  
Guy Helman ◽  
Swetha E. Murthy ◽  
Haoran Ji ◽  
Joanna Crawford ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
De Novo ◽  
Physiological Role ◽  
Congenital Nystagmus ◽  
Missense Mutations ◽  
Gene Encoding ◽  
Motor Delay ◽  
Mechanosensitive Ion Channels ◽  
Patch Clamp Electrophysiology

Mechanically activated (MA) ion channels convert physical forces into electrical signals. Despite the importance of this function, the involvement of mechanosensitive ion channels in human disease is poorly understood. Here we report heterozygous missense mutations in the gene encoding the MA ion channel TMEM63A that result in an infantile disorder resembling a hypomyelinating leukodystrophy. Four unrelated individuals presented with congenital nystagmus, motor delay, and deficient myelination on serial scans in infancy, prompting the diagnosis of Pelizaeus-Merzbacher (like) disease. Genomic sequencing revealed all four individuals carry heterozygous missense variants in the pore-forming domain of TMEM63A. These variants were confirmed to have arisende novoin three of the four individuals. While the physiological role of TMEM63A is incompletely understood, it is highly expressed in oligodendrocytes and it has recently been shown to be a mechanically activated (MA) ion channel. Using patch clamp electrophysiology, we demonstrated that each of the modelled variants results in strongly attenuated stretch-activated currents when expressed in naïve cells. Unexpectedly, the clinical evolution of all four individuals has been surprisingly favorable, with substantial improvements in neurological signs and developmental progression. In the three individuals with follow-up scans after four years of age, the myelin deficit had almost completely resolved. Our results suggest a previously unappreciated role for mechanosensitive ion channels in myelin development.

scholarly journals Naked mole-rat brain neurons are resistant to acid-induced cell death

2018 ◽  
Author(s):  
Zoé Husson ◽  
Ewan St John Smith
Keyword(s):  
Central Nervous System ◽  
Cell Death ◽  
Nervous System ◽  
Ion Channels ◽  
Hippocampal Neurons ◽  
Contributing Factors ◽  
Voltage Gated ◽  
Mole Rat ◽  
Naked Mole Rat ◽  
Brain Ph

AbstractRegulation of brain pH is a critical homeostatic process and changes in brain pH modulate various ion channels and receptors and thus neuronal excitability. Tissue acidosis, resulting from hypoxia or hypercapnia, can activate various proteins and ion channels, among which acid-sensing ion channels (ASICs) a family of primarily Na+permeable ion channels, which alongside classical excitotoxicity causes neuronal death. Naked mole-rats (NMRs,Heterocephalus glaber) are long-lived, fossorial, eusocial rodents that display remarkable behavioral/cellular hypoxia and hypercapnia resistance. In the central nervous system, ASIC subunit expression is similar between mouse and NMR with the exception of much lower expression of ASIC4 throughout the NMR brain. However, ASIC function and neuronal sensitivity to sustained acidosis has not been examined in the NMR brain. Here, we show with whole-cell patch-clamp electrophysiology of cultured NMR and mouse cortical and hippocampal neurons that NMR neurons have smaller voltage-gated Na+channel currents and more hyperpolarized resting membrane potentials. We further demonstrate that acid-mediated currents in NMR neurons are of smaller magnitude than in mouse, and that all currents in both species are fully blocked by the ASIC antagonist benzamil. We further demonstrate that NMR neurons show greater resistance to acid-induced cell death than mouse neurons. In summary, NMR neurons show significant cellular resistance to acidotoxicity compared to mouse neurons, contributing factors likely to be smaller ASIC-mediated currents and reduced NaV activity.AbbreviationsASIC, acid-sensing ion channel; CNS, central nervous system; DRG, dorsal root ganglion; NaV, voltage-gated Na+channel; NMR, naked mole-rat; TTX, tetrodotoxin

scholarly journals Briefing in Application of Machine Learning Methods in Ion Channel Prediction

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Hao Lin ◽  
Wei Chen
Keyword(s):  
Machine Learning ◽  
Ion Channels ◽  
Ion Channel ◽  
Inorganic Ions ◽  
Correct Identification ◽  
Biological Processes ◽  
Learning Methods ◽  
Channel Prediction ◽  
Machine Learning Methods ◽  
Wide Range

In cells, ion channels are one of the most important classes of membrane proteins which allow inorganic ions to move across the membrane. A wide range of biological processes are involved and regulated by the opening and closing of ion channels. Ion channels can be classified into numerous classes and different types of ion channels exhibit different functions. Thus, the correct identification of ion channels and their types using computational methods will provide in-depth insights into their function in various biological processes. In this review, we will briefly introduce and discuss the recent progress in ion channel prediction using machine learning methods.

Modelling activity-dependent changes of velocity in C-fibers

2017 ◽  
Vol 16 (1) ◽  
pp. 186-187
Author(s):  
J. Tigerholm ◽  
M.E. Petersson ◽  
O. Obreja ◽  
A. Lampert ◽  
R. Carr ◽  
...  
Keyword(s):  
Neuropathic Pain ◽  
Ion Channels ◽  
Ion Channel ◽  
Small Diameter ◽  
Intracellular Sodium ◽  
Low Frequencies ◽  
C Fibers ◽  
Wide Range ◽  
Activity Dependent ◽  
Insight Into

AbstractAimsWhen C-nociceptors are activated repeatedly using electrical stimulation at relatively low frequencies (0.125–2 Hz), their propagation velocity will decrease. This is referred to as activity-dependent slowing (ADS). The main reason why activity-dependent changes in velocity are of interest is that they can be recorded directly, using invasive methods (microneurography), in patients with chronic pain. Interestingly, in certain patients with neuropathic pain, reduced activity-dependent slowing of conduction has been observed, indicating that these axons have an increased excitability. Through a computational model, it is possible to link such velocity alterations with changes in active conductances, opening for an understanding the underlying excitability changes occurring in these patients.MethodsWe have developed a detailed multicompartment model of a C-nociceptor fiber. This model incorporates a wide range of voltage-gated ion channels (Nav1.7, Nav1.8, Nav1.9, Kdr, KA, KM, KNa and h) which were implemented across a detailed and realistic axon morphology.ResultsThe model predicts that the small diameter of the axon can accumulate intracellular sodium when it is repeatedly activated in a similar fashion as during single fiber microneurography. This increase of intracellular sodium concentration can shift the balance between ion channel currents, shift the membrane potential and membrane input resistance, and thereby generate activity-dependent changes of velocity, such as ADS as well as recovery cycle supernormality.ConclusionsOur results thus provide insight into how activity-dependent excitability changes can be generated in C-fibers. By identifying which ion channels are contributing to activity-dependent changes of velocity this could provide insight into ion channel alterations in neuropathic pain patients.

scholarly journals Nest Carbon Dioxide Masks GABA-Dependent Seizure Susceptibility in the Naked Mole-Rat

2020 ◽  
Vol 30 (11) ◽  
pp. 2068-2077.e4 ◽  
Author(s):  
Michael Zions ◽  
Edward F. Meehan ◽  
Michael E. Kress ◽  
Donald Thevalingam ◽  
Edmund C. Jenkins ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Seizure Susceptibility ◽  
Mole Rat ◽  
Naked Mole Rat
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