scholarly journals Quantum Calculations on Ion Channels: Why Are They More Useful Than Classical Calculations, and for Which Processes Are They Essential?

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 655
Author(s):  
Alisher M. Kariev ◽  
Michael E. Green
Keyword(s):  
Charge Transfer ◽  
Ion Channels ◽  
Correlation Energy ◽  
Force Fields ◽  
Critical Role ◽  
Atomic Scale ◽  
Quantum Calculations ◽  
Interatomic Distances ◽  
Classical Analogue ◽  
Exchange And Correlation

There are reasons to consider quantum calculations to be necessary for ion channels, for two types of reasons. The calculations must account for charge transfer, and the possible switching of hydrogen bonds, which are very difficult with classical force fields. Without understanding charge transfer and hydrogen bonding in detail, the channel cannot be understood. Thus, although classical approximations to the correct force fields are possible, they are unable to reproduce at least some details of the behavior of a system that has atomic scale. However, there is a second class of effects that is essentially quantum mechanical. There are two types of such phenomena: exchange and correlation energies, which have no classical analogues, and tunneling. Tunneling, an intrinsically quantum phenomenon, may well play a critical role in initiating a proton cascade critical to gating. As there is no classical analogue of tunneling, this cannot be approximated classically. Finally, there are energy terms, exchange and correlation energy, whose values can be approximated classically, but these approximations must be subsumed within classical terms, and as a result, will not have the correct dependence on interatomic distances. Charge transfer, and tunneling, require quantum calculations for ion channels. Some results of quantum calculations are shown.

Quantum Calculation of Proton and Other Charge Transfer Steps in Voltage Sensing in the Kv1.2 Channel

2019 ◽  
Author(s):  
Alisher M Kariev ◽  
Michael Green
Keyword(s):  
Charge Transfer ◽  
Energy Charge ◽  
Quantum Calculation ◽  
Quantum Calculations ◽  
Gating Current ◽  
Transmembrane Segment ◽  
Voltage Sensing ◽  
Standard Models ◽  
Charge Displacement ◽  
Voltage Sensing Domain

Quantum calculations on 976 atoms of the voltage sensing domain of the K<sub>v</sub>1.2 channel, with protons in several positions, give energy, charge transfer, and other properties. Motion of the S4 transmembrane segment that accounts for gating current in standard models is shown not to occur; there is H<sup>+ </sup>transfer instead. The potential at which two proton positions cross in energy approximately corresponds to the gating potential for the channel. The charge displacement seems approximately correct for the gating current. Two mutations are accounted for (Y266F, R300cit, cit =citrulline). The primary conclusion is that voltage sensing depends on H<sup>+</sup> transfer, not motion of arginine charges.

scholarly journals Emerging Roles for Ion Channels in Ovarian Cancer: Pathomechanisms and Pharmacological Treatment

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 668
Author(s):  
Concetta Altamura ◽  
Maria Raffaella Greco ◽  
Maria Rosaria Carratù ◽  
Rosa Angela Cardone ◽  
Jean-François Desaphy
Keyword(s):  
Ovarian Cancer ◽  
Ion Channels ◽  
Transient Receptor Potential ◽  
Critical Role ◽  
Gynecologic Cancer ◽  
Receptor Potential ◽  
Transient Receptor Potential Channels ◽  
Platinum Resistance

Ovarian cancer (OC) is the deadliest gynecologic cancer, due to late diagnosis, development of platinum resistance, and inadequate alternative therapy. It has been demonstrated that membrane ion channels play important roles in cancer processes, including cell proliferation, apoptosis, motility, and invasion. Here, we review the contribution of ion channels in the development and progression of OC, evaluating their potential in clinical management. Increased expression of voltage-gated and epithelial sodium channels has been detected in OC cells and tissues and shown to be involved in cancer proliferation and invasion. Potassium and calcium channels have been found to play a critical role in the control of cell cycle and in the resistance to apoptosis, promoting tumor growth and recurrence. Overexpression of chloride and transient receptor potential channels was found both in vitro and in vivo, supporting their contribution to OC. Furthermore, ion channels have been shown to influence the sensitivity of OC cells to neoplastic drugs, suggesting a critical role in chemotherapy resistance. The study of ion channels expression and function in OC can improve our understanding of pathophysiology and pave the way for identifying ion channels as potential targets for tumor diagnosis and treatment.

scholarly journals The description of friction of silicon MEMS with surface roughness: virtues and limitations of a stochastic Prandtl–Tomlinson model and the simulation of vibration-induced friction reduction

2010 ◽  
Vol 1 ◽  
pp. 163-171 ◽  
Author(s):  
W Merlijn van Spengen ◽  
Viviane Turq ◽  
Joost W M Frenken
Keyword(s):  
Surface Roughness ◽  
Critical Role ◽  
Measurement Data ◽  
Friction Model ◽  
Friction Reduction ◽  
Atomic Scale ◽  
Mems Devices ◽  
Tomlinson Model ◽  
Atomic Force ◽  
On Chip

We have replaced the periodic Prandtl–Tomlinson model with an atomic-scale friction model with a random roughness term describing the surface roughness of micro-electromechanical systems (MEMS) devices with sliding surfaces. This new model is shown to exhibit the same features as previously reported experimental MEMS friction loop data. The correlation function of the surface roughness is shown to play a critical role in the modelling. It is experimentally obtained by probing the sidewall surfaces of a MEMS device flipped upright in on-chip hinges with an AFM (atomic force microscope). The addition of a modulation term to the model allows us to also simulate the effect of vibration-induced friction reduction (normal-force modulation), as a function of both vibration amplitude and frequency. The results obtained agree very well with measurement data reported previously.

scholarly journals Identification of a putative binding site critical for general anesthetic activation of TRPA1

2017 ◽  
Vol 114 (14) ◽  
pp. 3762-3767 ◽  
Author(s):  
Hoai T. Ton ◽  
Thieu X. Phan ◽  
Ara M. Abramyan ◽  
Lei Shi ◽  
Gerard P. Ahern
Keyword(s):  
Ion Channels ◽  
Transient Receptor Potential ◽  
Transmembrane Domain ◽  
Halogen Bond ◽  
Critical Role ◽  
Sensory Nerves ◽  
Structural Basis ◽  
General Anesthetics ◽  
General Anesthetic ◽  
Potential Binding

General anesthetics suppress CNS activity by modulating the function of membrane ion channels, in particular, by enhancing activity of GABAA receptors. In contrast, several volatile (isoflurane, desflurane) and i.v. (propofol) general anesthetics excite peripheral sensory nerves to cause pain and irritation upon administration. These noxious anesthetics activate transient receptor potential ankyrin repeat 1 (TRPA1), a major nociceptive ion channel, but the underlying mechanisms and site of action are unknown. Here we exploit the observation that pungent anesthetics activate mammalian but not Drosophila TRPA1. Analysis of chimeric Drosophila and mouse TRPA1 channels reveal a critical role for the fifth transmembrane domain (S5) in sensing anesthetics. Interestingly, we show that anesthetics share with the antagonist A-967079 a potential binding pocket lined by residues in the S5, S6, and the first pore helix; isoflurane competitively disrupts A-967079 antagonism, and introducing these mammalian TRPA1 residues into dTRPA1 recapitulates anesthetic agonism. Furthermore, molecular modeling predicts that isoflurane and propofol bind to this pocket by forming H-bond and halogen-bond interactions with Ser-876, Met-915, and Met-956. Mutagenizing Met-915 or Met-956 selectively abolishes activation by isoflurane and propofol without affecting actions of A-967079 or the agonist, menthol. Thus, our combined experimental and computational results reveal the potential binding mode of noxious general anesthetics at TRPA1. These data may provide a structural basis for designing drugs to counter the noxious and vasorelaxant properties of general anesthetics and may prove useful in understanding effects of anesthetics on related ion channels.

Abstract 17319: Distinct Effects of Human Calmodulinopathy on the Function of Small Conductance Ca 2+ -Activated K + (SK) Channels

Circulation ◽  
2018 ◽  
Vol 138 (Suppl_1) ◽  
Author(s):  
Hannah A Ledford ◽  
Seojin Park ◽  
Duncan Muir ◽  
Wen Smith ◽  
Ryan L Woltz ◽  
...  
Keyword(s):  
Ion Channels ◽  
Intracellular Signaling ◽  
Critical Role ◽  
Dominant Negative ◽  
Polymorphic Ventricular Tachycardia ◽  
Dominant Negative Effect ◽  
Sk Channels ◽  
Channel Function ◽  
Sk Channel ◽  
Small Conductance

Background: Calmodulin (CaM) plays a critical role in intracellular signaling and regulation of Ca 2+ -dependent ion channels. Mutations in CALM1, CALM2, and CALM3 have recently been linked to cardiac arrhythmias, such as Long QT Syndrome (LQTS), catecholaminergic polymorphic ventricular tachycardia (CPVT), and familial idiopathic ventricular fibrillation (IVF). Small-conductance Ca 2+ - activated K + channels (SK) are voltage-independent channels that are regulated solely from beat-to-beat changes in intracellular calcium. CaM regulates the function of multiple ion channels, including SK channels, although the effect of CaM mutations on these channels is not yet understood. We hypothesize that human CaM mutations linked to sudden cardiac death disrupt SK channel function by distinct mechanisms. Methods and Results: We tested the effects of LQTS (CaM D96V , CaM D130G ), CPVT (CaM N54I , CaM N98S ), and IVF (CaM F90L ) CaM mutants compared to CaM WT on SK channel function. Using whole-cell voltage-clamp recordings, we found that CaM D96V and CaM D130G mutants significantly inhibited apamin-sensitive currents. Similarly, action potential studies in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) also revealed significant knockdown of apamin-sensitive currents. Immunofluorescent confocal microscopy confirmed that this effect was not due to changes in SK channel trafficking. Rather, co-immunoprecipitation studies showed a significant decrease in the association of these CaM mutants with the SK channel. Rosetta molecular modeling was used to identify a conformational change in CaM F90L structure compared to that of CaM WT . Conclusions: We found that CaM D96V and CaM D130G mutants significantly reduced apamin-sensitive currents, through a dominant negative effect on SK channel function. Consistent with our hypothesis, CaM F90L resulted in the least inhibitory effects. The data suggests that specific mutations with phenylalanine to leucine (CaM F90L ) may disrupt the interaction between apo-CaM with CaMBD on the SK2 channel.

scholarly journals Molecular-scale investigation of the oxidation behavior of chromia-forming alloys in high-temperature CO2

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Richard P. Oleksak ◽  
Rafik Addou ◽  
Bharat Gwalani ◽  
John P. Baltrus ◽  
Tao Liu ◽  
...  
Keyword(s):  
High Temperature ◽  
Power Systems ◽  
High Purity ◽  
Photoelectron Spectroscopy ◽  
Ambient Pressure ◽  
Critical Role ◽  
Atomic Scale ◽  
Atomic Diffusion ◽  
Carbon Transport

AbstractCurrent and future power systems require chromia-forming alloys compatible with high-temperature CO2. Important questions concerning the mechanisms of oxidation and carburization remain unanswered. Herein we shed light onto these processes by studying the very initial stages of oxidation of Fe22Cr and Fe22Ni22Cr model alloys. Ambient-pressure X-ray photoelectron spectroscopy enabled in situ analysis of the oxidizing surface under 1 mbar of flowing CO2 at temperatures up to 530 °C, while postexposure analyses revealed the structure and composition of the oxidized surface at the near-atomic scale. We found that gas purity played a critical role in the kinetics of the reaction, where high purity CO2 promoted the deposition of carbon and the selective oxidation of Cr. In contrast, no carbon deposition occurred in low purity CO2 and Fe oxidation ensued, thus highlighting the critical role of impurities in defining the early oxidation pathway of the alloy. The Cr-rich oxide formed on Fe22Cr in high purity CO2 was both thicker and more permeable to carbon compared to that formed on Fe22Ni22Cr, where carbon transport appeared to occur by atomic diffusion through the oxide. Alternatively, the Fe-rich oxide formed in low purity CO2 suggested carbon transport by molecular CO2.

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