Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel's pore: a modeling study

Worldwide Sodium Channel Conference, January 31st-February 2nd, 2024, Grindelwald, Switzerland

The following is a brief report of the inaugural Worldwide Sodium Channels Conference, held in Grindelwald, Switzerland, in January 2024. This excellent in-person conference followed the highly successful online Worldwide Sodium Channel Seminars series which started following the COVID-19 pandemic, in 2021. We present here our highlights of the 45 presentations delivered over the two-and-a-half-day conference, focusing on key outputs from each of the eight sessions.

Nonextensive realizations in interacting ion channels: Implications for mechano-electrical transducer mechanisms

We propose a theoretical model to investigate the thermodynamics of single and coupled two-state ion channels, associated with mechanoelectrical transduction (MET) and hair cell biophysics. The modeling was based on the Tsallis nonextensive statistical mechanics. The choice for a nonextensive framework in modeling ion channels is encouraged on the fact that we take into account the presence of interactions or long-range correlations in the dynamics of single and coupled ion channels. However, the basic assumptions that support Boltzmann-Gibbs statistics, traditionally used to model ion channel dynamics, state that the system is formed by independent or weakly interacting elements. Despite being well studied in many biological systems, the literature has not yet addressed the study of both entropy and mutual information related to isolated or physically interacting pairs of MET channels. Inspired by hair cell biophysics, we show how the presence of nonextensivity, or subadditivity and superadditivity modulates the nonextensive entropy and mutual information as functions of stereocilia displacements. We also observe that the magnitude of the interaction between the two channels, given by a nonextensive parameter, influences the amplitude of the nonextensive joint entropy and mutual information as functions of the hair cell displacements. Finally, we show how nonextensivity regulates the current versus displacement curve for a single and a pair of interacting two-state channels. The present findings shed light on the thermodynamic process involved in the molecular mechanisms of the auditory system.

Generalizing the Wells-Riley Infection Probability: A Superstatistical Scheme for Indoor Infection Risk Estimation

Recent evidence supports that air is the main transmission pathway of the recently identified SARS-CoV-2 coronavirus that causes COVID-19 disease. Estimating the infection risk associated with an indoor space remains an open problem due to insufficient data concerning COVID-19 outbreaks, as well as, methodological challenges arising from cases where environmental (i.e., out-of-host) and immunological (i.e., within-host) heterogeneities cannot be neglected. This work addresses these issues by introducing a generalization of the elementary Wells-Riley infection probability model. To this end, we adopted a superstatistical approach where the exposure rate parameter is gamma-distributed across subvolumes of the indoor space. This enabled us to construct a susceptible (S)-exposed (E)-infected (I) dynamics model where the Tsallis entropic index q quantifies the degree of departure from a well-mixed (i.e., homogeneous) indoor-air-environment state. A cumulative-dose mechanism is employed to describe infection activation in relation to a host's immunological profile. We corroborate that the six-foot rule cannot guarantee the biosafety of susceptible occupants, even for exposure times as short as 15 min. Overall, our work seeks to provide a minimal (in terms of the size of the parameter space) framework for more realistic indoor SEI dynamics explorations while highlighting their Tsallisian entropic origin and the crucial yet elusive role that the innate immune system can play in shaping them. This may be useful for scientists and decision makers interested in probing different indoor biosafety protocols more thoroughly and comprehensively, thus motivating the use of nonadditive entropies in the emerging field of indoor space epidemiology.

Hydropathicity-based prediction of pain-causing NaV1.7 variants

Background

Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant is of major clinical importance; it can aid in reducing costs of in vitro pathophysiological characterization of NaV1.7 variants, as well as, in the design of drug agents for counteracting pain-disease symptoms.

Results

In this work, we utilize spatial complexity of hydropathic effects toward predicting which NaV1.7 variants cause pain (and which are neutral) based on the location of corresponding mutation sites within the NaV1.7 structure. For that, we analyze topological and scaling hydropathic characteristics of the atomic environment around NaV1.7’s pore and probe their spatial correlation with mutation sites. We show that pain-related mutation sites occupy structural locations in proximity to a hydrophobic patch lining the pore while clustering at a critical hydropathic-interactions distance from the selectivity filter (SF). Taken together, these observations can differentiate pain-related NaV1.7 variants from neutral ones, i.e., NaV1.7 variants not causing pain disease, with 80.5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\%$$\end{document}% sensitivity and 93.7\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\%$$\end{document}% specificity [area under the receiver operating characteristics curve = 0.872].

Conclusions

Our findings suggest that maintaining hydrophobic NaV1.7 interior intact, as well as, a finely-tuned (dictated by hydropathic interactions) distance from the SF might be necessary molecular conditions for physiological NaV1.7 functioning. The main advantage for using the presented predictive scheme is its negligible computational cost, as well as, hydropathicity-based biophysical rationalization.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04119-2.