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Trofimov YA, Krylov NA, Minakov AS, Nadezhdin KD, Neuberger A, Sobolevsky AI, Efremov RG. Dynamic molecular portraits of ion-conducting pores characterize functional states of TRPV channels. Commun Chem 2024; 7:119. [PMID: 38824263 PMCID: PMC11144267 DOI: 10.1038/s42004-024-01198-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024] Open
Abstract
Structural biology is solving an ever-increasing number of snapshots of ion channel conformational ensembles. Deciphering ion channel mechanisms, however, requires understanding the ensemble dynamics beyond the static structures. Here, we present a molecular modeling-based approach characterizing the ion channel structural intermediates, or their "dynamic molecular portraits", by assessing water and ion conductivity along with the detailed evaluation of pore hydrophobicity and residue packing. We illustrate the power of this approach by analyzing structures of few vanilloid-subfamily transient receptor potential (TRPV) channels. Based on the pore architecture, there are three major states that are common for TRPVs, which we call α-closed, π-closed, and π-open. We show that the pore hydrophobicity and residue packing for the open state is most favorable for the pore conductance. On the contrary, the α-closed state is the most hydrophobic and always non-conducting. Our approach can also be used for structural and functional classification of ion channels.
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Affiliation(s)
- Yury A Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Xenakis MN. Generalizing the Wells-Riley Infection Probability: A Superstatistical Scheme for Indoor Infection Risk Estimation. ENTROPY (BASEL, SWITZERLAND) 2023; 25:896. [PMID: 37372240 DOI: 10.3390/e25060896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
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.
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Affiliation(s)
- Markos N Xenakis
- VTT Technical Research Centre of Finland Ltd., FI-02044 Espoo, Finland
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Xenakis MN, Kapetis D, Yang Y, Gerrits MM, Heijman J, Waxman SG, Lauria G, Faber CG, Westra RL, Lindsey PJ, Smeets HJ. Hydropathicity-based prediction of pain-causing NaV1.7 variants. BMC Bioinformatics 2021; 22:212. [PMID: 33892629 PMCID: PMC8063372 DOI: 10.1186/s12859-021-04119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/01/2021] [Indexed: 11/10/2022] Open
Abstract
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}
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\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.
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Affiliation(s)
- Makros N Xenakis
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands. .,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Dimos Kapetis
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN, 47907, USA.,Purdue Institute for Integrative Neuroscience, West Lafayette, IN, 47907, USA
| | - Monique M Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Stephen G Waxman
- Department of Neurology and Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA.,Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Via G.B. Grassi 74, 20157, Milan, Italy
| | - Catharina G Faber
- Department of Neurology, Maastricht University Medical Center, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Ronald L Westra
- Department of Data Science and Knowledge Engineering, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Patrick J Lindsey
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Oncology and Developmental Biology (GROW), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Hubert J Smeets
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
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Xenakis MN, Kapetis D, Yang Y, Heijman J, Waxman SG, Lauria G, Faber CG, Smeets HJ, Lindsey PJ, Westra RL. Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel's pore: a modeling study. J Biol Phys 2021; 47:61-77. [PMID: 33735400 PMCID: PMC7981368 DOI: 10.1007/s10867-021-09565-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/02/2021] [Indexed: 01/22/2023] Open
Abstract
Voltage-gated sodium channels (NavChs) are pore-forming membrane proteins that regulate the transport of sodium ions through the cell membrane. Understanding the structure and function of NavChs is of major biophysical, as well as clinical, importance given their key role in cellular pathophysiology. In this work, we provide a computational framework for modeling system-size-dependent, i.e., cumulative, atomic properties around a NavCh's pore. We illustrate our methodologies on the bacterial NavAb channel captured in a closed-pore state where we demonstrate that the atomic environment around its pore exhibits a bi-phasic spatial organization dictated by the structural separation of the pore domains (PDs) from the voltage-sensing domains (VSDs). Accordingly, a mathematical model describing packing of atoms around NavAb's pore is constructed that allows-under certain conservation conditions-for a power-law approximation of the cumulative hydropathic dipole field effect acting along NavAb's pore. This verified the non-extensitivity hypothesis for the closed-pore NavAb channel and revealed a long-range hydropathic interactions law regulating atom-packing around the NavAb's selectivity filter. Our model predicts a PDs-VSDs coupling energy of [Formula: see text] kcal/mol corresponding to a global maximum of the atom-packing energy profile. Crucially, we demonstrate for the first time how critical phenomena can emerge in a single-channel structure as a consequence of the non-extensive character of its atomic porous environment.
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Affiliation(s)
- Markos N Xenakis
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.
- Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Dimos Kapetis
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", via Celoria 11, 20133, Milan, Italy
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN, 47907, USA
- Purdue Institute for Integrative Neuroscience, West Lafayette, IN, 47907, USA
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Stephen G Waxman
- Department of Neurology and Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA
- Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", via Celoria 11, 20133, Milan, Italy
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, via G.B. Grassi 74, 20157, Milan, Italy
| | - Catharina G Faber
- Department of Neurology, Maastricht University Medical Center, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Hubert J Smeets
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
- Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Patrick J Lindsey
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
- Research School for Oncology and Developmental Biology (GROW), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Ronald L Westra
- Department of Data Science and Knowledge Engineering, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
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