1
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Niraula D, El Naqa I, Tuszynski JA, Gatenby RA. Modeling non-genetic information dynamics in cells using reservoir computing. iScience 2024; 27:109614. [PMID: 38632985 PMCID: PMC11022048 DOI: 10.1016/j.isci.2024.109614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Virtually all cells use energy-driven, ion-specific membrane pumps to maintain large transmembrane gradients of Na+, K+, Cl-, Mg++, and Ca++, but the corresponding evolutionary benefit remains unclear. We propose that these gradients enable a dynamic and versatile biological system that acquires, analyzes, and responds to environmental information. We hypothesize that environmental signals are transmitted into the cell by ion fluxes along pre-existing gradients through gated ion-specific membrane channels. The consequent changes in cytoplasmic ion concentration can generate a local response or orchestrate global/regional cellular dynamics through wire-like ion fluxes along pre-existing and self-assembling cytoskeleton to engage the endoplasmic reticulum, mitochondria, and nucleus.
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Affiliation(s)
- Dipesh Niraula
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Issam El Naqa
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Jack Adam Tuszynski
- Departments of Physics and Oncology, University of Alberta, Edmonton, AB, Canada
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Robert A. Gatenby
- Departments of Radiology and Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
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2
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Tenenbaum A. Energy condensation and dipole alignment in protein dynamics. Phys Rev E 2024; 109:044401. [PMID: 38755822 DOI: 10.1103/physreve.109.044401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The possibility that distant biomolecules in a cell interact via electromagnetic (e.m.) radiation was proposed many years ago to explain the high rate of encounters of partners in some enzymatic reactions. The results of two recent experiments designed to test the propensity of protein bovine serum albumin (BSA) to interact via e.m. radiation with other proteins were interpreted in a theoretical framework based on three main assumptions: (i) in order to experience this kind of interaction the protein must be in an out-of-equilibrium state; (ii) in this state there is a condensation of energy in low-frequency vibrational modes; and (iii) the hydration layers of water around the protein sustain the energy condensation. In the present paper we present the results of molecular dynamics simulations of BSA in four states: at equilibrium and out-of-equilibrium in water, and at room and high temperature in vacuum. By comparing physical properties of the system in the four states, our simulations provide a qualitative and quantitative assessment of the three assumptions on which the theoretical framework is based. Our results confirm the assumptions of the theoretical model showing energy condensation at low frequency and electretlike alignment between the protein's and the water's dipoles; they also allow a quantitative estimate of the contribution of the out-of-equilibrium state and of the water to the observed behavior of the protein. In particular, it has been found that in the out-of-equilibrium state the amplitude of the oscillation of the protein's dipole moment greatly increases, thereby enhancing a possible absorption or emission of e.m. radiation. The analysis of BSA's dynamics outlined in the present paper provides a procedure for checking the propensity of a biomolecule to interact via e.m. radiation with its biochemical partners.
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Affiliation(s)
- Alexander Tenenbaum
- Physics Department, Sapienza University, Piazzale Aldo Moro 5, 00185 Roma, Italy
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3
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Sasihithlu K, Scholes GD. Vibrational Dipole-Dipole Coupling and Long-Range Forces between Macromolecules. J Phys Chem B 2024; 128:1205-1208. [PMID: 38289630 DOI: 10.1021/acs.jpcb.3c08251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Long-range interactions between biomacromolecules are considered important for directing intracellular processes. Recent studies have posited that interactions between oscillating dipoles are well-suited to mediating long-range forces because they are weakly screened by a dielectric environment. Here, we extend these studies and present a quantum electrodynamic mechanism for resonant interactions between vibrational transition dipole moments of molecules. We explicitly consider the molecular charge density oscillations as IR transition dipoles. This gives a physical, molecular assignment to the idea of oscillating dipoles and allows us to develop explicit expressions for the interactions that can be quantified using parameters known from experiment. Moreover, in the same framework, we can describe van der Waals forces. We use numerical calculations to estimate the strength of resonant vibrational dipole-dipole interactions over long distances and compare these estimates to the van der Waals interaction. We find that the resonant vibrational dipole-dipole interactions dominate over the long range.
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Affiliation(s)
- Karthik Sasihithlu
- Department of Energy Science and Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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4
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Azizi K, Gori M, Morzan U, Hassanali A, Kurian P. Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution. PNAS NEXUS 2023; 2:pgad257. [PMID: 37575674 PMCID: PMC10416812 DOI: 10.1093/pnasnexus/pgad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023]
Abstract
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Matteo Gori
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Uriel Morzan
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Philip Kurian
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
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5
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Chierici F, Dogariu A, Tuszynski JA. Computational Investigation of the Ordered Water System Around Microtubules: Implications for Protein Interactions. Front Mol Biosci 2022; 9:884043. [PMID: 35547397 PMCID: PMC9083000 DOI: 10.3389/fmolb.2022.884043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
The existence of an exclusion zone in which particles of a colloidal suspension in water are repelled from hydrophilic surfaces has been experimentally demonstrated in numerous studies, especially in the case of Nafion surfaces. Various explanations have been proposed for the origin of this phenomenon, which is not completely understood yet. In particular, the existence of a fourth phase of water has been proposed by G. Pollack and if this theory is proven correct, its implications on our understanding of the properties of water, especially in biological systems, would be profound and could give rise to new medical therapies. Here, a simple approach based on the linearized Poisson-Boltzmann equation is developed in order to study the repulsive forces mediated by ordered water and involving the following interacting biomolecules: 1) microtubule and a tubulin dimer, 2) two tubulin dimers and 3) a tubulin sheet and a tubulin dimer. The choice of microtubules in this study is motivated because they could be a good candidate for the generation of an exclusion zone in the cell and these models could be a starting point for detailed experimental investigations of this phenomenon.
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Affiliation(s)
- Francesco Chierici
- DIMEAS, Politecnico di Torino, Torino, Italy
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, United States
- *Correspondence: Francesco Chierici,
| | - Aristide Dogariu
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, United States
| | - Jack A. Tuszynski
- DIMEAS, Politecnico di Torino, Torino, Italy
- Department of Physics, University of Alberta, Edmonton, AB, Canada
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6
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Lechelon M, Meriguet Y, Gori M, Ruffenach S, Nardecchia I, Floriani E, Coquillat D, Teppe F, Mailfert S, Marguet D, Ferrier P, Varani L, Sturgis J, Torres J, Pettini M. Experimental evidence for long-distance electrodynamic intermolecular forces. SCIENCE ADVANCES 2022; 8:eabl5855. [PMID: 35171677 PMCID: PMC8849397 DOI: 10.1126/sciadv.abl5855] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/22/2021] [Indexed: 05/31/2023]
Abstract
Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent experiments, on the basis of different physical effects detected by fluorescence correlation spectroscopy and terahertz spectroscopy, respectively, we demonstrate experimentally the activation of resonant electrodynamic intermolecular forces. This is an unprecedented experimental proof of principle of a physical phenomenon that, having been observed for biomacromolecules and with long-range action (up to 1000 Å), could be of importance for biology. In addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space.
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Affiliation(s)
- Mathias Lechelon
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Yoann Meriguet
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Matteo Gori
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Quantum Biology Lab, Howard University, 2400 6th St NW, Washington, DC 20059, USA
| | - Sandra Ruffenach
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Ilaria Nardecchia
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Elena Floriani
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
| | - Dominique Coquillat
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Teppe
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Sébastien Mailfert
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Didier Marguet
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Pierre Ferrier
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Luca Varani
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
| | - James Sturgis
- Laboratoire d’Ingenierie des Systèmes Macromoleculaires, Aix-Marseille Univ., CNRS, Marseille, France
| | - Jeremie Torres
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
| | - Marco Pettini
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
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7
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Maestri S, Merelli E, Pettini M. Agent-based models for detecting the driving forces of biomolecular interactions. Sci Rep 2022; 12:1878. [PMID: 35115584 PMCID: PMC8814177 DOI: 10.1038/s41598-021-04205-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.
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Affiliation(s)
- Stefano Maestri
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.,Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
| | - Emanuela Merelli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
| | - Marco Pettini
- Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
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8
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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9
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Transition between Random and Periodic Electron Currents on a DNA Chain. Int J Mol Sci 2021; 22:ijms22147361. [PMID: 34298980 PMCID: PMC8303785 DOI: 10.3390/ijms22147361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.
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10
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Energy transfer to the phonons of a macromolecule through light pumping. Sci Rep 2021; 11:6591. [PMID: 33758269 PMCID: PMC7988022 DOI: 10.1038/s41598-021-85856-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/22/2021] [Indexed: 12/23/2022] Open
Abstract
In the present paper we address the problem of the energy downconversion of the light absorbed by a protein into its internal vibrational modes. We consider the case in which the light receptors are fluorophores either naturally co-expressed with the protein or artificially covalently bound to some of its amino acids. In a recent work [Phys. Rev. X 8, 031061 (2018)], it has been experimentally found that by shining a laser light on the fluorophores attached to a protein the energy fed to it can be channeled into the normal mode of lowest frequency of vibration thus making the subunits of the protein coherently oscillate. Even if the phonon condensation phenomenon has been theoretically explained, the first step - the energy transfer from electronic excitation into phonon excitation - has been left open. The present work is aimed at filling this gap.
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11
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Manjula V, Prasad TV, Balakrishna K, Raju KCJ, Vishwam T. Influence of hydrogen bond networks in Glycerol / N-Methyl-2-Pyrrolidone mixtures studied by dielectric relaxation spectroscopy. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Investigation of the Electrical Properties of Microtubule Ensembles under Cell-Like Conditions. NANOMATERIALS 2020; 10:nano10020265. [PMID: 32033331 PMCID: PMC7075204 DOI: 10.3390/nano10020265] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
Microtubules are hollow cylindrical polymers composed of the highly negatively-charged (~23e), high dipole moment (1750 D) protein α, β- tubulin. While the roles of microtubules in chromosomal segregation, macromolecular transport, and cell migration are relatively well-understood, studies on the electrical properties of microtubules have only recently gained strong interest. Here, we show that while microtubules at physiological concentrations increase solution capacitance, free tubulin has no appreciable effect. Further, we observed a decrease in electrical resistance of solution, with charge transport peaking between 20-60 Hz in the presence of microtubules, consistent with recent findings that microtubules exhibit electric oscillations at such low frequencies. We were able to quantify the capacitance and resistance of the microtubules (MT) network at physiological tubulin concentrations to be 1.27 × 10-5 F and 9.74 × 104 Ω. Our results show that in addition to macromolecular transport, microtubules also act as charge storage devices through counterionic condensation across a broad frequency spectrum. We conclude with a hypothesis of an electrically tunable cytoskeleton where the dielectric properties of tubulin are polymerisation-state dependent.
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13
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Abstract
Biomacromolecules and engineered materials can achieve molecular recognition if they engage their ligand with properly oriented and chemically complementary moieties. Recently, there has been significant interest in fabricating recognitive soft materials, which possess specific affinity for biological analytes. We present a summary and evaluation of current recognitive materials for biosensing, drug delivery, and regenerative medicine applications. We highlight the impact of material composition on the extent and specificity of ligand adsorption, citing new theoretical and empirical evidence. We conclude with a guide for synthesizing and characterizing novel recognitive materials, as well as recommendations for ligand selection and experimental design.
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Affiliation(s)
- John R Clegg
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street Stop C0800, Austin, TX 78712, USA.
| | - Nicholas A Peppas
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street Stop C0800, Austin, TX 78712, USA. and McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX 78712, USA and Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, 107 W Dean Keeton Street Stop C0800, Austin, TX 78712, USA and Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 2409 University Ave. Stop A1900, Austin, TX 78712, USA and Department of Surgery and Perioperative Care, Dell Medical School, 1601 Trinity St., Bldg. B, Stop Z0800, Austin, TX 78712, USA and Department of Pediatrics, Dell Medical School, 1400 Barbara Jordan Blvd., Austin, TX 7872, USA
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14
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Fiscelli G, Rizzuto L, Passante R. Dispersion Interaction between Two Hydrogen Atoms in a Static Electric Field. PHYSICAL REVIEW LETTERS 2020; 124:013604. [PMID: 31976703 DOI: 10.1103/physrevlett.124.013604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Indexed: 06/10/2023]
Abstract
We consider the dispersion interaction between two ground-state hydrogen atoms, interacting with the quantum electromagnetic field in the vacuum state, in the presence of an external static electric field, both in the nonretarded and in the retarded Casimir-Polder regime. We show that the presence of the external field strongly modifies the dispersion interaction between the atoms, changing its space dependence. Moreover, we find that, for specific geometrical configurations of the two atoms with respect to the external field and/or the relative orientation of the fields acting on the two atoms, it is possible to change the character of the dispersion force, turning it from attractive to repulsive, or even make it vanishing. This new finding clearly shows the possibility to control and tailor interatomic dispersion interactions through external actions. By a numerical estimate of the field-modified interaction, we show that at typical interatomic distances the change of the interaction's strength can match or even outmatch the unperturbed interaction; this can be obtained for values of the external field that can be currently achieved in the laboratory, and sufficiently weak to be taken into account perturbatively.
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Affiliation(s)
- Giuseppe Fiscelli
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università degli Studi di Palermo, Via Archirafi 36, I-90123 Palermo, Italia and INFN, Laboratori Nazionali del Sud, I-95123 Catania, Italy
| | - Lucia Rizzuto
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università degli Studi di Palermo, Via Archirafi 36, I-90123 Palermo, Italia and INFN, Laboratori Nazionali del Sud, I-95123 Catania, Italy
| | - Roberto Passante
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università degli Studi di Palermo, Via Archirafi 36, I-90123 Palermo, Italia and INFN, Laboratori Nazionali del Sud, I-95123 Catania, Italy
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15
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Nishiyama A, Tanaka S, Tuszynski JA. Nonequilibrium quantum brain dynamics. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Fang W, Li GX, Xu J, Yang Y. Enhancement of long-distance Casimir-Polder interaction between an excited atom and a cavity made of metamaterials. OPTICS EXPRESS 2019; 27:37753-37770. [PMID: 31878551 DOI: 10.1364/oe.27.037753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Within the framework of macroscopic quantum electrodynamics, we investigate both the radiation force and the potential of Casimir-Polder type acting on an excited cold two-level atom in a cavity made of left-handed materials and topological insulators. As the time-reversal symmetry is broken on the surface of the topological insulators, the spontaneous emission of the atom placed near the focus point(s) exhibits anisotropic properties. While the potential wells are normally shallow for topological trivial dielectric, they may be amplified in the presence of topological magnetoelectric effect. We find that when there exists only one focus point in the cavity, it is possible to boost the forces or the potential wells by up to one order of magnitude. Meanwhile, the lifetime of the atom could be prolonged owing to the focus effect of the left-handed materials, where the emitted photons can trace back to the atom and reabsorbed by itself. Our results indicate the possibility in forming long-lived potential wells, which may have potential applications in trapping and guiding cold atoms far away from the surface.
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Gagnér VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G. Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Sci Rep 2019; 9:19281. [PMID: 31848402 PMCID: PMC6917748 DOI: 10.1038/s41598-019-55777-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.
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Affiliation(s)
- Viktor Ahlberg Gagnér
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ida Lundholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Helena Rodilla
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Gleb Bourenkov
- European Molecular Biology Laboratory Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
| | - Thomas Schneider
- European Molecular Biology Laboratory Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
| | - Jan Stake
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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18
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Stöhr M, Tkatchenko A. Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions. SCIENCE ADVANCES 2019; 5:eaax0024. [PMID: 31853494 PMCID: PMC6910842 DOI: 10.1126/sciadv.aax0024] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 05/05/2023]
Abstract
Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions-the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems.
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19
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Timsit Y, Bennequin D. Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives. Int J Mol Sci 2019; 20:ijms20122911. [PMID: 31207893 PMCID: PMC6627100 DOI: 10.3390/ijms20122911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
In the past few decades, studies on translation have converged towards the metaphor of a “ribosome nanomachine”; they also revealed intriguing ribosome properties challenging this view. Many studies have shown that to perform an accurate protein synthesis in a fluctuating cellular environment, ribosomes sense, transfer information and even make decisions. This complex “behaviour” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. We analyse here the significance of this analogy and establish a preliminary link between two fields: ribosome structure-function studies and the analysis of information processing systems. This cross-disciplinary analysis opens new perspectives about the mechanisms of information transfer and processing in ribosomes and may provide new conceptual frameworks for the understanding of the behaviours of unicellular organisms.
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Affiliation(s)
- Youri Timsit
- Mediterranean Institute of Oceanography UM 110, Aix-Marseille Université, CNRS, IRD, Campus de Luminy, 13288 Marseille, France.
| | - Daniel Bennequin
- Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG) Université Paris Diderot, bâtiment Sophie-Germain, 8, place Aurélie Nemours, 75013 Paris, France.
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20
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Abstract
We investigate the dynamics of a population of identical biomolecules mimicked as electric dipoles with random orientations and positions in space and oscillating with their intrinsic frequencies. The biomolecules, beyond being coupled among themselves via the dipolar interaction, are also driven by a common external energy supply. A collective mode emerges by decreasing the average distance among the molecules as testified by the emergence of a clear peak in the power spectrum of the total dipole moment. This is due to a coherent vibration of the most part of the molecules at a frequency definitely larger than their own frequencies corresponding to a partial cluster synchronization of the biomolecules. These results can be verified experimentally via spectroscopic investigations of the strength of the intermolecular electrodynamic interactions, thus being able to test the possible biological relevance of the observed macroscopic mode.
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21
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Notararigo V, Passante R, Rizzuto L. Resonance interaction energy between two entangled atoms in a photonic bandgap environment. Sci Rep 2018; 8:5193. [PMID: 29581454 PMCID: PMC5980077 DOI: 10.1038/s41598-018-23416-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/09/2018] [Indexed: 11/09/2022] Open
Abstract
We consider the resonance interaction energy between two identical entangled atoms, where one is in the excited state and the other in the ground state. They interact with the quantum electromagnetic field in the vacuum state and are placed in a photonic-bandgap environment with a dispersion relation quadratic near the gap edge and linear for low frequencies, while the atomic transition frequency is assumed to be inside the photonic gap and near its lower edge. This problem is strictly related to the coherent resonant energy transfer between atoms in external environments. The analysis involves both an isotropic three-dimensional model and the one-dimensional case. The resonance interaction asymptotically decays faster with distance compared to the free-space case, specifically as 1/r2 compared to the 1/r free-space dependence in the three-dimensional case, and as 1/r compared to the oscillatory dependence in free space for the one-dimensional case. Nonetheless, the interaction energy remains significant and much stronger than dispersion interactions between atoms. On the other hand, spontaneous emission is strongly suppressed by the environment and the correlated state is thus preserved by the spontaneous-decay decoherence effects. We conclude that our configuration is suitable for observing the elusive quantum resonance interaction between entangled atoms.
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Affiliation(s)
- Valentina Notararigo
- Department of Physics and Astronomy, University College London, Gower Street, London, WC1E 6BT, UK
| | - Roberto Passante
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Via Archirafi 36, I-90123, Palermo, Italy. .,INFN, Laboratori Nazionali del Sud, I-95123, Catania, Italy.
| | - Lucia Rizzuto
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Via Archirafi 36, I-90123, Palermo, Italy.,INFN, Laboratori Nazionali del Sud, I-95123, Catania, Italy
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22
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Kurian P, Capolupo A, Craddock TJA, Vitiello G. Water-mediated correlations in DNA-enzyme interactions. PHYSICS LETTERS. A 2018; 382:33-43. [PMID: 29403145 PMCID: PMC5796540 DOI: 10.1016/j.physleta.2017.10.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In this paper we consider dipole-mediated correlations between DNA and enzymes in the context of their water environment. Such correlations emerge from electric dipole-dipole interactions between aromatic ring structures in DNA and in enzymes. We show that there are matching collective modes between DNA and enzyme dipole fields, and that a dynamic time-averaged polarization vanishes in the water dipole field only if either DNA, enzyme, or both are absent from the sample. This persistent field may serve as the electromagnetic image that, in popular colloquialisms about DNA biochemistry, allows enzymes to "scan" or "read" the double helix. Topologically nontrivial configurations in the coherent ground state requiring clamplike enzyme behavior on the DNA may stem, ultimately, from spontaneously broken gauge symmetries.
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Affiliation(s)
- P. Kurian
- Quantum Biology Laboratory, National Human Genome Center and Department of Medicine, Howard University College of Medicine, Washington, DC 20059, USA
| | - A. Capolupo
- Università degli Studi di Salerno and INFN Gruppo Collegato di Salerno, 84084 Fisciano (Salerno), Italy
| | - T. J. A. Craddock
- Departments of Psychology and Neuroscience, Computer Science, and Clinical Immunology, and Clinical Systems Biology Group, Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - G. Vitiello
- Università degli Studi di Salerno and INFN Gruppo Collegato di Salerno, 84084 Fisciano (Salerno), Italy
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23
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Nardecchia I, Lechelon M, Gori M, Donato I, Preto J, Floriani E, Jaeger S, Mailfert S, Marguet D, Ferrier P, Pettini M. Detection of long-range electrostatic interactions between charged molecules by means of fluorescence correlation spectroscopy. Phys Rev E 2017; 96:022403. [PMID: 28950524 DOI: 10.1103/physreve.96.022403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/07/2022]
Abstract
In the present paper, an experimental feasibility study on the detection of long-range intermolecular interactions through three-dimensional molecular diffusion in solution is performed. This follows recent theoretical and numerical analyses reporting that long-range electrodynamic forces between biomolecules could be identified through deviations from Brownian diffusion. The suggested experimental technique was fluorescence correlation spectroscopy (FCS). By considering two oppositely charged molecular species in aqueous solution, namely, lysozymes and fluorescent dye molecules (Alexa488), the diffusion coefficient of the dyes has been measured for different values of the concentration of lysozyme, that is, for different average distances between the oppositely charged molecules. For our model, long-range interactions are of electrostatic origin, suggesting that their action radius can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular dynamics simulations provide a clear and unambiguous interpretation of the experimental results.
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Affiliation(s)
- Ilaria Nardecchia
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Mathias Lechelon
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | - Matteo Gori
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | - Irene Donato
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France
| | - Jordane Preto
- Department of Oncology, 3-336, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Elena Floriani
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | | | | | - Didier Marguet
- Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Marco Pettini
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
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24
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Preto J. Semi-classical statistical description of Fröhlich condensation. J Biol Phys 2017; 43:167-184. [PMID: 28197797 DOI: 10.1007/s10867-017-9442-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/03/2017] [Indexed: 12/23/2022] Open
Abstract
Fröhlich's model equations describing phonon condensation in open systems of biological relevance are reinvestigated within a semi-classical statistical framework. The main assumptions needed to deduce Fröhlich's rate equations are identified and it is shown how they lead us to write an appropriate form for the corresponding master equation. It is shown how solutions of the master equation can be numerically computed and can highlight typical features of the condensation effect. Our approach provides much more information compared to the existing ones as it allows to investigate the time evolution of the probability density function instead of following single averaged quantities. The current work is also motivated, on the one hand, by recent experimental evidences of long-lived excited modes in the protein structure of hen-egg white lysozyme, which were reported as a consequence of the condensation effect, and, on the other hand, by a growing interest in investigating long-range effects of electromagnetic origin and their influence on the dynamics of biochemical reactions.
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Affiliation(s)
- Jordane Preto
- Department of Oncology, 3-336, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada.
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25
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Preto J. Classical investigation of long-range coherence in biological systems. CHAOS (WOODBURY, N.Y.) 2016; 26:123116. [PMID: 28039969 DOI: 10.1063/1.4971963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Almost five decades ago, H. Fröhlich [H. Fröhlich, "Long-range coherence and energy storage in biological systems," Int. J. Quantum Chem. 2(5), 641-649 (1968)] reported, on a theoretical basis, that the excitation of quantum modes of vibration in contact with a thermal reservoir may lead to steady states, where under high enough rate of energy supply, only specific low-frequency modes of vibration are strongly excited. This nonlinear phenomenon was predicted to occur in biomolecular systems, which are known to exhibit complex vibrational spectral properties, especially in the terahertz frequency domain. However, since the effects of terahertz or lower-frequency modes are mainly classical at physiological temperatures, there are serious doubts that Fröhlich's quantum description can be applied to predict such a coherent behavior in a biological environment, as suggested by the author. In addition, a quantum formalism makes the phenomenon hard to investigate using realistic molecular dynamics simulations (MD) as they are usually based on the classical principles. In the current paper, we provide a general classical Hamiltonian description of a nonlinear open system composed of many degrees of freedom (biomolecular structure) excited by an external energy source. It is shown that a coherent behaviour similar to Fröhlich's effect is to be expected in the classical case for a given range of parameter values. Thus, the supplied energy is not completely thermalized but stored in a highly ordered fashion. The connection between our Hamiltonian description, carried out in the space of normal modes, and a more standard treatment in the physical space is emphasized in order to facilitate the prediction of the effect from MD simulations. It is shown how such a coherent phenomenon may induce long-range resonance effects that could be of critical importance at the biomolecular level. The present work is motivated by recent experimental evidences of long-lived excited low-frequency modes in protein structures, which were reported as a consequence of the Fröhlich's effect.
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Affiliation(s)
- Jordane Preto
- Department of Oncology, 3-336, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
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26
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Tuszynski JA, Wenger C, Friesen DE, Preto J. An Overview of Sub-Cellular Mechanisms Involved in the Action of TTFields. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E1128. [PMID: 27845746 PMCID: PMC5129338 DOI: 10.3390/ijerph13111128] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 10/23/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Long-standing research on electric and electromagnetic field interactions with biological cells and their subcellular structures has mainly focused on the low- and high-frequency regimes. Biological effects at intermediate frequencies between 100 and 300 kHz have been recently discovered and applied to cancer cells as a therapeutic modality called Tumor Treating Fields (TTFields). TTFields are clinically applied to disrupt cell division, primarily for the treatment of glioblastoma multiforme (GBM). In this review, we provide an assessment of possible physical interactions between 100 kHz range alternating electric fields and biological cells in general and their nano-scale subcellular structures in particular. This is intended to mechanistically elucidate the observed strong disruptive effects in cancer cells. Computational models of isolated cells subject to TTFields predict that for intermediate frequencies the intracellular electric field strength significantly increases and that peak dielectrophoretic forces develop in dividing cells. These findings are in agreement with in vitro observations of TTFields' disruptive effects on cellular function. We conclude that the most likely candidates to provide a quantitative explanation of these effects are ionic condensation waves around microtubules as well as dielectrophoretic effects on the dipole moments of microtubules. A less likely possibility is the involvement of actin filaments or ion channels.
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Affiliation(s)
- Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Cornelia Wenger
- The Institute of Biophysics and Biomedical Engineering, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal.
| | - Douglas E Friesen
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Jordane Preto
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
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27
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Gori M, Donato I, Floriani E, Nardecchia I, Pettini M. Random walk of passive tracers among randomly moving obstacles. Theor Biol Med Model 2016; 13:13. [PMID: 27075996 PMCID: PMC4831201 DOI: 10.1186/s12976-016-0038-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/19/2016] [Indexed: 12/03/2022] Open
Abstract
Background This study is mainly motivated by the need of understanding how the diffusion behavior of a biomolecule (or even of a larger object) is affected by other moving macromolecules, organelles, and so on, inside a living cell, whence the possibility of understanding whether or not a randomly walking biomolecule is also subject to a long-range force field driving it to its target. Method By means of the Continuous Time Random Walk (CTRW) technique the topic of random walk in random environment is here considered in the case of a passively diffusing particle among randomly moving and interacting obstacles. Results The relevant physical quantity which is worked out is the diffusion coefficient of the passive tracer which is computed as a function of the average inter-obstacles distance. Conclusions The results reported here suggest that if a biomolecule, let us call it a test molecule, moves towards its target in the presence of other independently interacting molecules, its motion can be considerably slowed down.
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Affiliation(s)
- Matteo Gori
- Aix-Marseille Université, Marseille, France.,CNRS Centre de Physique Théorique UMR7332, Marseille, 13288, France
| | - Irene Donato
- Aix-Marseille Université, Marseille, France.,CNRS Centre de Physique Théorique UMR7332, Marseille, 13288, France
| | - Elena Floriani
- Aix-Marseille Université, Marseille, France.,CNRS Centre de Physique Théorique UMR7332, Marseille, 13288, France
| | - Ilaria Nardecchia
- CNRS Centre de Physique Théorique UMR7332, Marseille, 13288, France.,Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, 13288, France
| | - Marco Pettini
- Aix-Marseille Université, Marseille, France. .,CNRS Centre de Physique Théorique UMR7332, Marseille, 13288, France.
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28
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Pokorný J, Pokorný J, Foletti A, Kobilková J, Vrba J, Vrba J. Mitochondrial Dysfunction and Disturbed Coherence: Gate to Cancer. Pharmaceuticals (Basel) 2015; 8:675-95. [PMID: 26437417 PMCID: PMC4695805 DOI: 10.3390/ph8040675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/06/2015] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
Continuous energy supply, a necessary condition for life, excites a state far from thermodynamic equilibrium, in particular coherent electric polar vibrations depending on water ordering in the cell. Disturbances in oxidative metabolism and coherence are a central issue in cancer development. Oxidative metabolism may be impaired by decreased pyruvate transfer to the mitochondrial matrix, either by parasitic consumption and/or mitochondrial dysfunction. This can in turn lead to disturbance in water molecules’ ordering, diminished power, and coherence of the electromagnetic field. In tumors with the Warburg (reverse Warburg) effect, mitochondrial dysfunction affects cancer cells (fibroblasts associated with cancer cells), and the electromagnetic field generated by microtubules in cancer cells has low power (high power due to transport of energy-rich metabolites from fibroblasts), disturbed coherence, and a shifted frequency spectrum according to changed power. Therapeutic strategies restoring mitochondrial function may trigger apoptosis in treated cells; yet, before this step is performed, induction (inhibition) of pyruvate dehydrogenase kinases (phosphatases) may restore the cancer state. In tumor tissues with the reverse Warburg effect, Caveolin-1 levels should be restored and the transport of energy-rich metabolites interrupted to cancer cells. In both cancer phenotypes, achieving permanently reversed mitochondrial dysfunction with metabolic-modulating drugs may be an effective, specific anti-cancer strategy.
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Affiliation(s)
- Jiří Pokorný
- Institute of Photonics and Electronics, Czech Academy of Sciences, Chaberská 57, 182 51 Prague 8, Czech Republic.
| | - Jan Pokorný
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic.
| | - Alberto Foletti
- Institute of Translational Pharmacology, National Research Council-CNR, Via Fosso del Cavaliere 100, Rome 00133, Italy.
- Clinical Biophysics International Research Group, via Maggio 21, Lugano 6900, Switzerland.
| | - Jitka Kobilková
- Department of Obstetrics and Gynaecology, 1st Faculty of Medicine, Charles University in Prague, Apolinářská 18, 128 00 Prague 2, Czech Republic.
| | - Jan Vrba
- Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic.
| | - Jan Vrba
- Faculty of Biomedical Engineering, Czech Technical University in Kladno, Sitná Square 3105, 272 01 Kladno, Czech Republic.
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