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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: 1] [Impact Index Per Article: 0.5] [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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Mercado-Uribe H, Guevara-Pantoja FJ, García-Muñoz W, García-Maldonado JS, Méndez-Alcaraz JM, Ruiz-Suárez JC. On the evolution of the exclusion zone produced by hydrophilic surfaces: A contracted description. J Chem Phys 2021; 154:194902. [PMID: 34240904 DOI: 10.1063/5.0043084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
After exciting scientific debates about its nature, the development of the exclusion zone, a region near hydrophilic surfaces from which charged colloidal particles are strongly expelled, has been finally traced back to the diffusiophoresis produced by unbalanced ion gradients. This was done by numerically solving the coupled Poisson equation for electrostatics, the two stationary Stokes equations for low Reynolds numbers in incompressible fluids, and the Nernst-Planck equation for mass transport. Recently, it has also been claimed that the leading mechanism behind the diffusiophoretic phenomenon is electrophoresis [Esplandiu et al., Soft Matter 16, 3717 (2020)]. In this paper, we analyze the evolution of the exclusion zone based on a one-component interaction model at the Langevin equation level, which leads to simple analytical expressions instead of the complex numerical scheme of previous works, yet being consistent with it. We manage to reproduce the evolution of the exclusion zone width and the mean-square displacements of colloidal particles we measure near Nafion, a perfluorinated polymer membrane material, along with all characteristic time regimes, in a unified way. Our findings are also strongly supported by complementary experiments using two parallel planar conductors kept at a fixed voltage, mimicking the hydrophilic surfaces, and some computer simulations.
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Affiliation(s)
- H Mercado-Uribe
- CINVESTAV-Monterrey, PIIT, 66600 Apodaca, Nuevo León, Mexico
| | | | - W García-Muñoz
- CINVESTAV-Monterrey, PIIT, 66600 Apodaca, Nuevo León, Mexico
| | - J S García-Maldonado
- Departamento de Física, CINVESTAV, Av. IPN 2508, Col. San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - J M Méndez-Alcaraz
- Departamento de Física, CINVESTAV, Av. IPN 2508, Col. San Pedro Zacatenco, 07360 Ciudad de México, Mexico
| | - J C Ruiz-Suárez
- CINVESTAV-Monterrey, PIIT, 66600 Apodaca, Nuevo León, Mexico
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Morelli AM, Ravera S, Calzia D, Panfoli I. An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane. Open Biol 2020; 9:180221. [PMID: 30966998 PMCID: PMC6501646 DOI: 10.1098/rsob.180221] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.
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Affiliation(s)
- Alessandro Maria Morelli
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Silvia Ravera
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
| | - Daniela Calzia
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Isabella Panfoli
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
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Sharma A, Adams C, Cashdollar BD, Li Z, Nguyen NV, Sai H, Shi J, Velchuru G, Zhu KZ, Pollack GH. Effect of Health-Promoting Agents on Exclusion-Zone Size. Dose Response 2018; 16:1559325818796937. [PMID: 30202249 PMCID: PMC6122250 DOI: 10.1177/1559325818796937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 12/03/2022] Open
Abstract
It is now well-confirmed that hydrophilic surfaces including those within the cell generate structural changes in water. This interfacial water is ordered and acquires features different from the bulk. Amongst those features is the exclusion of colloidal and molecular solutes from extensive regions next to the hydrophilic surface, thereby earning it the label of "exclusion zone" (EZ) water. The transition of ordered EZ water to bulk serves as an important trigger of many cellular physiological functions, and in turn cellular health. We tested physiological doses of half a dozen agents generally identified to restore or build health on the extent to which they build EZs. All agents known to enhance biological function resulted in EZ expansion. On the other hand, the weed killer, glyphosate, considerably diminished EZ size. While the expansion effect of the health-promoting agents was observed over a wide range of concentrations, excessive doses ultimately reduced EZ size. We hypothesize that EZ buildup may be a mechanistic feature underlying many health-promoting agents, while agents that impair health may act by diminishing the amount of EZ water.
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Affiliation(s)
- Abha Sharma
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Colby Adams
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | | | - Zheng Li
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Nam V. Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Himasri Sai
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Jiachun Shi
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Gautham Velchuru
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Kevin Z. Zhu
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
| | - Gerald H. Pollack
- Department of Bioengineering, University of Washington, Seattle, WA,
USA
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Riveros-Perez E, Riveros R. Water in the human body: An anesthesiologist's perspective on the connection between physicochemical properties of water and physiologic relevance. Ann Med Surg (Lond) 2017; 26:1-8. [PMID: 29904607 PMCID: PMC5904784 DOI: 10.1016/j.amsu.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/10/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022] Open
Abstract
The unique structure and multifaceted physicochemical properties of the water molecule, in addition to its universal presence in body compartments, make water a key player in multiple biological processes in human physiology. Since anesthesiologists deal with physiologic processes where water molecules are critical at different levels, and administer medications whose pharmacokinetics and pharmacodynamics depend on interaction with water molecules, we consider that exploration of basic science aspects related to water and its role in physiology and pharmacology is relevant to the practice of anesthesiology. The purpose of this paper is to delineate the physicochemical basis of water that are critical in enabling it to support various homeostatic processes. The role of water in the formation of solutions, modulation of surface tension and in homeostasis of body temperature, acid-base status and osmolarity, is analyzed. Relevance of molecular water interactions to the anesthesiologist is not limited to the realm of physiology and pathophysiology. Deep knowledge of the importance of water in volatile anesthetic effects on neurons opens a window to a new comprehensive understanding of complex cellular mechanisms underlying the practice of anesthesiology.
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Affiliation(s)
- Efraín Riveros-Perez
- Department of Anesthesiology and Perioperative Medicine, Augusta University, USA
| | - Ricardo Riveros
- Pediatric Anesthesiologist Nemours Children's Health System, Orlando, FL, USA
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