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Cao Y, Wei H, Jiang S, Lu T, Nie P, Yang C, Liu N, Lee I, Meng X, Wang W, Yuan Z. Effect of AQP4 and its palmitoylation on the permeability of exogenous reactive oxygen species: Insights from computational study. Int J Biol Macromol 2023; 253:127568. [PMID: 37866582 DOI: 10.1016/j.ijbiomac.2023.127568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Aquaporin 4 (AQP4) facilitates the transport of reactive oxygen species (ROS). Both cancer cells and the ionizing radiation microenvironment can induce posttranslational modifications (PTMs) in AQP4, which may affect its permeability to ROS. Because this ROS diffusion process is rapid, microscopic, and instantaneous within and outside cells, conventional experimental methods are inadequate for elucidating the molecular mechanisms involved. In this study, computational methods were employed to investigate the permeability of exogenous ROS mediated by radiation in AQP4 at a molecular scale. We constructed a simulation system incorporating AQP4 and AQP4-Cysp13 in a complex lipid environment with ROS. Long-timescale molecular dynamics simulations were conducted to assess the structural stability of both AQP4 and AQP4-Cysp13. Free energy calculations were utilized to determine the ROS transport capability of the two AQP4 proteins. Computational electrophysiology and channel structural analysis quantitatively evaluated changes in ROS transport capacity under various radiation-induced transmembrane voltage microenvironments. Our findings demonstrate the distinct transport capabilities of AQP4 channels for water molecules and various types of ROS and reveal a decrease in transport efficiency when AQP4 undergoes palmitoylation modification. In addition, we have simulated the radiation-induced alteration of cell membrane voltage, which significantly affected the ROS transport capacity. We propose that this research will enhance the understanding of the molecular mechanisms governing the transport of exogenous ROS by AQP4 and elucidate the influence of palmitoylation on ROS transport. This study will also help clarify how different structural features of AQP4 affect the transport of exogenous ROS mediated by radiotherapy, thereby providing a theoretical molecular basis for the development of new treatment strategies that combine with radiotherapy.
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Affiliation(s)
- Yipeng Cao
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China; National Supercomputer Center in Tianjin, 300457, PR China.
| | - Hui Wei
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Shengpeng Jiang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Tong Lu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Pengfei Nie
- National Supercomputer Center in Tianjin, 300457, PR China
| | - Chengwen Yang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Ningbo Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin 300071, PR China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, 300457, PR China.
| | - Wei Wang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China.
| | - Zhiyong Yuan
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China.
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Rahimi Z, Koslowski T, Lohrasebi A. Water purification modeling by functionalized hourglass-shape multilayer nano-channel. J Mol Graph Model 2023; 125:108599. [PMID: 37586129 DOI: 10.1016/j.jmgm.2023.108599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
In this study, inspired by the overall structure and operation of the aquaporin channel, graphene-based nanochannels are proposed to be used as potential membranes for the water purification process. To this end, an hourglass-shaped channel has been designed using the three-layer porous graphene sheets and the effects of some main channel's elements, such as the channel bending angle and attached functional groups to it, on the filtration performance have been examined by using molecular dynamics simulations. We find that a suitable bending channel shape can improve the channel efficiency, i.e. both the water permeability and the ion rejection rate of the suitable bent channels were more than for the straight channels. In addition, regarding the different functionalized channels, the half-functionalized channels were more efficient than the completed functionalized ones. Furthermore, by monitoring the dynamics of water molecules as they pass through the narrowest part of the channels, it was found that water molecule rotation assists water transport.
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Affiliation(s)
- Zeinab Rahimi
- Department of Physics, University of Isfahan, Isfahan, 8174673441, Iran; Institute for Physical Chemistry, University of Freiburg, Albertstrasse 21, D-79104, Freiburg, Germany
| | - Thorsten Koslowski
- Institute for Physical Chemistry, University of Freiburg, Albertstrasse 21, D-79104, Freiburg, Germany
| | - Amir Lohrasebi
- Department of Physics, University of Isfahan, Isfahan, 8174673441, Iran.
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Salehi N, Lohrasebi A, Bordbar AK. Preventing the amyloid-beta peptides accumulation on the cell membrane by applying GHz electric fields: A molecular dynamic simulation. J Mol Graph Model 2023; 123:108516. [PMID: 37216829 DOI: 10.1016/j.jmgm.2023.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease is associated with accumulating different amyloid peptides on the nerve cell membranes. The non-thermal effects of the GHz electric fields in this topic have yet to be well recognized. Hence, in this study, the impacts of 1 and 5 GHz electric fields on the amyloid peptide proteins accumulation on the cell membrane have been investigated, utilizing molecular dynamics (MD) simulation. The obtained results indicated that this range of electric fields did not significantly affect the peptide structure. Moreover, it was found that the peptide penetration into the membrane was increased as the field frequency was increased when the system was exposed to a 20 mv/nm oscillating electric field. In addition, it was observed that the protein-membrane interaction is reduced significantly in the presence of the 70 mv/nm electric field. The molecular level results reported in this study could be helpful in better understanding Alzheimer's disease.
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Affiliation(s)
- N Salehi
- Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran
| | - A Lohrasebi
- Department of Physics, University of Isfahan, Isfahan, 81746-73441, Iran.
| | - A K Bordbar
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
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Rahimi Z, Lohrasebi A. Impacts of external electric fields on the permeation of glycerol and water molecules through aquaglyceroporin-7: molecular dynamics simulation approach. Eur Phys J E Soft Matter 2023; 46:3. [PMID: 36656387 DOI: 10.1140/epje/s10189-023-00261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The aquaglyceroporin-7 (AQP7) protein channels facilitate the permeation of glycerol and water molecules through cell membranes by passive diffusion and play a crucial role in cell physiology. Considering the wide-spirit usage of radiofrequency electromagnetic fields in our daily life, in this study, the effects of constant and GHz electric fields were investigated on the dynamics of glycerol and water molecules inside the AQP7. To this end, four different molecular simulation groups were carried out in the absence and presence of electric fields. The results reveal that the free energy profile of the glycerol permeation inside the channel is reduced in the presence of the field of 0.2 mV/nm and the oscillating field of 10 GHz. In addition, exposing the channel to the electric field of 0.2 mV/nm assisted the water transport through the channel with no considerable effect on channel stability. These observations provide a framework for understanding how such fields could alter normal operation of protein channels, which may lead to disease beginning or being used in disease treatment. Glycerol and water molecules permeation through the aquaglyceroporin-7 channel can be influenced by application of external electric fields.
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Affiliation(s)
- Zeinab Rahimi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran
| | - Amir Lohrasebi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran.
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Pluhackova K, Schittny V, Bürkner P, Siligan C, Horner A. Multiple pore lining residues modulate water permeability of
GlpF. Protein Sci 2022; 31:e4431. [PMID: 36173178 PMCID: PMC9490802 DOI: 10.1002/pro.4431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Kristyna Pluhackova
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075 University of Stuttgart Stuttgart Germany
| | - Valentin Schittny
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule (ETH) Zurich Basel Switzerland
| | - Paul‐Christian Bürkner
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075 University of Stuttgart Stuttgart Germany
| | | | - Andreas Horner
- Institute of Biophysics Johannes Kepler University Linz Austria
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