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Guan L, Tan J, Qi B, Chen Y, Cao M, Zhang Q, Zou Y. Effects of an external static EF on the conformational transition of 5-HT1A receptor: A molecular dynamics simulation study. Biophys Chem 2024; 312:107283. [PMID: 38941873 DOI: 10.1016/j.bpc.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
The serotonin receptor subtype 1A (5-HT1AR), one of the G-protein-coupled receptor (GPCR) family, has been implicated in several neurological conditions. Understanding the activation and inactivation mechanism of 5-HT1AR at the molecular level is critical for discovering novel therapeutics in many diseases. Recently there has been a growing appreciation for the role of external electric fields (EFs) in influencing the structure and activity of biomolecules. In this study, we used molecular dynamics (MD) simulations to examine conformational features of active states of 5-HT1AR and investigate the effect of an external static EF with 0.02 V/nm applied on the active state of 5-HT1AR. Our results showed that the active state of 5-HT1AR maintained the native structure, while the EF led to structural modifications in 5-HT1AR, particularly inducing the inward movement of transmembrane helix 6 (TM6). Furthermore, it disturbed the conformational switches associated with activation in the CWxP, DRY, PIF, and NPxxY motifs, consequently predisposing an inclination towards the inactive-like conformation. We also found that the EF led to an overall increase in the dipole moment of 5-HT1AR, encompassing TM6 and pivotal amino acids. The analyses of conformational properties of TM6 showed that the changed secondary structure and decreased solvent exposure occurred upon the EF condition. The interaction of 5-HT1AR with the membrane lipid bilayer was also altered under the EF. Our findings reveal the molecular mechanism underlying the transition of 5-HT1AR conformation induced by external EFs, which offer potential novel insights into the prospect of employing structure-based EF applications for GPCRs.
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Affiliation(s)
- Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Yukang Chen
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Meng Cao
- Department of Physical Education, College of Sport, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518061, PR China
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, PR China
| | - Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China.
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Wu S, Yang X, Jing H, Chu Y, Yuan J, Zhu Z, Huang K. Effect of external electric fields on sulfur dioxide–water systems. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Tang J, Ma J, Guo L, Wang K, Yang Y, Bo W, Yang L, Jiang H, Wu Z, Zeng B, Gong Y. The Effect of KcsA Channel on Lipid Bilayer Electroporation Induced by Picosecond Pulse Trains. J Membr Biol 2020; 253:271-286. [PMID: 32405692 DOI: 10.1007/s00232-020-00123-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023]
Abstract
Membrane proteins are the major component of plasma membranes, and they play crucial roles in all organisms. To understand the influence of the presence of KcsA channel on cell membrane electroporation induced by picosecond pulse trains (psPT), in this paper, the electroporation of KcsA membrane protein system and bare lipid bilayer system (POPC) with the applied psPT are simulated using molecular dynamics (MD) method. First, we find that the average pore formation time of the KcsA system is longer than the bare system with the applied psPT. In the KcsA system, water protrusions appear more slowly. Then, the system size effects of psPT in the MD simulations are investigated. When the system size decreases, the average pore formation time of small KcsA membrane protein system is shorter than the bare system with the applied psPT. It is found that the psPT makes the protein fluctuation of small system increase greatly; meanwhile the instability of protein disturbs the water and then affects the water protrusion appearance time. Furthermore, it shows that the protein fluctuation of constant electric field is smaller than that of psPT and no field, and protein fluctuation increases with the psPT repetition frequency increasing.
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Affiliation(s)
- Jingchao Tang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,CNRS, UMR 7565, 54506, Vandoeuvre les Nancy, France
| | - Jialu Ma
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lianghao Guo
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Kaicheng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yang Yang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Wenfei Bo
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lixia Yang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Haibo Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Zhe Wu
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Baoqing Zeng
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
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In Vitro and MD Simulation Study to Explore Physicochemical Parameters for Antibacterial Peptide to Become Potent Anticancer Peptide. MOLECULAR THERAPY-ONCOLYTICS 2019; 16:7-19. [PMID: 31909181 PMCID: PMC6940675 DOI: 10.1016/j.omto.2019.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023]
Abstract
Although the physicochemical properties of antimicrobial peptides (AMPs) and anticancer peptides (ACPs) are very similar, it remains unclear which specific parameter(s) of ACPs confer the major anticancer activity. By answering how to construct a short AMP/ACP that could easily be synthesized in the most cost effective way plus conferring a maximum anticancer effect is a very important scientific breakthrough in the development of protein/peptide drugs. In this study, an 18-amino-acids antimicrobial peptide, AcrAP1 (named AP1-Z1), was used as a template. Bioinformatics algorithms were then performed to design its six mutants (AP1-Z3a, AP1-Z3b, AP1-Z5a, AP1-Z5b, AP1-Z7, and AP1-Z9). After a series of in vitro experiments plus intensive computational analysis, the data demonstrated that AP1-Z5a and AP1-Z5b induced both apoptosis and anti-angiogenic effects to achieve the maximum anticancer activity. Specifically, the most effective mutant, AP1-Z5b, exhibited high selectivity for the charged membrane in molecular dynamics simulations. These findings clearly demonstrated that both charge and hydrophobicity play an important role and are necessary to reach an optimum equilibrium for optimizing the anticancer activity of AMPs. Overall, the present study provides a very crucial theoretical basis and important scientific evidence on the key physicochemical parameters of ACP drugs development.
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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Han J, Pluhackova K, Bruns D, Böckmann RA. Synaptobrevin transmembrane domain determines the structure and dynamics of the SNARE motif and the linker region. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:855-65. [DOI: 10.1016/j.bbamem.2016.01.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/06/2016] [Accepted: 01/27/2016] [Indexed: 12/29/2022]
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Ritos K, Borg MK, Mottram NJ, Reese JM. Electric fields can control the transport of water in carbon nanotubes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0025. [PMID: 26712640 PMCID: PMC4696074 DOI: 10.1098/rsta.2015.0025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/12/2015] [Indexed: 06/05/2023]
Abstract
The properties of water confined inside nanotubes are of considerable scientific and technological interest. We use molecular dynamics to investigate the structure and average orientation of water flowing within a carbon nanotube. We find that water exhibits biaxial paranematic liquid crystal ordering both within the nanotube and close to its ends. This preferred molecular ordering is enhanced when an axial electric field is applied, affecting the water flow rate through the nanotube. A spatially patterned electric field can minimize nanotube entrance effects and significantly increase the flow rate.
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Affiliation(s)
- Konstantinos Ritos
- Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow G1 1XJ, UK
| | - Matthew K Borg
- School of Engineering, University of Edinburgh, Edinburgh EH9 3FB, UK
| | - Nigel J Mottram
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow G1 1XH, UK
| | - Jason M Reese
- School of Engineering, University of Edinburgh, Edinburgh EH9 3FB, UK
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English NJ, Waldron CJ. Perspectives on external electric fields in molecular simulation: progress, prospects and challenges. Phys Chem Chem Phys 2016; 17:12407-40. [PMID: 25903011 DOI: 10.1039/c5cp00629e] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.
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Affiliation(s)
- Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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Escoffre JM, Bellard E, Faurie C, Sébaï SC, Golzio M, Teissié J, Rols MP. Membrane disorder and phospholipid scrambling in electropermeabilized and viable cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1701-9. [PMID: 24583083 DOI: 10.1016/j.bbamem.2014.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/11/2014] [Accepted: 02/19/2014] [Indexed: 11/25/2022]
Abstract
Membrane electropermeabilization relies on the transient permeabilization of the plasma membrane of cells submitted to electric pulses. This method is widely used in cell biology and medicine due to its efficiency to transfer molecules while limiting loss of cell viability. However, very little is known about the consequences of membrane electropermeabilization at the molecular and cellular levels. Progress in the knowledge of the involved mechanisms is a biophysical challenge. As a transient loss of membrane cohesion is associated with membrane permeabilization, our main objective was to detect and visualize at the single-cell level the incidence of phospholipid scrambling and changes in membrane order. We performed studies using fluorescence microscopy with C6-NBD-PC and FM1-43 to monitor phospholipid scrambling and membrane order of mammalian cells. Millisecond permeabilizing pulses induced membrane disorganization by increasing the translocation of phosphatidylcholines according to an ATP-independent process. The pulses induced the formation of long-lived permeant structures that were present during membrane resealing, but were not associated with phosphatidylcholine internalization. These pulses resulted in a rapid phospholipid flip/flop within less than 1s and were exclusively restricted to the regions of the permeabilized membrane. Under such electrical conditions, phosphatidylserine externalization was not detected. Moreover, this electrically-mediated membrane disorganization was not correlated with loss of cell viability. Our results could support the existence of direct interactions between the movement of membrane zwitterionic phospholipids and the electric field.
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Affiliation(s)
- Jean-Michel Escoffre
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077, Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077, Toulouse, France
| | - Elisabeth Bellard
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077, Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077, Toulouse, France
| | - Cécile Faurie
- Matwin-Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux cedex, France
| | - Sarra C Sébaï
- Eviagenics, Immeuble Villejuif Biopark, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - Muriel Golzio
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077, Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077, Toulouse, France
| | - Justin Teissié
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077, Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077, Toulouse, France.
| | - Marie-Pierre Rols
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077, Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077, Toulouse, France.
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Abstract
Membrane electropermeabilization is the observation that the permeability of a cell membrane can be transiently increased when a micro-millisecond external electric field pulse is applied on a cell suspension or on a tissue. Applicative aspects for the transfer of foreign molecules (macromolecules) into the cytoplasm are routinely used. But only a limited knowledge about what is really occurring in the cell and its membranes at the molecular levels is available. This chapter is a critical attempt to report the present state of the art and to point out some of the still open problems. The experimental facts associated to membrane electropermeabilization are firstly reported. They are valid on biological and model systems. Secondly, soft matter approaches give access to the bioelectrochemical description of the thermodynamical constraints supporting the destabilization of simplified models of the biological membrane. It is indeed described as a thin dielectric leaflet, where a molecular transport takes place by electrophoresis and then diffusion. This naïve approach is due to the lack of details on the structural aspects affecting the living systems as shown in a third part. Membranes are part of the cell machinery. The critical property of cells as being an open system from the thermodynamical point of view is almost never present. Computer simulations are now contributing to our knowledge on electropermeabilization. The last part of this chapter is a (very) critical report of all the efforts that have been performed. The final conclusion remains that we still do not know all the details on the reversible structural and dynamical alterations of the cell membrane (and cytoplasm) supporting its electropermeabilization. We have a long way in basic and translational researches to reach a pertinent description.
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Affiliation(s)
- Justin Teissie
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
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Membrane-proximal tryptophans of synaptobrevin II stabilize priming of secretory vesicles. J Neurosci 2013; 32:15983-97. [PMID: 23136435 DOI: 10.1523/jneurosci.6282-11.2012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Trans-soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) receptor (SNARE) complexes formed between the SNARE motifs of synaptobrevin II, SNAP-25, and syntaxin play an essential role in Ca(2+)-regulated exocytosis. Apart from the well studied interactions of the SNARE domains, little is known about the functional relevance of other evolutionarily conserved structures in the SNARE proteins. Here, we show that substitution of two highly conserved tryptophan residues within the juxtamembrane domain (JMD) of the vesicular SNARE Synaptobrevin II (SybII) profoundly impairs priming of granules in mouse chromaffin cells without altering catecholamine release from single vesicles. Using molecular dynamic simulations of membrane-embedded SybII, we show that Trp residues of the JMD influence the electrostatic surface potential by controlling the position of neighboring lysine and arginine residues at the membrane-water interface. Our observations indicate a decisive role of the tryptophan moiety of SybII in keeping the vesicles in the release-ready state and support a model wherein tryptophan-mediated protein-lipid interactions assist in bridging the apposing membranes before fusion.
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Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:294-302. [PMID: 22001851 DOI: 10.1016/j.bbamem.2011.09.030] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/28/2011] [Accepted: 09/26/2011] [Indexed: 01/29/2023]
Abstract
Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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Daub CD, Bratko D, Luzar A. Nanoscale Wetting Under Electric Field from Molecular Simulations. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:155-79. [DOI: 10.1007/128_2011_188] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Gurtovenko AA, Anwar J, Vattulainen I. Defect-Mediated Trafficking across Cell Membranes: Insights from in Silico Modeling. Chem Rev 2010; 110:6077-103. [DOI: 10.1021/cr1000783] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Jamshed Anwar
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Ilpo Vattulainen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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Fiche JB, Laredo T, Tanchak O, Lipkowski J, Dutcher JR, Yada RY. Influence of an electric field on oriented films of DMPC/gramicidin bilayers: a circular dichroism study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1057-1066. [PMID: 20067313 DOI: 10.1021/la902325n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A film of oriented bilayers containing a mixture of gramicidin and dimyristoylphosphatidylcholine (DMPC) has been deposited on a fused-silica window coated with a 10 nm thick gold layer. The thin layer of gold allows the application of an electric potential across the film and the study of its influence on the structure and integrity of the bilayers. Electrochemical measurements, ellipsometry, and far-UV circular dichroism (CD) were employed to characterize the properties of the film of bilayers as a function of the potential applied to the gold electrode. For potentials across the film that are within the range approximately +300 to -150 mV the oriented film of bilayers is stable, and no change in the CD spectra of gramicidin molecule is observed. At more negative potentials, an increase in the film thickness and water content measured by ellipsometry indicated that the film swells and incorporates water, which causes a change in the circular dichroism spectrum of gramicidin molecules in the film. This transformation was interpreted as a change in the average orientation of gramicidin molecules within the film due to a decrease in the ordering of the molecules upon swelling.
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Affiliation(s)
- J B Fiche
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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van Uitert I, Le Gac S, van den Berg A. The influence of different membrane components on the electrical stability of bilayer lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:21-31. [DOI: 10.1016/j.bbamem.2009.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 10/01/2009] [Accepted: 10/06/2009] [Indexed: 11/25/2022]
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Hu Z, Jiang J. Chiral Separation of Racemic Phenylglycines in Thermolysin Crystal: A Molecular Simulation Study. J Phys Chem B 2009; 113:15851-7. [DOI: 10.1021/jp9055889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zhongqiao Hu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576
| | - Jianwen Jiang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576
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Schulz R, Kleinekathöfer U. Transitions between closed and open conformations of TolC: the effects of ions in simulations. Biophys J 2009; 96:3116-25. [PMID: 19383457 DOI: 10.1016/j.bpj.2009.01.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 01/06/2009] [Accepted: 01/14/2009] [Indexed: 11/19/2022] Open
Abstract
Bacteria, such as Escherichia coli, use multidrug efflux pumps to export toxic substrates through their cell membranes. Upon formation of an efflux pump, the aperture of its outer membrane protein TolC opens and thereby enables the extrusion of substrate molecules. The specialty of TolC is its ability to dock to different transporters, making it a highly versatile export protein. Within this study, the transition between two conformations of TolC that are both available as crystal structures was investigated using all-atom molecular dynamics simulations. To create a partially open conformation from a closed one, the stability of the periplasmic aperture was weakened by a double point mutation at the constricting ring, which removes some salt bridges and hydrogen bonds. These mutants, which showed partial opening in previous experiments, did not spontaneously open during a 20-ns equilibration at physiological values of the KCl solution. Detailed analysis of the constricting ring revealed that the cations of the solvent were able to constitute ionic bonds in place of the removed salt bridges, which inhibited the opening of the aperture in simulations. To remove the ions from these binding positions within the available simulation time, an extra force was applied onto the ions. To keep the effect of this additional force rather flexible, it was applied in form of an artificial external electric field perpendicular to the membrane. Depending on the field direction and the ion concentration, these simulations led to a partial opening. In experiments, this energy barrier for the ions can be overcome by thermal fluctuations on a longer timescale.
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Hu Z, Jiang J. Separation of amino acids in glucose isomerase crystal: Insight from molecular dynamics simulations. J Chromatogr A 2009; 1216:5122-9. [DOI: 10.1016/j.chroma.2009.04.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/21/2009] [Accepted: 04/24/2009] [Indexed: 10/20/2022]
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22
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Siu SWI, Böckmann RA. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J Phys Chem B 2009; 113:3195-202. [DOI: 10.1021/jp810302k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shirley W. I. Siu
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
| | - Rainer A Böckmann
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
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Hu Z, Jiang J. Electrophoresis in protein crystal: nonequilibrium molecular dynamics simulations. Biophys J 2008; 95:4148-56. [PMID: 18641079 PMCID: PMC2567938 DOI: 10.1529/biophysj.108.140160] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Accepted: 07/08/2008] [Indexed: 11/18/2022] Open
Abstract
Electrophoresis of a mixture of NaCl and CaCl2 in a lysozyme crystal is investigated using nonequilibrium molecular dynamics (MD) simulations. Upon exposure to an electric field, the stability of lysozyme is found to decrease slightly. This finding is demonstrated by increases in the root mean-square deviations of the heavy atoms of lysozyme, in the solvent-accessible surface area of hydrophobic residues, and in the number of hydrogen bonds between lysozyme and water. The solvent-accessible surface area of hydrophilic residues changes marginally, and the number of hydrogen bonds between lysozyme molecules decreases. Water molecules tend to align preferentially parallel to the electric field, and the dipole moment along the pore axis increases linearly with increasing field strength. Two pronounced layered structures are observed for Na+ and Ca2+ in the vicinity of protein surface, but only one enriched layer is observed for Cl-. The number distributions of all ions are nearly independent of the electric field. The water coordination numbers of all ions are smaller in the crystal than in aqueous bulk solution; however, the reverse is found for the Cl- coordination numbers of cations. Both the water and the Cl- coordination numbers are insensitive to the electric field. Ion diffusivities in the crystal are approximately 2 orders of magnitude smaller than those in aqueous bulk solution. The drift velocities of ions increase proportionally to the electric field, particularly at high strengths, and depend on ionic charge and coordination with oppositely charged ions. Electrical current exhibits a linear relationship with the field strength. The zero-field electrical conductivity is estimated to be 0.56 S/m, which is very close to 0.61 S/m as predicted by the Nernst-Einstein equation.
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Affiliation(s)
- Zhongqiao Hu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576
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Corvis Y, Korchowiec B, Korchowiec J, Badis M, Mironiuk-Puchalska E, Fokt I, Priebe W, Rogalska E. Complexation of metal ions in Langmuir films formed with two amphiphilic dioxadithia crown ethers. J Phys Chem B 2008; 112:10953-63. [PMID: 18698707 DOI: 10.1021/jp803072b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two new crown ethers presented in this study were synthesized in order to investigate two important features of ionophores, namely metal cation complexation and interfacial properties, and the way in which they interrelate. The two derivatives were conceived as analogs of membrane phospholipids with respect to their amphiphilicity and geometry. They contain a hydrophilic 1,1'-dioxo-3,3'-dithio-14-crown ether headgroup and bear two myristoyl or stearoyl lateral chains. The length of the myristoyl and stearoyl derivatives in an extended conformation is comparable with the thickness of the individual leaflets of cell membranes. The membrane-related and complexation properties of the two crown ether derivatives were studied in monomolecular films spread on pure water and on aqueous solutions of mono-, di-, and trivalent metal salts. The properties of the monolayers are described quantitatively using thermodynamic models. The compression isotherms of the monolayers formed on different subphases show a clear-cut differentiation of the monovalent and di- or trivalent cations with both ligands. This differentiation was interpreted in terms of conformational changes occurring in the crown ether derivatives upon complexation. Molecular modeling indicates that the mono- and divalent cations are coordinated differently by the ligands, yielding complexes with different conformations. The differences of the conformations of the mono- and di- or trivalent cation complexes may be important from the point of view of the interactions with lipid membranes and the biological activity of these potential ionophores.
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Affiliation(s)
- Yohann Corvis
- Groupe d'Etude des Vecteurs Supramoléculaires du Médicament, Faculté des Sciences, BP 239, UMR 7565 CNRS/Nancy Université, 54506 Vandoeuvre-lès-Nancy cedex, France
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Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J 2008; 95:1837-50. [PMID: 18469089 DOI: 10.1529/biophysj.108.129437] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane electroporation is the method to directly transfer bioactive substances such as drugs and genes into living cells, as well as preceding electrofusion. Although much information on the microscopic mechanism has been obtained both from experiment and simulation, the existence and nature of possible intermediates is still unclear. To elucidate intermediates of electropore formation by direct comparison with measured prepore formation kinetics, we have carried out 49 atomistic electroporation simulations on a palmitoyl-oleoyl-phosphatidylcholine bilayer for electric field strengths between 0.04 and 0.7 V/nm. A statistical theory is developed to facilitate direct comparison of experimental (macroscopic) prepore formation kinetics with the (single event) preporation times derived from the simulations, which also allows us to extract an effective number of lipids involved in each pore formation event. A linear dependency of the activation energy for prepore formation on the applied field is seen, with quantitative agreement between experiment and simulation. The distribution of preporation times suggests a four-state pore formation model. The model involves a first intermediate characterized by a differential tilt of the polar lipid headgroups on both leaflets, and a second intermediate (prepore), where a polar chain across the bilayer is formed by 3-4 lipid headgroups and several water molecules, thereby providing a microscopic explanation for the polarizable volume derived previously from the measured kinetics. An average pore radius of 0.47 +/- 0.15 nm is seen, in favorable agreement with conductance measurements and electrooptical experiments of lipid vesicles.
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Siu SWI, Vácha R, Jungwirth P, Böckmann RA. Biomolecular simulations of membranes: Physical properties from different force fields. J Chem Phys 2008; 128:125103. [DOI: 10.1063/1.2897760] [Citation(s) in RCA: 227] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bratko D, Daub CD, Luzar A. Field-exposed water in a nanopore: liquid or vapour? Phys Chem Chem Phys 2008; 10:6807-13. [DOI: 10.1039/b809072f] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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