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Zhu L, Zhao W, Yan Y, Liao X, Bourtsalas A, Dan Y, Xiao H, Chen X. Interaction between mechanosensitive channels embedded in lipid membrane. J Mech Behav Biomed Mater 2019; 103:103543. [PMID: 31783284 DOI: 10.1016/j.jmbbm.2019.103543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/07/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
The study of the gating mechanism of mechanosensitive channels opens a window to the exploration of how different mechanical stimuli induce adaptive cellular behaviors of both the protein and the lipid, across different time and length scales. In this work, through a molecular dynamics-decorated finite element method (MDeFEM), the gating behavior of mechanosensitive channels of small conductance (MscS) in Escherichia coli (E. coli) is studied upon membrane stretch or global bending. The local membrane curvature around MscS is incorporated, as well as multiple MscL (mechanosensitive channels of large conductance) molecules in proximity to MscS. The local membrane curvature is found to delay MscS opening and diminishes moderately upon membrane stretching. Mimicking the insertion of lysophosphatidylcholine (LPC) molecules into the lipid, both downward and upward bending can active MscS, as long as the global membrane curvature radius reaches 34 nm. Based on the different MscS pore evolutions observed with the presence of one or more MscLs nearby, we propose that when coreconstituted, multiple MscL molecules tend to be located at the local membrane curvature zone around MscS. In another word, as MscL "swims around" in the lipid bilayer, it can be trapped by the membrane's local curvature. Collectively, the current study provides valuable insights into the interplay between mechanosensitive channels and lipid membrane at structural and physical levels, and specific predictions are proposed for further experimental investigations.
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Affiliation(s)
- Liangliang Zhu
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Wei Zhao
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China
| | - Yuan Yan
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China
| | - Xiangbiao Liao
- Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
| | - Athanasios Bourtsalas
- Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
| | - Yong Dan
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China.
| | - Hang Xiao
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China.
| | - Xi Chen
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
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Gating and inactivation of mechanosensitive channels of small conductance: A continuum mechanics study. J Mech Behav Biomed Mater 2018; 90:502-514. [PMID: 30453114 DOI: 10.1016/j.jmbbm.2018.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/27/2018] [Accepted: 10/30/2018] [Indexed: 11/21/2022]
Abstract
Mechanosensitive channels of small conductance (MscS) in Escherichia coli (E. coli) serve as a paradigm for understanding the gating behaviors of the MscS family of ion channels. In this work, we develop a continuum mechanics framework to explore the conformational states of MscS during the gating transition. A complete gating transition trajectory from the closed to the open state along with partially open intermediates is obtained, and the open structure is close to the available structural model from crystallographic studies. The computational efficiency of the modeling framework makes it possible to explore the roles of various structural elements (e.g., loops that connect transmembrane helices) and specific interactions in the gating transition. It is observed that removing either the Asp62-Arg131 salt bridge or the Phe68-Leu111 non-polar interaction leads to essentially non-conducting structures even with a membrane tension close to the lysis limit. The loop connecting TM2 (the second transmembrane helix) and TM3 is found to be essential for force transmission during gating, while the loop connecting TM1 and TM2 does not make any major contribution. Based on the different structural evolutions observed when the TM3 kink is treated as a loop or a helical segment, we propose that the helical propensity of the kink plays a central role in inactivation; i.e., under prolonged sub-threshold membrane tension, transition of the initially flexible loop to a helical segment in TM3 may lead to MscS inactivation. Finally, the gating transition of MscS under different transmembrane voltages is explored and found to be essentially voltage independent. Collectively, results from the current continuum mechanics analysis provide further insights into the gating transition of MscS at structural and physical levels, and specific predictions are proposed for further experimental investigations.
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Bavi N, Martinac AD, Cortes DM, Bavi O, Ridone P, Nomura T, Hill AP, Martinac B, Perozo E. Structural Dynamics of the MscL C-terminal Domain. Sci Rep 2017; 7:17229. [PMID: 29222414 PMCID: PMC5722894 DOI: 10.1038/s41598-017-17396-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022] Open
Abstract
The large conductance mechanosensitive channel (MscL), acts as an osmoprotective emergency valve in bacteria by opening a large, water-filled pore in response to changes in membrane tension. In its closed configuration, the last 36 residues at the C-terminus form a bundle of five α-helices co-linear with the five-fold axis of symmetry. Here, we examined the structural dynamics of the C-terminus of EcMscL using site-directed spin labelling electron paramagnetic resonance (SDSL EPR) spectroscopy. These experiments were complemented with computational modelling including molecular dynamics (MD) simulations and finite element (FE) modelling. Our results show that under physiological conditions, the C-terminus is indeed an α-helical bundle, located near the five-fold symmetry axis of the molecule. Both experiments and computational modelling demonstrate that only the top part of the C-terminal domain (from the residue A110 to E118) dissociates during the channel gating, while the rest of the C-terminus stays assembled. This result is consistent with the view that the C-terminus functions as a molecular sieve and stabilizer of the oligomeric MscL structure as previously suggested.
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Affiliation(s)
- Navid Bavi
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- St. Vincent's Clinical School, The University of New South Wales, Darlinghurst (Sydney), New South Wales, 2010, Australia
| | - Adam D Martinac
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- School of Mechanical & Mining Engineering, University of Queensland, St. Lucia (Brisbane), QLD 4072, Brisbane, Australia
| | - D Marien Cortes
- Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Omid Bavi
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- Department of Physics, University of Tehran, Tehran, 1439955961, Iran
| | - Pietro Ridone
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- St. Vincent's Clinical School, The University of New South Wales, Darlinghurst (Sydney), New South Wales, 2010, Australia
| | - Takeshi Nomura
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- Department of Rehabilitation, Kyushu Nutrition Welfare University, Kitakyushu, 800-029, Japan
| | - Adam P Hill
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia
- St. Vincent's Clinical School, The University of New South Wales, Darlinghurst (Sydney), New South Wales, 2010, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, New South Wales, 2010, Australia.
- St. Vincent's Clinical School, The University of New South Wales, Darlinghurst (Sydney), New South Wales, 2010, Australia.
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th St, Chicago, Illinois, 60637, USA.
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Martinac AD, Bavi N, Bavi O, Martinac B. Pulling MscL open via N-terminal and TM1 helices: A computational study towards engineering an MscL nanovalve. PLoS One 2017; 12:e0183822. [PMID: 28859093 PMCID: PMC5578686 DOI: 10.1371/journal.pone.0183822] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/11/2017] [Indexed: 11/18/2022] Open
Abstract
There are great opportunities in the manipulation of bacterial mechanosensitive (MS) ion channels for specific and targeted drug delivery purposes. Recent research has shown that these ion channels have the potential to be converted into nanovalves through clever use of magnetic nanoparticles and magnetic fields. Using a combination of molecular dynamics (MD) simulations and the finite element (FE) modelling, this study investigates the theoretical feasibility of opening the MscL channel (MS channel of large conductance of E. coli) by applying mechanical force directly to its N-terminus. This region has already been reported to function as a major mechanosensor in this channel. The stress-strain behaviour of each MscL helix was obtained using all atom MD simulations. Using the same method, we simulated two models, the wild-type (WT) MscL and the G22N mutant MscL, both embedded in a POPE lipid bilayer. In addition to indicating the main interacting residues at the hydrophobic pore, their pairwise interaction energies were monitored during the channel gating. We implemented these inputs into our FE model of MscL using curve-fitting codes and continuum mechanics equations. In the FE model, the channel could be fully opened via pulling directly on the N-terminus and bottom of TM1 by mutating dominant van der Waals interactions in the channel pore; otherwise the stress generated on the channel protein can irreversibly unravel the N-secondary structure. This is a significant finding suggesting that applying force in this manner is sufficient to open an MscL nanovalve delivering various drugs used, for example, in cancer chemotherapy. More importantly, the FE model indicates that to fully operate an MscL nanovalve by pulling directly on the N-terminus and bottom of TM1, gain-of-function (GOF) mutants (e.g., G22N MscL) would have to be employed rather than the WT MscL channel.
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Affiliation(s)
- Adam D. Martinac
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Navid Bavi
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Omid Bavi
- Department of Physics, University of Tehran, Tehran, Iran
| | - Boris Martinac
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
- * E-mail:
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Anishkin A, Sukharev S. Channel disassembled: Pick, tweak, and soak parts to soften. Channels (Austin) 2017; 11:173-175. [PMID: 28166450 DOI: 10.1080/19336950.2017.1291213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Andriy Anishkin
- a Department of Biology , University of Maryland , College Park , MD , USA
| | - Sergei Sukharev
- a Department of Biology , University of Maryland , College Park , MD , USA
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Bavi N, Bavi O, Vossoughi M, Naghdabadi R, Hill AP, Martinac B, Jamali Y. Nanomechanical properties of MscL α helices: A steered molecular dynamics study. Channels (Austin) 2016; 11:209-223. [PMID: 27753526 DOI: 10.1080/19336950.2016.1249077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during stretching and high dependency of the elastic properties on the pulling rate. We estimated Young's moduli of the α-helices of MscL to vary between 0.2 and 12.5 GPa with TM2 helix being the stiffest. We also studied the effect of water on the properties of the pore-lining TM1 helix. In the absence of water, this helix exhibited a much stiffer response. By monitoring the number of hydrogen bonds, it appears that water acts like a 'lubricant' (softener) during TM1 helix elongation. These data shed light on another physical aspect underlying hydrophobic gating of MS channels, in particular MscL.
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Affiliation(s)
- N Bavi
- a Division of Molecular Cardiology and Biophysics , Victor Chang Cardiac Research Institute , Darlinghurst , NSW , Australia.,b St Vincent's Clinical School, Faculty of Medicine , University of New South Wales , Darlinghurst , NSW , Australia
| | - O Bavi
- c Institute for Nanoscience and Nanotechnology, Sharif University of Technology , Tehran , Iran
| | - M Vossoughi
- c Institute for Nanoscience and Nanotechnology, Sharif University of Technology , Tehran , Iran.,d Biochemical & Bioenvironmental Research Center (BBRC) , Tehran , Iran
| | - R Naghdabadi
- c Institute for Nanoscience and Nanotechnology, Sharif University of Technology , Tehran , Iran.,e Department of Mechanical Engineering , Sharif University of Technology , Tehran , Iran
| | - A P Hill
- a Division of Molecular Cardiology and Biophysics , Victor Chang Cardiac Research Institute , Darlinghurst , NSW , Australia
| | - B Martinac
- a Division of Molecular Cardiology and Biophysics , Victor Chang Cardiac Research Institute , Darlinghurst , NSW , Australia.,b St Vincent's Clinical School, Faculty of Medicine , University of New South Wales , Darlinghurst , NSW , Australia
| | - Y Jamali
- f Department of Mathematics , Tarbiat Modares University , Tehran , Iran.,g Computational Physical Sciences Research Laboratory , School of Nanoscience, Institute for Research in Fundamental Sciences (IPM) , Tehran , Iran
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