1
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Foley SL, Deserno M. Quantifying uncertainty in trans-membrane stresses and moments in simulation. Methods Enzymol 2024; 701:83-122. [PMID: 39025584 DOI: 10.1016/bs.mie.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The lateral stress profile of a lipid bilayer constitutes a valuable link between molecular simulation and mesoscopic elastic theory. Even though it is frequently calculated in simulations, its statistical precision (or that of observables derived from it) is often left unspecified. This omission can be problematic, as uncertainties are prerequisite to assessing statistical significance. In this chapter, we provide a comprehensive yet accessible overview of the statistical error analysis for the lateral stress profile. We detail two relatively simple but powerful techniques for generating error bars: block-averaging and bootstrapping. Combining these methods allows us to reliably estimate uncertainties, even in the presence of both temporal and spatial correlations, which are ubiquitous in simulation data. We illustrate these techniques with simple examples like stress moments, but also more complex observables such as the location of stress profile extrema and the monolayer neutral surface.
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Affiliation(s)
- Samuel L Foley
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States.
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, United States
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2
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Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules. MEMBRANES 2022; 12:membranes12040350. [PMID: 35448320 PMCID: PMC9032087 DOI: 10.3390/membranes12040350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a Staphylococcus aureus bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer’s electrostatic potential. Conducting asymmetric loading of molecules in only one leaflet, it was observed that anionic and cationic amphiphiles have a large impact on the Staphylococcus aureus membrane’s electrostatic potential and lateral pressure profile as compared to a symmetric distribution. Nonintuitively, we find that the cationic and anionic molecules induce a similar change in the electrostatic potential, which points to the complexity of membrane interfaces, and how asymmetry can induce biophysical consequences. Finally, we link changes in membrane structure to the rate of electroporation for the membranes, and again find a crucial impact of introducing asymmetry to the system. Understanding these physical mechanisms provides critical insights and viable pathways for the rational design of membrane-active molecules, where controlling the localization is key.
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3
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Specific adsorption and highly sensitive detection of methyl red in wastewater using an iron paste electrode modified with a molecularly imprinted polymer. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2021.107144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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4
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Grage SL, Culetto A, Ulrich AS, Weinschenk S. Membrane-Mediated Activity of Local Anesthetics. Mol Pharmacol 2021; 100:502-512. [PMID: 34475108 DOI: 10.1124/molpharm.121.000252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/19/2021] [Indexed: 01/06/2023] Open
Abstract
The activity of local anesthetics (LAs) has been attributed to the inhibition of ion channels, causing anesthesia. However, there is a growing body of research showing that LAs act on a wide range of receptors and channel proteins far beyond simple analgesia. The current concept of ligand recognition may no longer explain the multitude of protein targets influenced by LAs. We hypothesize that LAs can cause anesthesia without directly binding to the receptor proteins just by changing the physical properties of the lipid bilayer surrounding these proteins and ion channels based on LAs' amphiphilicity. It is possible that LAs act in one of the following ways: They 1) dissolve raft-like membrane microdomains, 2) impede nerve impulse propagation by lowering the lipid phase transition temperature, or 3) modulate the lateral pressure profile of the lipid bilayer. This could also explain the numerous additional effects of LAs besides anesthesia. Furthermore, the concepts of membrane-mediated activity and binding to ion channels do not have to exclude each other. If we were to consider LA as the middle part of a continuum between unspecific membrane-mediated activity on one end and highly specific ligand binding on the other end, we could describe LA as the link between the unspecific action of general anesthetics and toxins with their highly specific receptor binding. This comprehensive membrane-mediated model offers a fresh perspective to clinical and pharmaceutical research and therapeutic applications of local anesthetics. SIGNIFICANCE STATEMENT: Local anesthetics, according to the World Health Organization, belong to the most important drugs available to mankind. Their rediscovery as therapeutics and not only anesthetics marks a milestone in global pain therapy. The membrane-mediated mechanism of action proposed in this review can explain their puzzling variety of target proteins and their thus far inexplicable therapeutic effects. The new concept presented here places LAs on a continuum of structures and molecular mechanisms in between small general anesthetics and the more complex molecular toxins.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Anke Culetto
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Stefan Weinschenk
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
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5
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Rajeshwar T R, Anishkin A, Sukharev S, Vanegas JM. Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach. Biophys J 2020; 120:232-242. [PMID: 33333032 DOI: 10.1016/j.bpj.2020.11.2274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 02/02/2023] Open
Abstract
Membrane tension perceived by mechanosensitive (MS) proteins mediates cellular responses to mechanical stimuli and osmotic stresses, and it also guides multiple biological functions including cardiovascular control and development. In bacteria, MS channels function as tension-activated pores limiting excessive turgor pressure, with MS channel of large conductance (MscL) acting as an emergency release valve preventing cell lysis. Previous attempts to simulate gating transitions in MscL by either directly applying steering forces to the protein or by increasing the whole-system tension were not fully successful and often disrupted the integrity of the system. We present a novel, to our knowledge, locally distributed tension molecular dynamics (LDT-MD) simulation method that allows application of forces continuously distributed among lipids surrounding the channel using a specially constructed collective variable. We report reproducible and reversible transitions of MscL to the open state with measured parameters of lateral expansion and conductivity that exactly satisfy experimental values. The LDT-MD method enables exploration of the MscL-gating process with different pulling velocities and variable tension asymmetry between the inner and outer membrane leaflets. We use LDT-MD in combination with well-tempered metadynamics to reconstruct the tension-dependent free-energy landscape for the opening transition in MscL. The flexible definition of the LDT collective variable allows general application of our method to study mechanical activation of any membrane-embedded protein.
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Affiliation(s)
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, Maryland
| | - Juan M Vanegas
- Department of Physics, University of Vermont, Burlington, Vermont.
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6
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Complexity of seemingly simple lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183420. [DOI: 10.1016/j.bbamem.2020.183420] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
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7
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Jefferies D, Khalid S. Atomistic and coarse-grained simulations of membrane proteins: A practical guide. Methods 2020; 185:15-27. [PMID: 32084518 DOI: 10.1016/j.ymeth.2020.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are amphipathic macromolecules whose exposed hydrophobic surfaces promote interactions with lipid membranes. Membrane proteins are remarkably diverse in terms of chemical composition and correspondingly, their biological functions and general biophysical behavior. Conventional experimental techniques provide an approach to study specific properties of membrane proteins e.g. their surface features, the nature and abundance of stabilizing intramolecular forces, preferred bilayer orientation, and the characteristics of their annular lipid shells. Molecular modeling software-and in particular, the suite of molecular dynamics algorithms-enables a more comprehensive exploration of dynamic membrane protein behavior. Molecular dynamics methods enable users to produce stepwise trajectories of proteins on arbitrary spatiotemporal scales that enable the easy identification of dynamic interactions that are beyond the scope of conventional analytical techniques. This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions.
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Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.
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8
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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9
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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10
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Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018; 57:5418-5422. [PMID: 29528530 PMCID: PMC6142180 DOI: 10.1002/anie.201801498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/29/2022]
Abstract
Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating-associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg2+ ; whereas Na+ switches it to the expanded state, as revealed by MD simulations, small-angle X-ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure-function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.
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Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition Case Western Reserve University 10900 Euclid Ave, Cleveland, OH 44106-4988 (USA)
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
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11
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Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition; Case Western Reserve University; 10900 Euclid Ave Cleveland OH 44106-4988 USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
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12
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Melo M, Arnarez C, Sikkema H, Kumar N, Walko M, Berendsen HJC, Kocer A, Marrink SJ, Ingólfsson HI. High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. J Am Chem Soc 2017; 139:2664-2671. [PMID: 28122455 PMCID: PMC5343553 DOI: 10.1021/jacs.6b11091] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Indexed: 12/18/2022]
Abstract
The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight-chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL-bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.
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Affiliation(s)
- Manuel
N. Melo
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Clément Arnarez
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Hendrik Sikkema
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Neeraj Kumar
- Groningen
Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Martin Walko
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Herman J. C. Berendsen
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Armagan Kocer
- Department
of Neuroscience, University Medical Center
Groningen, University of Groningen, Antonius Deusinglaan 1, 99713 AV, Groningen, The
Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Groningen
Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG, Groningen, The Netherlands
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
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13
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Karamdad K, Law RV, Seddon JM, Brooks NJ, Ces O. Studying the effects of asymmetry on the bending rigidity of lipid membranes formed by microfluidics. Chem Commun (Camb) 2016; 52:5277-80. [PMID: 27001410 DOI: 10.1039/c5cc10307j] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this article we detail a robust high-throughput microfluidic platform capable of fabricating either symmetric or asymmetric giant unilamellar vesicles (GUVs) and characterise the mechanical properties of their membranes.
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Affiliation(s)
- K Karamdad
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. and Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - R V Law
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. and Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - J M Seddon
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. and Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - N J Brooks
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. and Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - O Ces
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. and Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
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14
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Bruhn DS, Lomholt MA, Khandelia H. Quantifying the Relationship between Curvature and Electric Potential in Lipid Bilayers. J Phys Chem B 2016; 120:4812-7. [DOI: 10.1021/acs.jpcb.6b03439] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dennis S. Bruhn
- MEMPHYS - Center for Biomembrane
Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Michael A. Lomholt
- MEMPHYS - Center for Biomembrane
Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Himanshu Khandelia
- MEMPHYS - Center for Biomembrane
Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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15
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Abstract
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
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16
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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17
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Ingólfsson HI, Thakur P, Herold KF, Hobart EA, Ramsey NB, Periole X, de Jong DH, Zwama M, Yilmaz D, Hall K, Maretzky T, Hemmings HC, Blobel C, Marrink SJ, Koçer A, Sack JT, Andersen OS. Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem Biol 2014; 9:1788-98. [PMID: 24901212 PMCID: PMC4136704 DOI: 10.1021/cb500086e] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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A wide
variety of phytochemicals are consumed for their perceived
health benefits. Many of these phytochemicals have been found to alter
numerous cell functions, but the mechanisms underlying their biological
activity tend to be poorly understood. Phenolic phytochemicals are
particularly promiscuous modifiers of membrane protein function, suggesting
that some of their actions may be due to a common, membrane bilayer-mediated
mechanism. To test whether bilayer perturbation may underlie this
diversity of actions, we examined five bioactive phenols reported
to have medicinal value: capsaicin from chili peppers, curcumin from
turmeric, EGCG from green tea, genistein from soybeans, and resveratrol
from grapes. We find that each of these widely consumed phytochemicals
alters lipid bilayer properties and the function of diverse membrane
proteins. Molecular dynamics simulations show that these phytochemicals
modify bilayer properties by localizing to the bilayer/solution interface.
Bilayer-modifying propensity was verified using a gramicidin-based
assay, and indiscriminate modulation of membrane protein function
was demonstrated using four proteins: membrane-anchored metalloproteases,
mechanosensitive ion channels, and voltage-dependent potassium and
sodium channels. Each protein exhibited similar responses to multiple
phytochemicals, consistent with a common, bilayer-mediated mechanism.
Our results suggest that many effects of amphiphilic phytochemicals
are due to cell membrane perturbations, rather than specific protein
binding.
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Affiliation(s)
| | - Pratima Thakur
- Dept.
Physiology and Membrane Biology, University of California, Davis, California, United States
| | | | | | | | | | | | | | | | - Katherine Hall
- Hospital for Special
Surgery, New York, New York, United States
| | | | | | - Carl Blobel
- Hospital for Special
Surgery, New York, New York, United States
| | | | | | - Jon T. Sack
- Dept.
Physiology and Membrane Biology, University of California, Davis, California, United States
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18
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Mukherjee N, Jose MD, Birkner JP, Walko M, Ingólfsson HI, Dimitrova A, Arnarez C, Marrink SJ, Koçer A. The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating. FASEB J 2014; 28:4292-302. [PMID: 24958207 DOI: 10.1096/fj.14-251579] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
One of the best-studied mechanosensitive channels is the mechanosensitive channel of large conductance (MscL). MscL senses tension in the membrane evoked by an osmotic down shock and directly couples it to large conformational changes leading to the opening of the channel. Spectroscopic techniques offer unique possibilities to monitor these conformational changes if it were possible to generate tension in the lipid bilayer, the native environment of MscL, during the measurements. To this end, asymmetric insertion of l-α-lysophosphatidylcholine (LPC) into the lipid bilayer has been effective; however, how LPC activates MscL is not fully understood. Here, the effects of LPC on tension-sensitive mutants of a bacterial MscL and on MscL homologs with different tension sensitivities are reported, leading to the conclusion that the mode of action of LPC is different from that of applied tension. Our results imply that LPC shifts the free energy of gating by interfering with MscL-membrane coupling. Furthermore, we demonstrate that the fine-tuned addition of LPC can be used for controlled activation of MscL in spectroscopic studies.
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Affiliation(s)
- Nobina Mukherjee
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Mac Donald Jose
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Jan Peter Birkner
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands; and
| | - Martin Walko
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Anna Dimitrova
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Clément Arnarez
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Armağan Koçer
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands; Neuroscience Department, University Medical Centre Groningen, Groningen, The Netherlands
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19
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Ha-Duong T. Coarse-grained models of the proteins backbone conformational dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:157-69. [PMID: 24446361 DOI: 10.1007/978-3-319-02970-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coarse-grained models are more and more frequently used in the studies of the proteins structural and dynamic properties, since the reduced number of degrees of freedom allows to enhance the conformational space exploration. This chapter attempts to provide an overview of the various coarse-grained models that were applied to study the functional conformational changes of the polypeptides main chain around their native state. It will more specifically discuss the methods used to represent the protein backbone flexibility and to account for the physico-chemical interactions that stabilize the secondary structure elements.
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Affiliation(s)
- Tap Ha-Duong
- BIOCIS - UMR CNRS 8076, Faculté de Pharmacie - Université Paris Sud, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France,
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20
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Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
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Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
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21
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Dékány Fraňová M, Vattulainen I, Samuli Ollila O. Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1406-11. [DOI: 10.1016/j.bbamem.2014.01.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/07/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
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22
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Vanegas JM, Torres-Sánchez A, Arroyo M. Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations. J Chem Theory Comput 2014; 10:691-702. [DOI: 10.1021/ct4008926] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Juan M. Vanegas
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | | | - Marino Arroyo
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
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23
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Abstract
We show using a minimalistic theoretical framework that phase transition decoupling in lipid bilayers is caused by a nonuniform stress profile due to an asymmetric distribution of lipids between the two leaflets. Applying this framework to vesicles, we demonstrate that their anomalous freezing is also caused by a stress asymmetry, but that this is due to lipid tail extension on freezing. Finally, we predict a previously unknown dependence of surface tension on temperature, find the phenomenon also in coarse grained molecular dynamics simulations, and suggest that it might have relevance in thermosensitive protein gating.
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Affiliation(s)
- Antti Lamberg
- Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan.
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24
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Sakakibara K, Fujisawa T, Hill JP, Ariga K. Conformational interchange of a carbohydrate by mechanical compression at the air–water interface. Phys Chem Chem Phys 2014; 16:10286-94. [DOI: 10.1039/c3cp55078h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Bagatolli LA, Mouritsen OG. Is the fluid mosaic (and the accompanying raft hypothesis) a suitable model to describe fundamental features of biological membranes? What may be missing? FRONTIERS IN PLANT SCIENCE 2013; 4:457. [PMID: 24312108 PMCID: PMC3826152 DOI: 10.3389/fpls.2013.00457] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/24/2013] [Indexed: 05/08/2023]
Abstract
The structure, dynamics, and stability of lipid bilayers are controlled by thermodynamic forces, leading to overall tensionless membranes with a distinct lateral organization and a conspicuous lateral pressure profile. Bilayers are also subject to built-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes leading to the formation of non-lamellar and curved structures. A key controller of the bilayer's propensity to form curved structures is the average molecular shape of the different lipid molecules. Via the curvature stress, molecular shape mediates a coupling to membrane-protein function and provides a set of physical mechanisms for formation of lipid domains and laterally differentiated regions in the plane of the membrane. Unfortunately, these relevant physical features of membranes are often ignored in the most popular models for biological membranes. Results from a number of experimental and theoretical studies emphasize the significance of these fundamental physical properties and call for a refinement of the fluid mosaic model (and the accompanying raft hypothesis).
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Affiliation(s)
- Luis A. Bagatolli
- Center for Biomembrane Physics (MEMPHYS), University of Southern DenmarkOdense, Denmark
- Membrane Biophysics and Biophotonics group, Department of Biochemistry and Molecular Biology, University of Southern DenmarkOdense, Denmark
- *Correspondence: Luis A. Bagatolli, Center for Biomembrane Physics (MEMPHYS), University of Southern Denmark, Campusvej 55, Odense 5230, Denmark e-mail:
| | - Ole G. Mouritsen
- Center for Biomembrane Physics (MEMPHYS), University of Southern DenmarkOdense, Denmark
- Department of Physics, Chemistry, and Pharmacy, University of Southern DenmarkOdense, Denmark
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27
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Hu M, de Jong DH, Marrink SJ, Deserno M. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discuss 2013; 161:365-82; discussion 419-59. [PMID: 23805750 DOI: 10.1039/c2fd20087b] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We calculate the Gaussian curvature modulus kappa of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We find the value kappa/kappa = -1.04 +/- 0.03 for the elastic ratio between the Gaussian and the mean curvature modulus and deduce kappa(m)/kappa(m) = -0.98 +/- 0.09 for the monolayer elastic ratio, where the latter is based on plausible assumptions for the distance z0 of the monolayer neutral surface from the bilayer midplane and the spontaneous lipid curvature K(0m). By also analyzing the lateral stress profile sigma0(z) of our system, two other lipid types and pertinent data from the literature, we show that determining K(0m) and kappa through the first and second moment of sigma0(z) gives rise to physically implausible values for these observables. This discrepancy, which we previously observed for a much simpler CG model, suggests that the moment conditions derived from simple continuum assumptions miss the effect of physically important correlations in the lipid bilayer.
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Affiliation(s)
- Mingyang Hu
- Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
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28
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Bennett WD, Tieleman DP. Computer simulations of lipid membrane domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1765-76. [DOI: 10.1016/j.bbamem.2013.03.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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29
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Haselwandter CA, Phillips R. Connection between oligomeric state and gating characteristics of mechanosensitive ion channels. PLoS Comput Biol 2013; 9:e1003055. [PMID: 23696720 PMCID: PMC3656111 DOI: 10.1371/journal.pcbi.1003055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 03/08/2013] [Indexed: 01/06/2023] Open
Abstract
The mechanosensitive channel of large conductance (MscL) is capable of transducing mechanical stimuli such as membrane tension into an electrochemical response. MscL provides a widely-studied model system for mechanotransduction and, more generally, for how bilayer mechanical properties regulate protein conformational changes. Much effort has been expended on the detailed experimental characterization of the molecular structure and biological function of MscL. However, despite its central significance, even basic issues such as the physiologically relevant oligomeric states and molecular structures of MscL remain a matter of debate. In particular, tetrameric, pentameric, and hexameric oligomeric states of MscL have been proposed, together with a range of detailed molecular structures of MscL in the closed and open channel states. Previous theoretical work has shown that the basic phenomenology of MscL gating can be understood using an elastic model describing the energetic cost of the thickness deformations induced by MscL in the surrounding lipid bilayer. Here, we generalize this elastic model to account for the proposed oligomeric states and hydrophobic shapes of MscL. We find that the oligomeric state and hydrophobic shape of MscL are reflected in the energetic cost of lipid bilayer deformations. We make quantitative predictions pertaining to the gating characteristics associated with various structural models of MscL and, in particular, show that different oligomeric states and hydrophobic shapes of MscL yield distinct membrane contributions to the gating energy and gating tension. Thus, the functional properties of MscL provide a signature of the oligomeric state and hydrophobic shape of MscL. Our results suggest that, in addition to the hydrophobic mismatch between membrane proteins and the surrounding lipid bilayer, the symmetry and shape of the hydrophobic surfaces of membrane proteins play an important role in the regulation of protein function by bilayer membranes.
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Affiliation(s)
- Christoph A. Haselwandter
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
- Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (CAH); (RP)
| | - Rob Phillips
- Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (CAH); (RP)
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30
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Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B 2013; 117:3516-30. [PMID: 23406326 DOI: 10.1021/jp311533p] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hybrid molecular dynamics simulations of atomistic (AA) solutes embedded in coarse-grained (CG) environment can substantially reduce the computational cost with respect to fully atomistic simulations. However, interfacing both levels of resolution is a major challenge that includes a balanced description of the relevant interactions. This is especially the case for polar solvents such as water, which screen the electrostatic interactions and thus require explicit electrostatic coupling between AA and CG subsystems. Here, we present and critically test computationally efficient hybrid AA/CG models. We combined the Gromos atomistic force field with the MARTINI coarse-grained force field. To enact electrostatic coupling, two recently developed CG water models with explicit electrostatic interactions were used: the polarizable MARTINI water model and the BMW model. The hybrid model was found to be sensitive to the strength of the AA-CG electrostatic coupling, which was adjusted through the relative dielectric permittivity εr(AA-CG). Potentials of mean force (PMFs) between pairs of amino acid side chain analogues in water and partitioning free enthalpies of uncharged amino acid side chain analogues between apolar solvent and water show significant differences between the hybrid simulations and the fully AA or CG simulations, in particular for charged and polar molecules. For apolar molecules, the results obtained with the hybrid AA/CG models are in better agreement with the fully atomistic results. The structures of atomistic ubiquitin solvated in CG water and of a single atomistic transmembrane α-helix and the transmembrane portion of an atomistic mechanosensitive channel in CG lipid bilayers were largely maintained during 50-100 ns of AA/CG simulations, partly due to an overstabilization of intramolecular interactions. This work highlights some key challenges on the way toward hybrid AA/CG models that are both computationally efficient and sufficiently accurate for biomolecular simulations.
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Affiliation(s)
- Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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31
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Ollila OHS, Lamberg A, Lehtivaara M, Koivuniemi A, Vattulainen I. Interfacial tension and surface pressure of high density lipoprotein, low density lipoprotein, and related lipid droplets. Biophys J 2013; 103:1236-44. [PMID: 22995496 DOI: 10.1016/j.bpj.2012.08.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 07/02/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022] Open
Abstract
Lipid droplets play a central role in energy storage and metabolism on a cellular scale. Their core is comprised of hydrophobic lipids covered by a surface region consisting of amphiphilic lipids and proteins. For example, high and low density lipoproteins (HDL and LDL, respectively) are essentially lipid droplets surrounded by specific proteins, their main function being to transport cholesterol. Interfacial tension and surface pressure of these particles are of great interest because they are related to the shape and the stability of the droplets and to protein adsorption at the interface. Here we use coarse-grained molecular-dynamics simulations to consider a number of related issues by calculating the interfacial tension in protein-free lipid droplets, and in HDL and LDL particles mimicking physiological conditions. First, our results suggest that the curvature dependence of interfacial tension becomes significant for particles with a radius of ∼5 nm, when the area per molecule in the surface region is <1.4 nm(2). Further, interfacial tensions in the used HDL and LDL models are essentially unaffected by single apo-proteins at the surface. Finally, interfacial tensions of lipoproteins are higher than in thermodynamically stable droplets, suggesting that HDL and LDL are kinetically trapped into a metastable state.
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32
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Liang C, Louhivuori M, Marrink SJ, Jansen TLC, Knoester J. Vibrational Spectra of a Mechanosensitive Channel. J Phys Chem Lett 2013; 4:448-452. [PMID: 26281739 DOI: 10.1021/jz3019258] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.
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Affiliation(s)
- Chungwen Liang
- †Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Martti Louhivuori
- ‡Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- ‡Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- †Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- †Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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33
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Coupling Membrane Elasticity and Structure to Protein Function. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/b978-0-12-411515-6.00004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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34
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Liu C, Faller R. Conformational, dynamical. and tensional study of tethered bilayer lipid membranes in coarse-grained molecular simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15907-15915. [PMID: 23092246 DOI: 10.1021/la303511p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Tethered bilayer lipid membranes (tBLMs) have attracted great interest recently due to their crucial roles in elucidating fundamental membrane characteristics and the implications in biochemical sensors and pharmaceutical drug carriers. Nevertheless, they have not yet been investigated computationally on the molecular scale. Here, we study tBLMs consisting of DOPCs (1,2-dioleoyl-sn-glycero-3-phosphocholine) as free lipids and pegylated DOPCs (on phosphate group) as tethers in water by a variation of the MARTINI model. By varying grafting densities and tether lengths, distinct conformational changes from planar to undulated bilayers are observed. Lateral diffusivities and lateral pressure profiles show that the dynamical and tensional states are specific to the system configurations. These results suggest that the conformations, fluidity, and elasticity of the tBLMs can be tuned and manipulated to conform to various requirements in theoretical investigations and technological applications.
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Affiliation(s)
- Chueh Liu
- Department of Chemical Engineering and Materials Science, University of California-Davis, Davis, California 95616, United States
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Schmidt TH, Kandt C. LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. J Chem Inf Model 2012; 52:2657-69. [DOI: 10.1021/ci3000453] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas H. Schmidt
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| | - Christian Kandt
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
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Deplazes E, Louhivuori M, Jayatilaka D, Marrink SJ, Corry B. Structural investigation of MscL gating using experimental data and coarse grained MD simulations. PLoS Comput Biol 2012; 8:e1002683. [PMID: 23028281 PMCID: PMC3447979 DOI: 10.1371/journal.pcbi.1002683] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/21/2012] [Indexed: 12/02/2022] Open
Abstract
The mechanosensitive channel of large conductance (MscL) has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation. Cells in biological organisms have to be able to respond to mechanical forces during processes such as touch, hearing, pain sensation and tissue growth. One way this is achieved is through mechanosensitive ion channels, membrane embedded proteins that initiate electrical signalling upon tension within the cell or cell membrane. The malfunction of such channels is also associated with a range of diseases including muscular dystrophy and cardiac arrhythmia. In this manuscript, we study in detail the mechanosensitive channel of large conductance (MscL) from bacteria, a model system in which to understand the principles of mechanosensation. Despite many years of investigative work the details of how the protein senses tension in the surrounding membrane remain unknown. By combining structural data from experiments with computer simulation we are able to model the open channel structure of the protein and report previously unobserved structural changes that might present a new mechanism of sensing tension. The methods developed in this paper are not limited to the study of mechanosensitive ion channels and may be useful in understanding the structure and function of other membrane proteins.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Perth, Australia
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Sezgin E, Schwille P. Model membrane platforms to study protein-membrane interactions. Mol Membr Biol 2012; 29:144-54. [DOI: 10.3109/09687688.2012.700490] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Hatch HW, Debenedetti PG. Molecular modeling of mechanical stresses on proteins in glassy matrices: Formalism. J Chem Phys 2012; 137:035103. [DOI: 10.1063/1.4734007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Orłowski A, Grzybek M, Bunker A, Pasenkiewicz-Gierula M, Vattulainen I, Männistö PT, Róg T. Strong preferences of dopamine and l-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism. J Neurochem 2012; 122:681-90. [DOI: 10.1111/j.1471-4159.2012.07813.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Karo J, Peterson P, Vendelin M. Molecular dynamics simulations of creatine kinase and adenine nucleotide translocase in mitochondrial membrane patch. J Biol Chem 2012; 287:7467-76. [PMID: 22241474 PMCID: PMC3293576 DOI: 10.1074/jbc.m111.332320] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies.
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Affiliation(s)
- Jaanus Karo
- Laboratory of Systems Biology, Institute of Cybernetics at Tallinn University of Technology, Akadeemia tee 21, 12618 Tallinn, Estonia
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Monticelli L, Barnoud J, Orlowski A, Vattulainen I. Interaction of C70 fullerene with the Kv1.2 potassium channel. Phys Chem Chem Phys 2012; 14:12526-33. [DOI: 10.1039/c2cp41117b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Vostrikov VV, Koeppe RE. Response of GWALP transmembrane peptides to changes in the tryptophan anchor positions. Biochemistry 2011; 50:7522-35. [PMID: 21800919 DOI: 10.1021/bi2006459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
While the interfacial partitioning of charged or aromatic anchor residues may determine the preferred orientations of transmembrane peptide helices, the dependence of helix orientation on anchor residue position is not well understood. When anchor residue locations are changed systematically, some adaptations of the peptide-lipid interactions may be required to compensate for the altered interfacial interactions. Recently, we have developed a novel transmembrane peptide, termed GW(5,19)ALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-ethanolamide), which proves to be a well-behaved sequence for an orderly investigation of protein-lipid interactions. Its roughly symmetric nature allows for shifting the anchoring Trp residues by one Leu-Ala pair inward (GW(7,17)ALP23) or outward (GW(3,21)ALP23), thus providing fine adjustments of the formal distance between the tryptophan residues. With no other obvious anchoring features present, we postulate that the inter-Trp distance may be crucial for aspects of the peptide-lipid interaction. Importantly, the amino acid composition is identical for each of the resulting related GWALP23 sequences, and the radial separation between the pairs of Trp residues on each side of the transmembrane α-helix remains similar. Here we address the adaptation of the aforementioned peptides to the varying Trp locations by means of solid-state (2)H nuclear magnetic resonance experiments in varying lipid bilayer membrane environments. All of the GW(x,y)ALP23 sequence isomers adopt transmembrane orientations in DOPC, DMPC, and DLPC environments, even when the Trp residues are quite closely spaced, in GW(7,17)ALP23. Furthermore, the dynamics for each peptide isomer are less extensive than for peptides possessing additional interfacial Trp residues. The helical secondary structure is maintained more strongly within the Trp-flanked core region than outside of the Trp boundaries. Deuterium-labeled tryptophan indole rings in the GW(x,y)ALP23 peptides provide additional insights into the behavior of the Trp side chains. A Trp side chain near the C-terminus adopts a different orientation and undergoes somewhat faster dynamics than a corresponding Trp side chain located an equivalent distance from the N-terminus. In contrast, as the inter-Trp distance changes, the variations among the average orientations of the Trp indole rings at either terminus are systematic yet fairly small. We conclude that subtle adjustments to the peptide tilt, and to the N- and C-terminal Trp side chain torsion angles, permit the GW(x,y)ALP23 peptides to maintain preferred transmembrane orientations while adapting to lipid bilayers with differing hydrophobic thicknesses.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States.
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