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Harris J, Chipot C, Roux B. Statistical Mechanical Theories of Membrane Permeability. J Phys Chem B 2024; 128:9183-9196. [PMID: 39283709 DOI: 10.1021/acs.jpcb.4c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
A popular theoretical framework to compute the permeability coefficient of a molecule is provided by the classic Smoluchowski-Kramers treatment of the steady-state diffusive flux across a free-energy barrier. Within this framework, commonly termed "inhomogeneous solubility-diffusion" (ISD), the permeability, P, is expressed in closed form in terms of the potential of mean force and position-dependent diffusivity of the molecule of interest along the membrane normal. In principle, both quantities can be calculated from all-atom MD simulations. Although several methods exist for calculating the position-dependent diffusivity, each of these is at best an estimate. In addition, the ISD model does not account for memory effects along the chosen reaction coordinate. For these reasons, it is important to seek alternative theoretical formulations to determine the permeability coefficient that are able to account for the factors ignored by the ISD approximation. Using Green-Kubo linear response theory, we establish the familiar constitutive relation between the flux density across the membrane and the difference in the concentration of a permeant molecule, j = PΔC. On this basis, we derive a time-correlation function expression for the nonequilibrium flux across a membrane that is reminiscent of the transmission coefficient in the reactive flux formalism treatment of transition rates. An analysis based on the transition path theory framework is exploited to derive alternative expressions for the permeability coefficient. The different strategies are illustrated with stochastic simulations based on the generalized Langevin equation in addition to unbiased molecular dynamics simulations of water permeation of a lipid bilayer.
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Affiliation(s)
- Jonathan Harris
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Université de Lorraine, Unité Mixte de Recherche n7019, B.P. 70239, 54506 cedex Vandœuvre-lès-Nancy, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
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2
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Matsubara Y, Okabe R, Masayama R, Watanabe NM, Umakoshi H, Kasahara K, Matubayasi N. A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation. J Chem Phys 2024; 161:024108. [PMID: 38984955 DOI: 10.1063/5.0214401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
We propose a theoretical approach to estimate the permeability coefficients of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic quantities for the reactive (R) phase that exists within the inner region of a membrane. One can evaluate these quantities using multiple MD trajectories starting from phase R. We apply the RP theory to the permeation of ethanol and methylamine at different concentrations (infinitely dilute and 1 mol % conditions of permeants). Under the 1 mol% condition, the present method yields a larger permeability coefficient for ethanol (0.12 ± 0.01 cm s-1) than for methylamine (0.069 ± 0.006 cm s-1), while the values of the permeability coefficient are satisfactorily close to those obtained from the brute-force MD simulations (0.18 ± 0.03 and 0.052 ± 0.005 cm s-1 for ethanol and methylamine, respectively). Moreover, upon analyzing the thermodynamic and kinetic contributions to the permeability, we clarify that a higher concentration dependency of permeability for ethanol, as compared to methylamine, arises from the sensitive nature of ethanol's free-energy barrier within the inner region of the membrane against ethanol concentration.
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Affiliation(s)
- Yuya Matsubara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryo Okabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ren Masayama
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nozomi Morishita Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Ando T, Fukuda S, Ngo KX, Flechsig H. High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action. Annu Rev Biophys 2024; 53:19-39. [PMID: 38060998 DOI: 10.1146/annurev-biophys-030722-113353] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Kien X Ngo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
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Abstract
This review focuses on nonlytic outer membrane vesicles (OMVs), a subtype of bacterial extracellular vesicles (BEVs) produced by Gram-negative organisms focusing on the mechanisms of their biogenesis, cargo, and function. Throughout, we highlight issues concerning the characterization of OMVs and distinguishing them from other types of BEVs. We also highlight the shortcomings of commonly used methodologies for the study of BEVs that impact the interpretation of their functionality and suggest solutions to standardize protocols for OMV studies.
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Affiliation(s)
| | - Simon R. Carding
- Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Chen J, Nan B. Flagellar Motor Transformed: Biophysical Perspectives of the Myxococcus xanthus Gliding Mechanism. Front Microbiol 2022; 13:891694. [PMID: 35602090 PMCID: PMC9120999 DOI: 10.3389/fmicb.2022.891694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Many bacteria move on solid surfaces using gliding motility, without involvement of flagella or pili. Gliding of Myxococcus xanthus is powered by a proton channel homologous to the stators in the bacterial flagellar motor. Instead of being fixed in place and driving the rotation of a circular protein track like the flagellar basal body, the gliding machinery of M. xanthus travels the length of the cell along helical trajectories, while mechanically engaging with the substrate. Such movement entails a different molecular mechanism to generate propulsion on the cell. In this perspective, we will discuss the similarities and differences between the M. xanthus gliding machinery and bacterial flagellar motor, and use biophysical principles to generate hypotheses about the operating mechanism, efficiency, sensitivity to control, and mechanosensing of M. xanthus gliding.
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Affiliation(s)
- Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, United States
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Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. NANOSCALE HORIZONS 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
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Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
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Bompard J, Maniti O, Aboukhachfe R, Ausserre D, Girard-Egrot A. BALM: Watching the Formation of Tethered Bilayer Lipid Membranes with Submicron Lateral Resolution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9457-9471. [PMID: 34324820 DOI: 10.1021/acs.langmuir.1c01184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tethered bilayer lipid membranes (tBLMs) are artificial membranes largely used for the in situ study of biological membranes and membrane-associated proteins. To date, the formation of these membranes was essentially monitored by surface averaging techniques like surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation monitoring (QCM-D), which cannot provide both local and real-time information in a single approach. Here, we report an original application of backside absorbing layer microscopy (BALM), a novel white-light wide-field optical microscopy, to study tBLMs. Thanks to the combination of sensitivity and resolution, BALM not only allowed the real-time quantitative monitoring of tBLM formation but also enabled the high-resolution visualization of local fluxes and matter exchanges taking place at each step of the process. Quantitative BALM measurements of the final layer thickness, reproduced in parallel with SPR, were consistent with the achievement of a continuous lipid bilayer. This finding was confirmed by BALM imaging, which additionally revealed the heterogeneity of the bilayer during its formation. While established real-time techniques, like SPR or QCM-D, view the surface as homogeneous, BALM showed the presence of surface patterns appearing in the first step of the tBLM formation process and governing subsequent matter adsorption or desorption steps. Finally, matter fluxes persisting even after rinsing at the end of the tBLM formation demonstrated the lasting presence of dispersed vesicular pockets with laterally fluctuating positions over the final single and continuous lipid bilayer. These new mechanistic insights into the tBLM formation process demonstrate the great potential of BALM in the study of complex biological systems.
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Affiliation(s)
- J Bompard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246, GEMBAS Team, Lederer building, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - O Maniti
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246, GEMBAS Team, Lederer building, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - R Aboukhachfe
- Lebanese University, Faculty of Technology, Hisbe Street, Saida, Lebanon
| | - D Ausserre
- Institut Molecules & Matériaux du Mans, IMMM CNRS UMR 6283, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France
| | - A Girard-Egrot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246, GEMBAS Team, Lederer building, 1 rue Victor Grignard, F-69622 Villeurbanne, France
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8
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Heath GR, Lin YC, Matin TR, Scheuring S. Structural dynamics of channels and transporters by high-speed atomic force microscopy. Methods Enzymol 2021; 652:127-159. [PMID: 34059280 DOI: 10.1016/bs.mie.2021.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Channels and transporters are vital for transmembrane transport of ions and solutes, and also of larger compounds such as lipids and macromolecules. Therefore, they are crucial in many biological processes such as sensing, signal transduction, and the regulation of the distribution of molecules. Dysfunctions of these membrane proteins are associated to numerous diseases, and their interaction with drugs is critical in medicine. Understanding the behavior of channels and transporters requires structural and dynamic information to decipher the molecular mechanisms underlying their function. High-Speed Atomic Force Microscopy (HS-AFM) now allows the study of single transmembrane channels and transporters in action under physiological conditions, i.e., at ambient temperature and pressure, in physiological buffer and in a membrane, and in a most direct, label-free manner. In this chapter, we discuss the HS-AFM sample preparation, application, and data analysis protocols to study the structural and conformational dynamics of membrane-embedded channels and transporters.
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Affiliation(s)
- George R Heath
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - Yi-Chih Lin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Tina R Matin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States; Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, United States.
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Abstract
Pore-forming proteins (PFPs) include virulence factors that are produced by many pathogenic bacteria. However, PFPs also comprise non-virulence factors, such as apoptotic Bcl2-like proteins, and also occur in non-pathogenic bacteria and indeed in all kingdoms of life. Pore-forming proteins are an ancient class of proteins, which are tremendously powerful in damaging cell membranes. In general, upon binding to lipid membranes, they convert from the soluble monomeric form into an oligomeric state, and then undergo a dramatic conformational change to form transmembrane pores. Thus, PFPs render the plasma membrane of their target cells permeable to solutes, potentially leading to cell death, or to more subtle manipulations of cellular functions. Recent cryo-EM and X-ray crystallography studies revealed high-resolution structures of several PFPs in their pre-pore and pore states, however many aspects regarding the cues that induce pore formation, the pre-pore to pore conformational transition, the mechanism of membrane permeation and associated dynamics are still less well understood, and direct visualization of the dynamics of these transitions are missing. Using high-speed atomic force microscopy (HS-AFM), the kinetics of oligomerization and the pre-pore to pore transition dynamics of various PFPs, such as Listeriolysin O (LLO), lysenin, and Perforin-2 (PFN2), could be studied. These studies revealed that LLO does not form pores of regular shape or size, but rather forms membrane inserted arcs that propagate and damage lipid membranes as lineactants. In contrast, lysenin forms stable pre-pore and pore nonameric rings and HS-AFM allowed to study their diffusion on and the pH-dependent insertion into the membrane. Similarly, PFN2 underwent pre-pore to pore transition upon acidification. The openness of the HS-AFM system allowed the transition to be imaged in real time and revealed that all observed molecules transitioned into the pore state within 3s. In this chapter, we detail protocols to prepare lipids, form supported lipid bilayers, and provide guidelines for real-time, real-space HS-AFM observations of PFPs in action.
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Casuso I, Redondo-Morata L, Rico F. Biological physics by high-speed atomic force microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190604. [PMID: 33100165 PMCID: PMC7661283 DOI: 10.1098/rsta.2019.0604] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.
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Affiliation(s)
- Ignacio Casuso
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
| | - Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, 59000 Lille, France
| | - Felix Rico
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
- e-mail:
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11
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Jiao F, Cannon KS, Lin YC, Gladfelter AS, Scheuring S. The hierarchical assembly of septins revealed by high-speed AFM. Nat Commun 2020; 11:5062. [PMID: 33033254 PMCID: PMC7545167 DOI: 10.1038/s41467-020-18778-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Septins are GTP-binding proteins involved in diverse cellular processes including division and membrane remodeling. Septins form linear, palindromic heteromeric complexes that can assemble in filaments and higher-order structures. Structural studies revealed various septin architectures, but questions concerning assembly-dynamics and -pathways persist. Here we used high-speed atomic force microscopy (HS-AFM) and kinetic modeling which allowed us to determine that septin filament assembly was a diffusion-driven process, while formation of higher-order structures was complex and involved self-templating. Slightly acidic pH and increased monovalent ion concentrations favor filament-assembly, -alignment and -pairing. Filament-alignment and -pairing further favored diffusion-driven assembly. Pairing is mediated by the septin N-termini face, and may occur symmetrically or staggered, likely important for the formation of higher-order structures of different shapes. Multilayered structures are templated by the morphology of the underlying layers. The septin C-termini face, namely the C-terminal extension of Cdc12, may be involved in membrane binding.
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Affiliation(s)
- Fang Jiao
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kevin S Cannon
- Department of Biology, University of North Carolina and Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yi-Chih Lin
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina and Chapel Hill, Chapel Hill, NC, 27599, USA
- Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
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Redondo-Morata L, Losada-Pérez P, Giannotti MI. Lipid bilayers: Phase behavior and nanomechanics. CURRENT TOPICS IN MEMBRANES 2020; 86:1-55. [PMID: 33837691 DOI: 10.1016/bs.ctm.2020.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipid membranes are involved in many physiological processes like recognition, signaling, fusion or remodeling of the cell membrane or some of its internal compartments. Within the cell, they are the ultimate barrier, while maintaining the fluidity or flexibility required for a myriad of processes, including membrane protein assembly. The physical properties of in vitro model membranes as model cell membranes have been extensively studied with a variety of techniques, from classical thermodynamics to advanced modern microscopies. Here we review the nanomechanics of solid-supported lipid membranes with a focus in their phase behavior. Relevant information obtained by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM) as complementary techniques in the nano/mesoscale interface is presented. Membrane morphological and mechanical characterization will be discussed in the framework of its phase behavior, phase transitions and coexistence, in simple and complex models, and upon the presence of cholesterol.
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Affiliation(s)
- Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, Lille, France
| | - Patricia Losada-Pérez
- Experimental Soft Matter and Thermal Physics (EST) Group, Department of Physics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marina Inés Giannotti
- Biomedical Research Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain; Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Barcelona, Spain.
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13
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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14
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Abstract
The notion that graded distributions of signals underlie the spatial organization of biological systems has long been a central pillar in the fields of cell and developmental biology. During morphogenesis, morphogens spread across tissues to guide development of the embryo. Similarly, a variety of dynamic gradients and pattern-forming networks have been discovered that shape subcellular organization. Here we discuss the principles of intracellular pattern formation by these intracellular morphogens and relate them to conceptually similar processes operating at the tissue scale. We will specifically review mechanisms for generating cellular asymmetry and consider how intracellular patterning networks are controlled and adapt to cellular geometry. Finally, we assess the general concept of intracellular gradients as a mechanism for positional control in light of current data, highlighting how the simple readout of fixed concentration thresholds fails to fully capture the complexity of spatial patterning processes occurring inside cells.
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Affiliation(s)
- Lars Hubatsch
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Nathan W Goehring
- The Francis Crick Institute, London, United Kingdom; Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
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15
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Qin X, Liu L, Lee SK, Alsina A, Liu T, Wu C, Park H, Yu C, Kim H, Chu J, Triller A, Tang BZ, Hyeon C, Park CY, Park H. Increased Confinement and Polydispersity of STIM1 and Orai1 after Ca 2+ Store Depletion. Biophys J 2019; 118:70-84. [PMID: 31818466 DOI: 10.1016/j.bpj.2019.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
STIM1 (a Ca2+ sensor in the endoplasmic reticulum (ER) membrane) and Orai1 (a pore-forming subunit of the Ca2+-release-activated calcium channel in the plasma membrane) diffuse in the ER membrane and plasma membrane, respectively. Upon depletion of Ca2+ stores in the ER, STIM1 translocates to the ER-plasma membrane junction and binds Orai1 to trigger store-operated Ca2+ entry. However, the motion of STIM1 and Orai1 during this process and its roles to Ca2+ entry is poorly understood. Here, we report real-time tracking of single STIM1 and Orai1 particles in the ER membrane and plasma membrane in living cells before and after Ca2+ store depletion. We found that the motion of single STIM1 and Orai1 particles exhibits anomalous diffusion both before and after store depletion, and their mobility-measured by the radius of gyration of the trajectories, mean-square displacement, and generalized diffusion coefficient-decreases drastically after store depletion. We also found that the measured displacement distribution is non-Gaussian, and the non-Gaussian parameter drastically increases after store depletion. Detailed analyses and simulations revealed that single STIM1 and Orai1 particles are confined in the compartmentalized membrane both before and after store depletion, and the changes in the motion after store depletion are explained by increased confinement and polydispersity of STIM1-Orai1 complexes formed at the ER-plasma membrane junctions. Further simulations showed that this increase in the confinement and polydispersity after store depletion localizes a rapid increase of Ca2+ influx, which can facilitate the rapid activation of local Ca2+ signaling pathways and the efficient replenishing of Ca2+ store in the ER in store-operated Ca2+ entry.
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Affiliation(s)
- Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lei Liu
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Adolfo Alsina
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hojeong Park
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hajin Kim
- Department of Biomedical Engineering and Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Antoine Triller
- Biologie Cellulaire de la Synapse N&P, IBENS, Institut de Biologie de L'ENS, Ecole Normale Supérieure, Paris, France
| | - Ben Zhong Tang
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Department of Chemistry, Kowloon, Hong Kong, China, Kowloon, Hong Kong, China
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Hyokeun Park
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Division of Life Science; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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16
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High-speed force spectroscopy: microsecond force measurements using ultrashort cantilevers. Biophys Rev 2019; 11:689-699. [PMID: 31588961 PMCID: PMC6815269 DOI: 10.1007/s12551-019-00585-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/27/2019] [Indexed: 10/25/2022] Open
Abstract
Complete understanding of the role of mechanical forces in biological processes requires knowledge of the mechanical properties of individual proteins and living cells. Moreover, the dynamic response of biological systems at the nano- and microscales span over several orders of magnitude in time, from sub-microseconds to several minutes. Thus, access to force measurements over a wide range of length and time scales is required. High-speed atomic force microscopy (HS-AFM) using ultrashort cantilevers has emerged as a tool to study the dynamics of biomolecules and cells at video rates. The adaptation of HS-AFM to perform high-speed force spectroscopy (HS-FS) allows probing protein unfolding and receptor/ligand unbinding up to the velocity of molecular dynamics (MD) simulations with sub-microsecond time resolution. Moreover, application of HS-FS on living cells allows probing the viscoelastic response at short time scales providing deep understanding of cytoskeleton dynamics. In this mini-review, we assess the principles and recent developments and applications of HS-FS using ultrashort cantilevers to probe molecular and cellular mechanics.
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17
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Goiko M, de Bruyn JR, Heit B. Membrane Diffusion Occurs by Continuous-Time Random Walk Sustained by Vesicular Trafficking. Biophys J 2019; 114:2887-2899. [PMID: 29925025 DOI: 10.1016/j.bpj.2018.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/06/2018] [Accepted: 04/16/2018] [Indexed: 10/28/2022] Open
Abstract
Diffusion in cellular membranes is regulated by processes that occur over a range of spatial and temporal scales. These processes include membrane fluidity, interprotein and interlipid interactions, interactions with membrane microdomains, interactions with the underlying cytoskeleton, and cellular processes that result in net membrane movement. The complex, non-Brownian diffusion that results from these processes has been difficult to characterize, and moreover, the impact of factors such as membrane recycling on membrane diffusion remains largely unexplored. We have used a careful statistical analysis of single-particle tracking data of the single-pass plasma membrane protein CD93 to show that the diffusion of this protein is well described by a continuous-time random walk in parallel with an aging process mediated by membrane corrals. The overall result is an evolution in the diffusion of CD93: proteins initially diffuse freely on the cell surface but over time become increasingly trapped within diffusion-limiting membrane corrals. Stable populations of freely diffusing and corralled CD93 are maintained by an endocytic/exocytic process in which corralled CD93 is selectively endocytosed, whereas freely diffusing CD93 is replenished by exocytosis of newly synthesized and recycled CD93. This trafficking not only maintained CD93 diffusivity but also maintained the heterogeneous distribution of CD93 in the plasma membrane. These results provide insight into the nature of the biological and biophysical processes that can lead to significantly non-Brownian diffusion of membrane proteins and demonstrate that ongoing membrane recycling is critical to maintaining steady-state diffusion and distribution of proteins in the plasma membrane.
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Affiliation(s)
- Maria Goiko
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - John R de Bruyn
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Centre for Human Immunology, The University of Western Ontario, London, Ontario, Canada.
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18
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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19
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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: 184] [Impact Index Per Article: 36.8] [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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20
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Clarkson CG, Johnson A, Leggett GJ, Geoghegan M. Slow polymer diffusion on brush-patterned surfaces in aqueous solution. NANOSCALE 2019; 11:6052-6061. [PMID: 30869707 DOI: 10.1039/c9nr00341j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A model system for the investigation of diffusional transport in compartmentalized nanosystems is described. Arrays of "corrals" enclosed within poly[oligo(ethylene glycol)methyl ether methacrylate] (POEGMA) "walls" were fabricated using double-exposure interferometric lithography to deprotect aminosilane films protected by a nitrophenyl group. In exposed regions, removal of the nitrophenyl group enabled attachment of an initiator for the atom-transfer radical polymerization of end-grafted POEGMA (brushes). Diffusion coefficients for poly(ethylene glycol) in these corrals were obtained by fluorescence correlation spectroscopy. Two modes of surface diffusion were observed: one which is similar to diffusion on the unpatterned surface and a very slow mode of surface diffusion that becomes increasingly important as confinement increases. Diffusion within the POEGMA brushes does not significantly contribute to the results.
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21
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Heath GR, Scheuring S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr Opin Struct Biol 2019; 57:93-102. [PMID: 30878714 DOI: 10.1016/j.sbi.2019.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
Recent advances in high-speed atomic force microscopy (HS-AFM) have made it possible to study the conformational dynamics of single unlabeled transmembrane channels and transporters. Improving environmental control with the integration of a non-disturbing buffer exchange system, which in turn allows the gradual change of conditions during HS-AFM operation, has provided a breakthrough toward the performance of structural titration experiments. Further advancements in temporal resolution with the use of line scanning and height spectroscopy techniques show how high-speed atomic force microscopy can measure millisecond to microsecond dynamics, pushing this method beyond current spatial and temporal limits offered by less direct techniques.
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Affiliation(s)
- George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA.
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22
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Smith DJ, Klauda JB, Sodt AJ. Simulation Best Practices for Lipid Membranes [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2019; 1:5966. [PMID: 36204133 PMCID: PMC9534443 DOI: 10.33011/livecoms.1.1.5966] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single- and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic- and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.
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Affiliation(s)
- David J. Smith
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering and Biophysics Program, University of Maryland, College Park, MD, USA
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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23
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Chavent M, Duncan AL, Rassam P, Birkholz O, Hélie J, Reddy T, Beliaev D, Hambly B, Piehler J, Kleanthous C, Sansom MSP. How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins. Nat Commun 2018; 9:2846. [PMID: 30030429 PMCID: PMC6054660 DOI: 10.1038/s41467-018-05255-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/15/2018] [Indexed: 01/07/2023] Open
Abstract
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs. In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, Toulouse, 31400, France
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401, Illkirch, France
| | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,SEMMLE, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Theoretical Biology and Biophysics, T-6, Los Alamos National Laboratory, Los Alamos, NM, 87525, USA
| | - Dmitry Beliaev
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Ben Hambly
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
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24
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Uchihashi T, Scheuring S. Applications of high-speed atomic force microscopy to real-time visualization of dynamic biomolecular processes. Biochim Biophys Acta Gen Subj 2018; 1862:229-240. [DOI: 10.1016/j.bbagen.2017.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
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25
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Molecular mechanisms of action of sphingomyelin-specific pore-forming toxin, lysenin. Semin Cell Dev Biol 2018; 73:188-198. [DOI: 10.1016/j.semcdb.2017.07.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 11/21/2022]
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26
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Zuttion F, Redondo-Morata L, Marchesi A, Casuso I. High-Resolution and High-Speed Atomic Force Microscope Imaging. Methods Mol Biol 2018; 1814:181-200. [PMID: 29956233 DOI: 10.1007/978-1-4939-8591-3_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of high-speed atomic force microscopy (HS-AFM) over the recent years has opened up new horizons for the study of structure, function and dynamics of biological molecules. HS-AFM is capable of 1000 times faster imaging than conventional AFM. This circumstance uniquely enables the observation of the dynamics of all the molecules present in the imaging area. Over the last 10 years, the HS-AFM has gone from a prototype-state technology that only a few labs in the world had access to (including ours) to an established commercialized technology that is present in tens of labs around the world. In this protocol chapter we share with the readers our practical know-how on high resolution HS-AFM imaging.
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Affiliation(s)
- Francesca Zuttion
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France
| | - Lorena Redondo-Morata
- Inserm U1019, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Arin Marchesi
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France
| | - Ignacio Casuso
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France.
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27
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Munguira ILB, Takahashi H, Casuso I, Scheuring S. Lysenin Toxin Membrane Insertion Is pH-Dependent but Independent of Neighboring Lysenins. Biophys J 2017; 113:2029-2036. [PMID: 29117526 DOI: 10.1016/j.bpj.2017.08.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/11/2017] [Indexed: 10/18/2022] Open
Abstract
Pore-forming toxins form a family of proteins that act as virulence factors of pathogenic bacteria, but similar proteins are found in all kingdoms of life, including the vertebrate immune system. They are secreted as soluble monomers that oligomerize on target membranes in the so-called prepore state; after activation, they insert into the membrane and adopt the pore state. Lysenin is a pore-forming toxin from the earthworm Eisenida foetida, of which both the soluble and membrane-inserted structures are solved. However, the activation and membrane-insertion mechanisms have remained elusive. Here, we used high-speed atomic force microscopy to directly visualize the membrane-insertion mechanism. Changing the environmental pH from pH 7.5 to below pH 6.0 favored membrane insertion. We detected a short α-helix in the soluble structure that comprised three glutamic acids (Glu92, Glu94, and Glu97) that we hypothesized may represent a pH-sensor (as in similar toxins, e.g., Listeriolysin). Mutant lysenin still can form pores, but mutating these glutamic acids to glutamines rendered the toxin pH-insensitive. On the other hand, toxins in the pore state did not favor insertion of neighboring prepores; indeed, pore insertion breaks the hexagonal ordered domains of prepores and separates from neighboring molecules in the membrane. pH-dependent activation of toxins may represent a common feature of pore-forming toxins. High-speed atomic force microscopy with single-molecule resolution at high temporal resolution and the possibility of exchanging buffers during the experiments presents itself as a unique tool for the study of toxin-state conversion.
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Affiliation(s)
- Ignacio L B Munguira
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Hirohide Takahashi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France; Departments of Anesthesiology and Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Ignacio Casuso
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France; Departments of Anesthesiology and Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
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28
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Abstract
Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor. Molecular dynamics simulation further suggested which other amino acid residues may also allosterically influence the pH-sensor. LLO was engineered to the point where it can, in a pH-regulated manner, perforate artificial and cellular membranes. The single mutant Tyr406Ala bound to membranes and oligomerized similarly to the wild-type LLO, however, the final membrane insertion step was pH-affected by the introduced mutation. We show that the mutant toxin can be activated at the surface of artificial membranes or living cells by a single wash with slightly acidic pH buffer. Y406A mutant has a high potential in development of novel nanobiotechnological applications such as controlled release of substances or as a sensor of environmental pH.
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29
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Norregaard K, Metzler R, Ritter CM, Berg-Sørensen K, Oddershede LB. Manipulation and Motion of Organelles and Single Molecules in Living Cells. Chem Rev 2017; 117:4342-4375. [PMID: 28156096 DOI: 10.1021/acs.chemrev.6b00638] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function. In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation and dynamics of single molecule and organelles are reviewed.
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Affiliation(s)
- Kamilla Norregaard
- Cluster for Molecular Imaging, Department of Biomedical Science and Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany
| | - Christine M Ritter
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
| | | | - Lene B Oddershede
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
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30
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Chipot C, Comer J. Subdiffusion in Membrane Permeation of Small Molecules. Sci Rep 2016; 6:35913. [PMID: 27805049 PMCID: PMC5090971 DOI: 10.1038/srep35913] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 10/05/2016] [Indexed: 12/22/2022] Open
Abstract
Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.
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Affiliation(s)
- Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7565, Université de Lorraine, B.P. 70239, 54506, Vandœuvre-lès-Nancy cedex, France
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, 1800 Denison Ave, Kansas State University, Manhattan, Kansas 66506, USA
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31
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Takahashi H, Miyagi A, Redondo-Morata L, Scheuring S. Temperature-Controlled High-Speed AFM: Real-Time Observation of Ripple Phase Transitions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:6106-6113. [PMID: 27647753 DOI: 10.1002/smll.201601549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 07/27/2016] [Indexed: 05/24/2023]
Abstract
With nanometer lateral and Angstrom vertical resolution, atomic force microscopy (AFM) has contributed unique data improving the understanding of lipid bilayers. Lipid bilayers are found in several different temperature-dependent states, termed phases; the main phases are solid and fluid phases. The transition temperature between solid and fluid phases is lipid composition specific. Under certain conditions some lipid bilayers adopt a so-called ripple phase, a structure where solid and fluid phase domains alternate with constant periodicity. Because of its narrow regime of existence and heterogeneity ripple phase and its transition dynamics remain poorly understood. Here, a temperature control device to high-speed atomic force microscopy (HS-AFM) to observe dynamics of phase transition from ripple phase to fluid phase reversibly in real time is developed and integrated. Based on HS-AFM imaging, the phase transition processes from ripple phase to fluid phase and from ripple phase to metastable ripple phase to fluid phase could be reversibly, phenomenologically, and quantitatively studied. The results here show phase transition hysteresis in fast cooling and heating processes, while both melting and condensation occur at 24.15 °C in quasi-steady state situation. A second metastable ripple phase with larger periodicity is formed at the ripple phase to fluid phase transition when the buffer contains Ca2+ . The presented temperature-controlled HS-AFM is a new unique experimental system to observe dynamics of temperature-sensitive processes at the nanoscopic level.
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Affiliation(s)
- Hirohide Takahashi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, 13009, Marseille, France
| | - Atsushi Miyagi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, 13009, Marseille, France
| | - Lorena Redondo-Morata
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, 13009, Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, 13009, Marseille, France
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Goiko M, de Bruyn JR, Heit B. Short-Lived Cages Restrict Protein Diffusion in the Plasma Membrane. Sci Rep 2016; 6:34987. [PMID: 27725698 PMCID: PMC5057110 DOI: 10.1038/srep34987] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/22/2016] [Indexed: 01/08/2023] Open
Abstract
The plasma membrane is a heterogeneous environment characterized by anomalous diffusion and the presence of microdomains that are molecularly distinct from the bulk membrane. Using single particle tracking of the C-type lectin CD93, we have identified for the first time the transient trapping of transmembrane proteins in cage-like microdomains which restrict protein diffusion. These cages are stabilized by actin-dependent confinement regions, but are separate structures with sizes and lifespans uncorrelated to those of the underlying actin corral. These membrane cages require cholesterol for their strength and stability, with cholesterol depletion decreasing both. Despite this, cages are much larger in size and are longer lived than lipid rafts, suggesting instead that cholesterol-dependent effects on membrane fluidity or molecular packing play a role in cage formation. This diffusional compartment in the plasma membrane has characteristics of both a diffusional barrier and a membrane microdomain, with a size and lifespan intermediate between short-lived microdomains such as lipid rafts and long-lasting diffusional barriers created by the actin cytoskeleton.
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Affiliation(s)
- Maria Goiko
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, N6A 5C1 Canada.,Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, N6A 3K7 Canada
| | - John R de Bruyn
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, N6A 3K7 Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, N6A 5C1 Canada.,Centre for Human Immunology, The University of Western Ontario, London, Ontario, N6A 5C1 Canada
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Ruan Y, Rezelj S, Bedina Zavec A, Anderluh G, Scheuring S. Listeriolysin O Membrane Damaging Activity Involves Arc Formation and Lineaction -- Implication for Listeria monocytogenes Escape from Phagocytic Vacuole. PLoS Pathog 2016; 12:e1005597. [PMID: 27104344 PMCID: PMC4841516 DOI: 10.1371/journal.ppat.1005597] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/04/2016] [Indexed: 12/15/2022] Open
Abstract
Listeriolysin-O (LLO) plays a crucial role during infection by Listeria monocytogenes. It enables escape of bacteria from phagocytic vacuole, which is the basis for its spread to other cells and tissues. It is not clear how LLO acts at phagosomal membranes to allow bacterial escape. The mechanism of action of LLO remains poorly understood, probably due to unavailability of suitable experimental tools that could monitor LLO membrane disruptive activity in real time. Here, we used high-speed atomic force microscopy (HS-AFM) featuring high spatio-temporal resolution on model membranes and optical microscopy on giant unilamellar vesicles (GUVs) to investigate LLO activity. We analyze the assembly kinetics of toxin oligomers, the prepore-to-pore transition dynamics and the membrane disruption in real time. We reveal that LLO toxin efficiency and mode of action as a membrane-disrupting agent varies strongly depending on the membrane cholesterol concentration and the environmental pH. We discovered that LLO is able to form arc pores as well as damage lipid membranes as a lineactant, and this leads to large-scale membrane defects. These results altogether provide a mechanistic basis of how large-scale membrane disruption leads to release of Listeria from the phagocytic vacuole in the cellular context.
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Affiliation(s)
- Yi Ruan
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Saša Rezelj
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Apolonija Bedina Zavec
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail: (SS); (GA)
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
- * E-mail: (SS); (GA)
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Cherstvy AG, Metzler R. Anomalous diffusion in time-fluctuating non-stationary diffusivity landscapes. Phys Chem Chem Phys 2016; 18:23840-52. [DOI: 10.1039/c6cp03101c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We investigate the diffusive and ergodic properties of massive and confined particles in a model disordered medium, in which the local diffusivity fluctuates in time while its mean has a power law dependence on the diffusion time.
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Affiliation(s)
- Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
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