1
|
Gh. MS, Wilhelm MJ, Dai HL. Observing mechanosensitive channels in action in living bacteria. BIOPHYSICAL REPORTS 2024; 4:100141. [PMID: 38189030 PMCID: PMC10765490 DOI: 10.1016/j.bpr.2023.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024]
Abstract
Mechanosensitive (MS) channels act to protect the cytoplasmic membrane (CM) of living cells from environmental changes in osmolarity. In this report, we demonstrate the use of time-resolved second-harmonic light scattering (SHS) as a means of experimentally observing the relative state (open versus closed) of MS channels in living bacteria suspended in different buffer solutions. Specifically, the state of the MS channels was selectively controlled by changing the composition of the suspension medium, inducing either a transient or persistent osmotic shock. SHS was then used to monitor transport of the SHG-active cation, malachite green, across the bacterial CM. When MS channels were forced open, malachite green cations were able to cross the CM at a rate at least two orders of magnitude faster compared with when the MS channels were closed. These observations were corroborated using both numerical model simulations and complementary fluorescence experiments, in which the propensity for the CM impermeant cation, propidium, to stain cells was shown to be contingent upon the relative state of the MS channels (i.e., cells with open MS channels fluoresced red, cells with closed MS channels did not). Application of time-resolved SHS to experimentally distinguish MS channels opened via osmotic shock versus chemical activation, as well as a general comparison with the patch-clamp method is discussed.
Collapse
Affiliation(s)
| | | | - Hai-Lung Dai
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| |
Collapse
|
2
|
Zhen W, Luo T, Wang Z, Jiang X, Yuan E, Weichselbaum RR, Lin W. Mechanoregulatory Cholesterol Oxidase-Functionalized Nanoscale Metal-Organic Framework Stimulates Pyroptosis and Reinvigorates T Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2305440. [PMID: 37635106 PMCID: PMC10840730 DOI: 10.1002/smll.202305440] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/27/2023] [Indexed: 08/29/2023]
Abstract
Cancer cells alter mechanical tension in their cell membranes. New interventions to regulate cell membrane tension present a potential strategy for cancer therapy. Herein, the increase of cell membrane tension by cholesterol oxidase (COD) via cholesterol depletion in vitro and the design of a COD-functionalized nanoscale metal-organic framework, Hf-TBP/COD, for cholesterol depletion and mechanoregulation of tumors in vivo, are reported. COD is found to deplete cholesterol and disrupt the mechanical properties of lipid bilayers, leading to decreased cell proliferation, migration, and tolerance to oxidative stress. Hf-TBP/COD increases mechanical tension of plasma membranes and osmotic fragility of cancer cells, which induces influx of calcium ions, inhibits cell migration, increases rupturing propensity for effective caspase-1 mediated pyroptosis, and decreases tolerance to oxidative stress. In the tumor microenvironment, Hf-TBP/COD downregulates multiple immunosuppressive checkpoints to reinvigorate T cells and enhance T cell infiltration. Compared to Hf-TBP, Hf-TBP/COD improves anti-tumor immune response and tumor growth inhibition from 54.3% and 79.8% to 91.7% and 95% in a subcutaneous triple-negative breast cancer model and a colon cancer model, respectively.
Collapse
Affiliation(s)
- Wenyao Zhen
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Radiation and Cellular Oncology, The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Taokun Luo
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Zitong Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaomin Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Radiation and Cellular Oncology, The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Eric Yuan
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology, The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Wenbin Lin
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Radiation and Cellular Oncology, The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
3
|
Abstract
The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.
Collapse
Affiliation(s)
- James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA;
| |
Collapse
|
4
|
Ramirez VI, Wray R, Blount P, King MD. The Effects of Airflow on the Mechanosensitive Channels of Escherichia coli MG1655 and the Impact of Survival Mechanisms Triggered. Microorganisms 2023; 11:2236. [PMID: 37764080 PMCID: PMC10534522 DOI: 10.3390/microorganisms11092236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Understanding how bacteria respond to ventilated environments is a crucial concept, especially when considering accurate airflow modeling and detection limits. To properly design facilities for aseptic conditions, we must minimize the parameters for pathogenic bacteria to thrive. Identifying how pathogenic bacteria continue to survive, particularly due to their multi-drug resistance characteristics, is necessary for designing sterile environments and minimizing pathogen exposure. A conserved characteristic among bacterial organisms is their ability to maintain intracellular homeostasis for survival and growth in hostile environments. Mechanosensitive (MS) channels are one of the characteristics that guide this phenomenon. Interestingly, during extreme stress, bacteria will forgo favorable homeostasis to execute fast-acting survival strategies. Physiological sensors, such as MS channels, that trigger this survival mechanism are not clearly understood, leaving a gap in how bacteria translate physical stress to an intracellular response. In this paper, we study the role of mechanosensitive ion channels that are potentially triggered by aerosolization. We hypothesize that change in antimicrobial uptake is affected by aerosolization stress. Bacteria regulate their defense mechanisms against antimicrobials, which leads to varying susceptibility. Based on this information we hypothesize that aerosolization stress affects the antimicrobial resistance defense mechanisms of Escherichia coli (E. coli). We analyzed the culturability of knockout E. coli strains with different numbers of mechanosensitive channels and compared antibiotic susceptibility under stressed and unstressed airflow conditions. As a result of this study, we can identify how the defensive mechanisms of resistant bacteria are triggered for their survival in built environments. By changing ventilation airflow velocity and observing the change in antibiotic responses, we show how pathogenic bacteria respond to ventilated environments via mechanosensitive ion channels.
Collapse
Affiliation(s)
- Violette I. Ramirez
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| | - Robin Wray
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paul Blount
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria D. King
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| |
Collapse
|
5
|
Mulhall EM, Gharpure A, Lee RM, Dubin AE, Aaron JS, Marshall KL, Spencer KR, Reiche MA, Henderson SC, Chew TL, Patapoutian A. Direct observation of the conformational states of PIEZO1. Nature 2023; 620:1117-1125. [PMID: 37587339 PMCID: PMC10468401 DOI: 10.1038/s41586-023-06427-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
PIEZOs are mechanosensitive ion channels that convert force into chemoelectric signals1,2 and have essential roles in diverse physiological settings3. In vitro studies have proposed that PIEZO channels transduce mechanical force through the deformation of extensive blades of transmembrane domains emanating from a central ion-conducting pore4-8. However, little is known about how these channels interact with their native environment and which molecular movements underlie activation. Here we directly observe the conformational dynamics of the blades of individual PIEZO1 molecules in a cell using nanoscopic fluorescence imaging. Compared with previous structural models of PIEZO1, we show that the blades are significantly expanded at rest by the bending stress exerted by the plasma membrane. The degree of expansion varies dramatically along the length of the blade, where decreased binding strength between subdomains can explain increased flexibility of the distal blade. Using chemical and mechanical modulators of PIEZO1, we show that blade expansion and channel activation are correlated. Our findings begin to uncover how PIEZO1 is activated in a native environment. More generally, as we reliably detect conformational shifts of single nanometres from populations of channels, we expect that this approach will serve as a framework for the structural analysis of membrane proteins through nanoscopic imaging.
Collapse
Affiliation(s)
- Eric M Mulhall
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Anant Gharpure
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Rachel M Lee
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Adrienne E Dubin
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Kara L Marshall
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Kathryn R Spencer
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Scott C Henderson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Ardem Patapoutian
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA.
| |
Collapse
|
6
|
Sawada Y, Nomura T, Martinac B, Sokabe M. A novel force transduction pathway from a tension sensor to the gate in the mechano-gating of MscL channel. Front Chem 2023; 11:1175443. [PMID: 37347044 PMCID: PMC10279863 DOI: 10.3389/fchem.2023.1175443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
The bacterial mechanosensitive channel of large conductance MscL is activated exclusively by increased tension in the membrane bilayer. Despite many proposed models for MscL opening, its precise mechano-gating mechanism, particularly how the received force at the tension sensor transmits to the gate remains incomplete. Previous studies have shown that along with amphipathic N-terminus located near the cytoplasmic surface of the membrane, Phe78 residue near the outer surface also acts as a "tension sensor," while Gly22 is a central constituent of the "hydrophobic gate." Present study focused on elucidating the force transmission mechanism from the sensor Phe78 in the outer transmembrane helix (TM2) to the gate in the inner transmembrane helix (TM1) of MscL by applying the patch clamp and molecular dynamics (MD) simulations to the wild type MscL channel and its single mutants at the sensor (F78N), the gate (G22N) and their combination (G22N/F78N) double mutant. F78N MscL resulted in a severe loss-of-function, while G22N MscL caused a gain-of-function channel exhibiting spontaneous openings at the resting membrane tension. We initially speculated that the spontaneous opening in G22N mutant might occur without tension acting on Phe78 residue. To test this hypothesis, we examined the (G22N/F78N) double mutant, which unexpectedly exhibited neither spontaneous activity nor activity by a relatively high membrane tension. To understand the underlying mechanism, we conducted MD simulations and analyzed the force transduction pathway. Results showed that the mutation at the tension sensor (F78N) in TM2 caused decreased interaction of this residue not only with lipids, but also with a group of amino acids (Ile32-Leu36-Ile40) in the neighboring TM1 helix, which resulted in an inefficient force transmission to the gate-constituting amino acids on TM1. This change also induced a slight tilting of TM1 towards the membrane plane and decreased the size of the channel pore at the gate, which seems to be the major mechanism for the inhibition of spontaneous opening of the double mutant channel. More importantly, the newly identified interaction between the TM2 (Phe78) and adjacent TM1 (Ile32-Leu36-Ile40) helices seems to be an essential force transmitting mechanism for the stretch-dependent activation of MscL given that substitution of any one of these four amino acids with Asn resulted in severe loss-of-function MscL as reported in our previous work.
Collapse
Affiliation(s)
- Yasuyuki Sawada
- Department of Physiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute of Materials Innovation, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
| | - Takeshi Nomura
- International Cooperative Research Project, Solution Oriented Research for Science and Technology (ICORP/SORST), Cell Mechanosensing, Japan Science and Technology Agency (JST), Nagoya, Japan
- Molecular Cardiology and Biophysics Division, Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Human Science and Environment, University of Hyogo, Himeji, Japan
| | - Boris Martinac
- Molecular Cardiology and Biophysics Division, Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Masahiro Sokabe
- Department of Physiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- International Cooperative Research Project, Solution Oriented Research for Science and Technology (ICORP/SORST), Cell Mechanosensing, Japan Science and Technology Agency (JST), Nagoya, Japan
- Human Information Systems Laboratories, Kanazawa Institute of Technology, Hakusan, Ishikawa, Japan
| |
Collapse
|
7
|
Wijerathne TD, Ozkan AD, Lacroix JJ. Microscopic mechanism of PIEZO1 activation by pressure-induced membrane stretch. J Gen Physiol 2023; 155:213842. [PMID: 36715688 PMCID: PMC9930135 DOI: 10.1085/jgp.202213260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Mechanosensitive PIEZO1 ion channels open in response to membrane stretch. Yet, the underlying microscopic mechanism of this activation remains unknown. To probe this mechanism, we used cell-attached pressure-clamp recordings to measure single channel currents at different steady-state negative pipette pressures, spanning the full range of the channel's pressure sensitivity. Pressure-dependent activation occurs through a sharp reduction of the mean shut duration and through a moderate increase of the mean open duration. Across all tested pressures, the distribution of open and shut dwell times best follows sums of two and three exponential components, respectively. As the magnitude of the pressure stimulus increases, the time constants of most of these exponential components gradually change, in opposite directions for open and shut dwell times, and to a similar extent. In addition, while the relative amplitudes of fast and slow components remain unchanged for open intervals, they fully reverse for shut intervals, further reducing the mean shut duration. Using two-dimensional dwell time analysis, Markov-chain modeling, and simulations, we identified a minimal five-states model which recapitulates essential characteristics of single channel data, including microscopic reversibility, correlations between adjacent open and shut intervals, and asymmetric modulation of dwell times by pressure. This study identifies a microscopic mechanism for the activation of PIEZO1 channels by pressure-induced membrane stretch and deepens our fundamental understanding of mechanotransduction by a vertebrate member of the PIEZO channel family.
Collapse
Affiliation(s)
- Tharaka D Wijerathne
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, CA, USA
| | - Alper D Ozkan
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, CA, USA
| | - Jérôme J Lacroix
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, CA, USA
| |
Collapse
|
8
|
Maingi V, Zhang Z, Thachuk C, Sarraf N, Chapman ER, Rothemund PWK. Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Nat Commun 2023; 14:1532. [PMID: 36941256 PMCID: PMC10027858 DOI: 10.1038/s41467-023-36996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
Collapse
Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
| | - Zhao Zhang
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Chris Thachuk
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
| | - Namita Sarraf
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Paul W K Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation + Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
9
|
Lane BJ, Pliotas C. Approaches for the modulation of mechanosensitive MscL channel pores. Front Chem 2023; 11:1162412. [PMID: 37021145 PMCID: PMC10069478 DOI: 10.3389/fchem.2023.1162412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
MscL was the first mechanosensitive ion channel identified in bacteria. The channel opens its large pore when the turgor pressure of the cytoplasm increases close to the lytic limit of the cellular membrane. Despite their ubiquity across organisms, their importance in biological processes, and the likelihood that they are one of the oldest mechanisms of sensory activation in cells, the exact molecular mechanism by which these channels sense changes in lateral tension is not fully understood. Modulation of the channel has been key to understanding important aspects of the structure and function of MscL, but a lack of molecular triggers of these channels hindered early developments in the field. Initial attempts to activate mechanosensitive channels and stabilize functionally relevant expanded or open states relied on mutations and associated post-translational modifications that were often cysteine reactive. These sulfhydryl reagents positioned at key residues have allowed the engineering of MscL channels for biotechnological purposes. Other studies have modulated MscL by altering membrane properties, such as lipid composition and physical properties. More recently, a variety of structurally distinct agonists have been shown bind to MscL directly, close to a transmembrane pocket that has been shown to have an important role in channel mechanical gating. These agonists have the potential to be developed further into antimicrobial therapies that target MscL, by considering the structural landscape and properties of these pockets.
Collapse
Affiliation(s)
- Benjamin J. Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| |
Collapse
|
10
|
Nano-scale solution of the Poisson-Nernst-Planck (PNP) equations in a fraction of two neighboring cells reveals the magnitude of intercellular electrochemical waves. PLoS Comput Biol 2023; 19:e1010895. [PMID: 36791152 PMCID: PMC9974139 DOI: 10.1371/journal.pcbi.1010895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/28/2023] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
The basic building blocks of the electrophysiology of cardiomyocytes are ion channels integrated in the cell membranes. Close to the ion channels there are very strong electrical and chemical gradients. However, these gradients extend for only a few nano-meters and are therefore commonly ignored in mathematical models. The full complexity of the dynamics is modelled by the Poisson-Nernst-Planck (PNP) equations but these equations must be solved using temporal and spatial scales of nano-seconds and nano-meters. Here we report solutions of the PNP equations in a fraction of two abuttal cells separated by a tiny extracellular space. We show that when only the potassium channels of the two cells are open, a stationary solution is reached with the well-known Debye layer close to the membranes. When the sodium channels of one of the cells are opened, a very strong and brief electrochemical wave emanates from the channels. If the extracellular space is sufficiently small and the number of sodium channels is sufficiently high, the wave extends all the way over to the neighboring cell and may therefore explain cardiac conduction even at very low levels of gap junctional coupling.
Collapse
|
11
|
Ma S, Zhang Y, Zhang X, Xie H, Tong Q, Yu K, Yang J. Dynamic Interactions Between Brilliant Green and MscL Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2023; 29:e202202106. [PMID: 36251739 DOI: 10.1002/chem.202202106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/22/2022]
Abstract
The mechanosensitive ion channel of large conductance (MscL) is a promising template for the development of new antibiotics due to its high conservation and uniqueness to microbes. Brilliant green (BG), a triarylmethane dye, has been identified as a new antibiotic targeted MscL. However, the detailed binding sites to MscL and the dynamic pathway of BG through the MscL channel remain unknown. Here, the dynamic interactions between BG and MscL were investigated using solid-state NMR spectroscopy and molecule dynamics (MD) simulations. Residue site-specific binding sites of BG to the MscL channel were identified by solid-state NMR. In addition, MD simulations revealed that BG conducts through the MscL channel via residues along the inner surface of the pore sequentially, in which the strong hydrophobic interactions between BG and hydrophobic residues F23 and I27 in the hydrophobic gate region of the MscL channel are major restrictions. Particularly, it was demonstrated that BG activates the MscL channel by reducing the hydrophobicity of the F23 in the gate region by water molecules that are bound to BG. Taken together, these simulations and experimental data provide novel insights into the dynamic interactions between BG and MscL, based on which new hydrophobic antibiotics and adjuvants targeting MscL can be developed.
Collapse
Affiliation(s)
- Shaojie Ma
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P.R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China
| | - Yan Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xuning Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P.R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China.,Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| |
Collapse
|
12
|
Saurabh A, Fazel M, Safar M, Sgouralis I, Pressé S. Single-photon smFRET. I: Theory and conceptual basis. BIOPHYSICAL REPORTS 2022; 3:100089. [PMID: 36582655 PMCID: PMC9793182 DOI: 10.1016/j.bpr.2022.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.
Collapse
Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennesse
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona,School of Molecular Sciences, Arizona State University, Tempe, Arizona,Corresponding author
| |
Collapse
|
13
|
Latham AP, Zhang B. Molecular Determinants for the Layering and Coarsening of Biological Condensates. AGGREGATE (HOBOKEN, N.J.) 2022; 3:e306. [PMID: 37065433 PMCID: PMC10101022 DOI: 10.1002/agt2.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many membraneless organelles, or biological condensates, form through phase separation, and play key roles in signal sensing and transcriptional regulation. While the functional importance of these condensates has inspired many studies to characterize their stability and spatial organization, the underlying principles that dictate these emergent properties are still being uncovered. In this review, we examine recent work on biological condensates, especially multicomponent systems. We focus on connecting molecular factors such as binding energy, valency, and stoichiometry with the interfacial tension, explaining the nontrivial interior organization in many condensates. We further discuss mechanisms that arrest condensate coalescence by lowering the surface tension or introducing kinetic barriers to stabilize the multidroplet state.
Collapse
Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
| |
Collapse
|
14
|
Characterising ion channel structure and dynamics using fluorescence spectroscopy techniques. Biochem Soc Trans 2022; 50:1427-1445. [DOI: 10.1042/bst20220605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Ion channels undergo major conformational changes that lead to channel opening and ion conductance. Deciphering these structure-function relationships is paramount to understanding channel physiology and pathophysiology. Cryo-electron microscopy, crystallography and computer modelling provide atomic-scale snapshots of channel conformations in non-cellular environments but lack dynamic information that can be linked to functional results. Biophysical techniques such as electrophysiology, on the other hand, provide functional data with no structural information of the processes involved. Fluorescence spectroscopy techniques help bridge this gap in simultaneously obtaining structure-function correlates. These include voltage-clamp fluorometry, Förster resonance energy transfer, ligand binding assays, single molecule fluorescence and their variations. These techniques can be employed to unearth several features of ion channel behaviour. For instance, they provide real time information on local and global rearrangements that are inherent to channel properties. They also lend insights in trafficking, expression, and assembly of ion channels on the membrane surface. These methods have the advantage that they can be carried out in either native or heterologous systems. In this review, we briefly explain the principles of fluorescence and how these have been translated to study ion channel function. We also report several recent advances in fluorescence spectroscopy that has helped address and improve our understanding of the biophysical behaviours of different ion channel families.
Collapse
|
15
|
Non-invasive imaging of ion concentration distribution around cell spheroids by electrical impedance tomographic sensor printed on circuit board under temporal compensation by ion transport impedance model. Biosens Bioelectron 2022; 212:114432. [DOI: 10.1016/j.bios.2022.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/29/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022]
|
16
|
Martinac B, Kung C. The force-from-lipid principle and its origin, a ‘ what is true for E. coli is true for the elephant’ refrain. J Neurogenet 2022; 36:44-54. [DOI: 10.1080/01677063.2022.2097674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Boris Martinac
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Clinical Medicine, UNSW Medicine & Health, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Ching Kung
- Laboratory of Molecular Biology and the Department of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| |
Collapse
|
17
|
Abstract
SignificanceOuter membrane porins play a crucial role in processes as varied as energy production, photosynthesis, and nutrient transport. They act as the gatekeepers between a gram-negative bacterium and its environment. Understanding how these proteins fold and function is important in improving our understanding and control of these processes. Here we use single-molecule methods to help resolve the apparent differences between the fast folding expected on a molecular scale and the slow kinetics observed in ensemble measurements in the laboratory.
Collapse
|
18
|
Immadisetty K, Polasa A, Shelton R, Moradi M. Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel. Comput Struct Biotechnol J 2022; 20:2539-2550. [PMID: 35685356 PMCID: PMC9156883 DOI: 10.1016/j.csbj.2022.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
Mechanosensitive channel of large conductance (MscL) detects and responds to changes in the pressure profile of cellular membranes and transduces the mechanical energy into electrical and/or chemical signals. MscL can be activated using ultrasonic or chemical activation methods to improve the absorption of medicines and bioactive compounds into cells. However, re-engineering chemical signals such as pH change can trigger channel activation in MscL. This study elucidates the activation mechanism of an engineered MscL at an atomic level through a combination of equilibrium and non-equilibrium (NE) molecular dynamics (MD) simulations. Comparing the wild-type (WT) and engineered MscL activation processes suggests that the two systems are likely associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various backbone-backbone hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are between the transmembrane helices 1 and 2 in engineered MscL channel. The orientation-based biasing approach for producing and optimizing an open MscL model used in this work is a promising way to characterize unknown protein functional states and investigate the activation processes in ion channels and transmembrane proteins in general. This work paves the way for a computational framework for engineering more efficient pH-sensing mechanosensitive channels.
Collapse
Affiliation(s)
- Kalyan Immadisetty
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Reid Shelton
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
- Corresponding author.
| |
Collapse
|
19
|
Zhang Y, Angiulli G, Martinac B, Cox CD, Walz T. Cyclodextrins for structural and functional studies of mechanosensitive channels. J Struct Biol X 2021; 5:100053. [PMID: 34816118 PMCID: PMC8593449 DOI: 10.1016/j.yjsbx.2021.100053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Mechanosensitive (MS) channels that are activated by the 'force-from-lipids' (FFL) principle rest in the membrane in a closed state but open a transmembrane pore in response to changes in the transmembrane pressure profile. The molecular implementations of the FFL principle vary widely between different MS channel families. The function of MS channels is often studied by patch-clamp electrophysiology, in which mechanical force or amphipathic molecules are used to activate the channels. Structural studies of MS channels in states other than the closed resting state typically relied on the use of mutant channels. Cyclodextrins (CDs) were recently introduced as a relatively easy and convenient approach to generate membrane tension. The principle is that CDs chelate hydrophobic molecules and can remove lipids from membranes, thus forcing the remaining lipids to cover more surface area and creating tension for membrane proteins residing in the membranes. CDs can be used to study the structure of MS channels in a membrane under tension by using single-particle cryo-electron microscopy to image the channels in nanodiscs after incubation with CDs as well as to characterize the function of MS channels by using patch-clamp electrophysiology to record the effect of CDs on channels inserted into membrane patches excised from proteoliposomes. Importantly, because incubation of membrane patches with CDs results in the activation of MscL, an MS channel that opens only shortly before membrane rupture, CD-mediated lipid removal appears to generate sufficient force to open most if not all types of MS channels that follow the FFL principle.
Collapse
Affiliation(s)
- Yixiao Zhang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA
| | - Gabriella Angiulli
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA
| | - Boris Martinac
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Charles D. Cox
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA
| |
Collapse
|
20
|
Arya S, Gourley AJ, Penedo JC, Blindauer CA, Stewart AJ. Fatty acids may influence insulin dynamics through modulation of albumin-Zn 2+ interactions. Bioessays 2021; 43:e2100172. [PMID: 34725844 DOI: 10.1002/bies.202100172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 01/02/2023]
Abstract
Insulin is stored within the pancreas in an inactive Zn2+ -bound hexameric form prior to release. Similarly, clinical insulins contain Zn2+ and form multimeric complexes. Upon release from the pancreas or upon injection, insulin only becomes active once Zn2+ disengages from the complex. In plasma and other extracellular fluids, the majority of Zn2+ is bound to human serum albumin (HSA), which plays a vital role in controlling insulin pharmacodynamics by enabling removal of Zn2+ . The Zn2+ -binding properties of HSA are attenuated by non-esterified fatty acids (NEFAs) also transported by HSA. Elevated NEFA concentrations are associated with obesity and type 2 diabetes. Here we present the hypothesis that higher NEFA levels in obese and/or diabetic individuals may contribute to insulin resistance and affect therapeutic insulin dose-response profiles, through modulation of HSA/Zn2+ dynamics. We envisage this novel concept to have important implications for personalized treatments and management of diabetes-related conditions in the future.
Collapse
Affiliation(s)
- Swati Arya
- School of Medicine, University of St. Andrews, St. Andrews, Fife, UK
| | - Adam J Gourley
- School of Medicine, University of St. Andrews, St. Andrews, Fife, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, UK
| | | | - Alan J Stewart
- School of Medicine, University of St. Andrews, St. Andrews, Fife, UK
| |
Collapse
|
21
|
Cyclodextrins increase membrane tension and are universal activators of mechanosensitive channels. Proc Natl Acad Sci U S A 2021; 118:2104820118. [PMID: 34475213 DOI: 10.1073/pnas.2104820118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
The bacterial mechanosensitive channel of small conductance (MscS) has been extensively studied to understand how mechanical forces are converted into the conformational changes that underlie mechanosensitive (MS) channel gating. We showed that lipid removal by β-cyclodextrin can mimic membrane tension. Here, we show that all cyclodextrins (CDs) can activate reconstituted Escherichia coli MscS, that MscS activation by CDs depends on CD-mediated lipid removal, and that the CD amount required to gate MscS scales with the channel's sensitivity to membrane tension. Importantly, cholesterol-loaded CDs do not activate MscS. CD-mediated lipid removal ultimately causes MscS desensitization, which we show is affected by the lipid environment. While many MS channels respond to membrane forces, generalized by the "force-from-lipids" principle, their different molecular architectures suggest that they use unique ways to convert mechanical forces into conformational changes. To test whether CDs can also be used to activate other MS channels, we chose to investigate the mechanosensitive channel of large conductance (MscL) and demonstrate that CDs can also activate this structurally unrelated channel. Since CDs can open the least tension-sensitive MS channel, MscL, they should be able to open any MS channel that responds to membrane tension. Thus, CDs emerge as a universal tool for the structural and functional characterization of unrelated MS channels.
Collapse
|
22
|
Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
Collapse
Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
| |
Collapse
|
23
|
Abstract
Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.
Collapse
Affiliation(s)
| | - Urs Jenal
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland; ,
| |
Collapse
|
24
|
White DS, Chowdhury S, Idikuda V, Zhang R, Retterer ST, Goldsmith RH, Chanda B. cAMP binding to closed pacemaker ion channels is non-cooperative. Nature 2021; 595:606-610. [PMID: 34194042 PMCID: PMC8513821 DOI: 10.1038/s41586-021-03686-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/02/2021] [Indexed: 12/17/2022]
Abstract
Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding1. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding2,3, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP5 and provide direct validation of the ligand-induced flip-state model6-9. This approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.
Collapse
Affiliation(s)
- David S White
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sandipan Chowdhury
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Vinay Idikuda
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
- Center for Investigation of Membrane Excitability Diseases, Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Ruohan Zhang
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Baron Chanda
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Investigation of Membrane Excitability Diseases, Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
25
|
Yang Z, Xu H, Wang J, Chen W, Zhao M. Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis. APPLIED SPECTROSCOPY 2021; 75:491-505. [PMID: 33825543 DOI: 10.1177/00037028211009973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.
Collapse
Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| |
Collapse
|
26
|
Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
Collapse
Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
| |
Collapse
|
27
|
Zhang X, Zhang Y, Tang S, Ma S, Shen Y, Chen Y, Tong Q, Li Y, Yang J. Hydrophobic Gate of Mechanosensitive Channel of Large Conductance in Lipid Bilayers Revealed by Solid-State NMR Spectroscopy. J Phys Chem B 2021; 125:2477-2490. [DOI: 10.1021/acs.jpcb.0c07487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xuning Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yan Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Siyang Tang
- Children’s Hospital and Department of Biophysics, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shaojie Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Yanke Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Tong
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuezhou Li
- Children’s Hospital and Department of Biophysics, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jun Yang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| |
Collapse
|
28
|
Han C, Kang H, Yi J, Kang M, Lee H, Kwon Y, Jung J, Lee J, Park J. Single-vesicle imaging and co-localization analysis for tetraspanin profiling of individual extracellular vesicles. J Extracell Vesicles 2021; 10:e12047. [PMID: 33456726 PMCID: PMC7797949 DOI: 10.1002/jev2.12047] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are secreted nano-sized vesicles that contain cellular proteins, lipids, and nucleic acids. Although EVs are expected to be biologically diverse, current analyses cannot adequately characterize this diversity because most are ensemble methods that inevitably average out information from diverse EVs. Here we describe a single vesicle analysis, which directly visualizes marker expressions of individual EVs using a total internal-reflection microscopy and analyzes their co-localization to investigate EV subpopulations. The single-vesicle imaging and co-localization analysis successfully illustrated the diversity of EVs and revealed distinct patterns of tetraspanin expressions. Application of the analysis demonstrated similarities and dissimilarities between the EV fractions that had been acquired from different conventional EV isolation methods. The analysis method developed in this study will provide a new and reliable tool for investigating characteristics of single EVs, and the findings of the analysis might increase understanding of the characteristics of EVs.
Collapse
Affiliation(s)
- Chungmin Han
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Hyejin Kang
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Johan Yi
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Minsu Kang
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Hyunjin Lee
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Yongmin Kwon
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Jaehun Jung
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Jingeol Lee
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| | - Jaesung Park
- Department of Mechanical Engineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeong-buk Republic of Korea
| |
Collapse
|
29
|
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.
Collapse
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.
| |
Collapse
|
30
|
Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
Collapse
|
31
|
Discoveries in structure and physiology of mechanically activated ion channels. Nature 2020; 587:567-576. [PMID: 33239794 DOI: 10.1038/s41586-020-2933-1] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/19/2020] [Indexed: 01/24/2023]
Abstract
The ability to sense physical forces is conserved across all organisms. Cells convert mechanical stimuli into electrical or chemical signals via mechanically activated ion channels. In recent years, the identification of new families of mechanosensitive ion channels-such as PIEZO and OSCA/TMEM63 channels-along with surprising insights into well-studied mechanosensitive channels have driven further developments in the mechanotransduction field. Several well-characterized mechanosensory roles such as touch, blood-pressure sensing and hearing are now linked with primary mechanotransducers. Unanticipated roles of mechanical force sensing continue to be uncovered. Furthermore, high-resolution structures representative of nearly every family of mechanically activated channel described so far have underscored their diversity while advancing our understanding of the biophysical mechanisms of pressure sensing. Here we summarize recent discoveries in the physiology and structures of known mechanically activated ion channel families and discuss their implications for understanding the mechanisms of mechanical force sensing.
Collapse
|
32
|
Kapsalis C, Ma Y, Bode BE, Pliotas C. In-Lipid Structure of Pressure-Sensitive Domains Hints Mechanosensitive Channel Functional Diversity. Biophys J 2020; 119:448-459. [PMID: 32621864 PMCID: PMC7376121 DOI: 10.1016/j.bpj.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis has been used as a structural model for rationalizing functional observations in multiple MscL orthologs. Although these orthologs adopt similar structural architectures, they reportedly present significant functional differences. Subtle structural discrepancies on mechanosensitive channel nanopockets are known to affect mechanical gating and may be linked to large variability in tension sensitivity among these membrane channels. Here, we modify the nanopocket regions of MscL from Escherichia coli and M. tuberculosis and employ PELDOR/DEER distance and 3pESEEM deuterium accessibility measurements to interrogate channel structure within lipids, in which both channels adopt a closed conformation. Significant in-lipid structural differences between the two constructs suggest a more compact E. coli MscL at the membrane inner-leaflet, as a consequence of a rotated TM2 helix. Observed differences within lipids could explain E. coli MscL’s higher tension sensitivity and should be taken into account in extrapolated models used for MscL gating rationalization.
Collapse
Affiliation(s)
- Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Yue Ma
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, St Andrews, United Kingdom.
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
| |
Collapse
|
33
|
Haylock S, Friddin MS, Hindley JW, Rodriguez E, Charalambous K, Booth PJ, Barter LMC, Ces O. Membrane protein mediated bilayer communication in networks of droplet interface bilayers. Commun Chem 2020; 3:77. [PMID: 34113722 PMCID: PMC7610947 DOI: 10.1038/s42004-020-0322-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Droplet interface bilayers (DIBs) are model membranes formed between lipid monolayer-encased water droplets in oil. Compared to conventional methods, one of the most unique properties of DIBs is that they can be connected together to generate multi-layered ‘tissue-like’ networks, however introducing communication pathways between these compartments typically relies on water-soluble pores that are unable to gate. Here, we show that network connectivity can instead be achieved using a water-insoluble membrane protein by successfully reconstituting a chemically activatable mutant of the mechanosensitive channel MscL into a network of DIBs. Moreover, we also show how the small molecule activator can diffuse through an open channel and across the neighbouring droplet to activate MscL present in an adjacent bilayer. This demonstration of membrane protein mediated bilayer communication could prove key toward developing the next generation of responsive bilayer networks capable of defining information flow inside a minimal tissue.
Collapse
Affiliation(s)
- Stuart Haylock
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Mark S Friddin
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - James W Hindley
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,fabriCELL, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Enrique Rodriguez
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Kalypso Charalambous
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Laura M C Barter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,fabriCELL, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| |
Collapse
|
34
|
Lam K, Tajkhorshid E. Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics. Biophys J 2020; 119:24-34. [PMID: 32533943 DOI: 10.1016/j.bpj.2020.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022] Open
Abstract
Organic fluorophores, such as Cy3 and Cy5, have been widely used as chemical labels to probe the structure and dynamics of membrane proteins. Although a number of previous studies have reported on the possibility of some of the water-soluble fluorophores to interact with lipid bilayers, detailed fluorophore-lipid interactions and, more importantly, the potential effect of such interactions on the natural dynamics of the labeled membrane proteins have not been well studied. We have performed a large set of all-atom molecular dynamics simulations employing the highly mobile membrane mimetic model to describe spontaneous partitioning of the fluorophores into lipid bilayers with different lipid compositions. Spontaneous membrane partitioning of Cy3 and Cy5 fluorophores captured in these simulations proceeds in two steps. Electrostatic interaction between the fluorophores and the lipid headgroups facilitates the initial, fast membrane association of the fluorophores, followed by slow insertion of hydrophobic moieties into the lipid bilayer core. After the conversion of the resulting membrane-bound systems to full-membrane representations, biased-exchange umbrella sampling simulations are performed for free energy calculations, revealing a higher energy barrier for partitioning into negatively charged (phosphatidylserine or phosphatidylcholine) membranes than purely zwitterionic (phosphatidylcholine or phosphatidylethanolamine) ones. Furthermore, the potential effect of fluorophore-lipid interactions on membrane proteins has been examined by covalently linking Cy5 to single- and multipass transmembrane helical proteins. Equilibrium simulations show strong position-dependent effects of Cy5-tagging on the structure and natural dynamics of membrane proteins. Interactions between the tagged protein and Cy5 were also observed. Our results suggest that fluorophore-lipid interactions can affect the structure and dynamics of membrane proteins to various extents, especially in systems with higher structural flexibility.
Collapse
Affiliation(s)
- Kin Lam
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| |
Collapse
|
35
|
Poblete-Castro I, Aravena-Carrasco C, Orellana-Saez M, Pacheco N, Cabrera A, Borrero-de Acuña JM. Engineering the Osmotic State of Pseudomonas putida KT2440 for Efficient Cell Disruption and Downstream Processing of Poly(3-Hydroxyalkanoates). Front Bioeng Biotechnol 2020; 8:161. [PMID: 32211393 PMCID: PMC7066983 DOI: 10.3389/fbioe.2020.00161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/17/2020] [Indexed: 11/17/2022] Open
Abstract
In the last decade, the development of novel programmable cell lytic systems based on different inducible genetic constructs like the holin–endolysin and lysozyme appears as a promising alternative to circumvent the use of costly enzymes and mechanical disrupters for downstream processing of intracellular microbial products. Despite the advances, upon activation of these systems the cellular disruption of the biocatalyst occurs in an extended period, thus delaying the recovery of poly(3-hydroxyalkanoate) (PHA). Herein the osmotic state of Pseudomonas putida KT2440 was engineered by inactivating the inner-membrane residing rescue valve MscL, which is responsible mainly for circumventing low-osmolarity challenges. Then the major outer membrane porin OprF and the specific porin OprE were overproduced during PHA producing conditions on decanoate-grown cells. The engineered P. putida strains carrying each porin showed no impairment on growth rate and final biomass and PHA yield after 48 h cultivation. Expression of both porins in tandem in the mutant strain KTΔmscL-oprFE led to a slight reduction of the biomass synthesis (∼10%) but higher PHA accumulation (%wt) relative to the cell dry mass. Each strain was then challenged to an osmotic upshift for 1 h and subsequently to a rapid passage to a hypotonic condition where the membrane stability of the KTΔmscL-oprFE suffered damage, resulting in a rapid reduction of cell viability. Cell disruption accounted for >95% of the cell population within 3 h as reported by colony forming units (CFU), FACS analyses, and transmission electron microscopy. PHA recovery yielded 94.2% of the biosynthesized biopolymer displaying no significant alterations on the final monomer composition. This study can serve as an efficient genetic platform for the recovery of any microbial intracellular compound allowing less unit operation steps for cellular disruption.
Collapse
Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Carla Aravena-Carrasco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Alex Cabrera
- Unidad de Citometría de Flujo, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Manuel Borrero-de Acuña
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
36
|
Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels. PHYSICAL REVIEW LETTERS 2020; 124:048102. [PMID: 32058787 DOI: 10.1103/physrevlett.124.048102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Indexed: 06/10/2023]
Abstract
Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.
Collapse
Affiliation(s)
- Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Smitha Hegde
- Centre for Synthetic and Systems Biology University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Raman Ganti
- Institute for Medical Engineering and Science Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
37
|
Life with Bacterial Mechanosensitive Channels, from Discovery to Physiology to Pharmacological Target. Microbiol Mol Biol Rev 2020; 84:84/1/e00055-19. [PMID: 31941768 DOI: 10.1128/mmbr.00055-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
General principles in biology have often been elucidated from the study of bacteria. This is true for the bacterial mechanosensitive channel of large conductance, MscL, the channel highlighted in this review. This channel functions as a last-ditch emergency release valve discharging cytoplasmic solutes upon decreases in osmotic environment. Opening the largest gated pore, MscL passes molecules up to 30 Å in diameter; exaggerated conformational changes yield advantages for study, including in vivo assays. MscL contains structural/functional themes that recur in higher organisms and help elucidate how other, structurally more complex, channels function. These features of MscL include (i) the ability to directly sense, and respond to, biophysical changes in the membrane, (ii) an α helix ("slide helix") or series of charges ("knot in a rope") at the cytoplasmic membrane boundary to guide transmembrane movements, and (iii) important subunit interfaces that, when disrupted, appear to cause the channel to gate inappropriately. MscL may also have medical applications: the modality of the MscL channel can be changed, suggesting its use as a triggered nanovalve in nanodevices, including those for drug targeting. In addition, recent studies have shown that the antibiotic streptomycin opens MscL and uses it as one of the primary paths to the cytoplasm. Moreover, the recent identification and study of novel specific agonist compounds demonstrate that the channel is a valid drug target. Such compounds may serve as novel-acting antibiotics and adjuvants, a way of permeabilizing the bacterial cell membrane and, thus, increasing the potency of commonly used antibiotics.
Collapse
|
38
|
Martinac B, Nikolaev YA, Silvani G, Bavi N, Romanov V, Nakayama Y, Martinac AD, Rohde P, Bavi O, Cox CD. Cell membrane mechanics and mechanosensory transduction. CURRENT TOPICS IN MEMBRANES 2020; 86:83-141. [DOI: 10.1016/bs.ctm.2020.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
39
|
Allosteric activation of an ion channel triggered by modification of mechanosensitive nano-pockets. Nat Commun 2019; 10:4619. [PMID: 31601809 PMCID: PMC6787021 DOI: 10.1038/s41467-019-12591-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/17/2019] [Indexed: 11/08/2022] Open
Abstract
Lipid availability within transmembrane nano-pockets of ion channels is linked with mechanosensation. However, the effect of hindering lipid-chain penetration into nano-pockets on channel structure has not been demonstrated. Here we identify nano-pockets on the large conductance mechanosensitive channel MscL, the high-pressure threshold channel. We restrict lipid-chain access to the nano-pockets by mutagenesis and sulfhydryl modification, and monitor channel conformation by PELDOR/DEER spectroscopy. For a single site located at the entrance of the nano-pockets and distal to the channel pore we generate an allosteric response in the absence of tension. Single-channel recordings reveal a significant decrease in the pressure activation threshold of the modified channel and a sub-conducting state in the absence of applied tension. Threshold is restored to wild-type levels upon reduction of the sulfhydryl modification. The modification associated with the conformational change restricts lipid access to the nano-pocket, interrupting the contact between the membrane and the channel that mediates mechanosensitivity.
Collapse
|
40
|
Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
|
41
|
Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
Collapse
Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
| | | | | |
Collapse
|
42
|
Dalgarno PA, Juan-Colás J, Hedley GJ, Piñeiro L, Novo M, Perez-Gonzalez C, Samuel IDW, Leake MC, Johnson S, Al-Soufi W, Penedo JC, Quinn SD. Unveiling the multi-step solubilization mechanism of sub-micron size vesicles by detergents. Sci Rep 2019; 9:12897. [PMID: 31501469 PMCID: PMC6733941 DOI: 10.1038/s41598-019-49210-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022] Open
Abstract
The solubilization of membranes by detergents is critical for many technological applications and has become widely used in biochemistry research to induce cell rupture, extract cell constituents, and to purify, reconstitute and crystallize membrane proteins. The thermodynamic details of solubilization have been extensively investigated, but the kinetic aspects remain poorly understood. Here we used a combination of single-vesicle Förster resonance energy transfer (svFRET), fluorescence correlation spectroscopy and quartz-crystal microbalance with dissipation monitoring to access the real-time kinetics and elementary solubilization steps of sub-micron sized vesicles, which are inaccessible by conventional diffraction-limited optical methods. Real-time injection of a non-ionic detergent, Triton X, induced biphasic solubilization kinetics of surface-immobilized vesicles labelled with the Dil/DiD FRET pair. The nanoscale sensitivity accessible by svFRET allowed us to unambiguously assign each kinetic step to distortions of the vesicle structure comprising an initial fast vesicle-swelling event followed by slow lipid loss and micellization. We expect the svFRET platform to be applicable beyond the sub-micron sizes studied here and become a unique tool to unravel the complex kinetics of detergent-lipid interactions.
Collapse
Affiliation(s)
- Paul A Dalgarno
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK.,Institute of Biological Physics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - José Juan-Colás
- Department of Electronic Engineering, University of York, Heslington, York, YO10 5DD, UK
| | - Gordon J Hedley
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK.,School of Chemistry, University of Glasgow, Glasgow, Scotland, G12 8QQ, United Kingdom
| | - Lucas Piñeiro
- Department of Physical Chemistry, Faculty of Science, University of Santiago de Compostela, Lugo, E-27002, Spain
| | - Mercedes Novo
- Department of Physical Chemistry, Faculty of Science, University of Santiago de Compostela, Lugo, E-27002, Spain
| | - Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK
| | - Ifor D W Samuel
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York, England, YO10 5DD, UK.,Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York, YO10 5DD, UK
| | - Wajih Al-Soufi
- Department of Physical Chemistry, Faculty of Science, University of Santiago de Compostela, Lugo, E-27002, Spain
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, UK.
| | - Steven D Quinn
- SUPA School of Physics and Astronomy, University of St. Andrews, North Haugh, Fife, KY16 9SS, UK. .,Department of Physics, University of York, Heslington, York, England, YO10 5DD, UK. .,Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| |
Collapse
|
43
|
Owada N, Yoshida M, Morita K, Yoshimura K. Temperature-sensitive mutants of MscL mechanosensitive channel. J Biochem 2019; 166:281-288. [PMID: 31143940 DOI: 10.1093/jb/mvz035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/25/2019] [Indexed: 01/15/2023] Open
Abstract
MscL is a mechanosensitive channel that undergoes a global conformational change upon application of membrane stretching. To elucidate how the structural stability and flexibility occur, we isolated temperature-sensitive (Ts) mutants of Escherichia coli MscL that allowed cell growth at 32°C but not at 42°C. Two Ts mutants, L86P and D127V, were identified. The L86P mutation occurred in the second transmembrane helix, TM2. Substitution of residues neighbouring L86 with proline also led to a Ts mutation, but the substitution of L86 with other amino acids did not result in a Ts phenotype, indicating that the Ts phenotype was due to a structural change of TM2 helix by the introduction of a proline residue. The D127V mutation was localized in the electrostatic belt of the bundle of cytoplasmic helices, indicating that stability of the pentameric bundle of the cytoplasmic helix affects MscL structure. Together, this study described a novel class of MscL mutations that were correlated with the thermodynamic stability of the MscL structure.
Collapse
Affiliation(s)
- Naoto Owada
- Department of Machinery and Control Systems, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama-shi, Saitama, Japan
| | - Megumi Yoshida
- Department of Machinery and Control Systems, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama-shi, Saitama, Japan
| | - Kohei Morita
- Department of Machinery and Control Systems, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama-shi, Saitama, Japan
| | - Kenjiro Yoshimura
- Department of Machinery and Control Systems, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama-shi, Saitama, Japan
| |
Collapse
|
44
|
Litwin DB, Durham RJ, Jayaraman V. Single-Molecule FRET Methods to Study Glutamate Receptors. Methods Mol Biol 2019; 1941:3-16. [PMID: 30707423 DOI: 10.1007/978-1-4939-9077-1_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Single-molecule fluorescence energy transfer methods allow us to determine the complete structural landscape between the donor and acceptor fluorophores introduced on the protein of interest. This method is particularly attractive to study ion channel proteins as single-molecule current recordings have been used to study the function of these proteins for several decades. Here we describe the smFRET method used to study glutamate receptors.
Collapse
Affiliation(s)
- Douglas B Litwin
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ryan J Durham
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, USA.
| |
Collapse
|
45
|
Litwin DB, Carrillo E, Shaikh SA, Berka V, Jayaraman V. The structural arrangement at intersubunit interfaces in homomeric kainate receptors. Sci Rep 2019; 9:6969. [PMID: 31061516 PMCID: PMC6502836 DOI: 10.1038/s41598-019-43360-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/23/2019] [Indexed: 02/02/2023] Open
Abstract
Kainate receptors are glutamate-gated cation-selective channels involved in excitatory synaptic signaling and are known to be modulated by ions. Prior functional and structural studies suggest that the dimer interface at the agonist-binding domain plays a key role in activation, desensitization, and ion modulation in kainate receptors. Here we have used fluorescence-based methods to investigate the changes and conformational heterogeneity at these interfaces associated with the resting, antagonist-bound, active, desensitized, and ion-modulated states of the receptor. These studies show that in the presence of Na+ ions the interfaces exist primarily in the coupled state in the apo, antagonist-bound and activated (open channel) states. Under desensitizing conditions, the largely decoupled dimer interface at the agonist-binding domain as seen in the cryo-EM structure is one of the states observed. However, in addition to this state there are several additional states with lower levels of decoupling. Replacing Na+ with Cs+ does not alter the FRET efficiencies of the states significantly, but shifts the population to the more decoupled states in both resting and desensitized states, which can be correlated with the lower activation seen in the presence of Cs+.
Collapse
Affiliation(s)
- Douglas B Litwin
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Elisa Carrillo
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Sana A Shaikh
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Vladimir Berka
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA.
| |
Collapse
|
46
|
Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
Collapse
Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| |
Collapse
|
47
|
Ganesan I, Theg SM. Structural considerations of folded protein import through the chloroplast TOC/TIC translocons. FEBS Lett 2019; 593:565-572. [PMID: 30775779 DOI: 10.1002/1873-3468.13342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 11/11/2022]
Abstract
Protein import into chloroplasts is carried out by the protein translocons at the outer and inner envelope membranes (TOC and TIC). Detailed structures for these translocons are lacking, with only a low-resolution TOC complex structure available. Recently, we showed that the TOC/TIC translocons can import folded proteins, a rather unique feat for a coupled double membrane system. We also determined the maximum functional TOC/TIC pore size to be 30-35 Å. Here, we discuss how such large pores could form and compare the structural dynamics of the pore-forming Toc75 subunit to its bacterial/mitochondrial Omp85 family homologs. We put forward structural models that can be empirically tested and also briefly review the pore dynamics of other protein translocons with known structures.
Collapse
Affiliation(s)
- Iniyan Ganesan
- Department of Plant Biology, University of California Davis, CA, USA
| | - Steven M Theg
- Department of Plant Biology, University of California Davis, CA, USA
| |
Collapse
|
48
|
Goujon A, Straková K, Sakai N, Matile S. Streptavidin interfacing as a general strategy to localize fluorescent membrane tension probes in cells. Chem Sci 2019; 10:310-319. [PMID: 30713639 PMCID: PMC6333237 DOI: 10.1039/c8sc03620a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
To image the mechanical properties of biological membranes, twisted push-pull mechanophores that respond to membrane tension by planarization in the ground state have been introduced recently. For their application in biological systems, these so-called fluorescent flippers will have to be localized to specific environments of cellular membranes. In this report, we explore streptavidin as a versatile connector between biotinylated flipper probes and biotinylated targets. Fluorescence spectroscopy and microscopy with LUVs and GUVs reveal the specific conditions needed for desthiobiotin-loaded streptavidin to deliver biotinylated flippers selectively to biotinylated membranes. Selectivity for biotinylated plasma membranes is also observed in HeLa cells, confirming the compatibility of this strategy with biological systems. Streptavidin interfacing does not affect the mechanosensitivity of the flipper probes, red shift in the excitation maximum and fluorescence lifetime increase with membrane order and tension, as demonstrated, inter alia, using FLIM.
Collapse
Affiliation(s)
- Antoine Goujon
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Karolína Straková
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Naomi Sakai
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Stefan Matile
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| |
Collapse
|
49
|
Colom A, Derivery E, Soleimanpour S, Tomba C, Molin MD, Sakai N, González-Gaitán M, Matile S, Roux A. A fluorescent membrane tension probe. Nat Chem 2018; 10:1118-1125. [PMID: 30150727 PMCID: PMC6197433 DOI: 10.1038/s41557-018-0127-3] [Citation(s) in RCA: 288] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/25/2018] [Indexed: 12/24/2022]
Abstract
Cells and organelles are delimited by lipid bilayers in which high deformability is essential to many cell processes, including motility, endocytosis and cell division. Membrane tension is therefore a major regulator of the cell processes that remodel membranes, albeit one that is very hard to measure in vivo. Here we show that a planarizable push-pull fluorescent probe called FliptR (fluorescent lipid tension reporter) can monitor changes in membrane tension by changing its fluorescence lifetime as a function of the twist between its fluorescent groups. The fluorescence lifetime depends linearly on membrane tension within cells, enabling an easy quantification of membrane tension by fluorescence lifetime imaging microscopy. We further show, using model membranes, that this linear dependency between lifetime of the probe and membrane tension relies on a membrane-tension-dependent lipid phase separation. We also provide calibration curves that enable accurate measurement of membrane tension using fluorescence lifetime imaging microscopy.
Collapse
Affiliation(s)
- Adai Colom
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Emmanuel Derivery
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Saeideh Soleimanpour
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caterina Tomba
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marta Dal Molin
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marcos González-Gaitán
- Biochemistry Department, University of Geneva, Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, Geneva, Switzerland.
- Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland.
- School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
50
|
Herrera N, Maksaev G, Haswell ES, Rees DC. Elucidating a role for the cytoplasmic domain in the Mycobacterium tuberculosis mechanosensitive channel of large conductance. Sci Rep 2018; 8:14566. [PMID: 30275500 PMCID: PMC6167328 DOI: 10.1038/s41598-018-32536-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/31/2018] [Indexed: 12/04/2022] Open
Abstract
Microbial survival in dynamic environments requires the ability to successfully respond to abrupt changes in osmolarity. The mechanosensitive channel of large conductance (MscL) is a ubiquitous channel that facilitates the survival of bacteria and archaea under severe osmotic downshock conditions by relieving excess turgor pressure in response to increased membrane tension. A prominent structural feature of MscL, the cytoplasmic C-terminal domain, has been suggested to influence channel assembly and function. In this report, we describe the X-ray crystal structure and electrophysiological properties of a C-terminal domain truncation of the Mycobacterium tuberculosis MscL (MtMscLΔC). A crystal structure of MtMscLΔC solubilized in the detergent n-dodecyl-β-D-maltopyranoside reveals the pentameric, closed state-like architecture for the membrane spanning region observed in the previously solved full-length MtMscL. Electrophysiological characterization demonstrates that MtMscLΔC retains mechanosensitivity, but with conductance and tension sensitivity more closely resembling full length EcMscL than MtMscL. This study establishes that the C-terminal domain of MtMscL is not required for oligomerization of the full-length channel, but rather influences the tension sensitivity and conductance properties of the channel. The collective picture that emerges from these data is that each MscL channel structure has characteristic features, highlighting the importance of studying multiple homologs.
Collapse
Affiliation(s)
- Nadia Herrera
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.,Division of Infectious Diseases, Department of Medicine University of California, San Francisco, San Francisco, CA, 94143-0654, USA
| | - Grigory Maksaev
- Department of Biology, NSF Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Department of Cell Biology and Physiology, Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Elizabeth S Haswell
- Department of Biology, NSF Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
| |
Collapse
|