1
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Ito KI, Sato Y, Toyabe S. Design of artificial molecular motor inheriting directionality and scalability. Biophys J 2024; 123:858-866. [PMID: 38425042 PMCID: PMC10995430 DOI: 10.1016/j.bpj.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Realizing artificial molecular motors with autonomous functionality and high performance is a major challenge in biophysics. Such motors not only provide new perspectives in biotechnology but also offer a novel approach for the bottom-up elucidation of biological molecular motors. Directionality and scalability are critical factors for practical applications. However, the simultaneous realization of both remains challenging. In this study, we propose a novel design for a rotary motor that can be fabricated using a currently available technology, DNA origami, and validate its functionality through simulations with practical parameters. We demonstrate that the motor rotates unidirectionally and processively in the direction defined by structural asymmetry, which induces kinetic asymmetry in motor motion. The motor also exhibits scalability, such that increasing the number of connections between the motor and stator allows for a larger speed, run length, and stall force.
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Affiliation(s)
- Kenta I Ito
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, Fukuoka, Japan
| | - Shoichi Toyabe
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan.
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2
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Miyamura Y, Nishikino T, Koiwa H, Homma M, Kojima S. Roles of linker region flanked by transmembrane and peptidoglycan binding region of PomB in energy conversion of the Vibrio flagellar motor. Genes Cells 2024; 29:282-289. [PMID: 38351850 DOI: 10.1111/gtc.13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 04/04/2024]
Abstract
The flagellar components of Vibrio spp., PomA and PomB, form a complex that transduces sodium ion and contributes to rotate flagella. The transmembrane protein PomB is attached to the basal body T-ring by its periplasmic region and has a plug segment following the transmembrane helix to prevent ion flux. Previously we showed that PomB deleted from E41 to R120 (Δ41-120) was functionally comparable to the full-length PomB. In this study, three deletions after the plug region, PomB (Δ61-120), PomB (Δ61-140), and PomB (Δ71-150), were generated. PomB (Δ61-120) conferred motility, whereas the other two mutants showed almost no motility in soft agar plate; however, we observed some swimming cells with speed comparable for the wild-type cells. When the two PomB mutants were introduced into a wild-type strain, the swimming ability was not affected by the mutant PomBs. Then, we purified the mutant PomAB complexes to confirm the stator formation. When plug mutations were introduced into the PomB mutants, the reduced motility by the deletion was rescued, suggesting that the stator was activated. Our results indicate that the deletions prevent the stator activation and the linker and plug regions, from E41 to S150, are not essential for the motor function of PomB but are important for its regulation.
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Affiliation(s)
- Yusuke Miyamura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tatsuro Nishikino
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hiroaki Koiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Michio Homma
- Division of Material Science and Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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3
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Redford SA, Colen J, Shivers JL, Zemsky S, Molaei M, Floyd C, Ruijgrok PV, Vitelli V, Bryant Z, Dinner AR, Gardel ML. Motor crosslinking augments elasticity in active nematics. Soft Matter 2024; 20:2480-2490. [PMID: 38385209 PMCID: PMC10933839 DOI: 10.1039/d3sm01176c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge concerning how hydrodynamic parameters depend on the properties of microscopic elements. In this work, we combine experiments and multiscale modeling to relate the structure and dynamics of active nematics composed of biopolymer filaments and molecular motors to their microscopic properties, in particular motor processivity, speed, and valency. We show that crosslinking of filaments by both motors and passive crosslinkers not only augments the contributions to nematic elasticity from excluded volume effects but dominates them. By altering motor kinetics we show that a competition between motor speed and crosslinking results in a nonmonotonic dependence of nematic flow on motor speed. By modulating passive filament crosslinking we show that energy transfer into nematic flow is in large part dictated by crosslinking. Thus motor proteins both generate activity and contribute to nematic elasticity. Our results provide new insights for rationally engineering active materials.
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Affiliation(s)
- Steven A Redford
- The Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
| | - Jonathan Colen
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jordan L Shivers
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Mehdi Molaei
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Carlos Floyd
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vincenzo Vitelli
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron R Dinner
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
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4
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Korosec CS, Unksov IN, Surendiran P, Lyttleton R, Curmi PMG, Angstmann CN, Eichhorn R, Linke H, Forde NR. Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle. Nat Commun 2024; 15:1511. [PMID: 38396042 PMCID: PMC10891099 DOI: 10.1038/s41467-024-45570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.
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Affiliation(s)
- Chapin S Korosec
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
- Department of Mathematics and Statistics, York University, Toronto, ON, M3J 1P3, Canada.
| | - Ivan N Unksov
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Pradheebha Surendiran
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Roman Lyttleton
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Christopher N Angstmann
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ralf Eichhorn
- Nordita, Royal Institute of Technology and Stockholm University, 106 91, Stockholm, Sweden
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden.
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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5
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Kaplan M, Yao Q, Jensen GJ. Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography. Int J Mol Sci 2023; 24:8292. [PMID: 37176000 PMCID: PMC10179241 DOI: 10.3390/ijms24098292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, USA
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6
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Hormeno S, Wilkinson OJ, Aicart-Ramos C, Kuppa S, Antony E, Dillingham MS, Moreno-Herrero F. Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA. Proc Natl Acad Sci U S A 2022; 119:e2112376119. [PMID: 35385349 PMCID: PMC9169624 DOI: 10.1073/pnas.2112376119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/01/2022] [Indexed: 01/17/2023] Open
Abstract
Human DNA helicase B (HELB) is a poorly characterized helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single-molecule approaches to characterize the biochemical activities of HELB protein with a particular focus on its interactions with Replication Protein A (RPA) and RPA–single-stranded DNA (ssDNA) filaments. HELB is a monomeric protein that binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5′ to 3′ direction accompanied by the formation of DNA loops. HELB also displays classical helicase activity, but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from ssDNA. This activity, which can allow other proteins access to ssDNA intermediates despite their shielding by RPA, may underpin the diverse roles of HELB in cellular DNA transactions.
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Affiliation(s)
- Silvia Hormeno
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Oliver J. Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Sahiti Kuppa
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Edwin Antony
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Mark S. Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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7
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Baker JE. A chemical thermodynamic model of motor enzymes unifies chemical-Fx and powerstroke models. Biophys J 2022; 121:1184-1193. [PMID: 35192841 PMCID: PMC9034244 DOI: 10.1016/j.bpj.2022.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
Molecular motors play a central role in many biological processes, ranging from pumping blood and breathing to growth and wound healing. Through motor-catalyzed chemical reactions, these nanomachines convert the chemical free energy from ATP hydrolysis into two different forms of mechanical work. Motor enzymes perform reversible work, wrev, through an intermediate step in their catalyzed reaction cycle referred to as a working step, and they perform Fx work when they move a distance, x, against a force, F. In a powerstroke model, wrev is performed when the working step stretches a spring within a given motor enzyme. In a chemical-Fx model, wrev is performed in generating a conserved Fx potential defined external to the motor enzyme. It is difficult to find any common ground between these models even though both have been shown to account for mechanochemical measurements of motor enzymes with reasonable accuracy. Here, I show that, by changing one simple assumption in each model, the powerstroke and chemical-Fx model can be reconciled through a chemical thermodynamic model. The formal and experimental justifications for changing these assumptions are presented. The result is a unifying model for mechanochemical coupling in motor enzymes first presented by A.V. Hill in 1938 that is consistent with single-molecule structural and mechanical data.
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Affiliation(s)
- Josh E Baker
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada.
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8
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Wang MD, Nicodemi M, Dekker NH, Gregor T, Holcman D, van Oijen AM, Manley S. Physics meets biology: The joining of two forces to further our understanding of cellular function. Mol Cell 2021; 81:3033-3037. [PMID: 34358454 DOI: 10.1016/j.molcel.2021.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Some biological questions are tough to solve through standard molecular and cell biological methods and naturally lend themselves to investigation by physical approaches. Below, a group of formally trained physicists discuss, among other things, how they apply physics to address biological questions and how physical approaches complement conventional biological approaches.
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9
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Liu K, Patteson AE, Banigan EJ, Schwarz JM. Dynamic Nuclear Structure Emerges from Chromatin Cross-Links and Motors. Phys Rev Lett 2021; 126:158101. [PMID: 33929233 DOI: 10.1103/physrevlett.126.158101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin protein filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical mechanisms, we develop a model of an active, cross-linked Rouse chain bound to a polymeric shell. System-sized correlated motions occur but require both motor activity and cross-links. Contractile motors, in particular, enhance chromosome dynamics by driving anomalous density fluctuations. Nuclear shape fluctuations depend on motor strength, cross-linking, and chromosome-lamina binding. Therefore, complex chromosome dynamics and nuclear shape emerge from a minimal, active chromosome-lamina system.
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Affiliation(s)
- Kuang Liu
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
| | - Alison E Patteson
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, MIT, Cambridge, Massachusetts 02139, USA
| | - J M Schwarz
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
- Indian Creek Farm, Ithaca, New York 14850, USA
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10
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Kapoor S, Kodesia A, Kalidas N, Ashish, Thakur KG. Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB. J Biol Chem 2021; 296:100308. [PMID: 33493516 PMCID: PMC7949163 DOI: 10.1016/j.jbc.2021.100308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022] Open
Abstract
The δ-proteobacteria Myxococcus xanthus displays social (S) and adventurous (A) motilities, which require pole-to-pole reversal of the motility regulator proteins. Mutual gliding motility protein C (MglC), a paralog of GTPase-activating protein Mutual gliding motility protein B (MglB), is a member of the polarity module involved in regulating motility. However, little is known about the structure and function of MglC. Here, we determined ∼1.85 Å resolution crystal structure of MglC using Selenomethionine Single-wavelength anomalous diffraction. The crystal structure revealed that, despite sharing <9% sequence identity, both MglB and MglC adopt a Regulatory Light Chain 7 family fold. However, MglC has a distinct ∼30° to 40° shift in the orientation of the functionally important α2 helix compared with other structural homologs. Using isothermal titration calorimetry and size-exclusion chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using small-angle X-ray scattering and molecular docking studies, we show that the MglBC complex consists of a MglC homodimer sandwiched between two homodimers of MglB. A combination of size-exclusion chromatography and site-directed mutagenesis studies confirmed the MglBC interacting interface obtained by molecular docking studies. Finally, we show that the C-terminal region of MglB, crucial for binding its established partner MglA, is not required for binding MglC. These studies suggest that the MglB uses distinct interfaces to bind MglA and MglC. Based on these data, we propose a model suggesting a new role for MglC in polarity reversal in M. xanthus.
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Affiliation(s)
- Srajan Kapoor
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Akriti Kodesia
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Nidhi Kalidas
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Ashish
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India.
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11
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Abstract
While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.
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Affiliation(s)
- Ignacio Casuso
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
| | - Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, 59000 Lille, France
| | - Felix Rico
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
- e-mail:
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12
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Deme JC, Johnson S, Vickery O, Aron A, Monkhouse H, Griffiths T, James RH, Berks BC, Coulton JW, Stansfeld PJ, Lea SM. Structures of the stator complex that drives rotation of the bacterial flagellum. Nat Microbiol 2020; 5:1553-1564. [PMID: 32929189 PMCID: PMC7610383 DOI: 10.1038/s41564-020-0788-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023]
Abstract
The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio mimicus, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric A5B2 subunit assembly where the five A subunits enclose the two B subunits. Comparison to structures of other ion-driven motors indicates that this A5B2 architecture is fundamental to bacterial systems that couple energy from ion flow to generate mechanical work at a distance and suggests that such events involve rotation in the motor structures.
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Affiliation(s)
- Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Owen Vickery
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Amy Aron
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Holly Monkhouse
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Thomas Griffiths
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - James W Coulton
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Département de Biochemie et Médecine Moleculaire, Université de Montréal, Montréal, Quebec, Canada
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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13
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Abstract
Animal cells form contractile structures to promote various functions, from cell motility to cell division. Force generation in these structures is often due to molecular motors such as myosin that require polar substrates for their function. Here, we propose a motor-free mechanism that can generate contraction in biopolymer networks without the need for polarity. This mechanism is based on active binding and unbinding of cross-linkers that breaks the principle of detailed balance, together with the asymmetric force-extension response of semiflexible biopolymers. We find that these two ingredients can generate steady state contraction via a nonthermal, ratchetlike process. We calculate the resulting force-velocity relation using both coarse-grained and microscopic models.
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Affiliation(s)
- Sihan Chen
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Tomer Markovich
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Fred C MacKintosh
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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14
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Abstract
The friction between cytoskeletal filaments is of central importance for the formation of cellular structures such as the mitotic spindle and the cytokinetic ring. This friction is caused by passive cross-linkers, yet the underlying mechanism and the dependence on cross-linker density are poorly understood. Here, we use theory and computer simulations to study the friction between two filaments that are cross-linked by passive proteins, which can hop between discrete binding sites while physically excluding each other. The simulations reveal that filaments move via rare discrete jumps, which are associated with free-energy barrier crossings. We identify the reaction coordinate that governs the relative microtubule movement and derive an exact analytical expression for the free-energy barrier and the friction coefficient. Our analysis not only elucidates the molecular mechanism underlying cross-linker-induced filament friction, but also predicts that the friction coefficient scales superexponentially with the density of cross-linkers.
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15
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Feizabadi MS, Alejilat RS, Duffy AB, Breslin JC, Akintola II. A Confirmation for the Positive Electric Charge of Bio-Molecular Motors through Utilizing a Novel Nano-Technology Approach In Vitro. Int J Mol Sci 2020; 21:ijms21144935. [PMID: 32668620 PMCID: PMC7404192 DOI: 10.3390/ijms21144935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
Abstract
Molecular motors are microtubule-based proteins which contribute to many cell functions, such as intracellular transportation and cell division. The details of the nature of the mutual interactions between motors and microtubules still needs to be extensively explored. However, electrostatic interaction is known as one of the key factors making motor-microtubule association possible. The association rate of molecular motors to microtubules is a way to observe and evaluate the charge of the bio-motors in vivo. Growing evidence indicates that microtubules with distinct structural compositions in terms of beta tubulin isotypes carry different charges. Therefore, the electrostatic-driven association rate of motors–microtubules, which is a base for identifying the charge of motors, can be more likely influenced. Here, we present a novel method to experimentally confirm the charge of molecular motors in vitro. The offered nanotechnology-based approach can validate the charge of motors in the absence of any cellular components through the observation and analysis of the changes that biomolecular motors can cause on the dynamic of charged microspheres inside a uniform electric field produced by a microscope slide-based nanocapacitor. This new in vitro experimental method is significant as it minimizes the intracellular factors that may interfere the electric charge that molecular motors carry.
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16
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Johnson S, Fong YH, Deme JC, Furlong EJ, Kuhlen L, Lea SM. Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation. Nat Microbiol 2020; 5:966-975. [PMID: 32284565 PMCID: PMC7320910 DOI: 10.1038/s41564-020-0703-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/05/2020] [Indexed: 11/14/2022]
Abstract
The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical propeller that is attached to a motor embedded in the inner membrane. The motor consists of a series of stator units surrounding a central rotor made up of two ring complexes, the MS-ring and the C-ring. Despite many studies, high-resolution structural information is still lacking for the MS-ring of the rotor, and proposed mismatches in stoichiometry between the two rings have long provided a source of confusion for the field. Here, we present structures of the Salmonella MS-ring, revealing a high level of variation in inter- and intrachain symmetry that provides a structural explanation for the ability of the MS-ring to function as a complex and elegant interface between the two main functions of the flagellum-protein secretion and rotation.
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Affiliation(s)
- Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucas Kuhlen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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17
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Jose R, Santen L. Self-Organized Lane Formation in Bidirectional Transport by Molecular Motors. Phys Rev Lett 2020; 124:198103. [PMID: 32469583 DOI: 10.1103/physrevlett.124.198103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Within cells, vesicles and proteins are actively transported several micrometers along the cytoskeletal filaments. The transport along microtubules is propelled by dynein and kinesin motors, which carry the cargo in opposite directions. Bidirectional intracellular transport is performed with great efficiency, even under strong confinement, as for example in the axon. For this kind of transport system, one would expect generically cluster formation. In this Letter, we discuss the effect of the recently observed self-enhanced binding affinity along the kinesin trajectories on the microtubule. We introduce a stochastic lattice-gas model, where the enhanced binding affinity is realized via a floor field. From Monte Carlo simulations and a mean-field analysis we show that this mechanism can lead to self-organized symmetry breaking and lane formation that indeed leads to efficient bidirectional transport in narrow environments.
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Affiliation(s)
- Robin Jose
- Department of Theoretical Physics & Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Ludger Santen
- Department of Theoretical Physics & Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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18
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Naganawa S, Ito M. MotP Subunit is Critical for Ion Selectivity and Evolution of a K +-Coupled Flagellar Motor. Biomolecules 2020; 10:biom10050691. [PMID: 32365619 PMCID: PMC7277484 DOI: 10.3390/biom10050691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/03/2023] Open
Abstract
The bacterial flagellar motor is a sophisticated nanomachine embedded in the cell envelope. The flagellar motor is driven by an electrochemical gradient of cations such as H+, Na+, and K+ through ion channels in stator complexes embedded in the cell membrane. The flagellum is believed to rotate as a result of electrostatic interaction forces between the stator and the rotor. In bacteria of the genus Bacillus and related species, the single transmembrane segment of MotB-type subunit protein (MotB and MotS) is critical for the selection of the H+ and Na+ coupling ions. Here, we constructed and characterized several hybrid stators combined with single Na+-coupled and dual Na+- and K+-coupled stator subunits, and we report that the MotP subunit is critical for the selection of K+. This result suggested that the K+ selectivity of the MotP/MotS complexes evolved from the single Na+-coupled stator MotP/MotS complexes. This finding will promote the understanding of the evolution of flagellar motors and the molecular mechanisms of coupling ion selectivity.
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Affiliation(s)
- Shun Naganawa
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan;
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan;
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe Saitama 350-8585, Japan
- Correspondence: ; Tel.: +81-276-82-9202
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19
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. Prog Nucl Magn Reson Spectrosc 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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20
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Abstract
Tissues transition between solid-like and fluid-like behavior, which has major implications for morphogenesis and disease. These transitions can occur due to changes in the intrinsic shape of constituent cells and cell motility. We consider an alternative mechanism by studying tissues that explore the energy landscape through stochastic dynamics, driven by turnover of junctional molecular motors. To identify the solid-fluid transition, we start with single-component tissues and show that the mean cell-shape index uniquely describes the effective diffusion coefficient of cell movements, which becomes finite at the transition. We generalize our approach to two-component tissues, and explore cell-sorting dynamics both due to differential adhesion and due to differential degree of junctional fluctuations. We recover some known characteristic scaling relations describing the sorting kinetics, and discover some discrepancies from these relations in the case of differential-fluctuations-driven sorting. Finally, we show that differential fluctuations efficiently sort two solid-like tissues with a fluid intercompartmental boundary.
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Affiliation(s)
- Matej Krajnc
- JoŽef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia. and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, USA
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21
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Huang YS, Fan CH, Hsu N, Chiu NH, Wu CY, Chang CY, Wu BH, Hong SR, Chang YC, Yan-Tang Wu A, Guo V, Chiang YC, Hsu WC, Chen L, Pin-Kuang Lai C, Yeh CK, Lin YC. Sonogenetic Modulation of Cellular Activities Using an Engineered Auditory-Sensing Protein. Nano Lett 2020; 20:1089-1100. [PMID: 31884787 DOI: 10.1021/acs.nanolett.9b04373] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biomolecules that respond to different external stimuli enable the remote control of genetically modified cells. We report herein a sonogenetic approach that can manipulate target cell activities by focused ultrasound stimulation. This system requires an ultrasound-responsive protein derived from an engineered auditory-sensing protein prestin. Heterologous expression of mouse prestin containing two parallel amino acid substitutions, N7T and N308S, that frequently exist in prestins from echolocating species endowed transfected mammalian cells with the ability to sense ultrasound. An ultrasound pulse of low frequency and low pressure efficiently evoked cellular calcium responses after transfecting with prestin(N7T, N308S). Moreover, pulsed ultrasound can also noninvasively stimulate target neurons expressing prestin(N7T, N308S) in deep regions of mouse brains. Our study delineates how an engineered auditory-sensing protein can cause mammalian cells to sense ultrasound stimulation. Moreover, our sonogenetic tools will serve as new strategies for noninvasive therapy in deep tissues.
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Affiliation(s)
- Yao-Shen Huang
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Ching-Hsiang Fan
- Department of Biomedical Engineering and Environmental Sciences , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Ning Hsu
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Nai-Hua Chiu
- Department of Biomedical Engineering and Environmental Sciences , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Chun-Yao Wu
- Department of Biomedical Engineering and Environmental Sciences , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Chu-Yuan Chang
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Bing-Huan Wu
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Shi-Rong Hong
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Ya-Chu Chang
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Anthony Yan-Tang Wu
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program , Academia Sinica , Taipei 106 , Taiwan
- Department and Graduate Institute of Pharmacology , National Taiwan University , Taipei 106 , Taiwan
| | - Vanessa Guo
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
| | - Yueh-Chen Chiang
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Wei-Chia Hsu
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Linyi Chen
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
- Department of Medical Science , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program , Academia Sinica , Taipei 106 , Taiwan
- Genome and Systems Biology Degree Program , National Taiwan University and Academia Sinica , Taipei 106 , Taiwan
| | - Chih-Kuang Yeh
- Department of Biomedical Engineering and Environmental Sciences , National Tsing Hua University , Hsinchu 300 , Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine , National Tsing Hua University , Hsinchu 300 , Taiwan
- Department of Medical Science , National Tsing Hua University , Hsinchu 300 , Taiwan
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22
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Zhou Q, Chen J, Luan Y, Vainikka PA, Thallmair S, Marrink SJ, Feringa BL, van Rijn P. Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Sci Adv 2020; 6:eaay2756. [PMID: 32064345 PMCID: PMC6989133 DOI: 10.1126/sciadv.aay2756] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/21/2019] [Indexed: 05/12/2023]
Abstract
Artificial rotary molecular motors convert energy into controlled motion and drive a system out of equilibrium with molecular precision. The molecular motion is harnessed to mediate the adsorbed protein layer and then ultimately to direct the fate of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). When influenced by the rotary motion of light-driven molecular motors grafted on surfaces, the adsorbed protein layer primes hBM-MSCs to differentiate into osteoblasts, while without rotation, multipotency is better maintained. We have shown that the signaling effects of the molecular motion are mediated by the adsorbed cell-instructing protein layer, influencing the focal adhesion-cytoskeleton actin transduction pathway and regulating the protein and gene expression of hBM-MSCs. This unique molecular-based platform paves the way for implementation of dynamic interfaces for stem cell control and provides an opportunity for novel dynamic biomaterial engineering for clinical applications.
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Affiliation(s)
- Qihui Zhou
- Institute for Translational Medicine, Department of Periodontology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266021, China
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Jiawen Chen
- Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Yafei Luan
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Petteri A. Vainikka
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Sebastian Thallmair
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Siewert J. Marrink
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Ben L. Feringa
- Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Patrick van Rijn
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
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23
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Striebel M, Graf IR, Frey E. A Mechanistic View of Collective Filament Motion in Active Nematic Networks. Biophys J 2019; 118:313-324. [PMID: 31843261 DOI: 10.1016/j.bpj.2019.11.3387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 01/05/2023] Open
Abstract
Protein filament networks are structures crucial for force generation and cell shape. A central open question is how collective filament dynamics emerges from interactions between individual network constituents. To address this question, we study a minimal but generic model for a nematic network in which filament sliding is driven by the action of motor proteins. Our theoretical analysis shows how the interplay between viscous drag on filaments and motor-induced forces governs force propagation through such interconnected filament networks. We find that the ratio between these antagonistic forces establishes the range of filament interaction, which determines how the local filament velocity depends on the polarity of the surrounding network. This force-propagation mechanism implies that the polarity-independent sliding observed in Xenopus egg extracts and in vitro experiments with purified components is a consequence of a large force-propagation length. We suggest how our predictions can be tested by tangible in vitro experiments whose feasibility is assessed with the help of simulations and an accompanying theoretical analysis.
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Affiliation(s)
- Moritz Striebel
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Isabella R Graf
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, München, Germany.
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24
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Inoue D, Gutmann G, Nitta T, Kabir AMR, Konagaya A, Tokuraku K, Sada K, Hess H, Kakugo A. Adaptation of Patterns of Motile Filaments under Dynamic Boundary Conditions. ACS Nano 2019; 13:12452-12460. [PMID: 31585030 DOI: 10.1021/acsnano.9b01450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Boundary conditions are important for pattern formation in active matter. However, it is still not well-understood how alterations in the boundary conditions (dynamic boundary conditions) impact pattern formation. To elucidate the effect of dynamic boundary conditions on the pattern formation by active matter, we investigate an in vitro gliding assay of microtubules on a deformable soft substrate. The dynamic boundary conditions were realized by applying mechanical stress through stretching and compression of the substrate during the gliding assay. A single cycle of stretch-and-compression (relaxation) of the substrate induces perpendicular alignment of microtubules relative to the stretch axis, whereas repeated cycles resulted in zigzag patterns of microtubules. Our model shows that the orientation angles of microtubules correspond to the direction to attain smooth movement without buckling, which is further amplified by the collective migration of the microtubules. Our results provide an insight into understanding the rich dynamics in self-organization arising in active matter subjected to time-dependent boundary conditions.
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Affiliation(s)
- Daisuke Inoue
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
| | - Greg Gutmann
- Department of Computer Science , Tokyo Institute of Technology , Yokohama 226-8502 , Japan
| | - Takahiro Nitta
- Applied Physics Course, Faculty of Engineering , Gifu University , Gifu 501-1193 , Japan
| | | | - Akihiko Konagaya
- Department of Computer Science , Tokyo Institute of Technology , Yokohama 226-8502 , Japan
| | - Kiyotaka Tokuraku
- Department of Applied Sciences , Muroran Institute of Technology , Muroran 050-8585 , Japan
| | - Kazuki Sada
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
- Graduate School of Chemical Sciences and Engineering , Hokkaido University , Sapporo 060-0810 , Japan
| | - Henry Hess
- Department of Biomedical Engineering , Columbia University , New York , New York 10027 , United States
| | - Akira Kakugo
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
- Graduate School of Chemical Sciences and Engineering , Hokkaido University , Sapporo 060-0810 , Japan
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25
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Blanchard AT, Bazrafshan AS, Yi J, Eisman JT, Yehl KM, Bian T, Mugler A, Salaita K. Highly Polyvalent DNA Motors Generate 100+ pN of Force via Autochemophoresis. Nano Lett 2019; 19:6977-6986. [PMID: 31402671 DOI: 10.1021/acs.nanolett.9b02311] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motor proteins such as myosin, kinesin, and dynein are essential to eukaryotic life and power countless processes including muscle contraction, wound closure, cargo transport, and cell division. The design of synthetic nanomachines that can reproduce the functions of these motors is a longstanding goal in the field of nanotechnology. DNA walkers, which are programmed to "walk" along defined tracks via the burnt bridge Brownian ratchet mechanism, are among the most promising synthetic mimics of these motor proteins. While these DNA-based motors can perform useful tasks such as cargo transport, they have not been shown to be capable of cooperating to generate large collective forces for tasks akin to muscle contraction. In this work, we demonstrate that highly polyvalent DNA motors (HPDMs), which can be viewed as cooperative teams of thousands of DNA walkers attached to a microsphere, can generate and sustain substantial forces in the 100+ pN regime. Specifically, we show that HPDMs can generate forces that can unzip and shear DNA duplexes (∼12 and ∼50 pN, respectively) and rupture biotin-streptavidin bonds (∼100-150 pN). To help explain these results, we present a variant of the burnt-bridge Brownian ratchet mechanism that we term autochemophoresis, wherein many individual force generating units generate a self-propagating chemomechanical gradient that produces large collective forces. In addition, we demonstrate the potential of this work to impact future engineering applications by harnessing HPDM autochemophoresis to deposit "molecular ink" via mechanical bond rupture. This work expands the capabilities of synthetic DNA motors to mimic the force-generating functions of biological motors. Our work also builds upon previous observations of autochemophoresis in bacterial transport processes, indicating that autochemophoresis may be a fundamental mechanism of pN-scale force generation in living systems.
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Alisina S Bazrafshan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jacob Yi
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Julia T Eisman
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Kevin M Yehl
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Teng Bian
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Andrew Mugler
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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26
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Xie P, Guo SK, Chen H. A Generalized Kinetic Model for Coupling between Stepping and ATP Hydrolysis of Kinesin Molecular Motors. Int J Mol Sci 2019; 20:ijms20194911. [PMID: 31623357 PMCID: PMC6801755 DOI: 10.3390/ijms20194911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 12/23/2022] Open
Abstract
A general kinetic model is presented for the chemomechanical coupling of dimeric kinesin molecular motors with and without extension of their neck linkers (NLs). A peculiar feature of the model is that the rate constants of ATPase activity of a kinesin head are independent of the strain on its NL, implying that the heads of the wild-type kinesin dimer and the mutant with extension of its NLs have the same force-independent rate constants of the ATPase activity. Based on the model, an analytical theory is presented on the force dependence of the dynamics of kinesin dimers with and without extension of their NLs at saturating ATP. With only a few adjustable parameters, diverse available single molecule data on the dynamics of various kinesin dimers, such as wild-type kinesin-1, kinesin-1 with mutated residues in the NLs, kinesin-1 with extension of the NLs and wild-type kinesin-2, under varying force and ATP concentration, can be reproduced very well. Additionally, we compare the power production among different kinesin dimers, showing that the mutation in the NLs reduces the power production and the extension of the NLs further reduces the power production.
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Affiliation(s)
- Ping Xie
- School of Materials Science and Energy Engineering, FoShan University, Guangdong 528000, China.
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Si-Kao Guo
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong 528000, China.
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27
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Abstract
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load experienced. Attached motor proteins move along the filament to one of its ends with a velocity that varies nonlinearly with the motor protein extension. The resultant force on the filament drives it out of equilibrium. The distance from equilibrium is reflected in the end-to-end distribution, modified bending stiffness, and a transition to spiral morphology of the polymer. The local stress dependence of activity results in correlated fluctuations in the speed and direction of the center of mass leading to a series of ballistic-diffusive crossovers in its dynamics.
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Affiliation(s)
- Nisha Gupta
- Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar - 140306, Punjab, India
| | - Abhishek Chaudhuri
- Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar - 140306, Punjab, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhaba National Institute, Anushaktigar, Mumbai 400094, India
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28
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Abstract
Most membrane proteins exist in complexes that carry out critical cellular functions and exhibit rich dynamics. The bacterial flagellar motor, a large membrane-spanning ion-driven rotary motor that propels the bacteria to swim, provides a canonical example. Rotation of the motor is driven by multiple torque-generating units (stators). Turnover of the stators has been shown previously, demonstrating the exchange of stator units between the motor and a membrane pool. But the details of the turnover kinetics remain unclear. Here, we directly measured the kinetics of stator turnover in individual motors via analysis of a large dataset of long-term high-resolution recordings of motor speed at high load. We found that the dwell time distribution of the stator units exhibits a multi-exponential shape, suggesting the existence of a hidden state in the turnover of the stators.
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29
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Wiegand T, Cadalbert R, von Schroetter C, Allain FHT, Meier BH. Segmental isotope labelling and solid-state NMR of a 12 × 59 kDa motor protein: identification of structural variability. J Biomol NMR 2018; 71:237-245. [PMID: 29948439 DOI: 10.1007/s10858-018-0196-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/01/2018] [Indexed: 05/26/2023]
Abstract
Segmental isotope labelling enables the NMR study of an individual domain within a multidomain protein, but still in the context of the entire full-length protein. Compared to the fully labelled protein, spectral overlap can be greatly reduced. We here describe segmental labelling of the (double-) hexameric DnaB helicase from Helicobacter pylori using a ligation approach. Solid-state spectra demonstrate that the ligated protein has the same structure and structural order as the directly expressed full-length protein. We uniformly 13C/15N labeled the N-terminal domain (147 residues) of the protein, while the C-terminal domain (311 residues) remained in natural abundance. The reduced signal overlap in solid-state NMR spectra allowed to identify structural "hotspots" for which the structure of the N-terminal domain in the context of the oligomeric full-length protein differs from the one in the isolated form. They are located near the linker between the two domains, in an α-helical hairpin.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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30
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Pecci A, Ma X, Savoia A, Adelstein RS. MYH9: Structure, functions and role of non-muscle myosin IIA in human disease. Gene 2018; 664:152-167. [PMID: 29679756 PMCID: PMC5970098 DOI: 10.1016/j.gene.2018.04.048] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022]
Abstract
The MYH9 gene encodes the heavy chain of non-muscle myosin IIA, a widely expressed cytoplasmic myosin that participates in a variety of processes requiring the generation of intracellular chemomechanical force and translocation of the actin cytoskeleton. Non-muscle myosin IIA functions are regulated by phosphorylation of its 20 kDa light chain, of the heavy chain, and by interactions with other proteins. Variants of MYH9 cause an autosomal-dominant disorder, termed MYH9-related disease, and may be involved in other conditions, such as chronic kidney disease, non-syndromic deafness, and cancer. This review discusses the structure of the MYH9 gene and its protein, as well as the regulation and physiologic functions of non-muscle myosin IIA with particular reference to embryonic development. Moreover, the review focuses on current knowledge about the role of MYH9 variants in human disease.
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Affiliation(s)
- Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation, University of Pavia, Piazzale Golgi, 27100 Pavia, Italy.
| | - Xuefei Ma
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bldg. 10 Room 6C-103B, 10 Center Drive, Bethesda, MD 20892-1583, USA.
| | - Anna Savoia
- Department of Medical Sciences, University of Trieste, via Dell'Istria, 65/1, I-34137 Trieste, Italy; IRCCS Burlo Garofolo, via Dell'Istria, 65/1, I-34137 Trieste, Italy.
| | - Robert S Adelstein
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bldg. 10 Room 6C-103B, 10 Center Drive, Bethesda, MD 20892-1583, USA.
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31
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Tjioe M, Ryoo H, Ishitsuka Y, Ge P, Bookwalter C, Huynh W, McKenney RJ, Trybus KM, Selvin PR. Magnetic Cytoskeleton Affinity Purification of Microtubule Motors Conjugated to Quantum Dots. Bioconjug Chem 2018; 29:2278-2286. [PMID: 29932650 PMCID: PMC6452869 DOI: 10.1021/acs.bioconjchem.8b00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We develop magnetic cytoskeleton affinity (MiCA) purification, which allows for rapid isolation of molecular motors conjugated to large multivalent quantum dots, in miniscule quantities, which is especially useful for single-molecule applications. When purifying labeled molecular motors, an excess of fluorophores or labels is usually used. However, large labels tend to sediment during the centrifugation step of microtubule affinity purification, a traditionally powerful technique for motor purification. This is solved with MiCA, and purification time is cut from 2 h to 20 min, a significant time-savings when it needs to be done daily. For kinesin, MiCA works with as little as 0.6 μg protein, with yield of ∼27%, compared to 41% with traditional purification. We show the utility of MiCA purification in a force-gliding assay with kinesin, allowing, for the first time, simultaneous determination of whether the force from each motor in a multiple-motor system drives or hinders microtubule movement. Furthermore, we demonstrate rapid purification of just 30 ng dynein-dynactin-BICD2N-QD (DDB-QD), ordinarily a difficult protein-complex to purify.
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Affiliation(s)
| | | | | | | | | | - Walter Huynh
- Department of Cellular and Molecular Pharmacology , University of California, San Francisco , San Francisco , California 94143 , United States
| | - Richard J McKenney
- Molecular & Cellular Biology , University of California, Davis , La Jolla , California 92093 , United States
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics , University of Vermont , Burlington , Vermont 05405 , United States
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32
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McElwee M, Vijayakrishnan S, Rixon F, Bhella D. Structure of the herpes simplex virus portal-vertex. PLoS Biol 2018; 16:e2006191. [PMID: 29924793 PMCID: PMC6028144 DOI: 10.1371/journal.pbio.2006191] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/02/2018] [Accepted: 06/06/2018] [Indexed: 12/04/2022] Open
Abstract
Herpesviruses include many important human pathogens such as herpes simplex virus, cytomegalovirus, varicella-zoster virus, and the oncogenic Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus. Herpes virions contain a large icosahedral capsid that has a portal at a unique 5-fold vertex, similar to that seen in the tailed bacteriophages. The portal is a molecular motor through which the viral genome enters the capsid during virion morphogenesis. The genome also exits the capsid through the portal-vertex when it is injected through the nuclear pore into the nucleus of a new host cell to initiate infection. Structural investigations of the herpesvirus portal-vertex have proven challenging, owing to the small size of the tail-like portal-vertex-associated tegument (PVAT) and the presence of the tegument layer that lays between the nucleocapsid and the viral envelope, obscuring the view of the portal-vertex. Here, we show the structure of the herpes simplex virus portal-vertex at subnanometer resolution, solved by electron cryomicroscopy (cryoEM) and single-particle 3D reconstruction. This led to a number of new discoveries, including the presence of two previously unknown portal-associated structures that occupy the sites normally taken by the penton and the Ta triplex. Our data revealed that the PVAT is composed of 10 copies of the C-terminal domain of pUL25, which are uniquely arranged as two tiers of star-shaped density. Our 3D reconstruction of the portal-vertex also shows that one end of the viral genome extends outside the portal in the manner described for some bacteriophages but not previously seen in any eukaryote viruses. Finally, we show that the viral genome is consistently packed in a highly ordered left-handed spool to form concentric shells of DNA. Our data provide new insights into the structure of a molecular machine critical to the biology of an important class of human pathogens.
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Affiliation(s)
- Marion McElwee
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Swetha Vijayakrishnan
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Frazer Rixon
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - David Bhella
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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33
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Rossmann FM, Beeby M. Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging. Acta Crystallogr D Struct Biol 2018; 74:585-594. [PMID: 29872008 PMCID: PMC6096493 DOI: 10.1107/s2059798318007945] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high-throughput, medium-resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors. Variations in the size and the number of torque-generating proteins in the motor visualized for the first time using ECT has shown that these variations have enabled bacteria to adapt their swimming torque to the environment. Much of the structural diversity can be explained in terms of scaffold structures that facilitate the incorporation of additional motor proteins, and more recent studies have begun to infer evolutionary pathways to higher torque-producing motors. This review seeks to highlight how the emerging power of ECT has enabled the inference of ancestral states from various bacterial species towards understanding how, and `why', flagellar motors have evolved from an ancestral motor to a diversity of variants with adapted or modified functions.
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Affiliation(s)
- Florian M. Rossmann
- Department of Life Sciences, Imperial College London, London SW7 2AZ, England
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London SW7 2AZ, England
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34
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Baeza A, Vallet-Regí M. Nanomotors for Nucleic Acid, Proteins, Pollutants and Cells Detection. Int J Mol Sci 2018; 19:E1579. [PMID: 29799489 PMCID: PMC6032312 DOI: 10.3390/ijms19061579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/14/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023] Open
Abstract
The development of nanomachines able to operate at the nanoscale, performing complex tasks such as drug delivery, precision surgery, or cell detection, constitutes one of the most important challenges in nanotechnology. The principles that rule the nanoscale are completely different from the ones which govern the macroscopic world and, therefore, the collaboration of scientists with expertise in different fields is required for the effective fabrication of these tiny machines. In this review, the most recent advances carried out in the synthesis and application of nanomachines for diagnosis applications will be presented in order to provide a picture of their potential in the detection of important biomolecules or pathogens in a selective and controlled manner.
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Affiliation(s)
- Alejandro Baeza
- Department of Chemistry in Pharmaceutical Sciences, School of Pharmacy, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11, 28029 Madrid, Spain.
| | - María Vallet-Regí
- Department of Chemistry in Pharmaceutical Sciences, School of Pharmacy, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11, 28029 Madrid, Spain.
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35
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Hahn A, Vonck J, Mills DJ, Meier T, Kühlbrandt W. Structure, mechanism, and regulation of the chloroplast ATP synthase. Science 2018; 360:eaat4318. [PMID: 29748256 PMCID: PMC7116070 DOI: 10.1126/science.aat4318] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022]
Abstract
The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded Fo motor drive ATP synthesis in the F1 head by rotary catalysis. We determined the high-resolution structure of the complete cF1Fo complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F1 head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
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Affiliation(s)
- Alexander Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.
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36
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Srivastava AP, Luo M, Zhou W, Symersky J, Bai D, Chambers MG, Faraldo-Gómez JD, Liao M, Mueller DM. High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane. Science 2018; 360:eaas9699. [PMID: 29650704 PMCID: PMC5948177 DOI: 10.1126/science.aas9699] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/30/2018] [Indexed: 01/06/2023]
Abstract
Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded Fo motor that rotates to drive ATP synthesis in the F1 subunit. We used single-particle cryo-electron microscopy (cryo-EM) to obtain structures of the full complex in a lipid bilayer in the absence or presence of the inhibitor oligomycin at 3.6- and 3.8-angstrom resolution, respectively. To limit conformational heterogeneity, we locked the rotor in a single conformation by fusing the F6 subunit of the stator with the δ subunit of the rotor. Assembly of the enzyme with the F6-δ fusion caused a twisting of the rotor and a 9° rotation of the Fo c10-ring in the direction of ATP synthesis, relative to the structure of isolated Fo Our cryo-EM structures show how F1 and Fo are coupled, give insight into the proton translocation pathway, and show how oligomycin blocks ATP synthesis.
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Affiliation(s)
- Anurag P Srivastava
- Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Min Luo
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Jindrich Symersky
- Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Dongyang Bai
- Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA.
| | - David M Mueller
- Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA.
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37
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Benoit MPMH, Sosa H. Use of Single Molecule Fluorescence Polarization Microscopy to Study Protein Conformation and Dynamics of Kinesin-Microtubule Complexes. Methods Mol Biol 2018; 1665:199-216. [PMID: 28940071 DOI: 10.1007/978-1-4939-7271-5_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single molecule fluorescence polarization microscopy (smFPM) is a technique that enables to monitor changes in the orientation of a single labeled protein domain. Here we describe a smFPM microscope set-up and protocols to investigate conformational changes associated with the movement of motor proteins along cytoskeletal tracks.
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Affiliation(s)
- Matthieu P M H Benoit
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Hernando Sosa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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38
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Kinoshita M, Furukawa Y, Uchiyama S, Imada K, Namba K, Minamino T. Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor. Biochem Biophys Res Commun 2017; 496:12-17. [PMID: 29294326 DOI: 10.1016/j.bbrc.2017.12.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022]
Abstract
The bacterial flagellar motor rotates in both counterclockwise (CCW) and clockwise (CW) directions. FliG, FliM and FliN form the C ring on the cytoplasmic face of the MS ring made of a transmembrane protein, FliF. The C ring acts not only as a rotor but also as a switch of the direction of motor rotation. FliG consists of three domains: FliGN, FliGM and FliGC. FliGN directly binds to FliF. Intermolecular interactions between FliGM and FliGC drive FliG ring formation. FliGM is responsible for the interaction with FliM. FliGC is involved in the interaction with the stator protein MotA. Adaptive remodeling of the C ring occurs when the motor switches between the CCW and CW states. However, it remained unknown how. Here, we report the effects of a CW-locked deletion mutation (ΔPEV) in FliG of Thermotaoga maritia (Tm-FliG) on FliG-FliG and FliG-FliM interactions. The PEV deletion stabilized the intramolecular interaction between FliGM and FliGC, thereby suppressing the oligomerization of Tm-FliGMC in solution. This deletion also induced a conformational change of HelixMC connecting FliGM and FliGC to reduce the binding affinity of Tm-FliGMC for FliM. We will discuss adaptive remodeling of the C ring responsible for flagellar motor switching.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan; Quantitative Biology Center, RIKEN, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan.
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39
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Wang X, Carlsson AE. A master equation approach to actin polymerization applied to endocytosis in yeast. PLoS Comput Biol 2017; 13:e1005901. [PMID: 29240771 PMCID: PMC5746272 DOI: 10.1371/journal.pcbi.1005901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/28/2017] [Accepted: 11/27/2017] [Indexed: 02/02/2023] Open
Abstract
We present a Master Equation approach to calculating polymerization dynamics and force generation by branched actin networks at membranes. The method treats the time evolution of the F-actin distribution in three dimensions, with branching included as a directional spreading term. It is validated by comparison with stochastic simulations of force generation by actin polymerization at obstacles coated with actin “nucleation promoting factors” (NPFs). The method is then used to treat the dynamics of actin polymerization and force generation during endocytosis in yeast, using a model in which NPFs form a ring around the endocytic site, centered by a spot of molecules attaching the actin network strongly to the membrane. We find that a spontaneous actin filament nucleation mechanism is required for adequate forces to drive the process, that partial inhibition of branching and polymerization lead to different characteristic responses, and that a limited range of polymerization-rate values provide effective invagination and obtain correct predictions for the effects of mutations in the active regions of the NPFs. Endocytosis is a dynamic process by which cells internalize substances from outside the cell. Especially in yeast, endocytosis is mechanically demanding due to the high pressure difference across the cell membrane, or turgor pressure. Polymerization of a branched actin network is the major process providing the mechanical force to overcome the turgor pressure. Understanding the kinetics of the actin network, and the mechanical interaction between the actin network and the cell membrane, is thus crucial for the study of endocytosis. We develop an efficient mathematical framework for actin dynamics that can realistically incorporate these two features, thus providing a practical method for quantitatively modeling actin dynamics during endocytosis. The resulting model mechanistically reveals that spontaneous nucleation at the center of the endocytic site is required for successful endocytosis, distinguishes the roles of branching and polymerization, and predicts several other experimentally testable outcomes. The accuracy and efficiency of the method, in describing both mechanics and chemistry, render it applicable to a broad field of membrane-bending processes.
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Affiliation(s)
- Xinxin Wang
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Anders E. Carlsson
- Department of Physics and NSF Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
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40
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Sakai T, Inoue Y, Terahara N, Namba K, Minamino T. A triangular loop of domain D1 of FlgE is essential for hook assembly but not for the mechanical function. Biochem Biophys Res Commun 2017; 495:1789-1794. [PMID: 29229393 DOI: 10.1016/j.bbrc.2017.12.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/07/2017] [Indexed: 01/10/2023]
Abstract
The bacterial flagellar hook is a short, curved tubular structure made of FlgE. The hook connects the basal body as a rotary motor and the filament as a helical propeller and functions as a universal joint to smoothly transmit torque produced by the motor to the filament. Salmonella FlgE consists of D0, Dc, D1 and D2 domains. Axial interactions between a triangular loop of domain D1 (D1-loop) and domain D2 are postulated to be responsible for hook supercoiling. In contrast, Bacillus FlgE lacks the D1-loop and domain D2. Here, to clarify the roles of the D1-loop and domain D2 in the mechanical function, we carried out deletion analysis of Salmonella FlgE. A deletion of the D1-loop conferred a loss-of-function phenotype whereas that of domain D2 did not. The D1-loop deletion inhibited hook polymerization. Suppressor mutations of the D1-loop deletion was located within FlgD, which acts as the hook cap to promote hook assembly. This suggests a possible interaction between the D1-loop of FlgE and FlgD. Suppressor mutant cells produced straight hooks, but retained the ability to form a flagellar bundle behind a cell body, suggesting that the loop deletion does not affect the bending flexibility of the Salmonella hook.
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Affiliation(s)
- Tomofumi Sakai
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Yumi Inoue
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Naoya Terahara
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan; Quantitative Biology Center, RIKEN, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan.
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41
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McFadden WM, McCall PM, Gardel ML, Munro EM. Filament turnover tunes both force generation and dissipation to control long-range flows in a model actomyosin cortex. PLoS Comput Biol 2017; 13:e1005811. [PMID: 29253848 PMCID: PMC5757993 DOI: 10.1371/journal.pcbi.1005811] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 01/08/2018] [Accepted: 10/09/2017] [Indexed: 11/23/2022] Open
Abstract
Actomyosin-based cortical flow is a fundamental engine for cellular morphogenesis. Cortical flows are generated by cross-linked networks of actin filaments and myosin motors, in which active stress produced by motor activity is opposed by passive resistance to network deformation. Continuous flow requires local remodeling through crosslink unbinding and and/or filament disassembly. But how local remodeling tunes stress production and dissipation, and how this in turn shapes long range flow, remains poorly understood. Here, we study a computational model for a cross-linked network with active motors based on minimal requirements for production and dissipation of contractile stress: Asymmetric filament compliance, spatial heterogeneity of motor activity, reversible cross-links and filament turnover. We characterize how the production and dissipation of network stress depend, individually, on cross-link dynamics and filament turnover, and how these dependencies combine to determine overall rates of cortical flow. Our analysis predicts that filament turnover is required to maintain active stress against external resistance and steady state flow in response to external stress. Steady state stress increases with filament lifetime up to a characteristic time τm, then decreases with lifetime above τm. Effective viscosity increases with filament lifetime up to a characteristic time τc, and then becomes independent of filament lifetime and sharply dependent on crosslink dynamics. These individual dependencies of active stress and effective viscosity define multiple regimes of steady state flow. In particular our model predicts that when filament lifetimes are shorter than both τc and τm, the dependencies of effective viscosity and steady state stress on filament turnover cancel one another, such that flow speed is insensitive to filament turnover, and shows a simple dependence on motor activity and crosslink dynamics. These results provide a framework for understanding how animal cells tune cortical flow through local control of network remodeling.
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Affiliation(s)
- William M. McFadden
- Biophysical Sciences Program, University of Chicago, Chicago, Illinois, United States of America
| | - Patrick M. McCall
- Department of Physics, University of Chicago, Chicago, Illinois, United States of America
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
| | - Margaret L. Gardel
- Department of Physics, University of Chicago, Chicago, Illinois, United States of America
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- James Franck Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Edwin M. Munro
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
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Terahara N, Kodera N, Uchihashi T, Ando T, Namba K, Minamino T. Na +-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor. Sci Adv 2017; 3:eaao4119. [PMID: 29109979 PMCID: PMC5665596 DOI: 10.1126/sciadv.aao4119] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/06/2017] [Indexed: 05/03/2023]
Abstract
The bacterial flagellar motor consists of a rotor and a dozen stator units and regulates the number of active stator units around the rotor in response to changes in the environment. The MotPS complex is a Na+-type stator unit in the Bacillus subtilis flagellar motor and binds to the peptidoglycan layer through the peptidoglycan-binding (PGB) domain of MotS to act as the stator. The MotPS complex is activated in response to an increase in the Na+ concentration in the environment, but the mechanism of this activation has remained unknown. We report that activation occurs by a Na+-induced folding and dimer formation of the PGB domain of MotS, as revealed in real-time imaging by high-speed atomic force microscopy. The MotPS complex showed two distinct ellipsoid domains connected by a flexible linker. A smaller domain, corresponding to the PGB domain, became structured and unstructured in the presence and absence of 150 mM NaCl, respectively. When the amino-terminal portion of the PGB domain adopted a partially stretched conformation in the presence of NaCl, the center-to-center distance between these two domains increased by up to 5 nm, allowing the PGB domain to reach and bind to the peptidoglycan layer. We propose that assembly of the MotPS complex into a motor proceeds by means of Na+-induced structural transitions of its PGB domain.
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Affiliation(s)
- Naoya Terahara
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Noriyuki Kodera
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takayuki Uchihashi
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Goban-cho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Quantitative Biology Center, RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Corresponding author. (T.M.); (K.N.)
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Corresponding author. (T.M.); (K.N.)
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43
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Wiegand T, Liao WC, Ong TC, Däpp A, Cadalbert R, Copéret C, Böckmann A, Meier BH. Protein-nucleotide contacts in motor proteins detected by DNP-enhanced solid-state NMR. J Biomol NMR 2017; 69:157-164. [PMID: 29119516 DOI: 10.1007/s10858-017-0144-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein-DNA and protein-ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein-DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy. Interactions are established by DNP-enhanced 31P-13C polarization-transfer experiments followed by the recording of a 2D 13C-13C correlation experiment. The NMR spectra were obtained in less than 2 days and allowed the identification of residues of the motor protein involved in nucleotide binding.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Wei-Chih Liao
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Ta Chung Ong
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Alexander Däpp
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Christophe Copéret
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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Xu Y, Fei J, Li G, Yuan T, Li J. Compartmentalized Assembly of Motor Protein Reconstituted on Protocell Membrane toward Highly Efficient Photophosphorylation. ACS Nano 2017; 11:10175-10183. [PMID: 28933821 DOI: 10.1021/acsnano.7b04747] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecule assembly and functionalization of protocells have achieved a great success. However, the yield efficiency of photophosphorylation in the present cell-like systems is limited. Herein, inspired by natural photobacteria, we construct a protocell membrane reconstituting motor protein for highly efficient light-mediated adenosine triphosphate (ATP) synthesis through a layer-by-layer technique. The assembled membrane, compartmentally integrating photoacid generator, proton conductor, and ATP synthase, possesses excellent transparency, fast proton production, and quick proton transportation. Remarkably, these favorable features permit the formation of a large proton gradient in a confined region to drive ATP synthase to produce ATP with high efficiency (873 ATP s-1). It is the highest among the existing artificial photophosphorylation systems. Such a biomimetic system provides a bioenergy-supplying scenario for early photosynthetic life and holds promise in remotely controlled ATP-consumed biosensors, biocatalysts, and biodevices.
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Affiliation(s)
- Youqian Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Guangle Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tingting Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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Iwase K, Tanaka M, Hirose K, Uyeda TQP, Honda H. Acceleration of the sliding movement of actin filaments with the use of a non-motile mutant myosin in in vitro motility assays driven by skeletal muscle heavy meromyosin. PLoS One 2017; 12:e0181171. [PMID: 28742155 PMCID: PMC5524339 DOI: 10.1371/journal.pone.0181171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 06/27/2017] [Indexed: 11/19/2022] Open
Abstract
We examined the movement of an actin filament sliding on a mixture of normal and genetically modified myosin molecules that were attached to a glass surface. For this purpose, we used a Dictyostelium G680V mutant myosin II whose release rates of Pi and ADP were highly suppressed relative to normal myosin, leading to a significantly extended life-time of the strongly bound state with actin and virtually no motility. When the mixing ratio of G680V mutant myosin II to skeletal muscle HMM (heavy myosin) was 0.01%, the actin filaments moved intermittently. When they moved, their sliding velocities were about two-fold faster than the velocity of skeletal HMM alone. Furthermore, sliding movements were also faster when the actin filaments were allowed to slide on skeletal muscle HMM-coated glass surfaces in the motility buffer solution containing G680V HMM. In this case no intermittent movement was observed. When the actin filaments used were copolymerized with a fusion protein consisting of Dictyostelium actin and Dictyostelium G680V myosin II motor domain, similar faster sliding movements were observed on skeletal muscle HMM-coated surfaces. The filament sliding velocities were about two-fold greater than the velocities of normal actin filaments. We found that the velocity of actin filaments sliding on skeletal muscle myosin molecules increased in the presence of a non-motile G680V mutant myosin motor.
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Affiliation(s)
- Kohei Iwase
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Masateru Tanaka
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Taro Q. P. Uyeda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hajime Honda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
- * E-mail:
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Abstract
Myosin VI (MVI) is the only known member of the myosin superfamily that, upon dimerization, walks processively toward the pointed end of the actin filament. The leading head of the dimer directs the trailing head forward with a power stroke, a conformational change of the motor domain exaggerated by the lever arm. Using a unique coarse-grained model for the power stroke of a single MVI, we provide the molecular basis for its motility. We show that the power stroke occurs in two major steps. First, the motor domain attains the poststroke conformation without directing the lever arm forward; and second, the lever arm reaches the poststroke orientation by undergoing a rotational diffusion. From the analysis of the trajectories, we discover that the potential that directs the rotating lever arm toward the poststroke conformation is almost flat, implying that the lever arm rotation is mostly uncoupled from the motor domain. Because a backward load comparable to the largest interhead tension in a MVI dimer prevents the rotation of the lever arm, our model suggests that the leading-head lever arm of a MVI dimer is uncoupled, in accord with the inference drawn from polarized total internal reflection fluorescence (polTIRF) experiments. Without any adjustable parameter, our simulations lead to quantitative agreement with polTIRF experiments, which validates the structural insights. Finally, in addition to making testable predictions, we also discuss the implications of our model in explaining the broad step-size distribution of the MVI stepping pattern.
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Affiliation(s)
- Mauro L Mugnai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742;
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742;
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
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47
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Abstract
Millisecond-scale conformational transitions represent a seminal challenge for traditional molecular dynamics simulations, even with the help of high-end supercomputer architectures. Such events are particularly relevant to the study of molecular motors-proteins or abiological constructs that convert chemical energy into mechanical work. Here, we present a hybrid-simulation scheme combining an array of methods including elastic network models, transition path sampling, and advanced free-energy methods, possibly in conjunction with generalized-ensemble schemes to deliver a viable option for capturing the millisecond-scale motor steps of biological motors. The methodology is already implemented in large measure in popular molecular dynamics programs, and it can leverage the massively parallel capabilities of petascale computers. The applicability of the hybrid method is demonstrated with two examples, namely cyclodextrin-based motors and V-type ATPases.
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Affiliation(s)
- Abhishek Singharoy
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801
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48
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Priya R, Gomez GA, Budnar S, Acharya BR, Czirok A, Yap AS, Neufeld Z. Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions. PLoS Comput Biol 2017; 13:e1005411. [PMID: 28273072 PMCID: PMC5362241 DOI: 10.1371/journal.pcbi.1005411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/22/2017] [Accepted: 02/07/2017] [Indexed: 12/24/2022] Open
Abstract
Mechanical coherence of cell layers is essential for epithelia to function as tissue barriers and to control active tissue dynamics during morphogenesis. RhoA signaling at adherens junctions plays a key role in this process by coupling cadherin-based cell-cell adhesion together with actomyosin contractility. Here we propose and analyze a mathematical model representing core interactions involved in the spatial localization of junctional RhoA signaling. We demonstrate how the interplay between biochemical signaling through positive feedback, combined with diffusion on the cell membrane and mechanical forces generated in the cortex, can determine the spatial distribution of RhoA signaling at cell-cell junctions. This dynamical mechanism relies on the balance between a propagating bistable signal that is opposed by an advective flow generated by an actomyosin stress gradient. Experimental observations on the behavior of the system when contractility is inhibited are in qualitative agreement with the predictions of the model.
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Affiliation(s)
- Rashmi Priya
- Institute for Molecular Bioscience, Division of Cell Biology and Molecular Medicine, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guillermo A. Gomez
- Institute for Molecular Bioscience, Division of Cell Biology and Molecular Medicine, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Srikanth Budnar
- Institute for Molecular Bioscience, Division of Cell Biology and Molecular Medicine, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Bipul R. Acharya
- Institute for Molecular Bioscience, Division of Cell Biology and Molecular Medicine, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Andras Czirok
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Alpha S. Yap
- Institute for Molecular Bioscience, Division of Cell Biology and Molecular Medicine, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Zoltan Neufeld
- School of Mathematics and Physics, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
- * E-mail:
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49
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Galburt EA, Tomko EJ. Conformational selection and induced fit as a useful framework for molecular motor mechanisms. Biophys Chem 2017; 223:11-16. [PMID: 28187350 DOI: 10.1016/j.bpc.2017.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/27/2017] [Accepted: 01/27/2017] [Indexed: 11/15/2022]
Abstract
The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these mechanisms of ligand binding and those underlying the translocation of molecular motors and the nucleic acid unwinding of helicases. The mechanism of biased motion exhibited by molecular motors is typically described as either a thermal ratchet or a power-stroke and nucleic acid helicases are characterized by either active or passive unwinding mechanisms. We posit that both Brownian ratchet translocation and passive unwinding are examples of conformational selection and that both power-stroke translocation and active unwinding are examples of induced fit. Furthermore, in ligand-binding reactions, both conformational selection and induced fit may exist in parallel leading to a ligand-dependent flux through the different mechanistic pathways. Given the mappings we describe, we propose that motors may be able to function via parallel ratchet and stroke mechanisms and that helicases may be able to function via parallel active and passive mechanisms.
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Affiliation(s)
- Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Eric J Tomko
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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50
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Bameta T, Das D, Das D, Padinhateeri R, Inamdar MM. Sufficient conditions for the additivity of stall forces generated by multiple filaments or motors. Phys Rev E 2017; 95:022406. [PMID: 28297971 DOI: 10.1103/physreve.95.022406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Molecular motors and cytoskeletal filaments work collectively most of the time under opposing forces. This opposing force may be due to cargo carried by motors or resistance coming from the cell membrane pressing against the cytoskeletal filaments. Some recent studies have shown that the collective maximum force (stall force) generated by multiple cytoskeletal filaments or molecular motors may not always be just a simple sum of the stall forces of the individual filaments or motors. To understand this excess or deficit in the collective force, we study a broad class of models of both cytoskeletal filaments and molecular motors. We argue that the stall force generated by a group of filaments or motors is additive, that is, the stall force of N number of filaments (motors) is N times the stall force of one filament (motor), when the system is reversible at stall. Conversely, we show that this additive property typically does not hold true when the system is irreversible at stall. We thus present a novel and unified understanding of the existing models exhibiting such non-addivity, and generalise our arguments by developing new models that demonstrate this phenomena. We also propose a quantity similar to thermodynamic efficiency to easily predict this deviation from stall-force additivity for filament and motor collectives.
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Affiliation(s)
- Tripti Bameta
- UM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Vidhyanagari Campus, Mumbai-400098, India
| | - Dipjyoti Das
- Department of Physics, Indian Institute of Technology, Bombay, Powai, Mumbai-400 076, India
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology, Bombay, Powai, Mumbai-400 076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400 076, India
| | - Mandar M Inamdar
- Department of Civil Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai-400 076, India
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