1
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Inoue D. Surface Passivation of Norland Optical Adhesive Improves the Guiding Efficiency of Gliding Microtubules in Microfluidic Devices. NANO LETTERS 2024; 24:10790-10795. [PMID: 39146458 DOI: 10.1021/acs.nanolett.4c02015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The microtubule-kinesin biomolecular motor system, which is vital for cellular function, holds significant promise for nanotechnological applications. In vitro gliding assays have demonstrated the ability to transport microcargo by propelling microtubules across kinesin-coated surfaces. However, the uncontrolled directional motion of microtubules has posed significant challenges, limiting the system's application for precise cargo delivery. Microfluidic devices provide a means to direct microtubule movement through their geometric features. Norland Optical Adhesive (NOA) is valued for its mold-free application in microfluidic device fabrication; however, microtubules often climb up channel walls, limiting controlled movement. In this study, a surface passivation method for NOA is introduced, using polyethylene glycol via a thiol-ene click reaction. This technique significantly improved the directional control and concentration of microtubules within NOA microchannels. This approach presents new possibilities for the precise application of biomolecular motors in nanotechnology, enabling advancements in the design of microfluidic systems for complex biomolecular manipulations.
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Affiliation(s)
- Daisuke Inoue
- Faculty of Design, Kyushu University, Shiobaru 4-9-1, Minami-Ku, Fukuoka 815-8540, Japan
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2
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Kawamata I, Nishiyama K, Matsumoto D, Ichiseki S, Keya JJ, Okuyama K, Ichikawa M, Kabir AMR, Sato Y, Inoue D, Murata S, Sada K, Kakugo A, Nomura SIM. Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller. SCIENCE ADVANCES 2024; 10:eadn4490. [PMID: 38820146 PMCID: PMC11141615 DOI: 10.1126/sciadv.adn4490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein-based multicomponent systems with robotic functionalities.
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Affiliation(s)
- Ibuki Kawamata
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kohei Nishiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Daiki Matsumoto
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Shosei Ichiseki
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Jakia J. Keya
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kohei Okuyama
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, Iizuka 820-8502, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | - Satoshi Murata
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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3
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Barakat JM, Modica KJ, Lu L, Anujarerat S, Choi KH, Takatori SC. Surface Topography Induces and Orients Nematic Swarms of Active Filaments: Considerations for Lab-On-A-Chip Devices. ACS APPLIED NANO MATERIALS 2024; 7:12142-12152. [PMID: 38808306 PMCID: PMC11129142 DOI: 10.1021/acsanm.4c02020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Surface-bound molecular motors can drive the collective motion of cytoskeletal filaments in the form of nematic bands and polar flocks in reconstituted gliding assays. Although these "swarming transitions" are an emergent property of active filament collisions, they can be controlled and guided by tuning the surface chemistry or topography of the substrate. To date, the impact of surface topography on collective motion in active nematics is only partially understood, with most experimental studies focusing on the escape of a single filament from etched channels. Since the late 1990s, significant progress has been made to utilize the nonequilibrium properties of active filaments and create a range of functional nanodevices relevant to biosensing and parallel computation; however, the complexity of these swarming transitions presents a challenge when attempting to increase filament surface concentrations. In this work, we etch shallow, linear trenches into glass substrates to induce the formation of swarming nematic bands and investigate the mechanisms by which surface topography regulates the two-dimensional (2D) collective motion of driven filamentous actin (F-actin). We demonstrate that nematic swarms only appear at intermediate trench spacings and vanish if the trenches are made too narrow, wide, or tortuous. To rationalize these results, we simulate the F-actin as self-propelled, semiflexible chains subject to a soft, spatially modulated potential that encodes the energetic cost of bending a filament along the edge of a trench. In our model, we hypothesize that an individual filament experiences a penalty when its projected end-to-end distance is smaller than the trench spacing ("bending and turning"). However, chains that span the channel width glide above the trenches in a force- and torque-free manner ("crowd-surfing"). Our simulations demonstrate that collections of filaments form nematic bands only at intermediate trench spacings, consistent with our experimental findings.
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Affiliation(s)
| | | | - Le Lu
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Stephanie Anujarerat
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kyu Hwan Choi
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Sho C. Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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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] [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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Kekic M, Hanson KL, Perumal AS, Solana G, Rajendran K, Dash S, Nicolau DV, Dobroiu S, Dos Remedios CG, Nicolau DV. Biosensing using antibody-modulated motility of actin filaments on myosin-coated surfaces. Biosens Bioelectron 2024; 246:115879. [PMID: 38056344 DOI: 10.1016/j.bios.2023.115879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Motor proteins, such as myosin and kinesin, are biological molecular motors involved in force generation and intracellular transport within living cells. The characteristics of molecular motors, i.e., their motility over long distances, their capacity of transporting cargoes, and their very efficient energy consumption, recommend them as potential operational elements of a new class of dynamic nano-devices, with potential applications in biosensing, analyte concentrators, and biocomputation. A possible design of a biosensor based on protein molecular motor comprises a surface with immobilized motors propelling cytoskeletal filaments, which are decorated with antibodies, presented as side-branches. Upon biomolecular recognition of these branches by secondary antibodies, the 'extensions' on the cytoskeletal filaments can achieve considerable lengths (longer than several diameters of the cytoskeletal filament carrier), thus geometrically impairing or halting motility. Because the filaments are several micrometers long, this sensing mechanism converts an event in the nanometer range, i.e., antibody-antigen sizes, into an event in the micrometer range: the visualization of the halting of motility of microns-long cytoskeletal filaments. Here we demonstrate the proof of concept of a sensing system comprising heavy-mero-myosin immobilized on surfaces propelling actin filaments decorated with actin antibodies, whose movement is halted upon the recognition with secondary anti-actin antibodies. Because antibodies to the actin-myosin system are involved in several rare diseases, the first possible application for such a device may be their prognosis and diagnosis. The results also provide insights into guidelines for designing highly sensitive and very fast biosensors powered by motor proteins.
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Affiliation(s)
- Murat Kekic
- Muscle Research Unit, Department of Anatomy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kristi L Hanson
- BioNanoEngineering Labs, Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | | | - Gerardin Solana
- BioNanoEngineering Labs, Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Kavya Rajendran
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, Quebec, H3A 0C3, Canada
| | - Shantoshini Dash
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, Quebec, H3A 0C3, Canada
| | - Dan V Nicolau
- BioNanoEngineering Labs, Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia; Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Faculty of Life Sciences & Medicine, King's College London, London SE1 1UL, UK
| | - Serban Dobroiu
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, Quebec, H3A 0C3, Canada
| | - Cristobal G Dos Remedios
- Muscle Research Unit, Department of Anatomy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Dan V Nicolau
- BioNanoEngineering Labs, Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia; Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, Quebec, H3A 0C3, Canada.
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6
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Salhotra A, Rahman MA, Ruijgrok PV, Meinecke CR, Ušaj M, Zemsky S, Lindberg FW, Surendiran P, Lyttleton RW, Linke H, Korten T, Bryant Z, Månsson A. Exploitation of Engineered Light-Switchable Myosin XI for Nanotechnological Applications. ACS NANO 2023; 17:17233-17244. [PMID: 37639711 PMCID: PMC10510702 DOI: 10.1021/acsnano.3c05137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
For certain nanotechnological applications of the contractile proteins actin and myosin, e.g., in biosensing and network-based biocomputation, it would be desirable to temporarily switch on/off motile function in parts of nanostructured devices, e.g., for sorting or programming. Myosin XI motor constructs, engineered with a light-switchable domain for switching actin motility between high and low velocities (light-sensitive motors (LSMs) below), are promising in this regard. However, they were not designed for use in nanotechnology, where longevity of operation, long shelf life, and selectivity of function in specific regions of a nanofabricated network are important. Here, we tested if these criteria can be fulfilled using existing LSM constructs or if additional developments will be required. We demonstrated extended shelf life as well as longevity of the actin-propelling function compared to those in previous studies. We also evaluated several approaches for selective immobilization with a maintained actin propelling function in dedicated nanochannels only. Whereas selectivity was feasible using certain nanopatterning combinations, the reproducibility was not satisfactory. In summary, the study demonstrates the feasibility of using engineered light-controlled myosin XI motors for myosin-driven actin transport in nanotechnological applications. Before use for, e.g., sorting or programming, additional work is however needed to achieve reproducibility of the nanofabrication and, further, optimize the motor properties.
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Affiliation(s)
- Aseem Salhotra
- Department
of Chemistry and Biomedical Sciences, Linnaeus
University, 39182 Kalmar, Sweden
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
| | - Mohammad A Rahman
- Department
of Chemistry and Biomedical Sciences, Linnaeus
University, 39182 Kalmar, Sweden
| | - Paul V Ruijgrok
- Department
of Bioengineering, Stanford University, 94305 Stanford, California, United
States
| | - Christoph R Meinecke
- Center
for Microtechnologies, Technische Universität
Chemnitz, 09126 Chemnitz, Germany
| | - Marko Ušaj
- Department
of Chemistry and Biomedical Sciences, Linnaeus
University, 39182 Kalmar, Sweden
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
| | - Sasha Zemsky
- Department
of Bioengineering, Stanford University, 94305 Stanford, California, United
States
| | - Frida W Lindberg
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
- Solid
State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Pradheebha Surendiran
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
- Solid
State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Roman W. Lyttleton
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
- Solid
State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Heiner Linke
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
- Solid
State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Till Korten
- B CUBE -
Center for Molecular Bioengineering and Physics of Life, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Zev Bryant
- Department
of Bioengineering, Stanford University, 94305 Stanford, California, United
States
| | - Alf Månsson
- Department
of Chemistry and Biomedical Sciences, Linnaeus
University, 39182 Kalmar, Sweden
- NanoLundLund
University, Box 118, 22100 Lund, Sweden
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7
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Inoue D, Ohashi K, Takasuka TE, Kakugo A. In Vitro Synthesis and Design of Kinesin Biomolecular Motors by Cell-Free Protein Synthesis. ACS Synth Biol 2023; 12:1624-1631. [PMID: 37219894 DOI: 10.1021/acssynbio.3c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Kinesin is a biomolecular motor that generates force and motility along microtubule cytoskeletons in cells. Owing to their ability to manipulate cellular nanoscale components, microtubule/kinesin systems show great promise as actuators of nanodevices. However, classical in vivo protein production has some limitations for the design and production of kinesins. Designing and producing kinesins is laborious, and conventional protein production requires specific facilities to create and contain recombinant organisms. Here, we demonstrated the in vitro synthesis and editing of functional kinesins using a wheat germ cell-free protein synthesis system. The synthesized kinesins propelled microtubules on a kinesin-coated substrate and showed a higher binding affinity with microtubules than E. coli-produced kinesins. We also successfully incorporated affinity tags into the kinesins by extending the original sequence of the DNA template by PCR. Our method will accelerate the study of biomolecular motor systems and encourage their wider use in various nanotechnology applications.
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Affiliation(s)
- Daisuke Inoue
- Faculty of Design, Kyushu University, Room 605, Building 3, Shiobaru 4-9-1, Minami-Ku, Fukuoka 815-8540, Japan
| | - Keisuke Ohashi
- Graduate School of Global Food Resources, Hokkaido University, Sapporo 060-0810, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
| | - Taichi E Takasuka
- Graduate School of Global Food Resources, Hokkaido University, Sapporo 060-0810, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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8
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Singhania A, Kalita S, Chettri P, Ghosh S. Accounts of applied molecular rotors and rotary motors: recent advances. NANOSCALE ADVANCES 2023; 5:3177-3208. [PMID: 37325522 PMCID: PMC10262963 DOI: 10.1039/d3na00010a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Molecular machines are nanoscale devices capable of performing mechanical works at molecular level. These systems could be a single molecule or a collection of component molecules that interrelate with one another to produce nanomechanical movements and resulting performances. The design of the components of molecular machine with bioinspired traits results in various nanomechanical motions. Some known molecular machines are rotors, motors, nanocars, gears, elevators, and so on based on their nanomechanical motion. The conversion of these individual nanomechanical motions to collective motions via integration into suitable platforms yields impressive macroscopic output at varied sizes. Instead of limited experimental acquaintances, the researchers demonstrated several applications of molecular machines in chemical transformation, energy conversion, gas/liquid separation, biomedical use, and soft material fabrication. As a result, the development of new molecular machines and their applications has accelerated over the previous two decades. This review highlights the design principles and application scopes of several rotors and rotary motor systems because these machines are used in real applications. This review also offers a systematic and thorough overview of current advancements in rotary motors, providing in-depth knowledge and predicting future problems and goals in this area.
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Affiliation(s)
- Anup Singhania
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Sudeshna Kalita
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prerna Chettri
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Subrata Ghosh
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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9
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Furuta K. Making motors work - potential applications in biocomputing and synthetic biology. J Cell Sci 2023; 136:290763. [PMID: 36852673 DOI: 10.1242/jcs.261035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Biomolecular motors exhibit outstanding functions, including efficient motion and force generation, as well as autonomous operation. In this Essay, I discuss how biomolecular motors can be engineered to be used in artificial systems and what future applications such systems might have.
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Affiliation(s)
- Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
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10
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Månsson A. The potential of myosin and actin in nanobiotechnology. J Cell Sci 2023; 136:292584. [PMID: 36861886 DOI: 10.1242/jcs.261025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Since the late 1990s, efforts have been made to utilize cytoskeletal filaments, propelled by molecular motors, for nanobiotechnological applications, for example, in biosensing and parallel computation. This work has led to in-depth insights into the advantages and challenges of such motor-based systems, and has yielded small-scale, proof-of-principle applications but, to date, no commercially viable devices. Additionally, these studies have also elucidated fundamental motor and filament properties, as well as providing other insights obtained from biophysical assays in which molecular motors and other proteins are immobilized on artificial surfaces. In this Perspective, I discuss the progress towards practically viable applications achieved so far using the myosin II-actin motor-filament system. I also highlight several fundamental pieces of insights derived from the studies. Finally, I consider what may be required to achieve real devices in the future or at least to allow future studies with a satisfactory cost-benefit ratio.
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Affiliation(s)
- Alf Månsson
- Department of Chemistry and Biomedical Science, Linnaeus University, SE-391 82 Kalmar, Sweden
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11
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Fundamental energy cost of finite-time parallelizable computing. Nat Commun 2023; 14:447. [PMID: 36707510 PMCID: PMC9883481 DOI: 10.1038/s41467-023-36020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
The fundamental energy cost of irreversible computing is given by the Landauer bound of [Formula: see text]/bit, where k is the Boltzmann constant and T is the temperature in Kelvin. However, this limit is only achievable for infinite-time processes. We here determine the fundamental energy cost of finite-time parallelizable computing within the framework of nonequilibrium thermodynamics. We apply these results to quantify the energetic advantage of parallel computing over serial computing. We find that the energy cost per operation of a parallel computer can be kept close to the Landauer limit even for large problem sizes, whereas that of a serial computer fundamentally diverges. We analyze, in particular, the effects of different degrees of parallelization and amounts of overhead, as well as the influence of non-ideal electronic hardware. We further discuss their implications in the context of current technology. Our findings provide a physical basis for the design of energy-efficient computers.
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12
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Meinecke CR, Heldt G, Blaudeck T, Lindberg FW, van Delft FCMJM, Rahman MA, Salhotra A, Månsson A, Linke H, Korten T, Diez S, Reuter D, Schulz SE. Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1046. [PMID: 36770052 PMCID: PMC9920894 DOI: 10.3390/ma16031046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Network-based biocomputation (NBC) relies on accurate guiding of biological agents through nanofabricated channels produced by lithographic patterning techniques. Here, we report on the large-scale, wafer-level fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography as the central method. To confirm the functionality of these NBC networks, we solve an instance of a classical non-deterministic-polynomial-time complete ("NP-complete") problem, the subset-sum problem. The propagation of cytoskeletal filaments, e.g., molecular motor-propelled microtubules or actin filaments, relies on a combination of physical and chemical guiding along the channels of an NBC network. Therefore, the nanofabricated channels have to fulfill specific requirements with respect to the biochemical treatment as well as the geometrical confienement, with walls surrounding the floors where functional molecular motors attach. We show how the material stack used for the NBC network can be optimized so that the motor-proteins attach themselves in functional form only to the floor of the channels. Further optimizations in the nanolithographic fabrication processes greatly improve the smoothness of the channel walls and floors, while optimizations in motor-protein expression and purification improve the activity of the motor proteins, and therefore, the motility of the filaments. Together, these optimizations provide us with the opportunity to increase the reliability of our NBC devices. In the future, we expect that these nanolithographic fabrication technologies will enable production of large-scale NBC networks intended to solve substantially larger combinatorial problems that are currently outside the capabilities of conventional software-based solvers.
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Affiliation(s)
- Christoph R. Meinecke
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Georg Heldt
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Thomas Blaudeck
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126 Chemnitz, Germany
| | - Frida W. Lindberg
- NanoLund and Solid State Physics, Lund University, 22100 Lund, Sweden
| | | | | | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, 22100 Lund, Sweden
| | - Till Korten
- B CUBE—Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefan Diez
- B CUBE—Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Danny Reuter
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Stefan E. Schulz
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126 Chemnitz, Germany
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13
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Průša J, Cifra M. Electro-detachment of kinesin motor domain from microtubule in silico. Comput Struct Biotechnol J 2023; 21:1349-1361. [PMID: 36814722 PMCID: PMC9939557 DOI: 10.1016/j.csbj.2023.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Kinesin is a motor protein essential in cellular functions, such as intracellular transport and cell-division, as well as for enabling nanoscopic transport in bio-nanotechnology. Therefore, for effective control of function for nanotechnological applications, it is important to be able to modify the function of kinesin. To circumvent the limitations of chemical modifications, here we identify another potential approach for kinesin control: the use of electric forces. Using full-atom molecular dynamics simulations (247,358 atoms, total time ∼ 4.4 μs), we demonstrate, for the first time, that the kinesin-1 motor domain can be detached from a microtubule by an intense electric field within the nanosecond timescale. We show that this effect is field-direction dependent and field-strength dependent. A detailed analysis of the electric forces and the work carried out by electric field acting on the microtubule-kinesin system shows that it is the combined action of the electric field pulling on the β-tubulin C-terminus and the electric-field-induced torque on the kinesin dipole moment that causes kinesin detachment from the microtubule. It is shown, for the first time in a mechanistic manner, that an electric field can dramatically affect molecular interactions in a heterologous functional protein assembly. Our results contribute to understanding of electromagnetic field-biomatter interactions on a molecular level, with potential biomedical and bio-nanotechnological applications for harnessing control of protein nanomotors.
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14
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Surendiran P, Meinecke CR, Salhotra A, Heldt G, Zhu J, Månsson A, Diez S, Reuter D, Kugler H, Linke H, Korten T. Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation. ACS NANOSCIENCE AU 2022; 2:396-403. [PMID: 36281252 PMCID: PMC9585575 DOI: 10.1021/acsnanoscienceau.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Information processing
by traditional, serial electronic processors
consumes an ever-increasing part of the global electricity supply.
An alternative, highly energy efficient, parallel computing paradigm
is network-based biocomputation (NBC). In NBC a given combinatorial
problem is encoded into a nanofabricated, modular network. Parallel
exploration of the network by a very large number of independent molecular-motor-propelled
protein filaments solves the encoded problem. Here we demonstrate
a significant scale-up of this technology by solving four instances
of Exact Cover, a nondeterministic polynomial time (NP) complete problem
with applications in resource scheduling. The difficulty of the largest
instances solved here is 128 times greater in comparison to the current
state of the art for NBC.
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Affiliation(s)
| | | | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Georg Heldt
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Jingyuan Zhu
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden D-01307, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden D-01307, Germany
| | - Danny Reuter
- Center for Microtechnologies, Technische Universität Chemnitz, Chemnitz D-09126, Germany
- Fraunhofer Institute for Electronic Nano Systems ENAS, Chemnitz, D-09126, Germany
| | - Hillel Kugler
- Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Till Korten
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
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15
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Unksov IN, Korosec CS, Surendiran P, Verardo D, Lyttleton R, Forde NR, Linke H. Through the Eyes of Creators: Observing Artificial Molecular Motors. ACS NANOSCIENCE AU 2022; 2:140-159. [PMID: 35726277 PMCID: PMC9204826 DOI: 10.1021/acsnanoscienceau.1c00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
![]()
Inspired by molecular
motors in biology, there has been significant
progress in building artificial molecular motors, using a number of
quite distinct approaches. As the constructs become more sophisticated,
there is also an increasing need to directly observe the motion of
artificial motors at the nanoscale and to characterize their performance.
Here, we review the most used methods that tackle those tasks. We
aim to help experimentalists with an overview of the available tools
used for different types of synthetic motors and to choose the method
most suited for the size of a motor and the desired measurements,
such as the generated force or distances in the moving system. Furthermore,
for many envisioned applications of synthetic motors, it will be a
requirement to guide and control directed motions. We therefore also
provide a perspective on how motors can be observed on structures
that allow for directional guidance, such as nanowires and microchannels.
Thus, this Review facilitates the future research on synthetic molecular
motors, where observations at a single-motor level and a detailed
characterization of motion will promote applications.
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Affiliation(s)
- Ivan N. Unksov
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Chapin S. Korosec
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | | | - Damiano Verardo
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
- AlignedBio AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Roman Lyttleton
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Nancy R. Forde
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | - Heiner Linke
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
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16
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Kang'iri SM, Nitta T. Motility resilience of molecular shuttles against defective motors. IEEE Trans Nanobioscience 2022; 21:439-444. [PMID: 35471882 DOI: 10.1109/tnb.2022.3170562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Myosin and kinesin are biomolecular motors found in living cells. By propelling their associated cytoskeletal filaments, these biomolecular motors facilitate force generation and material transport in the cells. When extracted, the biomolecular motors are promising candidates for in vitro applications such as biosensor devices, on account of their high operating efficiency and nanoscale size. However, during integration into these devices, some of the motors become defective due to unfavorable adhesion to the substrate surface. These defective motors inhibit the motility of the cytoskeletal filaments which make up the molecular shuttles used in the devices. Difficulties in controlling the fraction of active and defective motors in experiments discourage systematic studies concerning the resilience of the molecular shuttle motility against the impedance of defective motors. Here, we used mathematical modelling to systematically examine the resilience of the propulsion by these molecular shuttles against the impedance of the defective motors. The model showed that the fraction of active motors on the substrate is the essential factor determining the resilience of the molecular shuttle motility. Approximately 40% of active kinesin or 80% of active myosin motors are required to constitute continuous gliding of molecular shuttles in their respective substrates. The simplicity of the mathematical model in describing motility behavior offers utility in elucidating the mechanisms of the motility resilience of molecular shuttles.
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17
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Ibusuki R, Morishita T, Furuta A, Nakayama S, Yoshio M, Kojima H, Oiwa K, Furuta K. Programmable molecular transport achieved by engineering protein motors to move on DNA nanotubes. Science 2022; 375:1159-1164. [PMID: 35271337 DOI: 10.1126/science.abj5170] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intracellular transport is the basis of microscale logistics within cells and is powered by biomolecular motors. Mimicking transport for in vitro applications has been widely studied; however, the inflexibility in track design and control has hindered practical applications. Here, we developed protein-based motors that move on DNA nanotubes by combining a biomolecular motor dynein and DNA binding proteins. The new motors and DNA-based nanoarchitectures enabled us to arrange the binding sites on the track, locally control the direction of movement, and achieve multiplexed cargo transport by different motors. The integration of these technologies realized microscale cargo sorters and integrators that automatically transport molecules as programmed in DNA sequences on a branched DNA nanotube. Our system should provide a versatile, controllable platform for future applications.
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Affiliation(s)
- Ryota Ibusuki
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Tatsuya Morishita
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Akane Furuta
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan.,Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Shintaro Nakayama
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Maki Yoshio
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Hiroaki Kojima
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Kazuhiro Oiwa
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan.,Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
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18
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Sunada Y, Hatori K. Polymer-Carrying Ability of Actin Filaments Interacting with Myosin Motors in a Biological Motility System In Vitro. Macromol Biosci 2022; 22:e2100471. [PMID: 35261163 DOI: 10.1002/mabi.202100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/10/2022] [Indexed: 11/08/2022]
Abstract
The reconstituted motility system of actin-myosin is expected to be used in bioinspired transport devices, in which carried materials are attached to either moving actin filaments or walking myosin molecules. However, the dependence of the ability to transport on the size of the attached materials is still inadequately understood. Here, as carried materials, polyethylene glycols (PEGs) of various sizes are covalently bound to actin filaments, and the motility of PEG-attached filaments on a heavy meromyosin immobilized on a glass surface is observed via fluorescence microscopy. Full attachment of 2 kDa PEG, with an approximately 2 nm gyration radius, decreases the velocity and fraction of moving actin filaments by approximately 10% relative to unattached filaments. For the 5 kDa PEG, the fraction of moving filaments is decreased by approximately 70% even when the filaments contain only 20% PEG-attached actin. The attachment of both sizes of PEGs suppresses the actin-activated ATPase activity at the same level. These results suggest that actin filaments can carry PEGs up to 2 kDa having the same size as actin monomers, while the rate of ATP hydrolysis is limited. The size-dependence may provide a criterion for material delivery via actin filaments in nanotransport applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuma Sunada
- Department of Bio-Systems Engineering, Graduate School of Science and Engineering, Yamagata University, 4-3-16, Jyonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Kuniyuki Hatori
- Department of Bio-Systems Engineering, Graduate School of Science and Engineering, Yamagata University, 4-3-16, Jyonan, Yonezawa, Yamagata, 992-8510, Japan
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19
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Linking path and filament persistence lengths of microtubules gliding over kinesin. Sci Rep 2022; 12:3081. [PMID: 35197505 PMCID: PMC8866476 DOI: 10.1038/s41598-022-06941-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/02/2022] [Indexed: 02/06/2023] Open
Abstract
Microtubules and kinesin motor proteins are involved in intracellular transports in living cells. Such intracellular material transport systems can be reconstructed for utilisation in synthetic environments, and they are called molecular shuttles driven by kinesin motors. The performance of the molecular shuttles depends on the nature of their trajectories, which can be characterized by the path persistence length of microtubules. It has been theoretically predicted that the path persistence length should be equal to the filament persistence length of the microtubules, where the filament persistence length is a measure of microtubule flexural stiffness. However, previous experiments have shown that there is a significant discrepancy between the path and filament persistence lengths. Here, we showed how this discrepancy arises by using computer simulation. By simulating molecular shuttle movements under external forces, the discrepancy between the path and filament persistence lengths was reproduced as observed in experiments. Our close investigations of molecular shuttle movements revealed that the part of the microtubules bent due to the external force was extended more than it was assumed in the theory. By considering the extended length, we could elucidate the discrepancy. The insights obtained here are expected to lead to better control of molecular shuttle movements.
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20
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Nano/Micromotors in Active Matter. MICROMACHINES 2022; 13:mi13020307. [PMID: 35208431 PMCID: PMC8878230 DOI: 10.3390/mi13020307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023]
Abstract
Nano/micromotors (NMMs) are tiny objects capable of converting energy into mechanical motion. Recently, a wealth of active matter including synthetic colloids, cytoskeletons, bacteria, and cells have been used to construct NMMs. The self-sustained motion of active matter drives NMMs out of equilibrium, giving rise to rich dynamics and patterns. Alongside the spontaneous dynamics, external stimuli such as geometric confinements, light, magnetic field, and chemical potential are also harnessed to control the movements of NMMs, yielding new application paradigms of active matter. Here, we review the recent advances, both experimental and theoretical, in exploring biological NMMs. The unique dynamical features of collective NMMs are focused on, along with some possible applications of these intriguing systems.
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21
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Reuther C, Santos-Otte P, Grover R, Heldt G, Woehlke G, Diez S. Multiplication of Motor-Driven Microtubules for Nanotechnological Applications. NANO LETTERS 2022; 22:926-934. [PMID: 35050639 DOI: 10.1021/acs.nanolett.1c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microtubules gliding on motor-functionalized surfaces have been explored for various nanotechnological applications. However, when moving over large distances (several millimeters) and long times (tens of minutes), microtubules are lost due to surface detachment. Here, we demonstrate the multiplication of kinesin-1-driven microtubules that comprises two concurrent processes: (i) severing of microtubules by the enzyme spastin and (ii) elongation of microtubules by self-assembly of tubulin dimers at the microtubule ends. We managed to balance the individual processes such that the average length of the microtubules stayed roughly constant over time while their number increased. Moreover, we show microtubule multiplication in physical networks with topographical channel structures. Our method is expected to broaden the toolbox for microtubule-based in vitro applications by counteracting the microtubule loss from substrate surfaces. Among others, this will enable upscaling of network-based biocomputation, where it is vital to increase the number of microtubules during operation.
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Affiliation(s)
- Cordula Reuther
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Paula Santos-Otte
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Rahul Grover
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Georg Heldt
- Fraunhofer Institute for Electronic Nano Systems, 09126 Chemnitz, Germany
| | - Günther Woehlke
- Center for Functional Protein Assemblies, Technische Universität München, 85748 Garching, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
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22
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Kabir AMR, Munmun T, Hayashi T, Yasuda S, Kimura AP, Kinoshita M, Murata T, Sada K, Kakugo A. Controlling the Rigidity of Kinesin-Propelled Microtubules in an In Vitro Gliding Assay Using the Deep-Sea Osmolyte Trimethylamine N-Oxide. ACS OMEGA 2022; 7:3796-3803. [PMID: 35128287 PMCID: PMC8811939 DOI: 10.1021/acsomega.1c06699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
The biomolecular motor protein kinesin and its associated filamentous protein microtubule have been finding important nanotechnological applications in the recent years. Rigidity of the microtubules, which are propelled by kinesin motors in an in vitro gliding assay, is an important metric that determines the success of utilization of microtubules and kinesins in various applications, such as transportation, sensing, sorting, molecular robotics, etc. Therefore, regulating the rigidity of kinesin-propelled microtubules has been critical. In this work, we report a simple strategy to regulate the rigidity of kinesin-propelled microtubules in an in vitro gliding assay. We demonstrate that rigidity of the microtubules, propelled by kinesins in an in vitro gliding assay, can be modulated simply by using the natural osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of microtubules can be modulated over a wide range. Based on this strategy, we are able to reduce the persistence length of microtubules, a measure of microtubule rigidity, ∼8 fold by using TMAO at the concentration of 1.5 M. Furthermore, we found that the decreased rigidity of the kinesin-propelled microtubules can be restored upon elimination of TMAO from the in vitro gliding assay. Alteration in the rigidity of microtubules is accounted for by the non-uniformity of the force applied by kinesins along the microtubules in the presence of TMAO. This work offers a facile strategy to reversibly regulate the rigidity of kinesin-propelled microtubules in situ, which would widen the applications of the biomolecular motor kinesin and its associated protein microtubule in various fields.
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Affiliation(s)
| | - Tasrina Munmun
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomohiko Hayashi
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Atsushi P. Kimura
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masahiro Kinoshita
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Takeshi Murata
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, 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
| | - 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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23
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Nitta T, Wang Y, Du Z, Morishima K, Hiratsuka Y. A printable active network actuator built from an engineered biomolecular motor. NATURE MATERIALS 2021; 20:1149-1155. [PMID: 33875849 DOI: 10.1038/s41563-021-00969-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Leveraging the motion and force of individual molecular motors in a controlled manner to perform macroscopic tasks can provide substantial benefits to many applications, including robotics. Nonetheless, although millimetre-scale movement has been demonstrated with synthetic and biological molecular motors, their efficient integration into engineered systems that perform macroscopic tasks remains challenging. Here, we describe an active network capable of macroscopic actuation that is hierarchically assembled from an engineered kinesin, a biomolecular motor, and microtubules, resembling the contractile units in muscles. These contracting materials can be formed in desired areas using patterned ultraviolet illumination, allowing their incorporation into mechanically engineered systems, being also compatible with printing technologies. Due to the designed filamentous assembly of kinesins, the generated forces reach the micronewton range, enabling actuation of millimetre-scale mechanical components. These properties may be useful for the fabrication of soft robotic systems with advanced functionalities.
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Affiliation(s)
- Takahiro Nitta
- Applied Physics Course, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Yingzhe Wang
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Zhao Du
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan
| | - Keisuke Morishima
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Yuichi Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan.
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24
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Sharan P, Nsamela A, Lesher-Pérez SC, Simmchen J. Microfluidics for Microswimmers: Engineering Novel Swimmers and Constructing Swimming Lanes on the Microscale, a Tutorial Review. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007403. [PMID: 33949106 DOI: 10.1002/smll.202007403] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Indexed: 05/16/2023]
Abstract
This paper provides an updated review of recent advances in microfluidics applied to artificial and biohybrid microswimmers. Sharing the common regime of low Reynolds number, the two fields have been brought together to take advantage of the fluid characteristics at the microscale, benefitting microswimmer research multifold. First, microfluidics offer simple and relatively low-cost devices for high-fidelity production of microswimmers made of organic and inorganic materials in a variety of shapes and sizes. Microscale confinement and the corresponding fluid properties have demonstrated differential microswimmer behaviors in microchannels or in the presence of various types of physical or chemical stimuli. Custom environments to study these behaviors have been designed in large part with the help of microfluidics. Evaluating microswimmers in increasingly complex lab environments such as microfluidic systems can ensure more effective implementation for in-field applications. The benefits of microfluidics for the fabrication and evaluation of microswimmers are balanced by the potential use of microswimmers for sample manipulation and processing in microfluidic systems, a large obstacle in diagnostic and other testing platforms. In this review various ways in which these two complementary technology fields will enhance microswimmer development and implementation in various fields are introduced.
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Affiliation(s)
- Priyanka Sharan
- Chair of Physical Chemistry, TU Dresden, 01062, Dresden, Germany
| | | | | | - Juliane Simmchen
- Chair of Physical Chemistry, TU Dresden, 01062, Dresden, Germany
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25
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Afroze F, Inoue D, Farhana TI, Hiraiwa T, Akiyama R, Kabir AMR, Sada K, Kakugo A. Monopolar flocking of microtubules in collective motion. Biochem Biophys Res Commun 2021; 563:73-78. [PMID: 34062389 DOI: 10.1016/j.bbrc.2021.05.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Flocking is a fascinating coordinated behavior of living organisms or self-propelled particles (SPPs). Particularly, monopolar flocking has been attractive due to its potential applications in various fields. However, the underlying mechanism behind flocking and emergence of monopolar motion in flocking of SPPs has remained obscured. Here, we demonstrate monopolar flocking of kinesin-driven microtubules, a self-propelled biomolecular motor system. Microtubules with an intrinsic structural chirality preferentially move towards counter-clockwise direction. At high density, the CCW motion of microtubules facilitates monopolar flocking and formation of a spiral pattern. The monopolar flocking of microtubules is accounted for by a torque generated when the motion of microtubules was obstructed due to collisions. Our results shed light on flocking and emergence of monopolar motion in flocking of chiral active matters. This work will help regulate the polarity in collective motion of SPPs which in turn will widen their applications in nanotechnology, materials science and engineering.
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Affiliation(s)
- Farhana Afroze
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka, 815-8540, Japan
| | - Tamanna Ishrat Farhana
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore; Universal Biology Institute, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
| | | | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan.
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26
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Ruijgrok PV, Ghosh RP, Zemsky S, Nakamura M, Gong R, Ning L, Chen R, Vachharajani VT, Chu AE, Anand N, Eguchi RR, Huang PS, Lin MZ, Alushin GM, Liphardt JT, Bryant Z. Optical control of fast and processive engineered myosins in vitro and in living cells. Nat Chem Biol 2021; 17:540-548. [PMID: 33603247 PMCID: PMC10807509 DOI: 10.1038/s41589-021-00740-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
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Affiliation(s)
- Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Robert Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Vipul T Vachharajani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Alexander E Chu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Namrata Anand
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Gregory M Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Bio-X Institute, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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27
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Abstract
Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.
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28
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Henglein F, Shoham S, Vizel Y. Formal Semantics and Verification of Network-Based Biocomputation Circuits. LECTURE NOTES IN COMPUTER SCIENCE 2021. [PMCID: PMC7798404 DOI: 10.1007/978-3-030-67067-2_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Network-Based Biocomputation Circuits (NBCs) offer a new paradigm for solving complex computational problems by utilizing biological agents that operate in parallel to explore manufactured planar devices. The approach can also have future applications in diagnostics and medicine by combining NBCs computational power with the ability to interface with biological material. To realize this potential, devices should be designed in a way that ensures their correctness and robust operation. For this purpose, formal methods and tools can offer significant advantages by allowing investigation of design limitations and detection of errors before manufacturing and experimentation. Here we define a computational model for NBCs by providing formal semantics to NBC circuits. We present a formal verification-based approach and prototype tool that can assist in the design of NBCs by enabling verification of a given design’s correctness. Our tool allows verification of the correctness of NBC designs for several NP-Complete problems, including the Subset Sum, Exact Cover and Satisfiability problems and can be extended to other NBC implementations. Our approach is based on defining transition systems for NBCs and using temporal logic for specifying and proving properties of the design using model checking. Our formal model can also serve as a starting point for computational complexity studies of the power and limitations of NBC systems.
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29
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Kalra AP, Patel SD, Eakins BB, Riddell S, Kumar P, Winter P, Preto J, Carlson KW, Lewis JD, Rezania V, Tuszyński JA, Shankar K. Revealing and Attenuating the Electrostatic Properties of Tubulin and Its Polymers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2003560. [PMID: 33295102 DOI: 10.1002/smll.202003560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/17/2020] [Indexed: 06/12/2023]
Abstract
Tubulin is an electrostatically negative protein that forms cylindrical polymers termed microtubules, which are crucial for a variety of intracellular roles. Exploiting the electrostatic behavior of tubulin and microtubules within functional microfluidic and optoelectronic devices is limited due to the lack of understanding of tubulin behavior as a function of solvent composition. This work displays the tunability of tubulin surface charge using dimethyl sulfoxide (DMSO) for the first time. Increasing the DMSO volume fractions leads to the lowering of tubulin's negative surface charge, eventually causing it to become positive in solutions >80% DMSO. As determined by electrophoretic mobility measurements, this change in surface charge is directionally reversible, i.e., permitting control between -1.5 and + 0.2 cm2 (V s)-1 . When usually negative microtubules are exposed to these conditions, the positively charged tubulin forms tubulin sheets and aggregates, as revealed by an electrophoretic transport assay. Fluorescence-based experiments also indicate that tubulin sheets and aggregates colocalize with negatively charged g-C3 N4 sheets while microtubules do not, further verifying the presence of a positive surface charge. This study illustrates that tubulin and its polymers, in addition to being mechanically robust, are also electrically tunable.
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Affiliation(s)
- Aarat P Kalra
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Sahil D Patel
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Boden B Eakins
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Saralyn Riddell
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta, T6G 2V4, Canada
| | - Pawan Kumar
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta, T6G 2V4, Canada
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Jordane Preto
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, 69008, France
| | - Kris W Carlson
- Department of Neurosurgery, Beth Israel Deaconess Medical Centre, Harvard Medical School, Boston, MA, 02215, USA
| | - John D Lewis
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta, T5J 4S2, Canada
| | - Jack A Tuszyński
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta, T6G 2V4, Canada
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30
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Kalra AP, Eakins BB, Patel SD, Ciniero G, Rezania V, Shankar K, Tuszynski JA. All Wired Up: An Exploration of the Electrical Properties of Microtubules and Tubulin. ACS NANO 2020; 14:16301-16320. [PMID: 33213135 DOI: 10.1021/acsnano.0c06945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microtubules are hollow, cylindrical polymers of the protein α, β tubulin, that interact mechanochemically with a variety of macromolecules. Due to their mechanically robust nature, microtubules have gained attention as tracks for precisely directed transport of nanomaterials within lab-on-a-chip devices. Primarily due to the unusually negative tail-like C-termini of tubulin, recent work demonstrates that these biopolymers are also involved in a broad spectrum of intracellular electrical signaling. Microtubules and their electrostatic properties are discussed in this Review, followed by an evaluation of how these biopolymers respond mechanically to electrical stimuli, through microtubule migration, electrorotation and C-termini conformation changes. Literature focusing on how microtubules act as nanowires capable of intracellular ionic transport, charge storage, and ionic signal amplification is reviewed, illustrating how these biopolymers attenuate ionic movement in response to electrical stimuli. The Review ends with a discussion on the important questions, challenges, and future opportunities for intracellular microtubule-based electrical signaling.
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Affiliation(s)
- Aarat P Kalra
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2M9, Canada
| | - Boden B Eakins
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Sahil D Patel
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Gloria Ciniero
- Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino 10129, Italy
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta T5J 4S2, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2M9, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino 10129, Italy
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
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31
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Martinez H, Martinez NJD, Guo J, Lujan VR, Depoy J, Brumbach MT, Brinker CJ, Bachand GD. Effects of Surface Chemistry and Topology on the Kinesin-Driven Motility of Microtubule Shuttles. ACS APPLIED BIO MATERIALS 2020; 3:7908-7918. [DOI: 10.1021/acsabm.0c01035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Haneen Martinez
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | | | - Jimin Guo
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Victoria R. Lujan
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Jessica Depoy
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | | | - C. Jeffrey Brinker
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - George D. Bachand
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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32
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Mozneb M, Mirtaheri E, Sanabria AO, Li CZ. Bioelectronic properties of DNA, protein, cells and their applications for diagnostic medical devices. Biosens Bioelectron 2020; 167:112441. [PMID: 32763825 DOI: 10.1016/j.bios.2020.112441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/25/2023]
Abstract
From a couple of centuries ago, understanding physical properties of biological material, their interference with their natural host and their potential manipulation for employment as a conductor in medical devices, has gathered substantial interest in the field of bioelectronics. With the fast-emerging technologies for fabrication of diagnostic modalities, wearable biosensors and implantable devices, which electrical components are of essential importance, a need for developing novel conductors within such devices has evolved over the past decades. As the possibility of electron transport within small biological molecules, such as DNA and proteins, as well as larger elements such as cells was established, several discoveries of the modern charge characterization technologies were evolved. Development of Electrochemical Scanning Tunneling Microscopy and Nuclear Magnetic Resonance among many other techniques were of vital importance, following the discoveries made in sub-micron scales of biological material. This review covers the most recent understandings of electronic properties within different scale of biological material starting from nanometer range to millimeter-sized organs. We also discuss the state-of-the-art technology that's been made taking advantage of electronic properties of biological material for addressing diseases like Parkinson's Disease and Epilepsy.
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Affiliation(s)
- Maedeh Mozneb
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Elnaz Mirtaheri
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Arianna Ortega Sanabria
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Chen-Zhong Li
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
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33
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Akter M, Keya JJ, Kabir AMR, Asanuma H, Murayama K, Sada K, Kakugo A. Photo-regulated trajectories of gliding microtubules conjugated with DNA. Chem Commun (Camb) 2020; 56:7953-7956. [PMID: 32537622 DOI: 10.1039/d0cc03124k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We regulate the persistency in motion of kinesin-driven microtubules (MTs) simply using a photoresponsive DNA (pDNA) and ultraviolet (UV)-visible light. The path persistence length of MTs, which is a measure of the persistency in their motion, increases and decreases upon illuminating the MTs with UV and visible light respectively. Moreover, pDNA is found to work as a shield for MTs against damage under UV irradiation.
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Affiliation(s)
- Mousumi Akter
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | | | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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34
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Bassir Kazeruni NM, Rodriguez JB, Saper G, Hess H. Microtubule Detachment in Gliding Motility Assays Limits the Performance of Kinesin-Driven Molecular Shuttles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:7901-7907. [PMID: 32551689 DOI: 10.1021/acs.langmuir.0c01002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The creation of complex active nanosystems integrating cytoskeletal filaments propelled by surface-adhered motor proteins often relies on the filaments' ability to glide over up to meter-long distances. While theoretical considerations support this ability, we show that microtubule detachment (either spontaneous or triggered by a microtubule crossing event) is a non-negligible phenomenon that has been overlooked until now. The average gliding distance before spontaneous detachment was measured to be 30 ± 10 mm for a functional kinesin-1 density of 500 μm-2 and 9 ± 4 mm for a functional kinesin-1 density of 100 μm-2 at 1 mM ATP. Even microtubules longer than 3 μm detached, suggesting that spontaneous detachment is not caused by the stochastic absence of motors or their stochastic release due to a limited run length.
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Affiliation(s)
- Neda M Bassir Kazeruni
- Columbia University, 351L Engineering Terrace, MC 8904 1210 Amsterdam Avenue, New York, New York 10027, United States
| | - Juan B Rodriguez
- Columbia University, 351L Engineering Terrace, MC 8904 1210 Amsterdam Avenue, New York, New York 10027, United States
| | - Gadiel Saper
- Columbia University, 351L Engineering Terrace, MC 8904 1210 Amsterdam Avenue, New York, New York 10027, United States
| | - Henry Hess
- Columbia University, 351L Engineering Terrace, MC 8904 1210 Amsterdam Avenue, New York, New York 10027, United States
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35
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Positional Isomers of a Non-Nucleoside Substrate Differentially Affect Myosin Function. Biophys J 2020; 119:567-580. [PMID: 32652059 DOI: 10.1016/j.bpj.2020.06.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 11/22/2022] Open
Abstract
Molecular motors have evolved to transduce chemical energy from ATP into mechanical work to drive essential cellular processes, from muscle contraction to vesicular transport. Dysfunction of these motors is a root cause of many pathologies necessitating the need for intrinsic control over molecular motor function. Herein, we demonstrate that positional isomerism can be used as a simple and powerful tool to control the molecular motor of muscle, myosin. Using three isomers of a synthetic non-nucleoside triphosphate, we demonstrate that myosin's force- and motion-generating capacity can be dramatically altered at both the ensemble and single-molecule levels. By correlating our experimental results with computation, we show that each isomer exerts intrinsic control by affecting distinct steps in myosin's mechanochemical cycle. Our studies demonstrate that subtle variations in the structure of an abiotic energy source can be used to control the force and motility of myosin without altering myosin's structure.
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36
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Kabir AMR, Inoue D, Kakugo A. Molecular swarm robots: recent progress and future challenges. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2020; 21:323-332. [PMID: 32939158 PMCID: PMC7476543 DOI: 10.1080/14686996.2020.1761761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.
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Affiliation(s)
| | - Daisuke Inoue
- Faculty of Design, Department of Human Science, Kyushu University, Fukuoka, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
- CONTACT Akira Kakugo Hokkaido University, Sapporo shi, Kita ku, Kita 10, Nishi 8, Science building-7, Room-215, Sapporo060-0810, Japan
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37
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Keya JJ, Kabir AMR, Kakugo A. Synchronous operation of biomolecular engines. Biophys Rev 2020; 12:401-409. [PMID: 32125657 PMCID: PMC7242543 DOI: 10.1007/s12551-020-00651-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
Biomolecular motor systems are the smallest natural machines with an ability to convert chemical energy into mechanical work with remarkably high efficiency. Such attractive features enabled biomolecular motors to become classic tools in soft matter research over the past decade. For designing suitably engineered biomimetic systems, the biomolecular motors can potentially be used as molecular engines that can transform energy and ensure great advantages for the construction of bio-nanodevices and molecular robots. From the optimization of their prolonged lifetime to coordinate them into highly complex and ordered structures, enormous efforts have been devoted to make them useful in the synthetic environment. Synchronous operation of the biomolecular engines is one of the key criteria to coordinate them into certain different patterns, which depends on the local interaction of biomolecular motors. Utilizing chemical and physical stimuli, synchronization of biomolecular motor systems has become possible, which allows them to coordinate into different higher ordered patterns with different modes of functionality. Recently, programmed synchronous operation of the biomolecular engines has also been demonstrated, using a smart biomaterial to build up swarms reminiscent of nature. Here, we review the recent progress in the synchronized operation of biomolecular motors in engineered systems to explicitly program their interaction and further their applications. Such developments in the coordination of biomolecular motors have opened a broad way to explore the construction of future autonomous molecular machines and robots based on synchronization of biomolecular engines.
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Affiliation(s)
- Jakia Jannat Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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38
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Bugyi B, Kellermayer M. The discovery of actin: "to see what everyone else has seen, and to think what nobody has thought". J Muscle Res Cell Motil 2020; 41:3-9. [PMID: 31093826 PMCID: PMC7109165 DOI: 10.1007/s10974-019-09515-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Actin is among the most highly abundant and ubiquitous proteins in eukaryotic cells. The structure, dynamics and functional diversity of actin have continued to mesmerise cell and molecular biologists, biophysicists and physiologists for more than three quarters of a century. The discovery and initial characterization of actin, which took place in the laboratory of Albert Szent-Györgyi by Ilona Banga and Brúnó F. Straub during the second world war in Hungary, is a remarkable and inspiring moment in the history of science. Many of the early thoughts and ideas on the properties and functions of actin and particularly actomyosin, which are referred to in this short historical overview, resonate freshly even today.
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Affiliation(s)
- Beáta Bugyi
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs, 7624, Hungary.
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Tűzoltó str. 37-47, Budapest, IX, 1428, Hungary.
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39
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Xu XY, Huang XL, Li ZM, Gao J, Jiao ZQ, Wang Y, Ren RJ, Zhang HP, Jin XM. A scalable photonic computer solving the subset sum problem. SCIENCE ADVANCES 2020; 6:eaay5853. [PMID: 32064352 PMCID: PMC6994215 DOI: 10.1126/sciadv.aay5853] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
The subset sum problem (SSP) is a typical nondeterministic-polynomial-time (NP)-complete problem that is hard to solve efficiently in time with conventional computers. Photons have the unique features of high propagation speed, strong robustness, and low detectable energy level and therefore can be promising candidates to meet the challenge. Here, we present a scalable chip built-in photonic computer to efficiently solve the SSP. We map the problem into a three-dimensional waveguide network through a femtosecond laser direct writing technique. We show that the photons sufficiently dissipate into the networks and search for solutions in parallel. In the case of successive primes, our approach exhibits a dominant superiority in time consumption even compared with supercomputers. Our results confirm the ability of light to realize computations intractable for conventional computers, and suggest the SSP as a good benchmarking platform for the race between photonic and conventional computers on the way toward "photonic supremacy."
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Affiliation(s)
- Xiao-Yun Xu
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xuan-Lun Huang
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhan-Ming Li
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jun Gao
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhi-Qiang Jiao
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Yao Wang
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ruo-Jing Ren
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - H. P. Zhang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Min Jin
- Center for Integrated Quantum Information Technologies (IQIT), School of Physics and Astronomy and State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
- CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- Institute for Quantum Science and Engineering and Department of Physics, Southern University of Science and Technology, Shenzhen 518055, China
- Corresponding author.
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40
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Průša J, Cifra M. Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor. Sci Rep 2019; 9:19721. [PMID: 31873109 PMCID: PMC6928163 DOI: 10.1038/s41598-019-56052-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022] Open
Abstract
Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. To fulfill various nanotechnological tasks in engineered environments, the function of biological molecular motors can be altered by artificial chemical modifications. The drawback of this approach is the necessity of designing and creating a new motor construct for every new task. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors. To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. In the simulation, we exposed the kinesin motor domain to intense (100 MV/m) electric field up to 30 ns. We found that both the magnitude and angle of the kinesin dipole moment are affected. Furthermore, we found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor. These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. Our results contribute to developing novel electromagnetic methods for modulating the function of biomolecular matter at the nanoscale.
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Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, Prague, 18251, Czech Republic.,Faculty of Chemical Engineering, University of Chemistry and Technology Prague, Technicka 5, Prague, 16628, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, Prague, 18251, Czech Republic.
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41
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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] [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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42
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Rahman MA, Reuther C, Lindberg FW, Mengoni M, Salhotra A, Heldt G, Linke H, Diez S, Månsson A. Regeneration of Assembled, Molecular-Motor-Based Bionanodevices. NANO LETTERS 2019; 19:7155-7163. [PMID: 31512480 DOI: 10.1021/acs.nanolett.9b02738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The guided gliding of cytoskeletal filaments, driven by biomolecular motors on nano/microstructured chips, enables novel applications in biosensing and biocomputation. However, expensive and time-consuming chip production hampers the developments. It is therefore important to establish protocols to regenerate the chips, preferably without the need to dismantle the assembled microfluidic devices which contain the structured chips. We here describe a novel method toward this end. Specifically, we use the small, nonselective proteolytic enzyme, proteinase K to cleave all surface-adsorbed proteins, including myosin and kinesin motors. Subsequently, we apply a detergent (5% SDS or 0.05% Triton X100) to remove the protein remnants. After this procedure, fresh motor proteins and filaments can be added for new experiments. Both, silanized glass surfaces for actin-myosin motility and pure glass surfaces for microtubule-kinesin motility were repeatedly regenerated using this approach. Moreover, we demonstrate the applicability of the method for the regeneration of nano/microstructured silicon-based chips with selectively functionalized areas for supporting or suppressing gliding motility for both motor systems. The results substantiate the versatility and a promising broad use of the method for regenerating a wide range of protein-based nano/microdevices.
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Affiliation(s)
- Mohammad A Rahman
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
| | - Cordula Reuther
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | | | - Martina Mengoni
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
| | - Georg Heldt
- Fraunhofer Institute for Electronic Nano Systems , Chemnitz , Germany 09126
| | | | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
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43
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Abstract
Spin wave logic circuits using quantum oscillations of spins (magnons) as carriers of information have been proposed for next generation computing with reduced energy demands and the benefit of easy parallelization. Current realizations of magnonic devices have micrometer sized patterns. Here we demonstrate the feasibility of biogenic nanoparticle chains as the first step to truly nanoscale magnonics at room temperature. Our measurements on magnetosome chains (ca 12 magnetite crystals with 35 nm particle size each), combined with micromagnetic simulations, show that the topology of the magnon bands, namely anisotropy, band deformation, and band gaps are determined by local arrangement and orientation of particles, which in turn depends on the genotype of the bacteria. Our biomagnonic approach offers the exciting prospect of genetically engineering magnonic quantum states in nanoconfined geometries. By connecting mutants of magnetotactic bacteria with different arrangements of magnetite crystals, novel architectures for magnonic computing may be (self-) assembled. The capability to engineer magnon states in confined geometries is vital to future nano-magnonics. Here the authors demonstrate that the topology of the magnon bands is determined by the local arrangement and orientation of nanoparticles and can be controlled by the genotype of magnetotactic bacteria.
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44
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Affiliation(s)
- Gadiel Saper
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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45
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Browning AP, Woodhouse FG, Simpson MJ. Reversible signal transmission in an active mechanical metamaterial. Proc Math Phys Eng Sci 2019; 475:20190146. [PMID: 31423095 PMCID: PMC6694314 DOI: 10.1098/rspa.2019.0146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/11/2019] [Indexed: 01/01/2023] Open
Abstract
Mechanical metamaterials are designed to enable unique functionalities, but are typically limited by an initial energy state and require an independent energy input to function repeatedly. Our study introduces a theoretical active mechanical metamaterial that incorporates a biological reaction mechanism to overcome this key limitation of passive metamaterials. Our material allows for reversible mechanical signal transmission, where energy is reintroduced by the biologically motivated reaction mechanism. By analysing a coarse-grained continuous analogue of the discrete model, we find that signals can be propagated through the material by a travelling wave. Analysis of the continuum model provides the region of the parameter space that allows signal transmission, and reveals similarities with the well-known FitzHugh-Nagumo system. We also find explicit formulae that approximate the effect of the time scale of the reaction mechanism on the signal transmission speed, which is essential for controlling the material.
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Affiliation(s)
- Alexander P. Browning
- Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
| | | | - Matthew J. Simpson
- Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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46
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Andorfer R, Alper JD. From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1553. [PMID: 30740918 PMCID: PMC6881777 DOI: 10.1002/wnan.1553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/06/2022]
Abstract
As technology at the small scale is advancing, motile engineered microstructures are becoming useful in drug delivery, biomedicine, and lab-on-a-chip devices. However, traditional engineering methods and materials can be inefficient or functionally inadequate for small-scale applications. Increasingly, researchers are turning to the biology of the cytoskeleton, including microtubules, actin filaments, kinesins, dyneins, myosins, and associated proteins, for both inspiration and solutions. They are engineering structures with components that range from being entirely biological to being entirely synthetic mimics of biology and on scales that range from isotropic continuous networks to single isolated structures. Motile biological microstructures trace their origins from the development of assays used to study the cytoskeleton to the array of structures currently available today. We define 12 types of motile biological microstructures, based on four categories: entirely biological, modular, hybrid, and synthetic, and three scales: networks, clusters, and isolated structures. We highlight some key examples, the unique functionalities, and the potential applications of each microstructure type, and we summarize the quantitative models that enable engineering them. By categorizing the diversity of motile biological microstructures in this way, we aim to establish a framework to classify these structures, define the gaps in current research, and spur ideas to fill those gaps. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Nanotechnology Approaches to Biology > Cells at the Nanoscale Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Rachel Andorfer
- Department of Bioengineering, Clemson University, Clemson, South Carolina
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Joshua D. Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
- Eukaryotic Pathogen Innovations Center, Clemson University, Clemson, South Carolina
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47
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Bate TE, Jarvis EJ, Varney ME, Wu KT. Collective dynamics of microtubule-based 3D active fluids from single microtubules. SOFT MATTER 2019; 15:5006-5016. [PMID: 31165127 DOI: 10.1039/c9sm00123a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains unclear. In this work, the motion of single microtubules was characterized by means of 2D gliding assays and compared with the flows of 3D active fluids. While the scales of the two systems differ by ∼1000×, both were driven by processive, non-processive or an equal mixture of both molecular motor proteins. To search for the dynamic correlation between both systems, the motor activities were tuned by varying temperature and ATP concentration, and the changes in both systems were compared. Motor processivity played an important role in active fluid flows but only when the fluids were nearly motionless; otherwise, flows were dominated by hydrodynamic resistance controlled by sample size. Furthermore, while the motors' thermal reaction led active fluids to flow faster with increasing temperature, such temperature dependence could be reversed by introducing temperature-varying depletants, emphasizing the potential role of the depletant in designing an active fluid's temperature response. The temperature response of active fluids was nearly immediate (⪅10 s). Such a characteristic enables active fluids to be controlled with a temperature switch. Overall, this work not only clarifies the role of temperature in active fluid activity, but also sheds light on the underlying principles of the relationship between the collective dynamics of active fluids and the dynamics of their constituent single microtubules.
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Affiliation(s)
- Teagan E Bate
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA.
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48
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Abstract
Many filamentous fungi colonizing animal or plant tissue, waste matter, or soil must find optimal paths through the constraining geometries of their microenvironment. Imaging of live fungal growth in custom-built microfluidics structures revealed the intracellular mechanisms responsible for this remarkable efficiency. In meandering channels, the Spitzenkörper (an assembly of vesicles at the filament tip) acted like a natural gyroscope, conserving the directional memory of growth, while the fungal cytoskeleton organized along the shortest growth path. However, if an obstacle could not be negotiated, the directional memory was lost due to the disappearance of the Spitzenkörper gyroscope. This study can impact diverse environmental, industrial, and medical applications, from fungal pathogenicity in plants and animals to biology-inspired computation. Filamentous fungi that colonize microenvironments, such as animal or plant tissue or soil, must find optimal paths through their habitat, but the biological basis for negotiating growth in constrained environments is unknown. We used time-lapse live-cell imaging of Neurospora crassa in microfluidic environments to show how constraining geometries determine the intracellular processes responsible for fungal growth. We found that, if a hypha made contact with obstacles at acute angles, the Spitzenkörper (an assembly of vesicles) moved from the center of the apical dome closer to the obstacle, thus functioning as an internal gyroscope, which preserved the information regarding the initial growth direction. Additionally, the off-axis trajectory of the Spitzenkörper was tracked by microtubules exhibiting “cutting corner” patterns. By contrast, if a hypha made contact with an obstacle at near-orthogonal incidence, the directional memory was lost, due to the temporary collapse of the Spitzenkörper–microtubule system, followed by the formation of two “daughter” hyphae growing in opposite directions along the contour of the obstacle. Finally, a hypha passing a lateral opening in constraining channels continued to grow unperturbed, but a daughter hypha gradually branched into the opening and formed its own Spitzenkörper–microtubule system. These observations suggest that the Spitzenkörper–microtubule system is responsible for efficient space partitioning in microenvironments, but, in its absence during constraint-induced apical splitting and lateral branching, the directional memory is lost, and growth is driven solely by the isotropic turgor pressure. These results further our understanding of fungal growth in microenvironments relevant to environmental, industrial, and medical applications.
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49
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Rahman MA, Salhotra A, Månsson A. Comparative analysis of widely used methods to remove nonfunctional myosin heads for the in vitro motility assay. J Muscle Res Cell Motil 2019; 39:175-187. [PMID: 30850933 PMCID: PMC6494787 DOI: 10.1007/s10974-019-09505-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/27/2019] [Indexed: 11/28/2022]
Abstract
The in vitro motility assay allows studies of muscle contraction through observation of actin filament propulsion by surface-adsorbed myosin motors or motor fragments isolated from muscle. A possible problem is that motility may be compromised by nonfunctional, “dead”, motors, obtained in the isolation process. Here we investigate the effects on motile function of two approaches designed to eliminate the effects of these dead motors. We first tested the removal of heavy meromyosin (HMM) molecules with ATP-insensitive “dead” heads by pelleting them with actin filaments, using ultracentrifugation in the presence of 1 mM MgATP (“affinity purification”). Alternatively we incubated motility assay flow cells, after HMM surface adsorption, with non-fluorescent “blocking actin” (1 µM) to block the dead heads. Both affinity purification and use of blocking actin increased the fraction of motile filaments compared to control conditions. However, affinity purification significantly reduced the actin sliding speed in five out of seven experiments on silanized surfaces and in one out of four experiments on nitrocellulose surfaces. Similar effects on velocity were not observed with the use of blocking actin. However, a reduced speed was also seen (without affinity purification) if HMM or myosin subfragment 1 was mixed with 1 mM MgATP before and during surface adsorption. We conclude that affinity purification can produce unexpected effects that may complicate the interpretation of in vitro motility assays and other experiments with surface adsorbed HMM, e.g. single molecule mechanics experiments. The presence of MgATP during incubation with myosin motor fragments is critical for the complicating effects.
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Affiliation(s)
- Mohammad A Rahman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden
| | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden.
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50
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Libberton B, Binz M, van Zalinge H, Nicolau DV. Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries. Phys Rev E 2019; 99:012408. [PMID: 30780339 DOI: 10.1103/physreve.99.012408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 12/23/2022]
Abstract
Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.
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Affiliation(s)
- Ben Libberton
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Marie Binz
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Harm van Zalinge
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Dan V Nicolau
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
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