1
|
Quan MC, Mai DJ. Biomolecular Actuators for Soft Robots. Chem Rev 2025; 125:4974-5002. [PMID: 40331746 DOI: 10.1021/acs.chemrev.4c00811] [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: 05/08/2025]
Abstract
Biomolecules present promising stimuli-responsive mechanisms to revolutionize soft actuators. Proteins, peptides, and nucleic acids foster specific intermolecular interactions, and their boundless sequence design spaces encode precise actuation capabilities. Drawing inspiration from nature, biomolecular actuators harness existing stimuli-responsive properties to meet the needs of diverse applications. This review features biomolecular actuators that respond to a wide variety of stimuli to drive both user-directed and autonomous actuation. We discuss how advances in biomaterial fabrication accelerate prototyping of precise, custom actuators, and we identify biomolecules with untapped actuation potential. Finally, we highlight opportunities for multifunctional and reconfigurable biomolecules to improve the versatility and sustainability of next-generation soft actuators.
Collapse
Affiliation(s)
- Michelle C Quan
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
2
|
Tjahjono N, Penev ES, Yakobson BI. Possibilities and Limits of DNA-Enabled Programmable 2D Self-Assembly. ACS APPLIED MATERIALS & INTERFACES 2025; 17:28514-28522. [PMID: 40323029 DOI: 10.1021/acsami.5c01955] [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: 05/16/2025]
Abstract
Programmable self-assembly provides a promising avenue to improve upon traditional synthesis and create multicomponent materials with emergent properties and arbitrary nanoscale complexity. However, its most successful realizations utilizing DNA often use complicated arduous procedures that result in low yields. Here, we employ coarse-grained molecular dynamics to uncover the ranges of temperatures and misbinding strengths needed for successful one-pot self-assembly of generic, two-dimensional (2D), and distinguishable tiles. Analysis of the energies associated with a single-stranded DNA interacting with all other sequences within a mixture revealed that the success of DNA-based assembly is primarily determined by the strongest misbinding a given sequence can encounter with a sequence highly similar to its reverse complement. This enabled us to design optimized sequence ensembles with acceptably weak and consequently rare misbinding. An estimate is provided for the maximum size of, and complexity of sequences needed to synthesize self-assembled structures with high accuracy and yield, with potential relevance for DNA-functionalized low-dimensional materials for electronics and energy storage.
Collapse
Affiliation(s)
- Nicholas Tjahjono
- Department of Materials Science and NanoEngineering, Rice University, Houston, Texas 77005, United States
| | - Evgeni S Penev
- Department of Materials Science and NanoEngineering, Rice University, Houston, Texas 77005, United States
| | - Boris I Yakobson
- Department of Materials Science and NanoEngineering, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
3
|
Jiang R, Feng Q, Nong D, Kang YJ, Sept D, Hancock WO. Motor clustering enhances kinesin-driven vesicle transport. Biophys J 2025:S0006-3495(25)00279-6. [PMID: 40329534 DOI: 10.1016/j.bpj.2025.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 02/05/2025] [Accepted: 04/30/2025] [Indexed: 05/08/2025] Open
Abstract
Intracellular vesicles are typically transported by a small number of kinesin and dynein motors. However, the slow microtubule binding rate of kinesin-1 observed in in vitro biophysical studies suggests that long-range transport may require a high number of motors. To address the discrepancy in motor requirements between in vivo and in vitro studies, we reconstituted motility of 120-nm-diameter liposomes driven by multiple GFP-labeled kinesin-1 motors. Consistent with predictions based on previous binding rate measurements, we found that long-distance transport requires a high number of kinesin-1 motors. We hypothesized that this discrepancy from in vivo observations may arise from differences in motor organization and tested whether motor clustering can enhance transport efficiency using a DNA scaffold. Clustering just three motors increased liposome travel distances across a wide range of motor numbers. Our findings demonstrate that, independent of motor number, the arrangement of motors on a vesicle regulates transport distance, suggesting that differences in motor organization may explain the disparity between in vivo and in vitro motor requirements for long-range transport.
Collapse
Affiliation(s)
- Rui Jiang
- Intercollege Program in Integrative and Biomedical Physiology, Pennsylvania State University, University Park, Pennsylvania; Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Qingzhou Feng
- Molecular Cellular and Integrative Biomedical Sciences Program, Pennsylvania State University, University Park, Pennsylvania
| | - Daguan Nong
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - You Jung Kang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - William O Hancock
- Intercollege Program in Integrative and Biomedical Physiology, Pennsylvania State University, University Park, Pennsylvania; Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania; Molecular Cellular and Integrative Biomedical Sciences Program, Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania.
| |
Collapse
|
4
|
Peng CS, Zhang Y, Liu Q, Marti GE, Huang YWA, Südhof TC, Cui B, Chu S. Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms. Nat Chem Biol 2025; 21:648-656. [PMID: 39090313 PMCID: PMC11785820 DOI: 10.1038/s41589-024-01694-2] [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: 08/08/2023] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.
Collapse
Affiliation(s)
- Chunte Sam Peng
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunxiang Zhang
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - Qian Liu
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - G Edward Marti
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Yu-Wen Alvin Huang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Steven Chu
- Department of Physics, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
5
|
Murphy I, Bobilev K, Hayakawa D, Ikonen E, Videbæk TE, Dalal S, Ahmed WW, Ross JL, Rogers WB. A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity. PLoS One 2025; 20:e0319790. [PMID: 40258063 PMCID: PMC12011258 DOI: 10.1371/journal.pone.0319790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 02/08/2025] [Indexed: 04/23/2025] Open
Abstract
Attaching enzymes to nanostructures has proven useful to the study of enzyme functionality under controlled conditions and has led to new technologies. Often, the utility and interest of enzyme-tethered nanostructures lie in how the enzymatic activity is affected by how the enzymes are arranged in space. Therefore, being able to conjugate enzymes to nanostructures while preserving the enzymatic activity is essential. In this paper, we present a method to conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic activity. We show evidence of successful conjugation and quantify the variables that affect the conjugation yield. We also show that the enzymatic activity is unchanged after conjugation compared to the enzyme in its native state. Finally, we demonstrate the tethering of urease to nanostructures made using DNA origami with high site-specificity. Decorating nanostructures with enzymatically-active urease may prove to be useful in studying, or even utilizing, the functionality of urease in disciplines ranging from biotechnology to soft-matter physics. The techniques we present in this paper will enable researchers across these fields to modify enzymes without disrupting their functionality, thus allowing for more insightful studies into their behavior and utility.
Collapse
Affiliation(s)
- Ian Murphy
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Keren Bobilev
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daichi Hayakawa
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Eden Ikonen
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Thomas E. Videbæk
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Shibani Dalal
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Wylie W. Ahmed
- Laboratoire de Physique Théorique (LPT), Université de Toulouse, CNRS, UPS, Toulouse, France
- Molecular, Cellular and Developmental biology unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Department of Physics, California State University, Fullerton, California, United States of America
| | - Jennifer L. Ross
- Department of Physics, Syracuse University, Syracuse, New York, United States of America
| | - W. Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| |
Collapse
|
6
|
Abid Ali F, Zwetsloot AJ, Stone CE, Morgan TE, Wademan RF, Carter AP, Straube A. KIF1C activates and extends dynein movement through the FHF cargo adapter. Nat Struct Mol Biol 2025; 32:756-766. [PMID: 39747486 PMCID: PMC11996680 DOI: 10.1038/s41594-024-01418-z] [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: 10/26/2023] [Accepted: 10/03/2024] [Indexed: 01/04/2025]
Abstract
Cellular cargos move bidirectionally on microtubules by recruiting opposite polarity motors dynein and kinesin. These motors show codependence, where one requires the activity of the other, although the mechanism is unknown. Here we show that kinesin-3 KIF1C acts as both an activator and a processivity factor for dynein, using in vitro reconstitutions of human proteins. Activation requires only a fragment of the KIF1C nonmotor stalk binding the cargo adapter HOOK3. The interaction site is separate from the constitutive factors FTS and FHIP, which link HOOK3 to small G-proteins on cargos. We provide a structural model for the autoinhibited FTS-HOOK3-FHIP1B (an FHF complex) and explain how KIF1C relieves it. Collectively, we explain codependency by revealing how mutual activation of dynein and kinesin occurs through their shared adapter. Many adapters bind both dynein and kinesins, suggesting this mechanism could be generalized to other bidirectional complexes.
Collapse
Affiliation(s)
- Ferdos Abid Ali
- MRC Laboratory of Molecular Biology, Cambridge, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Alexander J Zwetsloot
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Caroline E Stone
- MRC Laboratory of Molecular Biology, Cambridge, UK
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | - Anne Straube
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.
| |
Collapse
|
7
|
Markus SM. Microtubule motors of opposite polarity cooperate rather than compete in cargo transport. Nat Struct Mol Biol 2025; 32:595-597. [PMID: 40133460 PMCID: PMC12061008 DOI: 10.1038/s41594-025-01524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]
Abstract
Microtubule-based cargo transport relies on the actions of dynein and kinesins, motors that walk in opposite directions yet act together to ensure appropriate distribution of cargos in cells. Research now provides mechanistic insights into how these seemingly antagonistic motors collaborate, rather than compete, to promote each other’s activities.
Collapse
Affiliation(s)
- Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
8
|
Leighton MP, Sivak DA. Flow of Energy and Information in Molecular Machines. Annu Rev Phys Chem 2025; 76:379-403. [PMID: 39952638 DOI: 10.1146/annurev-physchem-082423-030023] [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: 02/17/2025]
Abstract
Molecular machines transduce free energy between different forms throughout all living organisms. Unlike their macroscopic counterparts, molecular machines are characterized by stochastic fluctuations, overdamped dynamics, and soft components, and operate far from thermodynamic equilibrium. In addition, information is a relevant free energy resource for molecular machines, leading to new modes of operation for nanoscale engines. Toward the objective of engineering synthetic nanomachines, an important goal is to understand how molecular machines transduce free energy to perform their functions in biological systems. In this review, we discuss the nonequilibrium thermodynamics of free energy transduction within molecular machines, with a focus on quantifying energy and information flows between their components. We review results from theory, modeling, and inference from experiments that shed light on the internal thermodynamics of molecular machines, and ultimately explore what we can learn from considering these interactions.
Collapse
Affiliation(s)
- Matthew P Leighton
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada;
- Current affiliation: Department of Physics and Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA;
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada;
| |
Collapse
|
9
|
Huang YT, Tomishige M, Gross SP, Lai PY, Jun Y. Multiple kinesins speed up cargo transport in crowded environments by sharing load. Commun Biol 2025; 8:232. [PMID: 39948212 PMCID: PMC11825687 DOI: 10.1038/s42003-025-07573-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 01/17/2025] [Indexed: 02/16/2025] Open
Abstract
Kinesin motors transport cargoes along microtubules inside of cells. Although it is well known that the cargoes are typically carried by multiple kinesins and that the more motors used, the further the cargoes travel, it has been challenging to determine the number of motors moving a cargo and any instant. Further, there is no unified statement on the relationship between cargo velocity and motor number, especially in the presence of a very crowded cytoplasmic environment. Here, we use a non-invasive method to quantify instantaneous motor number, and use it to investigate the effects of crowded environments on cargo motion when it is carried by multiple kinesins. Our experiments reveal that the velocity of the cargo depends on the number of motors on the cargo and the size of the crowders in crowded environments. Our finding suggests that kinesin tension plays a role in collective motion, which has been confirmed through stochastic kinesin simulations. Overall, our study demonstrates the broad applicability of the non-invasive method to determine engaged motor numbers and sheds light on the intriguing interplay between macromolecular crowding, kinesin tension, and kinesin-mediated cargo transport.
Collapse
Affiliation(s)
- Ya-Ting Huang
- Department of Physics and Center for Complex Systems, National Central University, Taoyuan, 320, Taiwan
| | - Michio Tomishige
- Department of Physical Sciences, Aoyama Gakuin University, 252-5258, Kanagawa, Japan
| | - Steven P Gross
- Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Pik-Yin Lai
- Department of Physics and Center for Complex Systems, National Central University, Taoyuan, 320, Taiwan.
- Physics Division, National Center for Theoretical Sciences, Taipei, 10617, Taiwan.
| | - Yonggun Jun
- Department of Physics and Center for Complex Systems, National Central University, Taoyuan, 320, Taiwan.
| |
Collapse
|
10
|
Xia Q, Zhou M, Jiao K, Li B, Guo L, Wang L, Li J. Recent Advances in DNA-Templated Protein Patterning. SMALL METHODS 2025:e2401835. [PMID: 39895184 DOI: 10.1002/smtd.202401835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/13/2025] [Indexed: 02/04/2025]
Abstract
In recent decades, the advancement of DNA nanotechnology enables precise nanoscale organization of diverse functional materials with DNA templates. Particularly, a variety of DNA-templated protein patterns are constructed as powerful tools for programming biomimetic protein complexes. In this review, recent progress in DNA-templated protein patterning, including cutting-edge methods for arranging proteins with DNA templates, and protein patterns across varying dimensions are briefly summarized. Representative applications in biological analysis and biomedicine are discussed. DNA-protein patterns with programmable dynamics, which hold promise in precision diagnosis and therapeutics are highlighted. Finally, current challenges and opportunities in the fabrication and application of DNA-templated protein pattering are discussed.
Collapse
Affiliation(s)
- Qinglin Xia
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mo Zhou
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhangjiang Laboratory, 100 Haike Road, Shanghai, 201210, China
| | - Kai Jiao
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Bin Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linjie Guo
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Lihua Wang
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Jiang Li
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| |
Collapse
|
11
|
Abstract
Kinesins are a diverse superfamily of microtubule-based motors that perform fundamental roles in intracellular transport, cytoskeletal dynamics and cell division. These motors share a characteristic motor domain that powers unidirectional motility and force generation along microtubules, and they possess unique tail domains that recruit accessory proteins and facilitate oligomerization, regulation and cargo recognition. The location, direction and timing of kinesin-driven processes are tightly regulated by various cofactors, adaptors, microtubule tracks and microtubule-associated proteins. This Review focuses on recent structural and functional studies that reveal how members of the kinesin superfamily use the energy of ATP hydrolysis to transport cargoes, depolymerize microtubules and regulate microtubule dynamics. I also survey how accessory proteins and post-translational modifications regulate the autoinhibition, cargo binding and motility of some of the best-studied kinesins. Despite much progress, the mechanism and regulation of kinesins are still emerging, and unresolved questions can now be tackled using newly developed approaches in biophysics and structural biology.
Collapse
Affiliation(s)
- Ahmet Yildiz
- Physics Department, University of California at Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, USA.
| |
Collapse
|
12
|
Debrunner IS, Sommese RF, Sivaramakrishnan S. Engineering Synthetic Myosin Filaments Using DNA Nanotubes. Methods Mol Biol 2025; 2881:157-166. [PMID: 39704943 DOI: 10.1007/978-1-0716-4280-1_8] [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] [Indexed: 12/21/2024]
Abstract
Throughout the cell, motor proteins work together to drive numerous molecular processes and functions. For example, ensembles of myosin motors collectively transport vesicles and organelles, maintain membrane homeostasis, and drive muscle contraction. Studying these motors in groups has become increasingly important with work demonstrating the emergence of ensemble behavior distinct from individual motor behavior. One powerful technique that has been used in the last decade is DNA nanotechnology, which provides precise control over the spacing and organization of patterned motor proteins. Until recently, however, most studies combining DNA nanostructures and molecular motors have been confined to discrete DNA structures with limited attachment points for motor proteins. In this chapter, we describe a new approach for making synthetic motor filaments using DNA nanotubes. To begin, we present methods for preparing myosin VI-labeled nanotubes and testing these nanotubes using a general in vitro motility setup. We then describe how to modify this system to pattern motor proteins and effectors on the nanotubes. Overall, these nanotubes can easily be used to study large ensembles of molecular motors, such as muscle myosin or ciliary dynein, both proteins that work in large motor ensembles to drive key cellular functions.
Collapse
Affiliation(s)
- Ianna S Debrunner
- Molecular, Cellular, Developmental Biology and Genetics Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ruth F Sommese
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sivaraj Sivaramakrishnan
- Molecular, Cellular, Developmental Biology and Genetics Program, University of Minnesota, Minneapolis, MN, USA.
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
13
|
Gu S, Chen B, Xu X, Han F, Chen S. 3D Nanofabrication via Directed Material Assembly: Mechanism, Method, and Future. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025; 37:e2312915. [PMID: 39623887 PMCID: PMC11733727 DOI: 10.1002/adma.202312915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/27/2024] [Indexed: 01/16/2025]
Abstract
Fabrication of complex three-dimensional (3D) structures at nanoscale is the core of nanotechnology, as it enables the creation of various micro-/nano-devices such as micro-robots, metamaterials, sensors, photonic devices, etc. Among most 3D nanofabrication strategies, the guided material assembly, an efficient bottom-up approach capable of directly constructing designed structures from precise integration of material building blocks, possesses compelling advantages in diverse material compatibility, sufficient driving forces, facile processing steps, and nanoscale resolution. In this review, we focus on assembly-based fabrication methods capable of creating complex 3D nanostructures (instead of periodic or 2.5D-only structures). Recent advances are classified based on the different assembly mechanisms, i.e., assembly driven by chemical reactions, physical interactions, and the synergy of multiple microscopic interactions. The design principles of representative fabrication strategies with an emphasis on their respective advantages, e.g., structural design flexibility, material compatibility, resolution, or applications are analyzed. In the summary and outlook, existing challenges, as well as possible paths to solutions for future development are reviewed. We believe that with recent advances in assembly-based nanofabrication strategies, 3D nanofabrication has achieved tremendous progress in resolution, material generality, and manufacturing cost, for it to make a greater impact in the near future.
Collapse
Affiliation(s)
- Songyun Gu
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
| | - Bingxu Chen
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
| | - Xiayi Xu
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
- School of Biomedical Sciences and EngineeringGuangzhou International CampusSouth China University of TechnologyGuangzhou511442P. R. China
| | - Fei Han
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin150001P. R. China
| | - Shih‐Chi Chen
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
| |
Collapse
|
14
|
Tanwar S, Date S, Goel L, Wu L, Chatterjee A, Barman I. Raman Imaging of Targeted Drug Delivery with DNA-Based Nano-Optical Devices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402631. [PMID: 39707677 DOI: 10.1002/smll.202402631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 10/15/2024] [Indexed: 12/23/2024]
Abstract
Raman spectroscopy (RS) has emerged as a novel optical imaging modality by identifying molecular species through their bond vibrations, offering high specificity and sensitivity in molecule detection. However, its application in intracellular molecular probing has been limited due to challenges in combining vibrational tags with functional probes. DNA nanostructures, known for their high programmability, have been instrumental in fields like biomedicine and nanofabrication. So far, their ability to customize Raman signals remains largely untapped. In this study, a new class of Raman active DNA origami-based hybrid nanodevice (ND) for targeted cancer cell drug delivery and imaging is engineered. The ND is specifically engineered for metastatic prostate cancer treatment, featuring a legumain enzyme-responsive sequence for the controlled release of the chemotherapeutic agent doxorubicin. Integrating RS with precise targeting, the ND enables imaging of aggressive cancer cells and efficient drug delivery with minimal off-target effects. The developed device offers stimuli-responsive behavior, enhanced stability, exceptional tunability, and potent targeting abilities, positioning it as a highly promising strategy for advancing precision cancer imaging and therapy.
Collapse
Affiliation(s)
- Swati Tanwar
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Siddhi Date
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Linika Goel
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Arnab Chatterjee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
| |
Collapse
|
15
|
Utzschneider C, Suresh B, Sciortino A, Gaillard J, Schaeffer A, Pattanayak S, Joanny JF, Blanchoin L, Théry M. Force balance of opposing diffusive motors generates polarity-sorted microtubule patterns. Proc Natl Acad Sci U S A 2024; 121:e2406985121. [PMID: 39589887 PMCID: PMC11626118 DOI: 10.1073/pnas.2406985121] [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: 04/07/2024] [Accepted: 08/26/2024] [Indexed: 11/28/2024] Open
Abstract
The internal organization of cells is largely determined by the architecture and orientation of the microtubule network. Microtubules serve as polar tracks for the selective transport of specific molecular motors toward either their plus or minus ends. How both motors reciprocally move microtubules and organize the network's arrangement and polarity is unknown. Here, we combined experiments on reconstituted systems and theory to study the interaction of microtubules with both plus- and minus-end directed motors bound to a fluid membrane. Depending on motor concentrations, the system could lead either to the constant transport of microtubules or to their alignment, stacking, and immobilization in regular bands that separate motors into domains of opposite polarities. In bands, microtubules shared the same polarity and segregated the two opposing motors accordingly. These regular patterns resulted from the balance of forces produced by the two motors as they walked in opposite directions along microtubules. The system was maintained in a dynamic steady state in which the directional transport of microtubule-bound motors compensates for the random diffusion of lipid-bound motors. The size of motor domains depended on their respective concentrations. The constant flow of motors allowed the system to respond to variations in motor concentrations by moving microtubules to adapt to the new force balance. The polar sorting and linear arrangement of microtubules associated with the segregation of motors of opposite polarity are typical of cellular architectures, which these data may help to better understand.
Collapse
Affiliation(s)
- Clothilde Utzschneider
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, UMR5168, Université Grenoble-Alpes, CEA, INRA, CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble38054, France
| | - Bhagyanath Suresh
- CytoMorpho Lab, Chimie Biologie Innovation, UMR8132, Université Paris Sciences et Lettres, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, CEA, CNRS, Institut Pierre Gilles De Gennes, Paris75005, France
| | - Alfredo Sciortino
- CytoMorpho Lab, Chimie Biologie Innovation, UMR8132, Université Paris Sciences et Lettres, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, CEA, CNRS, Institut Pierre Gilles De Gennes, Paris75005, France
| | - Jérémie Gaillard
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, UMR5168, Université Grenoble-Alpes, CEA, INRA, CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble38054, France
| | - Alexandre Schaeffer
- CytoMorpho Lab, Chimie Biologie Innovation, UMR8132, Université Paris Sciences et Lettres, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, CEA, CNRS, Institut Pierre Gilles De Gennes, Paris75005, France
| | - Sudipta Pattanayak
- Collège de France, Université Paris Sciences et Lettres, Matière molle et biophysique, Paris75231, France
- Institut Curie, Université Paris Sciences et Lettres, Physique de la Cellule et Cancer, Paris Cedex 0574248, France
| | - Jean-François Joanny
- Collège de France, Université Paris Sciences et Lettres, Matière molle et biophysique, Paris75231, France
- Institut Curie, Université Paris Sciences et Lettres, Physique de la Cellule et Cancer, Paris Cedex 0574248, France
| | - Laurent Blanchoin
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, UMR5168, Université Grenoble-Alpes, CEA, INRA, CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble38054, France
- CytoMorpho Lab, Chimie Biologie Innovation, UMR8132, Université Paris Sciences et Lettres, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, CEA, CNRS, Institut Pierre Gilles De Gennes, Paris75005, France
| | - Manuel Théry
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, UMR5168, Université Grenoble-Alpes, CEA, INRA, CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble38054, France
- CytoMorpho Lab, Chimie Biologie Innovation, UMR8132, Université Paris Sciences et Lettres, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, CEA, CNRS, Institut Pierre Gilles De Gennes, Paris75005, France
| |
Collapse
|
16
|
Jongsma MLM, Bakker N, Voortman LM, Koning RI, Bos E, Akkermans JJLL, Janssen L, Neefjes J. Systems mapping of bidirectional endosomal transport through the crowded cell. Curr Biol 2024; 34:4476-4494.e11. [PMID: 39276769 PMCID: PMC11466077 DOI: 10.1016/j.cub.2024.08.026] [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: 02/16/2024] [Revised: 07/02/2024] [Accepted: 08/15/2024] [Indexed: 09/17/2024]
Abstract
Kinesin and dynein-dynactin motors move endosomes and other vesicles bidirectionally along microtubules, a process mainly studied under in vitro conditions. Here, we provide a physiological bidirectional transport model following color-coded, endogenously tagged transport-related proteins as they move through a crowded cellular environment. Late endosomes (LEs) surf bidirectionally on Protrudin-enriched endoplasmic reticulum (ER) membrane contact sites, while hopping and gliding along microtubules and bypassing cellular obstacles, such as mitochondria. During bidirectional transport, late endosomes do not switch between opposing Rab7 GTPase effectors, RILP and FYCO1, or their associated dynein and KIF5B motor proteins, respectively. In the endogenous setting, far fewer motors associate with endosomal membranes relative to effectors, implying coordination of transport with other aspects of endosome physiology through GTPase-regulated mechanisms. We find that directionality of transport is provided in part by various microtubule-associated proteins (MAPs), including MID1, EB1, and CEP169, which recruit Lis1-activated dynein motors to microtubule plus ends for transport of early and late endosomal populations. At these microtubule plus ends, activated dynein motors encounter the dynactin subunit p150glued and become competent for endosomal capture and minus-end movement in collaboration with membrane-associated Rab7-RILP. We show that endosomes surf over the ER through the crowded cell and move bidirectionally under the control of MAPs for motor activation and through motor replacement and capture by endosomal anchors.
Collapse
Affiliation(s)
- Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Nina Bakker
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Roman I Koning
- Electron Microscopy Facility, Department of Cell and Chemical Biology, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Erik Bos
- Electron Microscopy Facility, Department of Cell and Chemical Biology, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Jimmy J L L Akkermans
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Lennert Janssen
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| |
Collapse
|
17
|
Bensel BM, Previs SB, Bookwalter C, Trybus KM, Walcott S, Warshaw DM. Kinesin-1-transported liposomes prefer to go straight in 3D microtubule intersections by a mechanism shared by other molecular motors. Proc Natl Acad Sci U S A 2024; 121:e2407330121. [PMID: 38980901 PMCID: PMC11260143 DOI: 10.1073/pnas.2407330121] [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: 04/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024] Open
Abstract
Kinesin-1 ensembles maneuver vesicular cargoes through the three-dimensional (3D) intracellular microtubule (MT) network. To define how such cargoes navigate MT intersections, we first determined how many kinesins from an ensemble on a lipid-based cargo simultaneously engage a MT, and then determined the directional outcomes (straight, turn, terminate) for liposome cargoes at perpendicular MT intersections. Run lengths of 350-nm diameter liposomes decorated with up to 20, constitutively active, truncated kinesin-1 KIF5B (K543) were longer than single motor transported cargo, suggesting multiple motor engagement. However, detachment forces of lipid-coated beads with ~20 kinesins, measured using an optical trap, showed no more than three simultaneously engaged motors, with a single engaged kinesin predominating, indicating anticooperative MT binding. At two-dimensional (2D) and 3D in vitro MT intersections, liposomes frequently paused (~2 s), suggesting kinesins simultaneously bind both MTs and engage in a tug-of-war. Liposomes showed no directional outcome bias in 2D (1.1 straight:turn ratio) but preferentially went straight (1.8 straight:turn ratio) in 3D intersections. To explain these data, we developed a mathematical model of liposome transport incorporating the known mechanochemistry of kinesins, which diffuse on the liposome surface, and have stiff tails in both compression and extension that impact how motors engage the intersecting MTs. Our model predicts the ~3 engaged motor limit observed in the optical trap and the bias toward going straight in 3D intersections. The striking similarity of these results to our previous study of liposome transport by myosin Va suggests a "universal" mechanism by which cargoes navigate 3D intersections.
Collapse
Affiliation(s)
- Brandon M. Bensel
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
| | - Samantha Beck Previs
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
| | - Carol Bookwalter
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
| | - Kathleen M. Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
| | - Sam Walcott
- Department of Mathematical Sciences, and Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA01609
| | - David M. Warshaw
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
| |
Collapse
|
18
|
Umar AW, Ahmad N, Xu M. Reviving Natural Rubber Synthesis via Native/Large Nanodiscs. Polymers (Basel) 2024; 16:1468. [PMID: 38891415 PMCID: PMC11174458 DOI: 10.3390/polym16111468] [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: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of Hevea brasiliensis. NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.
Collapse
Affiliation(s)
- Abdul Wakeel Umar
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Ming Xu
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
- Guangdong-Hong Kong Joint Laboratory for Carbon Neutrality, Jiangmen Laboratory of Carbon Science and Technology, Jiangmen 529199, China
| |
Collapse
|
19
|
Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [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: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
Collapse
Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
| | | |
Collapse
|
20
|
Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
Collapse
Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
21
|
Yadav SA, Khatri D, Soni A, Khetan N, Athale CA. Wave-like oscillations of clamped microtubules driven by collective dynein transport. Biophys J 2024; 123:509-524. [PMID: 38258292 PMCID: PMC10912927 DOI: 10.1016/j.bpj.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/05/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Microtubules (MTs) are observed to move and buckle driven by ATP-dependent molecular motors in both mitotic and interphasic eukaryotic cells as well as in specialized structures such as flagella and cilia with a stereotypical geometry. In previous work, clamped MTs driven by a few kinesin motors were seen to buckle and occasionally flap in what was referred to as flagella-like motion. Theoretical models of active-filament dynamics and a following force have predicted that, with sufficient force and binding-unbinding, such clamped filaments should spontaneously undergo periodic buckling oscillations. However, a systematic experimental test of the theory and reconciliation to a model was lacking. Here, we have engineered a minimal system of MTs clamped at their plus ends and transported by a sheet of dynein motors that demonstrate the emergence of spontaneous traveling-wave oscillations along single filaments. The frequencies of tip oscillations are in the millihertz range and are statistically indistinguishable in the onset and recovery phases. We develop a 2D computational model of clamped MTs binding and unbinding stochastically to motors in a "gliding-assay" geometry. The simulated MTs oscillate with a frequency comparable to experiment. The model predicts the effect of MT length and motor density on qualitative transitions between distinct phases of flapping, regular oscillations, and looping. We develop an effective "order parameter" based on the relative deflection along the filament and orthogonal to it. The transitions predicted in simulations are validated by experimental data. These results demonstrate a role for geometry, MT buckling, and collective molecular motor activity in the emergence of oscillatory dynamics.
Collapse
Affiliation(s)
| | | | - Aman Soni
- Division of Biology, IISER Pune, Pune, India
| | - Neha Khetan
- Division of Biology, IISER Pune, Pune, India
| | | |
Collapse
|
22
|
Spratt J, Dias JM, Kolonelou C, Kiriako G, Engström E, Petrova E, Karampelias C, Cervenka I, Papanicolaou N, Lentini A, Reinius B, Andersson O, Ambrosetti E, Ruas JL, Teixeira AI. Multivalent insulin receptor activation using insulin-DNA origami nanostructures. NATURE NANOTECHNOLOGY 2024; 19:237-245. [PMID: 37813939 PMCID: PMC10873203 DOI: 10.1038/s41565-023-01507-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 08/15/2023] [Indexed: 10/11/2023]
Abstract
Insulin binds the insulin receptor (IR) and regulates anabolic processes in target tissues. Impaired IR signalling is associated with multiple diseases, including diabetes, cancer and neurodegenerative disorders. IRs have been reported to form nanoclusters at the cell membrane in several cell types, even in the absence of insulin binding. Here we exploit the nanoscale spatial organization of the IR to achieve controlled multivalent receptor activation. To control insulin nanoscale spatial organization and valency, we developed rod-like insulin-DNA origami nanostructures carrying different numbers of insulin molecules with defined spacings. Increasing the insulin valency per nanostructure markedly extended the residence time of insulin-DNA origami nanostructures at the receptors. Both insulin valency and spacing affected the levels of IR activation in adipocytes. Moreover, the multivalent insulin design associated with the highest levels of IR activation also induced insulin-mediated transcriptional responses more effectively than the corresponding monovalent insulin nanostructures. In an in vivo zebrafish model of diabetes, treatment with multivalent-but not monovalent-insulin nanostructures elicited a reduction in glucose levels. Our results show that the control of insulin multivalency and spatial organization with nanoscale precision modulates the IR responses, independent of the insulin concentration. Therefore, we propose insulin nanoscale organization as a design parameter in developing new insulin therapies.
Collapse
Affiliation(s)
- Joel Spratt
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - José M Dias
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Kolonelou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Georges Kiriako
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Enya Engström
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Petrova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christos Karampelias
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Igor Cervenka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Ambrosetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
23
|
Sen A, Chowdhury D, Kunwar A. Coordination, cooperation, competition, crowding and congestion of molecular motors: Theoretical models and computer simulations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:563-650. [PMID: 38960486 DOI: 10.1016/bs.apcsb.2023.12.005] [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: 07/05/2024]
Abstract
Cytoskeletal motor proteins are biological nanomachines that convert chemical energy into mechanical work to carry out various functions such as cell division, cell motility, cargo transport, muscle contraction, beating of cilia and flagella, and ciliogenesis. Most of these processes are driven by the collective operation of several motors in the crowded viscous intracellular environment. Imaging and manipulation of the motors with powerful experimental probes have been complemented by mathematical analysis and computer simulations of the corresponding theoretical models. In this article, we illustrate some of the key theoretical approaches used to understand how coordination, cooperation and competition of multiple motors in the crowded intra-cellular environment drive the processes that are essential for biological function of a cell. In spite of the focus on theory, experimentalists will also find this article as an useful summary of the progress made so far in understanding multiple motor systems.
Collapse
Affiliation(s)
- Aritra Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Debashish Chowdhury
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
| |
Collapse
|
24
|
Bauer J, Reichl A, Tinnefeld P. Kinetic Referencing Allows Identification of Epigenetic Cytosine Modifications by Single-Molecule Hybridization Kinetics and Superresolution DNA-PAINT Microscopy. ACS NANO 2024; 18:1496-1503. [PMID: 38157484 DOI: 10.1021/acsnano.3c08451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.
Collapse
Affiliation(s)
- Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Andreas Reichl
- Department of Chemistry, Ludwig-Maximilians-Universität München, Würmtalstraße 201, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| |
Collapse
|
25
|
Zhang Q, Wang W, Zhou S, Zhang R, Bischofberger I. Flow-induced periodic chiral structures in an achiral nematic liquid crystal. Nat Commun 2024; 15:7. [PMID: 38191525 PMCID: PMC10774319 DOI: 10.1038/s41467-023-43978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024] Open
Abstract
Supramolecular chirality typically originates from either chiral molecular building blocks or external chiral stimuli. Generating chirality in achiral systems in the absence of a chiral input, however, is non-trivial and necessitates spontaneous mirror symmetry breaking. Achiral nematic lyotropic chromonic liquid crystals have been reported to break mirror symmetry under strong surface or geometric constraints. Here we describe a previously unrecognised mechanism for creating chiral structures by subjecting the material to a pressure-driven flow in a microfluidic cell. The chirality arises from a periodic double-twist configuration of the liquid crystal and manifests as a striking stripe pattern. We show that the mirror symmetry breaking is triggered at regions of flow-induced biaxial-splay configurations of the director field, which are unstable to small perturbations and evolve into lower energy structures. The simplicity of this unique pathway to mirror symmetry breaking can shed light on the requirements for forming macroscopic chiral structures.
Collapse
Affiliation(s)
- Qing Zhang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Weiqiang Wang
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Shuang Zhou
- Department of Physics, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Rui Zhang
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China.
| | - Irmgard Bischofberger
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
26
|
Bensel BM, Previs S, Bookwalter C, Trybus KM, Walcott S, Warshaw DM. "Spatial Relationships Matter: Kinesin-1 Molecular Motors Transport Liposome Cargo Through 3D Microtubule Intersections In Vitro". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569616. [PMID: 38076816 PMCID: PMC10705568 DOI: 10.1101/2023.12.01.569616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Kinesin-1 ensembles maneuver vesicular cargoes through intersections in the 3-dimensional (3D) intracellular microtubule (MT) network. To characterize directional outcomes (straight, turn, terminate) at MT intersections, we challenge 350 nm fluid-like liposomes transported by ~10 constitutively active, truncated kinesin-1 KIF5B (K543) with perpendicular 2-dimensional (2D) and 3D intersections in vitro. Liposomes frequently pause at 2D and 3D intersections (~2s), suggesting that motor teams can simultaneously engage each MT and undergo a tug-of-war. Once resolved, the directional outcomes at 2D MT intersections have a straight to turn ratio of 1.1; whereas at 3D MT intersections, liposomes more frequently go straight (straight to turn ratio of 1.8), highlighting that spatial relationships at intersections bias directional outcomes. Using 3D super-resolution microscopy (STORM), we define the gap between intersecting MTs and the liposome azimuthal approach angle heading into the intersection. We develop an in silico model in which kinesin-1 motors diffuse on the liposome surface, simultaneously engage the intersecting MTs, generate forces and detach from MTs governed by the motors' mechanochemical cycle, and undergo a tug-of-war with the winning team determining the directional outcome in 3D. The model predicts that 1-3 motors typically engage the MT, consistent with optical trapping measurements. Modeled liposomes also predominantly go straight through 3D intersections over a range of intersection gaps and liposome approach angles, even when obstructed by the crossing MT. Our observations and modeling offer mechanistic insights into how cells might tune the MT cytoskeleton, cargo, and motors to modulate cargo transport.
Collapse
Affiliation(s)
- Brandon M Bensel
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Samantha Previs
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Carol Bookwalter
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Sam Walcott
- Department of Mathematical Sciences, Worcester Polytechnic Institute, Worcester, MA 01609
| | - David M Warshaw
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| |
Collapse
|
27
|
D'Souza AI, Grover R, Monzon GA, Santen L, Diez S. Vesicles driven by dynein and kinesin exhibit directional reversals without regulators. Nat Commun 2023; 14:7532. [PMID: 37985763 PMCID: PMC10662051 DOI: 10.1038/s41467-023-42605-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Intracellular vesicular transport along cytoskeletal filaments ensures targeted cargo delivery. Such transport is rarely unidirectional but rather bidirectional, with frequent directional reversals owing to the simultaneous presence of opposite-polarity motors. So far, it has been unclear whether such complex motility pattern results from the sole mechanical interplay between opposite-polarity motors or requires regulators. Here, we demonstrate that a minimal system, comprising purified Dynein-Dynactin-BICD2 (DDB) and kinesin-3 (KIF16B) attached to large unilamellar vesicles, faithfully reproduces in vivo cargo motility, including runs, pauses, and reversals. Remarkably, opposing motors do not affect vesicle velocity during runs. Our computational model reveals that the engagement of a small number of motors is pivotal for transitioning between runs and pauses. Taken together, our results suggest that motors bound to vesicular cargo transiently engage in a tug-of-war during pauses. Subsequently, stochastic motor attachment and detachment events can lead to directional reversals without the need for regulators.
Collapse
Affiliation(s)
- Ashwin I D'Souza
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Rahul Grover
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Gina A Monzon
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
- Center for Biophysics, Department of Physics, Saarland University, Saarbrücken, Germany
| | - Ludger Santen
- Center for Biophysics, Department of Physics, Saarland University, Saarbrücken, Germany.
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
28
|
Tayar AM, Caballero F, Anderberg T, Saleh OA, Cristina Marchetti M, Dogic Z. Controlling liquid-liquid phase behaviour with an active fluid. NATURE MATERIALS 2023; 22:1401-1408. [PMID: 37679525 DOI: 10.1038/s41563-023-01660-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Demixing binary liquids is a ubiquitous transition explained using a well-established thermodynamic formalism that requires the equality of intensive thermodynamics parameters across phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, but predicting and designing such out-of-equilibrium transitions remains a challenge. Here we study the liquid-liquid phase separation of attractive DNA nanostars driven away from equilibrium using a microtubule-based active fluid. We find that activity lowers the critical temperature and narrows the range of coexistence concentrations, but only in the presence of mechanical bonds between the liquid droplets and reconfiguring active fluid. Similar behaviours are observed in numerical simulations, suggesting that the activity suppression of the critical point is a generic feature of active liquid-liquid phase separation. Our work describes a versatile platform for building soft active materials with feedback control and providing an insight into self-organization in cell biology.
Collapse
Affiliation(s)
- Alexandra M Tayar
- Department of Physics, University of California, Santa Barbara, CA, USA.
| | | | - Trevor Anderberg
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Omar A Saleh
- Department of Physics, University of California, Santa Barbara, CA, USA
- Materials Department, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - M Cristina Marchetti
- Department of Physics, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
| |
Collapse
|
29
|
Chang C, Zheng T, Nettesheim G, Song H, Cho C, Crespi S, Shubeita G. On the use of thermal forces to probe kinesin's response to force. Front Mol Biosci 2023; 10:1260914. [PMID: 38028555 PMCID: PMC10644364 DOI: 10.3389/fmolb.2023.1260914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023] Open
Abstract
The stepping dynamics of cytoskeletal motor proteins determines the dynamics of cargo transport. In its native cellular environment, a molecular motor is subject to forces from several sources including thermal forces and forces ensuing from the interaction with other motors bound to the same cargo. Understanding how the individual motors respond to these forces can allow us to predict how they move their cargo when part of a team. Here, using simulation, we show that details of how the kinesin motor responds to small assisting forces-which, at the moment, are not experimentally constrained-can lead to significant changes in cargo dynamics. Using different models of the force-dependent detachment probability of the kinesin motor leads to different predictions on the run-length of the cargo they carry. These differences emerge from the thermal forces acting on the cargo and transmitted to the motor through the motor tail that tethers the motor head to the microtubule. We show that these differences appear for cargo carried by individual motors or motor teams, and use our findings to propose the use of thermal forces as a probe of kinesin's response to force in this otherwise inaccessible force regime.
Collapse
Affiliation(s)
- Chuan Chang
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tiantian Zheng
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Guilherme Nettesheim
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Hayoung Song
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Changhyun Cho
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuele Crespi
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Shubeita
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
30
|
Ma TC, Gicking AM, Feng Q, Hancock WO. Simulations suggest robust microtubule attachment of kinesin and dynein in antagonistic pairs. Biophys J 2023; 122:3299-3313. [PMID: 37464742 PMCID: PMC10465704 DOI: 10.1016/j.bpj.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 05/04/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Intracellular transport is propelled by kinesin and cytoplasmic dynein motors that carry membrane-bound vesicles and organelles bidirectionally along microtubule tracks. Much is known about these motors at the molecular scale, but many questions remain regarding how kinesin and dynein cooperate and compete during bidirectional cargo transport at the cellular level. The goal of the present study was to use a stochastic stepping model constructed by using published load-dependent properties of kinesin-1 and dynein-dynactin-BicD2 (DDB) to identify specific motor properties that determine the speed, directionality, and transport dynamics of a cargo carried by one kinesin and one dynein motor. Model performance was evaluated by comparing simulations to recently published experiments of kinesin-DDB pairs connected by complementary oligonucleotide linkers. Plotting the instantaneous velocity distributions from kinesin-DDB experiments revealed a single peak centered around zero velocity. In contrast, velocity distributions from simulations displayed a central peak around 100 nm/s, along with two side peaks corresponding to the unloaded kinesin and DDB velocities. We hypothesized that frequent motor detachment events and relatively slow motor reattachment rates resulted in periods in which only one motor is attached. To investigate this hypothesis, we varied specific model parameters and compared the resulting instantaneous velocity distributions, and we confirmed this systematic investigation using a machine-learning approach that minimized the residual sum of squares between the experimental and simulation velocity distributions. The experimental data were best recapitulated by a model in which the kinesin and dynein stall forces are matched, the motor detachment rates are independent of load, and the kinesin-1 reattachment rate is 50 s-1. These results provide new insights into motor dynamics during bidirectional transport and put forth hypotheses that can be tested by future experiments.
Collapse
Affiliation(s)
- Tzu-Chen Ma
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania.
| |
Collapse
|
31
|
Levin JT, Pan A, Barrett MT, Alushin GM. A platform for dissecting force sensitivity and multivalency in actin networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553463. [PMID: 37645911 PMCID: PMC10462062 DOI: 10.1101/2023.08.15.553463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The physical structure and dynamics of cells are supported by micron-scale actin networks with diverse geometries, protein compositions, and mechanical properties. These networks are composed of actin filaments and numerous actin binding proteins (ABPs), many of which engage multiple filaments simultaneously to crosslink them into specific functional architectures. Mechanical force has been shown to modulate the interactions between several ABPs and individual actin filaments, but it is unclear how this phenomenon contributes to the emergent force-responsive functional dynamics of actin networks. Here, we engineer filament linker complexes and combine them with photo-micropatterning of myosin motor proteins to produce an in vitro reconstitution platform for examining how force impacts the behavior of ABPs within multi-filament assemblies. Our system enables the monitoring of dozens of actin networks with varying architectures simultaneously using total internal reflection fluorescence microscopy, facilitating detailed dissection of the interplay between force-modulated ABP binding and network geometry. We apply our system to study a dimeric form of the critical cell-cell adhesion protein α-catenin, a model force-sensitive ABP. We find that myosin forces increase α-catenin's engagement of small filament bundles embedded within networks. This activity is absent in a force-sensing deficient mutant, whose binding scales linearly with bundle size in both the presence and absence of force. These data are consistent with filaments in smaller bundles bearing greater per-filament loads that enhance α-catenin binding, a mechanism that could equalize α-catenin's distribution across actin-myosin networks of varying sizes in cells to regularize their stability and composition.
Collapse
Affiliation(s)
- Joseph T. Levin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Ariel Pan
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Michael T. Barrett
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
32
|
Ahmad K, Javed A, Lanphere C, Coveney PV, Orlova EV, Howorka S. Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun 2023; 14:3630. [PMID: 37336895 DOI: 10.1038/s41467-023-38681-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/11/2023] [Indexed: 06/21/2023] Open
Abstract
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications.
Collapse
Affiliation(s)
- Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Abid Javed
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Conor Lanphere
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
- Advanced Research Computing Centre, University College London, London, WC1H 0AJ, UK.
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands.
| | - Elena V Orlova
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK.
| |
Collapse
|
33
|
O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
Collapse
Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
34
|
Zhang Y, Yang D, Wang P, Ke Y. Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes. ACS NANO 2023. [PMID: 37207344 DOI: 10.1021/acsnano.3c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway. A cohesive link was incorporated into the tile to induce intertube binding for the formation of DNA bundles. DNA bundles with length of dozens of micrometers and width of hundreds of nanometers were produced, whose assembly was revealed to be collectively determined by cationic strength and linker designs (binding strength, spacer length, linker position, etc.). Furthermore, multicomponent DNA bundles with programmable spatial features and compositions were realized by using various distinct tile designs. Lastly, we implemented dynamic capability into large DNA bundles to realize reversible reconfigurations among tile, tube, and bundles following specific molecular stimulations. We envision this assembly strategy can enrich the toolbox of DNA nanotechnology for rational design of large-size DNA materials of defined features and properties that may be applied to a variety of fields in materials science, synthetic biology, biomedical science, and beyond.
Collapse
Affiliation(s)
- Yunlong Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
35
|
Fukumoto K, Miyazono Y, Ueda T, Harada Y, Tadakuma H. Evaluating the effect of two-dimensional molecular layout on DNA origami-based transporters. NANOSCALE ADVANCES 2023; 5:2590-2601. [PMID: 37143804 PMCID: PMC10153088 DOI: 10.1039/d3na00088e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023]
Abstract
Cellular transport systems are sophisticated and efficient. Hence, one of the ultimate goals of nanotechnology is to design artificial transport systems rationally. However, the design principle has been elusive, because how motor layout affects motile activity has not been established, partially owing to the difficulty in achieving a precise layout of the motile elements. Here, we employed a DNA origami platform to evaluate the two-dimensional (2D) layout effect of kinesin motor proteins on transporter motility. We succeeded in accelerating the integration speed of the protein of interest (POI) to the DNA origami transporter by up to 700 times by introducing a positively charged poly-lysine tag (Lys-tag) into the POI (kinesin motor protein). This Lys-tag approach allowed us to construct and purify a transporter with high motor density, allowing a precise evaluation on the 2D layout effect. Our single-molecule imaging showed that the densely packed layout of kinesin decreased the run length of the transporter, although its velocity was moderately affected. These results indicate that steric hindrance is a critical parameter to be considered in the design of transport systems.
Collapse
Affiliation(s)
- Kodai Fukumoto
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University Osaka 560-0043 Japan
| | - Yuya Miyazono
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
| | - Takuya Ueda
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
- Graduate School of Science and Engineering, Waseda University Tokyo 162-8480 Japan
| | - Yoshie Harada
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Center for Quantum Information and Quantum Biology, Osaka University Osaka 560-0043 Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University Osaka 565-0871 Japan
| | - Hisashi Tadakuma
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
- School of Life Science and Technology, ShanghaiTech University Shanghai 201210 People's Republic of China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University Shanghai 201210 People's Republic of China
| |
Collapse
|
36
|
Geyer VF, Diez S. Horizontal Magnetic Tweezers to Directly Measure the Force-Velocity Relationship for Multiple Kinesin Motors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2300558. [PMID: 37035988 DOI: 10.1002/smll.202300558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Transport of intracellular cargo along cytoskeletal filaments is often achieved by the concerted action of multiple motor molecules. While single-molecule studies have provided profound insight into the mechano-chemical principles and force generation of individual motors, studies on multi-motor systems are less advanced. Here, a horizontal magnetic-tweezers setup is applied, capable of producing up to 150 pN of horizontal force onto 2.8 µm superparamagnetic beads, to motor-propelled cytoskeletal filaments. It is found that kinesin-1 driven microtubules decorated with individual beads display frequent transitions in their gliding velocities which we attribute to dynamic changes in the number of engaged motors. Applying defined temporal force-ramps the force-velocity relationship is directly measured for multi-motor transport. It is found that the stall forces of individual motors are approximately additive and collective backward motion of the transport system under super-stall forces is observed. The magnetic-tweezers apparatus is expected to be readily applicable to a wide range of molecular and cellular motility assays.
Collapse
Affiliation(s)
- Veikko F Geyer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| |
Collapse
|
37
|
Canty JT, Hensley A, Aslan M, Jack A, Yildiz A. TRAK adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport. Nat Commun 2023; 14:1376. [PMID: 36914620 PMCID: PMC10011603 DOI: 10.1038/s41467-023-36945-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Mitochondrial transport along microtubules is mediated by Miro1 and TRAK adaptors that recruit kinesin-1 and dynein-dynactin. To understand how these opposing motors are regulated during mitochondrial transport, we reconstitute the bidirectional transport of Miro1/TRAK along microtubules in vitro. We show that the coiled-coil domain of TRAK activates dynein-dynactin and enhances the motility of kinesin-1 activated by its cofactor MAP7. We find that TRAK adaptors that recruit both motors move towards kinesin-1's direction, whereas kinesin-1 is excluded from binding TRAK transported by dynein-dynactin, avoiding motor tug-of-war. We also test the predictions of the models that explain how mitochondrial transport stalls in regions with elevated Ca2+. Transport of Miro1/TRAK by kinesin-1 is not affected by Ca2+. Instead, we demonstrate that the microtubule docking protein syntaphilin induces resistive forces that stall kinesin-1 and dynein-driven motility. Our results suggest that mitochondrial transport stalls by Ca2+-mediated recruitment of syntaphilin to the mitochondrial membrane, not by disruption of the transport machinery.
Collapse
Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Cancer Immunology, Genentech Inc., 1 DNA Way, 94080, South San Francisco, CA, USA.
| | - Andrew Hensley
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Merve Aslan
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
| |
Collapse
|
38
|
Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
Collapse
Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| |
Collapse
|
39
|
Xu A, Basant A, Schleich S, Newsome TP, Way M. Kinesin-1 transports morphologically distinct intracellular virions during vaccinia infection. J Cell Sci 2023; 136:jcs260175. [PMID: 36093836 PMCID: PMC9659004 DOI: 10.1242/jcs.260175] [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: 04/27/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022] Open
Abstract
Intracellular mature viruses (IMVs) are the first and most abundant infectious form of vaccinia virus to assemble during its replication cycle. IMVs can undergo microtubule-based motility, but their directionality and the motor involved in their transport remain unknown. Here, we demonstrate that IMVs, like intracellular enveloped viruses (IEVs), the second form of vaccinia that are wrapped in Golgi-derived membranes, recruit kinesin-1 and undergo anterograde transport. In vitro reconstitution of virion transport in infected cell extracts revealed that IMVs and IEVs move toward microtubule plus ends with respective velocities of 0.66 and 0.56 µm/s. Quantitative imaging established that IMVs and IEVs recruit an average of 139 and 320 kinesin-1 motor complexes, respectively. In the absence of kinesin-1, there was a near-complete loss of in vitro motility and reduction in the intracellular spread of both types of virions. Our observations demonstrate that kinesin-1 transports two morphologically distinct forms of vaccinia. Reconstitution of vaccinia-based microtubule motility in vitro provides a new model to elucidate how motor number and regulation impacts transport of a bona fide kinesin-1 cargo.
Collapse
Affiliation(s)
- Amadeus Xu
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sibylle Schleich
- London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
| | - Timothy P. Newsome
- London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| |
Collapse
|
40
|
Wintersinger CM, Minev D, Ershova A, Sasaki HM, Gowri G, Berengut JF, Corea-Dilbert FE, Yin P, Shih WM. Multi-micron crisscross structures grown from DNA-origami slats. NATURE NANOTECHNOLOGY 2023; 18:281-289. [PMID: 36543881 PMCID: PMC10818227 DOI: 10.1038/s41565-022-01283-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Living systems achieve robust self-assembly across a wide range of length scales. In the synthetic realm, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes from a multitude of single-stranded components. To achieve greater complexity, subsequent hierarchical joining of origami can be pursued. However, erroneous and missing linkages restrict the number of unique origami that can be practically combined into a single design. Here we extend crisscross polymerization, a strategy previously demonstrated with single-stranded components, to DNA-origami 'slats' for fabrication of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ~2,000 strands that are combinatorially arranged to create unique DNA-origami slats, we realize finite structures composed of >1,000 uniquely addressable slats, with a mass exceeding 5 GDa, lateral dimensions of roughly 2 µm and a multitude of periodic structures. Robust production of target crisscross structures is enabled through strict control over initiation, rapid growth and minimal premature termination, and highly orthogonal binding specificities. Thus crisscross growth provides a route for prototyping and scalable production of structures integrating thousands of unique components (that is, origami slats) that each is sophisticated and molecularly precise.
Collapse
Affiliation(s)
- Christopher M Wintersinger
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dionis Minev
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anastasia Ershova
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Gokul Gowri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jonathan F Berengut
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - F Eduardo Corea-Dilbert
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
41
|
Karan C, Chaudhuri D. Cooperation and competition in the collective drive by motor proteins: mean active force, fluctuations, and self-load. SOFT MATTER 2023; 19:1834-1843. [PMID: 36789956 DOI: 10.1039/d2sm01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We consider the dynamics of a bio-filament under the collective drive of motor proteins. They are attached irreversibly to a substrate and undergo stochastic attachment-detachment with the filament to produce a directed force on it. We establish the dependence of the mean directed force and force correlations on the parameters describing the individual motor proteins using analytical theory and direct numerical simulations. The effective Langevin description for the filament motion gives mean-squared displacement, asymptotic diffusion constant, and mobility leading to an effective temperature. Finally, we show how competition between motor protein extensions generates a self-load, describable in terms of the effective temperature, affecting the filament motion.
Collapse
Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
42
|
Chiba K, Kita T, Anazawa Y, Niwa S. Insight into the regulation of axonal transport from the study of KIF1A-associated neurological disorder. J Cell Sci 2023; 136:286709. [PMID: 36655764 DOI: 10.1242/jcs.260742] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Neuronal function depends on axonal transport by kinesin superfamily proteins (KIFs). KIF1A is the molecular motor that transports synaptic vesicle precursors, synaptic vesicles, dense core vesicles and active zone precursors. KIF1A is regulated by an autoinhibitory mechanism; many studies, as well as the crystal structure of KIF1A paralogs, support a model whereby autoinhibited KIF1A is monomeric in solution, whereas activated KIF1A is dimeric on microtubules. KIF1A-associated neurological disorder (KAND) is a broad-spectrum neuropathy that is caused by mutations in KIF1A. More than 100 point mutations have been identified in KAND. In vitro assays show that most mutations are loss-of-function mutations that disrupt the motor activity of KIF1A, whereas some mutations disrupt its autoinhibition and abnormally hyperactivate KIF1A. Studies on disease model worms suggests that both loss-of-function and gain-of-function mutations cause KAND by affecting the axonal transport and localization of synaptic vesicles. In this Review, we discuss how the analysis of these mutations by molecular genetics, single-molecule assays and force measurements have helped to reveal the physiological significance of KIF1A function and regulation, and what physical parameters of KIF1A are fundamental to axonal transport.
Collapse
Affiliation(s)
- Kyoko Chiba
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Tomoki Kita
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuzu Anazawa
- Graduate School of Life Sciences, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan.,Department of Applied Physics, Graduate School of Engineering, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| |
Collapse
|
43
|
Büber E, Schröder T, Scheckenbach M, Dass M, Franquelim HG, Tinnefeld P. DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout. ACS NANO 2023; 17:3088-3097. [PMID: 36735241 DOI: 10.1021/acsnano.2c11981] [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: 06/18/2023]
Abstract
Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.
Collapse
Affiliation(s)
- Ece Büber
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, 80539Munich, Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152Martinsried, Germany
- Interfaculty Centre for Bioactive Matter, Leipzig University, c/o Deutscher Platz 5 (BBZ), 04109Leipzig, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| |
Collapse
|
44
|
Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
Collapse
Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| |
Collapse
|
45
|
Nair A, Greeny A, Rajendran R, Abdelgawad MA, Ghoneim MM, Raghavan RP, Sudevan ST, Mathew B, Kim H. KIF1A-Associated Neurological Disorder: An Overview of a Rare Mutational Disease. Pharmaceuticals (Basel) 2023; 16:147. [PMID: 37259299 PMCID: PMC9962247 DOI: 10.3390/ph16020147] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 10/03/2023] Open
Abstract
KIF1A-associated neurological diseases (KANDs) are a group of inherited conditions caused by changes in the microtubule (MT) motor protein KIF1A as a result of KIF1A gene mutations. Anterograde transport of membrane organelles is facilitated by the kinesin family protein encoded by the MT-based motor gene KIF1A. Variations in the KIF1A gene, which primarily affect the motor domain, disrupt its ability to transport synaptic vesicles containing synaptophysin and synaptotagmin leading to various neurological pathologies such as hereditary sensory neuropathy, autosomal dominant and recessive forms of spastic paraplegia, and different neurological conditions. These mutations are frequently misdiagnosed because they result from spontaneous, non-inherited genomic alterations. Whole-exome sequencing (WES), a cutting-edge method, assists neurologists in diagnosing the illness and in planning and choosing the best course of action. These conditions are simple to be identified in pediatric and have a life expectancy of 5-7 years. There is presently no permanent treatment for these illnesses, and researchers have not yet discovered a medicine to treat them. Scientists have more hope in gene therapy since it can be used to cure diseases brought on by mutations. In this review article, we discussed some of the experimental gene therapy methods, including gene replacement, gene knockdown, symptomatic gene therapy, and cell suicide gene therapy. It also covered its clinical symptoms, pathogenesis, current diagnostics, therapy, and research advances currently occurring in the field of KAND-related disorders. This review also explained the impact that gene therapy can be designed in this direction and afford the remarkable benefits to the patients and society.
Collapse
Affiliation(s)
- Ayushi Nair
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Alosh Greeny
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Roshni Pushpa Raghavan
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| |
Collapse
|
46
|
Li Q, Ferrare JT, Silver J, Wilson JO, Arteaga-Castaneda L, Qiu W, Vershinin M, King SJ, Neuman KC, Xu J. Cholesterol in the cargo membrane amplifies tau inhibition of kinesin-1-based transport. Proc Natl Acad Sci U S A 2023; 120:e2212507120. [PMID: 36626558 PMCID: PMC9934065 DOI: 10.1073/pnas.2212507120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023] Open
Abstract
Intracellular cargos are often membrane-enclosed and transported by microtubule-based motors in the presence of microtubule-associated proteins (MAPs). Whereas increasing evidence reveals how MAPs impact the interactions between motors and microtubules, critical questions remain about the impact of the cargo membrane on transport. Here we combined in vitro optical trapping with theoretical approaches to determine the effect of a lipid cargo membrane on kinesin-based transport in the presence of MAP tau. Our results demonstrate that attaching kinesin to a fluid lipid membrane reduces the inhibitory effect of tau on kinesin. Moreover, adding cholesterol, which reduces kinesin diffusion in the cargo membrane, amplifies the inhibitory effect of tau on kinesin binding in a dosage-dependent manner. We propose that reduction of kinesin diffusion in the cargo membrane underlies the effect of cholesterol on kinesin binding in the presence of tau, and we provide a simple model for this proposed mechanism. Our study establishes a direct link between cargo membrane cholesterol and MAP-based regulation of kinesin-1. The cholesterol effects uncovered here may more broadly extend to other lipid alterations that impact motor diffusion in the cargo membrane, including those associated with aging and neurological diseases.
Collapse
Affiliation(s)
- Qiaochu Li
- Department of Physics, University of California, Merced, CA95343
| | - James T. Ferrare
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jonathan Silver
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - John O. Wilson
- Department of Physics, University of California, Merced, CA95343
| | | | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, OR97331
| | - Michael Vershinin
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT84112
| | - Stephen J. King
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL32827
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jing Xu
- Department of Physics, University of California, Merced, CA95343
| |
Collapse
|
47
|
Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
Collapse
Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
48
|
Abstract
Coupling of motor proteins within arrays drives muscle contraction, flagellar beating, chromosome segregation, and other biological processes. Current models of motor coupling invoke either direct mechanical linkage or protein crowding, which rely on short-range motor-motor interactions. In contrast, coupling mechanisms that act at longer length scales remain largely unexplored. Here we report that microtubules can physically couple motor movement in the absence of detectable short-range interactions. The human kinesin-4 Kif4A changes the run length and velocity of other motors on the same microtubule in the dilute binding limit, when approximately 10-nm-sized motors are much farther apart than the motor size. This effect does not depend on specific motor-motor interactions because similar changes in Kif4A motility are induced by kinesin-1 motors. A micrometer-scale attractive interaction potential between motors is sufficient to recreate the experimental results in a biophysical model. Unexpectedly, our theory suggests that long-range microtubule-mediated coupling affects not only binding kinetics but also motor mechanochemistry. Therefore, the model predicts that motors can sense and respond to motors bound several micrometers away on a microtubule. Our results are consistent with a paradigm in which long-range motor interactions along the microtubule enable additional forms of collective motor behavior, possibly due to changes in the microtubule lattice.
Collapse
|
49
|
Behler KL, Honemann MN, Rita Silva‐Santos A, Dietz H, Weuster‐Botz D. Phage‐free production of artificial ssDNA with
Escherichia coli. Biotechnol Bioeng 2022; 119:2878-2889. [DOI: 10.1002/bit.28171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/09/2022] [Accepted: 06/19/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Karl L. Behler
- Technical University of Munich, School of Engineering and Design, Chair of Biochemical EngineeringGarching nearMunichGermany
| | - Maximilian N. Honemann
- Technical University of MunichDepartment of PhysicsGarching nearMunichGermany
- Technical University of MunichMunich Institute of Biomedical EngineeringGarching nearMunichGermany
| | | | - Hendrik Dietz
- Technical University of MunichDepartment of PhysicsGarching nearMunichGermany
- Technical University of MunichMunich Institute of Biomedical EngineeringGarching nearMunichGermany
| | - Dirk Weuster‐Botz
- Technical University of Munich, School of Engineering and Design, Chair of Biochemical EngineeringGarching nearMunichGermany
| |
Collapse
|
50
|
Abdellatef SA, Tadakuma H, Yan K, Fujiwara T, Fukumoto K, Kondo Y, Takazaki H, Boudria R, Yasunaga T, Higuchi H, Hirose K. Oscillatory movement of a dynein-microtubule complex crosslinked with DNA origami. eLife 2022; 11:76357. [PMID: 35749159 PMCID: PMC9232216 DOI: 10.7554/elife.76357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bending of cilia and flagella occurs when axonemal dynein molecules on one side of the axoneme produce force and move toward the microtubule (MT) minus end. These dyneins are then pulled back when the axoneme bends in the other direction, meaning oscillatory back and forth movement of dynein during repetitive bending of cilia/flagella. There are various factors that may regulate the dynein activity, e.g. the nexin-dynein regulatory complex, radial spokes, and central apparatus. In order to understand the basic mechanism of dynein’s oscillatory movement, we constructed a simple model system composed of MTs, outer-arm dyneins, and crosslinks between the MTs made of DNA origami. Electron microscopy (EM) showed pairs of parallel MTs crossbridged by patches of regularly arranged dynein molecules bound in two different orientations, depending on which of the MTs their tails bind to. The oppositely oriented dyneins are expected to produce opposing forces when the pair of MTs have the same polarity. Optical trapping experiments showed that the dynein-MT-DNA-origami complex actually oscillates back and forth after photolysis of caged ATP. Intriguingly, the complex, when held at one end, showed repetitive bending motions. The results show that a simple system composed of ensembles of oppositely oriented dyneins, MTs, and inter-MT crosslinkers, without any additional regulatory structures, has an intrinsic ability to cause oscillation and repetitive bending motions.
Collapse
Affiliation(s)
- Shimaa A Abdellatef
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Hisashi Tadakuma
- Institute for Protein Research, Osaka University, Osaka, Japan.,SLST and Gene Editing Center, ShanghaiTech University, Shanghai, China
| | - Kangmin Yan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Fujiwara
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kodai Fukumoto
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuichi Kondo
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Takazaki
- Institute for Protein Research, Osaka University, Osaka, Japan.,Kyushu Institute of Technology, Fukuoka, Japan
| | - Rofia Boudria
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Institut Pasteur, Paris, France
| | | | - Hideo Higuchi
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| |
Collapse
|