1
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Spudich JA. One must reconstitute the functions of interest from purified proteins. Front Physiol 2024; 15:1390186. [PMID: 38827995 PMCID: PMC11140241 DOI: 10.3389/fphys.2024.1390186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 06/05/2024] Open
Abstract
I am often asked by students and younger colleagues and now by the editors of this issue to tell the history of the development of the in vitro motility assay and the dual-beam single-molecule laser trap assay for myosin-driven actin filament movement, used widely as key assays for understanding how both muscle and nonmuscle myosin molecular motors work. As for all discoveries, the history of the development of the myosin assays involves many people who are not authors of the final publications, but without whom the assays would not have been developed as they are. Also, early experiences shape how one develops ideas and experiments, and influence future discoveries in major ways. I am pleased here to trace my own path and acknowledge the many individuals involved and my early science experiences that led to the work I and my students, postdoctoral fellows, and sabbatical visitors did to develop these assays. Mentors are too often overlooked in historical descriptions of discoveries, and my story starts with those who mentored me.
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Affiliation(s)
- James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States
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2
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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3
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Tan L, Lu J, Wang X, Liu G, Mu X, Hu K, Zhao S, Tian J. A DNAzyme-driven random biped DNA walking nanomachine for sensitive detection of uracil-DNA glycosylase activity. Analyst 2021; 146:5643-5649. [PMID: 34378556 DOI: 10.1039/d1an00440a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Highly specific and ultrasensitive detection of uracil-DNA glycosylase (UDG) activity is of great significance for maintaining genomic integrity and medical research of related diseases. Here, we constructed a random DNA walking nanomachine based on a DNAzyme for UDG activity detection on the AuNP (Au nanoparticle) surface. When UDG is present, the U bases in the Y structure are removed, resulting in AP sites, which will be cleaved by Endo-IV to generate a 3' concave end for Exo-III, causing the locking strand of the DNAzyme to be completely hydrolyzed by the Exo-III and release the walking strand to randomly pair with the substrate strand on the AuNP surface; then, the walking strand exerts its cleavage activity with the assistance of Mg2+ to cleave the substrate strand and keep the fluorophore 6-carboxyfluorescein (FAM) away from the surface of the AuNP, which restores the fluorescence signal of this system. In this way, sensitive detection of UDG can be realized, and the detection limit is as low as 3.69 × 10-6 U mL-1. In addition, we found that this method is highly specific to UDG and can be used to detect UDG specifically in complex samples, which has certain application prospects in biomedical research and clinical diagnosis related to UDG.
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Affiliation(s)
- Li Tan
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Jiangnan Lu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Xin Wang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Guang Liu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Xiaomei Mu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Kun Hu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
| | - Jianniao Tian
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guilin 541004, China.
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4
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Computational roles of intrinsic synaptic dynamics. Curr Opin Neurobiol 2021; 70:34-42. [PMID: 34303124 DOI: 10.1016/j.conb.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/14/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022]
Abstract
Conventional theories assume that long-term information storage in the brain is implemented by modifying synaptic efficacy. Recent experimental findings challenge this view by demonstrating that dendritic spine sizes, or their corresponding synaptic weights, are highly volatile even in the absence of neural activity. Here, we review previous computational works on the roles of these intrinsic synaptic dynamics. We first present the possibility for neuronal networks to sustain stable performance in their presence, and we then hypothesize that intrinsic dynamics could be more than mere noise to withstand, but they may improve information processing in the brain.
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5
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Hu YX, Wu GY, Wang XQ, Yin GQ, Zhang CW, Li X, Xu L, Yang HB. Acid-Activated Motion Switching of DB24C8 between Two Discrete Platinum(II) Metallacycles. Molecules 2021; 26:molecules26030716. [PMID: 33573149 PMCID: PMC7866548 DOI: 10.3390/molecules26030716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
The precise operation of molecular motion for constructing complicated mechanically interlocked molecules has received considerable attention and is still an energetic field of supramolecular chemistry. Herein, we reported the construction of two tris[2]pseudorotaxanes metallacycles with acid-base controllable molecular motion through self-sorting strategy and host-guest interaction. Firstly, two hexagonal Pt(II) metallacycles M1 and M2 decorated with different host-guest recognition sites have been constructed via coordination-driven self-assembly strategy. The binding of metallacycles M1 and M2 with dibenzo-24-crown-8 (DB24C8) to form tris[2]pseudorotaxanes complexes TPRM1 and TPRM2 have been investigated. Furthermore, by taking advantage of the strong binding affinity between the protonated metallacycle M2 and DB24C8, the addition of trifluoroacetic acid (TFA) as a stimulus successfully induces an acid-activated motion switching of DB24C8 between the discrete metallacycles M1 and M2. This research not only affords a highly efficient way to construct stimuli-responsive smart supramolecular systems but also offers prospects for precisely control multicomponent cooperative motion.
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Affiliation(s)
- Yi-Xiong Hu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
| | - Gui-Yuan Wu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China
| | - Xu-Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
| | - Guang-Qiang Yin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518055, China; (G.-Q.Y.); (X.L.)
| | - Chang-Wei Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
| | - Xiaopeng Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518055, China; (G.-Q.Y.); (X.L.)
| | - Lin Xu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
- Correspondence: (L.X.); (H.-B.Y.)
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China; (Y.-X.H.); (G.-Y.W.); (X.-Q.W.); (C.-W.Z.)
- Correspondence: (L.X.); (H.-B.Y.)
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6
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Robert-Paganin J, Pylypenko O, Kikuti C, Sweeney HL, Houdusse A. Force Generation by Myosin Motors: A Structural Perspective. Chem Rev 2019; 120:5-35. [PMID: 31689091 DOI: 10.1021/acs.chemrev.9b00264] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Generating force and movement is essential for the functions of cells and organisms. A variety of molecular motors that can move on tracks within cells have evolved to serve this role. How these motors interact with their tracks and how that, in turn, leads to the generation of force and movement is key to understanding the cellular roles that these motor-track systems serve. This review is focused on the best understood of these systems, which is the molecular motor myosin that moves on tracks of filamentous (F-) actin. The review highlights both the progress and the limits of our current understanding of how force generation can be controlled by F-actin-myosin interactions. What has emerged are insights they may serve as a framework for understanding the design principles of a number of types of molecular motors and their interactions with their tracks.
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Affiliation(s)
- Julien Robert-Paganin
- Structural Motility , UMR 144 CNRS/Curie Institute , 26 rue d'ulm , 75258 Paris cedex 05 , France
| | - Olena Pylypenko
- Structural Motility , UMR 144 CNRS/Curie Institute , 26 rue d'ulm , 75258 Paris cedex 05 , France
| | - Carlos Kikuti
- Structural Motility , UMR 144 CNRS/Curie Institute , 26 rue d'ulm , 75258 Paris cedex 05 , France
| | - H Lee Sweeney
- Department of Pharmacology & Therapeutics and the Myology Institute , University of Florida College of Medicine , PO Box 100267, Gainesville , Florida 32610-0267 , United States
| | - Anne Houdusse
- Structural Motility , UMR 144 CNRS/Curie Institute , 26 rue d'ulm , 75258 Paris cedex 05 , France
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7
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Is the cell really a machine? J Theor Biol 2019; 477:108-126. [PMID: 31173758 DOI: 10.1016/j.jtbi.2019.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 05/06/2019] [Accepted: 06/03/2019] [Indexed: 01/03/2023]
Abstract
It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.
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8
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Multi-Component Spirane Assemblies. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Yu G, Yung BC, Zhou Z, Mao Z, Chen X. Artificial Molecular Machines in Nanotheranostics. ACS NANO 2018; 12:7-12. [PMID: 29283247 DOI: 10.1021/acsnano.7b07851] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to their dynamic nature and excellent stimuli-responsiveness resulting from noncovalent driving forces, artificial molecular machines (AMMs) show great promise in cancer theranostics. In this Perspective, we introduce the potential applications of AMMs in controlled drug delivery, bioorthogonal catalysis, imaging, and cell membrane permeabilization, with the goal of enhancing cancer diagnosis and therapy. We expect this preliminary discussion will garner multidisciplinary interest from scientists to advance AMMs and to expand their future clinical applications.
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Affiliation(s)
- Guocan Yu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Bryant C Yung
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Zijian Zhou
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University , Hangzhou 310027, P.R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
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10
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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11
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Oshima H, Hayashi T, Kinoshita M. Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects. Biophys J 2017; 110:2496-2506. [PMID: 27276267 DOI: 10.1016/j.bpj.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 01/01/2023] Open
Abstract
Actomyosin is an important molecular motor, and the binding of actin and myosin is an essential research target in biophysics. Nevertheless, the physical factors driving or opposing the binding are still unclear. Here, we investigate the role of water in actin-myosin binding using the most reliable statistical-mechanical method currently available for assessing biomolecules immersed in water. This method is characterized as follows: water is treated not as a dielectric continuum but as an ensemble of molecules; the polyatomic structures of proteins are taken into consideration; and the binding free energy is decomposed into physically insightful entropic and energetic components by accounting for the hydration effect to its full extent. We find that the actin-myosin binding brings large gains of electrostatic and Lennard-Jones attractive interactions. However, these gains are accompanied by even larger losses of actin-water and myosin-water electrostatic and LJ attractive interactions. Although roughly half of the energy increase due to the losses is cancelled out by the energy decrease arising from structural reorganization of the water released upon binding, the remaining energy increase is still larger than the energy decrease brought by the gains mentioned above. Hence, the net change in system energy is positive, which opposes binding. Importantly, the binding is driven by a large gain of configurational entropy of water, which surpasses the positive change in system energy and the conformational entropy loss occurring for actin and myosin. The principal physical origin of the large water-entropy gain is as follows: the actin-myosin interface is closely packed with the achievement of high shape complementarity on the atomic level, leading to a large increase in the total volume available to the translational displacement of water molecules in the system and a resultant reduction of water crowding (i.e., entropic correlations among water molecules).
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Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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12
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YANAGIDA T, ISHII Y. Single molecule detection, thermal fluctuation and life. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:51-63. [PMID: 28190869 PMCID: PMC5422627 DOI: 10.2183/pjab.93.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines.
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Affiliation(s)
- Toshio YANAGIDA
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Center for Information and Neural Network (CiNet), Suita, Osaka, Japan
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
- World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Suita Osaka, Japan
| | - Yoshiharu ISHII
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
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13
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Gevorgyan A, Mkrtchyan S, Grigoryan T, Iaroshenko VO. Disilanes as oxygen scavengers and surrogates of hydrosilanes suitable for selective reduction of nitroarenes, phosphine oxides and other valuable substrates. Org Chem Front 2017. [DOI: 10.1039/c7qo00566k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this report, we demonstrate that the reaction of nitroarenes with hexamethyldisilane under various conditions affords a different range of compounds with excellent selectivity.
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Affiliation(s)
- Ashot Gevorgyan
- Homogeneous Catalysis and Molecular Design Research Group at the Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- PL-90-363 Łodź
- Poland
| | - Satenik Mkrtchyan
- Homogeneous Catalysis and Molecular Design Research Group at the Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- PL-90-363 Łodź
- Poland
| | - Tatevik Grigoryan
- Homogeneous Catalysis and Molecular Design Research Group at the Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- PL-90-363 Łodź
- Poland
| | - Viktor O. Iaroshenko
- Homogeneous Catalysis and Molecular Design Research Group at the Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- PL-90-363 Łodź
- Poland
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14
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Li W, Wang L, Jiang W. A catalytic assembled enzyme-free three-dimensional DNA walker and its sensing application. Chem Commun (Camb) 2017; 53:5527-5530. [DOI: 10.1039/c7cc02306e] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A novel and enzyme-free three-dimensional DNA walker powered by catalytic assembly has been constructed.
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Affiliation(s)
- Wei Li
- Key Laboratory of Natural Products Chemical Biological
- Ministry of Education
- School of Pharmacy
- Shandong University
- Jinan 250012
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biological
- Ministry of Education
- School of Pharmacy
- Shandong University
- Jinan 250012
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P. R. China
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15
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Andrecka J, Takagi Y, Mickolajczyk KJ, Lippert LG, Sellers JR, Hancock WO, Goldman YE, Kukura P. Interferometric Scattering Microscopy for the Study of Molecular Motors. Methods Enzymol 2016; 581:517-539. [PMID: 27793291 DOI: 10.1016/bs.mie.2016.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of molecular motor function has been greatly improved by the development of imaging modalities, which enable real-time observation of their motion at the single-molecule level. Here, we describe the use of a new method, interferometric scattering microscopy, for the investigation of motor protein dynamics by attaching and tracking the motion of metallic nanoparticle labels as small as 20nm diameter. Using myosin-5, kinesin-1, and dynein as examples, we describe the basic assays, labeling strategies, and principles of data analysis. Our approach is relevant not only for motor protein dynamics but also provides a general tool for single-particle tracking with high spatiotemporal precision, which overcomes the limitations of single-molecule fluorescence methods.
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Affiliation(s)
- J Andrecka
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Y Takagi
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - K J Mickolajczyk
- Pennsylvania State University, University Park, PA, United States; Intercollege Graduate Degree Program in Bioengineering, Pennsylvania State University, University Park, PA, United States
| | - L G Lippert
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - J R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - W O Hancock
- Pennsylvania State University, University Park, PA, United States; Intercollege Graduate Degree Program in Bioengineering, Pennsylvania State University, University Park, PA, United States
| | - Y E Goldman
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - P Kukura
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.
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16
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Zhang H, Lai M, Zuehlke A, Peng H, Li XF, Le XC. Binding-Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506312] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Zhang H, Lai M, Zuehlke A, Peng H, Li X, Le XC. Binding‐Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids. Angew Chem Int Ed Engl 2015; 54:14326-30. [DOI: 10.1002/anie.201506312] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/17/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058 (China)
| | - Albert Zuehlke
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Hanyong Peng
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Xing‐Fang Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - X. Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
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Abendroth JM, Bushuyev OS, Weiss PS, Barrett CJ. Controlling Motion at the Nanoscale: Rise of the Molecular Machines. ACS NANO 2015; 9:7746-68. [PMID: 26172380 DOI: 10.1021/acsnano.5b03367] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
As our understanding and control of intra- and intermolecular interactions evolve, ever more complex molecular systems are synthesized and assembled that are capable of performing work or completing sophisticated tasks at the molecular scale. Commonly referred to as molecular machines, these dynamic systems comprise an astonishingly diverse class of motifs and are designed to respond to a plethora of actuation stimuli. In this Review, we outline the conditions that distinguish simple switches and rotors from machines and draw from a variety of fields to highlight some of the most exciting recent examples of opportunities for driven molecular mechanics. Emphasis is placed on the need for controllable and hierarchical assembly of these molecular components to display measurable effects at the micro-, meso-, and macroscales. As in Nature, this strategy will lead to dramatic amplification of the work performed via the collective action of many machines organized in linear chains, on functionalized surfaces, or in three-dimensional assemblies.
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Affiliation(s)
- John M Abendroth
- California NanoSystems Institute and Department of Chemistry & Biochemistry, University of California , Los Angeles, Los Angeles, California 90095, United States
| | | | - Paul S Weiss
- California NanoSystems Institute and Department of Chemistry & Biochemistry, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
| | - Christopher J Barrett
- California NanoSystems Institute and Department of Chemistry & Biochemistry, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, McGill University , Montreal, QC, Canada
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19
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Andrecka J, Ortega Arroyo J, Takagi Y, de Wit G, Fineberg A, MacKinnon L, Young G, Sellers JR, Kukura P. Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy. eLife 2015. [PMID: 25748137 DOI: 10.7554/elife.05413.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Myosin 5a is a dual-headed molecular motor that transports cargo along actin filaments. By following the motion of individual heads with interferometric scattering microscopy at nm spatial and ms temporal precision we found that the detached head occupies a loosely fixed position to one side of actin from which it rebinds in a controlled manner while executing a step. Improving the spatial precision to the sub-nm regime provided evidence for an ångstrom-level structural transition in the motor domain associated with the power stroke. Simultaneous tracking of both heads revealed that consecutive steps follow identical paths to the same side of actin in a compass-like spinning motion demonstrating a symmetrical walking pattern. These results visualize many of the critical unknown aspects of the stepping mechanism of myosin 5 including head-head coordination, the origin of lever-arm motion and the spatiotemporal dynamics of the translocating head during individual steps.
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Affiliation(s)
- Joanna Andrecka
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jaime Ortega Arroyo
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Gabrielle de Wit
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adam Fineberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Lachlan MacKinnon
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
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20
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Andrecka J, Ortega Arroyo J, Takagi Y, de Wit G, Fineberg A, MacKinnon L, Young G, Sellers JR, Kukura P. Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy. eLife 2015; 4. [PMID: 25748137 PMCID: PMC4391024 DOI: 10.7554/elife.05413] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/05/2015] [Indexed: 01/21/2023] Open
Abstract
Myosin 5a is a dual-headed molecular motor that transports cargo along actin filaments. By following the motion of individual heads with interferometric scattering microscopy at nm spatial and ms temporal precision we found that the detached head occupies a loosely fixed position to one side of actin from which it rebinds in a controlled manner while executing a step. Improving the spatial precision to the sub-nm regime provided evidence for an ångstrom-level structural transition in the motor domain associated with the power stroke. Simultaneous tracking of both heads revealed that consecutive steps follow identical paths to the same side of actin in a compass-like spinning motion demonstrating a symmetrical walking pattern. These results visualize many of the critical unknown aspects of the stepping mechanism of myosin 5 including head-head coordination, the origin of lever-arm motion and the spatiotemporal dynamics of the translocating head during individual steps.
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Affiliation(s)
- Joanna Andrecka
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jaime Ortega Arroyo
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Gabrielle de Wit
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adam Fineberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Lachlan MacKinnon
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
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Noor A, Maloney DL, Lewis JEM, Lo WKC, Crowley JD. Acid-Base Driven Ligand Exchange with Palladium(II) “Click” Complexes. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201402197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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