1
|
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: 2.0] [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
|
2
|
Soppina P, Patel N, Shewale DJ, Rai A, Sivaramakrishnan S, Naik PK, Soppina V. Kinesin-3 motors are fine-tuned at the molecular level to endow distinct mechanical outputs. BMC Biol 2022; 20:177. [PMID: 35948971 PMCID: PMC9364601 DOI: 10.1186/s12915-022-01370-8] [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: 01/02/2022] [Accepted: 07/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. RESULTS We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B > KIF16B) show an inverse correlation with their microtubule-binding affinities (KIF1A < KIF13A < KIF13B < KIF16B). We demonstrate that this differential microtubule-binding affinity is largely contributed by the positively charged residues in loop8 of the kinesin-3 motor domain. Furthermore, microtubule gliding and cellular expression studies displayed significant microtubule bending that is influenced by the positively charged insert in the motor domain, K-loop, a hallmark of kinesin-3 family. CONCLUSIONS Together, we propose that a fine balance between the rate of ATP hydrolysis and microtubule affinity endows kinesin-3 motors with distinct mechanical outputs. The K-loop, a positively charged insert in the loop12 of the kinesin-3 motor domain promotes microtubule bending, an interesting phenomenon often observed in cells, which requires further investigation to understand its cellular and physiological significance.
Collapse
Affiliation(s)
- Pushpanjali Soppina
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.,Department of Biotechnology and Bioinformatics, Sambalpur University, Sambalpur, Orissa, 768019, India
| | - Nishaben Patel
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.,Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, 55455, USA
| | - Dipeshwari J Shewale
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Ashim Rai
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, 55455, USA
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, 55455, USA
| | - Pradeep K Naik
- Department of Biotechnology and Bioinformatics, Sambalpur University, Sambalpur, Orissa, 768019, India
| | - Virupakshi Soppina
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
| |
Collapse
|
3
|
Ariga T, Tateishi K, Tomishige M, Mizuno D. Noise-Induced Acceleration of Single Molecule Kinesin-1. PHYSICAL REVIEW LETTERS 2021; 127:178101. [PMID: 34739268 DOI: 10.1103/physrevlett.127.178101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
The movement of single kinesin molecules was observed while applying noisy external forces that mimic intracellular active fluctuations. We found kinesin accelerates under noise, especially when a large hindering load is added. The behavior quantitatively conformed to a theoretical model that describes the kinesin movement with simple two-state reactions. The universality of the kinetic theory suggests that intracellular enzymes share a similar noise-induced acceleration mechanism, i.e., active fluctuations in cells are not just noise but are utilized to promote various physiological processes.
Collapse
Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, 755-8505 Yamaguchi, Japan
| | - Keito Tateishi
- Graduate School of Medicine, Yamaguchi University, 755-8505 Yamaguchi, Japan
| | - Michio Tomishige
- Department of Physical Sciences, Aoyama Gakuin University, 252-5258 Kanagawa, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, 819-0395 Fukuoka, Japan
| |
Collapse
|
4
|
Ariga T, Tomishige M, Mizuno D. Experimental and theoretical energetics of walking molecular motors under fluctuating environments. Biophys Rev 2020; 12:503-510. [PMID: 32173796 DOI: 10.1007/s12551-020-00684-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/02/2020] [Indexed: 01/10/2023] Open
Abstract
Molecular motors are nonequilibrium open systems that convert chemical energy to mechanical work. Their energetics are essential for various dynamic processes in cells, but largely remain unknown because fluctuations typically arising in small systems prevent investigation of the nonequilibrium behavior of the motors in terms of thermodynamics. Recently, Harada and Sasa proposed a novel equality to measure the dissipation of nonequilibrium small systems. By utilizing this equality, we have investigated the nonequilibrium energetics of the single-molecule walking motor kinesin-1. The dissipation from kinesin movement was measured through the motion of an attached probe particle and its response to external forces, indicating that large hidden dissipation exists. In this short review, aiming to readers who are not familiar with nonequilibrium physics, we briefly introduce the theoretical basis of the dissipation measurement as well as our recent experimental results and mathematical model analysis and discuss the physiological implications of the hidden dissipation in kinesin. In addition, further perspectives on the efficiency of motors are added by considering their actual working environment: living cells.
Collapse
Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, Ube, Japan.
| | - Michio Tomishige
- Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan
| |
Collapse
|
5
|
Ems-McClung SC, Walczak CE. In Vitro FRET- and Fluorescence-Based Assays to Study Protein Conformation and Protein-Protein Interactions in Mitosis. Methods Mol Biol 2020; 2101:93-122. [PMID: 31879900 PMCID: PMC7189611 DOI: 10.1007/978-1-0716-0219-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proper cell division and the equal segregation of genetic material are essential for life. Cell division is mediated by the mitotic spindle, which is composed of microtubules (MTs) and MT-associated proteins that help align and segregate the chromosomes. The localization and characterization of many spindle proteins have been greatly aided by using GFP-tagged proteins in vivo, but these tools typically do not allow for understanding how their activity is regulated biochemically. With the recent explosion of the pallet of GFP-derived fluorescent proteins, fluorescence-based biosensors are becoming useful tools for the quantitative analysis of protein activity and protein-protein interactions. Here, we describe solution-based Förster resonance energy transfer (FRET) and fluorescence assays that can be used to quantify protein-protein interactions and to characterize protein conformations of MT-associated proteins involved in mitosis.
Collapse
Affiliation(s)
| | - Claire E Walczak
- Indiana University School of Medicine-Bloomington, Medical Sciences, Bloomington, IN, USA.
| |
Collapse
|
6
|
Ariga T, Tomishige M, Mizuno D. Nonequilibrium Energetics of Molecular Motor Kinesin. PHYSICAL REVIEW LETTERS 2018; 121:218101. [PMID: 30517811 DOI: 10.1103/physrevlett.121.218101] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/18/2018] [Indexed: 06/09/2023]
Abstract
Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum of the dissipation and work did not amount to the input free energy change, indicating large hidden dissipation exists. Possible sources of the hidden dissipation were explored by analyzing the Langevin dynamics of the probe, which incorporates the two-state Markov stepper as a kinesin model. We conclude that internal dissipation is dominant.
Collapse
Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| | - Michio Tomishige
- Department of Physics and Mathematics, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| |
Collapse
|
7
|
Pathak D, Thakur S, Mallik R. Fluorescence microscopy applied to intracellular transport by microtubule motors. J Biosci 2018; 43:437-445. [PMID: 30002263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Long-distance transport of many organelles inside eukaryotic cells is driven by the dynein and kinesin motors on microtubule filaments. More than 30 years since the discovery of these motors, unanswered questions include motor- organelle selectivity, structural determinants of processivity, collective behaviour of motors and track selection within the complex cytoskeletal architecture, to name a few. Fluorescence microscopy has been invaluable in addressing some of these questions. Here we present a review of some efforts to understand these sub-microscopic machines using fluorescence.
Collapse
Affiliation(s)
- Divya Pathak
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | | |
Collapse
|