1
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Wirth JO, Schentarra EM, Scheiderer L, Macarrón-Palacios V, Tarnawski M, Hell SW. Uncovering kinesin dynamics in neurites with MINFLUX. Commun Biol 2024; 7:661. [PMID: 38811803 PMCID: PMC11136979 DOI: 10.1038/s42003-024-06358-4] [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: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
Neurons grow neurites of several tens of micrometers in length, necessitating active transport from the cell body by motor proteins. By tracking fluorophores as minimally invasive labels, MINFLUX is able to quantify the motion of those proteins with nanometer/millisecond resolution. Here we study the substeps of a truncated kinesin-1 mutant in primary rat hippocampal neurons, which have so far been mainly observed on polymerized microtubules deposited onto glass coverslips. A gentle fixation protocol largely maintains the structure and surface modifications of the microtubules in the cell. By analyzing the time between the substeps, we identify the ATP-binding state of kinesin-1 and observe the associated rotation of the kinesin-1 head in neurites. We also observed kinesin-1 switching microtubules mid-walk, highlighting the potential of MINFLUX to study the details of active cellular transport.
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Affiliation(s)
- Jan Otto Wirth
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Eva-Maria Schentarra
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Lukas Scheiderer
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Victor Macarrón-Palacios
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany.
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany.
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2
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Xie P. ATP Concentration-Dependent Fractions of One-Head-Bound and Two-Head-Bound States of the Kinesin Motor during Its Chemomechanical Coupling Cycle. J Phys Chem Lett 2024; 15:3893-3899. [PMID: 38563569 DOI: 10.1021/acs.jpclett.4c00022] [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: 04/04/2024]
Abstract
Kinesin is a typical motor protein that can use the chemical energy of ATP hydrolysis to step processively on microtubules, alternating between one-head-bound and two-head-bound states. Some published experimental results showed that the duration of the one-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the two-head-bound state is independent of ATP concentration, indicating that ATP binding occurs in the one-head-bound state. On the contrary, other experimental results showed that the duration of the two-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the one-head-bound state increases slightly with a decrease in ATP concentration, indicating that ATP binding occurs mainly in the two-head-bound state. Here, we explain consistently and quantitatively these contradictory experimental results, resolving the controversy that is critical to the chemomechanical coupling mechanism of the kinesin motor.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China
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3
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Xie P. A Model for Chemomechanical Coupling of Kinesin-3 Motor. Cell Mol Bioeng 2024; 17:137-151. [PMID: 38737453 PMCID: PMC11082130 DOI: 10.1007/s12195-024-00795-1] [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: 10/19/2023] [Accepted: 01/11/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Kinesin-3 motor, which is in the monomeric and inactive form in solution, after cargo-induced dimerization can step on microtubules towards the plus end with a high velocity and a supperprocessivity, which is responsible for transporting the cargo in axons and dendrites. The kinesin-3 motor has a large initial landing rate to microtubules and spends the majority of its stepping cycle in a one-head-bound state. Under the load the kinesin-3 motor can dissociate more readily than the kinesin-1 motor. Methods To understand the physical origin of the peculiar features for the kinesin-3 motor, a model is presented here for its chemomechanical coupling. Based on the model the dynamics of the motor under no load, under the ramping load and under the constant load is studied analytically. Results The theoretical results explain well the available experimental data under no load and under the ramping load. For comparison, the corresponding available experimental data for the kinesin-1 motor under the ramping load are also explained. The predicted results of the velocity, dissociation rate and run length versus the constant load for the kinesin-3 motor are provided. Conclusions The study has strong implications for the chemomechanical coupling mechanism of the kinesin-3 dimer. The origin of the kinesin-3 dimer in the predominant one-head-bound state is due to the fact that the rate of ATP transition to ADP in the trailing head is much larger than that of ADP release from the MT-bound head. The study shows that the kinesin-3 ADP-head has an evidently longer interaction distance with microtubule than the kinesin-1 ADP-head, explaining why in the initial ADP state the kinesin-3 motor has the much larger landing rate than the kinesin-1 motor and why under the load the kinesin-3 motor can dissociate more readily than the kinesin-1 motor. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-024-00795-1.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing, 100190 China
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4
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Tanaka Y, Uchihashi T, Nakamura A. Product inhibition slow down the moving velocity of processive chitinase and sliding-intermediate state blocks re-binding of product. Arch Biochem Biophys 2024; 752:109854. [PMID: 38081338 DOI: 10.1016/j.abb.2023.109854] [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: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023]
Abstract
Processive movement is the key reaction for crystalline polymer degradation by enzyme. Product release is an important phenomenon in resetting the moving cycle, but how it affects chitinase kinetics was unknown. Therefore, we investigated the effect of diacetyl chitobiose (C2) on the biochemical activity and movement of chitinase A from Serratia marcescens (SmChiA). The apparent inhibition constant of C2 on crystalline chitin degradation of SmChiA was 159 μM. The binding position of C2 obtained by X-ray crystallography was at subsite +1, +2 and Trp275 interact with C2 at subsite +1. This binding state is consistent with the competitive inhibition obtained by biochemical analysis. The apparent inhibition constant of C2 on the moving velocity of high-speed (HS) AFM observations was 330 μM, which is close to the biochemical results, indicating that the main factor in crystalline chitin degradation is also the decrease in degradation activity due to inhibition of processive movement. The Trp275 is a key residue for making a sliding intermediate complex. SmChiA W275A showed weaker activity and affinity than WT against crystalline chitin because it is less processive than WT. In addition, biochemical apparent inhibition constant for C2 of SmChiA W275A was 45.6 μM. W275A mutant showed stronger C2 inhibition than WT even though the C2 binding affinity is weaker than WT. This result indicated that Trp275 is important for the interaction at subsite +1, but also important for making sliding intermediate complex and physically block the rebinding of C2 on the catalytic site for crystalline chitin degradation.
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Affiliation(s)
- Yoshiko Tanaka
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya,Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Aichi, 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka, 422-8529, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi, 444-8787, Japan.
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5
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Kita T, Sasaki K, Niwa S. Modeling the motion of disease-associated KIF1A heterodimers. Biophys J 2023; 122:4348-4359. [PMID: 37853694 PMCID: PMC10698283 DOI: 10.1016/j.bpj.2023.10.014] [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: 06/22/2023] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
KIF1A is a member of the kinesin-3 motor protein family that transports synaptic vesicle precursors in axons. Mutations in the Kif1a gene cause neuronal diseases. Most patients are heterozygous and have both mutated and intact KIF1A alleles, suggesting that heterodimers composed of wild-type KIF1A and mutant KIF1A are likely involved in pathogenesis. In this study, we propose mathematical models to describe the motility of KIF1A heterodimers composed of wild-type KIF1A and mutant KIF1A. Our models precisely describe run length, run time, and velocity of KIF1A heterodimers using a few parameters obtained from two homodimers. The first model is a simple hand-over-hand model in which stepping and detachment rates from a microtubule of each head are identical to those in the respective homodimers. Although the velocities of heterodimers expected from this model were in good agreement with the experimental results, this model underestimated the run lengths and run times of some heterodimeric motors. To address this discrepancy, we propose the tethered-head affinity model, in which we hypothesize a tethered head, in addition to a microtubule-binding head, contributes to microtubule binding in a vulnerable one-head-bound state. The run lengths and run times of the KIF1A heterodimers predicted by the tethered-head affinity model matched well with experimental results, suggesting a possibility that the tethered head affects the microtubule binding of KIF1A. Our models provide insights into how each head contributes to the processive movement of KIF1A and can be used to estimate motile parameters of KIF1A heterodimers.
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Affiliation(s)
- Tomoki Kita
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
| | - Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Shinsuke Niwa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, Miyagi, Japan.
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6
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Heidt A. Powerful microscope captures motor proteins in unprecedented detail. Nature 2023:10.1038/d41586-023-01906-0. [PMID: 37291475 DOI: 10.1038/d41586-023-01906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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7
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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.
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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
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8
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Chang YW, Tony Yang T, Chen MC, Liaw YG, Yin CF, Lin-Yan XQ, Huang TY, Hou JT, Hung YH, Hsu CL, Huang HC, Juan HF. Spatial and temporal dynamics of ATP synthase from mitochondria toward the cell surface. Commun Biol 2023; 6:427. [PMID: 37072500 PMCID: PMC10113393 DOI: 10.1038/s42003-023-04785-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/30/2023] [Indexed: 04/20/2023] Open
Abstract
Ectopic ATP synthase complex (eATP synthase), located on cancer cell surface, has been reported to possess catalytic activity that facilitates the generation of ATP in the extracellular environment to establish a suitable microenvironment and to be a potential target for cancer therapy. However, the mechanism of intracellular ATP synthase complex transport remains unclear. Using a combination of spatial proteomics, interaction proteomics, and transcriptomics analyses, we find ATP synthase complex is first assembled in the mitochondria and subsequently delivered to the cell surface along the microtubule via the interplay of dynamin-related protein 1 (DRP1) and kinesin family member 5B (KIF5B). We further demonstrate that the mitochondrial membrane fuses to the plasma membrane in turn to anchor ATP syntheses on the cell surface using super-resolution imaging and real-time fusion assay in live cells. Our results provide a blueprint of eATP synthase trafficking and contribute to the understanding of the dynamics of tumor progression.
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Grants
- 109-2221-E-010-012-MY3 Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)
- MOST 109-2221-E-010-011-MY3 Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)
- MOST 109-2327-B-006-004 Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)
- MOST 109-2320-B-002-017-MY3 Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)
- MOST 109-2221-E-002-161-MY3 Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)
- NTU-110L8808 Ministry of Education (Ministry of Education, Republic of China (Taiwan))
- NTU-CC-109L104702-2 Ministry of Education (Ministry of Education, Republic of China (Taiwan))
- NTU-110L7103 Ministry of Education (Ministry of Education, Republic of China (Taiwan))
- NTU-111L7107 Ministry of Education (Ministry of Education, Republic of China (Taiwan))
- NTU-CC-112L892102 Ministry of Education (Ministry of Education, Republic of China (Taiwan))
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Affiliation(s)
- Yi-Wen Chang
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - T Tony Yang
- Department of Electrical Engineering, National Taiwan University, Taipei, 106, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
| | - Min-Chun Chen
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Y-Geh Liaw
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Chieh-Fan Yin
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Xiu-Qi Lin-Yan
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Ting-Yu Huang
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Jen-Tzu Hou
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Hsuan Hung
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Chia-Lang Hsu
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.
| | - Hsueh-Fen Juan
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106, Taiwan.
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
- Center for Computational and Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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9
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Wirth JO, Scheiderer L, Engelhardt T, Engelhardt J, Matthias J, Hell SW. MINFLUX dissects the unimpeded walking of kinesin-1. Science 2023; 379:1004-1010. [PMID: 36893244 DOI: 10.1126/science.ade2650] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
We introduce an interferometric MINFLUX microscope that records protein movements with up to 1.7 nanometer per millisecond spatiotemporal precision. Such precision has previously required attaching disproportionately large beads to the protein, but MINFLUX requires the detection of only about 20 photons from an approximately 1-nanometer-sized fluorophore. Therefore, we were able to study the stepping of the motor protein kinesin-1 on microtubules at up to physiological adenosine-5'-triphosphate (ATP) concentrations. We uncovered rotations of the stalk and the heads of load-free kinesin during stepping and showed that ATP is taken up with a single head bound to the microtubule and that ATP hydrolysis occurs when both heads are bound. Our results show that MINFLUX quantifies (sub)millisecond conformational changes of proteins with minimal disturbance.
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Affiliation(s)
- Jan O Wirth
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lukas Scheiderer
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Tobias Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Johann Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jessica Matthias
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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10
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Průša J, Cifra M. Electro-detachment of kinesin motor domain from microtubule in silico. Comput Struct Biotechnol J 2023; 21:1349-1361. [PMID: 36814722 PMCID: PMC9939557 DOI: 10.1016/j.csbj.2023.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Kinesin is a motor protein essential in cellular functions, such as intracellular transport and cell-division, as well as for enabling nanoscopic transport in bio-nanotechnology. Therefore, for effective control of function for nanotechnological applications, it is important to be able to modify the function of kinesin. To circumvent the limitations of chemical modifications, here we identify another potential approach for kinesin control: the use of electric forces. Using full-atom molecular dynamics simulations (247,358 atoms, total time ∼ 4.4 μs), we demonstrate, for the first time, that the kinesin-1 motor domain can be detached from a microtubule by an intense electric field within the nanosecond timescale. We show that this effect is field-direction dependent and field-strength dependent. A detailed analysis of the electric forces and the work carried out by electric field acting on the microtubule-kinesin system shows that it is the combined action of the electric field pulling on the β-tubulin C-terminus and the electric-field-induced torque on the kinesin dipole moment that causes kinesin detachment from the microtubule. It is shown, for the first time in a mechanistic manner, that an electric field can dramatically affect molecular interactions in a heterologous functional protein assembly. Our results contribute to understanding of electromagnetic field-biomatter interactions on a molecular level, with potential biomedical and bio-nanotechnological applications for harnessing control of protein nanomotors.
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11
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Hu X, Dinu CZ. Microtubules and Quantum Dots Integration Leads to Conjugates with Applications in Biosensors and Bionanodevices. Methods Mol Biol 2022; 2430:133-148. [PMID: 35476330 DOI: 10.1007/978-1-0716-1983-4_9] [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: 06/14/2023]
Abstract
This chapter describes compiled methods for the formation and manipulation of microtubule-kinesin-carbon nanodots conjugates in user-defined synthetic environments. Specifically, by using inherited self-assembly and self-recognition properties of tubulin cytoskeletal protein and by interfacing this protein with lab synthesized carbon nanodots, bio-nano hybrid interfaces were formed. Further manipulation of such biohybrids under the mechanical cycle of kinesin 1 ATP-ase molecular motor led to their integration on user-controlled engineered surfaces. Presented methods are foreseen to lead to microtubule-molecular motor-hybrid based assemblies formation with applications ranging from biosensing, to nanoelectronics and single molecule printing, just to name a few.
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Affiliation(s)
- Xiao Hu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources, Morgantown, WV, USA
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cerasela Zoica Dinu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources, Morgantown, WV, USA.
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12
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Skinner DJ, Dunkel J. Estimating Entropy Production from Waiting Time Distributions. PHYSICAL REVIEW LETTERS 2021; 127:198101. [PMID: 34797138 DOI: 10.1103/physrevlett.127.198101] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication, or locomotion. Given time series observations of intra-, inter-, or multicellular processes, a key challenge is to detect nonequilibrium behavior and quantify the rate of free energy consumption. Obtaining reliable bounds on energy consumption and entropy production directly from experimental data remains difficult in practice, as many degrees of freedom typically are hidden to the observer, so that the accessible coarse-grained dynamics may not obviously violate detailed balance. Here, we introduce a novel method for bounding the entropy production of physical and living systems which uses only the waiting time statistics of hidden Markov processes and, hence, can be directly applied to experimental data. By determining a universal limiting curve, we infer entropy production bounds from experimental data for gene regulatory networks, mammalian behavioral dynamics, and numerous other biological processes. Further considering the asymptotic limit of increasingly precise biological timers, we estimate the necessary entropic cost of heartbeat regulation in humans, dogs, and mice.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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13
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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: 13] [Impact Index Per Article: 4.3] [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.
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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
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14
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Meng X, Sonn-Segev A, Schumacher A, Cole D, Young G, Thorpe S, Style RW, Dufresne ER, Kukura P. Micromirror Total Internal Reflection Microscopy for High-Performance Single Particle Tracking at Interfaces. ACS PHOTONICS 2021; 8:3111-3118. [PMID: 34692901 PMCID: PMC8532162 DOI: 10.1021/acsphotonics.1c01268] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 06/01/2023]
Abstract
Single particle tracking has found broad applications in the life and physical sciences, enabling the observation and characterization of nano- and microscopic motion. Fluorescence-based approaches are ideally suited for high-background environments, such as tracking lipids or proteins in or on cells, due to superior background rejection. Scattering-based detection is preferable when localization precision and imaging speed are paramount due to the in principle infinite photon budget. Here, we show that micromirror-based total internal reflection dark field microscopy enables background suppression previously only reported for interferometric scattering microscopy, resulting in nanometer localization precision at 6 μs exposure time for 20 nm gold nanoparticles with a 25 × 25 μm2 field of view. We demonstrate the capabilities of our implementation by characterizing sub-nanometer deterministic flows of 20 nm gold nanoparticles at liquid-liquid interfaces. Our results approach the optimal combination of background suppression, localization precision, and temporal resolution achievable with pure scattering-based imaging and tracking of nanoparticles at interfaces.
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Affiliation(s)
- Xuanhui Meng
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | - Adar Sonn-Segev
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | - Anne Schumacher
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | - Daniel Cole
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | - Gavin Young
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | - Stephen Thorpe
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
| | | | | | - Philipp Kukura
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K.
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15
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Unsupervised selection of optimal single-molecule time series idealization criterion. Biophys J 2021; 120:4472-4483. [PMID: 34487708 PMCID: PMC8553667 DOI: 10.1016/j.bpj.2021.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/22/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger data sets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The divisive segmentation and clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user-selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal/noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OCs based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence data sets, which often have signal/noise near the derived decision boundary and include time series of nonuniform length because of stochastic bleaching. Our approach, AutoDISC, allows unsupervised per-molecule optimization of DISC, which will substantially assist in the rapid analysis of high-throughput SM data sets with noisy samples and nonuniform time windows.
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16
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Priest L, Peters JS, Kukura P. Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins. Chem Rev 2021; 121:11937-11970. [PMID: 34587448 PMCID: PMC8517954 DOI: 10.1021/acs.chemrev.1c00271] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 02/02/2023]
Abstract
Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.
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Affiliation(s)
| | | | - Philipp Kukura
- Physical and Theoretical
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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17
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Bujak Ł, Holanová K, García Marín A, Henrichs V, Barvík I, Braun M, Lánský Z, Piliarik M. Fast Leaps between Millisecond Confinements Govern Ase1 Diffusion along Microtubules. SMALL METHODS 2021; 5:e2100370. [PMID: 34927934 DOI: 10.1002/smtd.202100370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/24/2021] [Indexed: 06/14/2023]
Abstract
Diffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, interferometric scattering microscopy is used to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. Millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments are resolved, revealing Ase1's mode of diffusive translocation along the microtubule's periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. It is anticipated that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, can provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.
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Affiliation(s)
- Łukasz Bujak
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Kristýna Holanová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Antonio García Marín
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Verena Henrichs
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 2026/5, Prague, 12116, Czech Republic
| | - Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Zdeněk Lánský
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
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18
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Abstract
Kinesin-1 is a motor protein that can step processively on microtubule by hydrolyzing ATP molecules, playing an essential role in intracellular transports. To better understand the mechanochemical coupling of the motor stepping cycle, numerous structural, biochemical, single molecule, theoretical modeling and numerical simulation studies have been undertaken for the kinesin-1 motor. Recently, a novel ultraresolution optical trapping method was employed to study the mechanics of the kinesin-1 motor and new results were supplemented to its stepping dynamics. In this commentary, the new single molecule results are explained well theoretically with one of the models presented in the literature for the mechanochemical coupling of the kinesin-1 motor. With the model, various prior experimental results for dynamics of different families of N-terminal kinesin motors have also been explained quantitatively.
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19
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Hasnain S, Mugnai ML, Thirumalai D. Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin. J Phys Chem B 2021; 125:10432-10444. [PMID: 34499499 DOI: 10.1021/acs.jpcb.1c02218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A substantial increase in the temporal resolution of the stepping of dimeric molecular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was employed to measure the stepping trajectories of conventional kinesin (Kin1) using the time-dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head, and (2) the rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.
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Affiliation(s)
- Sabeeha Hasnain
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
| | - Mauro L Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
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20
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Peng AW, Scharr AL, Caprara GA, Nettles D, Steele CR, Ricci AJ. Fluid Jet Stimulation of Auditory Hair Bundles Reveal Spatial Non-uniformities and Two Viscoelastic-Like Mechanisms. Front Cell Dev Biol 2021; 9:725101. [PMID: 34513845 PMCID: PMC8427531 DOI: 10.3389/fcell.2021.725101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
Hair cell mechanosensitivity resides in the sensory hair bundle, an apical protrusion of actin-filled stereocilia arranged in a staircase pattern. Hair bundle deflection activates mechano-electric transduction (MET) ion channels located near the tops of the shorter rows of stereocilia. The elicited macroscopic current is shaped by the hair bundle motion so that the mode of stimulation greatly influences the cell’s output. We present data quantifying the displacement of the whole outer hair cell bundle using high-speed imaging when stimulated with a fluid jet. We find a spatially non-uniform stimulation that results in splaying, where the hair bundle expands apart. Based on modeling, the splaying is predominantly due to fluid dynamics with a small contribution from hair bundle architecture. Additionally, in response to stimulation, the hair bundle exhibited a rapid motion followed by a slower motion in the same direction (creep) that is described by a double exponential process. The creep is consistent with originating from a linear passive system that can be modeled using two viscoelastic processes. These viscoelastic mechanisms are integral to describing the mechanics of the mammalian hair bundle.
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Affiliation(s)
- Anthony W Peng
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Alexandra L Scharr
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States.,Neuroscience Graduate Program, School of Medicine, Stanford University, Stanford, CA, United States
| | - Giusy A Caprara
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Dailey Nettles
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles R Steele
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States.,Department of Mechanical Engineering and Aeronautics and Astronautics, School of Engineering, Stanford University, Stanford, CA, United States
| | - Anthony J Ricci
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States.,Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA, United States
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21
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Goldtzvik Y, Thirumalai D. Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. J Chem Theory Comput 2021; 17:5358-5368. [PMID: 34251798 DOI: 10.1021/acs.jctc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conventional kinesin, a motor protein that transports cargo within cells, walks by taking multiple steps toward the plus end of the microtubule (MT). While significant progress has been made in understanding the details of the walking mechanism of kinesin, there are many unresolved issues. From a computational perspective, a central challenge is the large size of the system, which limits the scope of time scales accessible in standard computer simulations. Here, we create a general multiscale coarse-grained model for motors that enables us to simulate the stepping process of motors on polar tracks (actin and MT) with a focus on kinesin. Our approach greatly shortens the computation times without a significant loss in detail, thus allowing us to better describe the molecular basis of the stepping kinetics. The small number of parameters, which are determined by fitting to experimental data, allows us to develop an accurate method that may be adopted to simulate stepping in other molecular motors. The model enables us to simulate a large number of steps, which was not possible previously. We show in agreement with experiments that due to the docking of the neck linker (NL) of kinesin, sometimes deemed as the power stroke, the space explored diffusively by the tethered head is severely restricted, allowing the step to be completed in tens of microseconds. We predict that increasing the interaction strength between the NL and the motor head, achievable by mutations in the NL, decreases the stepping time but reaches a saturation value. Furthermore, the full three-dimensional dynamics of the cargo are fully resolved in our model, contributing to the predictive power and allowing us to study the important aspects of cargo-motor interactions.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
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22
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Loeff L, Kerssemakers JWJ, Joo C, Dekker C. AutoStepfinder: A fast and automated step detection method for single-molecule analysis. PATTERNS 2021; 2:100256. [PMID: 34036291 PMCID: PMC8134948 DOI: 10.1016/j.patter.2021.100256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 01/05/2023]
Abstract
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour. Fast, automated, and bias-free detection of steps within single-molecule trajectories Robust step detection without any prior knowledge on the data A dual-pass strategy for the detection of steps over a wide variety of scales A user-friendly interface for a simplified step fitting procedure
Single-molecule techniques have made it possible to track individual protein complexes in real time with a nanometer spatial resolution and a millisecond timescale. Accurate determination of the dynamic states within single-molecule time traces provides valuable kinetic information that underlie the function of biological macromolecules. Here, we present a new automated step detection method called AutoStepfinder, a versatile, robust, and easy-to-use algorithm that allows researchers to determine the kinetic states within single-molecule time trajectories without any bias.
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Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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23
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Vala M, Bujak Ł, García Marín A, Holanová K, Henrichs V, Braun M, Lánský Z, Piliarik M. Nanoscopic Structural Fluctuations of Disassembling Microtubules Revealed by Label-Free Super-Resolution Microscopy. SMALL METHODS 2021; 5:e2000985. [PMID: 34927839 DOI: 10.1002/smtd.202000985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/22/2020] [Indexed: 06/14/2023]
Abstract
Microtubules are cytoskeletal polymers of tubulin dimers assembled into protofilaments that constitute nanotubes undergoing periods of assembly and disassembly. Static electron micrographs suggest a structural transition of straight protofilaments into curved ones occurring at the tips of disassembling microtubules. However, these structural transitions have never been observed and the process of microtubule disassembly thus remains unclear. Here, label-free optical microscopy capable of selective imaging of the transient structural changes of protofilaments at the tip of a disassembling microtubule is introduced. Upon induced disassembly, the transition of ordered protofilaments into a disordered conformation is resolved at the tip of the microtubule. Imaging the unbinding of individual tubulin oligomers from the microtubule tip reveals transient pauses and relapses in the disassembly, concurrent with increased organization of protofilament segments at the microtubule tip. These findings show that microtubule disassembly is a discrete process and suggest a stochastic mechanism of switching from the disassembly to the assembly phase.
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Affiliation(s)
- Milan Vala
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Łukasz Bujak
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Antonio García Marín
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Kristýna Holanová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Verena Henrichs
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Zdeněk Lánský
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
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24
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Banerjee S, Chakraborty S, Sreepada A, Banerji D, Goyal S, Khurana Y, Haldar S. Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry. Annu Rev Biophys 2021; 50:419-445. [PMID: 33646813 DOI: 10.1146/annurev-biophys-090420-083836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
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Affiliation(s)
- Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Abhijit Sreepada
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Devshuvam Banerji
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shashwat Goyal
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Yajushi Khurana
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
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25
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Varela PF, Chenon M, Velours C, Verhey KJ, Ménétrey J, Gigant B. Structural snapshots of the kinesin-2 OSM-3 along its nucleotide cycle: implications for the ATP hydrolysis mechanism. FEBS Open Bio 2021; 11:564-577. [PMID: 33513284 PMCID: PMC7931232 DOI: 10.1002/2211-5463.13101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 11/09/2022] Open
Abstract
Motile kinesins are motor proteins that translocate along microtubules as they hydrolyze ATP. They share a conserved motor domain which harbors both ATPase and microtubule-binding activities. An ATP hydrolysis mechanism involving two water molecules has been proposed based on the structure of the kinesin-5 Eg5 bound to an ATP analog. Whether this mechanism is general in the kinesin superfamily remains uncertain. Here, we present structural snapshots of the motor domain of OSM-3 along its nucleotide cycle. OSM-3 belongs to the homodimeric kinesin-2 subfamily and is the Caenorhabditis elegans homologue of human KIF17. OSM-3 bound to ADP or devoid of a nucleotide shows features of ADP-kinesins with a docked neck linker. When bound to an ATP analog, OSM-3 adopts a conformation similar to those of several ATP-like kinesins, either isolated or bound to tubulin. Moreover, the OSM-3 nucleotide-binding site is virtually identical to that of ATP-like Eg5, demonstrating a shared ATPase mechanism. Therefore, our data extend to kinesin-2 the two-water ATP hydrolysis mechanism and further suggest that it is universal within the kinesin superfamily. PROTEIN DATABASE ENTRIES: 7A3Z, 7A40, 7A5E.
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Affiliation(s)
- Paloma F Varela
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Mélanie Chenon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Julie Ménétrey
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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26
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Sudhakar S, Abdosamadi MK, Jachowski TJ, Bugiel M, Jannasch A, Schäffer E. Germanium nanospheres for ultraresolution picotensiometry of kinesin motors. Science 2021; 371:371/6530/eabd9944. [PMID: 33574186 DOI: 10.1126/science.abd9944] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
Kinesin motors are essential for the transport of cellular cargo along microtubules. How the motors step, detach, and cooperate with each other is still unclear. To dissect the molecular motion of kinesin-1, we developed germanium nanospheres as ultraresolution optical trapping probes. We found that single motors took 4-nanometer center-of-mass steps. Furthermore, kinesin-1 never detached from microtubules under hindering load conditions. Instead, it slipped on microtubules in microsecond-long, 8-nanometer steps and remained in this slip state before detaching or reengaging in directed motion. Unexpectedly, reengagement and thus rescue of directed motion was more frequent. Our observations broaden our knowledge on the mechanochemical cycle and slip state of kinesin. This state and rescue need to be accounted for to understand long-range transport by teams of motors.
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Affiliation(s)
- Swathi Sudhakar
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Mohammad Kazem Abdosamadi
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Tobias Jörg Jachowski
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Michael Bugiel
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Anita Jannasch
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Erik Schäffer
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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27
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Zaniewski TM, Gicking AM, Fricks J, Hancock WO. A kinetic dissection of the fast and superprocessive kinesin-3 KIF1A reveals a predominant one-head-bound state during its chemomechanical cycle. J Biol Chem 2020; 295:17889-17903. [PMID: 33082143 PMCID: PMC7939386 DOI: 10.1074/jbc.ra120.014961] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The kinesin-3 family contains the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle and give rise to their unique properties are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to WT KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and -2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate-limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate-limiting transition in the KIF1A stepping cycle. Thus, KIF1A's activity can be explained by a fast rear-head detachment rate, a rate-limiting step of tethered-head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly bound post-hydrolysis state.
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Affiliation(s)
- Taylor M Zaniewski
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Allison M Gicking
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona, USA
| | - William O Hancock
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA.
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28
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Harashima T, Hasegawa Y, Kaneko S, Jono Y, Fujii S, Kiguchi M, Nishino T. Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance. Chem Sci 2020; 12:2217-2224. [PMID: 34163987 PMCID: PMC8179252 DOI: 10.1039/d0sc04449k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses. Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.![]()
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Affiliation(s)
- Takanori Harashima
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Yusuke Hasegawa
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Satoshi Kaneko
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Yuki Jono
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Shintaro Fujii
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Manabu Kiguchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
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29
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Toleikis A, Carter NJ, Cross RA. Backstepping Mechanism of Kinesin-1. Biophys J 2020; 119:1984-1994. [PMID: 33091340 PMCID: PMC7732724 DOI: 10.1016/j.bpj.2020.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023] Open
Abstract
Kinesin-1 is an ATP-driven molecular motor that transports cellular cargo along microtubules. At low loads, kinesin-1 almost always steps forward, toward microtubule plus ends, but at higher loads, it can also step backward. Backsteps are usually 8 nm but can be larger. These larger backward events of 16 nm, 24 nm, or more are thought to be slips rather than steps because they are too fast to consist of multiple, tightly coupled 8-nm steps. Here, we propose that not only these larger backsteps, but all kinesin-1 backsteps, are slips. We show first that kinesin waits before forward steps for less time than before backsteps and detachments; second, we show that kinesin waits for the same amount of time before backsteps and detachments; and third, we show that by varying the microtubule type, we can change the ratio of backsteps to detachments without affecting forward stepping. Our findings indicate that backsteps and detachments originate from the same state and that this state arises later in the mechanochemical cycle than the state that gives rise to forward steps. To explain our data, we propose that, in each cycle of ATP turnover, forward kinesin steps can only occur before Pi release, whereas backslips and detachments can only occur after Pi release. In the scheme we propose, Pi release gates access to a weak binding K⋅ADP-K⋅ADP state that can slip back along the microtubule, re-engage, release ADP, and try again to take an ATP-driven forward step. We predict that this rescued detachment pathway is key to maintaining kinesin processivity under load.
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Affiliation(s)
- Algirdas Toleikis
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Nicholas J Carter
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom.
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30
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Wedler V, Strauß F, Sudhakar S, Hermsdorf GL, Stierhof YD, Schäffer E. Polycationic gold nanorods as multipurpose in vitro microtubule markers. NANOSCALE ADVANCES 2020; 2:4003-4010. [PMID: 36132798 PMCID: PMC9417852 DOI: 10.1039/d0na00406e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/12/2020] [Indexed: 06/16/2023]
Abstract
Gold nanoparticles are intriguing because of their unique size- and shape-dependent chemical, electronic and optical properties. Gold nanorods (AuNRs) are particularly promising for various sensor applications due to their tip-enhanced plasmonic fields. For biomolecule attachment, AuNRs are often functionalized with proteins. However, by their intrinsic size such molecules block the most sensitive near-field region of the AuNRs. Here, we used short cationic thiols to functionalize AuNRs. We show that the functionalization layer is thin and that these polycationic AuNRs bind in vitro to negatively charged microtubules. Furthermore, we can plasmonically stimulate light emission from single AuNRs in the absence of any fluorophores and, therefore, use them as bleach- and blinkfree microtubule markers. We expect that polycationic AuNRs may be applicable to in vivo systems and other negatively charged molecules like DNA. In the long-term, microtubule-bound AuNRs can be used as ultrasensitive single-molecule sensors for molecular machines that interact with microtubules.
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Affiliation(s)
- Viktoria Wedler
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
| | - Fabian Strauß
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
| | - Swathi Sudhakar
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
| | - Gero Lutz Hermsdorf
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
| | - York-Dieter Stierhof
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
| | - Erik Schäffer
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP) Auf der Morgenstelle 32 72076 Tübingen Germany +49 7071 295042 +49 7071 2978831
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31
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Guo SK, Xie P. A common chemomechanical coupling model for orphan and conventional kinesin molecular motors. Biophys Chem 2020; 264:106427. [PMID: 32682233 DOI: 10.1016/j.bpc.2020.106427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/07/2020] [Accepted: 07/01/2020] [Indexed: 01/12/2023]
Abstract
Orphan and conventional kinesin dimers represent two families of the kinesin superfamily molecular motors. Conventional kinesin, having a 14-residue neck linker (NL) in each head, can step processively on microtubule (MT), with an ATP hydrolysis being coupled with a mechanical stepping under no load. Orphan kinesin phragmoplast-associated kinesin-related protein 2 (PAKRP2) dimer, despite having a NL of 32 residues in each head, can also step processively on MT and exhibits tight chemomechanical coupling under no load. However, the dynamic properties of the wild type PAKRP2 and the mutant one with each NL truncated to 14 residues are very different from those of the wild type conventional kinesin and the mutant one with each NL being replaced by the 32-residue NL from PAKRP2. Here, based on a common chemomechanical coupling model we study computationally the dynamics of the two families of the kinesin dimers, with the simulated results explaining quantitatively the available experimental data. The large differences in the dynamics between the two families of kinesin dimers arise mainly from different rate constants of NL docking and ATPase activity and different weak affinities of the head in ADP state for MT. The studies indicate that both the orphan kinesin PAKRP2 and conventional kinesin use the same mechanism for processive motility.
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Affiliation(s)
- Si-Kao Guo
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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32
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Okazaki KI, Nakamura A, Iino R. Chemical-State-Dependent Free Energy Profile from Single-Molecule Trajectories of Biomolecular Motors: Application to Processive Chitinase. J Phys Chem B 2020; 124:6475-6487. [DOI: 10.1021/acs.jpcb.0c02698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kei-ichi Okazaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Akihiko Nakamura
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Ryota Iino
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
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33
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Nakamura A, Okazaki KI, Furuta T, Sakurai M, Ando J, Iino R. Crystalline chitin hydrolase is a burnt-bridge Brownian motor. Biophys Physicobiol 2020; 17:51-58. [PMID: 33173714 PMCID: PMC7593131 DOI: 10.2142/biophysico.bsj-2020004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/27/2020] [Indexed: 12/01/2022] Open
Abstract
Motor proteins are essential units of life and are well-designed nanomachines working under thermal fluctuations. These proteins control moving direction by consuming chemical energy or by dissipating electrochemical potentials. Chitinase A from bacterium Serratia marcescens (SmChiA) processively moves along crystalline chitin by hydrolysis of a single polymer chain to soluble chitobiose. Recently, we directly observed the stepping motions of SmChiA labeled with a gold nanoparticle by dark-field scattering imaging to investigate the moving mechanism. Time constants analysis revealed that SmChiA moves back and forth along the chain freely, because forward and backward states have a similar free energy level. The similar probabilities of forward-step events (83.5%=69.3%+14.2%) from distributions of step sizes and chain-hydrolysis (86.3%=(1/2.9)/(1/2.9+1/18.3)×100) calculated from the ratios of time constants of hydrolysis and the backward step indicated that SmChiA moves forward as a result of shortening of the chain by a chitobiose unit, which stabilizes the backward state. Furthermore, X-ray crystal structures of sliding intermediate and molecular dynamics simulations showed that SmChiA slides forward and backward under thermal fluctuation without large conformational changes of the protein. Our results demonstrate that SmChiA is a burnt-bridge Brownian ratchet motor.
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Affiliation(s)
| | | | - Tadaomi Furuta
- Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Minoru Sakurai
- Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Jun Ando
- RIKEN, Wako, Saitama 351-0198, Japan
| | - Ryota Iino
- Institute for Molecular Science, Okazaki, Aichi 444-8787, Japan.,SOKENDAI, Hayama, Kanagawa 240-0193, Japan
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34
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Peng T, Li X, Li K, Nie Z, Tan W. DNA-Modulated Plasmon Resonance: Methods and Optical Applications. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14741-14760. [PMID: 32154704 DOI: 10.1021/acsami.9b23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.
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Affiliation(s)
- Tianhuan Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
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35
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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.
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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
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36
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Ando J, Shima T, Kanazawa R, Shimo-Kon R, Nakamura A, Yamamoto M, Kon T, Iino R. Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking. Sci Rep 2020; 10:1080. [PMID: 31974448 PMCID: PMC6978368 DOI: 10.1038/s41598-020-58070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic dynein is a dimeric motor protein which processively moves along microtubule. Its motor domain (head) hydrolyzes ATP and induces conformational changes of linker, stalk, and microtubule binding domain (MTBD) to trigger stepping motion. Here we applied scattering imaging of gold nanoparticle (AuNP) to visualize load-free stepping motion of processive dynein. We observed artificially-dimerized chimeric dynein, which has the head, linker, and stalk from Dictyostelium discoideum cytoplasmic dynein and the MTBD from human axonemal dynein, whose structure has been well-studied by cryo-electron microscopy. One head of a dimer was labeled with 30 nm AuNP, and stepping motions were observed with 100 μs time resolution and sub-nanometer localization precision at physiologically-relevant 1 mM ATP. We found 8 nm forward and backward steps and 5 nm side steps, consistent with on- and off-axes pitches of binding cleft between αβ-tubulin dimers on the microtubule. Probability of the forward step was 1.8 times higher than that of the backward step, and similar to those of the side steps. One-head bound states were not clearly observed, and the steps were limited by a single rate constant. Our results indicate dynein mainly moves with biased small stepping motion in which only backward steps are slightly suppressed.
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Affiliation(s)
- Jun Ando
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, 113-0033, Tokyo, Japan
| | - Riko Kanazawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Rieko Shimo-Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan
| | - Mayuko Yamamoto
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan. .,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan.
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37
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Blackwell R, Jung D, Bukenberger M, Smith AS. The Impact of Rate Formulations on Stochastic Molecular Motor Dynamics. Sci Rep 2019; 9:18373. [PMID: 31804523 PMCID: PMC6895049 DOI: 10.1038/s41598-019-54344-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/08/2019] [Indexed: 12/19/2022] Open
Abstract
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary to organize large structures on the short timescales necessary for biological function. The main mechanism of this transport is by cargo attachment to motors which walk in a directed fashion along intracellular filaments. There are a number of models which seek to describe the motion of motors with attached cargo, from detailed microscopic to coarse phenomenological descriptions. We focus on the intermediate-detailed discrete stochastic hopping models, and explore how cargo transport changes depending on the number of motors, motor interaction, system constraints and rate formulations, which are derived from common thermodynamic assumptions. We find that, despite obeying the same detailed balance constraint, the choice of rate formulation considerably affects the characteristics of the overall motion of the system, with one rate formulation exhibiting novel behavior of loaded motor groups moving faster than a single unloaded motor.
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Affiliation(s)
- R Blackwell
- PULS group, Physics Department and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander University Erlangen-Nürnberg, Cauerstrasse 3, 91058, Erlangen, Germany
| | - D Jung
- PULS group, Physics Department and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander University Erlangen-Nürnberg, Cauerstrasse 3, 91058, Erlangen, Germany
| | - M Bukenberger
- PULS group, Physics Department and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander University Erlangen-Nürnberg, Cauerstrasse 3, 91058, Erlangen, Germany
| | - A-S Smith
- PULS group, Physics Department and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander University Erlangen-Nürnberg, Cauerstrasse 3, 91058, Erlangen, Germany. .,Group for Computational Life Sciences, Division of Physical Chemistry, Insitut Rūder Bošković, Bijenička cesta 54, 10000, Zagreb, Croatia.
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38
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How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics. Proc Natl Acad Sci U S A 2019; 116:23091-23099. [PMID: 31659052 DOI: 10.1073/pnas.1913650116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Conventional kinesin, responsible for directional transport of cellular vesicles, takes multiple nearly uniform 8.2-nm steps by consuming one ATP molecule per step as it walks toward the plus end of the microtubule (MT). Despite decades of intensive experimental and theoretical studies, there are gaps in the elucidation of key steps in the catalytic cycle of kinesin. How the motor waits for ATP to bind to the leading head is controversial. Two experiments using a similar protocol have arrived at different conclusions. One asserts that kinesin waits for ATP in a state with both the heads bound to the MT, whereas the other shows that ATP binds to the leading head after the trailing head detaches. To discriminate between the 2 scenarios, we developed a minimal model, which analytically predicts the outcomes of a number of experimental observable quantities (the distribution of run length, the distribution of velocity [[Formula: see text]], and the randomness parameter) as a function of an external resistive force (F) and ATP concentration ([T]). The differences in the predicted bimodality in [Formula: see text] as a function of F between the 2 models may be amenable to experimental testing. Most importantly, we predict that the F and [T] dependence of the randomness parameters differ qualitatively depending on the waiting states. The randomness parameters as a function of F and [T] can be quantitatively measured from stepping trajectories with very little prejudice in data analysis. Therefore, an accurate measurement of the randomness parameter and the velocity distribution as a function of load and nucleotide concentration could resolve the apparent controversy.
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39
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Shi XX, Guo SK, Wang PY, Chen H, Xie P. All-atom molecular dynamics simulations reveal how kinesin transits from one-head-bound to two-heads-bound state. Proteins 2019; 88:545-557. [PMID: 31589786 DOI: 10.1002/prot.25833] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/19/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022]
Abstract
Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand-over-hand manner, transiting alternately between one-head-bound (1HB) and two-heads-bound (2HB) states. In 1HB state, one head bound by adenosine diphosphate (ADP) is detached from MT and the other head is bound to MT. Here, using all-atom molecular dynamics simulations we determined the position and orientation of the detached ADP-head relative to the MT-bound head in 1HB state. We showed that in 1HB state when the MT-bound head is in ADP or nucleotide-free state, with its neck linker being undocked, the detached ADP-head and the MT-bound head have the high binding energy, and after adenosine triphosphate (ATP) binds to the MT-bound head, with its neck linker being docked, the binding energy between the two heads is reduced greatly. These results reveal how the kinesin dimer retains 1HB state before ATP binding and how the dimer transits from 1HB to 2HB state after ATP binding. Key residues involved in the head-head interaction in 1HB state were identified.
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Affiliation(s)
- Xiao-Xuan Shi
- School of Material Science and Engineering, Central South University of Forestry and Technology, Changsha, China.,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Si-Kao Guo
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
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40
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Li C, Chen M, Lyzwa D, Cappellaro P. All-Optical Quantum Sensing of Rotational Brownian Motion of Magnetic Molecules. NANO LETTERS 2019; 19:7342-7348. [PMID: 31549847 DOI: 10.1021/acs.nanolett.9b02960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Sensing the local environment through the motional response of small molecules lays the foundation of many fundamental technologies. The information on local viscosity, for example, is contained in the random rotational Brownian motions of molecules. However, detection of the motions is challenging for molecules with sub-nanometer scale or high motional rates. Here we propose and experimentally demonstrate a novel method of detecting fast rotational Brownian motions of small magnetic molecules. With electronic spins as sensors, we are able to detect changes in motional rates, which yield different noise spectra and therefore different relaxation signals of the sensors. As a proof-of-principle demonstration, we experimentally implemented this method to detect the motions of gadolinium (Gd) complex molecules with nitrogen-vacancy (NV) centers in nanodiamonds. With all-optical measurements of the NV centers' longitudinal relaxation, we distinguished binary solutions with varying viscosities. Our method paves a new way for detecting fast motions of sub-nanometer sized magnetic molecules with better spatial resolution than conventional optical methods. It also provides a new tool in designing better contrast agents in magnetic resonance imaging.
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Affiliation(s)
- Changhao Li
- Research Laboratory of Electronics , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Nuclear Science and Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Mo Chen
- Research Laboratory of Electronics , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Mechanical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Dominika Lyzwa
- Research Laboratory of Electronics , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Paola Cappellaro
- Research Laboratory of Electronics , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Nuclear Science and Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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41
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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc Natl Acad Sci U S A 2019; 116:19777-19785. [PMID: 31506355 DOI: 10.1073/pnas.1818589116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5'-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F1-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.
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42
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Sharifi M, Attar F, Saboury AA, Akhtari K, Hooshmand N, Hasan A, El-Sayed MA, Falahati M. Plasmonic gold nanoparticles: Optical manipulation, imaging, drug delivery and therapy. J Control Release 2019; 311-312:170-189. [PMID: 31472191 DOI: 10.1016/j.jconrel.2019.08.032] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
Over the past two decades, the development of plasmonic nanoparticle (NPs), especially gold (Au) NPs, is being pursued more seriously in the medical fields such as imaging, drug delivery, and theranostic systems. However, there is no comprehensive review on the effect of the physical and chemical parameters of AuNPs on their plasmonic properties as well as the use of these unique characteristic in medical activities such as imaging and therapeutics. Therefore, in this literature the surface plasmon resonance (SPR) modeling of AuNPs was accurately captured toward precision medicine. Indeed, we investigated the importance of plasmonic properties of AuNPs in optical manipulation, imaging, drug delivery, and photothermal therapy (PTT) of cancerous cells based on their physicochemical properties. Finally, some challenges regarding the commercialization of AuNPs in future medicine such as, cytotoxicity, lack of standards for medical applications, high cost, and time-consuming process were discussed.
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Affiliation(s)
- Majid Sharifi
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute, Karaj, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Keivan Akhtari
- Department of Physics, University of Kurdistan, Sanandaj, Iran
| | - Nasrin Hooshmand
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Mostafa A El-Sayed
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States.
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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43
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Abstract
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.
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Affiliation(s)
- Aidan I Brown
- Department of Physics , University of California, San Diego , La Jolla , California 92093 , United States
| | - David A Sivak
- Department of Physics , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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44
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Brown AI, Sivak DA. Pulling cargo increases the precision of molecular motor progress. ACTA ACUST UNITED AC 2019. [DOI: 10.1209/0295-5075/126/40004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Mickolajczyk KJ, Cook ASI, Jevtha JP, Fricks J, Hancock WO. Insights into Kinesin-1 Stepping from Simulations and Tracking of Gold Nanoparticle-Labeled Motors. Biophys J 2019; 117:331-345. [PMID: 31301807 DOI: 10.1016/j.bpj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 02/02/2023] Open
Abstract
High-resolution tracking of gold nanoparticle-labeled proteins has emerged as a powerful technique for measuring the structural kinetics of processive enzymes and other biomacromolecules. These techniques use point spread function (PSF) fitting methods borrowed from single-molecule fluorescence imaging to determine molecular positions below the diffraction limit. However, compared to fluorescence, gold nanoparticle tracking experiments are performed at significantly higher frame rates and utilize much larger probes. In the current work, we use Brownian dynamics simulations of nanoparticle-labeled proteins to investigate the regimes in which the fundamental assumptions of PSF fitting hold and where they begin to break down. We find that because gold nanoparticles undergo tethered diffusion around their anchor point, PSF fitting cannot be extended to arbitrarily fast frame rates. Instead, camera exposure times that allow the nanoparticle to fully populate its stationary positional distribution achieve a spatial averaging that increases fitting precision. We furthermore find that changes in the rotational freedom of the tagged protein can lead to artifactual translations in the fitted particle position. Finally, we apply these lessons to dissect a standing controversy in the kinesin field over the structure of a dimer in the ATP waiting state. Combining new experiments with simulations, we determine that the rear kinesin head in the ATP waiting state is unbound but not displaced from its previous microtubule binding site and that apparent differences in separately published reports were simply due to differences in the gold nanoparticle attachment position. Our results highlight the importance of gold conjugation decisions and imaging parameters to high-resolution tracking results and will serve as a useful guide for the design of future gold nanoparticle tracking experiments.
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Affiliation(s)
- Keith J Mickolajczyk
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering
| | - Annan S I Cook
- Department of Biomedical Engineering; Department of Physics, Pennsylvania State University, University Park, Pennsylvania
| | | | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - William O Hancock
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering.
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46
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Shin K, Song S, Song YH, Hahn S, Kim JH, Lee G, Jeong IC, Sung J, Lee KT. Anomalous Dynamics of in Vivo Cargo Delivery by Motor Protein Multiplexes. J Phys Chem Lett 2019; 10:3071-3079. [PMID: 31117686 DOI: 10.1021/acs.jpclett.9b01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vesicle transport conducted by motor protein multiplexes (MPMs), which is ubiquitous among eukaryotes, shows anomalous and stochastic dynamics qualitatively different from the dynamics of thermal motion and artificial active matter; the relationship between in vivo vesicle-delivery dynamics and the underlying physicochemical processes is not yet quantitatively understood. Addressing this issue, we perform accurate tracking of individual vesicles, containing upconverting nanoparticles, transported by kinesin-dynein-multiplexes along axonal microtubules. The mean-square-displacement of vesicles along the microtubule exhibits unusual dynamic phase transitions that are seemingly inconsistent with the scaling behavior of the mean-first-passage time over the travel length. These paradoxical results and the vesicle displacement distribution are quantitatively explained and predicted by a multimode MPM model, developed in the current work, where ATP-hydrolysis-coupled motion of MPM has both unidirectional and bidirectional modes.
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Affiliation(s)
- Kyujin Shin
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - Sanggeun Song
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Yo Han Song
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - Seungsoo Hahn
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Da Vinci College of General Education , Chung-Ang University , Seoul 06974 , Korea
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
| | - Gibok Lee
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - In-Chun Jeong
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Kang Taek Lee
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
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47
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Zarrin A, Sivak DA, Brown AI. Breaking time-reversal symmetry for ratchet models of molecular machines. Phys Rev E 2019; 99:062127. [PMID: 31330673 DOI: 10.1103/physreve.99.062127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 06/10/2023]
Abstract
Biomolecular machines transduce free energy from one form to another to fulfill many important roles inside cells, with dissipation required to achieve directed progress. We investigate how to break time-reversal symmetry at a given dissipation cost by using deterministic protocols to drive systems over sawtooth potentials, which have frequently been used to model molecular machines as ratchets. Time asymmetry increases for sawtooth potentials with higher barriers and for driving potentials of intermediate width. For systems driven over a sawtooth potential according to a protocol, we find that symmetric sawtooths maximize time asymmetry, whereas earlier work examining ratchet models of molecular machines required asymmetric sawtooth potentials to achieve directed behavior. This distinction arises because deterministically driven machines are externally provided with direction, whereas autonomous machines must generate directed behavior.
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Affiliation(s)
- Arshia Zarrin
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Aidan I Brown
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
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48
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Affiliation(s)
- Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
| | - Daifei Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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49
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Budaitis BG, Jariwala S, Reinemann DN, Schimert KI, Scarabelli G, Grant BJ, Sept D, Lang MJ, Verhey KJ. Neck linker docking is critical for Kinesin-1 force generation in cells but at a cost to motor speed and processivity. eLife 2019; 8:44146. [PMID: 31084716 PMCID: PMC6533058 DOI: 10.7554/elife.44146] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are unclear. Furthermore, the necessity of NL docking for transport of membrane-bound cargo in cells has not been tested. We generated kinesin-1 motors impaired in CNB and/or N-latch formation based on molecular dynamics simulations. The mutant motors displayed reduced force output and inability to stall in optical trap assays but exhibited increased speeds, run lengths, and landing rates under unloaded conditions. NL docking thus enhances force production but at a cost to speed and processivity. In cells, teams of mutant motors were hindered in their ability to drive transport of Golgi elements (high-load cargo) but not peroxisomes (low-load cargo). These results demonstrate that the NL serves as a mechanical element for kinesin-1 transport under physiological conditions.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States
| | | | - Guido Scarabelli
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Barry J Grant
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - David Sept
- Biophysics Program, University of Michigan, Ann Arbor, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, United States
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States.,Biophysics Program, University of Michigan, Ann Arbor, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
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50
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Abstract
Interferometric scattering microscopy (iSCAT) is an extremely sensitive imaging method based on the efficient detection of light scattered by nanoscopic objects. The ability to, at least in principle, maintain high imaging contrast independent of the exposure time or the scattering cross section of the object allows for unique applications in single-particle tracking, label-free imaging of nanoscopic (dis)assembly, and quantitative single-molecule characterization. We illustrate these capabilities in areas as diverse as mechanistic studies of motor protein function, viral capsid assembly, and single-molecule mass measurement in solution. We anticipate that iSCAT will become a widely used approach to unravel previously hidden details of biomolecular dynamics and interactions.
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Affiliation(s)
- Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom; ,
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom; ,
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