1
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Unger BA, Wu CY, Choi AA, He C, Xu K. Hypersensitivity of the vimentin cytoskeleton to net-charge states and Coulomb repulsion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602555. [PMID: 39026705 PMCID: PMC11257561 DOI: 10.1101/2024.07.08.602555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
As with most intermediate filament systems, the hierarchical self-assembly of vimentin into nonpolar filaments requires no nucleators or energy input. Utilizing a set of live-cell, single-molecule, and super-resolution microscopy tools, here we show that in mammalian cells, the assembly and disassembly of the vimentin cytoskeleton is highly sensitive to the protein net charge state. Starting with the intriguing observation that the vimentin cytoskeleton fully disassembles under hypotonic stress yet reassembles within seconds upon osmotic pressure recovery, we pinpoint ionic strength as its underlying driving factor. Further modulating the pH and expressing differently charged constructs, we converge on a model in which the vimentin cytoskeleton is destabilized by Coulomb repulsion when its mass-accumulated negative charges (-18 per vimentin protein) along the filament are less screened or otherwise intensified, and stabilized when the charges are better screened or otherwise reduced. Generalizing this model to other intermediate filaments, we further show that whereas the negatively charged GFAP cytoskeleton is similarly subject to fast disassembly under hypotonic stress, the cytokeratin, as a copolymer of negatively and positively charged subunits, does not exhibit this behavior. Thus, in cells containing both vimentin and keratin cytoskeletons, hypotonic stress disassembles the former but not the latter. Together, our results both provide new handles for modulating cell behavior and call for new attention to the effects of net charges in intracellular protein interactions.
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Affiliation(s)
- Bret A. Unger
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Alexander A. Choi
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Changdong He
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Corresponding author: (K.X.)
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2
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Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
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Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
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3
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Choi AA, Xu K. Single-Molecule Diffusivity Quantification Unveils Ubiquitous Net Charge-Driven Protein-Protein Interaction. J Am Chem Soc 2024; 146:10973-10978. [PMID: 38576203 PMCID: PMC11023747 DOI: 10.1021/jacs.4c02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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4
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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5
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Liu Y, Shahid MA, Mao H, Chen J, Waddington M, Song KH, Zhang Y. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:403-413. [PMID: 37655169 PMCID: PMC10466381 DOI: 10.1021/cbmi.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
Multidimensional single-molecule localization microscopy (mSMLM) represents a paradigm shift in the realm of super-resolution microscopy techniques. It affords the simultaneous detection of single-molecule spatial locations at the nanoscale and functional information by interrogating the emission properties of switchable fluorophores. The latter is finely tuned to report its local environment through carefully manipulated laser illumination and single-molecule detection strategies. This Perspective highlights recent strides in mSMLM with a focus on fluorophore designs and their integration into mSMLM imaging systems. Particular interests are the accomplishments in simultaneous multiplexed super-resolution imaging, nanoscale polarity and hydrophobicity mapping, and single-molecule orientational imaging. Challenges and prospects in mSMLM are also discussed, which include the development of more vibrant and functional fluorescent probes, the optimization of optical implementation to judiciously utilize the photon budget, and the advancement of imaging analysis and machine learning techniques.
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Affiliation(s)
- Yunshu Liu
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Md Abul Shahid
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Hongjing Mao
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Jiahui Chen
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Michael Waddington
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Ki-Hee Song
- Quantum
Optics Research Division, Korea Atomic Energy
Research Institute, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
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6
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He C, Wu CY, Li W, Xu K. Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548239. [PMID: 37503034 PMCID: PMC10369965 DOI: 10.1101/2023.07.12.548239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.
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7
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Zhang Z, Chen H, Hu M, Wang D. Single-Molecule Tracking of Reagent Diffusion during Chemical Reactions. J Am Chem Soc 2023; 145:10512-10521. [PMID: 37079767 DOI: 10.1021/jacs.2c13172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Recent experiments have shown that the diffusion of reagent molecules is inconsistent with what the Stokes-Einstein equation predicts during a chemical reaction. Here, we used single-molecule tracking to observe the diffusion of reactive reagent molecules during click and Diels-Alder (DA) reactions. We found that the diffusion coefficient of the reagents remained unchanged within the experimental uncertainty upon the DA reaction. Yet, diffusion of reagent molecules is faster than predicted during the click reaction when the reagent concentration and catalyst concentration exceed a threshold. A stepwise analysis suggested that the fast diffusion scenario is due to the reaction but not the involvement of the tracer with the reaction itself. The present results provide experimental evidence on the faster-than-expected reagent diffusion during a CuAAC reaction in specific conditions and propose new insights into understanding this unexpected behavior.
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Affiliation(s)
- Zhengfu Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Hongbo Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Ming Hu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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8
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Choi AA, Xiang L, Li W, Xu K. Single-Molecule Displacement Mapping Indicates Unhindered Intracellular Diffusion of Small (≲1 kDa) Solutes. J Am Chem Soc 2023:10.1021/jacs.3c00597. [PMID: 37027457 PMCID: PMC10558625 DOI: 10.1021/jacs.3c00597] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (≲1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400 μs separation, we extend single-molecule displacement/diffusivity mapping (SMdM), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm2/s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ∼60-70% of that in vitro, up to ∼250 μm2/s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Limin Xiang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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9
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Park HH, Choi AA, Xu K. Size-Dependent Suppression of Molecular Diffusivity in Expandable Hydrogels: A Single-Molecule Study. J Phys Chem B 2023; 127:3333-3339. [PMID: 37011131 DOI: 10.1021/acs.jpcb.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
By repurposing the recently popularized expansion microscopy to control the meshwork size of hydrogels, we examine the size-dependent suppression of molecular diffusivity in the resultant tuned hydrogel nanomatrices over a wide range of polymer fractions of ∼0.14-7 wt %. With our recently developed single-molecule displacement/diffusivity mapping (SMdM) microscopy methods, we thus show that with a fixed meshwork size, larger molecules exhibit more impeded diffusion and that, for the same molecule, diffusion is progressively more suppressed as the meshwork size is reduced; this effect is more prominent for the larger molecules. Moreover, we show that the meshwork-induced obstruction of diffusion is uncoupled from the suppression of diffusion due to increased solution viscosities. Thus, the two mechanisms, respectively, being diffuser-size-dependent and independent, may separately scale down molecular diffusivity to produce the final diffusion slowdown in complex systems like the cell.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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10
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Park HH, Wang B, Moon S, Jepson T, Xu K. Machine-learning-powered extraction of molecular diffusivity from single-molecule images for super-resolution mapping. Commun Biol 2023; 6:336. [PMID: 36977778 PMCID: PMC10050076 DOI: 10.1038/s42003-023-04729-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
While critical to biological processes, molecular diffusion is difficult to quantify, and spatial mapping of local diffusivity is even more challenging. Here we report a machine-learning-enabled approach, pixels-to-diffusivity (Pix2D), to directly extract the diffusion coefficient D from single-molecule images, and consequently enable super-resolved D spatial mapping. Working with single-molecule images recorded at a fixed framerate under typical single-molecule localization microscopy (SMLM) conditions, Pix2D exploits the often undesired yet evident motion blur, i.e., the convolution of single-molecule motion trajectory during the frame recording time with the diffraction-limited point spread function (PSF) of the microscope. Whereas the stochastic nature of diffusion imprints diverse diffusion trajectories to different molecules diffusing at the same given D, we construct a convolutional neural network (CNN) model that takes a stack of single-molecule images as the input and evaluates a D-value as the output. We thus validate robust D evaluation and spatial mapping with simulated data, and with experimental data successfully characterize D differences for supported lipid bilayers of different compositions and resolve gel and fluidic phases at the nanoscale.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Bowen Wang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Suhong Moon
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Tyler Jepson
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA.
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11
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-Molecule Displacement Mapping Unveils Sign-Asymmetric Protein Charge Effects on Intraorganellar Diffusion. NANO LETTERS 2023; 23:1711-1716. [PMID: 36802676 PMCID: PMC10044514 DOI: 10.1021/acs.nanolett.2c04379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ∼40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, hence a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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Affiliation(s)
- Limin Xiang
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
- College of Chemistry and Molecular Sciences & TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Rui Yan
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Wan Li
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
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12
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525611. [PMID: 36747807 PMCID: PMC9900983 DOI: 10.1101/2023.01.26.525611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SM d M), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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13
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Choi AA, Xiang L, Li W, Xu K. Single-molecule displacement mapping indicates unhindered intracellular diffusion of small (<~1 kDa) solutes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525579. [PMID: 36747694 PMCID: PMC9900885 DOI: 10.1101/2023.01.26.525579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (<~1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400-μs separation, we extend single-molecule displacement/diffusivity mapping (SM d M), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm 2 /s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ~60-70% of that in vitro , up to ~250 μm 2 /s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water, but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments. Abstract Graphic
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14
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Rezaei-Ghaleh N, Agudo-Canalejo J, Griesinger C, Golestanian R. Response to Comment on "Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion" and "Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question". J Am Chem Soc 2022; 144:13441-13445. [PMID: 35919985 PMCID: PMC9354245 DOI: 10.1021/jacs.2c02850] [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] [Indexed: 11/29/2022]
Abstract
In their Comment
(DOI: 10.1021/jacs.2c02965) on two related publications by our
group (J. Am. Chem.
Soc.2022, 144, 1380–1388;
DOI: 10.1021/jacs.1c11754) and another (J. Am. Chem.
Soc.2021, 143, 20884–20890;
DOI: 10.1021/jacs.1c09455), Huang and Granick refer to the
diffusion NMR measurements of molecules during a copper-catalyzed
azide–alkyne cycloaddition (CuAAC) “click” reaction.
Here we respond to their comments and maintain that no measurable
diffusion enhancement was observed during the reaction. We expand
on the physical arguments presented in our original JACS Article regarding the appropriate reference state for the diffusion
coefficient and present new data showing that the use of other reference
states, as suggested by Huang and Granick, will still support our
conclusion that the two reactants and one product of the CuAAC reaction
do not exhibit boosted mobility during the reaction.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Jaime Agudo-Canalejo
- Department of Living Matter Physics, Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, D-37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Ramin Golestanian
- Department of Living Matter Physics, Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, D-37077 Göttingen, Germany.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
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15
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Losa J, Leupold S, Alonso-Martinez D, Vainikka P, Thallmair S, Tych KM, Marrink SJ, Heinemann M. Perspective: a stirring role for metabolism in cells. Mol Syst Biol 2022; 18:e10822. [PMID: 35362256 PMCID: PMC8972047 DOI: 10.15252/msb.202110822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Simeon Leupold
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Diego Alonso-Martinez
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Petteri Vainikka
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Katarzyna M Tych
- Chemical Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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