1
|
Frei MS, Sanchez SA, Liu L, Schneider F, Wang Z, Hakozaki H, Li Y, Lyons AC, Rohm TV, Olefsky JM, Shi L, Schöneberg J, Fraser SE, Mehta S, Wang Y, Zhang J. Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. bioRxiv 2024:2024.02.10.579766. [PMID: 38370804 PMCID: PMC10871310 DOI: 10.1101/2024.02.10.579766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Fluorescent biosensors revolutionized biomedical science by enabling the direct measurement of signaling activities in living cells, yet the current technology is limited in resolution and dimensionality. Here, we introduce highly sensitive chemigenetic kinase activity biosensors that combine the genetically encodable self-labeling protein tag HaloTag7 with bright far-red-emitting synthetic fluorophores. This technology enables five-color biosensor multiplexing, 4D activity imaging, and functional super-resolution imaging via stimulated emission depletion (STED) microscopy.
Collapse
Affiliation(s)
- Michelle S. Frei
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Samantha A. Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Falk Schneider
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zichen Wang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yajuan Li
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Theresa V. Rohm
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jerrold M. Olefsky
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lingyan Shi
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Johannes Schöneberg
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Scott E. Fraser
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Yingxiao Wang
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
2
|
Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Adrien Maria Vierdag WM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv 2024:arXiv:2401.13022v4. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
Collapse
Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | |
Collapse
|
3
|
Xia W, Veeragandham P, Cao Y, Xu Y, Rhyne TE, Qian J, Hung CW, Zhao P, Jones Y, Gao H, Liddle C, Yu RT, Downes M, Evans RM, Rydén M, Wabitsch M, Wang Z, Hakozaki H, Schöneberg J, Reilly SM, Huang J, Saltiel AR. Obesity causes mitochondrial fragmentation and dysfunction in white adipocytes due to RalA activation. Nat Metab 2024; 6:273-289. [PMID: 38286821 PMCID: PMC10896723 DOI: 10.1038/s42255-024-00978-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Mitochondrial dysfunction is a characteristic trait of human and rodent obesity, insulin resistance and fatty liver disease. Here we show that high-fat diet (HFD) feeding causes mitochondrial fragmentation in inguinal white adipocytes from male mice, leading to reduced oxidative capacity by a process dependent on the small GTPase RalA. RalA expression and activity are increased in white adipocytes after HFD. Targeted deletion of RalA in white adipocytes prevents fragmentation of mitochondria and diminishes HFD-induced weight gain by increasing fatty acid oxidation. Mechanistically, RalA increases fission in adipocytes by reversing the inhibitory Ser637 phosphorylation of the fission protein Drp1, leading to more mitochondrial fragmentation. Adipose tissue expression of the human homolog of Drp1, DNM1L, is positively correlated with obesity and insulin resistance. Thus, chronic activation of RalA plays a key role in repressing energy expenditure in obese adipose tissue by shifting the balance of mitochondrial dynamics toward excessive fission, contributing to weight gain and metabolic dysfunction.
Collapse
Affiliation(s)
- Wenmin Xia
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Preethi Veeragandham
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yu Cao
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yayun Xu
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Torrey E Rhyne
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaxin Qian
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chao-Wei Hung
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Peng Zhao
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ying Jones
- Electron Microscopy Core, Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Hui Gao
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research and Westmead Hospital, University of Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Ruth T Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institute (C2-94), Karolinska University Hospital, Stockholm, Sweden
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology and Diabetes, Ulm University Medical Center, Ulm, Germany
| | - Zichen Wang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Johannes Schöneberg
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Shannon M Reilly
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jianfeng Huang
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Alan R Saltiel
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Diego, San Diego, CA, USA.
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA.
| |
Collapse
|
4
|
Ortiz-Muñoz G, Brown M, Carbone CB, Pechuan-Jorge X, Rouilly V, Lindberg H, Ritter AT, Raghupathi G, Sun Q, Nicotra T, Mantri SR, Yang A, Doerr J, Nagarkar D, Darmanis S, Haley B, Mariathasan S, Wang Y, Gomez-Roca C, de Andrea CE, Spigel D, Wu T, Delamarre L, Schöneberg J, Modrusan Z, Price R, Turley SJ, Mellman I, Moussion C. In situ tumour arrays reveal early environmental control of cancer immunity. Nature 2023:10.1038/s41586-023-06132-2. [PMID: 37258670 DOI: 10.1038/s41586-023-06132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The immune phenotype of a tumour is a key predictor of its response to immunotherapy1-4. Patients who respond to checkpoint blockade generally present with immune-inflamed5-7 tumours that are highly infiltrated by T cells. However, not all inflamed tumours respond to therapy, and even lower response rates occur among tumours that lack T cells (immune desert) or that spatially exclude T cells to the periphery of the tumour lesion (immune excluded)8. Despite the importance of these tumour immune phenotypes in patients, little is known about their development, heterogeneity or dynamics owing to the technical difficulty of tracking these features in situ. Here we introduce skin tumour array by microporation (STAMP)-a preclinical approach that combines high-throughput time-lapse imaging with next-generation sequencing of tumour arrays. Using STAMP, we followed the development of thousands of arrayed tumours in vivo to show that tumour immune phenotypes and outcomes vary between adjacent tumours and are controlled by local factors within the tumour microenvironment. Particularly, the recruitment of T cells by fibroblasts and monocytes into the tumour core was supportive of T cell cytotoxic activity and tumour rejection. Tumour immune phenotypes were dynamic over time and an early conversion to an immune-inflamed phenotype was predictive of spontaneous or therapy-induced tumour rejection. Thus, STAMP captures the dynamic relationships of the spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Carlos Gomez-Roca
- IUCT, Institut Universitaire du Cancer de Toulouse, Toulouse, France
| | | | - David Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
| | - Thomas Wu
- Genentech, South San Francisco, CA, USA
| | | | - Johannes Schöneberg
- Department of Pharmacology, UCSD, San Diego, CA, USA
- Department of Chemistry & Biochemistry, UCSD, San Diego, CA, USA
| | | | | | | | | | | |
Collapse
|
5
|
Wang Z, Natekar P, Tea C, Tamir S, Hakozaki H, Schöneberg J. MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data. PLoS Comput Biol 2023; 19:e1011060. [PMID: 37083820 PMCID: PMC10184899 DOI: 10.1371/journal.pcbi.1011060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 05/15/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Mitochondria form a network in the cell that rapidly changes through fission, fusion, and motility. Dysregulation of this four-dimensional (4D: x,y,z,time) network is implicated in numerous diseases ranging from cancer to neurodegeneration. While lattice light-sheet microscopy has recently made it possible to image mitochondria in 4D, quantitative analysis methods for the resulting datasets have been lacking. Here we present MitoTNT, the first-in-class software for Mitochondrial Temporal Network Tracking in 4D live-cell fluorescence microscopy data. MitoTNT uses spatial proximity and network topology to compute an optimal tracking assignment. To validate the accuracy of tracking, we created a reaction-diffusion simulation to model mitochondrial network motion and remodeling events. We found that our tracking is >90% accurate for ground-truth simulations and agrees well with published motility results for experimental data. We used MitoTNT to quantify 4D mitochondrial networks from human induced pluripotent stem cells. First, we characterized sub-fragment motility and analyzed network branch motion patterns. We revealed that the skeleton node motion is correlated along branch nodes and is uncorrelated in time. Second, we identified fission and fusion events with high spatiotemporal resolution. We found that mitochondrial skeleton nodes near the fission/fusion sites move nearly twice as fast as random skeleton nodes and that microtubules play a role in mediating selective fission/fusion. Finally, we developed graph-based transport simulations that model how material would distribute on experimentally measured mitochondrial temporal networks. We showed that pharmacological perturbations increase network reachability but decrease network resilience through a combination of altered mitochondrial fission/fusion dynamics and motility. MitoTNT's easy-to-use tracking module, interactive 4D visualization capability, and powerful post-tracking analyses aim at making temporal network tracking accessible to the wider mitochondria research community.
Collapse
Affiliation(s)
- Zichen Wang
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Parth Natekar
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Challana Tea
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Sharon Tamir
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Johannes Schöneberg
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| |
Collapse
|
6
|
McMahon G, Rude M, Tea C, Wang Z, Natekar P, Hakozaki H, Schöneberg J. 4D mitochondrial biophysical parameters predict cell type in human organoid tissue. Biophys J 2023; 122:303a. [PMID: 36783518 DOI: 10.1016/j.bpj.2022.11.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Gillian McMahon
- Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - McKenna Rude
- Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Challana Tea
- Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Zichen Wang
- Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Parth Natekar
- Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Hiroyuki Hakozaki
- Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA; Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Johannes Schöneberg
- Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA; Pharmacology, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
7
|
Jin M, Shirazinejad C, Wang B, Yan A, Schöneberg J, Upadhyayula S, Xu K, Drubin DG. Branched actin networks are organized for asymmetric force production during clathrin-mediated endocytosis in mammalian cells. Nat Commun 2022; 13:3578. [PMID: 35732852 PMCID: PMC9217951 DOI: 10.1038/s41467-022-31207-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 06/08/2022] [Indexed: 01/15/2023] Open
Abstract
Actin assembly facilitates vesicle formation in several trafficking pathways, including clathrin-mediated endocytosis (CME). Interestingly, actin does not assemble at all CME sites in mammalian cells. How actin networks are organized with respect to mammalian CME sites and how assembly forces are harnessed, are not fully understood. Here, branched actin network geometry at CME sites was analyzed using three different advanced imaging approaches. When endocytic dynamics of unperturbed CME sites are compared, sites with actin assembly show a distinct signature, a delay between completion of coat expansion and vesicle scission, indicating that actin assembly occurs preferentially at stalled CME sites. In addition, N-WASP and the Arp2/3 complex are recruited to one side of CME sites, where they are positioned to stimulate asymmetric actin assembly and force production. We propose that actin assembles preferentially at stalled CME sites where it pulls vesicles into the cell asymmetrically, much as a bottle opener pulls off a bottle cap.
Collapse
Affiliation(s)
- Meiyan Jin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cyna Shirazinejad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Bowen Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Amy Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Pharmacology, and Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
8
|
Serwas D, Akamatsu M, Moayed A, Vegesna K, Vasan R, Hill JM, Schöneberg J, Davies KM, Rangamani P, Drubin DG. Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography. Dev Cell 2022; 57:1132-1145.e5. [PMID: 35504288 PMCID: PMC9165722 DOI: 10.1016/j.devcel.2022.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/18/2022] [Accepted: 04/07/2022] [Indexed: 01/26/2023]
Abstract
Actin assembly provides force for a multitude of cellular processes. Compared to actin-assembly-based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Here, cryo-electron tomography identified actin filament number, organization, and orientation during clathrin-mediated endocytosis in human SK-MEL-2 cells, showing that force generation is robust despite variance in network organization. Actin dynamics simulations incorporating a measured branch angle indicate that sufficient force to drive membrane internalization is generated through polymerization and that assembly is triggered from ∼4 founding "mother" filaments, consistent with tomography data. Hip1R actin filament anchoring points are present along the entire endocytic invagination, where simulations show that it is key to pulling force generation, and along the neck, where it targets filament growth and makes internalization more robust. Actin organization described here allowed direct translation of structure to mechanism with broad implications for other actin-driven processes.
Collapse
Affiliation(s)
- Daniel Serwas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amir Moayed
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Karthik Vegesna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer M Hill
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Karen M Davies
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
9
|
Abstract
Clathrin-mediated endocytosis (CME) robustness under elevated membrane tension is maintained by actin assembly-mediated force generation. However, whether more actin assembles at endocytic sites in response to increased load has not previously been investigated. Here actin network ultrastructure at CME sites was examined under low and high membrane tension. Actin and N-WASP spatial organization indicate that actin polymerization initiates at the base of clathrin-coated pits and that the network then grows away from the plasma membrane. Actin network height at individual CME sites was not coupled to coat shape, raising the possibility that local differences in mechanical load feed back on assembly. By manipulating membrane tension and Arp2/3 complex activity we tested the hypothesis that actin assembly at CME sites increases in response to elevated load. Indeed, in response to elevated membrane tension, actin grew higher, resulting in greater coverage of the clathrin coat, and CME slowed. When membrane tension was elevated and the Arp2/3 complex was inhibited, shallow clathrin-coated pits accumulated, indicating that this adaptive mechanism is especially crucial for coat curvature generation. We propose that actin assembly increases in response to increased load to ensure CME robustness over a range of plasma membrane tensions. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
Collapse
Affiliation(s)
- Charlotte Kaplan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
| | - Sam J Kenny
- Department of Chemistry, University of California, Berkeley, CA 94720-3220
| | - Xuyan Chen
- Department of Chemistry, University of California, Berkeley, CA 94720-3220
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220.,Center for Neural Circuits and Behavior, University of California, San Diego, CA 92093
| | - Ewa Sitarska
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA 94720-3220.,Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
| |
Collapse
|
10
|
Sun Y, Schöneberg J, Chen X, Jiang T, Kaplan C, Xu K, Pollard TD, Drubin DG. Direct comparison of clathrin-mediated endocytosis in budding and fission yeast reveals conserved and evolvable features. eLife 2019; 8:50749. [PMID: 31829937 PMCID: PMC6908435 DOI: 10.7554/elife.50749] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
Conserved proteins drive clathrin-mediated endocytosis (CME), which from yeast to humans involves a burst of actin assembly. To gain mechanistic insights into this process, we performed a side-by-side quantitative comparison of CME in two distantly related yeast species. Though endocytic protein abundance in S. pombe and S. cerevisiae is more similar than previously thought, membrane invagination speed and depth are two-fold greater in fission yeast. In both yeasts, accumulation of ~70 WASp molecules activates the Arp2/3 complex to drive membrane invagination. In contrast to budding yeast, WASp-mediated actin nucleation plays an essential role in fission yeast endocytosis. Genetics and live-cell imaging revealed core CME spatiodynamic similarities between the two yeasts, although the assembly of two zones of actin filaments is specific for fission yeast and not essential for CME. These studies identified conserved CME mechanisms and species-specific adaptations with broad implications that are expected to extend from yeast to humans.
Collapse
Affiliation(s)
- Yidi Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Xuyan Chen
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Tommy Jiang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Charlotte Kaplan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Thomas D Pollard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.,Department of Cell Biology, Yale University, New Haven, United States.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
11
|
Schöneberg J, Dambournet D, Liu T, Forster R, Hockemeyer D, Betzig E, Drubin D. 4D cell biology: Big data image analytics and lattice light‐sheet imaging reveal dynamics of clathrin‐mediated endocytosis in stem cell‐derived intestinal organoids. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.659.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
12
|
Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH, Carlson LA, Bahrami AH, Goldman DH, Ren X, Hummer G, Bustamante C, Hurley JH. ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 2019; 362:1423-1428. [PMID: 30573630 DOI: 10.1126/science.aat1839] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/17/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022]
Abstract
The endosomal sorting complexes required for transport (ESCRTs) catalyze reverse-topology scission from the inner face of membrane necks in HIV budding, multivesicular endosome biogenesis, cytokinesis, and other pathways. We encapsulated ESCRT-III subunits Snf7, Vps24, and Vps2 and the AAA+ ATPase (adenosine triphosphatase) Vps4 in giant vesicles from which membrane nanotubes reflecting the correct topology of scission could be pulled. Upon ATP release by photo-uncaging, this system generated forces within the nanotubes that led to membrane scission in a manner dependent upon Vps4 catalytic activity and Vps4 coupling to the ESCRT-III proteins. Imaging of scission revealed Snf7 and Vps4 puncta within nanotubes whose presence followed ATP release, correlated with force generation and nanotube constriction, and preceded scission. These observations directly verify long-standing predictions that ATP-hydrolyzing assemblies of ESCRT-III and Vps4 sever membranes.
Collapse
Affiliation(s)
- Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Mark Remec Pavlin
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shannon Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maurizio Righini
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Il-Hyung Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lars-Anders Carlson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amir Houshang Bahrami
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Daniel H Goldman
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University, Frankfurt/M, Germany
| | - Carlos Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
13
|
Schöneberg J, Dambournet D, Liu TL, Forster R, Hockemeyer D, Betzig E, Drubin DG. 4D Cell Biology: Big Data Image Analytics and Lattice Light-Sheet Imaging Reveal Dynamics of Clathrin-Mediated Endocytosis in Stem Cell-Derived Intestinal Organoids. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
14
|
Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Mol Cell 2019; 73:339-353.e6. [PMID: 30581147 PMCID: PMC6450660 DOI: 10.1016/j.molcel.2018.10.035] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/15/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.
Collapse
Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lindsey N Young
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyle L Morris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yukako Oe
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt/M, Germany
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
15
|
Schöneberg J, Dambournet D, Liu TL, Forster R, Hockemeyer D, Betzig E, Drubin DG. 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids. Mol Biol Cell 2018; 29:2959-2968. [PMID: 30188768 PMCID: PMC6329908 DOI: 10.1091/mbc.e18-06-0375] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue-scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice light-sheet imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70 × 60 × 40 µm xyz) at 5.7 s/frame. We developed an open-source data analysis package termed pyLattice to process the resulting large (∼60 Gb) movie data sets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from ∼35 cells at a time, resulting in ∼4000 processed tracks per movie. On the basis of their localization in the organoid, we classified CME tracks into apical, lateral, and basal events and found that CME dynamics is similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative high temporal and spatial resolution analysis of subcellular events within tissues.
Collapse
Affiliation(s)
| | - Daphné Dambournet
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Ryan Forster
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Eric Betzig
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720.,Department of Physics, University of California, Berkeley, Berkeley, CA 94720.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - David G Drubin
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| |
Collapse
|
16
|
Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Lamb TD, Hofmann KP, Spahn CMT, Heck M. It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods. Open Biol 2018; 8:180075. [PMID: 30068566 PMCID: PMC6119865 DOI: 10.1098/rsob.180075] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022] Open
Abstract
Among cyclic nucleotide phosphodiesterases (PDEs), PDE6 is unique in serving as an effector enzyme in G protein-coupled signal transduction. In retinal rods and cones, PDE6 is membrane-bound and activated to hydrolyse its substrate, cGMP, by binding of two active G protein α-subunits (Gα*). To investigate the activation mechanism of mammalian rod PDE6, we have collected functional and structural data, and analysed them by reaction-diffusion simulations. Gα* titration of membrane-bound PDE6 reveals a strong functional asymmetry of the enzyme with respect to the affinity of Gα* for its two binding sites on membrane-bound PDE6 and the enzymatic activity of the intermediary 1 : 1 Gα* · PDE6 complex. Employing cGMP and its 8-bromo analogue as substrates, we find that Gα* · PDE6 forms with high affinity but has virtually no cGMP hydrolytic activity. To fully activate PDE6, it takes a second copy of Gα* which binds with lower affinity, forming Gα* · PDE6 · Gα*. Reaction-diffusion simulations show that the functional asymmetry of membrane-bound PDE6 constitutes a coincidence switch and explains the lack of G protein-related noise in visual signal transduction. The high local concentration of Gα* generated by a light-activated rhodopsin molecule efficiently activates PDE6, whereas the low density of spontaneously activated Gα* fails to activate the effector enzyme.
Collapse
Affiliation(s)
- Bilal M Qureshi
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Microscopy and Cryo Electron Microscopy Group, Max-Planck Institut für Molekulare Genetik, Berlin, Germany
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2600, Australia
| | - Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Zentrum für Biophysik und Bioinformatik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Heck
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
17
|
Schöneberg J, Yan S, Bahrami AH, Righini M, Lee I, Pavlin M, Carlson L, Goldman D, Hummer G, Bustamante C, Hurley J. ESCRT membrane scission revealed by optical tweezers. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.542.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
18
|
Abstract
Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1DD that selectively perturbs the function of the Atg13-free state. Atg1DD shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.
Collapse
Affiliation(s)
- Mary G Lin
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Christopher W Davies
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
19
|
Schöneberg J, Yan S, Bahrami A, Righini M, Lee IH, Remec Pavlin M, Carlson LA, Goldman D, Hummer G, Bustamante C, Hurley J. ESCRT Membrane Scission Revealed by Optical Tweezers. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
20
|
Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F. Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat Commun 2017; 8:1095. [PMID: 29062047 PMCID: PMC5653669 DOI: 10.1038/s41467-017-01163-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25-109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.
Collapse
Affiliation(s)
- Fabian Paul
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, 14476, Potsdam, Germany
| | - Christoph Wehmeyer
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Esam T Abualrous
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Hao Wu
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Michael D Crabtree
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christian Freund
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, 14476, Potsdam, Germany
| | - Frank Noé
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
21
|
Schöneberg J, Lehmann M, Ullrich A, Posor Y, Lo WT, Lichtner G, Schmoranzer J, Haucke V, Noé F. Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat Commun 2017. [PMID: 28627515 PMCID: PMC5481832 DOI: 10.1038/ncomms15873] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) involves membrane-associated scaffolds of the bin-amphiphysin-rvs (BAR) domain protein family as well as the GTPase dynamin, and is accompanied and perhaps triggered by changes in local lipid composition. How protein recruitment, scaffold assembly and membrane deformation is spatiotemporally controlled and coupled to fission is poorly understood. We show by computational modelling and super-resolution imaging that phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] synthesis within the clathrin-coated area of endocytic intermediates triggers selective recruitment of the PX-BAR domain protein SNX9, as a result of complex interactions of endocytic proteins competing for phospholipids. The specific architecture induces positioning of SNX9 at the invagination neck where its self-assembly regulates membrane constriction, thereby providing a template for dynamin fission. These data explain how lipid conversion at endocytic pits couples local membrane constriction to fission. Our work demonstrates how computational modelling and super-resolution imaging can be combined to unravel function and mechanisms of complex cellular processes. The spatiotemporal regulation of membrane scaffolds recruitment and coupling between membrane deformation and fission in endocytosis are unclear. Here the authors show that lipid conversion at endocytic pits recruits SNX9, which couples local membrane constriction to fission in endocytosis.
Collapse
Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Martin Lehmann
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Alexander Ullrich
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - York Posor
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Wen-Ting Lo
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany
| | - Gregor Lichtner
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany.,Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany
| | - Jan Schmoranzer
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Volker Haucke
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany.,NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Virchowweg 6, Berlin 10117, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| |
Collapse
|
22
|
Schöneberg J, Otte F, Néel N, Weismann A, Mokrousov Y, Kröger J, Berndt R, Heinze S. Ballistic Anisotropic Magnetoresistance of Single-Atom Contacts. Nano Lett 2016; 16:1450-1454. [PMID: 26783634 DOI: 10.1021/acs.nanolett.5b05071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Anisotropic magnetoresistance, that is, the sensitivity of the electrical resistance of magnetic materials on the magnetization direction, is expected to be strongly enhanced in ballistic transport through nanoscale junctions. However, unambiguous experimental evidence of this effect is difficult to achieve. We utilize single-atom junctions to measure this ballistic anisotropic magnetoresistance (AMR). Single Co and Ir atoms are deposited on domains and domain walls of ferromagnetic Fe layers on W(110) to control their magnetization directions. They are contacted with nonmagnetic tips in a low-temperature scanning tunneling microscope to measure the junction conductances. Large changes of the magnetoresistance occur from the tunneling to the ballistic regime due to the competition of localized and delocalized d-orbitals, which are differently affected by spin-orbit coupling. This work shows that engineering the AMR at the single atom level is feasible.
Collapse
Affiliation(s)
| | | | - N Néel
- Institut für Physik, Technische Universität Ilmenau , D-98693 Ilmenau, Germany
| | | | - Y Mokrousov
- Peter Grünberg Institut and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA , D-52425 Jülich, Germany
| | - J Kröger
- Institut für Physik, Technische Universität Ilmenau , D-98693 Ilmenau, Germany
| | | | | |
Collapse
|
23
|
Schöneberg J, Hofmann KP, Heck M, Noé F. Response to comment "Transient complexes between dark rhodopsin and transducin: circumstantial evidence or physiological necessity?" by D. Dell'Orco and K.-W. Koch. Biophys J 2015; 108:778-9. [PMID: 25650945 DOI: 10.1016/j.bpj.2014.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 12/18/2014] [Indexed: 01/13/2023] Open
Affiliation(s)
| | | | - Martin Heck
- Institute for Medical Physics and Biophysics, Berlin, Germany.
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.
| |
Collapse
|
24
|
Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Hofmann KP, Spahn CMT, Heck M. Asymmetric properties of rod cGMP Phosphodiesterase 6 (PDE6): structural and functional analysis. BMC Pharmacol Toxicol 2015. [PMCID: PMC4565112 DOI: 10.1186/2050-6511-16-s1-a76] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|
25
|
Schöneberg J, Heck M, Hofmann KP, Noé F. Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes. Biophys J 2015; 107:1042-1053. [PMID: 25185540 DOI: 10.1016/j.bpj.2014.05.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 12/11/2022] Open
Abstract
Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R(∗)) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein.
Collapse
Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Martin Heck
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Berlin, Germany.
| | - Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
26
|
Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biol 2015; 11:e1004407. [PMID: 26367029 PMCID: PMC4569342 DOI: 10.1371/journal.pcbi.1004407] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/15/2015] [Indexed: 01/10/2023] Open
Abstract
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.
Collapse
Affiliation(s)
- Alexander Ullrich
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Mathias A. Böhme
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | | | - Harald Depner
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stephan J. Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
27
|
Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A. Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure 2015; 23:628-38. [PMID: 25728926 DOI: 10.1016/j.str.2015.01.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/16/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
The visual pigment rhodopsin belongs to the family of G protein-coupled receptors that can form higher oligomers. It is controversial whether rhodopsin forms oligomers and whether oligomers are functionally relevant. Here, we study rhodopsin organization in cryosections of dark-adapted mouse rod photoreceptors by cryoelectron tomography. We identify four hierarchical levels of organization. Rhodopsin forms dimers; at least ten dimers form a row. Rows form pairs (tracks) that are aligned parallel to the disk incisures. Particle-based simulation shows that the combination of tracks with fast precomplex formation, i.e. rapid association and dissociation between inactive rhodopsin and the G protein transducin, leads to kinetic trapping: rhodopsin first activates transducin from its own track, whereas recruitment of transducin from other tracks proceeds more slowly. The trap mechanism could produce uniform single-photon responses independent of rhodopsin lifetime. In general, tracks might provide a platform that coordinates the spatiotemporal interaction of signaling molecules.
Collapse
Affiliation(s)
- Monika Gunkel
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Johannes Schöneberg
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Weaam Alkhaldi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Stephan Irsen
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Frank Noé
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| | - Ashraf Al-Amoudi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| |
Collapse
|
28
|
Schöneberg J, Ullrich A, Noé F. Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophys 2014; 7:11. [PMID: 25737778 PMCID: PMC4347613 DOI: 10.1186/s13628-014-0011-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/29/2014] [Indexed: 11/17/2022]
Abstract
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics.
Collapse
Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Alexander Ullrich
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| |
Collapse
|
29
|
Abstract
We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
Collapse
|