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Bender SWB, Dreisler MW, Zhang M, Kæstel-Hansen J, Hatzakis NS. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nat Commun 2024; 15:1763. [PMID: 38409214 PMCID: PMC10897458 DOI: 10.1038/s41467-024-46106-0] [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] [Received: 05/10/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
The morphology of protein assemblies impacts their behaviour and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system- and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data: time-resolved insulin aggregates, and published data of dSTORM imaging of nuclear pore complexes, fibroblast growth receptor 1, sptPALM of Syntaxin 1a and dynamic live-cell PALM of ryanodine receptors. SEMORE extracts and quantifies all protein assemblies, their temporal morphology evolution and provides quantitative insights, e.g. classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being a time-aware framework can also support the rise of 4D super-resolution data.
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Affiliation(s)
- Steen W B Bender
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Marcus W Dreisler
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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Iversen JF, Bohr SSR, Pinholt HD, Moses ME, Iversen L, Christensen SM, Hatzakis NS, Zhang M. Single-Particle Tracking of Thermomyces lanuginosus Lipase Reveals How Mutations in the Lid Region Remodel Its Diffusion. Biomolecules 2023; 13:biom13040631. [PMID: 37189378 DOI: 10.3390/biom13040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The function of most lipases is controlled by the lid, which undergoes conformational changes at a water–lipid interface to expose the active site, thus activating catalysis. Understanding how lid mutations affect lipases’ function is important for designing improved variants. Lipases’ function has been found to correlate with their diffusion on the substrate surface. Here, we used single-particle tracking (SPT), a powerful tool for deciphering enzymes’ diffusional behavior, to study Thermomyces lanuginosus lipase (TLL) variants with different lid structures in a laundry-like application condition. Thousands of parallelized recorded trajectories and hidden Markov modeling (HMM) analysis allowed us to extract three interconverting diffusional states and quantify their abundance, microscopic transition rates, and the energy barriers for sampling them. Combining those findings with ensemble measurements, we determined that the overall activity variation in the application condition is dependent on surface binding and lipase mobility when bound. Specifically, the L4 variant with a TLL-like lid and wild-type (WT) TLL displayed similar ensemble activity, but WT bound stronger to the surface than L4, while L4 had a higher diffusion coefficient and thus activity when bound to the surface. These mechanistic elements can only be de-convoluted by our combined assays. Our findings offer fresh perspectives on the development of the next iteration of enzyme-based detergent.
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Affiliation(s)
- Josephine F. Iversen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Søren S.-R. Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Henrik D. Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | - Nikos S. Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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3
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Bohr F, Bohr SSR, Mishra NK, González-Foutel NS, Pinholt HD, Wu S, Nielsen EM, Zhang M, Kjaergaard M, Jensen KJ, Hatzakis NS. Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies. Commun Biol 2023; 6:178. [PMID: 36792809 PMCID: PMC9932072 DOI: 10.1038/s42003-022-04386-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 02/17/2023] Open
Abstract
Insulin formulations with diverse oligomerization states are the hallmark of interventions for the treatment of diabetes. Here using single-molecule recordings we firstly reveal that insulin oligomerization can operate via monomeric additions and secondly quantify the existence, abundance and kinetic characterization of diverse insulin assembly and disassembly pathways involving addition of monomeric, dimeric or tetrameric insulin species. We propose and experimentally validate a model where the insulin self-assembly pathway is rerouted, favoring monomeric or oligomeric assembly, by solution concentration, additives and formulations. Combining our practically complete kinetic characterization with rate simulations, we calculate the abundance of each oligomeric species from nM to mM offering mechanistic insights and the relative abundance of all oligomeric forms at concentrations relevant both for secreted and administrated insulin. These reveal a high abundance of all oligomers and a significant fraction of hexamer resulting in practically halved bioavailable monomer concentration. In addition to providing fundamental new insights, the results and toolbox presented here can be universally applied, contributing to the development of optimal insulin formulations and the deciphering of oligomerization mechanisms for additional proteins.
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Affiliation(s)
- Freja Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Narendra Kumar Mishra
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Nicolás Sebastian González-Foutel
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Physics Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shunliang Wu
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Milan Nielsen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Knud J Jensen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Zhou X, Sinkjær AW, Zhang M, Pinholt HD, Nielsen HM, Hatzakis NS, van de Weert M, Foderà V. Heterogeneous and Surface-Catalyzed Amyloid Aggregation Monitored by Spatially Resolved Fluorescence and Single Molecule Microscopy. J Phys Chem Lett 2023; 14:912-919. [PMID: 36669144 DOI: 10.1021/acs.jpclett.2c03400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Amyloid aggregation is associated with many diseases and may also occur in therapeutic protein formulations. Addition of co-solutes is a key strategy to modulate the stability of proteins in pharmaceutical formulations and select inhibitors for drug design in the context of diseases. However, the heterogeneous nature of this multicomponent system in terms of structures and mechanisms poses a number of challenges for the analysis of the chemical reaction. Using insulin as protein system and polysorbate 80 as co-solute, we combine a spatially resolved fluorescence approach with single molecule microscopy and machine learning methods to kinetically disentangle the different contributions from multiple species within a single aggregation experiment. We link the presence of interfaces to the degree of heterogeneity of the aggregation kinetics and retrieve the rate constants and underlying mechanisms for single aggregation events. Importantly, we report that the mechanism of inhibition of the self-assembly process depends on the details of the growth pathways of otherwise macroscopically identical species. This information can only be accessed by the analysis of single aggregate events, suggesting our method as a general tool for a comprehensive physicochemical characterization of self-assembly reactions.
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Affiliation(s)
- Xin Zhou
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Wilgaard Sinkjær
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hanne Mørck Nielsen
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
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Thorlaksen C, Stanciu AM, Busch Neergaard M, Hatzakis N, Foderà V, Groenning M. Morphological integrity of insulin amyloid-like aggregates depends on preparation methods and post-production treatments. Eur J Pharm Biopharm 2022; 179:147-155. [PMID: 36058445 DOI: 10.1016/j.ejpb.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 11/28/2022]
Abstract
Protein aggregates are often varying extensively in their morphological characteristics, which may lead to various biological outcomes, such as increased immunogenicity risk. However, isolation of aggregates with a specific morphology within an ensemble is often challenging. To gain vital knowledge on the effects of aggregate characteristics, samples containing a single morphology must be produced by direct control of the aggregation process. Moreover, the formed aggregates need to be in an aqueous solution suitable for biological assays, while keeping their morphology intact. Here we evaluated the dependence of morphology and integrity of amyloid-like fibrils and spherulites on preparation conditions and post-treatment methods. Samples containing either amyloid-like fibrils or spherulites produced from human insulin in acetic acid solutions are dependent on the presence of salt (NaCl). Moreover, mechanical shaking (600 rpm) inhibits spherulite formation, while only affecting the length of the formed fibrils compared to quiescent conditions. Besides shaking, the initial protein concentration in the formulation was found to control fibril length. Surprisingly, exchanging the solution used for aggregate formation to a physiologically relevant buffer, had a striking effect on the morphological integrity of the fibril and spherulite samples. Especially the secondary structure of one of our spherulite samples presented dramatic changes of the aggregated β-sheet content after exchanging the solution, emphasizing the importance of the aggregate stability. These results and considerations have profound implications on the data interpretation and should be implemented in the workflow for both fundamental characterization of aggregates as well as assays for evaluation of their corresponding biological effects.
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Affiliation(s)
- Camilla Thorlaksen
- Biophysical analysis, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark; Department of Pharmacy and Nanoscience Center University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Adriana-Maria Stanciu
- Biophysical analysis, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark; Department of Pharmacy and Nanoscience Center University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | - Nikos Hatzakis
- Department of Chemistry and Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; NovoNordisk Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 København N, Denmark
| | - Vito Foderà
- Department of Pharmacy and Nanoscience Center University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Minna Groenning
- Biophysical analysis, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark.
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