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Krainer G, Jacquat RPB, Schneider MM, Welsh TJ, Fan J, Peter QAE, Andrzejewska EA, Šneiderienė G, Czekalska MA, Ausserwoeger H, Chai L, Arter WE, Saar KL, Herling TW, Franzmann TM, Kosmoliaptsis V, Alberti S, Hartl FU, Lee SF, Knowles TPJ. Single-molecule digital sizing of proteins in solution. Nat Commun 2024; 15:7740. [PMID: 39231922 PMCID: PMC11375031 DOI: 10.1038/s41467-024-50825-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.
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Affiliation(s)
- Georg Krainer
- Institute of Molecular Biosciences (IMB), University of Graz, Humboldtstraße 50, 8010, Graz, Austria.
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Raphael P B Jacquat
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Matthias M Schneider
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Department of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jieyuan Fan
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Quentin A E Peter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hannes Ausserwoeger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Lin Chai
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kadi L Saar
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Therese W Herling
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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Halder B, Ghosh S, Khan T, Pal S, Das N, Sen P. Tracking heterogenous protein aggregation at nanoscale through fluorescence correlation spectroscopy. Photochem Photobiol 2024; 100:989-999. [PMID: 39032082 DOI: 10.1111/php.14004] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
Various biophysical techniques have been extensively employed to study protein aggregation due to its significance. Traditionally, these methods detect aggregation at micrometer length scales and micromolar concentrations. However, unlike in vitro, protein aggregation typically occurs at nanomolar concentrations in vivo. Here, using fluorescence correlation spectroscopy (FCS), we captured bromelain aggregation at concentrations as low as ~20 nM, surpassing the detection limit of traditional methods like thioflavin T fluorescence, scattering, and fluorescence microscopy by more than one order of magnitude. Moreover, using thioflavin T fluorescence-based FCS, we have detected larger aggregates at higher bromelain concentrations, which is undetectable in FCS otherwise. Importantly, our study reveals inherent heterogeneity in bromelain aggregation, inaccessible to ensemble-averaged techniques. The presented report may provide a platform for the characterization of premature aggregates at very low protein concentrations, which are thought to be functionally significant species in protein aggregation-induced diseases.
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Affiliation(s)
- Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shreya Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Subhendu Pal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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3
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Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
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Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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Bjarnason S, McIvor JAP, Prestel A, Demény KS, Bullerjahn JT, Kragelund BB, Mercadante D, Heidarsson PO. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nat Commun 2024; 15:1445. [PMID: 38365983 PMCID: PMC10873366 DOI: 10.1038/s41467-024-45847-2] [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: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jordan A P McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Andreas Prestel
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kinga S Demény
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jakob T Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Birthe B Kragelund
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland.
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Vespini V, Grilli S, Ferraro P, Rega R, Ottevaere H, Nie Y, Musto P, Pannico M. Label-Free Protein Analysis by Pyro-Electrohydrodynamic Jet Printing of Gold Nanoparticles. Front Bioeng Biotechnol 2022; 10:817736. [PMID: 35273956 PMCID: PMC8902359 DOI: 10.3389/fbioe.2022.817736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The pyro-electrohydrodynamic jet (p-jet) printing technology has been used for the fabrication of confined assemblies of gold nanoparticles with a round shape and a diameter ranging between 100 and 200 μm. The surface-enhanced Raman spectroscopy (SERS) performance of the p-jet substrate was evaluated by using Rhodamine 6G (R6G) as a reference. The results demonstrate that this kind of SERS substrate exhibits strong plasmonic effects and a significant reproducibility of the signal with a coefficient of variation below 15%. We tested the signal behavior also in case of the bovine serum albumin (BSA) as a model analyte, to demonstrate the affinity with biomolecules. Strong SERS activity was measured also for BSA across the whole spot area. The spectral patterns collected in different locations of the sensing area were highly reproducible. This observation was substantiated by multivariate analysis of the imaging datasets and opens the route towards a potential application of this kind of SERS substrate in biosensing.
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Affiliation(s)
- Veronica Vespini
- National Research Council of Italy (CNR-ISASI), Institute of Applied Sciences and Intelligent Systems, Pozzuoli, Italy
| | - Simonetta Grilli
- National Research Council of Italy (CNR-ISASI), Institute of Applied Sciences and Intelligent Systems, Pozzuoli, Italy
| | - Pietro Ferraro
- National Research Council of Italy (CNR-ISASI), Institute of Applied Sciences and Intelligent Systems, Pozzuoli, Italy
- *Correspondence: Pietro Ferraro, ; Pellegrino Musto,
| | - Romina Rega
- National Research Council of Italy (CNR-ISASI), Institute of Applied Sciences and Intelligent Systems, Pozzuoli, Italy
| | | | - Yunfeng Nie
- Vrije University of Brussels Pleinlaan, Brussels, Belgium
| | - Pellegrino Musto
- Composites and Biomaterials, National Research Council of Italy (CNR-IPCB), Institute for Polymers, Pozzuoli, Italy
- *Correspondence: Pietro Ferraro, ; Pellegrino Musto,
| | - Marianna Pannico
- Composites and Biomaterials, National Research Council of Italy (CNR-IPCB), Institute for Polymers, Pozzuoli, Italy
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Shen D, Bai Y, Liu Y. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells. Chembiochem 2021; 23:e202100443. [PMID: 34613660 DOI: 10.1002/cbic.202100443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/05/2021] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
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7
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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8
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Assenza S, Sassi AS, Kellner R, Schuler B, De Los Rios P, Barducci A. Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. eLife 2019; 8:e48491. [PMID: 31845888 PMCID: PMC7000219 DOI: 10.7554/elife.48491] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.
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Affiliation(s)
- Salvatore Assenza
- Laboratory of Food and Soft MaterialsETH ZürichZürichSwitzerland
- Departmento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadridSpain
| | - Alberto Stefano Sassi
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- IBM TJ Watson Research CenterYorktown HeightsNew YorkUnited States
| | - Ruth Kellner
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Benjamin Schuler
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
- Department of PhysicsUniversity of ZurichZurichSwitzerland
| | - Paolo De Los Rios
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS)INSERM, CNRS, Université de MontpellierMontpellierFrance
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Abstract
This Feature Article presents a view of the protein folding transition based on the hypothesis that Nature has built features within the sequences that enable a Shortcut to efficient folding. Nature's Shortcut is proposed to be the early establishment of a set of nonlocal weak contacts, constituting protein loops that significantly constrain regions of the collapsed disordered protein into a native-like low-resolution fluctuating topology of major sections of the backbone. Nature's establishment of this scaffold of nonlocal contacts is claimed to bypass what would otherwise be a nearly hopeless unaided search for the final three-dimensional structure in proteins longer than ∼100 amino acids. To support this main contention of the Feature Article, the loop hypothesis (LH) description of early folding events is experimentally tested with time-resolved Förster resonance energy transfer techniques for adenylate kinase, and the data are shown to be consistent with theoretical predictions from the sequential collapse model (SCM). The experimentally based LH and the theoretically founded SCM are argued to provide a unified picture of the role of nonlocal contacts as constituting Nature's Shortcut to protein folding. Importantly, the SCM is shown to reliably predict key nonlocal contacts utilizing only primary sequence information. This view on Nature's Shortcut is open to the protein community for further detailed assessment, including its practical consequences, by suitable application of advanced experimental and computational techniques.
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Affiliation(s)
| | - Elisha Haas
- The Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan 52900 , Israel
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10
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An Expanded Conformation of an Antibody Fab Region by X-Ray Scattering, Molecular Dynamics, and smFRET Identifies an Aggregation Mechanism. J Mol Biol 2019; 431:1409-1425. [PMID: 30776431 DOI: 10.1016/j.jmb.2019.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 11/20/2022]
Abstract
Protein aggregation is the underlying cause of many diseases, and also limits the usefulness of many natural and engineered proteins in biotechnology. Better mechanistic understanding and characterization of aggregation-prone states is needed to guide protein engineering, formulation, and drug-targeting strategies that prevent aggregation. While several final aggregated states-notably amyloids-have been characterized structurally, very little is known about the native structural conformers that initiate aggregation. We used a novel combination of small-angle x-ray scattering (SAXS), atomistic molecular dynamic simulations, single-molecule Förster resonance energy transfer, and aggregation-prone region predictions, to characterize structural changes in a native humanized Fab A33 antibody fragment, that correlated with the experimental aggregation kinetics. SAXS revealed increases in the native state radius of gyration, Rg, of 2.2% to 4.1%, at pH 5.5 and below, concomitant with accelerated aggregation. In a cutting-edge approach, we fitted the SAXS data to full MD simulations from the same conditions and located the conformational changes in the native state to the constant domain of the light chain (CL). This CL displacement was independently confirmed using single-molecule Förster resonance energy transfer measurements with two dual-labeled Fabs. These conformational changes were also found to increase the solvent exposure of a predicted APR, suggesting a likely mechanism through which they promote aggregation. Our findings provide a means by which aggregation-prone conformational states can be readily determined experimentally, and thus potentially used to guide protein engineering, or ligand binding strategies, with the aim of stabilizing the protein against aggregation.
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11
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Moosa MM, Ferreon JC, Ferreon ACM. Single-Molecule FRET Detection of Early-Stage Conformations in α-Synuclein Aggregation. Methods Mol Biol 2019; 1948:221-233. [PMID: 30771181 DOI: 10.1007/978-1-4939-9124-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Misfolding and aggregation of α-synuclein are linked to many neurodegenerative disorders, including Parkinson's and Alzheimer's disease. Despite intense research efforts, detailed structural characterization of early conformational transitions that initiate and drive α-synuclein aggregation remains elusive often due to the low sensitivity and ensemble averaging of commonly used techniques. Single-molecule Förster resonance energy transfer (smFRET) provides unique advantages in detecting minor conformations that initiate protein pathologic aggregation. In this chapter, we describe an smFRET-based method for characterizing early conformational conversions that are responsible for α-synuclein self-assembly and aggregation.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
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12
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Schwenk N, Mizaikoff B, Cárdenas S, López-Lorente ÁI. Gold-nanostar-based SERS substrates for studying protein aggregation processes. Analyst 2018; 143:5103-5111. [PMID: 30178815 DOI: 10.1039/c8an00804c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aggregation of proteins has been related to some neurodegenerative diseases such as Alzheimer's and Parkinson's among others. Raman spectroscopy is a useful technique for the investigation of protein conformation and of changes in their secondary structure. In this study, a surface enhanced Raman spectroscopy (SERS) substrate based on the immobilization of plasmonic gold nanostars on a glass slide via silanization of the surface has been prepared and characterized. Gold nanostars were synthesized via a seed-growth method using gold nanoparticles as seeds obtained via stainless steel as the reducing agent. The plasmonic substrate provided an enhancement of 5.7 × 102 fold, as shown for the Raman signal of crystal violet. Using this SERS-active substrate, the investigation of aggregation processes of bovine serum albumin (BSA) and myoglobin proteins upon temperature and solvent modification has been enabled with enhanced sensitivity. Both curve fitting and deconvolution of the amide I band, as well as 2D correlation analysis, were employed for the evaluation of the changes in the SERS spectra of the protein samples. The amide I band within the SERS spectra of the BSA protein revealed a decrease in the α-helix structures within the secondary structure of the protein while the presence of β-sheet structures increased with temperature and solvent concentration.
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Affiliation(s)
- Natalie Schwenk
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany
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13
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Microflow Imaging Analyses Reflect Mechanisms of Aggregate Formation: Comparing Protein Particle Data Sets Using the Kullback–Leibler Divergence. J Pharm Sci 2017; 106:1239-1248. [DOI: 10.1016/j.xphs.2017.01.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/21/2022]
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14
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Buell AK. The Nucleation of Protein Aggregates - From Crystals to Amyloid Fibrils. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 329:187-226. [DOI: 10.1016/bs.ircmb.2016.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Gambin Y, Polinkovsky M, Francois B, Giles N, Bhumkar A, Sierecki E. Confocal Spectroscopy to Study Dimerization, Oligomerization and Aggregation of Proteins: A Practical Guide. Int J Mol Sci 2016; 17:ijms17050655. [PMID: 27144560 PMCID: PMC4881481 DOI: 10.3390/ijms17050655] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein self-association is a key feature that can modulate the physiological role of proteins or lead to deleterious effects when uncontrolled. Protein oligomerization is a simple way to modify the activity of a protein, as the modulation of binding interfaces allows for self-activation or inhibition, or variation in the selectivity of binding partners. As such, dimerization and higher order oligomerization is a common feature in signaling proteins, for example, and more than 70% of enzymes have the potential to self-associate. On the other hand, protein aggregation can overcome the regulatory mechanisms of the cell and can have disastrous physiological effects. This is the case in a number of neurodegenerative diseases, where proteins, due to mutation or dysregulation later in life, start polymerizing and often fibrillate, leading to the creation of protein inclusion bodies in cells. Dimerization, well-defined oligomerization and random aggregation are often difficult to differentiate and characterize experimentally. Single molecule “counting” methods are particularly well suited to the study of self-oligomerization as they allow observation and quantification of behaviors in heterogeneous conditions. However, the extreme dilution of samples often causes weak complexes to dissociate, and rare events can be overlooked. Here, we discuss a straightforward alternative where the principles of single molecule detection are used at higher protein concentrations to quantify oligomers and aggregates in a background of monomers. We propose a practical guide for the use of confocal spectroscopy to quantify protein oligomerization status and also discuss about its use in monitoring changes in protein aggregation in drug screening assays.
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Affiliation(s)
- Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mark Polinkovsky
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bill Francois
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
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16
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Hakiminia F, Khalifeh K, Sajedi RH, Ranjbar B. Determination of structural elements on the folding reaction of mnemiopsin by spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 158:49-55. [PMID: 26803749 DOI: 10.1016/j.saa.2016.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/19/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
Mnemiopsin 1 is a member of photoprotein family, made up of 206 amino acid residues. These Ca(2+)-regulated photoproteins are responsible for light emission in a variety of marine cnidarians and ctenophores. They composed of an apoprotein, a single polypeptide chain of 25 kDa, molecular oxygen and the non-covalently bound chromophore. In this study, we examined whether three mutations, namely R39K, S128G and V183T affect the thermodynamic stability as well as refolding and unfolding kinetics of mnemiopsin 1. Conformational stability measurements using fluorescence and far-UV CD spectroscopies revealed that all variants unfold in multi-step manner in which the secondary and tertiary structures are lost in different steps. However kinetic studies showed that point mutation S128G destabilizes both kinetic intermediate and native conformation; while, these structural elements are stabilized in V183T. We also found that the stability of folded and intermediate states increases in R39K. We concluded that the initial packing of helical segments within the protein structure is more facilitated when Lys with smaller side chain is present in the protein chain.
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Affiliation(s)
- Forough Hakiminia
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, P.O. Box 45195-313, Zanjan, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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17
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Castello F, Casares S, Ruedas-Rama MJ, Orte A. The First Step of Amyloidogenic Aggregation. J Phys Chem B 2015; 119:8260-7. [PMID: 26039157 DOI: 10.1021/acs.jpcb.5b01957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural and dynamic characterization of the on-pathway intermediates involved in the mechanism of amyloid fibril formation is one of the major remaining biomedical challenges of our time. In addition to mature fibrils, various oligomeric structures are implicated in both the rate-limiting step of the nucleation process and the neuronal toxicity of amyloid deposition. Single-molecule fluorescence spectroscopy (SMFS) is an excellent tool for extracting most of the relevant information on these molecular systems, especially advanced multiparameter approaches, such as pulsed interleaved excitation (PIE). In our investigations of an amyloidogenic SH3 domain of α-spectrin, we have found dynamic oligomerization, even prior to incubation. Our single-molecule PIE experiments revealed that these species are small, mostly dimeric, and exhibit a loose and dynamic molecular organization. Furthermore, these experiments have allowed us to obtain quantitative information regarding the oligomer stability. These pre-amyloidogenic oligomers may potentially serve as the first target for fibrillization-prevention strategies.
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Affiliation(s)
- Fabio Castello
- †Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain
| | - Salvador Casares
- ‡Department of Physical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Maria J Ruedas-Rama
- †Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain
| | - Angel Orte
- †Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain
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18
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Narhi LO, Corvari V, Ripple DC, Afonina N, Cecchini I, Defelippis MR, Garidel P, Herre A, Koulov AV, Lubiniecki T, Mahler HC, Mangiagalli P, Nesta D, Perez-Ramirez B, Polozova A, Rossi M, Schmidt R, Simler R, Singh S, Spitznagel TM, Weiskopf A, Wuchner K. Subvisible (2-100 μm) Particle Analysis During Biotherapeutic Drug Product Development: Part 1, Considerations and Strategy. J Pharm Sci 2015; 104:1899-1908. [DOI: 10.1002/jps.24437] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 12/11/2022]
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19
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Quinn MK, Gnan N, James S, Ninarello A, Sciortino F, Zaccarelli E, McManus JJ. How fluorescent labelling alters the solution behaviour of proteins. Phys Chem Chem Phys 2015; 17:31177-87. [DOI: 10.1039/c5cp04463d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The impact of adding a fluorescent dye to a protein is examined using protein phase diagrams and numerical simulations. The addition of the dye is the equivalent of adding a large attractive patch to the surface of the protein, which results in significant changes to the protein solution behaviour.
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Affiliation(s)
- M. K. Quinn
- Department of Chemistry
- Maynooth University
- Maynooth
- Ireland
| | - N. Gnan
- CNR-ISC UOS Sapienza
- 00186 Roma
- Italy
| | - S. James
- Department of Chemistry
- Maynooth University
- Maynooth
- Ireland
| | - A. Ninarello
- Dipartimento di Fisica
- “Sapienza” Universita’ di Roma
- Roma
- Italy
| | - F. Sciortino
- CNR-ISC UOS Sapienza
- 00186 Roma
- Italy
- Dipartimento di Fisica
- “Sapienza” Universita’ di Roma
| | - E. Zaccarelli
- CNR-ISC UOS Sapienza
- 00186 Roma
- Italy
- Dipartimento di Fisica
- “Sapienza” Universita’ di Roma
| | - J. J. McManus
- Department of Chemistry
- Maynooth University
- Maynooth
- Ireland
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20
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Abstract
Single-molecule spectroscopy is widely used to study macromolecular dynamics. Although this technique provides unique information that cannot be obtained at the ensemble level, the possibility of studying fast molecular dynamics is limited by the number of photons detected per unit time (photon count rate), which is proportional to the illumination intensity. However, simply increasing the illumination intensity often does not help because of various photophysical and photochemical problems. In this Perspective, we show how to improve the dynamic range of single-molecule fluorescence spectroscopy at a given photon count rate by considering each and every photon and using a maximum likelihood method. For a photon trajectory with recorded photon colors and inter-photon times, the parameters of a model describing molecular dynamics are obtained by maximizing the appropriate likelihood function. We discuss various likelihood functions, their applicability, and the accuracy of the extracted parameters. The maximum likelihood method has been applied to analyze the experiments on fast two-state protein folding and to measure transition path times. Utilizing other information such as fluorescence lifetimes is discussed in the framework of two-dimensional FRET efficiency-lifetime histograms.
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Affiliation(s)
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892-0520
| | - Irina V. Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892-0520
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21
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Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein. Proc Natl Acad Sci U S A 2014; 111:13355-60. [PMID: 25165400 DOI: 10.1073/pnas.1407086111] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular chaperones are an essential part of the machinery that avoids protein aggregation and misfolding in vivo. However, understanding the molecular basis of how chaperones prevent such undesirable interactions requires the conformational changes within substrate proteins to be probed during chaperone action. Here we use single-molecule fluorescence spectroscopy to investigate how the DnaJ-DnaK chaperone system alters the conformational distribution of the denatured substrate protein rhodanese. We find that in a first step the ATP-independent binding of DnaJ to denatured rhodanese results in a compact denatured ensemble of the substrate protein. The following ATP-dependent binding of multiple DnaK molecules, however, leads to a surprisingly large expansion of denatured rhodanese. Molecular simulations indicate that hard-core repulsion between the multiple DnaK molecules provides the underlying mechanism for disrupting even strong interactions within the substrate protein and preparing it for processing by downstream chaperone systems.
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22
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Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation. Histochem Cell Biol 2014; 142:113-24. [PMID: 24696085 PMCID: PMC4072925 DOI: 10.1007/s00418-014-1213-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 10/31/2022]
Abstract
Studying the structure and dynamics of proteins in live cells is essential to understanding their physiological activities and mechanisms, and to validating in vitro characterization. Improvements in labeling and imaging technologies are starting to allow such in vivo studies; however, a number of technical challenges remain. Recently, we developed an electroporation-based protocol for internalization, which allows biomolecules labeled with organic fluorophores to be introduced at high efficiency into live E. coli (Crawford et al. in Biophys J 105 (11):2439-2450, 2013). Here, we address important challenges related to internalization of proteins, and optimize our method in terms of (1) electroporation buffer conditions; (2) removal of dye contaminants from stock protein samples; and (3) removal of non-internalized molecules from cell suspension after electroporation. We illustrate the usability of the optimized protocol by demonstrating high-efficiency internalization of a 10-kDa protein, the ω subunit of RNA polymerase. Provided that suggested control experiments are carried out, any fluorescently labeled protein of up to 60 kDa could be internalized using our method. Further, we probe the effect of electroporation voltage on internalization efficiency and cell viability and demonstrate that, whilst internalization increases with increased voltage, cell viability is compromised. However, due to the low number of damaged cells in our samples, the major fraction of loaded cells always corresponds to non-damaged cells. By taking care to include only viable cells into analysis, our method allows physiologically relevant studies to be performed, including in vivo measurements of protein diffusion, localization and intramolecular dynamics via single-molecule Förster resonance energy transfer.
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23
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Neupane K, Solanki A, Sosova I, Belov M, Woodside MT. Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy. PLoS One 2014; 9:e86495. [PMID: 24475132 PMCID: PMC3901707 DOI: 10.1371/journal.pone.0086495] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Oligomeric aggregates are widely suspected as toxic agents in diseases caused by protein aggregation, yet they remain poorly characterized, partly because they are challenging to isolate from a heterogeneous mixture of species. We developed an assay for characterizing structure, stability, and kinetics of individual oligomers at high resolution and sensitivity using single-molecule force spectroscopy, and applied it to observe the formation of transient structured aggregates within single oligomers of α-synuclein, an intrinsically-disordered protein linked to Parkinson's disease. Measurements of the molecular extension as the proteins unfolded under tension in optical tweezers revealed that even small oligomers could form numerous metastable structures, with a surprisingly broad range of sizes. Comparing the structures formed in monomers, dimers and tetramers, we found that the average mechanical stability increased with oligomer size. Most structures formed within a minute, with size-dependent rates. These results provide a new window onto the complex α-synuclein aggregation landscape, characterizing the microscopic structural heterogeneity and kinetics of different pathways.
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Affiliation(s)
- Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Allison Solanki
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Iveta Sosova
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Miro Belov
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Michael T. Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
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24
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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25
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Basak S, Chattopadhyay K. Studies of protein folding and dynamics using single molecule fluorescence spectroscopy. Phys Chem Chem Phys 2014; 16:11139-49. [DOI: 10.1039/c3cp55219e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Hoffmann A, Neupane K, Woodside MT. Single-molecule assays for investigating protein misfolding and aggregation. Phys Chem Chem Phys 2013; 15:7934-48. [PMID: 23612887 DOI: 10.1039/c3cp44564j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein misfolding and aggregation are relevant to many fields. Recently, their investigation has experienced a revival as a central topic in the research of numerous human diseases, including Parkinson's and Alzheimer's. Much has been learned from ensemble biochemical approaches, but the inherently heterogeneous nature of the underlying processes has obscured many important details. Single-molecule techniques offer unique capabilities to study heterogeneous systems, while providing high temporal and structural resolution to characterize them. In this Perspective, we give an overview of the single-molecule assays that have been applied to protein misfolding and aggregation, which are mainly based on fluorescence and force spectroscopy. We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches.
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Affiliation(s)
- Armin Hoffmann
- Department of Physics, University of Alberta, Edmonton, AB, Canada
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27
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Paredes JM, Casares S, Ruedas-Rama MJ, Fernandez E, Castello F, Varela L, Orte A. Early amyloidogenic oligomerization studied through fluorescence lifetime correlation spectroscopy. Int J Mol Sci 2012; 13:9400-9418. [PMID: 22949804 PMCID: PMC3431802 DOI: 10.3390/ijms13089400] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/13/2012] [Accepted: 07/19/2012] [Indexed: 12/20/2022] Open
Abstract
Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored the initial stages of amyloidogenic aggregation by employing fluorescence lifetime correlation spectroscopy (FLCS), an advanced modification of conventional fluorescence correlation spectroscopy (FCS) that utilizes time-resolved information. FLCS provides size distributions and kinetics for the oligomer growth of the SH3 domain of α-spectrin, whose N47A mutant forms amyloid fibrils at pH 3.2 and 37 °C in the presence of salt. The combination of FCS with additional fluorescence lifetime information provides an exciting approach to focus on the initial aggregation stages, allowing a better understanding of the fibrillization process, by providing multidimensional information, valuable in combination with other conventional methodologies.
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Affiliation(s)
- Jose M. Paredes
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Salvador Casares
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Maria J. Ruedas-Rama
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Elena Fernandez
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Fabio Castello
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Lorena Varela
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Angel Orte
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-958-243825; Fax: +34-958-244090
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28
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Direct observation of multiple misfolding pathways in a single prion protein molecule. Proc Natl Acad Sci U S A 2012; 109:5283-8. [PMID: 22421432 DOI: 10.1073/pnas.1107736109] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Single-molecule approaches offer a powerful tool for deciphering the mechanisms of misfolding by measuring the conformational fluctuations of a protein with high sensitivity. We applied single-molecule force spectroscopy to observe directly the misfolding of the prion protein PrP, a protein notable for having an infectious misfolded state that is able to propagate by recruiting natively folded PrP. By measuring folding trajectories of single PrP molecules held under tension in a high-resolution optical trap, we found that the native folding pathway involves only two states, without evidence for partially folded intermediates that have been proposed to mediate misfolding. Instead, frequent but fleeting transitions were observed into off-pathway intermediates. Three different misfolding pathways were detected, all starting from the unfolded state. Remarkably, the misfolding rate was even higher than the rate for native folding. A mutant PrP with higher aggregation propensity showed increased occupancy of some of the misfolded states, suggesting these states may act as intermediates during aggregation. These measurements of individual misfolding trajectories demonstrate the power of single-molecule approaches for characterizing misfolding directly by mapping out nonnative folding pathways.
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29
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Schuler B, Müller-Späth S, Soranno A, Nettels D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 2012; 896:21-45. [PMID: 22821515 DOI: 10.1007/978-1-4614-3704-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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30
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Borgia MB, Borgia A, Best RB, Steward A, Nettels D, Wunderlich B, Schuler B, Clarke J. Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature 2011; 474:662-5. [PMID: 21623368 PMCID: PMC3160465 DOI: 10.1038/nature10099] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/01/2011] [Indexed: 12/16/2022]
Abstract
A large range of debilitating medical conditions is linked to protein misfolding, which may compete with productive folding particularly in proteins containing multiple domains. Seventy-five per cent of the eukaryotic proteome consists of multidomain proteins, yet it is not understood how interdomain misfolding is avoided. It has been proposed that maintaining low sequence identity between covalently linked domains is a mechanism to avoid misfolding. Here we use single-molecule Förster resonance energy transfer to detect and quantify rare misfolding events in tandem immunoglobulin domains from the I band of titin under native conditions. About 5.5 per cent of molecules with identical domains misfold during refolding in vitro and form an unexpectedly stable state with an unfolding half-time of several days. Tandem arrays of immunoglobulin-like domains in humans show significantly lower sequence identity between neighbouring domains than between non-adjacent domains. In particular, the sequence identity of neighbouring domains has been found to be preferentially below 40 per cent. We observe no misfolding for a tandem of naturally neighbouring domains with low sequence identity (24 per cent), whereas misfolding occurs between domains that are 42 per cent identical. Coarse-grained molecular simulations predict the formation of domain-swapped structures that are in excellent agreement with the observed transfer efficiency of the misfolded species. We infer that the interactions underlying misfolding are very specific and result in a sequence-specific domain-swapping mechanism. Diversifying the sequence between neighbouring domains seems to be a successful evolutionary strategy to avoid misfolding in multidomain proteins.
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Affiliation(s)
- Madeleine B Borgia
- University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
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31
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Understanding protein adsorption phenomena at solid surfaces. Adv Colloid Interface Sci 2011; 162:87-106. [PMID: 21295764 DOI: 10.1016/j.cis.2010.12.007] [Citation(s) in RCA: 992] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/21/2010] [Accepted: 12/28/2010] [Indexed: 11/21/2022]
Abstract
Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas. Despite considerable progress in this field there are still widely differing and even contradictive opinions on how to explain the frequently observed phenomena such as structural rearrangements, cooperative adsorption, overshooting adsorption kinetics, or protein aggregation. In this review recent achievements and new perspectives on protein adsorption processes are comprehensively discussed. The main focus is put on commonly postulated mechanistic aspects and their translation into mathematical concepts and model descriptions. Relevant experimental and computational strategies to practically approach the field of protein adsorption mechanisms and their impact on current successes are outlined.
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32
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Ferreon ACM, Deniz AA. Protein folding at single-molecule resolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1021-9. [PMID: 21303706 DOI: 10.1016/j.bbapap.2011.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/22/2011] [Accepted: 01/25/2011] [Indexed: 12/15/2022]
Abstract
The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Allan Chris M Ferreon
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines MB-19, La Jolla, CA 92037, USA
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33
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Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc Natl Acad Sci U S A 2010; 107:11793-8. [PMID: 20547872 DOI: 10.1073/pnas.1002356107] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage.
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Qu P, Lu H, Ding X, Tao Y, Lu Z. Influences of urea and guanidine hydrochloride on the interaction of 6-thioguanine with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 74:1224-1228. [PMID: 19875331 DOI: 10.1016/j.saa.2009.09.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Revised: 08/11/2009] [Accepted: 09/24/2009] [Indexed: 05/28/2023]
Abstract
The interaction of 6-thioguanine (6-TG) and bovine serum albumin (BSA) in the absence and presence of denaturant (urea and Guanidine hydrochloride) was investigated by fluorescence spectroscopic techniques. Changes of fluorescence intensity both in F(304) and in F(348) of BSA reflected increasing participation of tyrosine fluorescence in the total emission with increasing denaturant, which indicated that energy transfer from tyrosyl residues to tryptophanyl residues became less efficient in the denatured tertiary protein structure. The quenching effects of 6-TG were shown not only on the native but also on the unfolded form of BSA. The quenching constants and binding constants were calculated from the fluorescence spectra of the BSA/6-TG complex both in the absence and presence of the denaturant. The data suggested that the quenching constants and binding constants of 6-TG for BSA decreased with increasing concentration of denaturant. The spectroscopic analysis also showed antidenaturant properties of 6-TG under both denaturant conditions.
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Affiliation(s)
- Peng Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Si Pai Lou 2#, Nanjing 210096, PR China
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Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A 2009; 106:20740-5. [PMID: 19933333 DOI: 10.1073/pnas.0900622106] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin alpha suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.
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Burrows SM, Pappas D. Comparison of methods to classify and quantify free and bound states of complexes using single molecule fluorescence anisotropy. Analyst 2009; 134:1911-21. [DOI: 10.1039/b905847h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Wahl M, Rahn HJ, Röhlicke T, Kell G, Nettels D, Hillger F, Schuler B, Erdmann R. Scalable time-correlated photon counting system with multiple independent input channels. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2008; 79:123113. [PMID: 19123551 DOI: 10.1063/1.3055912] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Time-correlated single photon counting continues to gain importance in a wide range of applications. Most prominently, it is used for time-resolved fluorescence measurements with sensitivity down to the single molecule level. While the primary goal of the method used to be the determination of fluorescence lifetimes upon optical excitation by short light pulses, recent modifications and refinements of instrumentation and methodology allow for the recovery of much more information from the detected photons, and enable entirely new applications. This is achieved most successfully by continuously recording individually detected photons with their arrival time and detection channel information (time tagging), thus avoiding premature data reduction and concomitant loss of information. An important property of the instrumentation used is the number of detection channels and the way they interrelate. Here we present a new instrument architecture that allows scalability in terms of the number of input channels while all channels are synchronized to picoseconds of relative timing and yet operate independent of each other. This is achieved by means of a modular design with independent crystal-locked time digitizers and a central processing unit for sorting and processing of the timing data. The modules communicate through high speed serial links supporting the full throughput rate of the time digitizers. Event processing is implemented in programmable logic, permitting classical histogramming, as well as time tagging of individual photons and their temporally ordered streaming to the host computer. Based on the time-ordered event data, any algorithms and methods for the analysis of fluorescence dynamics can be implemented not only in postprocessing but also in real time. Results from recently emerging single molecule applications are presented to demonstrate the capabilities of the instrument.
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Affiliation(s)
- Michael Wahl
- PicoQuant GmbH, Rudower Chaussee 29, D-12489 Berlin, Germany.
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Dukes KD, Rodenberg CF, Lammi RK. Monitoring the earliest amyloid-β oligomers via quantized photobleaching of dye-labeled peptides. Anal Biochem 2008; 382:29-34. [DOI: 10.1016/j.ab.2008.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 07/08/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
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Hillger F, Hänni D, Nettels D, Geister S, Grandin M, Textor M, Schuler B. Probing protein-chaperone interactions with single-molecule fluorescence spectroscopy. Angew Chem Int Ed Engl 2008; 47:6184-8. [PMID: 18618555 DOI: 10.1002/anie.200800298] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Frank Hillger
- Universität Zürich, Biochemisches Institut, 8057 Zürich, Switzerland
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Hillger F, Hänni D, Nettels D, Geister S, Grandin M, Textor M, Schuler B. Untersuchung von Protein-Chaperon-Wechselwirkungen mit Einzelmolekülspektroskopie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Schuler B, Eaton WA. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 2008; 18:16-26. [PMID: 18221865 DOI: 10.1016/j.sbi.2007.12.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/05/2007] [Accepted: 12/05/2007] [Indexed: 11/27/2022]
Abstract
A complete understanding of a protein-folding mechanism requires description of the distribution of microscopic pathways that connect the folded and unfolded states. This distribution can, in principle, be described by computer simulations and theoretical models of protein folding, but is hidden in conventional experiments on large ensembles of molecules because only average properties are measured. A long-term goal of single-molecule fluorescence studies is to time-resolve the structural events as individual molecules make transitions between folded and unfolded states. Although such studies are still in their infancy, the work till now shows great promise and has already produced novel and important information on current issues in protein folding that has been impossible or difficult to obtain from ensemble measurements.
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Affiliation(s)
- Benjamin Schuler
- Biochemisches Institut, Universität Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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