1
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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2
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Liang Q, Zhang Y, Zhang H, Wu S, Gong W, Perrett S. Reversible Redox-Dependent Conformational Switch of the C-Terminal α-Helical Lid of Human Hsp70 Observed by In-Cell NMR. ACS Chem Biol 2023; 18:176-183. [PMID: 36524733 DOI: 10.1021/acschembio.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glutathionylation of human stress-inducible Hsp70 (hHsp70) under oxidative stress conditions has been suggested to act as an on/off switch of hHsp70 chaperone activity and thus transfer redox signals to hHsp70 clients through a change in conformation. The mechanism of this switch involves unfolding of the C-terminal α-helical lid, SBDα, upon glutathionylation, which then binds to and blocks the hHsp70 substrate-binding site. This process is reversible and redox-regulated and has been demonstrated for purified protein in solution. Here, we found that this redox-regulated reversible process also occurs in the cellular environment. Using Escherichia coli as a model system, in-cell NMR data clearly indicate that hHsp70 SBDα undergoes a conformational transition from ordered to disordered after diamide stimulation. The disordered SBDα could spontaneously recover back to the helix bundle conformation over time. This oxidative-stress induced process also occurred in cell lysate, with a similar unfolding rate as in cells, but the refolding rate was significantly slower in cell lysate. Increased temperature accelerates this process. Under heat stress alone, unfolding of the SBDα could not be detected in cells. Our in-cell NMR results provide direct support for the molecular switch model of hHsp70 redox regulation and also demonstrate the power of in-cell NMR for real-time study of protein structures during biological processes in living cells.
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Affiliation(s)
- Qihui Liang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yiying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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3
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Yin M, Wang N, Wang Q, Xia H, Cheng X, Hu H, Zhang Z, Liu H. Cloning and expression of recombinant human superoxide dismutase 1 (hSOD1) in Bacillus subtilis 1012. Biotechnol Lett 2023; 45:125-135. [PMID: 36469194 DOI: 10.1007/s10529-022-03319-x] [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: 03/06/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE We aimed to clone and express the human Cu, Zn superoxide dismutase (hSOD1) in Bacillus subtilis 1012. Also, we investigated the expression level of hSOD1 under different induction conditions. RESULT As an essential member of the antioxidant defense system in vivo, hSOD1 has become a therapeutic agent against host diseases, such as oxygen toxicity, acute inflammation, and radiation injury. The recombinant hSOD1 was successfully secreted extracellularly into B. subtilis 1012. The expression conditions were optimized, including inoculum size, different media, temperatures, and inducer concentrations. Finally, the highest level of hSOD1 was produced as a soluble form in Super rich medium by 2% inoculum with 0.2 mM of IPTG at 37 °C after the induction for 24 h. Besides, 20 g/L of lactose also displayed the same inductive effect on hSOD1 expression as that of IPTG (0.2 mM). Finally, the specific activity of purified hSOD1 was determined to be 1625 U/mg in the presence of 800 μM of Cu2+ and 20 μM of Zn2+. CONCLUSIONS We propose that the B. subtilis 1012-hSOD1 strain system has great potential in future industrial applications.
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Affiliation(s)
- Mingzhu Yin
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China
| | - Nian Wang
- College of Basic Medical Sciences, Sun YAT-SEN University, No. 135, Xingang Xi Road, Guangzhou, 510275, People's Republic of China
| | - Qiqi Wang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China
| | - Hui Xia
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China
| | - Xue Cheng
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China
| | - Haiming Hu
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China
| | - Zhigang Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China.
| | - Hongtao Liu
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Wuhan, 430065, People's Republic of China.
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4
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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5
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Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High-Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022; 61:e202112645. [PMID: 35316563 DOI: 10.1002/anie.202112645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 01/16/2023]
Abstract
Protein aggregation is central to aging, disease and biotechnology. While there has been recent progress in defining structural features of cellular protein aggregates, many aspects remain unclear due to heterogeneity of aggregates presenting obstacles to characterization. Here we report high-resolution analysis of cellular inclusion bodies (IBs) of immature human superoxide dismutase (SOD1) mutants using NMR quenched amide hydrogen/deuterium exchange (qHDX), FTIR and Congo red binding. The extent of aggregation is correlated with mutant global stability and, notably, the free energy of native dimer dissociation, indicating contributions of native-like monomer associations to IB formation. This is further manifested by a common pattern of extensive protection against H/D exchange throughout nine mutant SOD1s despite their diverse characteristics. These results reveal multiple aggregation-prone regions in SOD1 and illuminate how aggregation may occur via an ensemble of pathways.
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Affiliation(s)
- Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael V Tarasca
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Bruna Siebeneichler
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Harmeen K Deol
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Tyler G B Soule
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Clinical Neurosciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Johnathan Almey
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Susan Kelso
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Gyana G Mishra
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Hilary Simon
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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6
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Moustafa A, Perbandt M, Liebau E, Betzel C, Falke S. Crystal structure of an extracellular superoxide dismutase from Onchocerca volvulus and implications for parasite-specific drug development. Acta Crystallogr F Struct Biol Commun 2022; 78:232-240. [PMID: 35647680 PMCID: PMC9158661 DOI: 10.1107/s2053230x22005350] [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: 04/05/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
An extracellular Cu/Zn superoxide dismutase from Onchocerca volvulus, the causative agent of human onchocerciasis, was purified and crystallized and the structure was solved at 1.55 Å resolution. The solution structure of the dimeric protein was verified using small-angle X-ray scattering. Initial docking studies utilizing previously identified superoxide dismutase inhibitors indicate the potential for future drug development targeting structural features outside the active site. Superoxide dismutases (SODs) are metalloproteins that are responsible for the dismutation of superoxide anion radicals. SODs are consequently protective against oxidative damage to cellular components. Among other protective mechanisms, the filarial parasite Onchocerca volvulus has a well developed defense system to scavenge toxic free radicals using SODs during migration and sojourning of the microfilariae and adult worms in the human body. O. volvulus is responsible for the neglected disease onchocerciasis or ‘river blindness’. In the present study, an extracellular Cu/Zn-SOD from O. volvulus (OvEC-SOD) was cloned, purified and crystallized to obtain structural insight into an attractive drug target with the potential to combat onchocerciasis. The recombinant OvEC-SOD forms a dimer and the protein structure was solved and refined to 1.55 Å resolution by X-ray crystallography. Interestingly, a sulfate ion supports the coordination of the conserved copper ion. The overall protein shape was verified by small-angle X-ray scattering. The enzyme shows a different surface charge distribution and different termini when compared with the homologous human SOD. A distinct hydrophobic cleft to which both protomers of the dimer contribute was utilized for a docking approach with compounds that have previously been identified as SOD inhibitors to highlight the potential for individual structure-based drug development.
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7
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Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High‐Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dalia Naser
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Michael V. Tarasca
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | | | - Anna Schaefer
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Harmeen K. Deol
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Tyler G. B. Soule
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Clinical Neurosciences University of Calgary Calgary, AB T2N 1N4 Canada
| | - Johnathan Almey
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Susan Kelso
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Molecular Genetics University of Toronto Toronto, ON M5S 1A1 Canada
| | - Gyana G. Mishra
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Biology University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Hilary Simon
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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9
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
A detailed knowledge
of the complex processes that make cells and
organisms alive is fundamental in order to understand diseases and
to develop novel drugs and therapeutic treatments. To this aim, biological
macromolecules should ideally be characterized at atomic resolution
directly within the cellular environment. Among the existing structural
techniques, solution NMR stands out as the only one able to investigate
at high resolution the structure and dynamic behavior of macromolecules
directly in living cells. With the advent of more sensitive NMR hardware
and new biotechnological tools, modern in-cell NMR approaches have
been established since the early 2000s. At the coming of age of in-cell
NMR, we provide a detailed overview of its developments and applications
in the 20 years that followed its inception. We review the existing
approaches for cell sample preparation and isotopic labeling, the
application of in-cell NMR to important biological questions, and
the development of NMR bioreactor devices, which greatly increase
the lifetime of the cells allowing real-time monitoring of intracellular
metabolites and proteins. Finally, we share our thoughts on the future
perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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10
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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11
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Polykretis P, Luchinat E, Boscaro F, Banci L. Methylglyoxal interaction with superoxide dismutase 1. Redox Biol 2020; 30:101421. [PMID: 31931282 PMCID: PMC6957824 DOI: 10.1016/j.redox.2019.101421] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 01/08/2023] Open
Abstract
Methylglyoxal (MG) is a highly reactive aldehyde spontaneously formed in human cells mainly as a by-product of glycolysis. Such endogenous metabolite reacts with proteins, nucleotides and lipids forming advanced glycation end-products (AGEs). MG binds to arginine, lysine and cysteine residues of proteins causing the formation of stable adducts that can interfere with protein function. Among the proteins affected by glycation, MG has been found to react with superoxide dismutase 1 (SOD1), a fundamental anti-oxidant enzyme that is abundantly expressed in neurons. Considering the high neuronal susceptibility to MG-induced oxidative stress, we sought to investigate by mass spectrometry and NMR spectroscopy which are the structural modifications induced on SOD1 by the reaction with MG. We show that MG reacts preferentially with the disulfide-reduced, demetallated form of SOD1, gradually causing its unfolding, and to a lesser extent, with the intermediate state of maturation – the reduced, zinc-bound homodimer – causing its gradual monomerization. These results suggest that MG could impair the correct maturation of SOD1 in vivo, thus both increasing cellular oxidative stress and promoting the cytotoxic misfolding and aggregation process of SOD1. MG forms stable adducts with the immature forms of SOD1. MG causes the unfolding of the apo-SOD1SH form. MG causes the monomerization of the E,Zn-SOD1SH form. In both forms, arginine 143 is more prone to interact with MG. The structural modifications caused by MG impair the correct maturation of SOD1.
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Affiliation(s)
- Panagis Polykretis
- Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale Morgagni 50, 50134, Florence, Italy
| | - Francesca Boscaro
- Mass Spectrometry Center (CISM), University of Florence, via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
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12
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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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13
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Cerofolini L, Giuntini S, Barbieri L, Pennestri M, Codina A, Fragai M, Banci L, Luchinat E, Ravera E. Real-Time Insights into Biological Events: In-Cell Processes and Protein-Ligand Interactions. Biophys J 2019; 116:239-247. [PMID: 30580921 PMCID: PMC6350048 DOI: 10.1016/j.bpj.2018.11.3132] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/30/2018] [Accepted: 11/27/2018] [Indexed: 11/15/2022] Open
Abstract
FlowNMR has the aim of continuously monitoring processes that occur in conditions that are not compatible with being carried out within a closed tube. However, it is sample intensive and not suitable for samples, such as proteins or living cells, that are often available in limited volumes and possibly low concentrations. We here propose a dialysis-based modification of a commercial flowNMR setup that allows for recycling the medium while confining the sample (proteins and cells) within the active volume of the tube. This approach is demonstrated in the specific cases of in-cell NMR and protein-based ligand studies.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy
| | | | - Anna Codina
- Bruker UK Limited, Banner Lane, Coventry, United Kingdom
| | - Marco Fragai
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Experimental and Clinical Biomedical Sciences, Mario Serio, University of Florence, Florence, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy.
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14
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In-Cell NMR: Analysis of Protein-Small Molecule Interactions, Metabolic Processes, and Protein Phosphorylation. Int J Mol Sci 2019; 20:ijms20020378. [PMID: 30658393 PMCID: PMC6359726 DOI: 10.3390/ijms20020378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables the non-invasive observation of biochemical processes, in living cells, at comparably high spectral and temporal resolution. Preferably, means of increasing the detection limit of this powerful analytical method need to be applied when observing cellular processes under physiological conditions, due to the low sensitivity inherent to the technique. In this review, a brief introduction to in-cell NMR, protein–small molecule interactions, posttranslational phosphorylation, and hyperpolarization NMR methods, used for the study of metabolites in cellulo, are presented. Recent examples of method development in all three fields are conceptually highlighted, and an outlook into future perspectives of this emerging area of NMR research is given.
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15
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Polykretis P, Cencetti F, Donati C, Luchinat E, Banci L. Cadmium effects on superoxide dismutase 1 in human cells revealed by NMR. Redox Biol 2019; 21:101102. [PMID: 30654299 PMCID: PMC6348768 DOI: 10.1016/j.redox.2019.101102] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 11/24/2022] Open
Abstract
Cadmium is a toxic pollutant that in recent decades has become more widespread in the environment due to anthropogenic activities, significantly increasing the risk of exposure. Concurrently, a continually growing body of research has begun to enumerate the harmful effects that this heavy metal has on human health. Consequently, additional research is required to better understand the mechanism and effects of cadmium at the molecular level. The main mechanism of cadmium toxicity is based on the indirect induction of severe oxidative stress, through several processes that unbalance the anti-oxidant cellular defence system, including the displacement of metals such as zinc from its native binding sites. Such mechanism was thought to alter the in vivo enzymatic activity of SOD1, one of the main antioxidant proteins of many tissues, including the central nervous system. SOD1 misfolding and aggregation is correlated with cytotoxicity in neurodegenerative diseases such as amyotrophic lateral sclerosis. We assessed the effect of cadmium on SOD1 folding and maturation pathway directly in human cells through in-cell NMR. Cadmium does not directly bind intracellular SOD1, instead causes the formation of its intramolecular disulfide bond in the zinc-bound form. Metallothionein overexpression is strongly induced by cadmium, reaching NMR-detectable levels. The intracellular availability of zinc modulates both SOD1 oxidation and metallothionein overexpression, strengthening the notion that zinc-loaded metallothioneins help maintaining the redox balance under cadmium-induced acute stress. Cadmium does not bind to superoxide dismutase 1 (SOD1) in human cells. In defect of zinc, cadmium causes the premature oxidation of SOD1. Cadmium induces the overexpression of metallothioneins to levels detectable by NMR. Zinc modulates metallothionein expression and attenuates SOD1 oxidation.
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Affiliation(s)
- Panagis Polykretis
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Cencetti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Chiara Donati
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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16
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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17
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Wall KP, Hough LE. In-Cell NMR within Budding Yeast Reveals Cytoplasmic Masking of Hydrophobic Residues of FG Repeats. Biophys J 2018; 115:1690-1695. [PMID: 30342747 PMCID: PMC6225093 DOI: 10.1016/j.bpj.2018.08.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022] Open
Abstract
In-cell NMR spectroscopy is a powerful tool to determine the properties of proteins and nucleic acids within living cells. In-cell NMR can give site-specific measurements of interactions, modifications, and dynamics as well as their modulation by the cellular environment. In-cell NMR requires selective incorporation of heavy isotopes into a protein of interest, either through the introduction of exogenously produced protein to a cell's interior or the selective overexpression of a protein. We developed conditions to allow the use of Saccharomyces cerevisiae, which was chosen because of its genetic tractability, as a eukaryotic expression system for in-cell NMR. We demonstrate this technique using a fragment of S. cerevisiae Nsp1, an FG Nup. FG Nups are intrinsically disordered proteins containing phenylalanine (F)-glycine (G) repeats and form the selective barrier within the nuclear pore complex. Yeast FG Nups have previously been shown to be maintained in a highly dynamic state within living bacteria as measured by in-cell NMR. Interactions thought to stabilize this dynamic state are also present in the protein's native organism, although site specificity of interaction is different between the two cytosols.
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Affiliation(s)
- Kathryn P Wall
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado, Boulder, Colorado.
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18
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The cysteine-reactive small molecule ebselen facilitates effective SOD1 maturation. Nat Commun 2018; 9:1693. [PMID: 29703933 PMCID: PMC5923229 DOI: 10.1038/s41467-018-04114-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/04/2018] [Indexed: 11/20/2022] Open
Abstract
Superoxide dismutase-1 (SOD1) mutants, including those with unaltered enzymatic activity, are known to cause amyotrophic lateral sclerosis (ALS). Several destabilizing factors contribute to pathogenicity including a reduced ability to complete the normal maturation process which comprises folding, metal cofactor acquisition, intra-subunit disulphide bond formation and dimerization. Immature SOD1 forms toxic oligomers and characteristic large insoluble aggregates within motor system cells. Here we report that the cysteine-reactive molecule ebselen efficiently confers the SOD1 intra-subunit disulphide and directs correct SOD1 folding, depopulating the globally unfolded precursor associated with aggregation and toxicity. Assisted formation of the unusual SOD1 cytosolic disulphide bond could have potential therapeutic applications. In less reducing environments, ebselen forms a selenylsulphide with Cys111 and restores the monomer–dimer equilibrium of A4V SOD1 to wild-type. Ebselen is therefore a potent bifunctional pharmacological chaperone for SOD1 that combines properties of the SOD1 chaperone hCCS and the recently licenced antioxidant drug, edaravone. Mutations in superoxide dismutase-1 (SOD1) cause amyotrophic lateral sclerosis (ALS). Here the authors present the SOD1 crystal structure bound to the small cysteine-reactive molecule ebselen and show that ebselen is a chaperone for SOD1.
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19
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New structural and functional insights from in-cell NMR. Emerg Top Life Sci 2018; 2:29-38. [PMID: 33525780 DOI: 10.1042/etls20170136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022]
Abstract
In recent years, it has become evident that structural characterization would gain significantly in terms of biological relevance if framed within a cellular context, while still maintaining the atomic resolution. Therefore, major efforts have been devoted to developing Cellular Structural Biology approaches. In this respect, in-cell NMR can provide and has provided relevant contributions to the field, not only to investigate the structural and dynamical properties of macromolecules in solution but, even more relevant, to understand functional processes directly in living cells and the factors that modulate them, such as exogenous molecules, partner proteins, and oxidative stress. In this commentary, we review and discuss some of the main contributions to the understanding of protein structural and functional properties achieved by in-cell NMR.
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20
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Lai YT, Yang Y, Hu L, Cheng T, Chang YY, Koohi-Moghadam M, Wang Y, Xia J, Wang J, Li H, Sun H. Integration of fluorescence imaging with proteomics enables visualization and identification of metallo-proteomes in living cells. Metallomics 2017; 9:38-47. [PMID: 27830853 DOI: 10.1039/c6mt00169f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Metalloproteins account for nearly one-third of proteins in proteomes. To date, the identification of metalloproteins relies mainly on protein purification and the subsequent characterization of bound metals, which often leads to losses of metal ions bound weakly and transiently. Herein, we developed a strategy to visualize and subsequently identify endogenous metalloproteins and metal-binding proteins in living cells via integration of fluorescence imaging with proteomics. We synthesized a "metal-tunable" fluorescent probe (denoted as Mn+-TRACER) that rapidly enters cells to target proteins with 4-40 fold fluorescence enhancements. By using Ni2+-TRACER as an example, we demonstrate the feasibility of tracking Ni2+-binding proteins in vitro, while cellular small molecules exhibit negligible interference on the labeling. We identified 44 Ni2+-binding proteins from microbes using Helicobacter pylori as a showcase. We further applied Cu2+-TRACER to mammalian cells and found 54 Cu2+-binding proteins. The strategy we report here provides a great opportunity to track various endogenous metallo-proteomes and to mine potential targets of metallodrugs.
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Affiliation(s)
- Yau-Tsz Lai
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Ya Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Ligang Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Tianfan Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Yuen-Yan Chang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Mohamad Koohi-Moghadam
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Yuchuan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Junwen Wang
- Center for Individualized Medicine & Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259 USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259 USA
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
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21
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Pauwels K, Lebrun P, Tompa P. To be disordered or not to be disordered: is that still a question for proteins in the cell? Cell Mol Life Sci 2017; 74:3185-3204. [PMID: 28612216 PMCID: PMC11107661 DOI: 10.1007/s00018-017-2561-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
Abstract
There is ample evidence that many proteins or regions of proteins lack a well-defined folded structure under native-like conditions. These are called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Whether this intrinsic disorder is also their main structural characteristic in living cells has been a matter of intense debate. The structural analysis of IDPs became an important challenge also because of their involvement in a plethora of human diseases, which made IDPs attractive targets for therapeutic development. Therefore, biophysical approaches are increasingly being employed to probe the structural and dynamical state of proteins, not only in isolation in a test tube, but also in a complex biological environment and even within intact cells. Here, we survey direct and indirect evidence that structural disorder is in fact the physiological state of many proteins in the proteome. The paradigmatic case of α-synuclein is used to illustrate the controversial nature of this topic.
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Affiliation(s)
- Kris Pauwels
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Pierre Lebrun
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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22
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The Role of Metal Binding in the Amyotrophic Lateral Sclerosis-Related Aggregation of Copper-Zinc Superoxide Dismutase. Molecules 2017; 22:molecules22091429. [PMID: 28850080 PMCID: PMC6151412 DOI: 10.3390/molecules22091429] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/22/2017] [Accepted: 08/27/2017] [Indexed: 12/13/2022] Open
Abstract
Protein misfolding and conformational changes are common hallmarks in many neurodegenerative diseases involving formation and deposition of toxic protein aggregates. Although many players are involved in the in vivo protein aggregation, physiological factors such as labile metal ions within the cellular environment are likely to play a key role. In this review, we elucidate the role of metal binding in the aggregation process of copper-zinc superoxide dismutase (SOD1) associated to amyotrophic lateral sclerosis (ALS). SOD1 is an extremely stable Cu-Zn metalloprotein in which metal binding is crucial for folding, enzymatic activity and maintenance of the native conformation. Indeed, demetalation in SOD1 is known to induce misfolding and aggregation in physiological conditions in vitro suggesting that metal binding could play a key role in the pathological aggregation of SOD1. In addition, this study includes recent advances on the role of aberrant metal coordination in promoting SOD1 aggregation, highlighting the influence of metal ion homeostasis in pathologic aggregation processes.
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23
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Luchinat E, Banci L. In-cell NMR: a topical review. IUCRJ 2017; 4:108-118. [PMID: 28250949 PMCID: PMC5330521 DOI: 10.1107/s2052252516020625] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Classical structural biology approaches allow structural characterization of biological macromolecules in vitro, far from their physiological context. Nowadays, thanks to the wealth of structural data available and to technological and methodological advances, the interest of the research community is gradually shifting from pure structural determination towards the study of functional aspects of biomolecules. Therefore, a cellular structural approach is ideally needed to characterize biological molecules, such as proteins, in their native cellular environment and the functional processes that they are involved in. In-cell NMR is a new application of high-resolution nuclear magnetic resonance spectroscopy that allows structural and dynamical features of proteins and other macromolecules to be analyzed directly in living cells. Owing to its challenging nature, this methodology has shown slow, but steady, development over the past 15 years. To date, several in-cell NMR approaches have been successfully applied to both bacterial and eukaryotic cells, including several human cell lines, and important structural and functional aspects have been elucidated. In this topical review, the major advances of in-cell NMR are summarized, with a special focus on recent developments in eukaryotic and mammalian cells.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center – CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Biomedical, Clinical and Experimental Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center – CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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24
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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25
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Müntener T, Häussinger D, Selenko P, Theillet FX. In-Cell Protein Structures from 2D NMR Experiments. J Phys Chem Lett 2016; 7:2821-5. [PMID: 27379949 DOI: 10.1021/acs.jpclett.6b01074] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures.
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Affiliation(s)
- Thomas Müntener
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Philipp Selenko
- Department of Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) , Robert Roessle Straße 10, 13125 Berlin, Germany
| | - Francois-Xavier Theillet
- Department of Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) , Robert Roessle Straße 10, 13125 Berlin, Germany
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26
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Fuccio C, Luchinat E, Barbieri L, Neri S, Fragai M. Algal autolysate medium to label proteins for NMR in mammalian cells. JOURNAL OF BIOMOLECULAR NMR 2016; 64:275-280. [PMID: 27106902 DOI: 10.1007/s10858-016-0026-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in (15)N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained.
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Affiliation(s)
- Carmelo Fuccio
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
- Department of Biomedical, Clinical and Experimental Sciences, University of Florence, Viale Morgagni 50, 50134, Florence, Italy
| | - Letizia Barbieri
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Sara Neri
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
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27
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Sequential protein expression and selective labeling for in-cell NMR in human cells. Biochim Biophys Acta Gen Subj 2016; 1860:527-33. [DOI: 10.1016/j.bbagen.2015.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/23/2022]
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Abstract
Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When this is done, important structural and functional features of macromolecules, which depend on their native network of interactions within the cell, may be lost. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that allows macromolecules to be analyzed in living cells, at the atomic level. In-cell NMR can be applied to several cellular systems to obtain biologically relevant structural and functional information. Here we summarize the existing approaches and focus on the applications to protein folding, interactions, and post-translational modifications.
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Affiliation(s)
- Enrico Luchinat
- From the Magnetic Resonance Center (CERM), the Department of Biomedical, Clinical and Experimental Sciences, and
| | - Lucia Banci
- From the Magnetic Resonance Center (CERM), the Department of Chemistry, University of Florence, Florence 50121, Italy
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29
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Direct structural evidence of protein redox regulation obtained by in-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:198-204. [PMID: 26589182 DOI: 10.1016/j.bbamcr.2015.11.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 12/30/2022]
Abstract
The redox properties of cellular environments are critical to many functional processes, and are strictly controlled in all living organisms. The glutathione-glutathione disulfide (GSH-GSSG) couple is the most abundant intracellular redox couple. A GSH redox potential can be calculated for each cellular compartment, which reflects the redox properties of that environment. This redox potential is often used to predict the redox state of a disulfide-containing protein, based on thermodynamic considerations. However, thiol-disulfide exchange reactions are often catalyzed by specific partners, and the distribution of the redox states of a protein may not correspond to the thermodynamic equilibrium with the GSH pool. Ideally, the protein redox state should be measured directly, bypassing the need to extrapolate from the GSH. Here, by in-cell NMR, we directly observe the redox state of three human proteins, Cox17, Mia40 and SOD1, in the cytoplasm of human and bacterial cells. We compare the observed distributions of redox states with those predicted by the GSH redox potential, and our results partially agree with the predictions. Discrepancies likely arise from the fact that the redox state of SOD1 is controlled by a specific partner, its copper chaperone (CCS), in a pathway which is not linked to the GSH redox potential. In principle, in-cell NMR allows determining whether redox proteins are at the equilibrium with GSH, or they are kinetically regulated. Such approach does not need assumptions on the redox potential of the environment, and provides a way to characterize each redox-regulating pathway separately.
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30
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Chattopadhyay M, Nwadibia E, Strong CD, Gralla EB, Valentine JS, Whitelegge JP. The Disulfide Bond, but Not Zinc or Dimerization, Controls Initiation and Seeded Growth in Amyotrophic Lateral Sclerosis-linked Cu,Zn Superoxide Dismutase (SOD1) Fibrillation. J Biol Chem 2015; 290:30624-36. [PMID: 26511321 DOI: 10.1074/jbc.m115.666503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 12/22/2022] Open
Abstract
Aggregation of copper-zinc superoxide dismutase (SOD1) is a defining feature of familial ALS caused by inherited mutations in the sod1 gene, and misfolded and aggregated forms of wild-type SOD1 are found in both sporadic and familial ALS cases. Mature SOD1 owes its exceptional stability to a number of post-translational modifications as follows: formation of the intramolecular disulfide bond, binding of copper and zinc, and dimerization. Loss of stability due to the failure to acquire one or more of these modifications is proposed to lead to aggregation in vivo. Previously, we showed that the presence of apo-, disulfide-reduced SOD1, the most immature form of SOD1, results in initiation of fibrillation of more mature forms that have an intact Cys-57-Cys-146 disulfide bond and are partially metallated. In this study, we examine the ability of each of the above post-translational modifications to modulate fibril initiation and seeded growth. Cobalt or zinc binding, despite conferring great structural stability, neither inhibits the initiation propensity of disulfide-reduced SOD1 nor consistently protects disulfide-oxidized SOD1 from being recruited into growing fibrils across wild-type and a number of ALS mutants. In contrast, reduction of the disulfide bond, known to be necessary for fibril initiation, also allows for faster recruitment during seeded amyloid growth. These results identify separate factors that differently influence seeded growth and initiation and indicate a lack of correlation between the overall thermodynamic stability of partially mature SOD1 states and their ability to initiate fibrillation or be recruited by a growing fibril.
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Affiliation(s)
- Madhuri Chattopadhyay
- From the Department of Chemistry and Biochemistry UCLA, Los Angeles, California 90095,
| | - Ekeoma Nwadibia
- From the Department of Chemistry and Biochemistry UCLA, Los Angeles, California 90095
| | - Cynthia D Strong
- the Department of Chemistry, Cornell College, Mt. Vernon, Iowa 52314, and
| | - Edith Butler Gralla
- From the Department of Chemistry and Biochemistry UCLA, Los Angeles, California 90095
| | | | - Julian P Whitelegge
- From the Department of Chemistry and Biochemistry UCLA, Los Angeles, California 90095, the The Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, California 90095
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31
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Leal SS, Cristóvão JS, Biesemeier A, Cardoso I, Gomes CM. Aberrant zinc binding to immature conformers of metal-free copper-zinc superoxide dismutase triggers amorphous aggregation. Metallomics 2015; 7:333-46. [PMID: 25554447 DOI: 10.1039/c4mt00278d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Superoxide dismutase 1 (SOD1) is a Cu/Zn metalloenzyme that aggregates in amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. Correct metal insertion during SOD1 biosynthesis is critical to prevent misfolding; however Zn(2+) can bind to the copper-site leading to an aberrantly metallated protein. These effects of Zn(2+) misligation on SOD1 aggregation remain to be explored, even though Zn(2+) levels are upregulated in ALS motor neurons. Here we use complementary biophysical methods to investigate Zn(2+) binding and its effects on the aggregation of three immature metal-free SOD1 conformers that represent biogenesis intermediates: dimeric, monomeric and reduced monomeric SOD1. Using isothermal titration calorimetry we determined that Zn(2+) binds to all conformers both at the zinc- as well as to the copper-site; however Zn(2+) binding mechanisms to the zinc-site have distinct characteristics across immature conformers. We show that this 'zinc overload' of immature SOD1 promotes intermolecular interactions, as evidenced by dynamic light scattering and ThT fluorescence kinetic studies. Analysis of aged zinc-induced aggregates by energy-dispersive X-ray and electron energy-loss spectroscopy shows that aggregates integrate some Zn(2+). In addition, electron diffraction analysis identifies nano-scaled crystalline materials and amyloid fibril-like reflections. Transmission electron microscopy reveals that Zn(2+) diverts the SOD1 aggregation pathway from fibrils to amorphous aggregate, and electrophoretic analysis evidences an increase in insoluble materials. Overall, we provide evidence that aberrant zinc coordination to immature conformers broadens the population of SOD1 misfolded species at early aggregation stages and provide evidence for a high structural polymorphism and heterogeneity of SOD1 aggregates.
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Affiliation(s)
- Sónia S Leal
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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32
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Barbieri L, Luchinat E, Banci L. Protein interaction patterns in different cellular environments are revealed by in-cell NMR. Sci Rep 2015; 5:14456. [PMID: 26399546 PMCID: PMC4585868 DOI: 10.1038/srep14456] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
In-cell NMR allows obtaining atomic-level information on biological macromolecules in their physiological environment. Soluble proteins may interact with the cellular environment in different ways: either specifically, with their functional partners, or non-specifically, with other cellular components. Such behaviour often causes the disappearance of the NMR signals. Here we show that by introducing mutations on the human protein profilin 1, used here as a test case, the in-cell NMR signals can be recovered. In human cells both specific and non-specific interactions are present, while in bacterial cells only the effect of non-specific interactions is observed. By comparing the NMR signal recovery pattern in human and bacterial cells, the relative contribution of each type of interaction can be assessed. This strategy allows detecting solution in-cell NMR spectra of soluble proteins without altering their fold, thus extending the applicability of in-cell NMR to a wider range of proteins.
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Affiliation(s)
- Letizia Barbieri
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.,Giotto Biotech S.r.l., Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.,Department of Biomedical, Clinical and Experimental Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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33
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Wang Y, Hu L, Yang X, Chang YY, Hu X, Li H, Sun H. On-line coupling of continuous-flow gel electrophoresis with inductively coupled plasma-mass spectrometry to quantitatively evaluate intracellular metal binding properties of metallochaperones HpHypA and HpHspA in E. coli cells. Metallomics 2015; 7:1399-406. [PMID: 26000660 DOI: 10.1039/c5mt00054h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
On-line coupling of gel electrophoresis with inductively coupled plasma-mass spectrometry (GE-ICP-MS) offers a strategy to monitor intracellular metals and their associated proteins simultaneously. Herein, we examine the feasibility of the GE-ICP-MS system in the quantitative analysis of intracellular metal binding properties using two Helicobacter pylori metallochaperones HypA and HspA overexpressed in E. coli cells as showcases. We show that parallel detection of metal and sulfur signals allows accurate quantification of intracellular metal-protein stoichiometries, even for metalloproteins that bind metal ions with micromolar affinities. Using this approach, we demonstrate that only a trace amount of Ni(2+) is associated with HpHypA in cells, distinct from the in vitro observation of stoichiometric binding, while HpHypA exhibits high fidelity towards its structural metal Zn(2+) with stoichiometric Zn(2+) binding. In contrast, HpHspA associates with Zn(2+), Ni(2+), Cu(2+) and Co(2+) from an essential metal pool with ca. 0.5 molar equivalents of total metals bound per HpHspA monomer. The metal binding properties of both HpHypA and HpHspA were altered by Bi(3+). The binding of both Zn(2+) and Ni(2+) to HpHypA was suppressed under the stress of Bi(3+) in cells, different from in vitro studies that showed that Bi(3+) interfered with Zn(2+) but not Ni(2+) binding. This study provides an analytical approach to investigate the intracellular metal selectivity of overexpressed metalloproteins.
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Affiliation(s)
- Yuchuan Wang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China.
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34
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In-cell NMR reveals potential precursor of toxic species from SOD1 fALS mutants. Nat Commun 2014; 5:5502. [PMID: 25429517 DOI: 10.1038/ncomms6502] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/07/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the superoxide dismutase 1 (SOD1) gene are related to familial cases of amyotrophic lateral sclerosis (fALS). Here we exploit in-cell NMR to characterize the protein folding and maturation of a series of fALS-linked SOD1 mutants in human cells and to obtain insight into their behaviour in the cellular context, at the molecular level. The effect of various mutations on SOD1 maturation are investigated by changing the availability of metal ions in the cells, and by coexpressing the copper chaperone for SOD1, hCCS. We observe for most of the mutants the occurrence of an unstructured SOD1 species, unable to bind zinc. This species may be a common precursor of potentially toxic oligomeric species, that are associated with fALS. Coexpression of hCCS in the presence of copper restores the correct maturation of the SOD1 mutants and prevents the formation of the unstructured species, confirming that hCCS also acts as a molecular chaperone.
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35
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Barbieri L, Luchinat E, Banci L. Structural insights of proteins in sub-cellular compartments: In-mitochondria NMR. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2492-6. [DOI: 10.1016/j.bbamcr.2014.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 10/25/2022]
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Abstract
Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biological functions. Whereas "looking into cells" is typically said in reference to optical microscopy, high-resolution in-cell and on-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful method that offers exciting new possibilities for structural and functional studies in and on live cells. In contrast to conventional imaging techniques, in- and on-cell NMR methods do not provide spatial information on cellular biomolecules. Instead, they enable atomic-resolution insights into the native cell states of proteins, nucleic acids, glycans, and lipids. Here we review recent advances and developments in both fields and discuss emerging concepts that have been delineated with these methods.
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Affiliation(s)
- Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, Maryland 20852-1448;
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37
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Lerche MH, Jensen PR, Karlsson M, Meier S. NMR insights into the inner workings of living cells. Anal Chem 2014; 87:119-32. [PMID: 25084065 DOI: 10.1021/ac501467x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mathilde H Lerche
- Albeda Research , Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
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38
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Felli IC, Gonnelli L, Pierattelli R. In-cell ¹³C NMR spectroscopy for the study of intrinsically disordered proteins. Nat Protoc 2014; 9:2005-16. [PMID: 25079425 DOI: 10.1038/nprot.2014.124] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A large number of proteins carry out their function in highly flexible and disordered states, lacking a well-defined 3D structure. These proteins, referred to as intrinsically disordered proteins (IDPs), are now in the spotlight of modern structural biology. Nuclear magnetic resonance (NMR) spectroscopy represents a unique tool for accessing atomic resolution information on IDPs in complex environments as whole cells, provided that the methods are optimized to their peculiar properties and to the characteristics of in-cell experiments. We describe procedures for the preparation of in-cell NMR samples, as well as for the setup of NMR experiments and their application to in-cell studies, using human α-synuclein overexpressed in Escherichia coli as an example. The expressed protein is labeled with (13)C and (15)N stable isotopes to enable the direct recording of (13)C-detected NMR experiments optimized for the properties of IDPs. The entire procedure covers 24 h, including cell transformation, cell growth overnight, setup of the spectrometer and NMR experiment recording.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Gonnelli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
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39
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Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. Intrazelluläre NMR- und EPR-Spektroskopie von biologischen Makromolekülen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311320] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. In-cell NMR and EPR spectroscopy of biomacromolecules. Angew Chem Int Ed Engl 2014; 53:10300-14. [PMID: 25070284 DOI: 10.1002/anie.201311320] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 12/21/2022]
Abstract
The dream of cell biologists is to be able to watch biological macromolecules perform their duties in the intracellular environment of live cells. Ideally, the observation of both the location and the conformation of these macromolecules with biophysical techniques is desired. The development of many fluorescence techniques, including superresolution fluorescence microscopy, has significantly enhanced our ability to spot proteins and other molecules in the crowded cellular environment. However, the observation of their structure and conformational changes while they attend their business is still very challenging. In principle, NMR and EPR spectroscopy can be used to investigate the conformation and dynamics of biological macromolecules in living cells. The development of in-cell magnetic resonance techniques has demonstrated the feasibility of this approach. Herein we review the different techniques with a focus on liquid-state in-cell NMR spectroscopy, provide an overview of applications, and discuss the challenges that lie ahead.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt (Germany)
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41
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Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS. Superoxide dismutases and superoxide reductases. Chem Rev 2014; 114:3854-918. [PMID: 24684599 PMCID: PMC4317059 DOI: 10.1021/cr4005296] [Citation(s) in RCA: 580] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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42
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Allen S, Dennison C. The importance of Zn(ii) binding by the human copper metallochaperone for Cu,Zn-superoxide dismutase. RSC Adv 2014. [DOI: 10.1039/c4ra03806a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Zn(ii) removal converts dimeric human CCS to a monomer that weakens its interaction with Cu,Zn-superoxide dismutase and may be disease causing.
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Affiliation(s)
- Stephen Allen
- Institute for Cell and Molecular Biosciences
- Medical School
- Newcastle University
- Newcastle upon Tyne, UK
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences
- Medical School
- Newcastle University
- Newcastle upon Tyne, UK
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43
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Li H, Sun H. In-cell NMR: an emerging approach for monitoring metal-related events in living cells. Metallomics 2014; 6:69-76. [DOI: 10.1039/c3mt00224a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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44
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Kosol S, Contreras-Martos S, Cedeño C, Tompa P. Structural characterization of intrinsically disordered proteins by NMR spectroscopy. Molecules 2013; 18:10802-28. [PMID: 24008243 PMCID: PMC6269831 DOI: 10.3390/molecules180910802] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/19/2013] [Accepted: 08/30/2013] [Indexed: 01/25/2023] Open
Abstract
Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as 13C-direct detected experiments, paramagnetic relaxation enhancements (PREs) or residual dipolar couplings (RDCs) for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.
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Affiliation(s)
- Simone Kosol
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
| | - Sara Contreras-Martos
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Cesyen Cedeño
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest 1518, Hungary
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
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45
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Ye Y, Liu X, Zhang Z, Wu Q, Jiang B, Jiang L, Zhang X, Liu M, Pielak GJ, Li C. 19F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells. Chemistry 2013; 19:12705-10. [DOI: 10.1002/chem.201301657] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 01/01/2023]
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46
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Danielsson J, Inomata K, Murayama S, Tochio H, Lang L, Shirakawa M, Oliveberg M. Pruning the ALS-associated protein SOD1 for in-cell NMR. J Am Chem Soc 2013; 135:10266-9. [PMID: 23819500 DOI: 10.1021/ja404425r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
To efficiently deliver isotope-labeled proteins into mammalian cells poses a main challenge for structural and functional analysis by in-cell NMR. In this study we have employed cell-penetrating peptides (CPPs) to deliver the ALS-associated protein superoxide dismutase (SOD1) into HeLa cells. Our results show that, although full-length SOD1 cannot be efficiently internalized, a variant in which the active-site loops IV and VII have been truncated (SOD1(ΔIVΔVII)) yields high cytosolic delivery. The reason for the enhanced delivery of SOD1(ΔIVΔVII) seems to be the elimination of negatively charged side chains, which alters the net charge of the CPP-SOD1 complex from neutral to +4. The internalized SOD1(ΔIVΔVII) protein displays high-resolution in-cell NMR spectra similar to, but not identical to, those of the lysate of the cells. Spectral differences are found mainly in the dynamic β strands 4, 5, and 7, triggered by partial protonation of the His moieties of the Cu-binding site. Accordingly, SOD1(ΔIVΔVII) doubles here as an internal pH probe, revealing cytosolic acidification under the experimental treatment. Taken together, these observations show that CPP delivery, albeit inefficient at first trials, can be tuned by protein engineering to allow atomic-resolution NMR studies of specific protein structures that have evaded other in-cell NMR approaches: in this case, the structurally elusive apoSOD1 barrel implicated as precursor for misfolding in ALS.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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47
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Banci L, Barbieri L, Bertini I, Luchinat E, Secci E, Zhao Y, Aricescu AR. Atomic-resolution monitoring of protein maturation in live human cells by NMR. Nat Chem Biol 2013; 9:297-9. [PMID: 23455544 PMCID: PMC4017183 DOI: 10.1038/nchembio.1202] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/31/2013] [Indexed: 12/15/2022]
Abstract
We used NMR directly in live human cells to describe the complete post-translational maturation process of human superoxide dismutase 1 (SOD1). We could follow, at atomic resolution, zinc binding, homodimer formation and copper uptake, and discover that copper chaperone for SOD1 (CCS) oxidation of the SOD1 intrasubunit disulfide bond occurs through both copper-dependent and independent mechanisms. Our approach represents a new strategy for structural investigation of endogeneously expressed proteins within a physiological (cellular) environment.
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Affiliation(s)
- Lucia Banci
- CERM, Magnetic Resonance Center, University of Florence, Florence, Italy.
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Li C, Liu M. Protein dynamics in living cells studied by in-cell NMR spectroscopy. FEBS Lett 2013; 587:1008-11. [PMID: 23318712 DOI: 10.1016/j.febslet.2012.12.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/18/2012] [Accepted: 12/18/2012] [Indexed: 01/06/2023]
Abstract
Most proteins function in cells where protein concentrations can reach 400 g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions.
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Affiliation(s)
- Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430072, PR China.
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Abstract
Isotope-assisted multi-dimensional NMR spectroscopy can now be applied to proteins inside living cells. The technique, called in-cell NMR, aims to investigate the structures, interactions and dynamics of proteins under their native conditions, ideally at an atomic resolution. The application has begun with bacterial cells but has now expanded to mammalian cultured cells, such as HeLa cells. The importance of the realization of such 'in-mammalian cell' NMR should be stressed, as these are the cells most often employed in cell biology. Hence, a substantially wide range of application would be possible in the near future once the technique has been well developed.
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Affiliation(s)
- Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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