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Doerner B, Della Sala F, Wang S, Webb SJ. Reaction, Recognition, Relay: Anhydride Hydrolysis Reported by Conformationally Responsive Fluorinated Foldamers in Micelles. Angew Chem Int Ed Engl 2024; 63:e202405924. [PMID: 38703400 DOI: 10.1002/anie.202405924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural membrane receptors are proteins that can report on changes in the concentration of external chemical messengers. Messenger binding to a receptor produces conformational changes that are relayed through the membrane into the cell; this information allows cells to adapt to changes in their environment. Artificial membrane receptors (R)-1 and (S)-1 are helical α-aminoisobutyric acid (Aib) foldamers that replicate key parts of this information relay. Solution-phase 19F NMR spectroscopy of zinc(II)-capped receptor 1, either in organic solvent or in membrane-mimetic micelles, showed messenger binding produced an enrichment of either left- or right-handed screw-sense; the chirality of the bound messenger was relayed to the other receptor terminus. Furthermore, in situ production of a chemical messenger in the external aqueous environment could be detected in real-time by a racemic mixture of receptor 1 in micelles. The hydrolysis of insoluble anhydrides produced carboxylate in the aqueous phase, which bound to the receptors and gave a distinct 19F NMR output from inside the hydrophobic region of the micelles.
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Affiliation(s)
- Benedicte Doerner
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Flavio Della Sala
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Siyuan Wang
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Simon J Webb
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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Heravi S, Power JVD, Yethiraj A, Booth V. The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α-synuclein. Protein Sci 2024; 33:e4894. [PMID: 38358134 PMCID: PMC10868423 DOI: 10.1002/pro.4894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 02/16/2024]
Abstract
α-synuclein is an intrinsically disordered protein (IDP) whose aggregation in presynaptic neuronal cells is a pathological hallmark of Lewy body formation and Parkinson's disease. This aggregation process is likely affected by the crowded macromolecular cellular environment. In this study, α-synuclein was studied in the presence of both a synthetic crowder, Ficoll70, and a biological crowder composed of lysed cells that better mimics the biocomplexity of the cellular environment. 15 N-1 H HSQC NMR results show similar α-synuclein chemical shifts in non-crowded and all crowded conditions implying that it remains similarly unstructured in all conditions. Nevertheless, both HSQC NMR and fluorescence measurements indicate that, only in the cell lysate, α-synuclein forms aggregates over a timescale of 48 h. 15 N-edited diffusion measurements indicate that all crowders slow down the α-synuclein's diffusivity. Interestingly, at high concentrations, α-synuclein diffuses faster in cell lysate than in Ficoll70, possibly due to additional soft (e.g., electrostatic or hydrophobic) interactions. 15 N-edited relaxation measurements show that some residues are more mobile in cell lysate than in Ficoll70; the rates that are most different are predominantly in hydrophobic residues. We thus examined cell lysates with reduced hydrophobicity and found slower dynamics (higher relaxation rates) in several α-synuclein residues. Taken together, these experiments suggest that while cell lysate does not substantially affect α-synuclein structure (HSQC spectra), it does affect chain dynamics and translational diffusion, and strongly affects aggregation over a timescale of days, in a manner that is different from either no crowder or an artificial crowder: soft hydrophobic interactions are implicated.
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Affiliation(s)
- Sina Heravi
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Jude Vincent Dobbin Power
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Anand Yethiraj
- Department of Physics and Physical OceanographyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Valerie Booth
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Department of Physics and Physical OceanographyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Pastore A, Temussi PA. Crowding revisited: Open questions and future perspectives. Trends Biochem Sci 2022; 47:1048-1058. [PMID: 35691783 DOI: 10.1016/j.tibs.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/12/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects protein stability is an important question heatedly discussed over the past 20 years. Theoretical estimations have suggested a 5-20°C effect of fold stabilisation. This estimate, however, is at variance with what has been verified experimentally that proposes only a limited increase of stability, opening the question whether some of the assumptions taken for granted should be reconsidered. The present review critically analyses the causes of this discrepancy and discusses the limitations and implications of the current concept of crowding.
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Affiliation(s)
- Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
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Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy. Int J Mol Sci 2022; 23:ijms23126781. [PMID: 35743221 PMCID: PMC9224231 DOI: 10.3390/ijms23126781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D 15N-1H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.
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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: 32] [Impact Index Per Article: 16.0] [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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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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Vale N, Alves C, Sharma V, Lázaro DF, Silva S, Gomes P, Outeiro TF. A new MAP-Rasagiline conjugate reduces α-synuclein inclusion formation in a cell model. Pharmacol Rep 2020; 72:456-464. [PMID: 32048262 DOI: 10.1007/s43440-019-00032-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disease of the elderly. Current therapies are only symptomatic, and have no disease-modifying effect. Therefore, disease progresses continuously over time, presenting with both motor and non-motor features. The precise molecular basis for PD is still elusive, but the aggregation of the protein alpha-synuclein (α-syn) is a key pathological hallmark of the disease and is, therefore, a major focus of current research. Considering the intrinsic properties of cell-penetrating peptides (CPPs) for mediating drug delivery of neurotherapeutics across the blood brain barrier (BBB), these might open novel opportunities for the development of new solutions for the treatment of brain-related aspects of PD and other neurodegenerative disorders. METHODS Here, we synthesized solid-phase CPPs using an amphipathic model peptide (MAP) conjugated with the drug Rasagiline (RAS), which we named RAS-MAP, and evaluated its effect on α-syn inclusion formation in a human cell-based model of synucleinopathy. RESULTS We found that treatment with RAS-MAP at low concentrations (1-3 µM) reduced α-syn aggregation in cells. CONCLUSIONS For the first time, we report that conjugation of a current drug used in the therapy of PD with CPP reduces α-syn aggregation, which might prove beneficial in PD and other synucleinopathies.
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Affiliation(s)
- Nuno Vale
- Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho, 45, 4200-135, Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Department of Molecular Pathology and Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
| | - Cláudia Alves
- Department of Chemistry and Biochemistry, Faculty of Sciences, LAQV/REQUIMTE, University of Porto, Rua do Campo Alegre, 687, 4169-007, Porto, Portugal
| | - Vaishali Sharma
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Diana F Lázaro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Sara Silva
- Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho, 45, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Paula Gomes
- Department of Chemistry and Biochemistry, Faculty of Sciences, LAQV/REQUIMTE, University of Porto, Rua do Campo Alegre, 687, 4169-007, Porto, Portugal
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany.,Max Planck Institute for Experimental Medicine, Göttingen, Germany.,Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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8
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Lo CH, Lim CKW, Ding Z, Wickramasinghe SP, Braun AR, Ashe KH, Rhoades E, Thomas DD, Sachs JN. Targeting the ensemble of heterogeneous tau oligomers in cells: A novel small molecule screening platform for tauopathies. Alzheimers Dement 2019; 15:1489-1502. [PMID: 31653529 DOI: 10.1016/j.jalz.2019.06.4954] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/30/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Understanding the heterogeneous pathology in Alzheimer's disease and related tauopathies is one of the most urgent and fundamental challenges facing the discovery of novel disease-modifying therapies. Through monitoring ensembles of toxic and nontoxic tau oligomers spontaneously formed in cells, our biosensor technology can identify tool compounds that modulate tau oligomer structure and toxicity, providing much needed insight into the nature and properties of toxic tau oligomers. BACKGROUND Tauopathies are a group of neurodegenerative disorders characterized by pathologic aggregation of the microtubule binding protein tau. Recent studies suggest that tau oligomers are the primary toxic species in tauopathies. NEW/UPDATED HYPOTHESIS We hypothesize that tau biosensors capable of monitoring tau oligomer conformation are able to identify tool compounds that modulate the structure and conformation of these tau assemblies, providing key insight into the unique structural fingerprints of toxic tau oligomers. These fingerprints will provide gravely needed biomarker profiles to improve staging of early tauopathy pathology and generate lead compounds for potential new therapeutics. Our time-resolved fluorescence resonance energy transfer biosensors provide us an exquisitely sensitive technique to monitor minute structural changes in monomer and oligomer conformation. In this proof-of-concept study, we identified a novel tool compound, MK-886, which directly binds tau, perturbs the conformation of toxic tau oligomers, and rescues tau-induced cytotoxicity. Furthermore, we show that MK-886 alters the conformation of tau monomer at the proline-rich and microtubule binding regions, stabilizing an on-pathway oligomer. MAJOR CHALLENGES FOR THE HYPOTHESIS Our approach monitors changes in the ensemble of assemblies that are spontaneously formed in cells but does not specifically isolate or enrich unique toxic tau species. However, time-resolved fluorescence resonance energy transfer does not provide high-resolution, atomic scale information, requiring additional experimental techniques to resolve the structural features stabilized by different tool compounds. LINKAGE TO OTHER MAJOR THEORIES Our biosensor technology is broadly applicable to other areas of tauopathy therapeutic development. These biosensors can be readily modified for different isoforms of tau, specific post-translational modifications, and familial Alzheimer's disease-associated mutations. We are eager to explore tau interactions with chaperone proteins, monitor cross-reactivity with other intrinsically disordered proteins, and target seeded oligomer pathology.
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Affiliation(s)
- Chih Hung Lo
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Colin Kin-Wye Lim
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Zhipeng Ding
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Sanjula P Wickramasinghe
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthony R Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Karen H Ashe
- Department of Neurology, University of Minnesota, Minneapolis, MN, USA; Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA; N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, USA; Geriatric Research, Education, and Clinical Centers, Veterans Affairs Medical Center, Minneapolis, MN, USA
| | - Elizabeth Rhoades
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA; Photonic Pharma LLC, Minneapolis, MN, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA.
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Sciolino N, Burz DS, Shekhtman A. In-Cell NMR Spectroscopy of Intrinsically Disordered Proteins. Proteomics 2019; 19:e1800055. [PMID: 30489014 DOI: 10.1002/pmic.201800055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/29/2018] [Indexed: 01/14/2023]
Abstract
This review summarizes the results of in-cell Nuclear Magnetic Resonance, NMR, spectroscopic investigations of the eukaryotic and prokaryotic intrinsically disordered proteins, IDPs: α-synuclein, prokaryotic ubiquitin-like protein, Pup, tubulin-related neuronal protein, Tau, phenylalanyl-glycyl-repeat-rich nucleoporins, FG Nups, and the negative regulator of flagellin synthesis, FlgM. The results show that the cellular behavior of IDPs may differ significantly from that observed in the test tube.
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Affiliation(s)
- Nicholas Sciolino
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
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10
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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Zigoneanu IG, Sims CE, Allbritton NL. Separation of peptide fragments of a protein kinase C substrate fused to a β-hairpin by capillary electrophoresis. Anal Bioanal Chem 2015; 407:8999-9008. [PMID: 26427499 PMCID: PMC4662605 DOI: 10.1007/s00216-015-9065-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/14/2015] [Accepted: 09/17/2015] [Indexed: 01/23/2023]
Abstract
Synthetic peptides incorporating well-folded β-hairpin peptides possess advantages in a variety of cell biology applications by virtue of increased resistance to proteolytic degradation. In this study, the WKpG β-hairpin peptide fused to a protein kinase C (PKC) substrate was synthesized, and capillary-electrophoretic separation conditions for this peptide and its proteolytic fragments were developed. Fragments of WKpG-PKC were generated by enzymatic treatment with trypsin and Pronase E to produce standards for identification of degradation fragments in a cellular lysate. A simple buffer system of 250 mM H3PO4, pH 1.5 enabled separation of WKpG-PKC and its fragments by capillary electrophoresis in less than 16 min. Using a cellular lysate produced from Ba/F3 cells, the β-hairpin-conjugated substrate and its PKCα-phosphorylated product could be detected and separated from peptidase-generated fragments produced in a cell lysate. The method has potential application for identification and quantification of WKpG-PKC and its fragments in complex biological systems when the peptide is used as a reporter to assay PKC activity.
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Affiliation(s)
- Imola G Zigoneanu
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, 27599, USA
- North Carolina State University, Raleigh, NC, 27695, USA
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nancy L Allbritton
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, 27599, USA.
- North Carolina State University, Raleigh, NC, 27695, USA.
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA.
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12
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Kristensen M, de Groot AM, Berthelsen J, Franzyk H, Sijts A, Nielsen HM. Conjugation of cell-penetrating peptides to parathyroid hormone affects its structure, potency, and transepithelial permeation. Bioconjug Chem 2015; 26:477-88. [PMID: 25611217 DOI: 10.1021/bc5005763] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Delivery of therapeutic peptides and proteins by the use of cell-penetrating peptides (CPPs) as carriers has been suggested as a feasible strategy. The aim of the present study was to investigate the effect of conjugating a series of well-known CPPs to the biologically active part of parathyroid hormone, i.e., PTH(1-34), and to evaluate the effect with regard to secondary structure, potency in Saos-2 cells, immunogenicity, safety, as well as the transepithelial permeation across monolayers by using the Caco-2 cell culture model. Further, co-administration of CPP and PTH(1-34) as an alternative to covalent conjugation was compared with regard to the transepithelial permeation. CPP-conjugated PTH(1-34) fusion peptides were successfully expressed in Escherichia coli and purified from inclusion bodies. No clear correlation between the degree of secondary structure of the CPP-conjugated PTH(1-34) fusion peptides and their potency was found, albeit a general decrease in permeation was observed for both N- and C-terminally CPP-conjugated PTH(1-34) as compared to native PTH(1-34). However, attachment of CPP to the N-terminus significantly increased permeation across Caco-2 cell monolayers as compared to the corresponding C-terminally CPP-conjugated PTH(1-34). In addition, the nonaarginine sequence proved to be the only CPP capable of increasing permeation when conjugated to PTH(1-34) as compared to co-administration of CPP and PTH(1-34). This enhancement effect was, however, associated with an unacceptably low level of cell viability. In conclusion, covalent conjugation of CPPs to PTH(1-34) influenced the secondary structure, potency, and transepithelial permeation efficiency of the resulting conjugate, and hence this approach appears not to be favorable as compared to co-administration when optimizing CPP-mediated permeation of PTH(1-34) across an intestinal epithelium.
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Affiliation(s)
- Mie Kristensen
- †Section for Biologics, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anne Marit de Groot
- §Division of Immunology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University. Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Jens Berthelsen
- ‡Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Henrik Franzyk
- ∥Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Alice Sijts
- §Division of Immunology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University. Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Hanne Mørck Nielsen
- †Section for Biologics, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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13
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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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14
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Marsh ENG, Suzuki Y. Using (19)F NMR to probe biological interactions of proteins and peptides. ACS Chem Biol 2014; 9:1242-50. [PMID: 24762032 DOI: 10.1021/cb500111u] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorine is a valuable probe for investigating the interactions of biological molecules because of its favorable NMR characteristics, its small size, and its near total absence from biology. Advances in biosynthetic methods allow fluorine to be introduced into peptides and proteins with high precision, and the increasing sensitivity of NMR spectrometers has facilitated the use of (19)F NMR to obtain molecular-level insights into a wide range of often-complex biological interactions. Here, we summarize the advantages of solution-state (19)F NMR for studying the interactions of peptides and proteins with other biological molecules, review methods for the production of fluorine-labeled materials, and describe some representative recent examples in which (19)F NMR has been used to study conformational changes in peptides and proteins and their interactions with other biological molecules.
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Affiliation(s)
- E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yuta Suzuki
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Kiviniemi A, Murtola M, Ingman P, Virta P. Synthesis of fluorine-labeled peptide nucleic acid building blocks as sensors for the 19F NMR spectroscopic detection of different hybridization modes. J Org Chem 2013; 78:5153-9. [PMID: 23638811 DOI: 10.1021/jo400014y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide nucleic acid (PNA) building blocks, bearing a fluorine sensor at C-5 of the uracil base [viz. trifluoromethyl and 3,3-bis(trifluoromethyl)-4,4,4-trifluorobut-1-ynyl], were synthesized and incorporated to a PNA strand, and their applicability for the monitoring of different hybridization modes by (19)F NMR spectroscopy was studied. Both sensors gave unique (19)F resonance shifts in NMR when the PNA was targeted to a complementary antiparallel DNA, antiparallel RNA, parallel DNA, and parallel RNA. The 5-trifluoromethyl-derived sensor was additionally applied for the monitoring of interconversions from a parallel DNA/PNA complex to an antiparallel RNA/PNA complex and from a PNA/PNA complex to two DNA/PNA complexes (i.e., double-duplex invasion).
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, 20014 Turku, Finland
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16
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Abstract
Intrinsically disordered proteins are important in signaling, regulation, and translocation. Understanding their diffusion under physiologically relevant conditions will yield insight into their functions. We used NMR to quantify the translational diffusion of a globular and a disordered protein in dilute solution and under crowded conditions. In dilute solution, the globular protein chymotrypsin inhibitor 2 (CI2, 7.4 kDa) diffuses faster than the disordered protein α-synuclein (14 kDa). Surprisingly, the opposite occurs under crowded conditions; α-synuclein diffuses faster than CI2, even though α-synuclein is larger than CI2. These data show that shape is a key parameter determining protein diffusion under crowded conditions, adding to the properties known to be affected by macromolecular crowding. The results also offer a clue about why many signaling proteins are disordered.
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Affiliation(s)
- Yaqiang Wang
- Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Laura A. Benton
- Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | | | - Gary J. Pielak
- Chemistry, University of North Carolina, Chapel Hill, NC 27599
- Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Corresponding Author:
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17
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Bellucci A, Zaltieri M, Navarria L, Grigoletto J, Missale C, Spano P. From α-synuclein to synaptic dysfunctions: new insights into the pathophysiology of Parkinson's disease. Brain Res 2012; 1476:183-202. [PMID: 22560500 DOI: 10.1016/j.brainres.2012.04.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/30/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
Alpha-synuclein is a natively unfolded protein playing a key role in the regulation of several neuronal synaptic functions in physiological and pathological conditions. Many studies, over the past years, have shown that it is actively involved in PD pathophysiology. Alpha-synuclein is integrated in a complex network of neuronal processes through the interaction with cytosolic and synaptic proteins. Hence, it is not the sole α-synuclein pathology but its effects on diverse protein partners and specific cellular pathways in the membrane and/or cytosolic districts such as endoplasmic reticulum/Golgi, axonal and synaptic compartments of dopaminergic neurons, that may cause the onset of neuronal cell dysfunction and degeneration which are among the key pathological features of the PD brain. Here we summarize a series of experimental data supporting that α-synuclein aggregation may induce dysfunction and degeneration of synapses via these multiple mechanisms. Taken together, these data add new insights into the complex mechanisms underlying synaptic derangement in PD and other α-synucleinopathies. This article is part of a Special Issue entitled: Brain Integration.
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Affiliation(s)
- Arianna Bellucci
- Division of Pharmacology, Department of Biomedical Sciences and Biotechnologies and National Institute of Neuroscience, University of Brescia, Brescia, Italy.
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