1
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Kunka A, Lacko D, Stourac J, Damborsky J, Prokop Z, Mazurenko S. CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic Acids Res 2022; 50:W145-W151. [PMID: 35580052 PMCID: PMC9252748 DOI: 10.1093/nar/gkac378] [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: 03/23/2022] [Revised: 04/20/2022] [Accepted: 05/14/2022] [Indexed: 11/24/2022] Open
Abstract
The importance of the quantitative description of protein unfolding and aggregation for the rational design of stability or understanding the molecular basis of protein misfolding diseases is well established. Protein thermostability is typically assessed by calorimetric or spectroscopic techniques that monitor different complementary signals during unfolding. The CalFitter webserver has already proved integral to deriving invaluable energy parameters by global data analysis. Here, we introduce CalFitter 2.0, which newly incorporates singular value decomposition (SVD) of multi-wavelength spectral datasets into the global fitting pipeline. Processed time- or temperature-evolved SVD components can now be fitted together with other experimental data types. Moreover, deconvoluted basis spectra provide spectral fingerprints of relevant macrostates populated during unfolding, which greatly enriches the information gains of the CalFitter output. The SVD analysis is fully automated in a highly interactive module, providing access to the results to users without any prior knowledge of the underlying mathematics. Additionally, a novel data uploading wizard has been implemented to facilitate rapid and easy uploading of multiple datasets. Together, the newly introduced changes significantly improve the user experience, making this software a unique, robust, and interactive platform for the analysis of protein thermal denaturation data. The webserver is freely accessible at https://loschmidt.chemi.muni.cz/calfitter.
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Affiliation(s)
- Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - David Lacko
- Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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2
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Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV, Sulatskaya AI. New findings on GFP-like protein application as fluorescent tags: Fibrillogenesis, oligomerization, and amorphous aggregation. Int J Biol Macromol 2021; 192:1304-1310. [PMID: 34687761 DOI: 10.1016/j.ijbiomac.2021.10.107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/19/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Green fluorescent proteins (GFP) are commonly used as fluorescent tags and biosensors in cell biology and medicine. However, the propensity of GFP-like proteins to aggregate and the consequence of intermolecular interaction for their application have not been thoroughly examined. In this work, alternative aggregation pathways of superfolder green fluorescent protein (sfGFP) were demonstrated using a spectroscopic and microscopic study of the samples prepared by equilibrium microdialysis. Besides oligomerization of native monomers, we showed for the first time the condition-specific formation by sfGFP of either amyloid fibrils (at increased temperature or acidity) or amorphous aggregates (at physiological conditions). Both types of sfGFP aggregates had lost green fluorescence and were toxic to cells. Thus, when using GFP-like proteins as fluorescent tags, one should take into account their high ability to form aggregates with lost unique visible fluorescence in the cellular environment, which affects cell viability. Moreover, the results of this work cast doubt on the correctness of the data on the fibrillogenesis of various amyloidogenic proteins obtained using their fusion with GFP-like proteins.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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3
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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4
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Wurm M, Ilhan S, Jandt U, Zeng AP. Direct and highly sensitive measurement of fluorescent molecules in bulk solutions using flow cytometry. Anal Biochem 2019; 570:32-42. [PMID: 30710511 DOI: 10.1016/j.ab.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 12/24/2018] [Accepted: 01/14/2019] [Indexed: 11/25/2022]
Abstract
Utilizing flow cytometry to monitor progress of bulk biochemical reactions and concentration of chemical species normally relies on the utilization of cells carrying intrinsic fluorescence or modified beads. We present a method for a simple measurement of the fluorescent marker molecule fluorescein and GFPuv in bulk solutions with high sensitivity using a CytoFLEX flow cytometer and without the need for modified beads. Polystyrene beads were used to trigger measurements based on their high scatter signal, to detect the fluorescence signal from two different fluorophores present in the sample solution. We report sensitivities of 33 pg/mL for fluorescein and 50 ng/mL for GFPuv. This method is comparable in sensitivity to a typical spectrometric fluorescence assay tested with fluorescein, and approximately ten times more sensitive for the measurement of GFPuv. PEG was added to the sample at a low concentration of 0.001% (w/v) to block unspecific GFPuv binding to the beads. The method was further applied to measure the GFPuv concentration in crude cell lysate samples used for cell free protein expression. An advantage of this method over spectrometric assays is the ability to differentiate signal subpopulations in the sample based on their individual fluorescence intensities.
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Affiliation(s)
- Matthias Wurm
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - Sibel Ilhan
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany.
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
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5
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Kesgin-Schaefer S, Heidemann J, Puchert A, Koelbel K, Yorke BA, Huse N, Pearson AR, Uetrecht C, Tidow H. Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway. FEBS J 2019; 286:2329-2340. [PMID: 30817081 DOI: 10.1111/febs.14797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 01/23/2023]
Abstract
Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 Å resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.
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Affiliation(s)
- Stephanie Kesgin-Schaefer
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Anke Puchert
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Knut Koelbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Briony A Yorke
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Nils Huse
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Arwen R Pearson
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
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6
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Melnik TN, Nagibina GS, Surin AK, Glukhova KA, Melnik BS. Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States. Mol Biol 2018. [DOI: 10.1134/s0026893318010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding. Proc Natl Acad Sci U S A 2017; 114:11052-11056. [PMID: 29073015 DOI: 10.1073/pnas.1704937114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Green fluorescent protein (GFP) variants are widely used as genetically encoded fluorescent fusion tags, and there is an increasing interest in engineering their structure to develop in vivo optical sensors, such as for optogenetics and force transduction. Ensemble experiments have shown that the fluorescence of GFP is quenched upon denaturation. Here we study the dependence of fluorescence on protein structure by driving single molecules of GFP into different conformational states with optical tweezers and simultaneously probing the chromophore with fluorescence. Our results show that fluorescence is lost during the earliest events in unfolding, 3.5 ms before secondary structure is disrupted. No fluorescence is observed from the unfolding intermediates or the ensemble of compact and extended states populated during refolding. We further demonstrate that GFP can be mechanically switched between emissive and dark states. These data definitively establish that complete structural integrity is necessary to observe single-molecule fluorescence of GFP.
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8
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Lento C, Wilson DJ. Unravelling the mysteries of sub-second biochemical processes using time-resolved mass spectrometry. Analyst 2017; 142:1640-1653. [DOI: 10.1039/c7an00338b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many important chemical and biochemical phenomena proceed on sub-second time scales.
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Affiliation(s)
| | - Derek J. Wilson
- Department of Chemistry
- York University
- Toronto
- Canada
- Centre for Research of Biomolecular Interactions
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9
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Glukhova KF, Marchenkov VV, Melnik TN, Melnik BS. Isoforms of green fluorescent protein differ from each other in solvent molecules 'trapped' inside this protein. J Biomol Struct Dyn 2016; 35:1215-1225. [PMID: 27045905 DOI: 10.1080/07391102.2016.1174737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Green fluorescent protein (GFP) has been studied quite thoroughly, however, up to now some experimental data have not been explained explicitly. For example, under native conditions this protein can have two isoforms differing in their mobility in gel. In this case, no differences between the isoforms are revealed under denaturing conditions. In order to understand the difference in the isoforms of this protein, we have investigated GFP-cycle3 using mass spectrometry, gel electrophoresis, size exclusion chromatography, microcalorimetry, and spectroscopy methods under varying conditions. We have also designed and studied three mutant forms of this protein with substitutions of amino acid residues inside the GFP barrel. The mutations have allowed us to influence the formation of different GFP isoforms. Each of the mutant proteins has predominantly only one isoform. As a result of the performed research, it can be concluded that most likely the GFP isoforms differ in the solvent molecules 'trapped' inside the GFP barrel. In their turn, these molecules have an effect on the protein charge and consequently on its mobility at electrophoresis under native conditions.
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Affiliation(s)
- Kseniya F Glukhova
- a Institute of Protein Research , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia
| | - Victor V Marchenkov
- a Institute of Protein Research , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia
| | - Tatiana N Melnik
- a Institute of Protein Research , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia
| | - Bogdan S Melnik
- a Institute of Protein Research , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia
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10
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Jain R, Kumar R, Kumar S, Chhabra R, Agarwal MC, Kumar R. Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c. Arch Biochem Biophys 2015; 585:52-63. [DOI: 10.1016/j.abb.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/26/2022]
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11
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Liuni P, Deng B, Wilson DJ. Comparing equilibrium and kinetic protein unfolding using time-resolved electrospray-coupled ion mobility mass spectrometry. Analyst 2015; 140:6973-9. [DOI: 10.1039/c5an00843c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We apply a new hyphenated method, TRESI-IMS-MS, to compare equilibrium and kinetic unfolding intermediates of cytochrome c.
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Affiliation(s)
- Peter Liuni
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Bin Deng
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Derek J. Wilson
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
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12
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Zimmer MH, Li B, Shahid RS, Peshkepija P, Zimmer M. Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins. Chem Phys 2014; 429:5-11. [PMID: 24465077 PMCID: PMC3899699 DOI: 10.1016/j.chemphys.2013.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Computational methods were used to generate the lowest energy conformations of the immature precyclized forms of the 28 naturally occurring GFP-like proteins deposited in the pdb. In all 28 GFP-like proteins, the beta-barrel contracts upon chromophore formation and becomes more rigid. Our prior analysis of over 260 distinct naturally occurring GFP-like proteins revealed that most of the conserved residues are located in the top and bottom of the barrel in the turns between the β-sheets.(1) Structural analyses, molecular dynamics simulations and the Anisotropic Network Model were used to explore the role of these conserved lid residues as possible folding nuclei. Our results are internally consistent and show that the conserved residues in the top and bottom lids undergo relatively less translational movement than other lid residues, and a number of these residues may play an important role as hinges or folding nuclei in the fluorescent proteins.
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Affiliation(s)
- Matthew H. Zimmer
- Chemistry Department, Connecticut College, New London, CT06320, USA
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Binsen Li
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Ramza S. Shahid
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Paola Peshkepija
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Marc Zimmer
- Chemistry Department, Connecticut College, New London, CT06320, USA
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13
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Jackson SE, Craggs TD, Huang JR. Understanding the folding of GFP using biophysical techniques. Expert Rev Proteomics 2014; 3:545-59. [PMID: 17078767 DOI: 10.1586/14789450.3.5.545] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Green fluorescent protein (GFP) and its many variants are probably the most widely used proteins in medical and biological research, having been extensively engineered to act as markers of gene expression and protein localization, indicators of protein-protein interactions and biosensors. GFP first folds, before it can undergo an autocatalytic cyclization and oxidation reaction to form the chromophore, and in many applications the folding efficiency of GFP is known to limit its use. Here, we review the recent literature on protein engineering studies that have improved the folding properties of GFP. In addition, we discuss in detail the biophysical work on the folding of GFP that is beginning to reveal how this large and complex structure forms.
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14
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Campanini B, Pioselli B, Raboni S, Felici P, Giordano I, D'Alfonso L, Collini M, Chirico G, Bettati S. Role of histidine 148 in stability and dynamics of a highly fluorescent GFP variant. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:770-9. [PMID: 23357652 DOI: 10.1016/j.bbapap.2013.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
The armory of GFP mutants available to biochemists and molecular biologists is huge. Design and selection of mutants are usually driven by tailored spectroscopic properties, but some key aspects of stability, folding and dynamics of selected GFP variants still need to be elucidated. We have prepared, expressed and characterized three H148 mutants of the highly fluorescent variant GFPmut2. H148 is known to be involved in the H-bonding network surrounding the chromophore, and all the three mutants, H148G, H148R and H148K, show increased pKa values of the chromophore. Only H148G GFPmut2 (Mut2G) gave good expression and purification yields, indicating that position 148 is critical for efficient folding in vivo. The chemical denaturation of Mut2G was monitored by fluorescence emission, absorbance and far-UV circular dichroism spectroscopy. The mutation has little effect on the spectroscopic properties of the protein and on its stability in solution. However, the unfolding kinetics of the protein encapsulated in wet nanoporous silica gels, a system that allows to stabilize conformations that are poorly or only transiently populated in solution, indicate that the unfolding pathway of Mut2G is markedly different from the parent molecule. In particular, encapsulation allowed to identify an unfolding intermediate that retains a native-like secondary structure despite a destructured chromophore environment. Thus, H148 is a critical residue not only for the chromophoric and photodynamic properties, but also for the correct folding of GFP, and its substitution has great impact on expression yields and stability of the mature protein.
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Affiliation(s)
- Barbara Campanini
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy.
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15
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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16
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Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, Kuwajima K. The Molten Globule of β2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding. J Mol Biol 2013; 425:273-91. [DOI: 10.1016/j.jmb.2012.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 01/06/2023]
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17
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Melnik TN, Povarnitsyna TV, Glukhov AS, Melnik BS. Multi-state proteins: approach allowing experimental determination of the formation order of structure elements in the green fluorescent protein. PLoS One 2012; 7:e48604. [PMID: 23155397 PMCID: PMC3498258 DOI: 10.1371/journal.pone.0048604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/26/2012] [Indexed: 11/19/2022] Open
Abstract
The most complex problem in studying multi-state protein folding is the determination of the sequence of formation of protein intermediate states. A far more complex issue is to determine at what stages of protein folding its various parts (secondary structure elements) develop. The structure and properties of different intermediate states depend in particular on these parts. An experimental approach, named μ-analysis, which allows understanding the order of formation of structural elements upon folding of a multi-state protein was used in this study. In this approach the same elements of the protein secondary structure are “tested” by substitutions of single hydrophobic amino acids and by incorporation of cysteine bridges. Single substitutions of hydrophobic amino acids contribute to yielding information on the late stages of protein folding while incorporation of ss-bridges allows obtaining data on the initial stages of folding. As a result of such an μ-analysis, we have determined the order of formation of beta-hairpins upon folding of the green fluorescent protein.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | | | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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18
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Distinct effects of guanidine thiocyanate on the structure of superfolder GFP. PLoS One 2012; 7:e48809. [PMID: 23144981 PMCID: PMC3492234 DOI: 10.1371/journal.pone.0048809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/05/2012] [Indexed: 11/22/2022] Open
Abstract
Having a high folding efficiency and a low tendency to aggregate, the superfolder GFP (sfGFP) offers a unique opportunity to study the folding of proteins that have a β-barrel topology. Here, we studied the unfolding–refolding of sfGFP that was induced by guanidine thiocyanate (GTC), which is a stronger denaturing agent than GdnHCl or urea. Structural perturbations of sfGFP were studied by spectroscopic methods (absorbance, fluorescence, and circular dichroism), by acrylamide quenching of tryptophan and green chromophore fluorescence, and by size-exclusion chromatography. Low concentrations of GTC (up to 0.1 M) induce subtle changes in the sfGFP structure. The pronounced changes in the visible absorption spectrum of sfGFP which are accompanied by a dramatic decrease in tryptophan and green chromophore fluorescence was recorded in the range 0–0.7 M GNC. These alterations of sfGFP characteristics that erroneously can be mixed up with appearance of intermediate state in fact have pure spectroscopic but not structural nature. Higher concentrations of GTC (from 0.7 to 1.7 M), induce a disruption of the sfGFP structure, that is manifested in simultaneous changes of all of the detected parameters. Full recovery of native properties of denaturated sfGFP was observed after denaturant removal. The refolding of sfGFP passes through the accumulation of the off-pathway intermediate state, in which inner alpha-helix and hence green chromophore and Trp57 are still not tuned up to (properly integrated into) the already formed β-barrel scaffold of protein. Incorporation of the chromophore in the β-barrel in the pathway of refolding and restoration of its ability to fluoresce occur in a narrow range of GTC concentrations from 1.0 to 0.7 M, and a correct insertion of Trp 57 occurs at concentrations ranging from 0.7 to 0 M GTC. These two processes determine the hysteresis of protein unfolding and refolding.
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Abstract
We use molecular simulations using a coarse-grained model to map the folding landscape of Green Fluorescent Protein (GFP), which is extensively used as a marker in cell biology and biotechnology. Thermal and Guanidinium chloride (GdmCl) induced unfolding of a variant of GFP, without the chromophore, occurs in an apparent two-state manner. The calculated midpoint of the equilibrium folding in GdmCl, taken into account using the Molecular Transfer Model (MTM), is in excellent agreement with the experiments. The melting temperatures decrease linearly as the concentrations of GdmCl and urea are increased. The structural features of rarely populated equilibrium intermediates, visible only in free energy profiles projected along a few order parameters, are remarkably similar to those identified in a number of ensemble experiments in GFP with the chromophore. The excellent agreement between simulations and experiments show that the equilibrium intermediates are stabilized by the chromophore. Folding kinetics, upon temperature quench, show that GFP first collapses and populates an ensemble of compact structures. Despite the seeming simplicity of the equilibrium folding, flux to the native state flows through multiple channels and can be described by the kinetic partitioning mechanism. Detailed analysis of the folding trajectories show that both equilibrium and several kinetic intermediates, including misfolded structures, are sampled during folding. Interestingly, the intermediates characterized in the simulations coincide with those identified in single molecule pulling experiments. Our predictions, amenable to experimental tests, show that MTM is a practical way to simulate the effect of denaturants on the folding of large proteins.
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20
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Tomoyori K, Nakamura T, Makabe K, Maki K, Saeki K, Kuwajima K. Sequential four-state folding/unfolding of goat α-lactalbumin and its N-terminal variants. Proteins 2012; 80:2191-206. [PMID: 22577070 DOI: 10.1002/prot.24109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/11/2012] [Accepted: 04/25/2012] [Indexed: 11/09/2022]
Abstract
Equilibria and kinetics of folding/unfolding of α-lactalbumin and its two N-terminal variants were studied by circular dichroism spectroscopy. The two variants were wild-type recombinant and Glu1-deletion (E1M) variants expressed in Escherichia coli. The presence of an extra methionine at the N terminus in recombinant α-lactalbumin destabilized the protein by 2 kcal/mol, while the stability was recovered in the E1M variant in which Glu1 was replaced by Met1. Kinetic folding/unfolding reactions of the proteins, induced by stopped-flow concentration jumps of guanidine hydrochloride, indicated the presence of a burst-phase in refolding, and gave chevron plots with significant curvatures in both the folding and unfolding limbs. The folding-limb curvature was interpreted in terms of accumulation of the burst-phase intermediate. However, there was no burst phase observed in the unfolding kinetics to interpret the unfolding-limb curvature. We thus assumed a sequential four-state mechanism, in which the folding from the burst-phase intermediate takes place via two transition states separated by a high-energy intermediate. We estimated changes in the free energies of the burst-phase intermediate and two transition states, caused by the N-terminal variations and also by the presence of stabilizing calcium ions. The Φ values at the N terminus and at the Ca(2+)-binding site thus obtained increased successively during folding, demonstrating the validity of the sequential mechanism. The stability and the folding behavior of the E1M variant were essentially identical to those of the authentic protein, allowing us to use this variant as a pseudo-wild-type α-lactalbumin in future studies.
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Affiliation(s)
- Katsuaki Tomoyori
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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21
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Bosisio C, Quercioli V, Chirico G, D'Alfonso L, Bettati S, Raboni S, Campanini B, Collini M. Effect of the point mutation H148G on GFPmut2 unfolding kinetics by fluorescence spectroscopy. Biophys Chem 2011; 157:24-32. [DOI: 10.1016/j.bpc.2011.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 02/09/2023]
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22
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Widakowich G, Zhang C, Harris S, Mitri K, Powers G, Troung KS, Hearn MTW. Effects of IMAC specific peptide tags on the stability of recombinant green fluorescent protein. Biotechnol Prog 2011; 27:1048-53. [DOI: 10.1002/btpr.546] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 07/21/2010] [Indexed: 11/09/2022]
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23
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Yu L, Li Y, Fan H, Duan J, Zhu Q, Li S. Analysis of marker compounds with anti-platelet aggregation effects in Mailuoning injection using platelet binding assay combined with HPLC-DAD-ESI-MS and solid-phase extraction technique. PHYTOCHEMICAL ANALYSIS : PCA 2011; 22:87-93. [PMID: 20799275 DOI: 10.1002/pca.1260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 06/16/2010] [Accepted: 06/16/2010] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Mailuoning is prepared from a traditional formula of Chinese medicines and widely used as an antithrombotic agent. In this study, the platelet binding assay was used as a novel biospecific separation and analysis method to explore its active constituents, which could be considered as marker compounds for quality control. OBJECTIVE To establish a rapid and simple method to predict marker compounds in herbal medicine injection and evaluate the effects of those compounds. MATERIAL AND METHODS Platelets were used to bind and separate constituents. Binding constituents were analysed and taken as potential active compounds for further evaluation. Solid-phase-extraction was adopted to improve sensitivity. HPLC-DAD and ESI-MS were used to determine the binding constituents. RESULTS Five compounds were extracted through the platelet binding process and identified as neochlorogenic acid, caffeic acid, isochlorogenic acid and their isomers. Caffeic acid was selected for the flow cytometric assay to test its effect on platelets activation, which was determined by CD62P (P-selectin) expression. The results indicated that caffeic acid could significantly inhibit platelet activation while chlorogenic acid did not. CONCLUSION Caffeic acid could be considered as a marker compound of Mailuoning injection due to its anti-platelet effect. The study also suggested that platelet binding assay combined with some preconcentration technique could be efficiently used to predict anti-platelet compounds in complicated herbal medicines.
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Affiliation(s)
- Li Yu
- Jiangsu Key laboratory for TCM formulae Research, Nanjing University of Chinese Medicine, Nanjing, China
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24
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Hsu STD, Blaser G, Behrens C, Cabrita LD, Dobson CM, Jackson SE. Folding study of Venus reveals a strong ion dependence of its yellow fluorescence under mildly acidic conditions. J Biol Chem 2009; 285:4859-69. [PMID: 19901033 DOI: 10.1074/jbc.m109.000695] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Venus is a yellow fluorescent protein that has been developed for its fast chromophore maturation rate and bright yellow fluorescence that is relatively insensitive to changes in pH and ion concentrations. Here, we present a detailed study of the stability and folding of Venus in the pH range from 6.0 to 8.0 using chemical denaturants and a variety of spectroscopic probes. By following hydrogen-deuterium exchange of (15)N-labeled Venus using NMR spectroscopy over 13 months, residue-specific free energies of unfolding of some highly protected amide groups have been determined. Exchange rates of less than one per year are observed for some amide groups. A super-stable core is identified for Venus and compared with that previously reported for green fluorescent protein. These results are discussed in terms of the stability and folding of fluorescent proteins. Under mildly acidic conditions, we show that Venus undergoes a drastic decrease in yellow fluorescence at relatively low concentrations of guanidinium chloride. A detailed study of this effect establishes that it is due to pH-dependent, nonspecific interactions of ions with the protein. In contrast to previous studies on enhanced green fluorescence protein variant S65T/T203Y, which showed a specific halide ion-binding site, NMR chemical shift mapping shows no evidence for specific ion binding. Instead, chemical shift perturbations are observed for many residues primarily located in both lids of the beta-barrel structure, which suggests that small scale structural rearrangements occur on increasing ionic strength under mildly acidic conditions and that these are propagated to the chromophore resulting in fluorescence quenching.
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Affiliation(s)
- Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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25
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Charged liposome affects the translation and folding steps of in vitro expression of green fluorescent protein. J Biosci Bioeng 2009; 108:450-4. [DOI: 10.1016/j.jbiosc.2009.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 05/11/2009] [Accepted: 05/19/2009] [Indexed: 11/18/2022]
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26
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Hsu STD, Blaser G, Jackson SE. The folding, stability and conformational dynamics of beta-barrel fluorescent proteins. Chem Soc Rev 2009; 38:2951-65. [PMID: 19771338 DOI: 10.1039/b908170b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review describes our current knowledge on the folding, stability and conformational dynamics of fluorescent proteins (FPs). The biophysical studies that have led to the elucidation of many of the key features of the complex energy landscape for folding for GFP and its variants are discussed. These illustrate some important issues surrounding how the large beta-barrel structure forms, and will be of interest to the protein folding community. In addition, the review highlights the importance of some of these results for the use of FPs in in vivo applications. The results should facilitate and aid in experimental designs of in vivo applications, as well as the interpretation of in vivo experimental data. The review is therefore of interest to all those working with FPs in vivo (103 references).
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Affiliation(s)
- Shang-Te Danny Hsu
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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27
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Bose HS, Whittal RM, Bose M, Debnath D. Hydrophobic core of the steroidogenic acute regulatory protein for cholesterol transport. Biochemistry 2009; 48:1198-209. [PMID: 19170610 DOI: 10.1021/bi801514e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The steroidogenic acute regulatory protein (StAR), the first family member of START (StAR-related lipid transport) proteins, plays an essential role by facilitating the movement of cholesterol from the outer to inner mitochondrial membrane. Wild-type and mutant StAR binds cholesterol with similar intensity, but only wild-type StAR can transport it to mitochondria. Here, we report that the hydrophobic core is crucial for biological activity of proteins with START domains. Wild-type StAR increased steroidogenic activity by 7-9-fold compared to mutant R182L StAR, but both of them showed similar near-UV CD spectra. The fluorescence maximum of wild-type StAR is red shifted in comparison to mutant StAR under identical urea concentration. TFE increased the alpha-helical contribution of wild-type StAR more than the mutant protein. Acrylamide quenching for the wild-type protein (K(SV) = 12.0 +/- 0.2-11.2 +/- 0.5 M(-1)) exceeded that of the mutant protein (K(SV) = 4 +/- 0.2 M(-1)). Consistent with these findings, the hydrophobic probe ANS bound wild-type StAR (K(app) = 8.1 x 10(5) M(-1)) to a greater degree than mutant StAR (K(app) = 3.75 x 10(5) M(-1)). Partial proteolysis examined by mass spectrometry suggests that only wild-type StAR has a protease-sensitive C-terminus, but not the mutant. Stopped-flow CD revealed that the time of unfolding of mutant StAR was 0.017 s. In contrast, the wild-type StAR protein is unfolded in 16.3 s. In summary, these results demonstrate that wild-type StAR adopts a very flexible form due to the accommodation of more water molecules, while mutant StAR is generated by an alternate folding pathway making it inactive.
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Affiliation(s)
- Himangshu S Bose
- Department of Biomedical Sciences, Mercer University School of Medicine and Memorial Health University Medical Center, Savannah, Georgia 31404, USA.
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28
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Walters J, Milam SL, Clark AC. Practical approaches to protein folding and assembly: spectroscopic strategies in thermodynamics and kinetics. Methods Enzymol 2009; 455:1-39. [PMID: 19289201 DOI: 10.1016/s0076-6879(08)04201-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We describe here the use of several spectroscopies, such as fluorescence emission, circular dichroism, and differential quenching by acrylamide, in examining the equilibrium and kinetic folding of proteins. The first section regarding equilibrium techniques provides practical information for determining the conformational stability of a protein. In addition, several equilibrium-folding models are discussed, from two-state monomer to four-state homodimer, providing a comprehensive protocol for interpretation of folding curves. The second section focuses on the experimental design and interpretation of kinetic data, such as burst-phase analysis and exponential fits, used in elucidating kinetic folding pathways. In addition, simulation programs are used routinely to support folding models generated by kinetic experiments, and the fundamentals of simulations are covered.
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Affiliation(s)
- Jad Walters
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
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29
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Stepanenko OV, Verkhusha VV, Shavlovsky MM, Kuznetsova IM, Uversky VN, Turoverov KK. Understanding the role of Arg96 in structure and stability of green fluorescent protein. Proteins 2008; 73:539-51. [PMID: 18470931 DOI: 10.1002/prot.22089] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Arg96 is a highly conservative residue known to catalyze spontaneous green fluorescent protein (GFP) chromophore biosynthesis. To understand a role of Arg96 in conformational stability and structural behavior of EGFP, the properties of a series of the EGFP mutants bearing substitutions at this position were studied using circular dichroism, steady state fluorescence spectroscopy, fluorescence lifetime, kinetics and equilibrium unfolding analysis, and acrylamide-induced fluorescence quenching. During the protein production and purification, high yield was achieved for EGFP/Arg96Cys variant, whereas EGFP/Arg96Ser and EGFP/Arg96Ala were characterized by essentially lower yields and no protein was produced when Arg96 was substituted by Gly. We have also shown that only EGFP/Arg96Cys possessed relatively fast chromophore maturation, whereas it took EGFP/Arg96Ser and EGFP/Arg96Ala about a year to develop a noticeable green fluorescence. The intensity of the characteristic green fluorescence measured for the EGFP/Arg96Cys and EGFP/Arg96Ser (or EGFP/Arg96Ala) was 5- and 50-times lower than that of the nonmodified EGFP. Intriguingly, EGFP/Arg96Cys was shown to be more stable than EGFP toward the GdmCl-induced unfolding both in kinetics and in the quasi-equilibrium experiments. In comparison with EGFP, tryptophan residues of EGFP/Arg96Cys were more accessible to the solvent. These data taken together suggest that besides established earlier crucial catalytic role, Arg96 is important for the overall folding and conformational stability of GFP.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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30
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Huang JR, Hsu STD, Christodoulou J, Jackson SE. The extremely slow-exchanging core and acid-denatured state of green fluorescent protein. HFSP JOURNAL 2008; 2:378-87. [PMID: 19436495 DOI: 10.2976/1.2976660] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/07/2008] [Indexed: 11/19/2022]
Abstract
Green fluorescent protein (GFP) is a large protein with a complex eleven-stranded beta-barrel structure. Previous studies have shown that it has a complex energy landscape for folding on which there are several intermediate states and a denatured state with significant residual structure. Here, we use two different types of HD exchange measurement and nuclear magnetic resonance (NMR) techniques to probe the energy landscape for folding of GFP in further detail. HD exchange experiments were performed over a wide range of conditions including different concentrations of denaturant. Results show that the penetration model dominates the exchange mechanism, consistent with the known stability and slow unfolding kinetics of GFP. HD exchange experiments at high pH establish that there is an extremely slow-exchanging superstable core of amide protons in GFP that are clustered and located in beta-strands 1, 2, 4, 5, and 6. These residues form part of a mini-beta-sheet which we propose constitutes a folding nucleus. Using a pulsed-labeling strategy, the acid-denatured state has been investigated and the residual structure observed in earlier studies shown to locate to beta-strands 1 and 3. There is some evidence that this residual structure is stabilized by a localized hydrophobic collapse of the polypeptide chain.
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31
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Abstract
Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape, followed by a very slow search and rearrangement step into the locked, active chromophore-containing structure. As we have shown previously, the substantial difference in time scales is what generates the observed hysteresis in thermodynamic folding. The interconversion between locked and the soft folding structures at intermediate denaturant concentrations is so slow that it is not observed under the typical experimental observation time. Simulations of a coarse-grained model were used to describe the fast folding event as well as identify native-like intermediates on energy landscapes enroute to the fluorescent native fold. Interestingly, these simulations reveal structural features of the slow dynamic transition to chromophore activation. Experimental evidence presented here shows that the trapped, native-like intermediate has structural heterogeneity in residues previously linked to chromophore formation. We propose that the final step of GFP folding is a "locking" mechanism leading to chromophore formation and high stability. The combination of previous experimental work and current simulation work is explained in the context of a dual-basin folding mechanism described above.
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32
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Orte A, Craggs TD, White SS, Jackson SE, Klenerman D. Evidence of an Intermediate and Parallel Pathways in Protein Unfolding from Single-Molecule Fluorescence. J Am Chem Soc 2008; 130:7898-907. [DOI: 10.1021/ja709973m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angel Orte
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Timothy D. Craggs
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Samuel S. White
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sophie E. Jackson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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33
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Abstract
Guanidine induced equilibrium and kinetic folding of a variant of green fluorescent protein (F99S/M153T/V163A, GFPuv) was studied. Using manual mixing and stopped-flow techniques, we combined different probes, including tryptophan fluorescence, chromophore fluorescence and reactivity with DTNB, to trace the spontaneous and TF-assisted folding of guanidine denatured GFPuv. We found that both unfolding and refolding of GFPuv occurred in a stepwise manner and a stable intermediate was populated under equilibrium conditions. The thermodynamic parameters obtained show that the intermediate state of GFPuv is quite compact compared to the denatured state and most of the green fluorescence is retained in this state. By studying GFPuv folding assisted by TF and a number of TF mutants, we found that wild-type TF catalyzes proline isomerization and accelerates the folding rate at low TF concentrations, but retards GFPuv folding and decelerates the folding rate at high TF concentrations. This reflects the two activities of TF, as an enzyme and as a chaperone. A general mechanism of TF assisted protein folding is discussed.
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Affiliation(s)
- Jiang-Bi Xie
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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34
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Andrews BT, Schoenfish AR, Roy M, Waldo G, Jennings PA. The rough energy landscape of superfolder GFP is linked to the chromophore. J Mol Biol 2007; 373:476-90. [PMID: 17822714 PMCID: PMC2695656 DOI: 10.1016/j.jmb.2007.07.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 07/18/2007] [Accepted: 07/29/2007] [Indexed: 10/22/2022]
Abstract
Many green fluorescent protein (GFP) variants have been developed for use as fluorescent tags, and recently a superfolder GFP (sfGFP) has been developed as a robust folding reporter. This new variant shows increased stability and improved folding kinetics, as well as 100% recovery of native protein after denaturation. Here, we characterize sfGFP, and find that this variant exhibits hysteresis as unfolding and refolding equilibrium titration curves are non-coincident even after equilibration for more than eight half-lives as estimated from kinetic unfolding and refolding studies. This hysteresis is attributed to trapping in a native-like intermediate state. Mutational studies directed towards inhibiting chromophore formation indicate that the novel backbone cyclization is responsible for the hysteresis observed in equilibrium titrations of sfGFP. Slow equilibration and the presence of intermediates imply a rough landscape. However, de novo folding in the absence of the chromophore is dominated by a smoother energy landscape than that sampled during unfolding and refolding of the post-translationally modified polypeptide.
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Affiliation(s)
- Benjamin T. Andrews
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | - Andrea R. Schoenfish
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | - Melinda Roy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | | | - Patricia A. Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
- Corresponding author, E-mail:
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35
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Huang JR, Craggs TD, Christodoulou J, Jackson SE. Stable intermediate states and high energy barriers in the unfolding of GFP. J Mol Biol 2007; 370:356-71. [PMID: 17512539 DOI: 10.1016/j.jmb.2007.04.039] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 04/05/2007] [Accepted: 04/16/2007] [Indexed: 11/24/2022]
Abstract
We present a study of the denaturation of a truncated, cycle3 variant of green fluorescent protein (GFP). Chemical denaturation is used to unfold the protein, with changes in structure being monitored by the green fluorescence, tyrosine fluorescence and far-UV circular dichroism. The results show that the denaturation behaviour of GFP is complex compared to many small proteins: equilibrium is established only very slowly, over the time course of weeks, suggesting that there are high folding/unfolding energy barriers. Unfolding kinetics confirm that the rates of unfolding at low concentrations of denaturant are very low, consistent with the slow establishment of the equilibrium. In addition, we find that GFP significantly populates an intermediate state under equilibrium conditions, which is compact and stable with respect to the unfolded state (m(IU)=4.6 kcal mol(-1) M(-1) and Delta G(IU)=12.5 kcal mol(-1)). The global and local stability of GFP was probed further by measuring the hydrogen/deuterium (H/D) NMR exchange rates of more than 157 assigned amide protons. Analysis at two different values of pH showed that amide protons within the beta-barrel structure exchange at the EX2 limit, consequently, free energies of exchange could be calculated and compared to those obtained from the denaturation-curve studies providing further support for the three-state model and the existence of a stable intermediate state. Analysis reveals that amide protons in beta-strands 7, 8, 9 and 10 have, on average, higher exchange rates than others in the beta-barrel, suggesting that there is greater flexibility in this region of the protein. Forty or so amide protons were found which do not undergo significant exchange even after several months and these are clustered into a core region encompassing most of the beta-strands, at least at one end of the barrel structure. It is likely that these residues play an important role in stabilizing the structure of the intermediate state. The intermediate state observed in the chemical denaturation studies described here, is similar to that observed at pH 4 in other studies.
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Affiliation(s)
- Jie-rong Huang
- Chemistry Department, Lensfield Road, University of Cambridge, Cambridge CB2 1EW, UK
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