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Lolli G, Raboni S, Pasqualetto E, Benoni R, Campanini B, Ronda L, Mozzarelli A, Bettati S, Battistutta R. Insight into GFPmut2 pH Dependence by Single Crystal Microspectrophotometry and X-ray Crystallography. J Phys Chem B 2018; 122:11326-11337. [PMID: 30179482 DOI: 10.1021/acs.jpcb.8b07260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fluorescence of Green Fluorescent Protein (wtGFP) and variants has been exploited in distinct applications in cellular and analytical biology. GFPs emission depends on the population of the protonated (A-state) and deprotonated (B-state) forms of the chromophore. Whereas wtGFP is pH-independent, mutants in which Ser65 is replaced by either threonine or alanine (as in GFPmut2) are pH-dependent, with a p Ka around 6. Given the wtGFP pH-independence, only the structure of the protonated form was determined. The deprotonated form was deduced on the basis of the crystal structure of the Ser65Thr mutant at basic pH, assuming that it corresponds to the conformation populated in solution. Here, we present an investigation where structures of the protonated and deprotonated forms of GFPmut2 were determined from crystals grown in either MPD at pH 6 or PEG at pH 8.5, and moved to either higher or lower pH. Both crystal forms of GFPmut2 were titrated monitoring the process via polarized absorption microspectrophotometry in order to precisely correlate the protonation process with the structures. We found that (i) in solution, chromophore titration is not thermodynamically coupled with any residue and Glu222 is always protonated independent of the protonation state of the chromophore; (ii) the lack of coupling is reflected in the structural behavior of the chromophore and Glu222 environments, with only the former showing variations with pH; (iii) titrations of low-pH and high-pH grown crystals exhibit a Hill coefficient of about 0.75, indicating an anticooperative behavior not observed in solution; (iv) structures where pH was changed in the crystal point to Glu222 as the ionizable group responsible for the outset of the anticooperative behavior; and (v) in GFPmut2 the canonical GFP proton wire involving the chromophore is not interrupted at the level of Ser205 and Glu222 at basic pH as in the Ser65Thr mutant. This allows proposing the structure of the deprotonated state of GFPmut2 as an alternative model for the analogous state of wtGFP.
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Affiliation(s)
- Graziano Lolli
- Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy
| | - Samanta Raboni
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Elisa Pasqualetto
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
| | - Roberto Benoni
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Luca Ronda
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
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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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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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Rusciano G, De Luca AC, Pesce G, Sasso A. Raman Tweezers as a Diagnostic Tool of Hemoglobin-Related Blood Disorders. SENSORS (BASEL, SWITZERLAND) 2008; 8:7818-7832. [PMID: 27873960 PMCID: PMC3790991 DOI: 10.3390/s8127818] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 11/28/2008] [Accepted: 11/28/2008] [Indexed: 11/16/2022]
Abstract
This review presents the development of a Raman Tweezers system for detecting hemoglobin-related blood disorders at a single cell level. The study demonstrates that the molecular fingerprint insight provided by Raman analysis holds great promise for distinguishing between healthy and diseased cells in the field of biomedicine. Herein a Raman Tweezers system has been applied to investigate the effects of thalassemia, a blood disease quite diffuse in the Mediterranean Sea region. By resonant excitation of hemoglobin Raman bands, we examined the oxygenation capability of normal, alpha- and beta-thalassemic erythrocytes. A reduction of this fundamental red blood cell function, particularly severe for beta-thalassemia, has been found. Raman spectroscopy was also used to draw hemoglobin distribution inside single erythrocytes; the results confirmed the characteristic anomaly (target shape), occurring in thalassemia and some other blood disorders. The success of resonance Raman spectroscopy for thalassemia detection reported in this review provide an interesting starting point to explore the application of a Raman Tweezers system in the analysis of several blood disorders.
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Affiliation(s)
- Giulia Rusciano
- Università di Napoli Federico II / Complesso Univ. M. S. Angelo, Via Cinthia 80126, Napoli, Italy
- CNISM- Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia, UdR Napoli, Italy
| | - Anna C. De Luca
- Università di Napoli Federico II / Complesso Univ. M. S. Angelo, Via Cinthia 80126, Napoli, Italy
- CNISM- Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia, UdR Napoli, Italy
| | - Giuseppe Pesce
- Università di Napoli Federico II / Complesso Univ. M. S. Angelo, Via Cinthia 80126, Napoli, Italy
- CNISM- Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia, UdR Napoli, Italy
| | - Antonio Sasso
- Università di Napoli Federico II / Complesso Univ. M. S. Angelo, Via Cinthia 80126, Napoli, Italy
- CNISM- Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia, UdR Napoli, Italy
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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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Mallam AL, Jackson SE. Use of protein engineering techniques to elucidate protein folding pathways. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 84:57-113. [PMID: 19121700 DOI: 10.1016/s0079-6603(08)00403-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Anna L Mallam
- Department of Chemistry, Cambridge, CB2 1EW, United Kingdom
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Cannone F, Collini M, Chirico G, Baldini G, Bettati S, Campanini B, Mozzarelli A. Environment effects on the oscillatory unfolding kinetics of GFP. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:795-803. [PMID: 17429619 DOI: 10.1007/s00249-007-0160-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 03/13/2007] [Accepted: 03/20/2007] [Indexed: 11/29/2022]
Abstract
The chromophore of a green fluorescent protein (GFP) mutant engineered to enhance emission and stability is known to display erratic switchings among a few of its chemical substates and, in particular, between the anionic A and the neutral N substates, whose difference is associated with a proton exchange and a consequent conformation rearrangement. However, when close to unfolding, the A-N switchings suddenly become very regular as shown by fluorescence oscillations that have been recently observed for molecules embedded in wet silica gel. In order to establish whether the matrix hosting the protein is responsible for these oscillations, we investigated the effect of another medium (silanized surfaces), of a different denaturant (urea) and of cosolvents (D(2)O and glycerol). The occurrence of periodic A-N switchings, in the last milliseconds before GFP unfolding, is observed under all investigated conditions, together with three specific frequency values that characterize the pre-unfolding fluorescence. Urea and guanidinium, the denaturants employed in order to unfold GFP, do not lead to appreciable differences in the observed switching parameters, whereas the different media embedding the protein give rise only to frequency shifts that scale with the viscosity of the host. The periodicity of the GFP A-N switchings and their dependence on cosolvents suggest that they could be associated with oscillatory motions between meta-stable conformations of the beta-barrel surrounding the chromophore near protein unfolding.
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Affiliation(s)
- Fabio Cannone
- Department of Physics, University of Milano-Bicocca, Milan, Italy
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