1
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Guercia E, Berti F, De Zorzi R, Navarini L, Geremia S, Medagli B, De Conto M, Cassetta A, Forzato C. On the Cholesterol Raising Effect of Coffee Diterpenes Cafestol and 16- O-Methylcafestol: Interaction with Farnesoid X Receptor. Int J Mol Sci 2024; 25:6096. [PMID: 38892285 PMCID: PMC11173301 DOI: 10.3390/ijms25116096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The diterpene cafestol represents the most potent cholesterol-elevating compound known in the human diet, being responsible for more than 80% of the effect of coffee on serum lipids, with a mechanism still not fully clarified. In the present study, the interaction of cafestol and 16-O-methylcafestol with the stabilized ligand-binding domain (LBD) of the Farnesoid X Receptor was evaluated by fluorescence and circular dichroism. Fluorescence quenching was observed with both cafestol and 16-O-methylcafestol due to an interaction occurring in the close environment of the tryptophan W454 residue of the protein, as confirmed by docking and molecular dynamics. A conformational change of the protein was also observed by circular dichroism, particularly for cafestol. These results provide evidence at the molecular level of the interactions of FXR with the coffee diterpenes, confirming that cafestol can act as an agonist of FXR, causing an enhancement of the cholesterol level in blood serum.
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Affiliation(s)
- Elena Guercia
- Aromalab, illycaffè S.p.A., Area Science Park, Località Padriciano 99, 34149 Trieste, Italy; (E.G.); (L.N.)
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
| | - Luciano Navarini
- Aromalab, illycaffè S.p.A., Area Science Park, Località Padriciano 99, 34149 Trieste, Italy; (E.G.); (L.N.)
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
| | - Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
| | - Marco De Conto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
| | - Alberto Cassetta
- CNR-Institute of Crystallography, Area Science Park, SS. 14, Km 163.5, Basovizza, 34149 Trieste, Italy;
| | - Cristina Forzato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy; (F.B.); (S.G.); (B.M.); (M.D.C.)
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2
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Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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3
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Nandy T, Singh PC. Photophysical Properties of Noncanonical Amino Acid 7-Fluorotryptophan Sharply Different from Those of Canonical Derivative Tryptophan: Spectroscopic and Quantum Chemical Calculations. J Phys Chem B 2021; 125:6214-6221. [PMID: 34081478 DOI: 10.1021/acs.jpcb.1c03319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to the limited number of naturally existing canonical amino acids, several noncanonical amino acids have been designed to understand the diverse complex biological functions. Fluorinated amino acids are one of the important noncanonical amino acids that have been used to understand the different complex processes of proteins. In this study, the photophysical properties of the noncanonical amino acid 7-fluorotryptophan (7F-Trp) in different solvents have been investigated using extensive spectroscopic as well as quantum chemical calculation methods and compared with those of tryptophan (Trp). The spectroscopic and quantum chemical calculation data suggest that unlike Trp, 7F-Trp can be used to detect the excited-state proton transfer from solvents depending on its acidity, which makes 7F-Trp a potential candidate for sensing the excited-state proton transfer from the solvent molecules.
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Affiliation(s)
- Tonima Nandy
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
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4
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Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. J Phys Chem B 2021; 125:1009-1019. [PMID: 33492970 DOI: 10.1021/acs.jpcb.0c08085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite many studies on ligand-modulated protein mechanics, a comparative analysis of the role of ligand binding site on any specific protein fold is yet to be made. In this study, we explore the role of ligand binding site on the mechanical properties of β-grasp fold proteins, namely, ubiquitin and small ubiquitin related modifier 1 (SUMO1). The terminal segments directly connected through hydrogen bonds constitute the β-clamp geometry (or mechanical clamp), which confers high mechanical resilience to the β-grasp fold. Here, we study ubiquitin complexed with CUE2-1, a ubiquitin-binding domain (UBD) from yeast endonuclease protein Cue2, using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations. Our study reveals that CUE2-1 does not alter the mechanical properties of ubiquitin, despite directly interacting with its β-clamp. To explore the role of ligand binding site, we compare the mechanical properties of the ubiquitin/CUE2-1 complex with that of previously studied SUMO1/S12, another β-grasp protein complex, using SMD simulations. Simulations on the SUMO1/S12 complex corroborate previous experimentally observed enhancement in the mechanical stability of SUMO1, even though S12 binds away from the β-clamp. Differences in ligand binding-induced structural impact at the transition state of the two complexes explain the differences in ligand modulated protein mechanics. Contrary to previous reports, our study demonstrates that direct binding of ligands to the mechanical clamp does not necessarily alter the mechanical stability of β-grasp fold proteins. Rather, binding interactions away from the clamp can reinforce protein stability provided by the β-grasp fold. Our study highlights the importance of binding site and binding modes of ligands in modulating the mechanical stability of β-grasp fold proteins.
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Affiliation(s)
- Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
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5
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Fluorine induced conformational switching and modulation in photophysical properties of 7-fluorotryptophan: Spectroscopic, quantum chemical calculation and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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6
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Biswas B, Singh PC. The role of fluorocarbon group in the hydrogen bond network, photophysical and solvation dynamics of fluorinated molecules. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2019.109414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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8
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Jacob MH, D'Souza RN, Schwarzlose T, Wang X, Huang F, Haas E, Nau WM. Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding. J Phys Chem B 2018; 122:4445-4456. [PMID: 29617564 DOI: 10.1021/acs.jpcb.8b00879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.
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Affiliation(s)
- Maik H Jacob
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Roy N D'Souza
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Thomas Schwarzlose
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Xiaojuan Wang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Fang Huang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Elisha Haas
- Department of Life Science , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Werner M Nau
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany.,Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
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9
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Kenward C, Shin K, Rainey JK. Mixed Fluorotryptophan Substitutions at the Same Residue Expand the Versatility of 19
F Protein NMR Spectroscopy. Chemistry 2018; 24:3391-3396. [DOI: 10.1002/chem.201705638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Calem Kenward
- Department of Biochemistry & Molecular Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
- Department of Chemistry; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
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10
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Mondal S, Chaterjee S, Halder R, Jana B, Singh PC. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. J Phys Chem B 2017; 121:7681-7688. [PMID: 28737391 DOI: 10.1021/acs.jpcb.7b03420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Soumit Chaterjee
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Ritaban Halder
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Jana
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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11
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Chen H, Lin C, Xiong C, Liu Z, Zhang Y. One-pot synthesis of fluorescent 2,4-dialkenylindoles by rhodium-catalyzed dual C–H functionalization. Org Chem Front 2017. [DOI: 10.1039/c6qo00755d] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A one-pot synthesis of fluorescent 2,4-dialkenylindoles by rhodium-catalyzed dual C–H bond alkenylation of indoles.
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Affiliation(s)
- Hui Chen
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Cong Lin
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Chunhua Xiong
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou
- China
| | - Zhanxiang Liu
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Yuhong Zhang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
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12
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Xu J, Chen B, Callis P, Muiño PL, Rozeboom H, Broos J, Toptygin D, Brand L, Knutson JR. Picosecond fluorescence dynamics of tryptophan and 5-fluorotryptophan in monellin: slow water-protein relaxation unmasked. J Phys Chem B 2015; 119:4230-9. [PMID: 25710196 PMCID: PMC7477844 DOI: 10.1021/acs.jpcb.5b01651] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time dependent fluorescence Stokes (emission wavelength) shifts (TDFSS) from tryptophan (Trp) following sub-picosecond excitation are increasingly used to investigate protein dynamics, most recently enabling active research interest into water dynamics near the surface of proteins. Unlike many fluorescence probes, both the efficiency and the wavelength of Trp fluorescence in proteins are highly sensitive to microenvironment, and Stokes shifts can be dominated by the well-known heterogeneous nature of protein structure, leading to what we call pseudo-TDFSS: shifts that arise from differential decay rates of subpopulations. Here we emphasize a novel, general method that obviates pseudo-TDFSS by replacing Trp by 5-fluorotryptophan (5Ftrp), a fluorescent analogue with higher ionization potential and greatly suppressed electron-transfer quenching. 5FTrp slows and suppresses pseudo-TDFSS, thereby providing a clearer view of genuine relaxation caused by solvent and protein response. This procedure is applied to the sweet-tasting protein monellin which has uniquely been the subject of ultrafast studies in two different laboratories (Peon, J.; et al. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10964; Xu, J.; et al. J. Am. Chem. Soc. 2006, 128, 1214) that led to disparate interpretations of a 20 ps transient. They differed because of the pseudo-TDFSS present. The current study exploiting special properties of 5FTrp strongly supports the conclusion that both lifetime heterogeneity-based TDFSS and environment relaxation-based TDFSS are present in monellin and 5FTrp-monellin. The original experiments on monellin were most likely dominated by pseudo-TDFSS, whereas, in the present investigation of 5FTrp-monellin, the TDFSS is dominated by relaxation and any residual pseudo-TDFSS is overwhelmed and/or slowed to irrelevance.
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Affiliation(s)
- Jianhua Xu
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Binbin Chen
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Patrik Callis
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Pedro L. Muiño
- Department of Chemistry, Saint Francis University, Loretto, Pennsylvania 15940, United States
| | - Henriëtte Rozeboom
- Department of Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jaap Broos
- Department of Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Ludwig Brand
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jay R. Knutson
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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14
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Norouzy A, Assaf KI, Zhang S, Jacob MH, Nau WM. Coulomb Repulsion in Short Polypeptides. J Phys Chem B 2014; 119:33-43. [DOI: 10.1021/jp508263a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Amir Norouzy
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Khaleel I. Assaf
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Shuai Zhang
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Maik H. Jacob
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Werner M. Nau
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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15
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Deng X, Wu D. Highly sensitive photoluminescence energy transfer detection for 2,4,6-trinitrophenol using photoluminescent carbon nanodots. RSC Adv 2014. [DOI: 10.1039/c4ra06683a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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16
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Abstract
Biosynthetic incorporation of Trp analogs in a protein can help in its characterization using fluorescence spectroscopy and other methodologies like NMR and phosphorescence. Here a protocol is presented resulting in the efficient incorporation of Trp analogs in a recombinant protein, using an Escherichia coli Trp auxotroph. An overview of recent developments in the Trp analog incorporation field is also presented.
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Affiliation(s)
- Jaap Broos
- Laboratory of Biophysical Chemistry and Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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17
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Kishore M, Krishnamoorthy G, Udgaonkar JB. Critical Evaluation of the Two-State Model Describing the Equilibrium Unfolding of the PI3K SH3 Domain by Time-Resolved Fluorescence Resonance Energy Transfer. Biochemistry 2013; 52:9482-96. [DOI: 10.1021/bi401337k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Megha Kishore
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - G. Krishnamoorthy
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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18
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Banerjee S. Induction of protein conformational change inside the charged electrospray droplet. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:193-204. [PMID: 23378092 DOI: 10.1002/jms.3148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 06/01/2023]
Abstract
The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process.
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Affiliation(s)
- Shibdas Banerjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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19
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Jacob MH, Dsouza RN, Ghosh I, Norouzy A, Schwarzlose T, Nau WM. Diffusion-Enhanced Förster Resonance Energy Transfer and the Effects of External Quenchers and the Donor Quantum Yield. J Phys Chem B 2012; 117:185-98. [DOI: 10.1021/jp310381f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maik H. Jacob
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
| | - Roy N. Dsouza
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
| | - Indrajit Ghosh
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
| | - Amir Norouzy
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
| | - Thomas Schwarzlose
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
| | - Werner M. Nau
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany
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Singh TS, Rao BJ, Krishnamoorthy G. GTP binding leads to narrowing of the conformer population while preserving the structure of the RNA aptamer: a site-specific time-resolved fluorescence dynamics study. Biochemistry 2012; 51:9260-9. [PMID: 23110669 DOI: 10.1021/bi301110u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we employed a combination of steady-state and time-resolved fluorescence spectroscopy and studied the site-specific dynamics in a GTP aptamer using 2-aminopurine as a fluorescent probe. We compared the dynamics of the GTP-bound aptamer with that of the free aptamer as well as when it is denatured. GTP binding leads to an overall compaction of structure in the aptamer. The general pattern of fluorescence lifetimes and correlation times scanned across several locations in the aptamer does not seem to change following GTP binding. However, a remarkable narrowing of the lifetime distribution of the aptamer ensues following its compaction by GTP binding. Interestingly, such a "conformational narrowing" is evident from the lifetime readouts of the nucleotide belonging to the stem as well as the "bulge" part of the aptamer, independent of whether it is directly interacting with GTP. Taken together, these results underscore the importance of an overall intrinsic structure associated with the free aptamer that is further modulated following GTP binding. This work provides strong support for the "conformational selection" hypothesis of ligand binding.
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Affiliation(s)
- T Sanjoy Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
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Serrano AL, Bilsel O, Gai F. Native state conformational heterogeneity of HP35 revealed by time-resolved FRET. J Phys Chem B 2012; 116:10631-8. [PMID: 22891809 DOI: 10.1021/jp211296e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The villin headpiece subdomain (HP35) has become one of the most widely used model systems in protein folding studies, due to its small size and ultrafast folding kinetics. Here, we use HP35 as a test bed to show that the fluorescence decay kinetics of an unnatural amino acid, p-cyanophenylalanine (Phe(CN)), which are modulated by a nearby quencher (e.g., tryptophan or 7-azatryptophan) through the mechanism of fluorescence resonance energy transfer (FRET), can be used to detect protein conformational heterogeneity. This method is based on the notion that protein conformations having different donor-acceptor distances and interconverting slowly compared to the fluorescence lifetime of the donor (Phe(CN)) would exhibit different donor fluorescence lifetimes. Our results provide strong evidence suggesting that the native free energy basin of HP35 is populated with conformations that differ mostly in the position and mean helicity of the C-terminal helix. This finding is consistent with several previous experimental and computational studies. Moreover, this result holds strong implications for computational investigation of the folding mechanism of HP35.
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Affiliation(s)
- Arnaldo L Serrano
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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