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Asamoto DK, Kozachenko IA, López-Peña I, Kim JE. Bimolecular quenching of tryptophan fluorescence in a membrane protein: Evolution of local solvation and environment during folding into a bilayer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119919. [PMID: 34004426 DOI: 10.1016/j.saa.2021.119919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
Fluorescence spectroscopy, including Stern-Volmer quenching, is a valuable tool for the study of protein dynamics. Changes in protein solvation during the folding reaction of a membrane protein, Outer membrane protein A (OmpA), into lipid bilayers was probed with bimolecular fluorescence quenching with acrylamide quencher. Six single-tryptophan OmpA mutants (W7, W15, W57, W102, W129, and W143) allowed for site-specific investigations at varying locations within the transmembrane β-barrel domain. A sphere-of-action quenching model that combines both static and dynamic components gave rise to Stern-Volmer quenching constants, KD, for OmpA denatured in 8.0 M urea, aggregated in 0.5 M urea, adsorbed onto small unilamellar vesicles (SUVs), and folded in SUVs (t = 6 hrs). The average KD values were KDdenatured(6.4M-1)>KDaggregated5.9M-1>KDadsorbed(1.9M-1)>KDfolded(0.6M-1). With knowledge of the fluorescence lifetimes in the absence of quencher, the bimolecular quenching constants, kq, were derived; the evolution of kq (and therefore KD)during the folding reaction into SUVs (t = 0 hr to t = 6 hrs) revealed desolvation timescales, τdesolv of 41-46 min (W7, W15, W57, W102), 27 min (W129), and 15 min (W143). The evolution of λmax during folding revealed fast and slow components, τenvironmentfast and τenvironmentslow of 7-13 min and 25-84 min, respectively, for all mutants. For the five lipid- facing mutants (W7, W15, W57, W129, and W143), the general trend was τenvironmentfast7-13min<τdesolv15-46min≤τenvironmentslow(25-84min). These results suggest that there is an initial fast step in which there is a large change in polarity to a hydrophobic environment, followed by a slower desolvation process during evolution within the hydrophobic environment. These results complement previous mechanisms of concerted folding and provide insights into site-specific changes in solvation during formation of native β-barrel structure.
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Affiliation(s)
- DeeAnn K Asamoto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Ivan A Kozachenko
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States.
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2
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Liu F, Zhang J. Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study. J Biochem 2020; 168:417-425. [DOI: 10.1093/jb/mvaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/02/2023] Open
Abstract
AbstractHuman catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.
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Affiliation(s)
- Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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3
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Wang L, Dong J, Li R, Zhao P, Kong J, Li L. Elucidation of binding mechanism of dibutyl phthalate on bovine serum albumin by spectroscopic analysis and molecular docking method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118044. [PMID: 31954361 DOI: 10.1016/j.saa.2020.118044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Dibutyl phthalate has been illegally used in beverages and directly affects the human health. Herein, the interaction occurred between dibutyl phthalate and bovine serum albumin was studied. The experimental results demonstrated that dibutyl phthalate could bind to bovine serum albumin and statically quench the intrinsic fluorescence of this protein. Circular dichroism measurements proved that the binding of dibutyl phthalate would lead to an obvious decrease of α-helix content in the bovine serum albumin. Molecular docking analysis clarified the fluorescence quenching mechanism, size distribution and zeta potential variation, conformational change of BSA, the site marker competitive fluorescence quenching and the interaction mechanism of dibutyl phthalate to bovine serum albumin. This work provided a useful information for the binding of dibutyl phthalate to protein.
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Affiliation(s)
- Lei Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China
| | - Jianfang Dong
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China; Department of Material Science, Shandong Polytechnic Technician College, Liaocheng 252027, China
| | - Rui Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China
| | - Peiran Zhao
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China.
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4
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Ahmed IA, Rodgers JM, Eng C, Troxler T, Gai F. PET and FRET utility of an amino acid pair: tryptophan and 4-cyanotryptophan. Phys Chem Chem Phys 2019; 21:12843-12849. [PMID: 31179453 PMCID: PMC6587589 DOI: 10.1039/c9cp02126d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methods based on fluorescence resonance energy transfer (FRET) and photo-induced electron transfer (PET) are widely used in the biological sciences, employing mostly dye-based FRET and PET pairs. While very useful and important, dye-based reporters are not always applicable without concern, for example, in cases where the fluorophore size needs to be minimized. Therefore, development and characterization of smaller, ideally amino acid-based PET and FRET pairs will expand the biological spectroscopy toolbox to enable new applications. Herein, we show that, depending on the excitation wavelength, tryptophan and 4-cyanotrptophan can interact with each other via the mechanism of either energy or electron transfer, hence constituting a dual FRET and PET pair. The biological utility of this amino acid pair is further demonstrated by applying it to study the end-to-end collision rate of a short peptide, the mode of interaction between a ligand and BSA, and the activity of a protease.
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Affiliation(s)
- Ismail A. Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M. Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina Eng
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Thomas Troxler
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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Angulo G, Rosspeintner A, Lang B, Vauthey E. Optical transient absorption experiments reveal the failure of formal kinetics in diffusion assisted electron transfer reactions. Phys Chem Chem Phys 2018; 20:25531-25546. [DOI: 10.1039/c8cp05153d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge separation yield is shown to be strongly influenced by the distance dependence of the reactivity, viscosity and concentration and cannot be disentangled from the preceding events.
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Affiliation(s)
- Gonzalo Angulo
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Geneva
- Switzerland
| | - Bernhard Lang
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Geneva
- Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Geneva
- Switzerland
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6
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Kumpulainen T, Lang B, Rosspeintner A, Vauthey E. Ultrafast Elementary Photochemical Processes of Organic Molecules in Liquid Solution. Chem Rev 2016; 117:10826-10939. [DOI: 10.1021/acs.chemrev.6b00491] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tatu Kumpulainen
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Bernhard Lang
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
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7
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Angulo G, Rosspeintner A, Koch M, Vauthey E. Comment on "Observation of the Marcus Inverted Region for Bimolecular Photoinduced Electron-Transfer Reactions in Viscous Media". J Phys Chem B 2016; 120:9800-3. [PMID: 27536949 DOI: 10.1021/acs.jpcb.6b06610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gonzalo Angulo
- Institute of Physical Chemistry, Polish Academy of Sciences , 44/52 Kasprzaka, 01-224 Warsaw, Poland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry, University of Geneva , 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Marius Koch
- Department of Chemistry, Princeton University , 08540 Princeton, New Jersey, United States
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva , 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
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8
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Liu S, Lv P, Li D, Guo X, Zhang B, Yu M, Li D, Xiong Y, Zhang L, Tian C. K(+) preference at the NaK channel entrance revealed by fluorescence lifetime and anisotropy analysis of site-specifically incorporated (7-hydroxycoumarin-4-yl)ethylglycine. Chem Commun (Camb) 2015; 51:15971-4. [PMID: 26382573 DOI: 10.1039/c5cc06124e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescent unnatural amino acid, (7-hydroxycoumarin-4-yl)ethylglycine (HC), was site-specifically incorporated at the Phe69 site, close to the entrance of the selectivity filter of the NaK channel. Decreased fluorescence lifetime and elevated time-resolved anisotropy of NaK-F69HC in buffers with high K(+)/Na(+) molar ratios indicated the K(+) preference at the entrance of the NaK channel, consistent with previous crystal structure results of the NaK channel.
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Affiliation(s)
- Sanling Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, P. R. China.
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9
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Mintzer MR, Troxler T, Gai F. p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides. Phys Chem Chem Phys 2015; 17:7881-7. [PMID: 25716887 PMCID: PMC4357573 DOI: 10.1039/c5cp00050e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C≡N stretching frequency and fluorescence quantum yield of p-cyanophenylalanine are sensitive to environment. As such, this unnatural amino acid has found broad applications, ranging from studying how proteins fold to determining the local electric field of membranes. Herein, we demonstrate that the fluorescence of p-cyanophenylalanine can be quenched by selenomethionine through an electron transfer process occurring at short distances, thus further expanding its spectroscopic utility. Using this fluorophore-quencher pair, we are able to show that short polyproline peptides (1-4 prolines) are not rigid; instead, they sample a bimodal conformational distribution.
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Affiliation(s)
- Mary Rose Mintzer
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104
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10
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Meadows CW, Ou R, Klinman JP. Picosecond-resolved fluorescent probes at functionally distinct tryptophans within a thermophilic alcohol dehydrogenase: relationship of temperature-dependent changes in fluorescence to catalysis. J Phys Chem B 2014; 118:6049-61. [PMID: 24892947 PMCID: PMC4056859 DOI: 10.1021/jp500825x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two single-tryptophan variants were generated in a thermophilic alcohol dehydrogenase with the goal of correlating temperature-dependent changes in local fluorescence with the previously demonstrated catalytic break at ca. 30 °C (Kohen et al., Nature 1999, 399, 496). One tryptophan variant, W87in, resides at the active site within van der Waals contact of bound alcohol substrate; the other variant, W167in, is a remote-site surface reporter located >25 Å from the active site. Picosecond-resolved fluorescence measurements were used to analyze fluorescence lifetimes, time-dependent Stokes shifts, and the extent of collisional quenching at Trp87 and Trp167 as a function of temperature. A subnanosecond fluorescence decay rate constant has been detected for W87in that is ascribed to the proximity of the active site Zn(2+) and shows a break in behavior at 30 °C. For the remainder of the reported lifetime measurements, there is no detectable break between 10 and 50 °C, in contrast with previously reported hydrogen/deuterium exchange experiments that revealed a temperature-dependent break analogous to catalysis (Liang et al., Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9556). We conclude that the motions that lead to the rigidification of ht-ADH below 30 °C are likely to be dominated by global processes slower than the picosecond to nanosecond motions measured herein. In the case of collisional quenching of fluorescence by acrylamide, W87in and W167in behave in a similar manner that resembles free tryptophan in water. Stokes shift measurements, by contrast, show distinctive behaviors in which the active-site tryptophan relaxation is highly temperature-dependent, whereas the solvent-exposed tryptophan's dynamics are temperature-independent. These data are concluded to reflect a significantly constrained environment surrounding the active site Trp87 that both increases the magnitude of the Stokes shift and its temperature-dependence. The results are discussed in the context of spatially distinct differences in enthalpic barriers for protein conformational sampling that may be related to catalysis.
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Affiliation(s)
- Corey W Meadows
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and the §California Institute for Quantitative Biosciences, University of California, Berkeley , Berkeley, California 94720, United States
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11
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Strambini GB, Gonnelli M. Acrylonitrile quenching of trp phosphorescence in proteins: a probe of the internal flexibility of the globular fold. Biophys J 2010; 99:944-52. [PMID: 20682273 DOI: 10.1016/j.bpj.2010.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/12/2010] [Accepted: 05/17/2010] [Indexed: 10/19/2022] Open
Abstract
Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O(2) and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) =k(0) exp[-(r -r(0))/r(e)], with an attenuation length r(e) = 0.03 nm and a contact rate k(0) = 3.6 x 10(10) s(-1). At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 x 10(9) M(-1)s(-1) for free Trp in water, in proteins kq ranged from 6.5 x 10(6) M(-1)s(-1) for superficial sites to 1.3 x 10(2) M(-1)s(-1) for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.
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12
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Strambini GB, Gonnelli M. Fluorescence Quenching of Buried Trp Residues by Acrylamide Does Not Require Penetration of the Protein Fold. J Phys Chem B 2009; 114:1089-93. [DOI: 10.1021/jp909567q] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Margherita Gonnelli
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 56124 Pisa, Italy
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13
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Duda T, Bharill S, Wojtas I, Yadav P, Gryczynski I, Gryczynski Z, Sharma RK. Atrial natriuretic factor receptor guanylate cyclase signaling: new ATP-regulated transduction motif. Mol Cell Biochem 2009; 324:39-53. [PMID: 19137266 DOI: 10.1007/s11010-008-9983-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 11/28/2008] [Indexed: 11/25/2022]
Abstract
ANF-RGC membrane guanylate cyclase is the receptor for the hypotensive peptide hormones, atrial natriuretic factor (ANF) and type B natriuretic peptide (BNP). It is a single transmembrane spanning protein. Binding the hormone to the extracellular domain activates its intracellular catalytic domain. This results in accelerated production of cyclic GMP, a second messenger in controlling blood pressure, cardiac vasculature, and fluid secretion. ATP is the obligatory transducer of the ANF signal. It works through its ATP regulated module, ARM, which is juxtaposed to the C-terminal side of the transmembrane domain. Upon interaction, ATP induces a cascade of temporal and spatial changes in the ARM, which, finally, result in activation of the catalytic module. Although the exact nature and the details of these changes are not known, some of these have been stereographed in the simulated three-dimensional model of the ARM and validated biochemically. Through comprehensive techniques of steady state, time-resolved tryptophan fluorescence and Forster Resonance Energy Transfer (FRET), site-directed and deletion-mutagenesis, and reconstitution, the present study validates and explains the mechanism of the model-based predicted transduction role of the ARM's structural motif, (669)WTAPELL(675). This motif is critical in the ATP-dependent ANF signaling. Molecular modeling shows that ATP binding exposes the (669)WTAPELL(675) motif, the exposure, in turn, facilitates its interaction and activation of the catalytic module. These principles of the model have been experimentally validated. This knowledge brings us a step closer to our understanding of the mechanism by which the ATP-dependent spatial changes within the ARM cause ANF signaling of ANF-RGC.
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Affiliation(s)
- Teresa Duda
- Unit of Regulatory & Molecular Biology, Division of Biochemistry and Molecular Biology, Salus University, Elkins Park, PA 19027, USA.
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14
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Bharill S, Sarkar P, Ballin JD, Gryczynski I, Wilson GM, Gryczynski Z. Fluorescence intensity decays of 2-aminopurine solutions: lifetime distribution approach. Anal Biochem 2008; 377:141-9. [PMID: 18406333 DOI: 10.1016/j.ab.2008.03.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 03/11/2008] [Accepted: 03/14/2008] [Indexed: 11/28/2022]
Abstract
The fluorescent adenine analog 2-aminopurine (2AP) has been used extensively to monitor conformational changes and macromolecular binding events involving nucleic acids because its fluorescence properties are highly sensitive to changes in chemical environment. Furthermore, site-specific incorporation of 2AP permits local DNA and RNA conformational events to be discriminated from the global structural changes monitored by UV-Vis spectroscopy and circular dichroism. However, although the steady-state fluorescence properties of 2AP have been well defined in diverse settings, interpretation of 2AP fluorescence lifetime parameters has been hampered by the heterogeneous nature of multiexponential 2AP intensity decays observed across populations of microenvironments. To resolve this problem, we tested the utility of multiexponential versus continuous Lorentzian lifetime distribution models to describe fluorescence intensity decays from 2AP in diverse chemical backgrounds and within the context of RNA. Heterogeneity was introduced into 2AP intensity decays by mixing solvents of differing polarities or by adding quenchers under high viscosity to evaluate the transient effect. Heterogeneity of 2AP fluorescence within the context of a synthetic RNA hairpin was introduced by structural remodeling using a magnesium salt. In each case except folded RNA (which required a bimodal distribution), 2AP lifetime properties were well described by single Lorentzian distribution functions, abrogating the need to introduce additional discrete lifetime subpopulations. Rather, heterogeneity in fluorescence decay processes was accommodated by the breadth of each distribution. This approach also permitted solvent relaxation effects on 2AP emission to be assessed by comparing lifetime distributions at multiple wavelengths. Together, these studies provide a new perspective for the interpretation of 2AP fluorescence lifetime properties that will further the utility of this fluorophore in analyses of the complex and heterogeneous structural microenvironments associated with nucleic acids.
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Affiliation(s)
- Shashank Bharill
- Center for Commercialization of Fluorescence Technologies, Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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15
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16
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Kunz M, Kintrup M, Hillen W, Schneider S. Conformational Changes Induced in the Tet Repressor Protein TetR(B) upon Operator or Anhydrotetracycline Binding as Revealed by Time-resolved Fluorescence Spectroscopy on Single Tryptophan Mutants ¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720035cciitt2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Andrade SM, Costa SMB. Fluorescence quenching of Acridine Orange in microemulsions induced by the non-steroidal anti-inflammatory drug Piroxicam. Photochem Photobiol Sci 2003; 2:605-10. [PMID: 12803085 DOI: 10.1039/b300097d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The singlet excited-state quenching of Acridine Orange (AO) by methyl viologen (MV2+) and the non-steroidal anti-inflammatory drug Piroxicam (Prx), incorporated in sodium bis(2-ethylhexyl) sulfosuccinate (AOT)/isooctane/water and Triton X-100 (Trx-100)/cyclohexane-hexanol/water (w/o) microemulsions, was followed by steady- and transient-state fluorescence. The water content was varied by using different values of omega 0 (omega 0 = [H2O]/[S]) at fixed AOT (0.1 M) and Trx-100 (0.2 M) concentrations. In AOT, MV2+ resides at the interface, while Prx partitions between the interface and bulk water, but considerably biased towards the latter compared to AO. The quenching process efficiency increases with increasing omega 0, but reaches a diffusional value similar to that of free water only for the case of Prx, underlining the electrostatic effect of the AOT interface. The quenching process in Trx-100 microemulsions is more efficient for Prx than for MV2+, pointing to a similar polyoxyethylene intra-chain location for the former and AO. In both cases, data obtained allowed the microviscosity of the aqueous interior at different omega 0 to be extrapolated and indicate an increase in eta w values with water content, reflecting changes in the shape of Trx-100 microemulsions, which occur at omega 0 = 8.
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Affiliation(s)
- Suzana M Andrade
- Centro de Química Estrutural, Complexo 1, Instituto Superior Técnico, 1049-001 Lisboa, Portugal.
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18
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de Oliveira AH, Giglio JR, Andrião-Escarso SH, Ward RJ. The effect of resonance energy homotransfer on the intrinsic tryptophan fluorescence emission of the bothropstoxin-I dimer. Biochem Biophys Res Commun 2001; 284:1011-5. [PMID: 11409896 DOI: 10.1006/bbrc.2001.5073] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bothopstoxin-I (BthTX-I) is a homodimeric Lys49-PLA2 homologue from the venom of Bothrops jararacussu in which a single Trp77 residue is located at the dimer interface. Intrinsic tryptophan fluorescence emission (ITFE) quenching by iodide and acrylamide has confirmed that a dimer to monomer transition occurs on reducing the pH from 7.0 to 5.0. Both the monomer and the dimer showed an excitation wavelength-dependent increase in the fluorescence emission maximum, however the excitation curve of the dimer was blue-shifted with respect to the monomeric form. No differences in the absorption or circular dichroism spectra between pH 5.0 and 7.0 were observed, suggesting that this curve shift is due neither to altered electronic ground states nor to exciton coupling of the Trp residues. We suggest that fluorescence resonance energy homotransfer between Trp77 residues at the BthTX-I dimer interface results in excitation of an acceptor Trp population which demonstrates a red-shifted fluorescence emission.
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Affiliation(s)
- A H de Oliveira
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP, Brazil
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Abstract
During the past several years there has been debate about the origins of nonexponential intensity decays of intrinsic tryptophan (trp) fluorescence of proteins, especially for single tryptophan proteins (STP). In this review we summarize the data from diverse sources suggesting that time-dependent spectral relaxation is a ubiquitous feature of protein fluorescence. For most proteins, the observations from numerous laboratories have shown that for trp residues in proteins (1) the mean decay times increase with increasing observation wavelength; (2) decay associated spectra generally show longer decay times for the longer wavelength components; and (3) collisional quenching of proteins usually results in emission spectral shifts to shorter wavelengths. Additional evidence for spectral relaxation comes from the time-resolved emission spectra that usually shows time-dependent shifts to longer wavelengths. These overall observations are consistent with spectral relaxation in proteins occurring on a subnanosecond timescale. These results suggest that spectral relaxation is a significant if not dominant source of nonexponential decay in STP, and should be considered in any interpretation of nonexponential decay of intrinsic protein fluorescence.
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Affiliation(s)
- J R Lakowicz
- University of Maryland School of Medicine, Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, Baltimore, USA
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20
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Kunz M, Kintrup M, Hillen W, Schneider S. Conformational changes induced in the Tet repressor protein TetR(B) upon operator or anhydrotetracycline binding as revealed by time-resolved fluorescence spectroscopy on single tryptophan mutants. Photochem Photobiol 2000; 72:35-48. [PMID: 10911727 DOI: 10.1562/0031-8655(2000)072<0035:cciitt>2.0.co;2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have analyzed the tryptophan (trp) fluorescence-decay kinetics of single trp mutants of the Tet repressor protein in the free, the tet operator and anhydrotetracycline (atc)-bound states. The position of the single trp varies between residues 164 and 171, in close proximity to one entrance of the tetracycline-binding pocket. A good fit of the trp fluorescence decay needed generally three exponentials. The decay times vary with detection wavelength, the extent of this variation being correlated to the variation of the emission maximum. Quenching experiments with neutral (acrylamide), cationic (N-methylpyridinium chloride) and anionic quencher (KI) support the interpretation of the three fluorescence components within a conformer model. Operator and atc binding change the ratio of the relative amplitudes of the medium- and long-lived component, thus pointing to structural changes as indicated also by the changes in decay time. Since the fluorescence decay is different between the free, atc- and operator-bound states we conclude that the protein structure is different in each of these three states. The fluorescence quenching constants reflect not only the variation in solvent exposure with position, but also the fact that the net surface charge in this region is negative, because the quenching constants by the cationic quencher are up to 10-fold higher. The atc fluorescence appears to decay monoexponentially with about the same decay time for all mutants, except W170, in which the trp residue sterically interferes with atc.
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Affiliation(s)
- M Kunz
- Institut für Physikalische und Theoretische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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21
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Kreimer DI, Malak H, Lakowicz JR, Trakhanov S, Villar E, Shnyrov VL. Thermodynamics and dynamics of histidine-binding protein, the water-soluble receptor of histidine permease. Implications for the transport of high and low affinity ligands. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4242-52. [PMID: 10866829 DOI: 10.1046/j.1432-1033.2000.01470.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacterial histidine permease is a model system for ABC transporters (traffic ATPases). The water-soluble receptor of this permease, HisJ, binds L-histidine and L-arginine (tightly) and L-lysine and L-ornithine (less tightly) in the periplasm, interacts with the membrane-bound complex (HisQMP2) and induces its ATPase activity, which results in ligand translocation. HisJ is a two-domain protein; in the absence of ligand, the cleft between two domains is open and binding of substrate stabilizes the closed conformation. Surprisingly, various liganded HisJ forms display substantial differences in their physicochemical characteristics and capacity to induce the ATPase. This is due to either different effects of the individual ligands on the respective closed structures, or to different equilibria being reached for each ligand between the open liganded form and the closed liganded form [Wolf, A. , Lee, K.C., Kirsch, J.F. & Ames, G.F.-L. (1996) J. Biol. Chem. 271, 21243-21250]. In this work, time-resolved measurements of the decay of intrinsic HisJ fluorescence and of the decay of the anisotropy of the fluorescence, as well as the analysis of the steady-state near UV CD and fluorescence spectra, rule out the model in which the differences between liganded complexes reflect different equilibria. The decay of the anisotropy of the fluorescence shows that liganded complexes differ dramatically in their large-scale conformational dynamics. Differential scanning calorimetry (DSC) curves for the HisJ thermal unfolding are well described by a scheme of equilibrium two-state unfolding of two independent domains, which can be ascribed to the two-domain structure of HisJ. This is true both for apo-HisJ at various pH values, and for HisJ in the presence of its ligands at varying concentrations, at pH 8.3. The DSC and structural data suggest that all ligands interact more extensively with the larger domain. A qualitative model for the HisJ conformational dynamics employing the idea of a twisting movement of the domains is proposed, which explains the difference in the efficacy of the ATPase induction by the various liganded HisJ forms.
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Affiliation(s)
- D I Kreimer
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, USA
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22
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Abstract
Apolipophorin III (apoLp-III) is an exchangeable apolipoprotein whose structure is represented as a bundle of five amphipathic alpha-helices. In order to study the properties of the helical domains of apolipophorin III, we designed and obtained five single-tryptophan mutants of Locusta migratoria apoLp-III. The proteins were studied by UV absorption spectroscopy, time-resolved and steady-state fluorescence spectroscopy, and circular dichroism. Fluorescence anisotropy, near-UV CD and solute fluorescence quenching studies indicate that the Trp residues in helices 1 (N-terminal) and 5 (C-terminal) have the highest conformational flexibility. These two residues also showed the highest degree of hydration. Trp residues in helices 3 and 4 display the lowest mobility, as assessed by fluorescence anisotropy and near UV CD. The Trp residue in helix 2 is protected from the solvent but shows high mobility. As inferred from the properties of the Trp residues, helices 1 and 5 appear to have the highest conformational flexibility. Helix 2 has an intermediate mobility, whereas helices 3 and 4 appear to constitute a highly ordered domain. From the configuration of the helices in the tertiary structure of the protein, we estimated the relative strength of the five interhelical interactions of apoLp-III. These interactions can be ordered according to their apparent stabilizing strengths as: helix 3-helix 4 > helix 2-helix 3 > helix 4-helix 1 approximately helix 2-helix 5 > helix 1-helix 5. A new model for the conformational change that is expected to occur upon binding of the apolipoprotein to lipid is proposed. This model is significantly different from the currently accepted model (Breiter, D. R., Kanost, M. R., Benning, M. M., Wesemberg, G., Law, J. H., Wells, M. A., Rayment, I., and Holden, M. (1991) Biochemistry 30, 603-608). The model presented here predicts that the relaxation of the tertiary structure and the concomitant exposure of the hydrophobic core take place through the disruption of the weak interhelical contacts between helices 1 and 5. To some extent, the weakness of the helix 1-helix 5 interaction would be due to the parallel arrangement of these helices.
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Affiliation(s)
- J L Soulages
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA.
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23
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Lopez MM, Zelent B, Kosk-Kosicka D. Effects of volatile anesthetic on the Ca2+-ATPase activation by dimerization. Distance-dependent quenching analysis and fluorescence energy transfer studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3345-50. [PMID: 10824122 DOI: 10.1046/j.1432-1327.2000.01367.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phenomenological distance-dependent quenching (DDQ) model was employed to investigate the character of the interaction between volatile anesthetics (VAs) and the plasma membrane Ca2+-ATPase (PMCA). The simultaneous analysis of the frequency-domain and steady-state data of tryptophan (Trp) fluorescence quenching by a VA points to a specific character of the apparent quenching effect of the VA, possibly arising from a significant contribution of static quenching. The apparent contributions of both static and dynamic quenching may be due to VA binding in the PMCA, which results in the modification of the conformational substates of the enzyme. To characterize further the molecular consequences of VA binding, we investigated its effects on the process of PMCA activation by self-association. VA shifted the equilibrium from enzyme dimers to monomers, as monitored by the loss of fluorescence energy transfer. The shift was apparently due to the VA-induced decrease in the affinity of PMCA molecules for self-association. Addition of a large molecular mass dextran to increase the proximity between enzyme monomers induced re-association of the VA-impaired PMCA, while the Ca2+-ATPase activity was not recovered. The results are congruent with a dual VA effect on PMCA, a shift in the monomer/dimer equilibrium, and an inactivation of both monomers and dimers.
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Affiliation(s)
- M M Lopez
- Department of Anesthesiology/Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
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25
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Zelent B, Kuśba J, Gryczynski I, Johnson ML, Lakowicz JR. Time-resolved and steady-state fluorescence quenching of N-acetyl-L-tryptophanamide by acrylamide and iodide. Biophys Chem 1998; 73:53-75. [PMID: 9697300 PMCID: PMC6905192 DOI: 10.1016/s0301-4622(98)00137-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We examined the time-resolved and steady-state fluorescence quenching of N-acetyl-L-tryptophanamide (NATA) by acrylamide and iodide, over a range of viscosities in propylene glycol. The quenching of NATA by acrylamide and iodide results in heterogeneity of the intensity decay which increases with the quencher concentration. We attribute the complex decays of NATA to transient effects in diffusion and the nature of the fluorophore-quencher interaction. These data were compared using the phenomenological radiation boundary condition (RBC) and distance-dependent quenching (DDQ) models for collisional quenching. We used global analysis of the time-resolved frequency-domain and steady-state data to select between the models. Consideration of both the frequency-domain and steady state data demonstrate that the quenching rate depends exponentially on the fluorophore-quencher distance, indicating the validity of the DDQ model. The rate constants for acrylamide and iodide quenching, at the constant distance of 5 A, were found to be near 10(13) s-1 and 10(9) s-1, respectively. These rates reflect electron transfer and exchange interactions as the probable quenching mechanisms, respectively.
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Affiliation(s)
- Bogumil Zelent
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Józef Kuśba
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Ignacy Gryczynski
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Michael L. Johnson
- Department of Pharmacology, Box 448, Room 561, Jordan Hall, University of Virginia, Charlottesville, VA 22908, USA
| | - Joseph R. Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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26
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Distance-dependent quenching of Nile Blue fluorescence byN,N-diethylaniline observed by frequency-domain fluorometry. J Fluoresc 1996; 6:187-94. [DOI: 10.1007/bf00732821] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/1996] [Accepted: 08/07/1996] [Indexed: 11/26/2022]
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Zelent B, Kuśba J, Gryczynski I, Johnson ML, Lakowicz JR. Distance-Dependent Fluorescence Quenching of p-Bis[2-(5-phenyloxazolyl)]benzene by Various Quenchers. ACTA ACUST UNITED AC 1996; 100:18592-18602. [PMID: 34032396 DOI: 10.1021/jp9618688] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report results of frequency-domain and steady-state measurements of the fluorescence quenching of p-bis-[2-(5-phenyloxazolyl)]benzene (POPOP) when quenched by bromoform (CHBr3), methyl iodide (CH3I), potassium iodide (KI), 1,2,4-trimethoxybenzene (TMB), or N,N-diethylaniline (DEA). The quenching efficiency of these compounds decreased in the order DEA, TMB, KI, CH3I, CHBr3. In the case of DEA and TMB the measurements clearly confirm the applicability of the exponential distance-dependent quenching (DDQ) model, in which the bimolecular quenching rate k(r) depends exponentially on the fluorophore–quencher separation r, k(r) = ka exp[−(r − a)/re], where a is the distance of closest approach. Simultaneous analysis of the frequency-domain and steady-state data significantly improved resolution of the recovered molecular parameters ka and re. The data for DEA and TMB cannot be satisfactorily fit using either the Smoluchowski or Collins–Kimball radiation boundary condition (RBC) model. The quenching behavior of the less efficient quenchers KI, CH3I, and CHBr3 can be adequately described with both the DDQ and RBC models, but this may be a simple consequence of less efficient quenching. The efficiency of quenching is discussed on the basis of the mechanisms of interaction between the fluorophore and quencher molecules, which involves electron transfer and/or heavy atom effects.
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Affiliation(s)
- Bogumil Zelent
- Center for Fluorescence Spectroscopy, Department of Biological Chemistry, and Medical BiotechnologyCenter, UniVersity of Maryland at Baltimore, School of Medicine, 108 N. Greene Street,Baltimore, Maryland 21201
| | - Józef Kuśba
- Faculty of Applied Physics and Mathematics,Technical UniVersity of Gdan ́sk, ul. Narutowicza 11/12, 80-952 Gdan ́sk, Poland
| | - Ignacy Gryczynski
- Center for Fluorescence Spectroscopy, Department of Biological Chemistry, and Medical BiotechnologyCenter, UniVersity of Maryland at Baltimore, School of Medicine, 108 N. Greene Street,Baltimore, Maryland 21201
| | - Michael L Johnson
- Department of Pharmacology, Box 448, Jordan Hall, Room 561,UniVersity of Virginia, CharlottesVille, Virginia 22908
| | - Joseph R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biological Chemistry, and Medical BiotechnologyCenter, UniVersity of Maryland at Baltimore, School of Medicine, 108 N. Greene Street,Baltimore, Maryland 21201
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Distance-dependent fluorescence quenching ofN-acetyl-L-tryptophanamide by acrylamide. J Fluoresc 1993; 3:199-207. [PMID: 24234834 DOI: 10.1007/bf00862743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/1993] [Indexed: 10/26/2022]
Abstract
We examined the time-dependent intensity decays ofN-acetyl-L-tryptophanamide (NATA) when collisionally quenched by acrylamide in propylene glycol over a range of temperatures. The intensity decays of NATA became increasingly heterogeneous in the presence of acrylamide. The NATA intensity decays were not consistent with the Collins-Kimball radiation boundary condition (RBC) model for quenching. The steady-state Stern-Volmer plots show significant upward curvature, and quenching of NATA by acrylamide was observed even in vitrified propylene glycol, where translational diffusion cannot occur during the lifetime of the excited state. These frequencydomain and steady-state data indicate a through-space quenching interaction between NATA and acrylamide, and the results are consistent with a rate constant for quenching that depends exponentially on the fluorophore-quencher separation distance. The exponential distance-dependent rate of quenching also explains the upward curvature of the Stern-Volmer plot, and the steady-state data aid in determining the interaction distance between NATA and acrylamide. These results suggest that the distance-dependent quenching rates need to be considered in the interpretation of acrylamide quenching of proteins.
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