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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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2
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Julien O, Wang G, Jonckheer A, Engelborghs Y, Sykes BD. Tryptophan side chain conformers monitored by NMR and time-resolved fluorescence spectroscopies. Proteins 2011; 80:239-45. [DOI: 10.1002/prot.23198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/19/2011] [Accepted: 09/04/2011] [Indexed: 11/08/2022]
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3
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Tourné-Péteilh C, Lerner DA, Charnay C, Nicole L, Bégu S, Devoisselle JM. The potential of ordered mesoporous silica for the storage of drugs: the example of a pentapeptide encapsulated in a MSU-tween 80. Chemphyschem 2003; 4:281-6. [PMID: 12674601 DOI: 10.1002/cphc.200390045] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Corine Tourné-Péteilh
- UMR CNRS/ENSCM 5618, Université de Montpellier I, 15 Avenue Ch. Flahault, 34060 Montpellier, France
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4
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Broos J, Pas HH, Robillard GT. The smallest resonance energy transfer acceptor for tryptophan. J Am Chem Soc 2002; 124:6812-3. [PMID: 12059187 DOI: 10.1021/ja017812v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The utility of diazirine ligands as acceptors in resonance energy transfer (RET) distance measurements with tryptophan or tryptophan analogues as donor is reported. The principle is demonstrated for a diazirine derivative of d-mannitol, 2-azi-2-deoxy-d-arabino-hexitol, and single-tryptophan-containing mutants of the mannitol transporter, EIImtl, from E. coli. The Förster distance is 10 A for the tryptophan-diazirine donor-acceptor couple, allowing the measurement of distances up to 17 A. The versatility of tryptophan as an intrinsic spectroscopic probe in protein chemistry and the small size of the diazirine group makes this a very attractive donor-acceptor couple for accurate RET distance information in protein chemistry.
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Affiliation(s)
- Jaap Broos
- Department of Biochemistry and Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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5
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Sau AK, Chen CA, Cowan JA, Mazumdar S, Mitra S. Steady-state and time-resolved fluorescence studies on wild type and mutant chromatium vinosum high potential iron proteins: holo- and apo-forms. Biophys J 2001; 81:2320-30. [PMID: 11566801 PMCID: PMC1301702 DOI: 10.1016/s0006-3495(01)75878-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Detailed circular dichroism (CD), steady-state and time-resolved tryptophan fluorescence studies on the holo- and apo- forms of high potential iron protein (HiPIP) from Chromatium vinosum and its mutant protein have been carried out to investigate conformational properties of the protein. CD studies showed that the protein does not have any significant secondary structure elements in the holo- or apo- HiPIP, indicating that the metal cluster does not have any effect on formation of secondary structure in the protein. Steady-state fluorescence quenching studies however, suggested that removal of the iron-sulfur ([Fe(4)S(4)](3+)) cluster from the protein leads to an increase in the solvent accessibility of tryptophans, indicating change in the tertiary structure of the protein. CD studies on the holo- and apo- HiPIP also showed that removal of the metal prosthetic group drastically affects the tertiary structure of the protein. Time-resolved fluorescence decay of the wild type protein was fitted to a four-exponentials model and that of the W80N mutant was fitted to a three-exponentials model. The time-resolved fluorescence decay was also analyzed by maximum entropy method (MEM). The results of the MEM analysis agreed with those obtained from discrete exponentials model analysis. Studies on the wild type and mutants helped to assign the fast picosecond lifetime component to the W80 residue, which exhibits fast fluorescence energy transfer to the [Fe(4)S(4)](3+) cluster of the protein. Decay-associated fluorescence spectra of each tryptophan residues were calculated from the time-resolved fluorescence results at different emission wavelengths. The results suggested that W80 is in the hydrophobic core of the protein, but W60 and W76 are partially or completely exposed to the solvent.
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Affiliation(s)
- A K Sau
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400 005, India
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6
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Ababou A, Bombarda E. On the involvement of electron transfer reactions in the fluorescence decay kinetics heterogeneity of proteins. Protein Sci 2001; 10:2102-13. [PMID: 11567101 PMCID: PMC2374218 DOI: 10.1110/ps.05501] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Time-resolved fluorescence study of single tryptophan-containing proteins, nuclease, ribonuclease T1, protein G, glucagon, and mastoparan, has been carried out. Three different methods were used for the analysis of fluorescence decays: the iterative reconvolution method, as reviewed and developed in our laboratory, the maximum entropy method, and the recent method that we called "energy transfer" method. All the proteins show heterogeneous fluorescence kinetics (multiexponential decay). The origin of this heterogeneity is interpreted in terms of current theories of electron transfer process, which treat the electron transfer process as a radiationless transition. The theoretical electron transfer rate was calculated assuming the peptide bond carbonyl as the acceptor site. The good agreement between experimental and theoretical electron-transfer rates leads us to suggest that the electron-transfer process is the principal quenching mechanism of Trp fluorescence in proteins, resulting in heterogeneous fluorescence kinetics. Furthermore, the origin of apparent homogeneous fluorescence kinetics (monoexponential decay) in some proteins also can be explained on the basis of electron-transfer mechanism.
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Affiliation(s)
- A Ababou
- Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Université Louis Pasteur, Strasbourg 1, Illkirch, France.
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7
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Malnasi-Csizmadia A, Kovacs M, Woolley RJ, Botchway SW, Bagshaw CR. The dynamics of the relay loop tryptophan residue in the Dictyostelium myosin motor domain and the origin of spectroscopic signals. J Biol Chem 2001; 276:19483-90. [PMID: 11278775 DOI: 10.1074/jbc.m010886200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Steady-state and time-resolved fluorescence measurements were performed on a Dictyostelium discoideum myosin II motor domain construct retaining a single tryptophan residue at position 501, located on the relay loop. Other tryptophan residues were mutated to phenylalanine. The Trp-501 residue showed a large enhancement in fluorescence in the presence of ATP and a small quench in the presence of ADP as a result of perturbing both the ground and excited state processes. Fluorescence lifetime and quantum yield measurements indicated that at least three microstates of Trp-501 were present in all nucleotide states examined, and these could not be assigned to a particular gross conformation of the motor domain. Enhancement in emission intensity was associated with a reduction of the contribution from a statically quenched component and an increase in a component with a 5-ns lifetime, with little change in the contribution from a 1-ns lifetime component. Anisotropy measurements indicated that the Trp-501 side chain was relatively immobile in all nucleotide states, and the fluorescence was effectively depolarized by rotation of the whole motor domain with a correlation time on 50-70 ns. Overall these data suggest that the backbone of the relay loop remains structured throughout the myosin ATPase cycle but that the Trp-501 side chain experiences a different weighting in local environments provided by surrounding residues as the adjacent converter domain rolls around the relay loop.
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Affiliation(s)
- A Malnasi-Csizmadia
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
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8
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Malicka J, Groth M, Karolczak J, Czaplewski C, Liwo A, Wiczk W. Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues. Biopolymers 2001; 58:447-57. [PMID: 11180057 DOI: 10.1002/1097-0282(20010405)58:4<447::aid-bip1020>3.0.co;2-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fluorescence decay of tryptophan is a sensitive indicator of its local environment within a peptide or protein. In this study we carried out fluorescence measurements of the tryptophan residue of cyclic enkephalin analogues of a general formula X-c[D-Dab(2)-Gly(3)-Trp(4)-Y(5)] where X = Cbz or H and Y = D- or L-Leu, in four solvents [water, methanol, acetonitrile, and dimethyl sulfoxide (DMSO)]. An analysis of the tryptophan fluorescence decays using a discrete-exponential model indicates that tryptophan fluorescence decay can be described by a double exponential function in all solvents studied. Lifetime distribution analysis yields a bimodal distribution in protic solvents (water and methanol), whereas an asymmetric, unimodal distribution in an aprotic solvent (DMSO) and uni- or bimodal distributions in acetonitrile solution, depending on leucine configuration. The data are interpreted in terms of the rotamer model, in which the modality and the relative proportions of the lifetime components are related to the population distribution of tryptophan chi(1) rotamers about the C(alpha)--C(beta) bond. The chirality of the Leu(5) residue and solvent properties affect the local environment of the tryptophan residue and therefore influence the distribution of side-chain rotamers. These results are consistent with the results of theoretical conformational calculations.
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Affiliation(s)
- J Malicka
- University of Gdańsk, Faculty of Chemistry, Sobieskiego 18, 80-952 Gdańsk, Poland
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9
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Rzeska A, Malicka J, Stachowiak K, Szymańska A, Łankiewicz L, Wiczk W. Photophysics of phenylalanine analogues. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00394-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Rzeska A, Stachowiak K, Malicka J, Łankiewicz L, Wiczk W. Photophysics of phenylalanine analogues. J Photochem Photobiol A Chem 2000. [DOI: 10.1016/s1010-6030(00)00229-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Larive CK, Lunte SM, Zhong M, Perkins MD, Wilson GS, Gokulrangan G, Williams T, Afroz F, Schöneich C, Derrick TS, Middaugh CR, Bogdanowich-Knipp S. Separation and analysis of peptides and proteins. Anal Chem 1999; 71:389R-423R. [PMID: 10409086 DOI: 10.1021/a1990013o] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C K Larive
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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12
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Hudson BS, Huston JM, Soto-Campos G. A Reversible “Dark State” Mechanism for Complexity of the Fluorescence of Tryptophan in Proteins. J Phys Chem A 1999. [DOI: 10.1021/jp983585g] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bruce S. Hudson
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100 and Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Joseph M. Huston
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100 and Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Gerardo Soto-Campos
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100 and Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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13
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Hudson BS. An Ionization/Recombination Mechanism for Complexity of the Fluorescence of Tryptophan in Proteins. Acc Chem Res 1998. [DOI: 10.1021/ar960227s] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bruce S. Hudson
- Department of Chemistry Syracuse University Syracuse, New York 13244-4100
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