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Paschenko VZ, Gorokhov VV, Korvatovsky BN, Knox PP, Grishanova NP, Goryachev SN. A Study of the Temperature Dependence of Tryptophan Fluorescence Lifetime in the Range of –170 to +20°С in Various Solvents. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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2
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Prokopowicz M, Jarmuła A, Casamayou-Boucau Y, Gordon F, Ryder A, Sobich J, Maj P, Cieśla J, Zieliński Z, Fita P, Rode W. Advanced Spectroscopy and APBS Modeling for Determination of the Role of His190 and Trp103 in Mouse Thymidylate Synthase Interaction with Selected dUMP Analogues. Int J Mol Sci 2021; 22:2661. [PMID: 33800923 PMCID: PMC7962005 DOI: 10.3390/ijms22052661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
A homo-dimeric enzyme, thymidylate synthase (TS), has been a long-standing molecular target in chemotherapy. To further elucidate properties and interactions with ligands of wild-type mouse thymidylate synthase (mTS) and its two single mutants, H190A and W103G, spectroscopic and theoretical investigations have been employed. In these mutants, histidine at position 190 and tryptophan at position 103 are substituted with alanine and glycine, respectively. Several emission-based spectroscopy methods used in the paper demonstrate an especially important role for Trp 103 in TS ligands binding. In addition, the Advanced Poisson-Boltzmann Solver (APBS) results show considerable differences in the distribution of electrostatic potential around Trp 103, as compared to distributions observed for all remaining Trp residues in the mTS family of structures. Together, spectroscopic and APBS results reveal a possible interplay between Trp 103 and His190, which contributes to a reduction in enzymatic activity in the case of H190A mutation. Comparison of electrostatic potential for mTS complexes, and their mutants, with the substrate, dUMP, and inhibitors, FdUMP and N4-OH-dCMP, suggests its weaker influence on the enzyme-ligand interactions in N4OH-dCMP-mTS compared to dUMP-mTS and FdUMP-mTS complexes. This difference may be crucial for the explanation of the "abortive reaction" inhibitory mechanism of N4OH-dCMP towards TS. In addition, based on structural analyses and the H190A mutant capacity to form a denaturation-resistant complex with N4-OH-dCMP in the mTHF-dependent reaction, His190 is apparently responsible for a strong preference of the enzyme active center for the anti rotamer of the imino inhibitor form.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, MISMaP College, University of Warsaw, ul. Banacha 2C, 02-097 Warsaw, Poland
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Yannick Casamayou-Boucau
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Fiona Gordon
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Alan Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Justyna Sobich
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Maj
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Joanna Cieśla
- Faculty of Chemistry, Warsaw University of Technology, ul Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Fita
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
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Kumaran R, Gayathri S, Augustine Arul Prasad T, Dhenadhayalan N, Keerthiga R, Sureka S, Jeevitha K, Karthick P. Fluorescence and quantum mechanical approach on the interaction of amides and their role on the stability and coexistence of the rotamer conformations of L-tryptophan in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 243:118791. [PMID: 32810781 DOI: 10.1016/j.saa.2020.118791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Photophysical investigation on the fluorescence decay characteristics of L-tryptophan and a derivative N-acetyl-L-tryptophanamide (NATA) with alkyl amides were carried out in water. L-tryptophan exists in the zwitterionic form and exhibits a biexponential lifetime which is correlated to the existence of rotamer structures. Addition of formamide (F) and dimethylformamide (DMF) results in a decrease in the fluorescence lifetime and its proportion of the most stable structure of L-tryptophan wherein acetamide (ACM) results in an increase of the same. Interestingly, all the amides result in the formation of the lifetime of the rotamer whose lifetime doesn't exist initially and the lifetime and its distribution increases irrespective of the nature of amide. The interaction between L-tryptophan and amide is attributed to hydrogen-bonding such that these interactions influence the relative proportion of the existence of individual rotamers in the presence of amides.Strikingly, in the case of NATA that does not exhibit rotamer structures; the fluorescence lifetime is quenched in the presence of F, whereas ACM and DMF result in a larger fold of enhancement resulting in two different lifetimes. The variation in the fluorescence lifetime and amplitude of the various conformers of L-tryptophan and of NATA is completely governed by the concentration of the amides in solution such that the microenvironment surrounding the fluorophores are completely reorganised. The hydrogen-bonding functional groups in amides that are responsible for the coexistence of rotamers are elucidated and well supported by quantum mechanical (QM) studies. Time-correlated single-photon counting(TCSPC) technique is used as a probe as well as marker in establishing the variation in the lifetime properties of L-tryptophan and NATA with non-fluorescent hydrogen-bonding solutes in water which promotes this as fascinating field of research in the context of fluorescence properties of a complicated amino acid-like tryptophan.
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Affiliation(s)
- Rajendran Kumaran
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India.
| | - Somasundaram Gayathri
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Thomas Augustine Arul Prasad
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | | | - Ravichandran Keerthiga
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Suresh Sureka
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Kumar Jeevitha
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Pargunan Karthick
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
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Knox PP, Gorokhov VV, Korvatovsky BN, Grishanova NP, Goryachev SN, Paschenko VZ. Specific features of the temperature dependence of tryptophan fluorescence lifetime in the temperature range of −170–20 °C. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Knox PP, Korvatovskiy BN, Gorokhov VV, Goryachev SN, Mamedov MD, Paschenko VZ. Comparison of tryptophan fluorescence lifetimes in cyanobacterial photosystem I frozen in the light and in the dark. PHOTOSYNTHESIS RESEARCH 2019; 139:441-448. [PMID: 30353420 DOI: 10.1007/s11120-018-0595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
The dependence on temperature of tryptophan fluorescence lifetime in trimeric photosystem I (PSI) complexes from cyanobacteria Synechocystis sp. PCC 6803 during the heating of pre-frozen to - 180 °C in the dark or in the light-activated preparations has been studied. Fluorescence lifetime in samples frozen in the light was longer than in samples frozen in the dark. For samples in 65% glycerol at λreg = 335 nm and at 20 °C, the lifetime of components were as follows: τ1 ≈ 1.2 ns, τ2 ≈ 4.9 ns, and τ3 ≈ 20 ns. The contribution of the first component was negligible. To analyze the contribution of components 2 and 3 derived from frozen-thawed samples, two temperature ranges from - 180 to - 90 °C and above - 90 °C are considered. In doing so, the contributions of these components appear antiphase course to each other. The dependence on temperature of these contributions is explained by the influence of the microconformational protein dynamics on the tryptophan fluorescence lifetime. In the present work, a comparative analysis of temperature-dependent conformational dynamics and electron transfer in cyanobacterial PSI (Schlodder et al., in Biochemistry 37:9466-9476, 1998) and Rhodobacter sphaeroides reaction center complexes (Knox et al., in J Photochem Photobiol B 180:140-148, 2018) was also carried out.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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6
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Noguchi H, Mylemans B, De Zitter E, Van Meervelt L, Tame JRH, Voet A. Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies. Biochem Biophys Res Commun 2018; 497:1038-1042. [PMID: 29481797 DOI: 10.1016/j.bbrc.2018.02.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 01/29/2023]
Abstract
β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Elke De Zitter
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium.
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7
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Knox PP, Gorokhov VV, Korvatovskiy BN, Lukashev EP, Goryachev SN, Paschenko VZ, Rubin AB. The effect of light and temperature on the dynamic state of Rhodobacter sphaeroides reaction centers proteins determined from changes in tryptophan fluorescence lifetime and P +Q A- recombination kinetics. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 180:140-148. [PMID: 29413697 DOI: 10.1016/j.jphotobiol.2018.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 11/26/2022]
Abstract
The temperature dependencies of the rate of dark recombination of separated charges between the photoactive bacteriochlorophyll and the primary quinone acceptor (QA) in photosynthetic reaction centers (RCs) of the purple bacteria Rhodobacter sphaeroides (Rb. sphaeroides) were investigated. Measurements were performed in water-glycerol and trehalose environments after freezing to -180 °C in the dark and under actinic light with subsequent heating. Simultaneously, the RC tryptophanyl fluorescence lifetime in the spectral range between 323 and 348 nm was measured under these conditions. A correlation was found between the temperature dependencies of the functional and dynamic parameters of RCs in different solvent mixtures. For the first time, differences in the average fluorescence lifetime of tryptophanyl residues were measured between RCs frozen in the dark and in the actinic light. The obtained results can be explained by the RC transitions between different conformational states and the dynamic processes in the structure of the hydrogen bonds of RCs. We assumed that RCs exist in two main microconformations - "fast" and "slow", which are characterized by different rates of P+ and QA- recombination reactions. The "fast" conformation is induced in frozen RCs in the dark, while the "slow" conformation of RC occurs when the RC preparation is frozen under actinic light. An explanation of the temperature dependencies of tryptophan fluorescence lifetimes in RC proteins was made under the assumption that temperature changes affect mainly the electron transfer from the indole ring of the tryptophan molecule to the nearest amide or carboxyl groups.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene P Lukashev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Andrew B Rubin
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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8
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Resolving the 3D spatial orientation of helix I in the closed state of the colicin E1 channel domain by FRET. Insights into the integration mechanism. Arch Biochem Biophys 2016; 608:52-73. [DOI: 10.1016/j.abb.2016.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/27/2016] [Accepted: 08/08/2016] [Indexed: 11/13/2022]
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9
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Mozziconacci O, Schöneich C. Effect of Conformation on the Photodegradation of Trp- And Cystine-Containing Cyclic Peptides: Octreotide and Somatostatin. Mol Pharm 2014; 11:3537-46. [DOI: 10.1021/mp5003174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Olivier Mozziconacci
- Department of Pharmaceutical
Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, United States
| | - Christian Schöneich
- Department of Pharmaceutical
Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, United States
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10
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Eisenberg AS, Juszczak LJ. The broken ring: reduced aromaticity in Lys-Trp cations and high pH tautomer correlates with lower quantum yield and shorter lifetimes. J Phys Chem B 2014; 118:7059-69. [PMID: 24882092 PMCID: PMC4165537 DOI: 10.1021/jp503355h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several nonradiative processes compete with tryptophan fluorescence emission. The difficulty in spectral interpretation lies in associating specific molecular environmental features with these processes and thereby utilizing the fluorescence spectral data to identify the local environment of tryptophan. Here, spectroscopic and molecular modeling study of Lys-Trp dipeptide charged species shows that backbone-ring interactions are undistinguished. Instead, quantum mechanical ground state isosurfaces reveal variations in indole π electron distribution and density that parallel charge (as a function of pK(1), pK(2), and pK(R)) on the backbone and residues. A pattern of aromaticity-associated quantum yield and fluorescence lifetime changes emerges. Where quantum yield is high, isosurfaces have a charge distribution similar to the highest occupied molecular orbital (HOMO) of indole, which is the dominant fluorescent ground state of the (1)L(a) transition dipole moment. Where quantum yield is low, isosurface charge distribution over the ring is uneven, diminished, and even found off ring. At pH 13, the indole amine is deprotonated, and Lys-Trp quantum yield is extremely low due to tautomer structure that concentrates charge on the indole amine; the isosurface charge distribution bears scant resemblance to the indole HOMO. Such greatly diminished fluorescence has been observed for proteins where the indole nitrogen is hydrogen bonded, lending credence to the association of aromaticity changes with diminished quantum yield in proteins as well. Thus tryptophan ground state isosurfaces are an indicator of indole aromaticity, signaling the partition of excitation energy between radiative and nonradiative processes.
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Affiliation(s)
- Azaria Solomon Eisenberg
- Department of Chemistry, Brooklyn College of The City University of New York , 2900 Bedford Ave., Brooklyn, NY 11210, United States
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11
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Callis PR. Simulating electrostatic effects on electronic transitions in proteins. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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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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13
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Sicchieri LB, Monteiro AM, Samad RE, Ito AS, Neto AMF, Vieira ND, Gidlund M, Courrol LC. Study of tryptophan lifetime fluorescence following low-density lipoprotein modification. APPLIED SPECTROSCOPY 2013; 67:379-384. [PMID: 23601537 DOI: 10.1366/12-06780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this paper we report the effects of the irradiation of low-density lipoprotein (LDL) by ultra-short laser pulses to obtain in vitro alterations mimicking proatherogenic modifications occurring in vivo in LDL. The modifications by metallic ions (copper and iron) and ultra-short laser pulses were studied by fluorescence steady state and time-resolved lifetime measurements. The results demonstrate that the modifications caused by ultra-short laser pulses and by iron affect the tryptophan residues of apolipoprotein B-100 (Apo-B), slightly decreasing fluorescent lifetimes, with almost no modifications in pre-exponential factors, indicating preservation of structural properties around the fluorophore. On the other hand, oxidation by copper strongly affects the Apo-B protein associated with LDL. We describe a fast, inexpensive, and nondestructive fluorescence-based method that is readily accessible to provide the LDL particle characterization.
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Affiliation(s)
- Letícia Bonfante Sicchieri
- Centro de Lasers e Aplicações, Instituto de Pesquisas Energéticas e Nucleares-Comissão Nacional de Energia Nuclear, Avenida Lineu Prestes 2242, São Paulo-SP, 05508, Brazil
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14
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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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15
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Chakraborty J, Das N, Halder UC. Unfolding diminishes fluorescence resonance energy transfer (FRET) of lysine modified β-lactoglobulin: Relevance towards anti-HIV binding. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 102:1-10. [DOI: 10.1016/j.jphotobiol.2010.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 08/26/2010] [Accepted: 08/28/2010] [Indexed: 11/25/2022]
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16
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de Foresta B, Vincent M, Gallay J, Garrigos M. Interaction with membrane mimics of transmembrane fragments 16 and 17 from the human multidrug resistance ABC transporter 1 (hMRP1/ABCC1) and two of their tryptophan variants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:401-14. [DOI: 10.1016/j.bbamem.2009.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 11/12/2009] [Accepted: 11/30/2009] [Indexed: 10/20/2022]
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17
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Moors SLC, Jonckheer A, De Maeyer M, Engelborghs Y, Ceulemans A. Tryptophan conformations associated with partial unfolding in ribonuclease T1. Biophys J 2009; 97:1778-86. [PMID: 19751684 DOI: 10.1016/j.bpj.2009.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/06/2009] [Accepted: 07/14/2009] [Indexed: 11/29/2022] Open
Abstract
The origin of the biexponential fluorescence decay of Trp in ribonuclease T1 under mildly destabilizing conditions, such as increased pH or temperature, or the presence of detergent, is still not understood. We have performed two extended replica-exchange molecular dynamics simulations to obtain a detailed representation of the native state at two protonation states corresponding to a high and low pH. At high pH, the appearance of partially unfolded states is evident. We found that this pH-induced destabilization originates from increased global repulsion as well as reduced local favorable electrostatic interactions and reduced H-bonding strength of His(27), His(40), and His(92). At high pH, alternative tryptophan rotamers appear and are linked to a distorted environment of the tryptophan, which also acts as a separate source of ground-state heterogeneity. The total population of these alternative conformations agrees well with the amplitude of the experimentally observed secondary fluorescence lifetime.
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Affiliation(s)
- Samuel L C Moors
- Laboratory of Quantum Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium.
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18
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Otosu T, Nishimoto E, Yamashita S. Multiple conformational state of human serum albumin around single tryptophan residue at various pH revealed by time-resolved fluorescence spectroscopy. J Biochem 2009; 147:191-200. [DOI: 10.1093/jb/mvp175] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Quentmeier S, Quentmeier CC, Walla PJ, Gericke KH. Two-color two-photon excitation of intrinsic protein fluorescence: label-free observation of proteolytic digestion of bovine serum albumin. Chemphyschem 2009; 10:1607-13. [PMID: 19156800 DOI: 10.1002/cphc.200800586] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two-color two-photon (2c2p) excitation fluorescence is used to monitor the enzymatic cleavage of bovine serum albumin (BSA) by subtilisin. Fluorescence is generated by irradiation with spatially and temporally overlapping femtosecond laser beams resulting in simultaneous absorption of an 800 and a 400 nm photon. Thereby, excitation of the fluorescent amino acid tryptophan present in BSA corresponds to an effective one-photon wavelength of 266 nm. The progress of protein cleavage is monitored by time-resolved fluorescence analysis. The fluorescence lifetime of tryptophan decreases during the reaction. This demonstrates a novel label-free multiphoton observation technique for conformational changes of proteins containing tryptophan. Due to the strong 2c2p fluorescence signal it is suitable for fast evaluation and monitoring of protein reactions. The course of the reaction is monitored simultaneously by gel electrophoresis. In contrast to conventional one-photon techniques, 2c2p excitation enables label-free protein fluorescence studies without irradiating the sample with UV light. Due to the dependence of the excitation on the power of both laser beams, excitation is limited to a relatively small focal volume. This results in dramatically reduced overall photodamage compared to direct UV irradiation. This method can be easily extended to microscopy imaging techniques.
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Affiliation(s)
- Stefan Quentmeier
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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20
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Ganesan A, Moore BD, Kelly SM, Price NC, Rolinski OJ, Birch DJS, Dunkin IR, Halling PJ. Optical Spectroscopic Methods for Probing the Conformational Stability of Immobilised Enzymes. Chemphyschem 2009; 10:1492-9. [DOI: 10.1002/cphc.200800759] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashok Ganesan
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL (United Kingdom), Fax: (+44) 141‐548‐4822
- XstalBio Limited, University Avenue, Glasgow G12 8QQ (United Kingdom)
| | - Barry D. Moore
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL (United Kingdom), Fax: (+44) 141‐548‐4822
- XstalBio Limited, University Avenue, Glasgow G12 8QQ (United Kingdom)
| | - Sharon M. Kelly
- Division of Molecular and Cellular Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, University Avenue, Glasgow G12 8QQ (United Kingdom)
| | - Nicholas C. Price
- Division of Molecular and Cellular Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, University Avenue, Glasgow G12 8QQ (United Kingdom)
| | - Olaf J. Rolinski
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG (United Kingdom)
| | - David J. S. Birch
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG (United Kingdom)
| | - Ian R. Dunkin
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL (United Kingdom), Fax: (+44) 141‐548‐4822
| | - Peter J. Halling
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL (United Kingdom), Fax: (+44) 141‐548‐4822
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21
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Otosu T, Nishimoto E, Yamashita S. Fluorescence Decay Characteristics of Indole Compounds Revealed by Time-Resolved Area-Normalized Emission Spectroscopy. J Phys Chem A 2009; 113:2847-53. [DOI: 10.1021/jp8078937] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuhiro Otosu
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Etsuko Nishimoto
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Shoji Yamashita
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
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22
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Romani AP, Ito AS. Interaction of adrenocorticotropin peptides with microheterogeneous systems — A fluorescence study. Biophys Chem 2009; 139:92-8. [DOI: 10.1016/j.bpc.2008.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/20/2008] [Accepted: 10/22/2008] [Indexed: 11/28/2022]
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23
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Callis PR. Exploring the Electrostatic Landscape of Proteins with Tryptophan Fluorescence. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Maglia G, Jonckheer A, De Maeyer M, Frère JM, Engelborghs Y. An unusual red-edge excitation and time-dependent Stokes shift in the single tryptophan mutant protein DD-carboxypeptidase from Streptomyces: the role of dynamics and tryptophan rotamers. Protein Sci 2008; 17:352-61. [PMID: 18096643 PMCID: PMC2222716 DOI: 10.1110/ps.073147608] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/18/2007] [Accepted: 10/31/2007] [Indexed: 10/22/2022]
Abstract
The fluorescence emission of the single tryptophan (W233) of the mutant protein DD-carboxypeptidase from streptomyces is characterized by a red-edge excitation shift (REES), i.e., the phenomenon that the wavelength of maximum emission depends on the excitation wavelength. This phenomenon is an indication for a strongly reduced dynamic environment of the single tryptophan, which has a very low accessibility to the solvent. The REES shows, however, an unusual temperature and time dependence. This, together with the fluorescence lifetime analysis, showing three resolvable lifetimes, can be explained by the presence of three rotameric states that can be identified using the Dead-End Elimination method. The three individual lifetimes increase with increasing emission wavelength, indicating the presence of restricted protein dynamics within the rotameric states. This is confirmed by time-resolved anisotropy measurements that show dynamics within the rotamers but not among the rotamers. The global picture is that of a protein with a single buried tryptophan showing strongly restricted dynamics within three distinct rotameric states with different emission spectra and an anisotropic environment.
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Affiliation(s)
- Giovanni Maglia
- Laboratory of Biomolecular Dynamics, Department of Chemistry, University of Leuven, Celestijnenlaan 200 G, B-3001 Leuven, Belgium
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25
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Witter R, Nozirov F, Sternberg U, Cross TA, Ulrich AS, Fu R. Solid-state 19F NMR spectroscopy reveals that Trp41 participates in the gating mechanism of the M2 proton channel of influenza A virus. J Am Chem Soc 2007; 130:918-24. [PMID: 18163621 DOI: 10.1021/ja0754305] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The integral membrane protein M2 of influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH. The side chain of His37 in the transmembrane alpha-helix is known to play an important role in the pH activation of the proton channel. It has also been suggested that Trp41, which is located in an adjacent turn of the helix, forms part of the gating mechanism. Here, a synthetic 25-residue peptide containing the M2 transmembrane domain was labeled with 6F-Trp41 and studied in lipid membranes by solid-state 19F NMR. We monitored the pH-dependent differences in the 19F dipolar couplings and motionally narrowed chemical shift anisotropies of this 6F-Trp41 residue, and we discuss the pH activation mechanism of the H+ channel. At pH 8.0, the structural parameters implicate an inactivated state, while at pH 5.3 the tryptophan conformation represents the activated state. With the aid of COSMOS force field simulations, we have obtained new side-chain torsion angles for Trp41 in the inactivated state (chi1 = -100 degrees +/- 10 degrees , chi2 = +110 degrees +/- 10 degrees ), and we predict a most probable activated state with chi1 = -50 degrees +/- 10 degrees and chi2 = +115 degrees +/- 10 degrees . We have also validated the torsion angles of His37 in the inactivated state as chi1 = -175 degrees +/- 10 degrees and chi2 = -170 degrees +/- 10 degrees .
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Affiliation(s)
- Raiker Witter
- Forschungszentrum Karlsruhe, IBG, POB 3640, 76021 Karlsruhe, Germany
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26
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Tryptophan fluorescence reveals the presence of long-range interactions in the denatured state of ribonuclease Sa. Biophys J 2007; 94:2288-96. [PMID: 18065473 DOI: 10.1529/biophysj.107.116954] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Characterizing the denatured state ensemble is crucial to understanding protein stability and the mechanism of protein folding. The aim of this research was to see if fluorescence could be used to gain new information on the denatured state ensemble. Ribonuclease Sa (RNase Sa) contains no Trp residues. We made five variants of RNase Sa by adding Trp residues at locations where they are found in other members of the microbial ribonuclease family. To better understand the protein denatured state, we also studied the fluorescence properties of the following peptides: N-acetyl-Trp-amide (NATA), N-acetyl-Ala-Trp-Ala-amide (AWA), N-acetyl-Ala-Ala-Trp-Ala-Ala-amide (AAWAA), and the five pentapeptides with the same sequence as the Trp substitution sites in RNase Sa. The major conclusions are: 1), the wavelength of maximum fluorescence intensity, lambda(max), does not differ significantly for the peptides and the denatured proteins; 2), the fluorescence intensity at lambda(max), I(F), differs significantly for the five Trp containing variants of RNase Sa; 3), the I(F) differences for the denatured proteins are mirrored in the peptides, showing that the short-range effects giving rise to the I(F) differences in the peptides are also present in the proteins; 4) the I(F) values for the denatured proteins are more than 30% greater than for the peptides, showing the presence of long-range effects in the proteins; 5), fluorescence quenching of Trp by acrylamide and iodide is more than 50% greater in the peptides than in the denatured proteins, showing that long-range effects limit the accessibility of the quenchers to the Trp side chains in the proteins; and 6), these results show that nonlocal effects in the denatured states of proteins influence Trp fluorescence and accessibility significantly.
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27
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Kloppmann E, Ullmann GM, Becker T. An extended dead-end elimination algorithm to determine gap-free lists of low energy states. J Comput Chem 2007; 28:2325-35. [PMID: 17471458 DOI: 10.1002/jcc.20749] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle.
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Affiliation(s)
- Edda Kloppmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, 95447 Bayreuth, Germany
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28
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Munson CA, Kelepouris L, Baker GA, Baker SN, Blanchard GJ, Bright FV. On the behavior of indole-containing species sequestered within reverse micelles at sub-zero temperatures. APPLIED SPECTROSCOPY 2007; 61:537-47. [PMID: 17555624 DOI: 10.1366/000370207780807795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We report on the effects of temperature (+30 to -100 degrees C) on the fluorescence from N-acetyl tryptophanamide (NATA) and human serum albumin (HSA) sequestered within Aerosol-OT (AOT) reversed micelles. NATA reports simultaneously from the polar and non-polar side of the reverse micelle interface. As the sample temperature decreases, the relative fraction of NATA molecules associated with the polar side increases. This redistribution process is characterized by DeltaH = -14.8 +/- 0.6 kJ/mol and DeltaS = -54 +/- 2 J/(K mol). The activation energy for thermal quenching (E(a,TQ)) associated with the polar side NATA molecules is 6.7 kJ/mol before the micelles have shed water and 1.0 kJ/mol after water shedding (below approximately -20 degrees C). The time-resolved fluorescence intensity decay for tryptophan-214 in HSA is triple exponential. We suggest that these lifetimes arise from three indole residue conformations in equilibrium. Cooling the sample causes a freezing-in of the least quenched conformer; the other conformers are frozen out. The E(a,TQ) value for the shortest lifetime component is 6 kJ/mol. The E(a,TQ) for the long and intermediate lifetime components are equivalent (approximately 1.5 kJ/mol).
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Affiliation(s)
- Chase A Munson
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, The State University of New York, Buffalo, NY 14260-3000, USA
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29
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Dehareng D, Dive G. Charge Transfer Study through the Determination of the Ionization Energies of Tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the Inclusion of One Glycine in Alanine and Leucine Containing Peptides. J Phys Chem A 2006; 110:11975-87. [PMID: 17064186 DOI: 10.1021/jp064255w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH(2) terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH(2)=CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH(2) terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide.
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Affiliation(s)
- Dominique Dehareng
- Centre d'Ingéniérie des Protéines, Institut de Chimie B6a, Sart Tilman, B4000, Liège, Belgium.
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30
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Losi A, Ghiraldelli E, Jansen S, Gärtner W. Mutational effects on protein structural changes and interdomain interactions in the blue-light sensing LOV protein YtvA. Photochem Photobiol 2006; 81:1145-52. [PMID: 16022561 DOI: 10.1562/2005-05-25-ra-541] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutagenesis studies on the phototropin-related protein YtvA from Bacillus subtilis have revealed the role of selected structural elements in interdomain communication. The LOV (light, oxygen, voltage) domain of YtvA undergoes light-driven reactions similar to that of phot-LOV, with reversible formation of a covalent flavin-cysteine adduct. The mutated proteins Ytva-E105L and YtvA-E56Q have been studied by UV fluorescence and circular dichroism (CD) spectroscopy. E105 (L in phototropin) is located at the solvent-exposed surface of the LOV domain central beta-sheet, demonstrated to participate in interdomain interaction in phototropin. CD data show that YtvA-E105L has a lower alpha-helix content in the dark and undergoes larger light-driven conformational changes than YtvA-WT. The E56Q mutation breaks the E56-K97 salt bridge, a structural element highly conserved within the LOV series. In YtvA-E56Q the CD spectrum is the same as in YtvA-WT, although the conserved W103 becomes more exposed to the solvent and the dark-recovery kinetics is slower. These results indicate that the E56-K97 salt bridge stabilizes locally the protein structure and participates in the regulation of the photocycle but has negligible effects on the overall structure. The E105L mutation, instead, highlights the involvement of the central beta-sheet in the light-driven conformational changes in LOV proteins.
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Affiliation(s)
- Aba Losi
- Department of Physics, University of Parma, Italy
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31
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Romani AP, Marquezin CA, Soares AEE, Ito AS. Study of the interaction between Apis mellifera venom and micro-heterogeneous systems. J Fluoresc 2006; 16:423-30. [PMID: 16791506 DOI: 10.1007/s10895-006-0077-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Accepted: 01/23/2006] [Indexed: 10/24/2022]
Abstract
The bee venom, used in treatment of inflammatory and articular diseases, is a complex mixture of peptides and enzymes and the presence of tryptophan allows the investigation by fluorescence techniques. Steady state and time-resolved fluorescence spectroscopy were used to study the interaction between bee venom extracted from Apis mellifera and three micro heterogeneous systems: sodium dodecylsulphate (SDS) micelles, sodium dodecylsulphate-poly(ethylene oxide) (SDS-PEO) aggregates, and the polymeric micelles LUTROL F127, formed by poly(ethylene oxide)-poly(propylene oxide)- poly(ethylene oxide). Fluorescence parameters in buffer solution were typical of peptides containing tryptophan exposed to the aqueous medium, and they gradually changed upon the addition of surfactant and polymeric micelles, demonstrating the interaction of the peptides with the micro heterogeneous systems. Quenching experiments were carried out using the N-alkylpyridinium ions (ethyl, hexyl, and dodecyl) as quenchers. In buffer solution the quenching has low efficiency and is independent of the alkyl chain length of the quencher. In the presence of the micro heterogeneous systems the extent of static and dynamic quenching enhanced, showing that both fluorophore and quenchers reside in the microvolume of the aggregates. The more hydrophobic quencher (dodecyl pyridinium ion) provides higher values for K (SV) and dynamic quenching constants, and SDS-PEO aggregates are most efficient to promote interaction between peptides and alkyl pyridinium ions. The results proved that bee venom interacts with drug delivery micelles of the copolymer LUTROL F127.
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Affiliation(s)
- Ana Paula Romani
- Departamento de Física e Matemática, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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32
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Moors SLC, Hellings M, De Maeyer M, Engelborghs Y, Ceulemans A. Tryptophan rotamers as evidenced by X-ray, fluorescence lifetimes, and molecular dynamics modeling. Biophys J 2006; 91:816-23. [PMID: 16698786 PMCID: PMC1563760 DOI: 10.1529/biophysj.106.085100] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the native-state dynamics of the Bacillus caldolyticus cold-shock protein mutant Bc-Csp L66E, using fluorescence and appropriate molecular dynamics methods. Two fluorescence lifetimes were found, the amplitudes of which agree very well with tryptophan rotamer populations, obtained from parallel tempering calculations. Rotamer lifetimes were predicted by transition-state theory from high-temperature simulations. Transition pathways were extracted from the transition rates between individual rotameric states. The molecular dynamics also reveal the loop fluctuations in the native state.
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Affiliation(s)
- Samuel L C Moors
- Laboratory of Quantum Chemistry, University of Leuven, Leuven, Belgium
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33
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Pan CP, Callis PR, Barkley MD. Dependence of Tryptophan Emission Wavelength on Conformation in Cyclic Hexapeptides. J Phys Chem B 2006; 110:7009-16. [PMID: 16571015 DOI: 10.1021/jp056164p] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The wavelength of maximum emission of tryptophan depends on the local electrostatic environment of the indole chromophore. The time-resolved emission spectra of seven rigid cyclic hexapeptides containing a single tryptophan residue were measured. The emission maxima of the three decay-associated spectra for the seven peptides ranged from 341 to 359 nm, suggesting that different tryptophan rotamers have different emission maxima even in the case of solvent-exposed tryptophans. This conclusion is supported by quantum mechanical/molecular dynamics simulations of the six canonical side chain rotamers of tryptophan in solvated hexapeptides. The calculated range of emission maxima for the tryptophan rotamers of the seven peptides is 344-365 nm. The precision of the wavelength calculations and the peptide, water, and charged side chain contributions to the spectral shifts are examined. The results indicate that the emission maxima of decay-associated spectra can aid in the assignment of fluorescence lifetimes to tryptophan rotamers.
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Affiliation(s)
- Chia-Pin Pan
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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34
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Chen L, Ferreira JAB, Costa SMB, Cabrita GJM, Otzen DE, Melo EP. Compaction of Ribosomal Protein S6 by Sucrose Occurs Only Under Native Conditions. Biochemistry 2006; 45:2189-99. [PMID: 16475807 DOI: 10.1021/bi051490g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of osmolyte sucrose on the stability and compaction of the folded and unfolded states of ribosomal protein S6 from Thermus thermophilus was analyzed. Confirming previous results obtained with sodium sulfate and trehalose, refolding stopped-flow measurements of S6 show that sucrose favors the conversion of the unfolded state ensemble to a highly compact structure (75% as compact as the folded state). This conversion occurs when the unfolded state is suddenly placed under native conditions and the compact state accumulates in a transient off-folding pathway. This effect of sucrose on the compaction of the unfolded state ensemble is counteracted by guanidinium hydrochloride. The compact state does not accumulate at higher guanidinium concentrations and the unfolded state ensemble does not display increased compaction in the presence of 6 M guanidinium as evaluated by collisional quenching of tryptophan fluorescence. In contrast, accessibility of the tryptophan residue of folded S6 above 1 M sucrose concentration decreased as a result of an increased compaction of the folded state. Unfolding stopped-flow measurements of S6 reflect this increased compaction of the folded state, but the unfolding pathway is not affected by sucrose. Compaction of folded and unfolded S6 induced by sucrose occurs under native conditions indicating that decreased protein conformational entropy significantly contributes to the mechanism of protein stabilization by osmolytes.
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Affiliation(s)
- LuYang Chen
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais 1049-001, Lisboa, Portugal
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35
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Fernandez RM, Vieira RFF, Nakaie CR, Lamy MT, Ito AS. Acid-base titration of melanocortin peptides: evidence of Trp rotational conformers interconversion. Biopolymers 2005; 80:643-50. [PMID: 15657882 DOI: 10.1002/bip.20210] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tryptophantime-resolved fluorescence was used to monitor acid-base titration properties of alpha-melanocyte stimulating hormone (alpha-MSH) and the biologically more potent analog [Nle4, D-Phe7]alpha -MSH (NDP-MSH), labeled or not with the paramagnetic amino acid probe 2,2,6,6-tetramthylpiperidine-N-oxyl-4-amino-4-carboxylic acid (Toac). Global analysis of fluorescence decay profiles measured in the pH range between 2.0 and 11.0 showed that, for each peptide, the data could be well fitted to three lifetimes whose values remained constant. The less populated short lifetime component changed little with pH and was ascribed to Trp g+ chi1 rotamer, in which electron transfer deactivation predominates over fluorescence. The long and intermediate lifetime preexponential factors interconverted along that pH interval and the result was interpreted as due to interconversion between Trp g- and trans chi1 rotamers, driven by conformational changes promoted by modifications in the ionization state of side-chain residues. The differences in the extent of interconversion in alpha-MSH and NDP-MSH are indicative of structural differences between the peptides, while titration curves suggest structural similarities between each peptide and its Toac-labeled species, in aqueous solution. Though less sensitive than fluorescence, the Toac electron spin resonance (ESR) isotropic hyperfine splitting parameter can also monitor the titration of side-chain residues located relatively far from the probe.
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36
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Hellings M, Engelborghs Y, Deckmyn H, Vanhoorelbeke K, Schiphorst ME, Akkerman JWN, De Maeyer M. Experimental indication for the existence of multiple Trp rotamers in von Willebrand Factor A3 domain. Proteins 2005; 57:596-601. [PMID: 15382239 DOI: 10.1002/prot.20227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The first step in both normal haemostasis and arterial thrombosis is the interaction between collagen, von Willebrand factor (vWF), and glycoprotein Ib. The A3 domain of vWF forms the principal binding site for collagen type I and type III. Inhibition of the vWF-collagen interaction by an anti-human vWF monoclonal antibody (MoAb) 82D6A3 can be a potential way to prevent arterial thrombosis. Identification of the epitope of MoAb 82D6A3 showed recently that the consensus sequence SPWR obtained by phage display could adopt the conformation of the discontinuous epitope. Modelling showed that Trp982 in the vWF had to obtain a more solvent accessible conformation. We performed a detailed fluorescence study of Trp982 in the vWF A3. Using the method described by Hellings et al. (Biophys J 2003;85:1894-1902), we were able to identify two different low-energy Trp982 rotamers and to link them with their experimentally derived fluorescence lifetimes. Fluorescence anisotropy showed no interconversion in the nanosecond timescale between the two different rotameric states. With these experiments, we gather strong indications for the existence of an exposed rotamer conformation and a rotamer that corresponds to the one observed in the X-ray structure. These results strongly support the modeling work (Vanhoorelbeke et al., J Biol Chem 2003;278:37815-37821).
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Affiliation(s)
- Mario Hellings
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Leuven, Belgium
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Fernandez RM, Vieira RFF, Nakaie CR, Ito AS, Lamy MT. Peptide-lipid interaction monitored by spin labeled biologically active melanocortin peptides. Peptides 2005; 26:1825-34. [PMID: 16006009 DOI: 10.1016/j.peptides.2004.12.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 12/07/2004] [Indexed: 10/25/2022]
Abstract
The present work comparatively analyzes the interaction of alpha-MSH and its more potent and long-acting analog [Nle4, D-Phe7]alpha-MSH (NDP-MSH) with lipid bilayers. The peptides were spin labeled with Toac (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) at the N-terminal, as those derivatives had been previously shown to keep their full biological activity. Due to the special rigidity of the Toac covalent binding to the peptide molecule, this spin label is highly sensitive to the peptide backbone conformation and dynamics. The peptides were investigated both by the electron spin resonance (ESR) of Toac0 and the time resolved fluorescence of Trp9 present in the peptides. The Toac0 ESR of the membrane-bound peptides indicates that the two peptides are inserted into the bilayer, close to the bilayer surface, in rather similar environments. A residue titration around pKa 7.5, possibly that of His6, can be clearly monitored by peptide-lipid partition. Trp9 time resolved fluorescence indicates that the peptides, and their Toac-labeled derivatives, present rather similar conformations when membrane bound, though Trp9 in NDP-MSH, and in its Toac-labeled derivative, goes somewhat further down into the bilayer. Yet, Toac0 ESR signal shows that the Toac-labeled N-terminal of NDP-MSH is in a shallower position in the bilayer, as compared to the hormone.
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Affiliation(s)
- Roberto M Fernandez
- Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970, São Paulo, SP, Brazil
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Liu T, Callis PR, Hesp BH, de Groot M, Buma WJ, Broos J. Ionization potentials of fluoroindoles and the origin of nonexponential tryptophan fluorescence decay in proteins. J Am Chem Soc 2005; 127:4104-13. [PMID: 15771548 DOI: 10.1021/ja043154d] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work reports an explanation for the unusual monoexponential fluorescence decay of 5-fluorotryptophan (5FTrp) in single-Trp mutant proteins [Broos, J.; Maddalena, F.; Hesp, B. H. J. Am. Chem. Soc. 2004, 126, 22-23] and substantially clarifies the origin of the ubiquitous nonexponential fluorescence decay of tryptophan in proteins. Our results strongly suggest that the extent of nonexponential fluorescence decay is governed primarily by the efficiency of electron transfer (ET) quenching by a nearby amide group in the peptide bond. Fluoro substitution increases the ionization potential (IP) of indole, thereby suppressing the ET rate, leading to a longer average lifetime and therefore a more homogeneous decay. We report experimental IPs for a number of substituted indoles including 5-fluoroindole, 5-fluoro-3-methylindole, and 6-fluoroindole, along with accurate ab initio calculations of the IPs for these and 20 related molecules. The results predict the IP of 5-fluorotryptophan to be 0.19 eV higher than that of tryptophan. 5-Fluoro substitution does not measurably alter the excitation-induced change in permanent dipole moment nor does it change the fluorescent state from 1La to 1Lb. In combination with electronic structure information this argues that the increased IP and the decreased excitation energy of the 1La state, together 0.3 eV, are solely responsible for the strong reduction of electron transfer quenching. 6-Fluoro substitution is predicted to increase the IP by a mere 0.09 eV. In agreement with our conclusions, the fluorescence decay curves of 6-fluorotryptophan-containing proteins are well fit using only two decay times compared to three required for Trp.
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Affiliation(s)
- Tiqing Liu
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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Somers KRF, Krüger P, Bucikiewicz S, De Maeyer M, Engelborghs Y, Ceulemans A. Protein simulations: the absorption spectrum of barnase point mutants. Protein Sci 2005; 13:1823-31. [PMID: 15215525 PMCID: PMC2279920 DOI: 10.1110/ps.04652804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The near-UV absorption spectra of barnase double-point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared-Amber5.0, CHARMM-c27b1, and GROMOS96-using indole as the fluorescent probe. It was found that calculated absorption spectra reproduce experimental values very well, provided detailed charge cloud descriptions are included. These calculations further sustain the hypothesis that different tryptophan rotamers can be present in proteins. Molecular dynamics calculations of the double-point mutants also point to the structural effect of counter ions.
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Affiliation(s)
- Ken R F Somers
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
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Abstract
The peptide bond quenches tryptophan fluorescence by excited-state electron transfer, which probably accounts for most of the variation in fluorescence intensity of peptides and proteins. A series of seven peptides was designed with a single tryptophan, identical amino acid composition, and peptide bond as the only known quenching group. The solution structure and side-chain chi(1) rotamer populations of the peptides were determined by one-dimensional and two-dimensional (1)H-NMR. All peptides have a single backbone conformation. The -, psi-angles and chi(1) rotamer populations of tryptophan vary with position in the sequence. The peptides have fluorescence emission maxima of 350-355 nm, quantum yields of 0.04-0.24, and triple exponential fluorescence decays with lifetimes of 4.4-6.6, 1.4-3.2, and 0.2-1.0 ns at 5 degrees C. Lifetimes were correlated with ground-state conformers in six peptides by assigning the major lifetime component to the major NMR-determined chi(1) rotamer. In five peptides the chi(1) = -60 degrees rotamer of tryptophan has lifetimes of 2.7-5.5 ns, depending on local backbone conformation. In one peptide the chi(1) = 180 degrees rotamer has a 0.5-ns lifetime. This series of small peptides vividly demonstrates the dominant role of peptide bond quenching in tryptophan fluorescence.
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Affiliation(s)
- Chia-Pin Pan
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
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Mohan GS, Chiu PT, Southern CA, O'Hara PB. Steady State and Multifrequency Phase Fluorometry Studies of Binding Site Flexibility in Related Antibodies. J Phys Chem A 2004. [DOI: 10.1021/jp049330m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gopi S. Mohan
- Department of Chemistry, Amherst College, Amherst Massachusetts 01002
| | - Philip T. Chiu
- Department of Chemistry, Amherst College, Amherst Massachusetts 01002
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Callis PR, Liu T. Quantitative Prediction of Fluorescence Quantum Yields for Tryptophan in Proteins. J Phys Chem B 2004. [DOI: 10.1021/jp0310551] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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