1
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López-Peña I, Lee CT, Rivera JJ, Kim JE. Role of the Triplet State and Protein Dynamics in the Formation and Stability of the Tryptophan Radical in an Apoazurin Mutant. J Phys Chem B 2022; 126:6751-6761. [PMID: 35977067 PMCID: PMC9483921 DOI: 10.1021/acs.jpcb.2c02441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The protein, azurin,
has enabled the study of the tryptophan radical.
Upon UV excitation of tyrosine-deficient apoazurin and in the presence
of a Co(III) electron acceptor, the neutral radical (W48•)
is formed. The lifetime of W48• in apoazurin is 41 s, which
is shorter than the lifetime of several hours in Zn-substituted azurin.
Molecular dynamics simulations revealed enhanced fluctuations of apoazurin
which likely destabilize W48•. The photophysics of W48 was
investigated to probe the precursor state for ET. The phosphorescence
intensity was eliminated in the presence of an electron acceptor while
the fluorescence was unchanged; this quenching of the phosphorescence
is attributed to ET. The kinetics associated with W48• were
examined with a model that incorporates intersystem crossing, ET,
deprotonation, and decay of the cation radical. The estimated rate
constants for ET (6 × 106 s–1) and
deprotonation (3 × 105 s–1) are
in agreement with a photoinduced mechanism where W48• is derived
from the triplet state. The triplet as the precursor state for ET
was supported by photolysis of apoazurin with 280 nm in the absence
and presence of triplet-absorbing 405 nm light. Absorption bands from
the neutral radical were observed only in the presence of blue light.
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Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Joel J Rivera
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
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2
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Mitra S, Ainavarapu SRK, Dasgupta J. Long-Range Charge Delocalization Mediates the Ultrafast Ligand-to-Metal Charge Transfer Dynamics at the Cu 2+-Active Site in Azurin. J Phys Chem B 2022; 126:5390-5399. [PMID: 35797135 DOI: 10.1021/acs.jpcb.2c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The blue color metalloprotein in azurin has traditionally been attributed to the intense cysteine-to-Cu2+ ligand-to-metal charge transfer transition centered at 628 nm. Although resonance Raman measurements of the Cu2+ active site have implied that the LMCT transition electronically couples to the protein scaffold well beyond its primary metal-ligand coordination shell, the structural extent of this electronic coupling and visualization of the protein-mediated charge transfer dynamics have remained elusive. Here, using femtosecond broadband transient absorption and impulsive Raman spectroscopy, we provide direct evidence for a rapid relaxation between two distinct charge transfer states, having different spatial delocalization, within ∼300 fs followed by recombination of charges in subpicosecond time scales. We invoke the formation of a protein-centered radical cation, possibly Trp48 or a Phe residue, within 100 fs substantiating the long-range electronic coupling for the first time beyond the traditional copper active site. The Raman spectra of the excited CT state show the presence of protein-centric vibrations along with the vibrational modes assigned to the copper active site. Our results demonstrate a large delocalization length scale of the initially populated CT state, thereby highlighting the possibility of exploiting azurin photochemistry for energy conversion techniques.
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Affiliation(s)
- Soumyajit Mitra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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3
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Patel R, Clark AK, DeStefano G, DeStefano I, Gogoj H, Gray E, Patel AY, Hauner JT, Caputo GA, Vaden TD. Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids. Biochem Biophys Rep 2022; 30:101242. [PMID: 35280523 PMCID: PMC8907678 DOI: 10.1016/j.bbrep.2022.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 12/01/2022] Open
Abstract
The thermal unfolding of the copper redox protein azurin was studied in the presence of four different dipeptide-based ionic liquids (ILs) utilizing tetramethylguanidinium as the cation. The four dipeptides have different sequences including the amino acids Ser and Asp: TMG-AspAsp, TMG-SerSer, TMG-SerAsp, and TMG-AspSer. Thermal unfolding curves generated from temperature-dependent fluorescence spectroscopy experiments showed that TMG-AspAsp and TMG-SerSer have minor destabilizing effects on the protein while TMG-AspSer and TMG-SerAsp strongly destabilize azurin. Red-shifted fluorescence signatures in the 25 °C correlate with the observed protein destabilization in the solutions with TMG-AspSer and TMG-SerAsp. These signals could correspond to interactions between the Asp residue in the dipeptide and the azurin Trp residue in the unfolded state. These results, supported by appropriate control experiments, suggest that dipeptide sequence-specific interactions lead to selective protein destabilization and motivate further studies of TMG-dipeptide ILs.
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Affiliation(s)
- Roshani Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Austin K. Clark
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Gabriella DeStefano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Isabella DeStefano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Hunter Gogoj
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Erin Gray
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Joshua T. Hauner
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
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4
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Mouli MSSV, Agrawal HG, Kumar M, Mishra AK. Luminescent and morphological behavior of the aromatic dipeptide pair having singular structural variability. LUMINESCENCE 2022. [PMID: 35560861 DOI: 10.1002/bio.4275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/15/2022] [Accepted: 05/07/2022] [Indexed: 11/07/2022]
Abstract
In the present manuscript, the luminescence and the self-assembly behavior of the two aromatic dipeptides having singular structure variable are investigated. The terminally protected dipeptides tryptophan-tyrosine (WYp ) and tryptophan-phenylalanine (WFp ) were synthesized using standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; while the influence was more pronounced in case of the WYp entity when compared to WFp . Interesting morphological variation was observed for WFp and WYp , wherein discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signifies the influence of the singular structural variation on modulating the overall functional behavior of the short peptides motifs.
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Affiliation(s)
- M S S Vinod Mouli
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Harsha Gopal Agrawal
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Mohit Kumar
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Ashutosh Kumar Mishra
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
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5
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Serrano FA, Yukl ET. Contributions of Conformational Flexibility to High-Affinity Zinc Binding in the Solute Binding Protein AztC. ACS OMEGA 2022; 7:3768-3774. [PMID: 35128285 PMCID: PMC8811889 DOI: 10.1021/acsomega.1c06639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Bacteria rely on ATP binding cassette (ABC) transporters for the import of various nutrients. Bacterial ABC importers utilize an extracellular solute binding protein (SBP) to bind the substrate with high affinity and specificity and deliver it to the membrane permease for transport. The essential metals iron, manganese, and zinc are bound and transported by the cluster A-I SBPs. Crystal structures exist for the metal-bound and metal-free forms of several cluster A-I SBPs that show relatively subtle conformational changes that accompany metal binding. Recent solution studies and molecular dynamics simulations indicate a more complex conformational landscape for the cluster A-I SBPs, suggesting that changes in protein dynamics upon metal binding may have an important role in recognition by the membrane permease and effective transport. Here, we investigate conformational states and dynamics in the cluster A-I SBP AztC fromParacoccus denitrificans, characterizing its unusual intrinsic fluorescence behavior and thermodynamics of zinc binding. These data suggest a dynamic equilibrium of at least two conformational states in the apo form and compensatory changes in the holo that provide for a significant entropic contribution to zinc binding. Correlation with available crystal structures suggests that the formation of a Trp-Phe π-stacking interaction in the metal-bound form may mediate the observed changes in fluorescence. The conformational dynamics identified here for AztC are likely applicable to other cluster A-I SBPs with relevance to their exploitation as potential antibiotic drug targets.
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Affiliation(s)
- Fred A. Serrano
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Erik T. Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
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6
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Malik A, Albogami S, Alsenaidy AM, Aldbass AM, Alsenaidy MA, Khan ST. Spectral and thermal properties of novel eye lens ζ-crystallin. Int J Biol Macromol 2017; 102:1052-1058. [DOI: 10.1016/j.ijbiomac.2017.04.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/13/2017] [Accepted: 04/16/2017] [Indexed: 01/19/2023]
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7
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Bartoccini F, Bartolucci S, Mari M, Piersanti G. A simple, modular synthesis of C4-substituted tryptophan derivatives. Org Biomol Chem 2016; 14:10095-10100. [DOI: 10.1039/c6ob01791f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A straightforward, rapid, versatile, regio- and chemoselective approach for the synthesis of C4-substituted tryptophan derivatives is reported.
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Affiliation(s)
- F. Bartoccini
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - S. Bartolucci
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - M. Mari
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - G. Piersanti
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
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8
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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9
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Ghisaidoobe ABT, Chung SJ. Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques. Int J Mol Sci 2014; 15:22518-38. [PMID: 25490136 PMCID: PMC4284722 DOI: 10.3390/ijms151222518] [Citation(s) in RCA: 517] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 12/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ EX ≈ 280 nm, λ EM ≈ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.
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Affiliation(s)
| | - Sang J Chung
- Department of Chemistry, Dongguk University, Seoul 100-715, Korea.
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10
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Dow BA, Sukumar N, Matos JO, Choi M, Schulte A, Tatulian SA, Davidson VL. The sole tryptophan of amicyanin enhances its thermal stability but does not influence the electronic properties of the type 1 copper site. Arch Biochem Biophys 2014; 550-551:20-7. [PMID: 24704124 DOI: 10.1016/j.abb.2014.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
The cupredoxin amicyanin possesses a single tryptophan residue, Trp45. Its fluorescence is quenched when copper is bound even though it is separated by 10.1Å. Mutation of Trp45 to Ala, Phe, Leu and Lys resulted in undetectable protein expression. A W45Y amicyanin variant was isolated. The W45Y mutation did not alter the spectroscopic properties or intrinsic redox potential of amicyanin, but increased the pKa value for the pH-dependent redox potential by 0.5 units. This is due to a hydrogen-bond involving the His95 copper ligand which is present in reduced W45Y amicyanin but not in native amicyanin. The W45Y mutation significantly decreased the thermal stability of amicyanin, as determined by changes in the visible absorbance of oxidized amicyanin and in the circular dichroism spectra for oxidized, reduced and apo forms of amicyanin. Comparison of the crystal structures suggests that the decreased stability of W45Y amicyanin may be attributed to the loss of a strong interior hydrogen bond between Trp45 and Tyr90 in native amicyanin which links two of the β-sheets that comprise the overall structure of amicyanin. Thus, Trp45 is critical for stabilizing the structure of amicyanin but it does not influence the electronic properties of the copper which quenches its fluorescence.
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Affiliation(s)
- Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | - Narayanasami Sukumar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, United States.
| | - Jason O Matos
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States; Department of Physics, University of Central Florida, Orlando, FL 32816, United States
| | - Moonsung Choi
- Seoul National University of Science and Technology, College of Energy and Biotechnology, Department of Optometry, Seoul 139-743, Republic of Korea
| | - Alfons Schulte
- Department of Physics, University of Central Florida, Orlando, FL 32816, United States
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States.
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11
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Girotto S, Cendron L, Bisaglia M, Tessari I, Mammi S, Zanotti G, Bubacco L. DJ-1 is a copper chaperone acting on SOD1 activation. J Biol Chem 2014; 289:10887-10899. [PMID: 24567322 DOI: 10.1074/jbc.m113.535112] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lack of oxidative stress control is a common and often prime feature observed in many neurodegenerative diseases. Both DJ-1 and SOD1, proteins involved in familial Parkinson disease and amyotrophic lateral sclerosis, respectively, play a protective role against oxidative stress. Impaired activity and modified expression of both proteins have been observed in different neurodegenerative diseases. A potential cooperative action of DJ-1 and SOD1 in the same oxidative stress response pathway may be suggested based on a copper-mediated interaction between the two proteins reported here. To investigate the mechanisms underlying the antioxidative function of DJ-1 in relation to SOD1 activity, we investigated the ability of DJ-1 to bind copper ions. We structurally characterized a novel copper binding site involving Cys-106, and we investigated, using different techniques, the kinetics of DJ-1 binding to copper ions. The copper transfer between the two proteins was also examined using both fluorescence spectroscopy and specific biochemical assays for SOD1 activity. The structural and functional analysis of the novel DJ-1 copper binding site led us to identify a putative role for DJ-1 as a copper chaperone. Alteration of the coordination geometry of the copper ion in DJ-1 may be correlated to the physiological role of the protein, to a potential failure in metal transfer to SOD1, and to successive implications in neurodegenerative etiopathogenesis.
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Affiliation(s)
- Stefania Girotto
- Department of Chemical Sciences, University of Padova, via Marzolo, 1 35131 Padova, Italy; Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego, 30 16163 Genoa, Italy
| | - Laura Cendron
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy; Department of Biology, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy
| | - Marco Bisaglia
- Department of Biology, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy
| | - Isabella Tessari
- Department of Biology, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy
| | - Stefano Mammi
- Department of Chemical Sciences, University of Padova, via Marzolo, 1 35131 Padova, Italy
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Via Ugo Bassi, 58b 35121 Padova, Italy.
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12
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Raman R, Ptak CP, Hsieh CL, Oswald RE, Chang YF, Sharma Y. The perturbation of tryptophan fluorescence by phenylalanine to alanine mutations identifies the hydrophobic core in a subset of bacterial Ig-like domains. Biochemistry 2013; 52:4589-91. [PMID: 23800025 DOI: 10.1021/bi400128r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many host-parasite interactions are mediated via surface-exposed proteins containing bacterial immunoglobulin-like (Big) domains. Here, we utilize the spectral properties of a conserved Trp to provide evidence that, along with a Phe, these residues are positioned within the hydrophobic core of a subset of Big_2 domains. The mutation of the Phe to Ala decreases Big_2 domain stability and impairs the ability of LigBCen2 to bind to the host protein, fibronectin.
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Affiliation(s)
- Rajeev Raman
- Centre for Cellular and Molecular Biology (CCMB), CSIR , Uppal Road, Hyderabad 500 007, India
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13
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Tryptophan-Tryptophan Energy Transfer and Classification of Tryptophan Residues in Proteins Using a Therapeutic Monoclonal Antibody as a Model. J Fluoresc 2010; 21:275-88. [DOI: 10.1007/s10895-010-0715-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
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14
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Chang YC, Oas TG. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand. Biochemistry 2010; 49:5086-96. [PMID: 20476778 DOI: 10.1021/bi100222h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.
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Affiliation(s)
- Yu-Chu Chang
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
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15
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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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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Sanghamitra NJM, Mazumdar S. Conformational Dynamics Coupled to Protonation Equilibrium at the CuA Site of Thermus thermophilus: Insights into the Origin of Thermostability. Biochemistry 2008; 47:1309-18. [DOI: 10.1021/bi701783x] [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)
- Nusrat J. M. Sanghamitra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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18
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19
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Eftink MR. Fluorescence techniques for studying protein structure. METHODS OF BIOCHEMICAL ANALYSIS 2006; 35:127-205. [PMID: 2002770 DOI: 10.1002/9780470110560.ch3] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M R Eftink
- Department of Chemistry, University of Mississippi
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20
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Wlodarczyk J, Kierdaszuk B. A new approach to interpretation of heterogeneity of fluorescence decay: effect of induced tautomeric shift and enzyme-->ligand fluorescence resonance energy transfer. Biophys Chem 2006; 123:146-53. [PMID: 16765509 DOI: 10.1016/j.bpc.2006.05.014] [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] [Received: 12/16/2005] [Revised: 05/12/2006] [Accepted: 05/14/2006] [Indexed: 11/21/2022]
Abstract
Fluorescence decays in protein-ligand complexes are described by a new efficient model of continuous distribution of fluorescence lifetimes, and compared with multi-exponential models. Resulted analytical power-like decay function provides good fits to highly complex fluorescence kinetics. Moreover, this is a manifestation of so-called Tsallis q-exponential function, which is suitable for description of the systems with long-range interactions, memory effect, as well as with fluctuations of the characteristic lifetime of fluorescence. The proposed decay function was used to study effect of the interaction of E. coli purine nucleoside phosphorylase (PNP-I, the product of the deoD gene) with its specific inhibitor, viz. formycin A (FA), on fluorescence decays of ligand and enzyme tyrosine residues, in the presence of orthophosphate (P(i), a natural co-substrate). The power-like function provides new information about enzyme-ligand complex formation based on the excited state mean lifetime, heterogeneity parameter (q) and a number (N) of decay channels obtained from the variance of gamma distribution of fluorescence decay rates. With FA, which exists as a 85:15 mixture of the N(1)-H and N(2)-H tautomeric forms in aqueous solution, fluorescence intensity decay (lambda(exc)/lambda(em) 270/335 nm) is described by q approximately 1 and N approximately 200. Consequently power-like decay function converges to the single-exponential form, and lifetime distribution to the Dirac delta function. In contrast, selective excitation of the N(2)-H tautomer at higher wavelength led to a highly heterogenic fluorescence decay characterized by q>1 and 10-fold lower number of decay channels. Heterogeneity of fluorescence decays of both PNP-I and FA is enhanced by PNP-FA-P(i) complex formation, reflecting a shift of the tautomeric equilibrium of FA in favor of the N(2)-H species, and fluorescence resonance energy transfer (FRET) from protein tyrosine residue (Tyr160) to the bound N(2)-H tautomer. Moreover, proposed model is simple, and objectively describes heterogeneous nature of studied systems.
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Affiliation(s)
- Jakub Wlodarczyk
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki i Wigury Street, 02089 Warsaw, Poland
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21
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Affiliation(s)
- Catherine A Royer
- Centre de Biochimie Structurale, 29, rue de Navacelles 34090 Montpellier Cedex France
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22
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Pompa PP, Biasco A, Cingolani R, Rinaldi R, Verbeet MP, Canters GW. Structural stability study of protein monolayers in air. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 69:032901. [PMID: 15089340 DOI: 10.1103/physreve.69.032901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Indexed: 05/24/2023]
Abstract
The assessment of the folding and of the structural stability of a protein in air, upon immobilization in the solid state, represents a critical point from both a fundamental point of view and for the development of solid state nanobioelectronics. The recent demonstrations by Rinaldi et al. [R. Rinaldi et al., Adv. Mater. 14, 1453 (2002); Appl. Phys. Lett. 82, 472 (2003); Ann. (N.Y.) Acad. Sci. 1006, 187 (2003)] of protein-based solid state devices and transistors working in air have raised an intriguing question about the behavior of a biomolecule under nonphysiological conditions. The operation principle of the realized devices is based on the physiological electron transfer function of the metalloprotein azurin. This means that azurin should retain its shape and functionality also in the solid state when utilized in air and at room temperature. In this Brief Report, we prove this claim by analyzing the conformational state of the azurin monolayers developed for such devices by means of intrinsic fluorescence spectroscopy. We show that the immobilization of azurins in the solid state under nonliquid conditions, by means of a specific chemisorption process, does not necessarily lead to protein denaturation. This result is of great importance because it opens up interesting perspectives for the development of solid state hybrid nanodevices for electronic applications requiring nonliquid environments.
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Affiliation(s)
- P P Pompa
- Department of Innovation Engineering, University of Lecce, Via per Arnesano, 73100 Lecce, Italy
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23
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Włodarczyk J, Kierdaszuk B. Interpretation of fluorescence decays using a power-like model. Biophys J 2003; 85:589-98. [PMID: 12829513 PMCID: PMC1303114 DOI: 10.1016/s0006-3495(03)74503-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2003] [Accepted: 03/19/2003] [Indexed: 11/28/2022] Open
Abstract
A power-like decay function, characterized by the mean excited-state lifetime and relative variance of lifetime fluctuation around the mean value, was applied in analysis of fluorescence decays measured with the aid of time-correlated single photon counting. We have examined the fluorescence decay, in neutral aqueous medium, of tyrosine (L-tyrosine and N-acetyl-L-tyrosinamide), and of the tyrosine residues in a tryptophan-free protein, the enzyme purine nucleoside phosphorylase from Escherichia coli in a complex with formycin A (an inhibitor), and orthophosphate (a co-substrate). Tryptophan fluorescence decay was examined in neutral aqueous medium for L-tryptophan, N-acetyl-L-tryptophanamide, and for two tryptophan residues in horse liver alcohol dehydrogenase. To detect solvent effect, fluorescence decay of Nz-acetyl-L-tryptophanamide in aqueous medium was compared with that in dioxan. Hitherto, complex fluorescence decays have usually been analyzed with the aid of a multiexponential model, but interpretation of the individual exponential terms (i.e., pre-exponential amplitudes and fluorescence lifetimes), has not been adequately characterized. In such cases the intensity decays were also analyzed in terms of the lifetime distribution as a consequence of an interaction of fluorophore with environment. We show that the power-like decay function, which can be directly obtained from the gamma distribution of fluorescence lifetimes, is simpler and provides good fits to highly complex fluorescence decays as well as to a purely single-exponential decay. Possible interpretation of the power-like model is discussed.
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Affiliation(s)
- Jakub Włodarczyk
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
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24
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Abstract
Tryptophan fluorescence wavelength is widely used as a tool to monitor changes in proteins and to make inferences regarding local structure and dynamics. We have predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins, starting with crystal structures and using a hybrid quantum mechanical-classical molecular dynamics method with the assumption that only electrostatic interactions of the tryptophan ring electron density with the surrounding protein and solvent affect the transition energy. With only one adjustable parameter, the scaling of the quantum mechanical atomic charges as seen by the protein/solvent environment, the mean absolute deviation between predicted and observed fluorescence maximum wavelength is 6 nm. The modeling of electrostatic interactions, including hydration, in proteins is vital to understanding function and structure, and this study helps to assess the effectiveness of current electrostatic models.
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Affiliation(s)
- J T Vivian
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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25
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Vincent M, Gilles AM, Li de la Sierra IM, Briozzo P, Bârzu O, Gallay J. Nanosecond Fluorescence Dynamic Stokes Shift of Tryptophan in a Protein Matrix. J Phys Chem B 2000. [DOI: 10.1021/jp000638x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michel Vincent
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Anne-Marie Gilles
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Inès M. Li de la Sierra
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Pierre Briozzo
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Octavian Bârzu
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Jacques Gallay
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
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26
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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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27
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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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28
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Sau AK, Mitra S. Steady state and picosecond time-resolved fluorescence studies on native, desulpho and deflavo xanthine oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:273-82. [PMID: 11018718 DOI: 10.1016/s0167-4838(00)00136-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Steady state and time-resolved fluorescence studies on native, desulpho and deflavo xanthine oxidase (XO) have been carried out to investigate the conformational changes associated with the replacement of the molybdenum double bonded sulphur by oxygen and the removal of the flavin adenine dinucleotide (FAD). The steady state quenching experiments of the intrinsic tryptophan residues of the enzyme show that all the nine tryptophans are accessible to neutral quencher, acrylamide, in the native as well as desulpho and deflavo enzymes. However, the number of the tryptophan residues accessible to the ionic quenchers, potassium iodide and cesium chloride, increases upon removal of the FAD centre from the enzyme. This indicates that two tryptophan residues move out from the core of the enzyme to the solvent upon the removal of the FAD. The time-resolved fluorescence studies were carried out on the native, desulpho and deflavo XO by means of the time-correlated single photon counting technique, and the data were analysed by discrete exponential and maximum entropy methods. The results show that the fluorescence decay curve fitted best to a three-exponential model with lifetimes tau(1)=0.4, tau(2)=1.4 and tau(3)=3.0 ns for the native and desulpho XO, and tau(1)=0.7, tau(2)=1.7 and tau(3)=4.8 ns for the deflavo XO. The replacement of the molybdenum double bonded sulphur by oxygen in the desulpho enzyme does not cause any significant change of the lifetime components. However, removal of the FAD centre causes a significant change in the shortest and longest lifetime components indicating a conformational change in the deflavo XO possibly in the flavin domain. Decay-associated emission spectra at various emission wavelengths have been used to determine the origin of the lifetimes. The results show that tau(1) and tau(3) of the native and desulpho XO originate from the tryptophan residues which are completely or partially accessible to the solvent but tau(2) corresponds to those residues which are buried in the core of the enzyme and not exposed to the solvent. For deflavo enzyme, tau(2) is red shifted compared to the native enzyme indicating the movement of tryptophan residues from the core of the enzyme to the solvents.
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Affiliation(s)
- A K Sau
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, 400 005, Mumbai, India.
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29
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Moncrieffe MC, Venyaminov SY, Miller TE, Guzman G, Potter JD, Prendergast FG. Optical spectroscopic characterization of single tryptophan mutants of chicken skeletal troponin C: evidence for interdomain interaction. Biochemistry 1999; 38:11973-83. [PMID: 10508400 DOI: 10.1021/bi982048j] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of metal ion binding on the optical spectroscopic properties and temperature stability of two single tryptophan mutants of chicken skeletal TnC, F78W and F154W, have been examined. The absence of tyrosine and other tryptophan residues allowed the unambiguous assignment of the spectral signal from the introduced Trp residue. Changes in the molar ellipticity values in the far-UV CD spectra of the mutant proteins on metal ion binding were similar to those of wild-type TnC suggesting that the introduction of the Trp residue had no effect on the total secondary structure content. The fluorescence and near-UV absorbance data reveal that, in the apo state, Trp-78 is buried while Trp-154 is exposed to solvent. Additionally, the highly resolved (1)L(b) band of Trp-78 seen in the near-UV absorbance and CD spectra of the apo state of F78W suggest that this residue is likely in a rigid molecular environment. In the calcium-saturated state, Trp-154 becomes buried while the solvent accessibility of Trp-78 increases. The fluorescence emission and near-UV CD of Trp-78 in the N-terminal domain were sensitive to calcium binding at the C-terminal domain sites. Measurements of the temperature stability reveal that events occurring in the N-terminal domain affect the stability of the C-terminal domain and vice versa. This, coupled with the titration data, strongly suggests that there are interactions between the N- and C-terminal domains of TnC.
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Affiliation(s)
- M C Moncrieffe
- Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, Minnesota 55905, USA
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30
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Chen HM, Dimagno TJ, Wang W, Leung E, Lee CH, Chan SI. The effect of Glu75 of staphylococcal nuclease on enzyme activity, protein stability and protein unfolding. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:599-609. [PMID: 10215875 DOI: 10.1046/j.1432-1327.1999.00317.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Staphylococcal nuclease mutants, E57G and E75G, were generated. A comparison of the kinetic parameters both for mutants and wild-type protein shows that the Michaelis constants (Km) were almost identical for the wild-type protein and E57G mutant. An approximately 30-fold decrease in Km compared with the wild-type protein was observed for the E75G mutant. The turnover numbers for the enzyme (kcat) were higher with both the wild-type protein and the E57G mutant (3.88 +/- 0.21 x 103 s-1 and 3.71 +/- 0.28 x 103 s-1) than with the E75G mutant (3.04 +/- 0.02 x 102 s-1). The results of thermal denaturation with differential scanning microcalorimetry indicate that the excess calorimetric enthalpy of denaturations, DeltaHcal, was almost identical for the wild-type protein and E57G mutant (84.1 +/- 6.2 kcal.mol-1 and 79.3 +/- 7.1 kcal.mol-1, respectively). An approximately twofold decrease in DeltaHcal compared with the wild-type protein was observed for the E75G mutant (42.7 +/- 5.5 kcal.mol-1). These outcomes imply that Glu at position 75 plays a significant role in maintaining enzyme activity and protein stability. Further study of the unfolding of the wild-type protein and E75G mutant was conducted by using time-resolved fluorescence with a picosecond laser pulse. Two fluorescent lifetimes were found in the subnanosecond time range. The faster lifetime (tau2) did not generally vary with either pH or the concentration of guanidinium hydrochloride (GdmHCl) in the wild-type protein and the E75G mutant. The slow lifetime (tau1), however, did vary with these parameters and was faster as the protein is unfolded by either pH or GdmHCl denaturation. The midpoints of the transition for tau1 are pH 3.5 and 5.8 for the wild-type protein and E75G mutant, respectively, and the GdmHCl concentrations are 1.1 m and 0.6 m for the wild-type protein and E75G mutant, respectively. Parallel steady-state fluorescence measurements have also been carried out and the results are in general agreement with the time-resolved fluorescence experiments, indicating that Glu at position 75 plays an important role in protein unfolding.
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Affiliation(s)
- H M Chen
- Department of Biochemistry, Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
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31
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Kroes SJ, Canters GW, Gilardi G, van Hoek A, Visser AJ. Time-resolved fluorescence study of azurin variants: conformational heterogeneity and tryptophan mobility. Biophys J 1998; 75:2441-50. [PMID: 9788939 PMCID: PMC1299918 DOI: 10.1016/s0006-3495(98)77688-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Time-resolved fluorescence and time resolved fluorescence anisotropy studies have been performed on wild-type azurin from Pseudomonas aeruginosa and two variants to study the mobility of Trp48. The two azurin variants in which the microenvironment of Trp48 was changed comprised the single mutations Ile7Ser and Phe110Ser. The experiments were performed on the holo-Cu(I), holo-Cu(II), and apo- forms at various pH values, viscosities, and temperatures; two distinct parts of the emission spectrum were selected for detection. Two prominent subnanosecond lifetimes in the fluorescence decays of the Cu(II) proteins could be observed. The decay of apo-azurin also consists of more than one component. The occurrence of more than one component in the fluorescence decays is explained by conformational heterogeneity. The anisotropy decay results appeared to be different for wild-type and mutated azurins. Phe110Ser and Ile7Ser azurin show more mobility of the Trp48 residue, as reflected in the order parameter.
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Affiliation(s)
- S J Kroes
- Leiden Institute of Chemistry, Gorlaeus Laboratories, 2300 RA Leiden, The Netherlands
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32
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Probing the relation between protein structure and intrinsic tryptophan fluorescence using superrepressor mutants of thetrp repressor. J Fluoresc 1998. [DOI: 10.1007/bf02758230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Affiliation(s)
- M R Eftink
- Department of Chemistry, University of Mississippi, University 38677, USA
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34
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Callis PR. 1La and 1Lb transitions of tryptophan: applications of theory and experimental observations to fluorescence of proteins. Methods Enzymol 1997; 278:113-50. [PMID: 9170312 DOI: 10.1016/s0076-6879(97)78009-1] [Citation(s) in RCA: 217] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- P R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman 59717, USA
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35
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Dahms TE, Szabo AG. Conformational heterogeneity in crystalline proteins: time-resolved fluorescence studies. Methods Enzymol 1997; 278:202-21. [PMID: 9170315 DOI: 10.1016/s0076-6879(97)78012-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- T E Dahms
- Department of Biochemistry, University of Ottawa, Ontario, Canada
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36
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Mei G, Gilardi G, Venanzi M, Rosato N, Canters GW, Agró AF. Probing the structure and mobility of Pseudomonas aeruginosa azurin by circular dichroism and dynamic fluorescence anisotropy. Protein Sci 1996; 5:2248-54. [PMID: 8931143 PMCID: PMC2143279 DOI: 10.1002/pro.5560051111] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The UV dynamic fluorescence and CD of several Pseudomonas aeruginosa azurins bearing single amino acid mutation have been studied. Two classes of mutants were examined. In the first class, two hydrophobic residues in the core of the protein, Ile 7 and Phe 110, nearest to the azurin single tryptophan Trp 48, were substituted by a serine (mutants 17S and F110S). In the second class, two residues in the outer sphere of the copper ligand field were changed, obtaining the following mutants: M44K, H35F, H35L, and H35Q. All these proteins showed two fluorescence lifetimes in the copper-containing form, but only one in the copper-free form. The lifetime of the latter derivatives was different from either those of the metal-bound samples, definitely ruling out the presence of apo-like species in the holo protein. Copper-free 17S and F110S showed a more complex fluorescence decay profile requiring a distribution of lifetimes rather than a single lifetime. Holo F110S was also better fitted, in the limit of confidence, with two distributions rather than a pair of lifetimes. Time-resolved anisotropy of these two mutants as well as of wild-type (wt) protein showed two components (rotational times for wt < or = 200 ps and 7 ns, respectively). These components were not affected significantly by copper removal in the case of wt protein. Instead, the short rotational component of the mutants dropped dramatically to values near zero, indicating a much greater mobility of the tryptophanyl residue in the mutant apo azurins. These data were supported by CD measurements showing a small effect of the copper presence in the region below 250 nm, i.e., in the secondary structure, but almost a collapse of the aromatic asymmetry at 270-295 nm related to a relaxation of the structural constraint around the tryptophan. Altogether these data show that copper does not play a structural role in wt azurin, whereas it is crucial in the stabilization of 17S and F110S mutants. Furthermore, although the metal site geometry is rigidly kept in wt apo-azurin, it regains the native form only in the presence of the metal in the "core" mutants. This finding is important for the theory of entatic states in metalloproteins (Williams RJP, 1995, Eur J Biochem 234:363-381).
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Affiliation(s)
- G Mei
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Universitá di Roma Tor Vergata, Italy
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37
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Hansen JE, Steel DG, Gafni A. Detection of a pH-dependent conformational change in azurin by time-resolved phosphorescence. Biophys J 1996; 71:2138-43. [PMID: 8889189 PMCID: PMC1233681 DOI: 10.1016/s0006-3495(96)79414-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Azurin, a blue copper protein from the bacterial species Pseudomonas aeruginosa, contains a single tryptophan residue. Previous fluorescence measurements indicate that this residue is highly constrained and unusually inaccessible to water. In the apoprotein this residue also possesses a long-lived room-temperature phosphorescence (RTP), the nonexponential decay of which can be resolved into two major components associated with lifetimes of 417 and 592 ms, which likely originate from at least two conformations of the protein. The relative weights of these two decay components change with pH in good correlation with a change in protonation of His-35, which has been studied in Cu(II) azurin. Interestingly, the structural changes characterized in earlier work have little effect on the fluorescence decay and appear to occur away from the tryptophan residue. However, in the present work, the two RTP lifetimes suggest conformations with different structural rigidities in the vicinity of the tryptophan residue. The active conformation that predominates below a pH of 5.6 has the shorter lifetime and is less rigid. Phosphorescence decays of several metal derivatives of azurin were also measured and revealed strong similarities to that of apoazurin, indicating that the structural constraints upon the metal-binding site are imposed predominately by the protein.
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Affiliation(s)
- J E Hansen
- University of Michigan, Institute of Gerontology, Ann Arbor, 48109-2007 USA
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38
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Bandivadekar KR, Deshpande VV. Structure-function relationship of xylanase: fluorimetric analysis of the tryptophan environment. Biochem J 1996; 315 ( Pt 2):583-7. [PMID: 8615833 PMCID: PMC1217236 DOI: 10.1042/bj3150583] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Involvement of one out of three tryptophan residues in the active site of the low-molecular-mass xylanase from Chainia has been demonstrated previously [Deshpande, Hinge and Rao (1990) Biochim. Biophys. Acta 1041, 172-177]. The work described here aims at: (i) deducing the structure-function relationship for the tryptophan residue involved at the active site (a) by correlating the effect of N-bromosuccinimide (NBS) on the fluorescence and activity, and (b) by assessing the ability of xylan to protect against decrease in fluorescence versus activity of NBS-treated enzyme; and (ii) probing into the environment of the tryptophan residues by studying the quenching of their fluorescence by various solute quenchers in the presence and absence of guanidine hydrochloride (Gdn.HCl). Complete inactivation of the NBS-treated enzyme occurs well before the loss of fluorescence. Full protection by xylan (0.5%) of the inactivation of enzyme by NBS compared with 30% protection for the decrease in fluorescence confirms the participation of a single tryptophan at the substrate-binding site of the xylanase. The xylanase exhibited a rather low fluorescence emission maximum at 310 nm. There was no shift in the emission maximum on treatment of the enzyme with Gdn.HCl (6.5 M), indicating the rigidity of the microenvironment around tryptophan residues. The quenching studies with acrylamide suggested the occurrence of both collisional as well as static quenching processes. The enzyme retained full activity as well as the characteristic emission maximum at 310 nm in the presence of acrylamide (100 mM), indicating that quenching of fluorescence by acrylamide is a physical process. Acrylamide was more efficient as a quencher than CsCl or KBr. Treatment of the enzyme with Gdn.HCl resulted in an increase in accessibility of the quenchers to the fluorophore as suggested by an increase in the Stern-Volmer quenching constants (K(SV)) of the solute quenchers. The analysis of K(SV) and V values of KBr and CsCl suggests that the overall tryptophan microenvironment in the xylanase from Chainia is slightly electronegative.
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Affiliation(s)
- K R Bandivadekar
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
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39
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Abstract
The wavelength dependent fluorescence decay properties of bovine prothrombin fragment 1 have been investigated employing a picosecond time-correlated single photon counting technique. All observations are discussed with using the crystal structure (Soriano-Garcia et al., Biochemistry 31:2554-2566, 1992). Fluorescence lifetimes distribution and conventional multiexponential analysis, as well as acrylamide quenching studies lead to the identification of six distinguishable tryptophan excited-states. Accessibility to the quencher and the known structure are used to associate a fluorescence decay of the tryptophan present in the Gla domain (Trp42) with two red shifted components (2.3 and 4.9 ns). The two kringle domain tryptophans (Trp90 and Trp126) exhibit four decay times (0.06, 0.24, 0.68, and 2.3 ns), which are blue shifted. The calcium-induced fluorescence quenching is a result of static quenching: the five decay times remain unchanged, whereas the fluorescence intensity of Trp42 is decreased. The static quenching process is a consequence of a ground state interaction between the Cys18-Cys23 disulfide bridge and Trp42. The monomolecular equilibrium constant for this disulfide-pi-electron interaction is found as 4.8.
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Affiliation(s)
- M Hof
- Department of Physical Chemistry, Charles University, Prague, Czech Republic
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40
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Time-resolved fluorescence study of the single tryptophan in thiocyanate and azide derivatives of horseradish peroxidase: Implication for apH-induced conformational change in the heme cavity. J CHEM SCI 1995. [DOI: 10.1007/bf02840806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Döring K, Konermann L, Surrey T, Jähnig F. A long lifetime component in the tryptophan fluorescence of some proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 1995; 23:423-32. [PMID: 7729367 DOI: 10.1007/bf00196829] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tryptophan fluorescence of two membrane proteins (outer membrane protein A and lactose permease), a 21-residue hydrophobic peptide, three soluble proteins (rat serum albumin, ribonuclease T1, and azurin), and N-acetyltryptophanamide (NATA) was investigated by time-resolved measurements extended over 65 ns. A long lifetime component with a characteristic time of 25 ns and an amplitude below 1% was found for outer membrane protein A, lactose permease, the peptide in lipid membranes, and azurin in water, but not for rat serum albumin, ribonuclease T1, and NATA in water. When outer membrane protein A was dissolved and unfolded in guanidinum hydrochloride, the long lifetime component disappeared. Hence, a hydrophobic environment seems to be a necessary requirement for the long lifetime component to be present. However, NATA dissolved in butanol does not exhibit the long lifetime component, while the peptide dissolved in the same solvent under conditions which preserve its helical structure does show the long lifetime. Thus, a regular secondary structure for the polypeptide chain to which the tryptophan residue belongs seems to be a second necessary requirement for the long lifetime component to be present. The long lifetime component may therefore be seen in the context of protein substates.
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Affiliation(s)
- K Döring
- Max-Planck-Institut für Biologie, Abteilung Membranbiochemie, Tübingen, Germany
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42
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Das TK, Mazumdar S. pH-induced conformational perturbation in horseradish peroxidase. Picosecond tryptophan fluorescence studies on native and cyanide-modified enzymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 227:823-8. [PMID: 7867643 DOI: 10.1111/j.1432-1033.1995.tb20207.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fluorescence-decay characteristics of the single tryptophan present in horseradish peroxidase (HRP) have been studied using dye-laser pulses and single-photon counting techniques. The decay was found to be dominated by a picosecond-lifetime component, with small contributions from two other lifetime components in the nanosecond range. The distance of the tryptophan residue was estimated from the fluorescence-energy transfer to the heme moiety using Förster's theory. The tryptophan residue was found to be approximately 1.2 nm from the heme moiety at neutral pH. Detailed analysis of the fluorescence-decay profiles using the maximum-entropy method (MEM) has been carried out. The results of the MEM analysis also showed a maximum amplitude peak at approximately 45 ps (at pH approximately 7) with a very small (< 5%) contribution from two other components. Similar results were obtained with the cyanide derivative of the enzyme (HRPCN) where the major lifetime component was found to be 58 ps at neutral pH. The picosecond component of fluorescence lifetimes of native HRP as well as of HRPCN were found to increase with decrease in pH in the range pH 6-3.5. Moreover, the native enzyme showed significant increase in the magnitude of this fast lifetime component at pH above 8. Such increase in the major lifetime component possibly indicated a conformational perturbation caused by pH change in the enzyme. However, the pH dependence of HRPCN, which is devoid of alkaline transition, showed that the shortest lifetime component remains almost unchanged over the pH range 6-11. This result showed that the alkaline transition in native HRP is associated with a structural change in the distal region of the heme center, which is absent in the cyanide-ligated enzyme. The results have been discussed with respect to understanding the pH-induced effects associated with salt bridge and hydrogen-bonding network in HRP.
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Affiliation(s)
- T K Das
- Chemical Physics Group, Tata Institute of Fundamental Research, Bombay, India
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43
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Tanaka F, Tamai N, Mataga N, Tonomura B, Hiromi K. Analysis of internal motion of single tryptophan in Streptomyces subtilisin inhibitor from its picosecond time-resolved fluorescence. Biophys J 1994; 67:874-80. [PMID: 7948700 PMCID: PMC1225430 DOI: 10.1016/s0006-3495(94)80548-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A mode of internal motion of single tryptophan, Trp 86, of Streptomyces subtilisin inhibitor, was analyzed from its time-resolved fluorescence. The intensity and anisotropy decays of Trp 86 were measured in the picosecond range. These decays were analyzed with theoretical expressions derived assuming that the indole ring of tryptophan as an asymmetric rotor rotates around covalent bonds connecting indole with the peptide chain and an effective quencher of fluorescence of Trp 86 is the nearby SS bond of Cys 35-Cys 50. First, the intensity decays at 6 degrees, 20 degrees, and 40 degrees C were analyzed, and then the both decays of the intensity and anisotropy at 20 degrees C were simultaneously simulated with common parameters. Constants concerning geometrical structures of the protein used for the analysis were obtained from x-ray crystallographic data. Best fit between the observed and calculated decay curves was obtained by a nonlinear least squares method by adjusting a quenching constant averaged over the rotational angles, koq height of the potential energy, p, and three of six diffusion coefficients, Dxx, Dyy, Dzz, Dxy, Dyz, and Dzx, as variable parameters. The obtained results revealed that the internal motion of the indole ring became faster, the quenching rate of the fluorescence of Trp 86 was enhanced and the height of potential energy became lower at higher temperatures, and suggested that Trp 86 was wobbling around the long axis of the indole ring in the protein.
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44
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Bajzer Z, Prendergast FG. A model for multiexponential tryptophan fluorescence intensity decay in proteins. Biophys J 1993; 65:2313-23. [PMID: 8312471 PMCID: PMC1225973 DOI: 10.1016/s0006-3495(93)81325-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Tryptophan fluorescence intensity decay in proteins is modeled by multiexponential functions characterized by lifetimes and preexponential factors. Commonly, multiple conformations of the protein are invoked to explain the recovery of two or more lifetimes from the experimental data. However, in many proteins the structure seems to preclude the possibility of multiple conformers sufficiently different from one another to justify such an inference. We present here another plausible multiexponential model based on the assumption that an energetically excited donor surrounded by N acceptor molecules decays by specific radiative and radiationless relaxation processes, and by transferring its energy to acceptors present in or close to the protein matrix. If interactions between the acceptors themselves and back energy transfer are neglected, we show that the intensity decay function contain 2N exponential components characterized by the unperturbed donor lifetime, by energy transfer rates and a probability of occurrence for the corresponding process. We applied this model to the fluorescence decay of holo- and apoazurin, ribonuclease T1, and the reduced single tryptophan mutant (W28F) of thioredoxin. Use of a multiexponential model for the analysis of the fluorescence intensity decay can therefore be justified, without invoking multiple protein conformations.
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Affiliation(s)
- Z Bajzer
- Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, Minnesota 55905
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45
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Tyrosine hypochromism and absence of tyrosine-tryptophan energy transfer in phospholipase A2 and ribonuclease T1. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)85146-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Royer CA. Investigation of the structural determinants of the intrinsic fluorescence emission of the trp repressor using single tryptophan mutants. Biophys J 1992; 63:741-50. [PMID: 1420911 PMCID: PMC1262207 DOI: 10.1016/s0006-3495(92)81658-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The fluorescence decay properties of wild-type trp repressor (TR) have been characterized by carrying out a multi-emission wavelength study of the frequency response profiles. The decay is best analyzed in terms of a single exponential decay near 0.5 ns and a distribution of lifetimes centered near 3-4 ns. By comparing the recovered decay associated spectra and lifetime values with the structure of the repressor, tentative assignments of the two decay components recovered from the analysis to the two tryptophan residues, W19 and W99, of the protein have been made. These assignments consist of linking the short, red emitting component to emission from W99 and most of the longer bluer emitting lifetime distribution to emission from W19. Next, single tryptophan mutants of the repressor in which one of each of the tryptophan residues was substituted by phenylalanine were used to confirm the preliminary assignments, inasmuch as the 0.5-ns component is clearly due to emission from tryptophan 99, and much of the decay responsible for the recovered distribution emanates from tryptophan 19. The data demonstrate, however, that the decay of the wild-type protein is not completely resolvable due both to the large number of components in the wild-type emission (at least five) as well as to the fact that three of the five lifetime components are very close in value. The fluorescence decay of the wild-type decay is well described as a combination of the components found in each of the mutants. However, whereas the linear combination analysis of the 15 data sets (5 from the wild-type and each mutant) yields a good fit for the components recovered previously for the two mutants, the amplitudes of these components in the wild-type are not recovered in the expected ratios. Because of the dominance of the blue shifted emission in the wild-type protein, it is most likely that subtle structural differences in the wild-type as compared with the mutants, rather than energy transfer from tryptophan 19 to 99, are responsible for this failure of the linear combination hypothesis.
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Affiliation(s)
- C A Royer
- School of Pharmacy, University of Wisconsin-Madison 53706
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47
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Klemens FK, McMillin DR. Room-temperature phosphorescence from azurin derivatives. Phosphorescence quenching in oxidized native azurin. Photochem Photobiol 1992; 55:671-6. [PMID: 1528979 DOI: 10.1111/j.1751-1097.1992.tb08509.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The tryptophan phosphorescence from a series of derivatives of Pseudomonas aeruginosa azurin has been monitored at 30 degrees C in pH 8.5 buffer solution. The phosphorescence lifetimes fall in the range of 230-270 ms for deoxygenated solutions of derivatives containing Cd(II), Cu(I), Co(II), Ni(II), Hg(II) or apoazurin. A weak signal with a lifetime of ca 130 ms is observed from solutions of oxidized native azurin, but this component is ascribed to a modified form of azurin in solution, i.e. protein heterogeneity, on the basis of the unique sensitivity to quenching by dioxygen. Aside from this minor component, the tryptophan phosphorescence in the Cu(II) protein appears to be fully quenched. The quenching is assigned an electron-transfer mechanism involving transient reduction of the metal center. The same mechanism is deemed to be responsible for fluorescence quenching in oxidized native azurin as well. These observations are of interest because aromatic groups like tryptophan may be conduits for physiological electron-transfer processes involving the copper center.
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Affiliation(s)
- F K Klemens
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-1393
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48
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Nar H, Huber R, Messerschmidt A, Filippou AC, Barth M, Jaquinod M, van de Kamp M, Canters GW. Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 205:1123-9. [PMID: 1576995 DOI: 10.1111/j.1432-1033.1992.tb16881.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Azurin*, a by-product of heterologous expression of the gene encoding the blue copper protein azurin from Pseudomonas aeruginosa in Escherichia coli, was characterized by chemical analysis and electrospray ionization mass spectrometry, and its structure determined by X-ray crystallography. It was shown that azurin* is native azurin with its copper atom replaced by zinc in the metal binding site. Zinc is probably incorporated in the apo-protein after its expression and transport into the periplasm. Holo-azurin can be reconstituted from azurin* by prolonged exposure of the protein to high copper ion concentrations or unfolding of the protein and refolding in the presence of copper ions. An X-ray crystallographic analysis of azurin* at 0.21-nm resolution revealed that the overall structure of azurin is not perturbed by the metal exchange. However, the geometry of the co-ordination sphere changes from trigonal bipyramidal in the case of copper azurin to distorted tetrahedral for the zinc protein. The copper ligand Met121 is no longer co-ordinated to zinc which adopts a position close to the carbonyl oxygen atom from residue Gly45. The polypeptide structure surrounding the metal site undergoes moderate reorganization upon zinc binding. The largest displacement observed is for the carbonyl oxygen from residue Gly45, which is involved in copper and zinc binding. It moves by 0.03 nm towards the zinc, thereby reducing its distance to the metal from 0.29 nm in the copper protein to 0.23 nm in the derivative.
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Affiliation(s)
- H Nar
- Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Federal Republic of Germany
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49
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Chabbert M, Hillen W, Hansen D, Takahashi M, Bousquet JA. Structural analysis of the operator binding domain of Tn10-encoded Tet repressor: a time-resolved fluorescence and anisotropy study. Biochemistry 1992; 31:1951-60. [PMID: 1311199 DOI: 10.1021/bi00122a008] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An engineered Tn10-encoded Tet repressor, bearing a single Trp residue at position 43, in the putative alpha-helix-turn-alpha-helix motif of the operator binding domain, was studied by time-resolved fluorescence and anisotropy. Fluorescence intensity decay data suggested the existence of two classes of Trp-43, defined by different lifetimes. Analysis of anisotropy data were consistent with a model in which each class was defined by a different lifetime, rotational correlation time, and fluorescence emission maximum. The long-lifetime class had a red-shifted spectrum, similar to that of tryptophan zwitterion in water, and a short rotational correlation time. In contrast, the spectrum of the short-lifetime class was blue-shifted 10 nm compared to that of the long-lifetime class. Its correlation time was similar to that of the protein, which showed that Trp in this class was entirely constrained. Trp in this latter class could not be quenched by iodide, whereas most of the long-lifetime class was easily accessible. Presence of disruptive agents, such as 1 M GuCl or 3 M KCl, did not alter markedly the lifetimes but increased the weight of the short-lifetime component. In the same time, the rotational correlation time of this component was dramatically reduced. Taken together, our data suggest that the long-lifetime class could correspond to the tryptophan residues exposed to solvent whereas the short-lifetime class would correspond to the tryptophan residues embedded inside the hydrophobic core holding the helix-turn-helix motif. Destabilization of hydrophobic interactions would lead to an increase in the weight of the latter class for entropic reasons. Analysis of the fluorescence parameters of Trp-43 could provide structural information on the operator binding domain of Tet repressor.
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Affiliation(s)
- M Chabbert
- CNRS UA 491, Faculté de Pharmacie de Strasbourg, Illkirch, France
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50
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Fluorescence and molecular dynamics study of the internal motion of the buried tryptophan in bacteriophage T4 lysozyme: Effects of temperature and alteration of nonbonded networks. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87077-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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