1
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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2
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Addabbo RM, Dalphin MD, Mecha MF, Liu Y, Staikos A, Guzman-Luna V, Cavagnero S. Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis. J Phys Chem B 2020; 124:6488-6507. [DOI: 10.1021/acs.jpcb.0c03039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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3
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Kozer N, Clayton AHA. In-cell structural dynamics of an EGF receptor during ligand-induced dimer-oligomer transition. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 49:21-37. [PMID: 31740999 DOI: 10.1007/s00249-019-01410-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a membrane protein that regulates cell proliferation, differentiation and survival, and is a drug target for cancer therapy. Ligand-induced activation of the EGFR kinase is generally regarded to require ligand-bound-dimers, while phosphorylation and down-stream signalling is modulated by oligomers. Recent work has unveiled changes in EGFR dynamics from ligand-induced dimerization in membranes extracted from cells, however, less is known about the changes in EGFR dynamics that accompany the ligand-induced oligomerization in a live cell environment. Here, we determine the dynamics of a c-terminal GFP tag attached to EGFR in the unliganded dimer and in the liganded oligomers. By means of the single-frequency polarized phasor ellipse approach we extracted two correlation times on the sub-nanosecond and super-nanosecond timescales, respectively. EGF binding to the EGFR-GFP dimer lengthened the sub-nanosecond correlation time (from 0.1 to 1.3 ns) and shortened the super-nanosecond correlation time (from 210 to 56 ns) of the c-terminal GFP probe. The sub-nanosecond depolarization processes were assigned to electronic energy migration between proximal GFPs in the EGFR dimer or oligomer, while the super-nanosecond correlation times were assigned to nanosecond fluctuations of the GFP probe in the EGFR complex. Accordingly, these results show that ligand binding increased the average separation between the c-terminal tags and increased their rotational mobility. We propose that the dynamics are linked to an inhibitory function of the c-terminal tail in the un-liganded dimer and to the requirement of facile stochastic switching between kinase activation and cytoplasmic adaptor/effector binding in the active oligomers.
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Affiliation(s)
- Noga Kozer
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, School of Science, Swinburne University of Technology, Melbourne, Australia
| | - Andrew H A Clayton
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, School of Science, Swinburne University of Technology, Melbourne, Australia.
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4
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Peulen TO, Opanasyuk O, Seidel CAM. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately. J Phys Chem B 2017; 121:8211-8241. [PMID: 28709377 PMCID: PMC5592652 DOI: 10.1021/acs.jpcb.7b03441] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Förster resonance energy transfer
(FRET) measurements from
a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the
structure and dynamics of DA labeled macromolecules. Accurate descriptions
of FRET measurements by molecular models are complicated because the
fluorophores are usually coupled to the macromolecule via flexible
long linkers allowing for diffusional exchange between multiple states
with different fluorescence properties caused by distinct environmental
quenching, dye mobilities, and variable DA distances. It is often
assumed for the analysis of fluorescence intensity decays that DA
distances and D quenching are uncorrelated (homogeneous quenching
by FRET) and that the exchange between distinct fluorophore states
is slow (quasistatic). This allows us to introduce the FRET-induced
donor decay, εD(t), a function solely
depending on the species fraction distribution of the rate constants
of energy transfer by FRET, for a convenient joint analysis of fluorescence
decays of FRET and reference samples by integrated graphical and analytical
procedures. Additionally, we developed a simulation toolkit to model
dye diffusion, fluorescence quenching by the protein surface, and
FRET. A benchmark study with simulated fluorescence decays of 500
protein structures demonstrates that the quasistatic homogeneous model
works very well and recovers for single conformations the average
DA distances with an accuracy of < 2%. For more complex
cases, where proteins adopt multiple conformations with significantly
different dye environments (heterogeneous case), we introduce a general
analysis framework and evaluate its power in resolving heterogeneities
in DA distances. The developed fast simulation methods, relying on
Brownian dynamics of a coarse-grained dye in its sterically accessible
volume, allow us to incorporate structural information in the decay
analysis for heterogeneous cases by relating dye states with protein
conformations to pave the way for fluorescence and FRET-based dynamic
structural biology. Finally, we present theories and simulations to
assess the accuracy and precision of steady-state and time-resolved
FRET measurements in resolving DA distances on the single-molecule
and ensemble level and provide a rigorous framework for estimating
approximation, systematic, and statistical errors.
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Affiliation(s)
- Thomas-Otavio Peulen
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Oleg Opanasyuk
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
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5
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Bogh SA, Bora I, Rosenberg M, Thyrhaug E, Laursen BW, Sørensen TJ. Azadioxatriangulenium: exploring the effect of a 20 ns fluorescence lifetime in fluorescence anisotropy measurements. Methods Appl Fluoresc 2015; 3:045001. [PMID: 29148501 DOI: 10.1088/2050-6120/3/4/045001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Azaoxatriangulenium (ADOTA) has been shown to be highly emissive despite a moderate molar absorption coefficient of the primary electronic transition. As a result, the fluorescence lifetime is ~20 ns, longer than all commonly used red fluorescent organic probes. The electronic transitions in ADOTA are highly polarised (r 0 = 0.38), which in combination with the long fluorescence lifetime extents the size-range of biomolecular weights that can be detected in fluorescence polarisation-based experiments. Here, the rotational dynamics of bovine serum albumin (BSA) are monitored with three different ADOTA derivatives, differing only in constitution of the reactive linker. A detailed study of the degree of labelling, the steady-state anisotropy, and the time-resolved anisotropy of the three different ADOTA-BSA conjugates are reported. The fluorescence quantum yields (ϕ fl) of the free dyes in PBS solution are determined to be ~55%, which is reduced to ~20% in the ADOTA-BSA conjugates. Despite the reduction in ϕ fl, a ~20 ns intensity averaged lifetime is maintained, allowing for the rotational dynamics of BSA to be monitored for up to 100 ns. Thus, ADOTA can be used in fluorescence polarisation assays to fill the gap between commonly used organic dyes and the long luminescence lifetime transition metal complexes. This allows for efficient steady-state fluorescence polarisation assays for detecting binding of analytes with molecular weights of up to 100 kDa.
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Affiliation(s)
- Sidsel A Bogh
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
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6
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Bora I, Bogh SA, Santella M, Rosenberg M, Sørensen TJ, Laursen BW. Azadioxatriangulenium: Synthesis and Photophysical Properties of Reactive Dyes for Bioconjugation. European J Org Chem 2015; 2015:6351-6358. [PMID: 27047257 DOI: 10.1002/ejoc.201500888] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Azadioxatriangulenium (ADOTA) is a fluorescent triangulenium dye with a long fluorescence lifetime, highly polarized transitions and emission in the red part of the visible spectrum. These properties make the chromophore suited for application in fluorescence polarization/anisotropy assay. To be useful for these applications, reactive forms of the dyes must be available in significant quantities. Here, the synthesis and photophysical properties of amine-reactive NHS esters and a thiol-reactive maleimide derivate of ADOTA are reported. The synthesis involves two steps of nucleophilic bridge forming reactions starting from tris(2,6-dimethoxyphenyl) methylium tetrafluoroborate, which can readily be made on 100 gram scale. In the third and final step the reactive NHS or maleimide groups are formed. The beneficial photophysical properties of the ADOTA chromophore are maintained in these derivatives, and we conclude that these systems are ideal to study protein motion and protein-protein interactions for systems of up towards 1000 kDa.
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Affiliation(s)
- Ilkay Bora
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - Sidsel A Bogh
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - Marco Santella
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - Martin Rosenberg
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - Thomas Just Sørensen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - Bo W Laursen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
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7
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Samatanga B, Klostermeier D. DEAD-box RNA helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and RNA duplex recognition. Nucleic Acids Res 2014; 42:10644-54. [PMID: 25123660 PMCID: PMC4176333 DOI: 10.1093/nar/gku747] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We therefore investigated dsRNA and nucleotide binding by the helicase cores and the isolated N- and C-terminal RecA domains (RecA_N, RecA_C) of the DEAD-box proteins Hera and YxiN by steady-state and time-resolved fluorescence methods. Both helicases bind nucleotides predominantly via RecA_N, in agreement with previous studies on Mss116, and with a universal, modular function of RecA_N in nucleotide recognition. In contrast, dsRNA recognition is different: Hera interacts with dsRNA in the absence of nucleotide, involving both RecA domains, whereas for YxiN neither RecA_N nor RecA_C binds dsRNA, and the complete core only interacts with dsRNA after nucleotide has been bound. DEAD-box proteins thus cover a continuum from complete functional independence of their domains, exemplified by Mss116, to various degrees of inter-domain cooperation in dsRNA binding. The different degrees of domain communication and of thermodynamic linkage between dsRNA and nucleotide binding have important implications on the mechanism of dsRNA unwinding, and may help direct RNA helicases to their respective cellular processes.
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Affiliation(s)
- Brighton Samatanga
- Institute for Physical Chemistry, University of Muenster, Correnstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Correnstrasse 30, 48149 Muenster, Germany
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8
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Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S. Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics. ACS Chem Biol 2013; 8:1195-204. [PMID: 23517476 DOI: 10.1021/cb400030n] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crucial molecular events accompanying protein folding in the cell are still largely unexplored. As nascent polypeptides emerge from the ribosomal exit tunnel, they come in close proximity with the highly negatively charged ribosomal surface. How is the nascent polypeptide influenced by the ribosomal surface? We address this question via the intrinsically disordered protein PIR and a number of its variably charged mutants. Two different populations are identified: one is highly spatially biased, and the other is highly dynamic. The more negatively charged nascent polypeptides emerging from the ribosome are richer in the extremely dynamic population. Hence, nascent proteins with a net negative charge are less likely to interact with the ribosome. Surprisingly, the amplitude of the local motions of the highly dynamic population is much wider than that of disordered polypeptides under physiological conditions, implying that proximity to the ribosomal surface enhances the molecular flexibility of a subpopulation of the nascent protein, much like a denaturing agent would. This effect could be important for a proper structural channeling of the nascent protein and the prevention of cotranslational kinetic trapping. Interestingly, a significant population of the highly spatially biased nascent chain, probably interacting extensively with the ribosome, is present even for very negatively charged nascent proteins. This "sticking" effect likely serves to protect nascent proteins (e.g., from cotranslational aggregation). In all, our results highlight the influence of the ribosome in nascent protein dynamics and show that the ribosome's function in protein biogenesis extends well beyond catalysis of peptide bond formation.
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Affiliation(s)
- Anders M. Knight
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Peter H. Culviner
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Neşe Kurt-Yilmaz
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Taisong Zou
- Department of Physics, Center
for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - S. Banu Ozkan
- Department of Physics, Center
for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
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9
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James NG, Ross JA, Stefl M, Jameson DM. Applications of phasor plots to in vitro protein studies. Anal Biochem 2010; 410:70-6. [PMID: 21078289 DOI: 10.1016/j.ab.2010.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
In a recent article, we described the application of phasor analysis to fluorescence intensity decay data on in vitro samples. As detailed in that article, this method provides researchers with a simple graphical method for viewing lifetime data that can be used to quantify individual components of a mixture as well as to identify excited state reactions. In the current article, we extend the use of in vitro phasor analysis to intrinsic protein fluorescence. We show how alterations in the excited state properties of tryptophan residues are easily visualized using the phasor method. Specifically, we demonstrate that protein-ligand and protein-protein interactions can result in unique shifts in the location of phasor points, indicative of protein conformational changes. Application of the method to a rapid kinetic experiment is also shown. Finally, we show that the unfolding of lysozyme with either urea or guanidine hydrochloride results in different phasor trajectories, indicative of unique denaturation pathways.
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Affiliation(s)
- Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
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10
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Luschtinetz F, Dosche C, Kumke MU. Influence of Streptavidin on the Absorption and Fluorescence Properties of Cyanine Dyes. Bioconjug Chem 2009; 20:576-82. [DOI: 10.1021/bc800497v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Franziska Luschtinetz
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24−25, 14476 Potsdam-Golm, Germany
| | - Carsten Dosche
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24−25, 14476 Potsdam-Golm, Germany
| | - Michael U. Kumke
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24−25, 14476 Potsdam-Golm, Germany
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11
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Hemmilá I, Mukkala VM. Time-Resolution in Fluorometry Technologies, Labels, and Applications in Bioanalytical Assays. Crit Rev Clin Lab Sci 2008. [DOI: 10.1080/20014091084254] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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12
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Yu P, Lasagna M, Pawlyk AC, Reinhart GD, Pettigrew DW. IIAGlc Inhibition of Glycerol Kinase: A Communications Network Tunes Protein Motions at the Allosteric Site. Biochemistry 2007; 46:12355-65. [DOI: 10.1021/bi7010948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Yu
- Department of Biochemistry and Biophysics and Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843-2128
| | - Mauricio Lasagna
- Department of Biochemistry and Biophysics and Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843-2128
| | - Aaron C. Pawlyk
- Department of Biochemistry and Biophysics and Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843-2128
| | - Gregory D. Reinhart
- Department of Biochemistry and Biophysics and Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843-2128
| | - Donald W. Pettigrew
- Department of Biochemistry and Biophysics and Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843-2128
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13
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Abstract
Glucose/galactose binding protein (GGBP) functions in two different larger systems of proteins used by enteric bacteria for molecular recognition and signaling. Here we report on the thermodynamics of conformational equilibrium distributions of GGBP. Three fluorescence components appear at zero glucose concentration and systematically transition to three components at high glucose concentration. Fluorescence anisotropy correlations, fluorescent lifetimes, thermodynamics, computational structure minimization, and literature work were used to assign the three components as open, closed, and twisted conformations of the protein. The existence of three states at all glucose concentrations indicates that the protein continuously fluctuates about its conformational state space via thermally driven state transitions; glucose biases the populations by reorganizing the free energy profile. These results and their implications are discussed in terms of the two types of specific and nonspecific interactions GGBP has with cytoplasmic membrane proteins.
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Affiliation(s)
- Troy C Messina
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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14
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Steege KE, Wang J, Uhrich KE, Castner EW. Local Polarity and Microviscosity in the Hydrophobic Cores of Amphiphilic Star-like and Scorpion-like Macromolecules. Macromolecules 2007. [DOI: 10.1021/ma061779l] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Karen E. Steege
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
| | - Jinzhong Wang
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
| | - Kathryn E. Uhrich
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
| | - Edward W. Castner
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
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15
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Funston AM, Fadeeva TA, Wishart JF, Castner EW. Fluorescence Probing of Temperature-Dependent Dynamics and Friction in Ionic Liquid Local Environments. J Phys Chem B 2007; 111:4963-77. [PMID: 17439268 DOI: 10.1021/jp068298o] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The solvation dynamics and local orientational friction for a series of four ionic liquids have been probed using coumarin 153 (C153) as a function of temperature. These ionic liquids are comprised of nonaromatic organic cations paired with a common anion, bis(trifluoromethylsulfonyl)imide (NTf(2)-). The specific liquids are as follows: N-methyl-tri-N-butylammonium NTf(2)- (N(1444)+/NTf(2)-), N-hexyl-tri-N-butylammonium NTf(2)- (N(6444)+/NTf(2)-), N-methyl-N-butylpyrrolidinium NTf(2)- (Pyrr(14)+/NTf(2)-), and N-methyl-N-ethoxyethylpyrrolidinium NTf(2)- (Pyrr(1(2O2))+/NTf(2)-). The observed solvation dynamics and fluorescence depolarization dynamics occur over a broad range of time scales that can only be adequately fit by functions including three or more exponential components. Stretched exponential distributions cannot adequately fit our data. The solvation and reorientational dynamics of the C153 probe are studied over a range of temperatures from 278.2 to 353.2 K. For both the solvation dynamics and the probe reorientational dynamics, the observed temperature dependence is well fit by a Vogel-Tammann-Fulcher law. To correlate the observed microscopic dynamics with macroscopic physical properties, temperature-dependent viscosities are also measured. Differential scanning calorimetry is used to study the thermodynamics of the phase transitions from the liquid to supercooled liquid to glassy states. For the two tetraalkylammonium liquids, the observed melting transitions occur near 300 K, so we are able to study the dynamics in a clearly supercooled regime. Very long time scale orientational relaxation time constants dynamics on the order of 100 ns are observed in the C153 fluorescence anisotropy. These are interpreted to arise from long-lived local structures in the environment surrounding the C153 probe.
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Affiliation(s)
- Alison M Funston
- School of Chemistry, University of Melbourne, Melbourne, Australia
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16
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Vishwasrao HD, Heikal AA, Kasischke KA, Webb WW. Conformational dependence of intracellular NADH on metabolic state revealed by associated fluorescence anisotropy. J Biol Chem 2005; 280:25119-26. [PMID: 15863500 DOI: 10.1074/jbc.m502475200] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Global analysis of fluorescence and associated anisotropy decays of intrinsic tissue fluorescence offers a sensitive and non-invasive probe of the metabolically critical free/enzyme-bound states of intracellular NADH in neural tissue. Using this technique, we demonstrate that the response of NADH to the metabolic transition from normoxia to hypoxia is more complex than a simple increase in NADH concentration. The concentration of free NADH, and that of an enzyme bound form with a relatively low lifetime, increases preferentially over that of other enzyme bound NADH species. Concomitantly, the intracellular viscosity is reduced, likely due to the osmotic swelling of mitochondria. These conformation and environmental changes effectively decrease the tissue fluorescence average lifetime, causing the usual total fluorescence increase measurements to significantly underestimate the calculated concentration increase. This new discrimination of changes in NADH concentration, conformation, and environment provides the foundation for quantitative functional imaging of neural energy metabolism.
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Affiliation(s)
- Harshad D Vishwasrao
- Howard Hughes Medical Institute, Center for Neurobiology & Behavior, Columbia University, New York, New York 10032, USA
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17
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Vyleta NP, Coley AL, Laws WR. Resolution of Molecular Dynamics by Time-Resolved Fluorescence Anisotropy: Verification of Two Kinetic Models. J Phys Chem A 2004. [DOI: 10.1021/jp049707o] [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)
| | - Abram L. Coley
- Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - William R. Laws
- Department of Chemistry, University of Montana, Missoula, Montana 59812
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18
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Pion E, Bombarda E, Stiegler P, Ullmann GM, Mély Y, de Murcia G, Gérard D. Poly(ADP-ribose) polymerase-1 dimerizes at a 5' recessed DNA end in vitro: a fluorescence study. Biochemistry 2003; 42:12409-17. [PMID: 14567702 DOI: 10.1021/bi0344432] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of poly(ADP-ribose) polymerase-1 (PARP-1) is an immediate cellular reaction to DNA strand breakage as induced by alkylating agents, ionizing radiation, or oxidants. The resulting formation of protein-bound poly(ADP-ribose) facilitates survival of proliferating cells under conditions of DNA damage probably via its contribution to DNA base excision repair. In this study, we investigated the association of the amino-terminal DNA binding domain of human PARP-1 (hPARP-1 DBD) with a 5' recessed oligonucleotide mimicking a telomeric DNA end. We used the fluorescence of the Trp residues naturally occurring in the zinc finger domain of hPARP-1 DBD. Fluorescence intensity and fluorescence anisotropy measurements consistently show that the binding stoichiometry is two proteins per DNA molecule. hPARP-1 was found to bind the 5' recessed DNA end with a binding constant of approximately 10(14) M(-2) if a cooperative binding model is assumed. These results indicate that hPARP-1 DBD dimerizes during binding to the DNA target site. A footprint experiment shows that hPARP-1 DBD is asymmetrically positioned at the junction between the double-stranded and the single-stranded telomeric repeat. The largest contribution to the stability of the complex is given by nonionic interactions. Moreover, time-resolved fluorescence measurements are in line with the involvement of one Trp residue in the stacking interaction with DNA bases. Taken together, our data open new perspectives for interpretation of the selective binding of hPARP-1 to the junction between double- and single-stranded DNA.
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Affiliation(s)
- Emmanuelle Pion
- UMR 7034 du CNRS, Laboratoire de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, Faculté de Pharmacie, Université Louis Pasteur, 74, Route du Rhin, F-67401 Illkirch Cedex, France
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19
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Simon-Lukasik KV, Persikov AV, Brodsky B, Ramshaw JAM, Laws WR, Alexander Ross JB, Ludescher RD. Fluorescence determination of tryptophan side-chain accessibility and dynamics in triple-helical collagen-like peptides. Biophys J 2003; 84:501-8. [PMID: 12524302 PMCID: PMC1302630 DOI: 10.1016/s0006-3495(03)74869-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2002] [Accepted: 08/21/2002] [Indexed: 11/23/2022] Open
Abstract
We report tryptophan fluorescence measurements of emission intensity, iodide quenching, and anisotropy that describe the environment and dynamics at X and Y sites in stable collagen-like peptides of sequence (Gly-X-Y)(n). About 90% of tryptophans at both sites have similar solvent exposed fluorescence properties and a lifetime of 8.5-9 ns. Analysis of anisotropy decays using an associative model indicates that these long lifetime populations undergo rapid depolarizing motion with a 0.5 ns correlation time; however, the extent of fast motion at the Y site is considerably less than the essentially unrestricted motion at the X site. About 10% of tryptophans at both sites have a shorter ( approximately 3 ns) lifetime indicating proximity to a protein quenching group; these minor populations are immobile on the peptide surface, depolarizing only by overall trimer rotation. Iodide quenching indicates that tryptophans at the X site are more accessible to solvent. Side chains at X sites are more solvent accessible and considerably more mobile than residues at Y sites and can more readily fluctuate among alternate intermolecular interactions in collagen fibrils. This fluorescence analysis of collagen-like peptides lays a foundation for studies on the structure, dynamics, and function of collagen and of triple-helical junctions in gelatin gels.
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20
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Feinstein E, Deikus G, Rusinova E, Rachofsky EL, Ross JBA, Laws WR. Constrained analysis of fluorescence anisotropy decay:application to experimental protein dynamics. Biophys J 2003; 84:599-611. [PMID: 12524313 PMCID: PMC1302641 DOI: 10.1016/s0006-3495(03)74880-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Hydrodynamic properties as well as structural dynamics of proteins can be investigated by the well-established experimental method of fluorescence anisotropy decay. Successful use of this method depends on determination of the correct kinetic model, the extent of cross-correlation between parameters in the fitting function, and differences between the timescales of the depolarizing motions and the fluorophore's fluorescence lifetime. We have tested the utility of an independently measured steady-state anisotropy value as a constraint during data analysis to reduce parameter cross correlation and to increase the timescales over which anisotropy decay parameters can be recovered accurately for two calcium-binding proteins. Mutant rat F102W parvalbumin was used as a model system because its single tryptophan residue exhibits monoexponential fluorescence intensity and anisotropy decay kinetics. Cod parvalbumin, a protein with a single tryptophan residue that exhibits multiexponential fluorescence decay kinetics, was also examined as a more complex model. Anisotropy decays were measured for both proteins as a function of solution viscosity to vary hydrodynamic parameters. The use of the steady-state anisotropy as a constraint significantly improved the precision and accuracy of recovered parameters for both proteins, particularly for viscosities at which the protein's rotational correlation time was much longer than the fluorescence lifetime. Thus, basic hydrodynamic properties of larger biomolecules can now be determined with more precision and accuracy by fluorescence anisotropy decay.
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Affiliation(s)
- Efraim Feinstein
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
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21
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Engelborghs Y. The analysis of time resolved protein fluorescence in multi-tryptophan proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:2255-2270. [PMID: 11603842 DOI: 10.1016/s1386-1425(01)00485-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the last decades, considerable progress has been made in the analysis of the fluorescence decay of proteins with more than one tryptophan. The construction of single tryptophan containing proteins has shown that the lifetimes of the wild type proteins are often the linear combinations of the family lifetimes of the contributing tryptophan residues. Additivity is not followed when energy transfer takes place among tryptophan residues or when the structure of the remaining protein is altered upon the modification. Progress has also been made in the interpretation of the value of the lifetime and the linkage with the immediate environment. Probably all the irreversible processes leading to return to the ground state have been catalogued and their rate constants are documented. Also, the process of electron transfer to the peptide carbonyl is becoming more and more documented and is linked to the rotameric state of tryptophan. Reversible excited state processes are also being considered, including reversible interconversions between rotamers. Interesting information about tryptophan and its environment comes also from anisotropy measurements for proteins in the native, the denatured and the molten globule states. Alterations of protein fluorescence due to the effects of ligand binding or side chain modifications can be analyzed via the ratio of the quantum yields of the modified protein and the reference state. Using the ratio of quantum yields and the (amplitude weighted) average lifetime, three factors can be identified: (1) a change in the apparent radiative rate constant reflecting either static quenching or an intrinsic change in the radiative properties; (2) a change in dynamic quenching; and (3) a change in the balance of the populations of the microstates or local static quenching.
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Affiliation(s)
- Y Engelborghs
- Laboratory of Biomolecular Dynamics, University of Leuven, Belgium.
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22
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Bajzer Z, Moncrieffe MC, Penzar I, Prendergast FG. Complex homogeneous and heterogeneous fluorescence anisotropy decays: enhancing analysis accuracy. Biophys J 2001; 81:1765-75. [PMID: 11509386 PMCID: PMC1301651 DOI: 10.1016/s0006-3495(01)75827-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In biological macromolecules, fluorophores often exhibit multiple depolarizing motions that require multiple lifetimes and rotational relaxation times to define fluorescence intensity and anisotropy decays. The related analysis of time-correlated single-photon counting data becomes uncertain due to the multitude of decay parameters and numerical sensitivity to deconvolution of the instrument response function (IRF) via discretization of integrals. By using simulations we show that improved discretizations based on quadratic and cubic local approximations of the IRF yield more accurate estimation of short rotational relaxation times and lifetimes than the commonly used Grinvald-Steinberg discretization, which in turn appears more reliable than two discretizations based on linear local approximations of the IRF. In addition, our simulation suggests that cubic approximation is the most advantageous in discriminating complex heterogeneous and homogeneous anisotropy decay. We show that among three different information criteria, the Akaike information criterion is best suited for detection of heterogeneity in rotational relaxation times. It is capable of detecting heterogeneity even when anisotropy decay appears homogeneous within statistical errors of estimation.
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Affiliation(s)
- Z Bajzer
- Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, Minnesota 55905, USA.
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23
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de Oliveira AH, Giglio JR, Andrião-Escarso SH, Ward RJ. The effect of resonance energy homotransfer on the intrinsic tryptophan fluorescence emission of the bothropstoxin-I dimer. Biochem Biophys Res Commun 2001; 284:1011-5. [PMID: 11409896 DOI: 10.1006/bbrc.2001.5073] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bothopstoxin-I (BthTX-I) is a homodimeric Lys49-PLA2 homologue from the venom of Bothrops jararacussu in which a single Trp77 residue is located at the dimer interface. Intrinsic tryptophan fluorescence emission (ITFE) quenching by iodide and acrylamide has confirmed that a dimer to monomer transition occurs on reducing the pH from 7.0 to 5.0. Both the monomer and the dimer showed an excitation wavelength-dependent increase in the fluorescence emission maximum, however the excitation curve of the dimer was blue-shifted with respect to the monomeric form. No differences in the absorption or circular dichroism spectra between pH 5.0 and 7.0 were observed, suggesting that this curve shift is due neither to altered electronic ground states nor to exciton coupling of the Trp residues. We suggest that fluorescence resonance energy homotransfer between Trp77 residues at the BthTX-I dimer interface results in excitation of an acceptor Trp population which demonstrates a red-shifted fluorescence emission.
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Affiliation(s)
- A H de Oliveira
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP, Brazil
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24
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de Oliveira AH, Giglio JR, Andrião-Escarso SH, Ito AS, Ward RJ. A pH-induced dissociation of the dimeric form of a lysine 49-phospholipase A2 abolishes Ca2+-independent membrane damaging activity. Biochemistry 2001; 40:6912-20. [PMID: 11389606 DOI: 10.1021/bi0026728] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrolysis of phospholipids by class II phospholipase A2 (PLA2) involves a Ca2+ ion cofactor bound to the Asp49 residue in the active site region. In the lysine 49 phospholipase A2 homologues (Lys49-PLA2), the Asp49 residue is substituted by Lys, and consequently the Lys49-PLA2s show no Ca2+ binding and no detectable phospholipid hydrolysis. Nevertheless, the Lys49-PLA2s demonstrate membrane damaging activity by an incompletely understood Ca2+-independent mechanism of action. Using a combination of steady-state and time-resolved fluorescence techniques, we have examined the effect of pH on the monomer-dimer equilibrium of bothropstoxin I (BthTX-I), a Lys49-PLA2 from the venom of Bothrops jararacussu which contains a single Trp77 residue located at the dimer interface. At pH 5.0, we observe a decreased quantum yield, a decreased rotational correlation time, and an increased bimolecular quenching rate constant with iodide. These results are consistent with a pH-induced dissociation of the BthTX-I dimer, with the consequent exposure of the Trp77 residue to aqueous solvent. In the presence of liposomes, membrane damaging activity is observed only under conditions in which the dimeric form of the BthTX-I is favored. These results demonstrate that the dimeric form of the protein is essential for the initiation of the Ca2+-independent membrane damaging activity.
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Affiliation(s)
- A H de Oliveira
- Department of Chemistry, FFCLRP-USP, Universidade de São Paulo, Ribeirão Preto-SP, Brazil
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25
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Rachofsky EL, Laws WR. Kinetic models and data analysis methods for fluorescence anisotropy decay. Methods Enzymol 2001; 321:216-38. [PMID: 10909060 DOI: 10.1016/s0076-6879(00)21196-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- E L Rachofsky
- Department of Biochemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
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26
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Linderoth NA, Simon MN, Rodionova NA, Cadene M, Laws WR, Chait BT, Sastry S. Biophysical analysis of the endoplasmic reticulum-resident chaperone/heat shock protein gp96/GRP94 and its complex with peptide antigen. Biochemistry 2001; 40:1483-95. [PMID: 11170476 DOI: 10.1021/bi0016218] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Animals vaccinated with heat shock protein (HSP)--peptide complexes develop specific protective immunity against cancers from which the HSPs were originally isolated. This autologous specific immunity has been demonstrated using a number of HSP--peptide antigen complexes. A prototypical HSP-based cancer vaccine is the gp96--peptide antigen complex, which is currently undergoing human clinical trials. Here, we analyzed the structure of a recombinant wild-type and a mutant gp96 protein and their peptide complexes using a number of biophysical techniques. Gel filtration chromatography, dynamic light scattering, and equilibrium analytical ultracentrifugation demonstrated that both a wild-type gp96 and a gp96 mutant lacking a dimerization domain formed higher order structures. More detailed analysis using scanning transmission electron microscopy indicated that both the wild-type and dimerization deletion mutant gp96 protein were organized, unexpectedly, into large aggregates. Size distributions ranged from dimers to octamers and higher. Circular dichroism and intrinsic Trp fluorescence suggested that the gp96 dimerization domain deletion mutant protein was more compact than the wild-type gp96. A fluorescent peptide antigen was synthesized, and the peptide-binding properties of wild-type and the dimerization domain deletion mutant gp96 were studied. Fluorescence lifetime and anisotropy decay showed that the bound antigenic peptide was located in a hydrophobic pocket, with considerable free space for the rotation of the probe. Deletion of the dimerization domain affected the peptide-binding microenvironment, although peptide-binding affinity was reduced by only a small extent. Peptide--gp96 complexes were extremely stable, persisting for many days in the cold. The extraordinary stability of peptide--gp96 complexes and the plasticity of the peptide-binding pocket support the proposed relay of diverse peptides to MHC and/or other molecules via molecular recognition.
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MESH Headings
- Animals
- Antigen Presentation
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Chromatography, Affinity
- Chromatography, High Pressure Liquid
- Circular Dichroism
- Drug Stability
- Endoplasmic Reticulum/chemistry
- Endoplasmic Reticulum/metabolism
- Fluorescence Polarization
- HSP70 Heat-Shock Proteins/chemistry
- HSP70 Heat-Shock Proteins/genetics
- HSP70 Heat-Shock Proteins/metabolism
- Heat-Shock Proteins/chemistry
- Heat-Shock Proteins/genetics
- Heat-Shock Proteins/metabolism
- Light
- Macromolecular Substances
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mutagenesis, Site-Directed
- Peptides/chemistry
- Peptides/immunology
- Peptides/metabolism
- Protein Binding/genetics
- Scattering, Radiation
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Ultracentrifugation
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Affiliation(s)
- N A Linderoth
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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27
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Ayala-Sanmartin J, Vincent M, Sopkova J, Gallay J. Modulation by Ca(2+) and by membrane binding of the dynamics of domain III of annexin 2 (p36) and the annexin 2-p11 complex (p90): implications for their biochemical properties. Biochemistry 2000; 39:15179-89. [PMID: 11106497 DOI: 10.1021/bi000501x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The modulation of the local structure and dynamics of domain III of annexin 2 (Anx2), in both the monomeric (p36) and heterotetrameric forms (p90), by calcium and by membrane binding was studied by time-resolved fluorescence intensity and anisotropy measurements of the single tryptophan residue (W212). The results yield the same dominant excited-state lifetime (1.4 ns) in both p36 and p90, suggesting that the conformation and environment of W212 are very similar. The fluorescence anisotropy decay data were analyzed by associative (two-dimensional) as well as nonassociative (one-dimensional) models. Although no statistical criterion is decisive for one model versus the other, only the associative model allows recovery of a physically relevant value of the Brownian rotational correlation of the protein. Using the associative model, a nanosecond flexibility is detectable in p90 but not in p36. When Ca(2+) binds in the millimolar concentration range to both forms of Anx2, a conformational change takes place leading to an increase of the major excited-state lifetime (2.6 ns) and to a suppression of the W212 local flexibility of p90. Binding to membranes of either p36 or p90 in the presence of Ca(2+) does not induce any conformational change other than that provoked by Ca(2+) binding alone. The W212 local flexibility in both proteins increases significantly, however, in their membrane-bound forms. In the presence of membranes, the conformation change of domain III in p90 displays a sensitivity to Ca(2+) 2 orders of magnitude higher than that of p36, reaching intracellular sub-micromolar concentration ranges. This higher Ca(2+) sensitivity correlates with the Ca(2+)-dependent membrane aggregation but not with their Ca(2+)-dependent binding to membranes. The significance of these structural and dynamical changes for the function of the protein is discussed.
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Affiliation(s)
- J Ayala-Sanmartin
- Unité de Biologie Cellulaire et Moléculaire de la Sécrétion, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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28
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Tcherkasskaya O, Ptitsyn OB, Knutson JR. Nanosecond dynamics of tryptophans in different conformational states of apomyoglobin proteins. Biochemistry 2000; 39:1879-89. [PMID: 10677239 DOI: 10.1021/bi992117+] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence anisotropy kinetics were employed to quantify the nanosecond mobility of tryptophan residues in different conformational states (native, molten globule, unfolded) of apomyoglobins. Of particular interest is the similarity between the fluorescence anisotropy decays of tryptophans in the native and molten globule states. We find that, in these compact states, tryptophan residues rotate rapidly within a cone of semiangle 22-25 degrees and a correlation time of 0.5 ns, in addition to rotating together with the whole protein with a correlation time of 7-11 ns. The similar nanosecond dynamics of tryptophan residues in both states suggests that the conformation changes that distinguish the molten globule and native states of apomyoglobins originate from either subtle, slow rearrangements or fast changes distant from these tryptophans.
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Affiliation(s)
- O Tcherkasskaya
- Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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