1
|
Samarasinghe TN, Zeng Y, Johnson CK. Microchip Electrophoresis Assay for Calmodulin Binding Proteins. J Sep Sci 2021; 44:895-902. [PMID: 34321981 DOI: 10.1002/jssc.202000884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The calcium signaling protein calmodulin regulates numerous intracellular processes. We introduce a sensitive microchip assay to separate and detect calmodulin binding proteins. The assay utilizes an optimized microchip electrophoresis protein separation platform with laser-induced fluorescence detection. Fluorescence-labeled calmodulin modified with a photoreactive diazirine crosslinker allowed selective detection of calmodulin binding proteins. We demonstrate successful in-vitro crosslinking of calmodulin with two calmodulin binding proteins, calcineurin and nitric oxide synthase. We compare the efficacy of commonly applied electrophoretic separation modes: microchip capillary zone electrophoresis, microchip micellar electrokinetic chromatography/gel electrophoresis, and nanoparticle colloidal arrays. Out of the methods tested, polydymethylsiloxane/glass chips with microchip zone electrophoresis gave the poorest separation, whereas sieving methods in which electro-osmotic flow was suppressed gave the best separation of photoproducts of calmodulin conjugated with calmodulin binding proteins.
Collapse
Affiliation(s)
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| |
Collapse
|
2
|
YUCA ESRA, TAMERLER CANDAN. Self Assembled Recombinant Proteins on Metallic Nanoparticles As Bimodal Imaging Probes. JOM (WARRENDALE, PA. : 1989) 2019; 71:1281-1290. [PMID: 34149269 PMCID: PMC8211090 DOI: 10.1007/s11837-018-03325-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/28/2018] [Indexed: 05/12/2023]
Abstract
Combining multiple modalities is at the center of developing new methods for sensing and imaging that are required for comprehensive understanding of events at the molecular level. Various imaging modalities have been developed using metallic nanoparticles owning to their exceptional physical and chemical properties. Due to their localized surface plasmon resonance characteristics, gold and silver nanoparticles exhibit unique optoelectronic properties commonly used in biomedical sciences and engineering. Self assembled monolayers or physical adsorption have previously been adapted to functionalize the surfaces of nanoparticles with biomolecules for targeted imaging. However, depending on differences among the functional groups used on the nanoparticle surface, wide variation in the displayed biomolecular property to recognize its target may result. In the last decade, the properties of inorganic binding peptides have been proven advantageous to assemble selective functional nano-entities or proteins onto nanoparticles surfaces. Herein we explored formation of self-assembled hybrid metallic nano-architectures that are composed of gold and silver nanoparticles with fluorescent proteins, for use as bimodal imaging probes. We employed metal binding peptide-based assembly to self assemble green fluorescence protein onto metallic substrates of various geometries. Assembly of the green fluorescent proteins, genetically engineered to incorporate gold- or silver-binding peptides onto metallic nanoparticles, resulted in the generation of hybrid-, biomodal-imaging probes in a single step. Green fluorescent activity on gold and silver surfaces can be been monitored using both plasmonic and fluorescent signatures. Our results demonstrate a novel bimodal imaging system that can be finely tuned with respect to nanoparticle size and protein concentration. Resulting hybrid probes may mitigate the limitation of depth penetration into biological tissues as well as providing high signal-to-noise ratio and sensitivity.
Collapse
Affiliation(s)
- ESRA YUCA
- Institute for Bioengineering Research, University of Kansas, Lawrence-KS, 66045, USA
- Molecular Biology and Genetics, Yildiz Technical University, Istanbul 34210, Turkey
| | - CANDAN TAMERLER
- Institute for Bioengineering Research, University of Kansas, Lawrence-KS, 66045, USA
- Bioengineering Program, University of Kansas, Lawrence-KS, 66045, USA
- Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
3
|
Arnett DC, Bailey SK, Johnson CK. Exploring the conformations of nitric oxide synthase with fluorescence. Front Biosci (Landmark Ed) 2018; 23:2133-2145. [PMID: 29772550 DOI: 10.2741/4694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multi-domain oxidoreductases are a family of enzymes that catalyze oxidation-reduction reactions through a series of electron transfers. Efficient electron transfer requires a sequence of protein conformations that position electron donor and acceptor domains in close proximity to each other so that electron transfer can occur efficiently. An example is mammalian nitric oxide synthase (NOS), which consists of an N-terminal oxygenase domain containing heme and a C-terminal reductase domain containing NADPH/FAD and FMN subdomains. We describe the use of time-resolved and single-molecule fluorescence to detect and characterize the conformations and conformational dynamics of the neuronal and endothelial isoforms of NOS. Fluorescence signals are provided by a fluorescent dye attached to the Ca2+-signaling protein calmodulin (CaM), which regulates NOS activity. Time-resolved fluorescence decays reveal the presence of at least four underlying conformational states that are differentiated by the extent of fluorescence quenching. Single-molecule fluorescence displays transitions between conformational states on the time scales of milliseconds to seconds. This review describes the type of information available by analysis of time-resolved and single-molecule fluorescence experiments.
Collapse
Affiliation(s)
- David C Arnett
- Department of Chemistry, Northwestern College, 101 7th Street SW, Orange City, IA 51041
| | - Sheila K Bailey
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045,
| |
Collapse
|
4
|
Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies. Bioconjug Chem 2017; 28:2804-2814. [DOI: 10.1021/acs.bioconjchem.7b00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yijia Xiong
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| | - Nicole R. Ford
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Karen A. Hecht
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
- Department
of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas C. Squier
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| |
Collapse
|
5
|
Sadoine M, Cerminara M, Kempf N, Gerrits M, Fitter J, Katranidis A. Selective Double-Labeling of Cell-Free Synthesized Proteins for More Accurate smFRET Studies. Anal Chem 2017; 89:11278-11285. [DOI: 10.1021/acs.analchem.7b01639] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mayuri Sadoine
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | - Michele Cerminara
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | - Noémie Kempf
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | | | - Jörg Fitter
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
- 1. Physikalisches
Institut (IA), RWTH Aachen, 52062 Aachen, Germany
| | | |
Collapse
|
6
|
Kim TJ, Yoo JY, Shim WS. Substitution with a Single Cysteine in the Green Fluorescent Protein-Based Calcium Indicator GCaMP3 Enhances Calcium Sensitivity. J Fluoresc 2017; 27:2187-2193. [PMID: 28791525 DOI: 10.1007/s10895-017-2159-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/31/2017] [Indexed: 11/25/2022]
Abstract
Genetically encoded calcium indicators (GECI) such as GCaMP3 are attracting significant attention as a good option for measuring intracellular calcium levels. Recently, a modified GCaMP3 called dCys-GCaMP3 was developed by replacing two threonine residues with cysteines. dCys-GCaMP3 proved to be a better calcium indicator, but it was not clear how and why the two cysteine residues were able to enhance the protein's calcium sensitivity. The aim of the present study was to investigate the possible roles of these cysteine residues in dCys-GCaMP3. dCys-GCaMP3 (Thr330Cys;Thr364Cys) exhibited enhanced fluorescence intensity compared to the canonical GCaMP3 in calcium imaging experiments. However, substitution of a single residue at position 330 with cysteine (Thr330Cys) also afforded comparable sensitivity to GCaMP3. In contrast, the other single residue substitution at position 364 with cysteine (Thr364Cys) failed to enhance calcium sensitivity, showing that cysteine at position 330 is essential to improve calcium sensitivity. Thr330Cys substitution in the GCaMP3 or "Cys330-GCaMP3" showed significantly reduced background fluorescence, and the fluorescence intensity was proportional to the amount of DNA used to transfect the cells used in the study. The substitute had to be cysteine, because replacement with other amino acids such as alanine, valine, and aspartate did not improve GCaMP3's calcium sensitivity. Cys330-GCaMP3 outperformed a synthetic calcium-specific indicator, Fluo-3, in various calcium imaging experiments. Thus, the present study asserts that substituting the threonine at position 330 in GCaMP3 with cysteine is essential to enhance calcium sensitivity, and suggests that Cys330-GCaMP3 can be used as a potent fluorescent calcium indicator to measure intracellular calcium levels.
Collapse
Affiliation(s)
- Tae Joon Kim
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea
| | - Ji Young Yoo
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea
| | - Won-Sik Shim
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea. .,Gachon Institute of Pharmaceutical Sciences, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea.
| |
Collapse
|
7
|
Hedison TM, Hay S, Scrutton NS. A perspective on conformational control of electron transfer in nitric oxide synthases. Nitric Oxide 2017; 63:61-67. [PMID: 27619338 PMCID: PMC5295631 DOI: 10.1016/j.niox.2016.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 01/20/2023]
Abstract
This perspective reviews single molecule and ensemble fluorescence spectroscopy studies of the three tissue specific nitric oxide synthase (NOS) isoenzymes and the related diflavin oxidoreductase cytochrome P450 reductase. The focus is on the role of protein dynamics and the protein conformational landscape and we discuss how recent fluorescence-based studies have helped in illustrating how the nature of the NOS conformational landscape relates to enzyme turnover and catalysis.
Collapse
Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
8
|
Hedison TM, Leferink NGH, Hay S, Scrutton NS. Correlating Calmodulin Landscapes with Chemical Catalysis in Neuronal Nitric Oxide Synthase using Time-Resolved FRET and a 5-Deazaflavin Thermodynamic Trap. ACS Catal 2016; 6:5170-5180. [PMID: 27563493 PMCID: PMC4993522 DOI: 10.1021/acscatal.6b01280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/23/2016] [Indexed: 11/28/2022]
Abstract
![]()
A major challenge in enzymology is
the need to correlate the dynamic
properties of enzymes with, and understand the impact on, their catalytic
cycles. This is especially the case with large, multicenter enzymes
such as the nitric oxide synthases (NOSs), where the importance of
dynamics has been inferred from a variety of structural, single-molecule,
and ensemble spectroscopic approaches but where motions have not been
correlated experimentally with mechanistic steps in the reaction cycle.
Here we take such an approach. Using time-resolved spectroscopy employing
absorbance and Förster resonance energy transfer (FRET) and
exploiting the properties of a flavin analogue (5-deazaflavin mononucleotide
(5-dFMN)) and isotopically labeled nicotinamide coenzymes, we correlate
the timing of CaM structural changes when bound to neuronal nitric
oxide synthase (nNOS) with the nNOS catalytic cycle. We show that
remodeling of CaM occurs early in the electron transfer sequence (FAD
reduction), not at later points in the reaction cycle (e.g., FMN reduction).
Conformational changes are tightly correlated with FAD reduction kinetics
and reflect a transient “opening” and then “closure”
of the bound CaM molecule. We infer that displacement of the C-terminal
tail on binding NADPH and subsequent FAD reduction are the likely
triggers of conformational change. By combining the use of cofactor/coenzyme
analogues and time-resolved FRET/absorbance spectrophotometry, we
show how the reaction cycles of complex enzymes can be simplified,
enabling a detailed study of the relationship between protein dynamics
and reaction cycle chemistry—an approach that can also be used
with other complex multicenter enzymes.
Collapse
Affiliation(s)
- Tobias M. Hedison
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sam Hay
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| |
Collapse
|
9
|
Johnson CK, Harms GS. Tracking and localization of calmodulin in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2017-26. [DOI: 10.1016/j.bbamcr.2016.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023]
|
10
|
DeVore MS, Braimah A, Benson DR, Johnson CK. Single-Molecule FRET States, Conformational Interchange, and Conformational Selection by Dye Labels in Calmodulin. J Phys Chem B 2016; 120:4357-64. [PMID: 27111039 DOI: 10.1021/acs.jpcb.6b00864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the roles of measurement time scale and the nature of the fluorophores in the FRET states measured for calmodulin, a calcium signaling protein known to undergo pronounced conformational changes. The measured FRET distributions depend markedly on the measurement time scale (nanosecond or microsecond). Comparison of FRET distributions measured by donor fluorescence decay with FRET distributions recovered from single-molecule burst measurements binned over time scales of 90 μs to 1 ms reveals conformational averaging over the intervening time regimes. We find further that, particularly in the presence of saturating Ca(2+), the nature of the measured single-molecule FRET distribution depends markedly on the identity of the FRET pair. The results suggest interchange between conformational states on time scales of hundreds of microseconds or less. Interaction with a fluorophore such as the dye Texas Red alters both the nature of the measured FRET distributions and the dynamics of conformational interchange. The results further suggest that the fluorophore may not be merely a benign reporter of protein conformations in FRET studies, but may in fact alter the conformational landscape.
Collapse
Affiliation(s)
- Matthew S DeVore
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66045, United States
| | - Adebayo Braimah
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66045, United States
| | - David R Benson
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66045, United States
| | - Carey K Johnson
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66045, United States
| |
Collapse
|
11
|
Arnett DC, Persechini A, Tran QK, Black DJ, Johnson CK. Fluorescence quenching studies of structure and dynamics in calmodulin-eNOS complexes. FEBS Lett 2015; 589:1173-8. [PMID: 25871521 DOI: 10.1016/j.febslet.2015.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/17/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Abstract
Activation of endothelial nitric oxide synthase (eNOS) by calmodulin (CaM) facilitates formation of a sequence of conformational states that is not well understood. Fluorescence decays of fluorescently labeled CaM bound to eNOS reveal four distinct conformational states and single-molecule fluorescence trajectories show multiple fluorescence states with transitions between states occurring on time scales of milliseconds to seconds. A model is proposed relating fluorescence quenching states to enzyme conformations. Specifically, we propose that the most highly quenched state corresponds to CaM docked to an oxygenase domain of the enzyme. In single-molecule trajectories, this state occurs with time lags consistent with the oxygenase activity of the enzyme.
Collapse
Affiliation(s)
- David C Arnett
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; Department of Chemistry, Northwestern College, Orange City, IA 51041, USA
| | - Anthony Persechini
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - Quang-Kim Tran
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - D J Black
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| |
Collapse
|
12
|
Orevi T, Lerner E, Rahamim G, Amir D, Haas E. Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics. Methods Mol Biol 2014; 1076:113-169. [PMID: 24108626 DOI: 10.1007/978-1-62703-649-8_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Most proteins are nanomachines that are selected to execute specific functions and therefore should have some degree of flexibility. The driving force that excites specific motions of domains and smaller chain elements is the thermal fluctuations of the solvent bath which are channeled to selected modes of motions by the structural constraints. Consequently characterization of the ensembles of conformers of proteins and their dynamics should be expressed in statistical terms, i.e., determination of probability distributions of the various conformers. This can be achieved by measurements of time-resolved dynamic non-radiative excitation energy transfer (trFRET) within ensembles of site specifically labeled protein molecules. Distributions of intramolecular segmental end-to-end distances and their fast fluctuations can be determined, and fast and slow conformational transitions within selected sections of the molecule can be monitored and analyzed. Both ensemble and single-molecule detection methods can be applied for data collection. In combination with synchronization methods, time-resolved FRET was also used for studies of fast conformational transitions, in particular the folding/unfolding transitions.
Collapse
Affiliation(s)
- Tomer Orevi
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | | | | | | | | |
Collapse
|
13
|
DeVore MS, Gull SF, Johnson CK. Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy. Chem Phys 2013; 422:10.1016/j.chemphys.2012.11.018. [PMID: 24223465 PMCID: PMC3819237 DOI: 10.1016/j.chemphys.2012.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.
Collapse
Affiliation(s)
- Matthew S. DeVore
- Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States
| | - Stephen F. Gull
- Astrophysics Group, Department of Physics, Cambridge University, Cambridge CB3 0HE, United Kingdom
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States
| |
Collapse
|
14
|
Hellstrand E, Kukora S, Shuman CF, Steenbergen S, Thulin E, Kohli A, Krouse B, Linse S, Åkerfeldt KS. Förster resonance energy transfer studies of calmodulin produced by native protein ligation reveal inter-domain electrostatic repulsion. FEBS J 2013; 280:2675-87. [DOI: 10.1111/febs.12269] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/11/2013] [Accepted: 03/26/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Erik Hellstrand
- Biophysical Chemistry, Chemical Centre; Lund University; Sweden
| | | | | | | | - Eva Thulin
- Biochemistry and Structural Biology, Chemical Centre; Lund University; Sweden
| | - Anita Kohli
- Department of Chemistry; Haverford College; PA; USA
| | - Beth Krouse
- Department of Chemistry; Haverford College; PA; USA
| | - Sara Linse
- Biochemistry and Structural Biology, Chemical Centre; Lund University; Sweden
| | | |
Collapse
|
15
|
Structural insights into neuronal K+ channel-calmodulin complexes. Proc Natl Acad Sci U S A 2012; 109:13579-83. [PMID: 22869708 DOI: 10.1073/pnas.1207606109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Calmodulin (CaM) is a ubiquitous intracellular calcium sensor that directly binds to and modulates a wide variety of ion channels. Despite the large repository of high-resolution structures of CaM bound to peptide fragments derived from ion channels, there is no structural information about CaM bound to a fully folded ion channel at the plasma membrane. To determine the location of CaM docked to a functioning KCNQ K(+) channel, we developed an intracellular tethered blocker approach to measure distances between CaM residues and the ion-conducting pathway. Combining these distance restraints with structural bioinformatics, we generated an archetypal quaternary structural model of an ion channel-CaM complex in the open state. These models place CaM close to the cytoplasmic gate, where it is well positioned to modulate channel function.
Collapse
|
16
|
Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:189-98. [DOI: 10.1007/s00249-011-0772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 11/27/2022]
|
17
|
Backović M, Price ES, Johnson CK, Ralston JP. A distribution-based method to resolve single-molecule Förster resonance energy transfer observations. J Chem Phys 2011; 134:145101. [PMID: 21495770 DOI: 10.1063/1.3568946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a new approach to analyze single-molecule Förster resonance energy transfer (FRET) data. The method recognizes that FRET efficiencies assumed by traditional ensemble methods are unobservable for single molecules. We propose instead a method to predict distributions of FRET parameters obtained directly from the data. Distributions of FRET rates, given the data, are precisely defined using Bayesian methods and increase the information derived from the data. Benchmark comparisons find that the response time of the new method outperforms traditional methods of averaging. Our approach makes no assumption about the number or distribution of underlying FRET states. The new method also yields information about joint parameter distributions going beyond the standard framework of FRET analysis. For example, the running distribution of FRET means contains more information than any conceivable single measure of FRET efficiency. The method is tested against simulated data and then applied to a pilot-study sample of calmodulin molecules immobilized in lipid vesicles, revealing evidence for multiple dynamical states.
Collapse
Affiliation(s)
- Mihailo Backović
- Department of Physics & Astronomy. University of Kansas, Lawrence, Kansas 66045, USA.
| | | | | | | |
Collapse
|
18
|
Abstract
Fluorescence correlation spectroscopy (FCS) can be coupled with Förster resonance energy transfer (FRET) to detect intramolecular dynamics of proteins on the microsecond time scale. Here we describe application of FRET-FCS to detect fluctuations within the N-terminal and C-terminal domains of the Ca(2+)-signaling protein calmodulin. Intramolecular fluctuations were resolved by global fitting of the two fluorescence autocorrelation functions (green-green and red-red) together with the two cross-correlation functions (green-red and red-green). To match the Förster radius for FRET to the dimensions of the N-terminal and C-terminal domains, a near-infrared acceptor fluorophore (Atto 740) was coupled with a green-emitting donor (Alexa Fluor 488). Fluctuations were detected in both domains on the time scale of 30 to 40 μs. In the N-terminal domain, the amplitude of the fluctuations was dependent on occupancy of Ca(2+) binding sites. A high amplitude of dynamics in apo-calmodulin (in the absence of Ca(2+)) was nearly abolished at a high Ca(2+) concentration. For the C-terminal domain, the dynamic amplitude changed little with Ca(2+) concentration. The Ca(2+) dependence of dynamics for the N-terminal domain suggests that the fluctuations detected by FCS in the N-terminal domain are coupled to the opening and closing of the EF-hand Ca(2+)-binding loops.
Collapse
Affiliation(s)
| | - Marek Aleksiejew
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| |
Collapse
|
19
|
Chang WH, Liu Y. Bio-Orthogonal Protein Labeling Methods for Single Molecule FRET. J CHIN CHEM SOC-TAIP 2010. [DOI: 10.1002/jccs.201000073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Price ES, DeVore MS, Johnson CK. Detecting intramolecular dynamics and multiple Förster resonance energy transfer states by fluorescence correlation spectroscopy. J Phys Chem B 2010; 114:5895-902. [PMID: 20392129 PMCID: PMC2910717 DOI: 10.1021/jp912125z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a robust method for the detection of intramolecular dynamics in proteins but is also susceptible to interference from other dynamic processes such as triplet kinetics and photobleaching. We describe an approach for the detection of intramolecular dynamics in proteins labeled with a FRET dye pair based on global fitting to the two autocorrelation functions (green-green and red-red) and the two cross-correlation functions (green-red and red-green). We applied the method to detect intramolecular dynamics in the Ca(2+) signaling protein calmodulin. Dynamics were detected on the 100 mus time scale in Ca(2+)-activated calmodulin, whereas in apocalmodulin dynamics were not detected on this time scale. Control measurements on a polyproline FRET construct (Gly-Pro(15)-Cys) demonstrate the reliability of the method for isolating intramolecular dynamics from other dynamic processes on the microsecond time scale and confirm the absence of intramolecular dynamics of polyproline. We further show the sensitivity of the initial amplitudes of the FCS auto- and cross-correlation functions to the presence of multiple FRET states, static or dynamic. The FCS measurements also show that the diffusion of Ca(2+)-calmodulin is slower than that of apocalmodulin, indicating either a larger average hydrodynamic radius or shape effects resulting in a slower translational diffusion.
Collapse
Affiliation(s)
- E. Shane Price
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | | | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| |
Collapse
|
21
|
Homouz D, Sanabria H, Waxham MN, Cheung MS. Modulation of calmodulin plasticity by the effect of macromolecular crowding. J Mol Biol 2009; 391:933-43. [PMID: 19577574 PMCID: PMC2728162 DOI: 10.1016/j.jmb.2009.06.073] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/24/2009] [Accepted: 06/28/2009] [Indexed: 11/20/2022]
Abstract
In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.
Collapse
Affiliation(s)
| | - Hugo Sanabria
- Department of Neurobiology and Anatomy, UTHSC-Houston
| | | | | |
Collapse
|
22
|
Kuiper JM, Pluta R, Huibers WHC, Fusetti F, Geertsma ER, Poolman B. A method for site-specific labeling of multiple protein thiols. Protein Sci 2009; 18:1033-41. [PMID: 19388048 DOI: 10.1002/pro.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a generic method for the site-specific and differential labeling of multiple cysteine residues in one protein. Phenyl arsenic oxide has been employed as a protecting group of two closely spaced thiols, allowing first labeling of a single thiol. Subsequently, the protecting group is removed, making available a reactive dithiol site for labeling with a second probe. For proof-of-principle, single and triple Cys mutants of the sulphate binding protein of an ABC transporter were constructed. The closely spaced thiols were engineered on the basis of the crystal structure of the protein and placed in different types of secondary structure elements and at different spacing. We show that phenyl arsenic oxide is a good protecting group for thiols spaced 6.3-7.3 A. Proteins were labeled with two different fluorescent labels and the labeling ratios were determined with UV-Vis spectroscopy and MALDI-Tof mass spectrometry. The average labeling efficiency was approximately 80% for the single thiol and 65-90% for the dithiol site.
Collapse
Affiliation(s)
- Johanna M Kuiper
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
23
|
González-Andrade M, Figueroa M, Rodríguez-Sotres R, Mata R, Sosa-Peinado A. An alternative assay to discover potential calmodulin inhibitors using a human fluorophore-labeled CaM protein. Anal Biochem 2009; 387:64-70. [DOI: 10.1016/j.ab.2009.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/11/2008] [Accepted: 01/09/2009] [Indexed: 10/21/2022]
|
24
|
Fekner T, Li X, Lee MM, Chan MK. A pyrrolysine analogue for protein click chemistry. Angew Chem Int Ed Engl 2009; 48:1633-5. [PMID: 19156778 DOI: 10.1002/anie.200805420] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ignoring the STOP sign: A pyrrolysine analogue bearing a terminal alkyne was site-specifically incorporated into recombinant calmodulin (CaM) through a UAG codon. The resulting protein was labeled with an azide-containing dye using a copper(I)-catalyzed click reaction. Subsequent application of an orthogonal cysteine tagging method yielded a CaM labeled with two distinct fluorophores that enabled its study by FRET spectroscopy.
Collapse
Affiliation(s)
- Tomasz Fekner
- Department of Chemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
25
|
Fekner T, Li X, Lee M, Chan M. A Pyrrolysine Analogue for Protein Click Chemistry. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805420] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
26
|
Liyanage MR, Zaidi A, Johnson CK. Fluorescence polarization assay for calmodulin binding to plasma membrane Ca2+-ATPase: dependence on enzyme and Ca2+ concentrations. Anal Biochem 2008; 385:1-6. [PMID: 19000896 DOI: 10.1016/j.ab.2008.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 10/17/2008] [Accepted: 10/18/2008] [Indexed: 10/21/2022]
Abstract
Calmodulin (CaM) is a Ca2+ signaling protein that binds to a wide variety of target proteins, and it is important to establish methods for rapid characterization of these interactions. Here we report the use of fluorescence polarization (FP) to measure the Kd for the interaction of CaM with the plasma membrane Ca2+-ATPase (PMCA), a Ca2+ pump regulated by binding of CaM. Previous assays of PMCA-CaM interactions were indirect, based on activity or kinetics measurements. We also investigated the Ca2+ dependence of CaM binding to PMCA. FP assays directly detect CaM-target interactions and are rapid, sensitive, and suitable for high-throughput screening assay formats. Values for the dissociation constant K(d) in the nanomolar range are readily measured. We measured the changes in anisotropy of CaM labeled with Oregon Green 488 on titration with PMCA, yielding a K(d) value of CaM with PMCA (5.8 +/- 0.5 nM) consistent with previous indirect measurements. We also report the binding affinity of CaM with oxidatively modified PMCA (K(d) = 9.8 +/- 2.0 nM), indicating that the previously reported loss in CaM-stimulated activity for oxidatively modified PMCA is not a result of reduced CaM binding. The Ca2+ dependence follows a simple Hill plot demonstrating cooperative binding of Ca2+ to the binding sites in CaM.
Collapse
|
27
|
Spratt DE, Taiakina V, Palmer M, Guillemette JG. FRET conformational analysis of calmodulin binding to nitric oxide synthase peptides and enzymes. Biochemistry 2008; 47:12006-17. [PMID: 18947187 DOI: 10.1021/bi801418s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calmodulin (CaM) is a ubiquitous Ca (2+)-sensor protein that binds and activates the nitric oxide synthase (NOS) enzymes. We have used fluorescence resonance energy transfer (FRET) to examine the conformational transitions of CaM induced by its binding to synthetic nitric oxide synthase (NOS) CaM-binding domain peptides and full length heme-free constitutive NOS (cNOS) enzymes over a range of physiologically relevant free Ca (2+) concentrations. We demonstrate for the first time that the domains of CaM collapse when associated with Ca (2+)-independent inducible NOS CaM-binding domain, similar to the previously solved crystal structures of CaM bound to the Ca (2+)-dependent cNOS peptides. We show that the association of CaM is not detectable with the cNOS peptides at low free Ca (2+) concentrations (<40 nM). In contrast, we demonstrate that CaM associates with the cNOS holo-enzymes in the absence of Ca (2+) and that the Ca (2+)-dependent transition occurs at a lower free Ca (2+) concentration with the cNOS holo-enzymes. Our results suggest that other regions outside of the CaM-binding domain in the cNOS enzymes are involved in the recruitment and binding of CaM. We also demonstrate that CaM binds to the cNOS enzymes in a sequential manner with the Ca (2+)-replete C-lobe binding first followed by the Ca (2+)-replete N-lobe. This novel FRET study helps to clarify some of the observed similarities and differences between the Ca (2+)-dependent/independent interaction between CaM and the NOS isozymes.
Collapse
Affiliation(s)
- Donald E Spratt
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | | | | | | |
Collapse
|
28
|
Priddy TS, Price ES, Johnson CK, Carlson GM. Single molecule analyses of the conformational substates of calmodulin bound to the phosphorylase kinase complex. Protein Sci 2007; 16:1017-23. [PMID: 17525461 PMCID: PMC2206654 DOI: 10.1110/ps.062747407] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The four integral delta subunits of the phosphorylase kinase (PhK) complex are identical to calmodulin (CaM) and confer Ca(2+) sensitivity to the enzyme, but bind independently of Ca(2+). In addition to binding Ca(2+), an obligatory activator of PhK's phosphoryltransferase activity, the delta subunits transmit allosteric signals to PhK's remaining alpha, beta, and gamma subunits in activating the enzyme. Under mild conditions about 10% of the delta subunits can be exchanged for exogenous CaM. In this study, a CaM double-mutant derivatized with a fluorescent donor-acceptor pair (CaM-DA) was exchanged for delta to assess the conformational substates of PhKdelta by single molecule fluorescence resonance energy transfer (FRET) +/-Ca(2+). The exchanged subunits were determined to occupy distinct conformations, depending on the absence or presence of Ca(2+), as observed by alterations of the compact, mid-length, and extended populations of their FRET distance distributions. Specifically, the combined predominant mid-length and less common compact conformations of PhKdelta became less abundant in the presence of Ca(2+), with the delta subunits assuming more extended conformations. This behavior is in contrast to the compact forms commonly observed for many of CaM's Ca(2+)-dependent interactions with other proteins. In addition, the conformational distributions of the exchanged PhKdelta subunits were distinct from those of CaM-DA free in solution, +/-Ca(2+), as well as from exogenous CaM bound to the PhK complex as delta'. The distinction between delta and delta' is that the latter binds only in the presence of Ca(2+), but stoichiometrically and at a different location in the complex than delta.
Collapse
Affiliation(s)
- Timothy S Priddy
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | | | | | | |
Collapse
|
29
|
Slaughter BD, Bieber-Urbauer RJ, Johnson CK. Single-molecule tracking of sub-millisecond domain motion in calmodulin. J Phys Chem B 2007; 109:12658-62. [PMID: 16852567 DOI: 10.1021/jp051666o] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used single-pair fluorescence resonance energy transfer (spFRET) to track distance changes between domains of fluorescently labeled calmodulin (CaM) on the sub-millisecond time scale. In most cases, CaM remained in the same conformational substate over time periods of up to 1 ms, showing that conformational interchange occurs on a longer time scale. However, in some instances, apparent transitions between conformational substates could be detected. The magnitude of sub-millisecond motion within the dominant conformational substate also revealed fluctuations in distance between domains that were dependent on pH and ionic strength.
Collapse
|
30
|
Slaughter BD, Bieber Urbauer RJ, Urbauer JL, Johnson CK. Mechanism of calmodulin recognition of the binding domain of isoform 1b of the plasma membrane Ca(2+)-ATPase: kinetic pathway and effects of methionine oxidation. Biochemistry 2007; 46:4045-54. [PMID: 17343368 PMCID: PMC2597417 DOI: 10.1021/bi602481u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calmodulin (CaM) binds to a domain near the C-terminus of the plasma membrane Ca2+-ATPase (PMCA), causing the release of this domain and relief of its autoinhibitory function. We investigated the kinetics of dissociation and binding of Ca2+-CaM with a 28-residue peptide [C28W(1b)] corresponding to the CaM-binding domain of isoform 1b of PMCA. CaM was labeled with a fluorescent probe on either the N-terminal domain at residue 34 or the C-terminal domain at residue 110. Formation of complexes of CaM with C28W(1b) results in a decrease in the fluorescence yield of the fluorophore, allowing the kinetics of dissociation or binding to be detected. Using a maximum entropy method, we determined the minimum number and magnitudes of rate constants required to fit the data. Comparison of the fluorescence changes for CaM labeled on the C-terminal or N-terminal domain suggests sequential and ordered binding of the C-terminal and N-terminal domains of CaM with C28W(1b). For dissociation of C28W(1b) from CaM labeled on the N-terminal domain, we observed three time constants, indicating the presence of two intermediate states in the dissociation pathway. However, for CaM labeled on the C-terminal domain, we observed only two time constants, suggesting that the fluorescence label on the C-terminal domain was not sensitive to one of the kinetic steps. The results were modeled by a kinetic mechanism in which an initial complex forms upon binding of the C-terminal domain of CaM to C28W(1b), followed by binding of the N-terminal domain, and then formation of a tight binding complex. Oxidation of methionine residues in CaM resulted in significant perturbations to the binding kinetics. The rate of formation of a tight binding complex was reduced, consistent with the poorer effectiveness of oxidized CaM in activating the Ca2+ pump.
Collapse
Affiliation(s)
- Brian D. Slaughter
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence Kansas 66045-7582
| | - Ramona J. Bieber Urbauer
- Department of Chemistry and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia. 30602
| | - Jeffrey L. Urbauer
- Department of Chemistry and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia. 30602
| | - Carey K. Johnson
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence Kansas 66045-7582
| |
Collapse
|
31
|
|
32
|
Unruh JR, Price ES, Molla RG, Hui R, Johnson CK. Evaluation of a femtosecond fiber laser for two-photon fluorescence correlation spectroscopy. Microsc Res Tech 2006; 69:891-3. [PMID: 16886226 DOI: 10.1002/jemt.20358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This work evaluates a femtosecond fiber laser for use in two-photon fluorescence fluctuation spectroscopy. Fiber lasers present an attractive alternative to Ti:Sapphire systems because of their compact size and portability. Autocorrelation of the second harmonic generation signal from the laser demonstrates that its stability is sufficient for two-photon fluorescence correlation spectroscopy. Fluorescence correlation spectroscopy autocorrelation traces were well fit by a Gaussian-Lorentzian squared model with a beam waist near the diffraction limit for the 810 nm wavelength. A photon counting histogram collected with this system also fit nicely to a single-species model, further demonstrating the quality of the focal shape. The authors conclude that the output from the femtosecond fiber laser is sufficiently stable and has a high enough quality beam shape for fluctuation fluorescence methods, and thus represents an effective, compact, readily portable two-photon excitation source.
Collapse
Affiliation(s)
- Jay R Unruh
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | | | | | | | | |
Collapse
|
33
|
Abstract
Single-molecule fluorescence measurements can provide a new perspective on the conformations, dynamics, and interactions of proteins. Recent examples are described illustrating the application of single-molecule fluorescence spectroscopy to calcium signaling proteins with an emphasis on the new information available in single-molecule fluorescence burst measurements, resonance energy transfer, and polarization modulation methods. Calcium signaling pathways are crucial in many cellular processes. The calcium binding protein calmodulin (CaM) serves as a molecular switch to regulate a network of calcium signaling pathways. Single-molecule spectroscopic methods can yield insights into conformations and dynamics of CaM and CaM-regulated proteins. Examples include studies of the conformations and dynamics of CaM, binding of target peptides, and interaction with the plasma-membrane Ca2+ pump. Single-molecule resonance energy transfer measurements revealed conformational substates of CaM, and single-molecule polarization modulation spectroscopy was used to probe interactions between CaM and the plasma-membrane Ca2+-ATPase.
Collapse
Affiliation(s)
- Carey K Johnson
- Department of Chemistry, 1251 Wescoe Drive, University of Kansas, Lawrence, Kansas 66045-7582, USA.
| |
Collapse
|
34
|
Lyubchenko YL, Sherman S, Shlyakhtenko LS, Uversky VN. Nanoimaging for protein misfolding and related diseases. J Cell Biochem 2006; 99:52-70. [PMID: 16823798 PMCID: PMC1557678 DOI: 10.1002/jcb.20989] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Misfolding and aggregation of proteins is a common thread linking a number of important human health problems. The misfolded and aggregated proteins are inducers of cellular stress and activators of immunity in neurodegenerative diseases. They might possess clear cytotoxic properties, being responsible for the dysfunction and loss of cells in the affected organs. Despite the crucial importance of protein misfolding and abnormal interactions, very little is currently known about the molecular mechanism underlying these processes. Factors that lead to protein misfolding and aggregation in vitro are poorly understood, not to mention the complexities involved in the formation of protein nanoparticles with different morphologies (e.g., the nanopores) in vivo. A better understanding of the molecular mechanisms of misfolding and aggregation might facilitate development of the rational approaches to prevent pathologies mediated by protein misfolding. The conventional tools currently available to researchers can only provide an averaged picture of a living system, whereas much of the subtle or short-lived information is lost. We believe that the existing and emerging nanotools might help solving these problems by opening the entirely novel pathways for the development of early diagnostic and therapeutic approaches. This article summarizes recent advances of the nanoscience in detection and characterization of misfolded protein conformations. Based on these findings, we outline our view on the nanoscience development towards identification intracellular nanomachines and/or multicomponent complexes critically involved in protein misfolding.
Collapse
Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA.
| | | | | | | |
Collapse
|
35
|
Sharov V, Dremina E, Galeva N, Williams T, Schöneich C. Quantitative mapping of oxidation-sensitive cysteine residues in SERCA in vivo and in vitro by HPLC-electrospray-tandem MS: selective protein oxidation during biological aging. Biochem J 2006; 394:605-15. [PMID: 16307534 PMCID: PMC1383710 DOI: 10.1042/bj20051214] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The selective reversible S-glutathiolation of specific SERCA (sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase) cysteine residues represents a novel physiologic pathway of NO (nitric oxide)-dependent arterial smooth muscle relaxation [Adachi, Weisbrod, Pimentel, Ying, Sharov, Schöneich and Cohen (2004) Nat. Med. 10, 1200-1207]. This mechanism may be impaired through the irreversible oxidation of functionally important cysteine residues as a consequence of oxidative stress and aging. To establish whether in vivo aging and in vitro oxidation by peroxynitrite result in the loss of such functionally important cysteine residues of SERCA, we have developed and optimized a quantitative method to monitor the oxidation state of the individual SERCA cysteine residues using a maleimide-based fluorescence dye, TG1 (ThioGlo 1), as a label for cysteine residues that have not been altered by oxidation and are not involved in disulphide bridges. A high efficiency for TG1 labelling of such residues and the chemical structure of cysteine-TG1 adducts were validated by MS analysis of model peptides, model proteins and rat skeletal muscle SERCA1. Tryptic peptides containing 18 out of a total of 24 cysteine residues were identified by HPLC-ESI (electrospray ionization)-MS/MS (tandem MS). Two cysteine residues, at positions 344 and 349, were detected in the form of an internal disulphide bridge, and another 16 were found to be labelled with TG1. Using HPLC-ESI-MS, we quantitatively mapped peroxynitrite oxidation of eight cysteine residues (positions 364, 417, 420, 498, 525, 674, 675 and 938), some of which are involved in the control of SERCA activity. Biological aging resulted in the partial modification of cysteine residues 377, 498, 525, 561, 614, 636, 674, 675, 774 and 938. Neither peroxynitrite exposure nor biological aging affected the apparent SERCA1 ATP affinity. Our data show an age-dependent loss of cysteine residues (approx. 2.8 mol of cysteine/mol of SERCA1), which may be partially responsible for the age-dependent decrease in the specific Ca2+-ATPase activity (by 40%).
Collapse
Affiliation(s)
- Victor S. Sharov
- *Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, U.S.A
| | - Elena S. Dremina
- *Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, U.S.A
| | - Nadezhda A. Galeva
- †Mass Spectrometry Laboratory, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, U.S.A
| | - Todd D. Williams
- †Mass Spectrometry Laboratory, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, U.S.A
| | - Christian Schöneich
- *Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, U.S.A
- To whom correspondence should be addressed (email )
| |
Collapse
|
36
|
Slaughter BD, Unruh JR, Price ES, Huynh JL, Bieber Urbauer RJ, Johnson CK. Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy. J Am Chem Soc 2005; 127:12107-14. [PMID: 16117552 DOI: 10.1021/ja0526315] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.
Collapse
Affiliation(s)
- Brian D Slaughter
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582, USA
| | | | | | | | | | | |
Collapse
|
37
|
Allen MW, Urbauer RJB, Johnson CK. Single-molecule assays of calmodulin target binding detected with a calmodulin energy-transfer construct. Anal Chem 2005; 76:3630-7. [PMID: 15228334 DOI: 10.1021/ac0497656] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have detected single-molecule binding interactions of a target peptide with the calcium-signaling protein calmodulin (CaM) immobilized in an agarose gel, and we have demonstrated the application of a single-molecule binding assay to measure the binding strength of CaM with the CaM-binding domain of calmodulin-dependent protein kinase II (CaMKII). The results demonstrate the potential for ultrasensitive assays of CaM-target interactions and the measurement of a picomolar dissociation constant. To detect single-molecule protein interactions, single-molecule assays require that the analyte molecule be confined to the focal spot of the objective for the time scale of the measurement. We demonstrate the deleterious effect of surface immobilization on CaM. As an alternative to surface immobilization, we have constructed a CaM/maltose binding protein fusion protein, which renders CaM translationally immobile in a low weight percent agarose gel. The target binding functionality of CaM assayed in agarose gels is in good agreement with solution assays. The utility of the construct for detecting interactions with CaM targets was demonstrated in a single-molecule assay of binding interactions of MBP-CaM with the CaMKII CaM-binding domain peptide. A value of 103 +/- 35 pM for the dissociation constant of this interaction was determined by simple counting of fluorescent molecules.
Collapse
Affiliation(s)
- Michael W Allen
- Department of Chemistry and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | | | | |
Collapse
|
38
|
Johnson CK, Osborn KD, Allen MW, Slaughter BD. Single-molecule fluorescence spectroscopy: new probes of protein function and dynamics. Physiology (Bethesda) 2005; 20:10-4. [PMID: 15653834 DOI: 10.1152/physiol.00037.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Single-molecule fluorescence methods provide new tools for the study of biological systems. Single-pair fluorescence resonance energy transfer has provided detailed information about dynamics and structure of the Ca2+-signaling protein calmodulin. Single-molecule polarization modulation spectroscopy has probed the mechanism by which calmodulin activates the plasma membrane Ca2+ pump.
Collapse
Affiliation(s)
- Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.
| | | | | | | |
Collapse
|
39
|
Osborn KD, Zaidi A, Mandal A, Urbauer RJB, Johnson CK. Single-molecule dynamics of the calcium-dependent activation of plasma-membrane Ca2+-ATPase by calmodulin. Biophys J 2005; 87:1892-9. [PMID: 15446271 PMCID: PMC1304593 DOI: 10.1529/biophysj.103.039404] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plasma membrane calcium-ATPase (PMCA) helps to control cytosolic calcium levels by pumping out excess Ca2+. PMCA is regulated by the Ca2+ signaling protein calmodulin (CaM), which stimulates PMCA activity by binding to an autoinhibitory domain of PMCA. We used single-molecule polarization methods to investigate the mechanism of regulation of the PMCA by CaM fluorescently labeled with tetramethylrhodamine. The orientational mobility of PMCA-CaM complexes was determined from the extent of modulation of single-molecule fluorescence upon excitation with a rotating polarization. At a high Ca2+ concentration, the distribution of modulation depths reveals that CaM bound to PMCA is orientationally mobile, as expected for a dissociated autoinhibitory domain of PMCA. In contrast, at a reduced Ca2+ concentration a population of PMCA-CaM complexes appears with significantly reduced orientational mobility. This population can be attributed to PMCA-CaM complexes in which the autoinhibitory domain is not dissociated, and thus the PMCA is inactive. The presence of these complexes demonstrates the inadequacy of a two-state model of Ca2+ pump activation and suggests a regulatory role for the low-mobility state of the complex. When ATP is present, only the high-mobility state is detected, revealing an altered interaction between the autoinhibitory and nucleotide-binding domains.
Collapse
Affiliation(s)
- Kenneth D Osborn
- Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, USA
| | | | | | | | | |
Collapse
|
40
|
Smith JJ, Conrad DW, Cuneo MJ, Hellinga HW. Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms. Protein Sci 2004; 14:64-73. [PMID: 15576565 PMCID: PMC2253321 DOI: 10.1110/ps.04965405] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Covalent modification is an important strategy for introducing new functions into proteins. As engineered proteins become more sophisticated, it is often desirable to introduce multiple, modifications involving several different functionalities in a site-specific manner. Such orthogonal labeling schemes require independent labeling of differentially reactive nucleophilic amino acid side chains. We have developed two protein-mediated protection schemes that permit independent labeling of multiple thiols. These schemes exploit metal coordination or disulfide bond formation to reversibly protect cysteines in a Cys(2)His(2) zinc finger domain. We constructed a variety of N- and C-terminal fusions of these domains with maltose-binding protein, which were labeled with two or three different fluorophores. Multiple modifications were made by reacting an unprotected cysteine in MBP first, deprotecting the zinc finger, and then reacting the zinc finger cysteines. The fusion proteins were orthogonally labeled with two different fluorophores, which exhibited intramolecular fluorescene resonance energy transfer (FRET). These conjugates showed up to a threefold ratiometric change in emission intensities in response to maltose binding. We also demonstrated that the metal- and redox-mediated protection methods can be combined to produce triple independent modifications, and prepared a protein labeled with three different fluorophores that exhibited a FRET relay. Finally, labeled glucose-binding protein was covalently patterned on glass slides using thiol-mediated immobilization chemistries. Together, these experiments demonstrated that reversible thiol protection schemes provide a rapid, straightforward method for producing multiple, site-specific modifications.
Collapse
Affiliation(s)
- J Jefferson Smith
- Duke University Medical Center, Department of Biochemistry, Box 3711, Research Drive, 415 Nanaline Duke Building, Durham, NC 27710, USA
| | | | | | | |
Collapse
|
41
|
Tang J, Mei E, Green C, Kaplan J, DeGrado WF, Smith AB, Hochstrasser RM. Probing Structural Dynamics of Individual Calmodulin:Peptide Complexes in Hydrogels by Single-Molecule Confocal Microscopy. J Phys Chem B 2004. [DOI: 10.1021/jp0480798] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianyong Tang
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Erwen Mei
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Clive Green
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Justin Kaplan
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - William F. DeGrado
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Amos B. Smith
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Robin M. Hochstrasser
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
42
|
Slaughter BD, Allen MW, Unruh JR, Bieber Urbauer RJ, Johnson CK. Single-Molecule Resonance Energy Transfer and Fluorescence Correlation Spectroscopy of Calmodulin in Solution. J Phys Chem B 2004. [DOI: 10.1021/jp040098u] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian D. Slaughter
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582
| | - Michael W. Allen
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582
| | - Jay R. Unruh
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582
| | - Ramona J. Bieber Urbauer
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582
| | - Carey K. Johnson
- Department of Chemistry, 1251 Wescoe Hall Drive, University of Kansas, Lawrence, Kansas 66045-7582
| |
Collapse
|