Accurate High-Throughput Structure Mapping and Prediction with Transition Metal Ion FRET

Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

doi:10.1016/j.str.2012.11.013

Cited by 31 publications

(35 citation statements)

References 43 publications

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“…8 E). In addition, the quenching by transition metals has been shown to exhibit the steep distance and metal dependence predicted for FRET (Latt et al, 1972;Taraska et al, 2009a,b;Yu et al, 2013). Although we cannot rule out a small contribution from other forms of energy transfer, these results are consistent with FRET being the primary mechanism for fluorescence quenching by transition metals.…”

Section: Discussionsupporting

confidence: 70%

“…The efficiency of energy transfer is simply the fraction of fluorescence quenched upon addition of Co 2+ (E = 1  F CO /F). The efficiency of energy transfer can also be estimated from the decrease in the fluorescence Spectral properties of L-ANAP make it an ideal donor for tmFRET with Co 2+ tmFRET is a powerful method for measuring distances between a small-molecule fluorophore and a nonfluorescent transition metal (Taraska and Zagotta, 2010 , and Ni 2+ absorb visible light and can therefore accept energy transfer from a nearby donor fluorophore and quench the donor's fluorescence (Latt et al, 1970(Latt et al, , 1972Horrocks et al, 1975;Richmond et al, 2000;Sandtner et al, 2007;Taraska et al, 2009a,b;Yu et al, 2013). The degree of quenching is a direct measure of FRET efficiency.…”

Section: +mentioning

confidence: 99%

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Measuring distances between TRPV1 and the plasma membrane using a noncanonical amino acid and transition metal ion FRET

Zagotta¹,

Gordon²,

Senning³

et al. 2016

J Cell Biol

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Despite recent advances, the structure and dynamics of membrane proteins in cell membranes remain elusive. We implemented transition metal ion fluorescence resonance energy transfer (tmFRET) to measure distances between sites on the N-terminal ankyrin repeat domains (ARDs) of the pain-transducing ion channel TRPV1 and the intracellular surface of the plasma membrane. To preserve the native context, we used unroofed cells, and to specifically label sites in TRPV1, we incorporated a fluorescent, noncanonical amino acid, L-ANAP. A metal chelating lipid was used to decorate the plasma membrane with high-density/high-affinity metal-binding sites. The fluorescence resonance energy transfer (FRET) efficiencies between L-ANAP in TRPV1 and Co 2+ bound to the plasma membrane were consistent with the arrangement of the ARDs in recent cryoelectron microscopy structures of TRPV1. No change in tmFRET was observed with the TRPV1 agonist capsaicin. These results demonstrate the power of tmFRET for measuring structure and rearrangements of membrane proteins relative to the cell membrane.

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Section: Discussionsupporting

confidence: 70%

Section: +mentioning

confidence: 99%

Measuring distances between TRPV1 and the plasma membrane using a noncanonical amino acid and transition metal ion FRET

Zagotta¹,

Gordon²,

Senning³

et al. 2016

J Cell Biol

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“…Because static quenching by Co 2+ -NTA would not reduce the lifetime of rhodamine B, we can rule out any significant contribution from static quenching to our data (Lakowicz, 2006;Taraska and Zagotta, 2010). In addition, the quenching by transition metals has been shown to exhibit the steep distance and metal dependence predicted for FRET (Latt et al, 1972;Taraska et al, 2009a,b;Yu et al, 2013). Although we cannot rule out a small contribution from other forms of energy transfer, these results are consistent with FRET being the primary mechanism for fluorescence quenching by transition metals.…”

Section: Online Supplemental Materialsmentioning

confidence: 71%

“…These emission spectra have been corrected for an inner filter effect (prominent at the highest concentration; see Eq. 1) and suggest a FRET-based mechanism for quenching (Taraska et al, 2009a,b;Yu et al, 2013). The efficiency of energy transfer is simply the fraction of fluorescence quenched upon addition of Co 2+ -NTA (see Eq.…”

Section: Online Supplemental Materialsmentioning

confidence: 99%

“…e d u ; or William N. Zagotta: z a g o t t a @ u w . e d u Abbreviations used in this paper: FRET, fluorescence resonance energy transfer; PCF, patch-clamp fluorometry; TIRF, total internal reflection fluorescence; tmFRET, transition metal ion FRET.donor and a nonfluorescent transition metal ion as an acceptor (Latt et al, 1970(Latt et al, , 1972Horrocks et al, 1975;Richmond et al, 2000;Sandtner et al, 2007; Taraska et al, 2009a,b;Yu et al, 2013). Transition metal ions such as Ni 2+ , Co 2+ , and Cu 2+ have broad absorption spectra that overlap the emission spectra of visible light fluorophores (see Miessler and Tarr [1999] pages 361-380 for a discussion of electronic spectra of coordination compounds).…”

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Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane

Gordon¹,

Senning²,

Aman³

et al. 2016

J Cell Biol

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The plasma membrane is a major site of signal detection, transduction, and propagation in cells. Understanding cell signaling dynamics at the plasma membrane requires approaches that can detect changes in membrane architecture over molecular distances (10-100 Å) and biological time scales (milliseconds to seconds). Methods that provide access to dynamics at the intracellular surface of the plasma membrane would be especially powerful. Fluorescence resonance energy transfer (FRET) was first applied to studies of membrane dynamics by Keller et al. (1977), who recognized that fluorescent probes incorporated into membranes could be used as an indicator of mixing of the two membranes during membrane fusion. FRET occurs when the emission spectrum of a donor fluorophore overlaps with the absorption spectrum of an acceptor, and the donor and acceptor are in close proximity (Lakowicz, 2006;Taraska and Zagotta, 2010). FRET is steeply distance dependent, and each donor-acceptor pair has a characteristic distance at which the FRET efficiency is 50% (R 0 ), where the amount of FRET is optimally sensitive to changes in distance. The R 0 value for fluorescein and rhodamine, for example, is 60 Å (Delgadillo and Parkhurst, 2010), making them an ideal FRET pair for quantifying membrane fusion (Keller et al., 1977).Transition metal ion FRET (tmFRET) is a method to probe the shorter distances typical of the conformational landscape of proteins (Taraska and Zagotta, 2010). tmFRET is a form of FRET that uses a fluorophore as a Correspondence to Sharona E. Gordon: s e g @ u w . e d u ; or William N. Zagotta: z a g o t t a @ u w . e d u Abbreviations used in this paper: FRET, fluorescence resonance energy transfer; PCF, patch-clamp fluorometry; TIRF, total internal reflection fluorescence; tmFRET, transition metal ion FRET.donor and a nonfluorescent transition metal ion as an acceptor (Latt et al., 1970(Latt et al., , 1972Horrocks et al., 1975;Richmond et al., 2000;Sandtner et al., 2007; Taraska et al., 2009a,b;Yu et al., 2013). Transition metal ions such as Ni 2+ , Co 2+ , and Cu 2+ have broad absorption spectra that overlap the emission spectra of visible light fluorophores (see Miessler and Tarr [1999] pages 361-380 for a discussion of electronic spectra of coordination compounds). Transition metals can therefore accept energy transfer from a nearby donor fluorophore and quench the donor's fluorescence. The degree of quenching is a direct measure of the FRET efficiency (Lakowicz, 2006;Taraska et al., 2009a). The FRET efficiency is steeply dependent on distance between the donor and acceptor, allowing tmFRET to serve as a molecular ruler for distances in the membrane. The main advantages of tmFRET over classical FRET methods are (a) R 0 is very short (10-20 Å), allowing short-range interactions to be studied; (b) the transition metals have multiple transition dipoles, reducing the orientation dependence of FRET (Horrocks et al., 1975); (c) the metals can be reversibly bound to native and introduced binding sites; and (d) different...

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Understanding the activation mechanism of Thermomyces lanuginosus lipase using rational design and tryptophan‐induced fluorescence quenching

Skjold-Jørgensen

Vind

Svendsen

et al. 2016

Euro J Lipid Sci & Tech

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The attractiveness of lipases as industrial biocatalysts underlines the importance of understanding their molecular action in detail, helping future efforts to improve performance and applicability. Lipases represent a special class of carboxyl ester hydrolases, which act on long‐chained water insoluble acyl‐glycerols at the water‐lipid interface. This heterogeneous catalysis makes it very difficult to monitor the structural changes taking place in the enzyme during activation in its preferred milieu. In this review, we cover recent developments toward a deeper understanding of the interfacial activation phenomenon of lipases and discuss a selection of biophysical methods suitable for studying lipase activation. For many lipases, such as that from Thermomyces lanuginosus, a structural domain called the “lid” is directly involved in the activation process. This has been shown through alteration of the lid‐residue composition using rational design. The resulting lid‐mutants have highlighted the lid's role in governing enzymatic activity and interfacial activation. Moreover, a recently developed fluorescence‐based technique called the Tryptophan Induced Quenching method has proved to enable the direct measurement of lipase activation in water‐ethanol mixtures, and thus represents an intriguing method to gain further insight into the structural movements taking place at the water‐lipid interface. Practical applications: Lipases are important industrial biocatalysts widely used in industrial applications including detergent, leather, paper, fuel, fine chemicals, baking, cosmetics, and food. Knowledge of structural changes of lipase upon activation and identification of the amino acids involved in lipase activation is crucial for design of new variants with improved or new properties. Rational design of the lid‐region in lipases has an interesting potential for optimization of lipase function and adapting them to different environments. In order to leverage on the design of new lipase variants and their altered function, methods that enable direct measurement of lipase action directly in solution, in real time, are desired. In this context, fluorescence based methods have shown great potential and provides interesting perspectives for probing the delicate movements occurring in lipases upon activation. Interfacial activation of lipases and the lid movements studied by rational design, fluorescence quenching methods, and solvent effect – polarity driven activation.

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Accurate High-Throughput Structure Mapping and Prediction with Transition Metal Ion FRET

Cited by 31 publications

References 43 publications

Measuring distances between TRPV1 and the plasma membrane using a noncanonical amino acid and transition metal ion FRET

Measuring distances between TRPV1 and the plasma membrane using a noncanonical amino acid and transition metal ion FRET

Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane

Understanding the activation mechanism of Thermomyces lanuginosus lipase using rational design and tryptophan‐induced fluorescence quenching

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