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Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study
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10.1063/1.2835611
/content/aip/journal/jcp/128/11/10.1063/1.2835611
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/11/10.1063/1.2835611

Figures

Image of FIG. 1.
FIG. 1.

Folding of a two-domain protein as manifested by 2D FRET, where each domain has been tagged with a donor-acceptor FRET pair. (A) For uncoupled domains, states of the protein form a rectangle in the plane. (B) Kinetic coupling between conformational dynamics of each domain alters the rate constants of folding and unfolding; structural coupling between two domains alters their FRET efficiencies such that the states no longer form a rectangle.

Image of FIG. 2.
FIG. 2.

Correlation functions for two coupled domains. The cross-correlation function is plotted for , (thin solid line), , (dashed line), and , (dotted line). See text for the definition of the coupling parameters. The heavy solid line shows the autocorrelation functions for all three cases, which are indistinguishable in this plot.

Image of FIG. 3.
FIG. 3.

A cartoon depiction of structure 1 (top) and structure 2 (bottom). Native contact points are shown as open circles. FRET donor and acceptor dyes are shown as filled circles.

Image of FIG. 4.
FIG. 4.

Top: The average FRET efficiency as a function of for the donor-acceptor pair {1,61} of structure 1. Bottom: The characteristic relaxation times (points), (dashed line), and (solid line) as a function of for structure 1. See Eqs. (32)–(34) for the definition of these times.

Image of FIG. 5.
FIG. 5.

Contour plot of the joint probability distribution of the FRET efficiency at for structure 1. The FRET pairs are defined by and . Also shown are the points for each state and straight lines showing the connectivity of all possible paths. The lines and provide provide examples of elementary transitions with and without structural coupling between the FRET pairs, respectively (see Fig. 6).

Image of FIG. 6.
FIG. 6.

A cartoon showing the rearrangements of the chain in the transition and highlighted in Fig. 5, with dye molecules shown as filled circles.

Image of FIG. 7.
FIG. 7.

Top: The correlation functions (solid line), (dotted line), and (dashed line) plotted for structure 1 at . The FRET pairs are defined by and . Bottom: Same correlation functions plotted on a semilogarithmic scale. The heavy solid line is plotted vs , where is the lowest nonzero eigenvalue of the matrix .

Image of FIG. 8.
FIG. 8.

Top: The correlation functions (solid line), (dotted line), and (dashed line) plotted for structure 1 at . The FRET pairs are defined by and . Bottom: Same correlation functions plotted on a semilogarithmic scale. The heavy solid line is plotted vs , where is the lowest nonzero eigenvalue of the matrix . Note the the cross-correlation function is indistinguishable from .

Image of FIG. 9.
FIG. 9.

Contour plot of the joint probability distribution of the FRET efficiency at for structure 2. The FRET pairs are defined by and . Also shown are the points for each state and straight lines showing the connectivity of all possible paths.

Image of FIG. 10.
FIG. 10.

Top: The correlation functions (solid line), (dotted line), and (dashed line) plotted for structure 2 at . The FRET pairs defined by and . Bottom: Same correlation functions plotted on a semilogarithmic scale. The heavy solid line is plotted vs , where is the lowest nonzero eigenvalue of the matrix .

Tables

Generic image for table
Table I.

The correlation coefficients for structure 1, where and are for FRET pairs attached to the monomers of the corresponding row and column contacts of the table element.

Generic image for table
Table II.

for structure 1, where and are for FRET pairs attached to the monomers of the corresponding row and column contacts of the table element.

Generic image for table
Table III.

The correlation coefficients for structure 2, where and are for FRET pairs attached to the monomers of the corresponding row and column contacts of the table element.

Generic image for table
Table IV.

for structure 2 where and are for FRET pairs attached to the monomers of the corresponding row and column contacts of the table element.

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/content/aip/journal/jcp/128/11/10.1063/1.2835611
2008-03-17
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/11/10.1063/1.2835611
10.1063/1.2835611
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