Structure, Volume 21

Supplemental Information

Accurate High-Throughput Structure Mapping

and Prediction with Transition Metal Ion FRET

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

Taraska

Inventory of Supplemental Information

Supplementary Figure S1, related to Figure 2. Anisotropy values for fluorophore-labled

MBP. Anisotropy measured for MBP proteins labeled with mBBr (filled bars) or F5M

(open bars) without and with 14 μM maltose.

Supplementary Figure S2, related to Figure 2. Complete tmFRET data set for F5M donor-

labeled proteins and copper acceptors.

Supplementary Figure S3, related to Figure 2. Complete tmFRET data set for F5M donor-

labeled proteins and nickel acceptors.

Supplementary Figure S4, related to Figure 2. Complete tmFRET data set for mBBr

donor-labeled proteins and copper acceptors.

Supplementary Figure S5, related to Figure 2. Complete tmFRET data set for mBBr

donor-labeled proteins and nickel acceptors.

Supplementary Figure S6, related to Figure 3. Lifetime measurements of transition metal

ion induced-quenching. (a) Fluorescence lifetime of the K137C/K189H/T193H mutant

labeled with mBBr without (black) and with (red) 100 μM copper. (b) Fluorescence lifetime

of K137C/D197H/N201H mutant labeled with mBBr without (black) and with (red) 100 μM

copper. (c) Metal-dependent changes in liftetime for both mutants. (d) Comparison of

FRET values obtained from steady-state measurements and values generated from the

lifetime measurements.

Supplementary Figure S7, related to Figure 3. Ligand-binding titration curve with

increasing concentrations of maltose while keeping protein (E322C/K305H/E309H) and

copper concentration (10 mM) constant.

Supplementary Figure S8, related to Figure 4. Simulations of MBP conformational

transitions. A total of 6 simulations were performed under different conditions: with FRET

constraints and guiding force both off (green), FRET constraints on and guiding force off

(red), FRET constraints off and guiding force on (black), FRET constraints and guiding

force both on, with different guiding factors (0.5 - blue, 1.0 - cyan and 1.5 - magenta). The

RMSD between the simulated structures and the APO state crystal structure (protein data

bank:1OMP) is plotted.

Supplementary Figure S9, related to Figure 4. Simulations of MBP conformational

transitions. 100 structures generated with Xplor-NIH using rigid body/torsion angle

simulated annealing. Simulations without or with 4 tmFRET derived FRET constraints are

shown. The RMSD between the simulated structures and the APO state crystal structure

(protein data bank:1OMP) is plotted.

 

 

Supplementary Figure S1, related to Figure 2. Anisotropy values for fluorophore-labled MBP.

Anisotropy measured for MBP proteins labeled with mBBr (filled bars) or F5M (open bars)

without and with 14 M maltose.

   

 

Supplementary Figure S2, related to Figure 2. Complete tmFRET data set for F5M donor-

labeled proteins and copper acceptors.

Supplementary Figure S3, related to Figure 2. Complete tmFRET data set for F5M donor-

labeled proteins and nickel acceptors.

Supplementary Figure S4, related to Figure 2. Complete tmFRET data set for mBBr donor-

labeled proteins and copper acceptors.

   

 

Supplementary Figure S5, related to Figure 2. Complete tmFRET data set for mBBr donor-

labeled proteins and nickel acceptors.

   

 

 

Supplementary Figure S6, related to Figure 3. Lifetime measurements of transition metal ion

induced-quenching. (a) Fluorescence lifetime of the K137C/K189H/T193H mutant labeled with

mBBr without (black) and with (red) 100 μM copper. (b) Fluorescence lifetime of

K137C/D197H/N201H mutant labeled with mBBr without (black) and with (red) 100 μM

copper. (c) Metal-dependent changes in liftetime for both mutants. (d) Comparison of FRET

values obtained from steady-state measurements and values generated from the lifetime

measurements.

   

 

 

Supplementary Figure S7, related to Figure 3. Ligand-binding titration curve with increasing

concentrations of maltose while keeping protein (E322C/K305H/E309H) and copper

concentration (10 mM) constant.

   

 

 

Supplementary Figure S8, related to Figure 4. Simulations of MBP conformational

transitions. A total of 6 simulations were performed under different conditions: with FRET

constraints and guiding force both off (green), FRET constraints on and guiding force off (red),

FRET constraints off and guiding force on (black), FRET constraints and guiding force both on,

with different guiding factors (0.5 - blue, 1.0 - cyan and 1.5 - magenta). The RMSD between the

simulated structure and the APO state crystal structure (protein data bank:1OMP) is plotted.

   

 

 

Supplementary Figure S9, related to Figure 4. Simulations of MBP conformational

transitions. 100 structures generated with Xplor-NIH using rigid body/torsion angle simulated

annealing. Simulations without or with 4 tmFRET derived FRET constraints are shown. The

RMSD between the simulated structures and the APO state crystal structure (protein data

bank:1OMP) is plotted.