Lane: 1. Spectra BR protein ladder 2. PFD 3. TERM 4. 3-way connector 5. 2-way connector
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1 kda Lane: 1. Spectra BR protein ladder 2. PFD 3. TERM 4. 3-way connector 5. 2-way connector Supplementary Figure 1. SDS-PAGE of acterially expressed and purified proteins. A representative gel of proteins purified via the four different techniques used in this study. The PFD protein purified y ion-exchange chromatography followed y hydrophoic interaction chromatography, the hexahistidine-tagged TERM protein purified using nickel-nta affinity chromatography, and the streptagged 2-way and 3-way connector proteins purified y Streptactin affinity chromatography.
2 [ ] x 1-3 deg dmol -1 cm PFD filament 2-way connector 3-way connector [ ] x 1-3 deg dmol -1 cm PFD filament 2-way connector 3-way connector Wavelength (nm) Temperature ( C) Supplementary Figure 2. Secondary structure and thermal staility of the PFD and connector proteins. a, Far-UV circular dichroism spectra of PFD and the 2-way and 3-way connectors. All the proteins had a predominantly helical conformation with minima near 28 and 222 nm., The thermal staility of the PFD and connector proteins was measured y thermal ramps performed y heating from 25 C to 1 C at a rate of 1 C/min. Ellipticity was measured at 222 nm in 1 C intervals.
3 kda Band intensity T M = 63.3 C c 37 Temperature ( C) Tryptophan fluorescence maximum T M = 84.1 C Temperature ( C)
4 Supplementary Figure 3. The 3-way connector trimerizers into highly thermal-stale assemlies. a, SDS-PAGE gel analysis of the 3-way connector demonstrates a trimeric structure that is denatured y high temperature into monomers. The samples in 2% SDS were incuated at varying temperatures for 5 min., The intensity of the trimer ands in a were quantified y densitometric analysis. The data were fitted to a sigmoidal curve and had an apparent T m of 63.3 ±.5 C. c, Unfolding curve of the foldon domain within the 3-way connector was recorded y measuring the fluorescence emission maxima of the sole tryptophan residue of foldon at an excitation wavelength of 295 nm as a function of increasing temperature. The data are the means of three separate experiments and had an apparent T m of 84.1 ±.2 C when fitted to a sigmoidal curve.
5 kda Lane: 1. Spectra BR protein ladder 2. 1 μm 2-way connector 3. 1 μm 3-way connector 4. 1 μm PFD 5. 1 μm PFD 6. 1 μm 2-way connector + 1 μm PFD 7. 1 μm 2-way connector + 1 μm PFD 8. 1 μm 3-way connector + 1 μm PFD 9. 1 μm 3-way connector + 1 μm PFD 2-way connector 15 3-way connector PFD Supplementary Figure 4. The engineered connector proteins attach to PFD filaments. An SDS- PAGE gel was used to show the inding of the two- and three-way connector proteins to PFD filaments following a pull-down assay. The two-way and three-way connectors contain a strep-tag and ind Streptactin resin; however, an equal or 1-fold molar excess of PFD does not ind the resin and is washed away. When the connector proteins are refolded in the presence of an equal or 1-fold molar excess of PFD, the connectors attach to oth PFD and the Streptactin, resulting in co-elution of oth proteins.
6 1 8 2-way 3 K 2-way 353 K ns β-sheet 2 ns loop RMSF (Å) 6 4 hinge Residue numer α-helix X1 X2 α-helix X1 X2 β-sheets β-sheets α-helix c way 3 K 3-way 353 K d Side view Top view RMSF (Å) Residue numer α-helix X1 X2 α-helix foldon β-sheets β-sheets Supplementary Figure 5. The structural flexiility of the engineered connector proteins during all-atom molecular dynamic (MD) simulations. All simulations were performed at 3K or 353K for 2 ns. a, The root mean square fluctuations (RMSF) of C α atoms in the two-way connector during the simulation., Protein models of the two-way connector at the start of the simulation (green) and after 2 ns simulation (lue). c, The RMSF of the three-way connector during the simulation. d, Superimposed structure of the initial three-way connector model (green) and after 2 ns simulation (lue).
7 [ ] x 1-3 deg dmol -1 cm PFD TERM-(E-coil) TERM-(K-coil) TERM-(E-coil + K-coil) [ ] x 1-3 deg dmol -1 cm PFD TERM-(E-coil) TERM-(K-coil) Wavelength (nm) Temperature ( C) Supplementary Figure 6. The secondary structure and thermal staility of TERM-(E-coil) and TERM-(K-coil). a, Far-UV circular dichroism spectra of PFD, and the TERM-(E-coil) and TERM-(K-coil) proteins either individually or comined., The thermal staility of PFD, TERM-(E-coil), and the TERM-(K-coil) was measured y a thermal ramp performed y heating from 25 C to 1 C at a rate of 1 C/min. Ellipticity was measured at 222 nm in 1 C intervals.
8 1. 1. Bound protein ( M) K d =.585 μm Bound protein ( M) K d =.622 μm TERM-(K-coil)-mVenus ( M) TERM-mVenus ( M) Supplementary Figure 7. Determination of equilirium inding constant (K d ). a, The K d etween TERM-(E-coil)-mCerulean3 and TERM-(K-coil)-mVenus. Bound protein determined from FRET data as a function of free TERM-(K-coil)-mVenus concentration, fitted y a hyperola with B max = 1 μm TERM-(E-coil)-mCerulean3 and K d =.585 μm., The K d etween the TERM dimer (TERMmCerulean3 and TERM-mVenus) using steady-state FRET assays. Bound protein determined from FRET data as a function of free TERM-mVenus concentration, fitted y a hyperola with B max = 1 μm TERM-mCerulean3 and K d =.622 μm. Data for all measurements are the means of three separate experiments.
9 1:1 TERM-(K-coil): PFD 1:4 TERM-(K-coil): PFD PFD alone 1 8 1:2 TERM-(K-coil): PFD PFD Filament numer Filament length (nm) Supplementary Figure 8. The length of PFD filaments can e controlled y the engineered aitprey proteins. a, Denatured PFD was mixed with various ratios of the TERM-(K-coil) protein, refolded and imaged y TEM. Scale ars = 25 nm., Filament lengths were measured in digitized TEM images such as those in a and plotted as distriutions of length (n=5 filaments).
10 kda Lane: 1. Spectra BR protein ladder 2. TERM-(E-coil) 3. TERM-(K-coil)-foldon (Strep tag) 4. TERM-(E-coil) + TERM(-K-coil)-foldon (Strep tag) TERM-(E-coil) TERM-(K-coil)-foldon-Strep TERM-(K-coil)-foldon-Strep TERM-(E-coil) Foldon domain Streptactin resin Supplementary Figure 9. The engineered TERM-(K-coil) inds to a three-way connector that contains the TERM-(E-coil). A pull-down assay was used to show that the TERM-(K-coil) protein was ale to ind to the three-way connector containing the TERM-(E-coil) sequence and a strep-tag affinity sequence. The TERM-(E-coil)-foldon three-way connector was ale to ind to Streptactin resin, therey pulling along the ound TERM-(K-coil) which lacks the strep tag. Susequently, the eluted proteins were examined on an SDS-PAGE gel.
11 Supplementary Figure 1. Nanoparticle arrays on protein filament templates. a, TEM of 5-nm gold nanoparticles assemled along a PFD filament. Incuation of a 5-fold molar excess of gold nanoparticles prevented cross-linking etween individual filaments (scale ar = 1 nm)., The three-way connector was used to assemle three filaments that could susequently e templated with gold nanoparticles into defined structures (scale ar = 2 nm).
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