Incorporation of Sensing Modalities Into De Novo Designed Fluorescence-activating Proteins

Jason C. Klima, Lindsey A. Doyle, Justin Daho Lee, Michael Rappleye, Lauren A. Gagnon, Min Yen Lee, Emilia P. Barros, Anastassia A. Vorobieva, Jiayi Dou, Samantha Bremner, Jacob S. Quon, Cameron M. Chow, Lauren Carter, David L. Mack, Rommie E. Amaro, Joshua C. Vaughan, Andre Berndt, Barry L. Stoddard, David Baker

Correspondence to: [email protected]; [email protected]

Contents:

• pdbs.tar.gz: Computational design models for the 59 extended loop decoys, 5 refined extended loop7 decoys, 8 circularly permuted mFAP2a or mFAP2b decoys, 12 circularly permuted mFAP2a or mFAP2b decoys with de novo designed linkers, and mFAP10, mFAP2a and mFAP2b decoys.

• valls.tar.gz: β-barrel loop fragment databases used to design the extended loop library.

• Supplementary_Note_3.ipynb: Python script to design combinatorial library of linkers for grafting one EF-hand motif onto loop7 of mFAP2b.

• Supplementary_Note_4.py: PyRosetta script to circularly permute mFAP2a and mFAP2b.

• Supplementary_Table_1_left.json: Machine-readable Supplementary Table 1 (left)

• Supplementary_Table_1_center.json: Machine-readable Supplementary Table 1 (center)

• Supplementary_Table_1_right.json: Machine-readable Supplementary Table 1 (right)

• Supplementary_Table_2.json: Machine-readable Supplementary Table 2

• D1T.fa.params: Full-atom parameterization for DFHBI-1T chromophore.

• D1T.cen.params: Centroid parameterization for DFHBI-1T chromophore.

• HBI.fa.params: Full-atom parameterization for DFHBI chromophore.

• HBI.cen.params: Centroid parameterization for DFHBI chromophore.

To download and extract on the terminal command line:

git clone https://github.com/klimaj/mFAPs.git && cd mFAPs && tar -xzf pdbs.tar.gz && tar -xzf valls.tar.gz