SYNZIPs

SYNZIPs are synthetic heterodimeric coiled coils that form a diverse set of interaction connectivities. Many of these interactions have been validated bothin vitro and in vivo. This toolbox of interaction modules and their associated specification sheets provides a large set of well characterized protein interaction parts for molecular engineering.

Specification Sheets

YNZIP “spec sheets” are the full data for SYNZIP pairs that have been biophysically characterized and validated in at least one in vivo assay.
Alignments are taken either from the crystal structure, or are manually curated hypothetical alignments.
The interaction table entries are as follows:
Protein microarray (pa) is the arrayscore score generated from Reinke et al. 2010, ranging from 0 to 11, 0 being the strongest interaction. The two scores represent reciprocal measurements where each protein is printed on the surface and probed with the interacting partner and vice versa. The Y2H scores indicate colony growth on the respective selection media with “-” indicating no growth ranging to “+++” indicating maximum growth. These scores are manually curated from inspection of plate images and heatmap plots. MAPK scores are the fractional GFP intensities calculated as described in in the methods and range from 0 to 1, 0 being the strongest interaction. The two scores indicate a each zipper either fused to Ste5 or Msg5, unless noted otherwise.
Potential interactors are defined as: show interaction on protein microarray in at least one direction with an arrayscore score < 0.5, show an interaction in Y2H in at least one direction of the reciprocal measurements with a pixel count > 1000. Interactions that are weak in one assay(ie. protein microarray) and strong in the other(ie. Y2H), are indicated as interactors for the weaker assay.
All error bars show ±1 standard deviation of measurement replicates.
All three versions of the pENTR vector constructs, as well as the MBP-SZ-His6x constructs are available for all SYNZIPs in the following “spec sheets.”

Download SYNZIP Spec Sheets.

 

Data

SYNZIP sequences

Doanload txt, csv, or xls format.

SYNZIP stuctures

SYNZIP1:2 complex at PDB
SYNZIP5:6 complex at PDB

SYNZIP interactions

Info file .txt    
    SYNZIP protein microarray maximum signal.csv, average signal.csv
    SYNZIP Y2H (-histidine) interactions maximum signal.csv, average signal.csv
    SYNZIP Y2H (-uracil) interactions maximum signal.csv, average signal.csv

 

The SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains
K. Evan Thompson, Caleb J. Bashor, Wendell A. Lim & Amy E. Keating
ACS Synthetic Biology. In press 2012. at ACS Synthetic Biology

A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering
Aaron W. Reinke, Robert A. Grant, Amy E. Keating.
J Am Chem Soc. 2010 May 5;132(17):6025-31. PMID: 20387835 

Design of protein-interaction specificity gives selective bZIP-binding peptides
Gevorg Grigoryan, Aaron W. Reinke, Amy E. Keating
Nature, 458, 859-864 (2009). PMID: 19370028