Journal: eLife

Article Title: Encounter complexes and dimensionality reduction in protein–protein association

doi: 10.7554/eLife.01370

Figure Lengend Snippet: Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs PIPER energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003

Article Snippet: DB: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use.

Techniques: Generated, Sampling