Analysis of selective, high protein–protein binding interaction of cohesin–dockerin complex using biosensing methods

Optical biosensors that use fluorescence are promising tools for the analysis of target materials such as protein, DNA and other biomaterial. To analyze the binding properties of a protein–protein interaction, we constructed fluorescent biomarkers based on the cohesin–dockerin interaction, which coordinates the assembly of cellulolytic enzymes and scaffolding proteins to produce a cell surface multiprotein complex known as the “cellulosome” in some anaerobic bacteria. Our 2D-PAGE results displayed diverse binding profiles to the dockerin containing cellulosomal proteins produced by Clostridium cellulovorans grown on different carbon sources, such as Avicel, xylan and AXP (Avicel:xylan:pectin (3:1:1)). Fluorescence intensity analysis indicated that EngE and EngH bound more efficiently to Coh6 than to Coh2 or Coh9 (2-fold to 6-fold and 1.5-fold to 5-fold, respectively), while others cellulosomal proteins displayed similar results. In addition, both an enzyme-linked interaction assay (ELIA) and surface plasmon resonance (SPR) analyses demonstrated that both EngE and EngH preferentially bound cohesin6 versus the other two cohesin molecules. This work demonstrated the analysis of the binding patterns between interacting proteins using fluorescent biomarkers. We also illustrated the potential of this sensitive approach to quantify specific target analytical materials via the example of the cohesin–dockerin interaction.

► We constructed fluorescent cohesin markers selected by amino acid differences.
► Fluorescent intensity reflected the distinct interactions between cohesins and dockerin containing proteins in 2D-PAGE.
► Certain proteins had higher selective binding affinities than others, depending on the cohesin markers.
► ELIA and SPR analyses established quantitative binding affinity differences.