Imagine jostling and bumping your way around a crowded dance floor. The lights are low and the music is loud. You are trying to connect with a blind date. And all you have to go on is the person's name. It might take you most of the evening to find your companion.
Proteins inside the cell face a similar problem as the couple trying to meet for the first time on a congested dance floor. The cellular interior is jam-packed with a large number and variety of proteins. In this setting, proteins have a difficult time making their way to their biochemical partners.
New research, however, indicates that the structures of proteins are carefully fine-tuned so that these biomolecules can successfully find and interact with their biochemical mates.1
Many proteins must interact with other proteins to carry out their prescribed function in the cell. These protein-protein interactions (PPIs) out of necessity must be highly specific. If the wrong proteins bind to each other their interaction is of no use to the cell.
PPIs are complicated by the crowded cellular environment. Low protein concentrations of suitable mates further compound the problem. In the cellular milieu, proteins are much more likely to encounter promiscuous interaction partners than the ones necessary for them to execute their function.
Biochemists have long wondered how highly specific PPIs, so critical to the cell's operation, take place in a cellular interior teeming with myriad proteins.
Scientists from Harvard University and the Massachusetts Institute of Technology recently determined that protein structure is carefully optimized to suppress promiscuous interactions, allowing them to readily find their biochemical companions. Protein surfaces appear to be designed so that the binding of randomly associated proteins is much weaker than the binding when the appropriate proteins encounter each other.
It's as if the proteins that are trying to meet on the cell's crowded dance floor are sporting an unusually colored boutonniere or some other distinguishing feature that makes them easy to pick out in a crowd. All the while, unsuitable partners get a quick brush-off.
The last half century of research into the structure-function relationships of biochemical systems has consistently demonstrated that the function of biomolecules critically depends on an exacting location and spatial orientation of its chemical constituents. The finely tuned PPIs comprise the latest example of this precise arrangement uncovered by biochemists.
Precision and fine-tuning do not arise by happenstance. Rather, they come about only as a result of careful planning and a commitment to executing designs with the best craftsmanship possible. Fine-tuning is a hallmark of intelligent design. This feature dominates the best human designs and is often synonymous with exceptional quality. Similarly, the fine-tuning and precision of biochemical systems as exemplified by PPIs points to the work of a Divine Designer.
1 Eric J. Deeds et al., "Robust Protein-Protein Interactions in Crowded Cellular Environments," Proceedings of the National Academy of Sciences, USA 104 (September 18, 2007): 14952-57.