Reasons to Believe

Protein-Protein Interactions Fine-Tune the Case for Intelligent Design

I recently bumped into an acquaintance outside the Staples Center after a Lakers game.  Neither of us was aware the other was at the game. Yet, even if we had known and were intentionally keeping an eye out for one another, we probably would never have been able to connect; the crowds at Lakers games are just too heavy.

Proteins inside the cell face a similar problem. The cell interior is jam-packed with a large number and variety of proteins. Even the simplest bacterium harbors several thousand different types of proteins with numerous copies of each biomolecule existing in the cell’s interior. In many instances, proteins must interact and bind in a highly specific manner with other proteins to carry out their function. These protein-protein interactions (PPIs) are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

The jam-packed environment of the cell complicates things. Just like two friends searching for one another in a crowd, proteins are more likely to encounter a protein “stranger” than the desired “friend.”

Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions with “strangers.” Recently, Harvard scientists identified some of the key factors that control PPIs.1 Their research adds to the body of evidence that supports the notion that life’s chemistry is designed, stemming from the work of a Creator.


Factors Controlling PPIs

As I wrote previously, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions between protein “strangers.” The most recent work by the Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also carefully designed.

Proteins that do not engage in PPIs have surfaces that prevent these biomolecules from accidently interacting with other proteins. Because of this structural feature, these proteins can exist at relatively high levels inside the cell. Proteins that interact with only one other protein have specific regions on their surfaces designed to promote the PPI. The remainder of the surfaces are designed to eschew PPIs.

Proteins that interact with at least two other proteins also possess specially designed regions that promote binding with their multiple partners. These multi-partner proteins are much more likely to take part in unintended interactions with the wrong partners because more of their surface is devoted to PPIs. To control unwanted interactions, the concentration of these particular proteins is carefully balanced inside the cell.

In other words, protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life. As I point out in my book The Cell’s Design, high-precision structures and interactions, exemplified by PPIs, are hallmark features of biochemical systems and, by analogy to fine-tuned human designs, point to the work of a Creator.



Subjects: Biochemical Design

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana


  1. Muyoung Heo, Sergei Maslov, and Eugene Shakhnovich, “Topology of Protein Interaction Network Shapes Protein Abundances and Strengths of Their Functional and Nonspecific Interactions,” Proceedings of the National Academy of Sciences, USA 108 (March 8, 2011): 4258–63.