Proteins Through a Systems Architect's Eyes

An engineer can think about proteins as active components with interfaces and state, but their interfaces are molecular surfaces whose shapes, charge and energies change with…

I approach proteins with an occupational habit: I want to draw boxes and arrows. That habit is useful because architecture forces questions about state, boundaries, interfaces, resources and failure. It is dangerous because natural systems were not designed to respect our diagrams.

Proteins begin as amino-acid chains, but their biological roles depend on folding, chemical modification, concentration, location, binding partners and the surrounding physical conditions. Sequence constrains function without specifying every event that will occur.

Where does state live?

Software gives us the expectation that important state should have an owner. Natural systems often distribute state across structure, concentrations, relationships and history. A snapshot can therefore tell us less than the process that produced it.

Where are the interfaces?

An engineer can think about proteins as active components with interfaces and state, but their interfaces are molecular surfaces whose shapes, charge and energies change with conditions.

Engineered interfaces are declarations. Natural boundaries are often material: membranes, tissues, ecological borders, channels, gradients or social conventions. They can leak, adapt and participate in the behavior they constrain.

What is the failure model?

A compiled binary assumes a comparatively stable machine model. Proteins are part of a medium in which machine, component and environment are all physical and mutually modifying.

Failure analysis is useful because normal operation hides assumptions. A healthy component can coexist with an unhealthy whole. A local optimization can damage the larger system. Robustness at one level can create fragility at another.

History is part of the architecture

Structural biology connected linear sequence to three-dimensional molecular form and made it clear that sequence alone is not a complete description of function.

In a designed system, legacy structure may be accidental baggage. In an evolved or historically accumulated system, legacy structure can be the reason the current architecture exists at all. The path is not documentation around the system; sometimes it is part of the system.

The zoom test

A good architectural description should survive zooming. Going down a level should reveal mechanisms capable of implementing the higher-level pattern. Going up should reveal regularities that justify discussing the larger entity in its own vocabulary.

Proteins remind us that information must become physical organization before it can do work.

At what point does encoded possibility become physical function?

Reading trail

These links are starting points for the scientific and historical ideas. The systems interpretation, analogies and conclusions here are my own.