How Do Proteins Function?

Two proteins or other large molecules of complementary shape and surface charge-patterns upon being brought together will develop multiple attractions including hydrogen-bonds to one another, such fit and collective attraction being called an affinity and such collective bond a complex.

Protein complexing is so generally specific in its requirements of complementary shape and charge-pattern as to be described as “lock-and-key”.

And protein complexing is a fundamental mechanism of protein function:

The conformation-determining attractions and bonds of and within the protein itself can be considered intramolecular or internal complexing.

Cytostructural proteins complex with one another to form the internal structural framework of the cell called the cytoskeleton.

And every cell contains protein enzymes catalyzing—accelerating—the chemical reactions used by that cell, which reactions would otherwise run too slowly to be of use:

Body cells typically each synthesize thousands of different enzymes, and many molecules of each, each more or less specifically catalyzing its specific reaction operating upon its specific substrate(s) or reactant(s) (the phrase "lock-and-key" was first applied to enzyme specificity). And each enzyme catalyzes its reaction largely through, and its specificity is that of, not so much its complexing with its substrate(s) as with its reaction's rate-determining transition state, the highest-energy state through which that reaction must proceed, stabilizing and therefore lowering the energy of that state, allowing lower-energy passage through that state, increasing the probability that a given enzyme-substrate complex will have the energy needed to pass through that state, and therefore, in the cell or other reaction mixture where many such complexes are forming and dissociating, increasing the number of such able to pass through that state and their reactions proceed to completion at any given time, and therefore the overall rate of reaction.

In addition, many enzymes catalyze water-sensitive reactions in their hydrophobic cores.

More complicatedly, many if not most proteins function by virtue of conformation changes, changing back and forth between two or more conformations in the course and by way of function, a phenomenon called allostery, and complexing is frequently combined in protein function with allosteric conformation changes. Protein complexing of one molecule causing an allosteric conformation change in that protein enabling or preventing subsequent complexing of another molecule is a central mechanism of protein function and control in the cell; for example, some enzymes, including some acting as cell switches, sensors or governors, are activated or deactivated—turned on or off—by conformation changes caused by complexing with or dissociating from the appropriate molecules, some used specifically as signals. And other protein enzymes catalyze the degradation of fuel and use the energy yielded to repetitively alter their conformations and shapes, acting as motors and machines.