Proteins as Nanomachines

Proteins work like giant machines. They are made up of thousands of small molecules and atoms, these atoms and molecules react in various ways to change shape. Some simple as enzymes using one chemical to break apart apart oxygen and hydrogen in water, or some highly more complicated (the ones I'm going to talk about), like protein chaperonin, and ATP synthase. ATP synthase is a protein used in mitochondria to produce ATP. What happens is they are placed against a hydrogen ion gradient. Hydrogen ions flow down the gradient at high speeds changing the conformation of the countless atoms in ATP synthase to cause an inorganic phosphate functional group to bond covalently with an Adenosine Diphosphate (ADP), molecule. By using energy such as hydrogen ion's physical movement against an ATP synthase protein is a way to create molecular energy. My proposed idea which has already been brought up as an idea many time before, is creating proteins artificially on the molecular level to perform work. By assembling various parts a protein can be synthesized and utilized to perform work. The experiment would be creating a protein molecule in some way using DNA splicing, or mechanically building them. The protein will be hand crafted as a vessel to embark into a cell undetected and destroy a eukaryotic cell's nucleus. By using various forms of molecular energy
you could power the protein by allowing it to hold it's own fuel. The protein is made on the atomic and molecular level thus functions such as how atoms and chemicals interact with it physically
can be determined and modified.

This is highly theoretical, but given I'm entering into Biology with an intent of getting a medical degree and Ph.D in genetics I figure I will be going into this field.

Left: (Molecular Model of ATP synthase protein. note: these are all peptides and polypeptides)