The biophysics of energy converting model proteins is presented as a general set of three postulates with fifteen corollaries for fifteen subtypes of molecular machines. All of the molecular machines utilize a common structural transition, an inverse temperature transition characterized by increased hydrophobic folding and/or assembly as the temperature is increased through a transition temperature range identified by Tt. These molecular machines, which can be polymers (e.g., proteins or protein-based polymers), are capable of interconverting the free energies involving the six intensive variables of mechanical force, temperature, pressure, chemical potential, electrochemical potential, and electromagnetic radiation.
First-order molecular machines of the Tt-type are molecular engines which, with the appropriate energy input, can result in the production of useful mechanical motion. Postulate I is for the thermally-driven molecular engine. Postulate II with four corollaries is for the four cases where the energy inputs drive hydrophobic folding by lowering the temperature, Tt, at which the inverse temperature transition occurs. This is called the ΔTt-mechanism. The four energy inputs that have been shown to change the value of Tt are due to changes (1) in concentrations of chemicals, (2) in oxidative state of attached prosthetic groups, (3) in pressure, and (4) resulting from the absorption of light by attached chromophores. Postulate III with ten corollaries are for the ten pairwise energy conversions involving the intensive variables listed above exclusive of mechanical force. These energy conversions utilize the hydrophobic association transition but do not result in the motion implicit in the folding or assembly process. These are second-order molecular machines of the Tt-type.
The physical basis for the ΔTt-mechanism of energy conversion of Postulates II and III is proposed to arise due to competition for hydration between apolar (hydrophobic) and polar moieties. This competition is capable of effecting large changes in pKa values of Glu, Asp, Lys and His residues. This mechanism is proposed to be a dominant process in protein folding, assembly, and function.