Proteins as Molecular Machines

Abstract

The analysis of various biological energy-transducing systems and processes carried out in preceding chapters shows that in all cases we are dealing with the functioning of certain mechanical constructions, machines of rather small dimensions down to molecular ones, which ensure the elementary acts of coupling between energy-donating and energy-accepting chemical reactions. Expressions such as “a protein is a machine”, “an enzyme is a machine”, and “energy-transducing constructions” have now become stock phrases. Usually, however, these statements remain just words, and do not bear any definite meaning. The main reason for that is the fact that in spite of all the talk concerning the “machineness” of proteins in general, and of enzymes in particular, most scientists, when considering chemical properties of biopolymers, use standard approaches of chemical thermodynamics and chemical kinetics developed over the last 100 years for reactions of low-molecular compounds in gaseous phase and dilute solutions. These approaches are based essentially on classical statistical physics of ergodic systems, i.e., on the assumption that these systems have only thermal degrees of freedom with fast enough energy exchange between them. If, however, biologically active macromolecules are machines, it means that during their functioning specific mechanical degrees of freedem interacting only weakly with thermal ones must be excited.