The role of geometry and elastic strains in dynamic states of proteins

A theory is developed, where a linear macromolecule with geometrically constrained ends, elastically strained, exchanging energy with the solvent molecules through random collisions may provide a mechanism for the following specific functions in proteins: a) Induction of transient, oriented strains in substrates during transition between conformations. b) External variation of the rigidity and geometry of the active site. More generally, a macromolecule in solution possessing appropriate geometrical and elastic properties constitutes a machine, whose possible operations have common features with biological function such as passive transport, enzymatic catalysis and active transport. The theory suggests a quantitative law by which new information about the dynamical state of the protein molecule can be elucidated from the Arrhenius plot. It predicts a relationship between the rate of catalysis and the local viscosity of the solution.