UC Irvine

This chapter outlines the general aspects of protein states and protein motions and discusses the way water may be involved. It illustrates some examples to explain concepts and processes. The chapter distinguishes two different types of motions: equilibrium fluctuations (EF) and functionally important motions (FIMs). In EF, a resting protein moves from one substate to another, but does not change its state. A FIM describes the motion from one state to the other. The magnitude of the equilibrium fluctuations is determined by equilibrium thermodynamics. EF and FIMs are related through generalized fluctuation–dissipation theorems. The relations provide the basis for the study of the characteristic time of spontaneous fluctuations using perturbation methods. The study of the effect of hydration on the hierarchy of tiers explores the way water affects the EF of a protein and the way FIMs are triggered. The cross-correlation between protein EF and EF of the bound water is important for the existence of FIMs. © 1986, Elsevier Inc. All rights reserved.