Statistical Thermodynamics on the Binding of Biomolecules

Abstract

The binding of biomolecules in water plays an essential role in the expression of life phenomena. In this chapter, we show that the underlying mechanism of this binding can be clarified by calculating the thermodynamic quantities based on statistical mechanics. The three types of biomolecule binding are analyzed within a theoretical framework: (I) the binding between a soft peptide (a portion of protein) and a rigid RNA, (II) the one-to-many molecular recognition by a soft peptide accompanying target-dependent structuring, and (III) the actin–myosin binding. Types (I) and (II) are related to pharmacological applications, and type (III) is an elementary process for muscle contraction. These apparently different binding processes share the same underlying mechanism, which can be characterized using a unified theoretical framework. The binding is driven by a large gain of water entropy in the entire system. This gain primarily originates from the reduction of “water crowding,” which is attributed to a large overlap of the biomolecule excluded volumes (EV) upon binding, referred to as the entropic EV effect. Such a large EV overlap is achieved by the formation of sufficiently high shape complementarity on an atomic level within the binding interface. The electrostatic complementarity within the interface is ensured as much as possible to compensate for the energetic loss due to dehydration. Although the elimination of biomolecule fluctuations within the binding interface causes a large conformational entropy loss, it is surpassed by these complementarity formations when the binding is accomplished.